Post Doc Computational - Cold Spring Harbor Laboratory - Cold Spring Harbor, NY   
Familiarity with UNIX. Professor McCombie is seeking highly motivated Postdoctoral Fellows in Statistical Genomics and Human Genetics for his group at the...
From Cold Spring Harbor Laboratory - Wed, 12 Apr 2017 05:15:08 GMT - View all Cold Spring Harbor, NY jobs
          Post-doctoral Fellow - Functional & Chemical Genomics - Oklahoma Medical Research Foundation - Oklahoma City, OK   
*Posting Number: * 0001040 *Working Title: * Post-doctoral Fellow *Classification* : On-going *Status* : Full-Time *Department: * Functional &...
From Indeed - Tue, 27 Jun 2017 19:39:34 GMT - View all Oklahoma City, OK jobs
          Post Doc Computational - Cold Spring Harbor Laboratory - Cold Spring Harbor, NY   
Gronau I, Arbiza L, Mohammed J, Siepel A. Kuhlwilm M, Gronau I, Hubisz MJ, de Filippo C, Prado J, et al. Postdoctoral Positions in Computational Genomics....
From Cold Spring Harbor Laboratory - Wed, 29 Mar 2017 17:25:11 GMT - View all Cold Spring Harbor, NY jobs
          Post-doctoral Fellow - Functional & Chemical Genomics - Oklahoma Medical Research Foundation - Oklahoma City, OK   
A postdoctoral fellow position is available immediately in the laboratory of Dr. Functional & Chemical Genomics - Yoon....
From Indeed - Tue, 27 Jun 2017 19:39:34 GMT - View all Oklahoma City, OK jobs
          Research Technician I - Cold Spring Harbor Laboratory - Cold Spring Harbor, NY   
The core will collaborate with CSHL and other regional investigators to design, execute, and interpret single-cell genomics experiments, as well as develop...
From Cold Spring Harbor Laboratory - Wed, 21 Jun 2017 19:55:00 GMT - View all Cold Spring Harbor, NY jobs
          Dorsal Forebrain-Specific Deficiency of Reelin-Dab1 Signal Causes Behavioral Abnormalities Related to Psychiatric Disorders   
Abstract
Reelin-Dab1 signaling is involved in brain development and neuronal functions. The abnormalities in the signaling through either reduction of Reelin and Dab1 gene expressions or the genomic mutations in the brain have been reported to be associated with psychiatric disorders. However, it has not been clear if the deficiency in Reelin-Dab1 signaling is responsible for symptoms of the disorders. Here, to examine the function of Reelin-Dab1 signaling in the forebrain, we generated dorsal forebrain-specific Dab1 conditional knockout mouse (Dab1 cKO) and performed a behavioral test battery on the Dab1 cKO mice. Although conventional Dab1 null mutant mice exhibit cerebellar atrophy and cerebellar ataxia, the Dab1 cKO mice had normal cerebellum and showed no motor dysfunction. Dab1 cKO mice exhibited behavioral abnormalities, including hyperactivity, decreased anxiety-like behavior, and impairment of working memory, which are reminiscent of symptoms observed in patients with psychiatric disorders such as schizophrenia and bipolar disorder. These results suggest that deficiency of Reelin-Dab1 signal in the dorsal forebrain is involved in the pathogenesis of some symptoms of human psychiatric disorders.

          Mother Cells Pass on DNA Damage to Offspring   
Some dividing human cells pass on low-level DNA damage to offspring, causing daughter cells to pause in a quiescent, or dormant, state previously thought to be random in origin.

          Gene Mutations Linked to Early-Onset of Pancreatitis in Children   
Genetic mutations and a family history of pancreatitis are often associated with an early-onset of the disease in children. The research study was published in iThe Journal of Pediatrics.

          Identifying Genes that Influence the Timing of Puberty   
A genomic analysis that influences the timing of puberty in men and women was conducted to date and about 389 genetic signals were associated with puberty timing.

          Post Doc Computational - Cold Spring Harbor Laboratory - Cold Spring Harbor, NY   
Familiarity with UNIX. Professor McCombie is seeking highly motivated Postdoctoral Fellows in Statistical Genomics and Human Genetics for his group at the...
From Cold Spring Harbor Laboratory - Wed, 12 Apr 2017 05:15:08 GMT - View all Cold Spring Harbor, NY jobs
          IT Deskside Support - Bilingual - Eurofins Canada - Toronto, ON   
We are also number one in the field of environmental laboratory services and one of the global market leaders in agroscience, genomics, discovery pharmacology,...
From Indeed - Fri, 09 Jun 2017 12:58:51 GMT - View all Toronto, ON jobs
          Laboratory Analyst I - Food Microbiology - Eurofins-Experchem Inc. - Toronto, ON   
It is also number one in the field of environmental laboratory services and one of the global market leaders in agro science, genomics, discovery pharmacology,...
From Indeed - Thu, 11 May 2017 23:32:46 GMT - View all Toronto, ON jobs
          Could studying deaf horses shed light on treatment in humans?   

Over the years, Chemistry Prof. Koren Lipsett has owned and rescued horses. Today, they are a focus of her research on deafness in humans.

“My research lab focuses on genomic studies so we can understand human disease,” said Lipsett.

Prof. LipsettSo far, Lipsett and her students have looked at blind cats, fibroblast growth factor (hair length) in cattle, and for the past seven years, deafness in horses. They hope by researching these issues and genetic diseases in large mammals, it will help researchers better understand how to treat human genetic disorders, like congenital blindness and deafness.

Suzanne E. DiNello-Schleicher ’10, a biology and chemistry double major who is today a veterinarian, was the inspiration behind the horse project. One day in Lipsett’s lab, she was doing some preliminary research on the Internet and came across a story about a deaf colt.

“Because she’s a horse person and a vet person, she said, ‘maybe we can pursue this,’” said Lipsett. “Well it turns out the family that owned that particular horse also had the parents and siblings in this pedigree of Spanish Mustangs. Not just one offspring was deaf. There were two deaf offspring that came from the same stallion and two different mares. So that started the project.”

Working with larger mammals has its benefits, Lipsett says. For one, large mammals, as opposed to mice and rats, live longer. If, during transitional research, researchers are completing a treatment study, this allows scientists to study long-term implications. It’s humane: Lipsett uses hair plucked from the horse’s mane. It’s convenient: she uses her own horse and horses from the SPCA as experimental controls. She is currently working with a family from Virginia who owned deaf horses with white coats and blue eyes—the phenotype that studies have shown to correlate with deafness in other animals, like the Siberian Husky.

This knowledge helped Lipsett’s lab narrow down their focus to a candidate gene called the KIT gene.

Prof. Lipsett in the lab

“In [other cases of mammals] that had deafness, white pigmentation, and blue eyes, it has come down to the KIT gene,” said Lipsett. “That particular gene is complex, but that’s not the only one that has been found—there are 5 or 6 genes that we identified as candidate genes. And our job is to methodically go through, sequencing those genes, to see if we can find the mutation.”

The process involves examining the gene’s exons, the segments of the DNA that contain the coding information, or set of instructions, that translate to the protein of interest, for example.

Benjamin Gantz ’16 was responsible for examining exon-21 in the KIT gene. They ran into several issues with designing primers, which is the first step to sequencing a gene.

“Ben got to a point where we understood where the problem was, and by the time he graduated we a had a good understanding of what to do next,” said Lipsett.

“Ben would say, ‘wow, I’m doing real science,’ and I’d say, ‘You've been doing real science the whole time!’ Because you need to think outside the box. There’s no canned answer.”

“Many students have worked on this project before me. It was amazing to be able to pick up where they left off and continue this research,” echoed Gantz. “In independent research labs like Dr. Lipsett's, you are determining the answers to questions that no one on the planet knows. Other scientists may use our research to further their own understanding or study, but our findings will be a starting point for them.”

Over the years, several students have worked on pieces of the project that have been published, like Kaytie Innamorati ’14, who is currently conducting research on Alzheimer’s Disease as a Ph.D. candidate at Drexel University. She is listed as a co-author on the abstract, “Determining the genetic basis of equine deafness via candidate gene studies.” Also, Alecia Achimovich ’16, a Ph.D. candidate at The University of Virginia, is a co-author with Kaytie on a recent abstract.

Prof. Koren Lipsett working in the lab

Today, Lipsett says the research is at the point where they have narrowed down which genes to focus on, and now it’s about consolidating the data order to identify a putative gene mutation. As with the blind cat study, the next step will be to explore the mechanism of pathology that will help define how the gene mutation translated to disease symptoms like blindness or deafness.

“We care about this because we can directly correlate it to human studies,” said Lipsett. “The more we understand the gene function in a mammal model, the more likely we can understand the equivalent function in humans. Then, we can apply that knowledge to characterize and potentially treat the genetic disorder.”

A biological career pathway

Lipsett didn’t start working with DNA until she came to Gettysburg. But looking at her journey, the path to that research seemed inevitable.

“I loved biochemistry in college,” she said. “I didn’t do genomics, I did protein studies. It’s related to the biological system, and that’s what’s exciting to me. My work evolved slowly, as in any research career. You don’t necessarily stay in the same track, but your research takes you down new tracks and lets you solve cool new problems.”

Prof. Koren LipsettDuring Lipsett’s postdoctoral research at Johns Hopkins University, she studied metabolic pathways at the genomic level and how specific genes, and the gene products, participate in a given biological pathway. She and her colleagues worked on identifying the gene corresponding to an enzyme involved in the aflatoxin biosynthetic pathway in fungus, furthering their understanding of the pathways in natural product biosynthesis. For example, aflatoxins are a family of carcinogenic toxins that are produced by fungi and can be found contaminating grain and peanuts (peanut butter). Aflatoxin can cause liver cancer. In the United States, we screen our crops for the contaminant, but other countries might not.

“My interest is studying these pathways,” she said. Because nature produces antifungal, anticancer and antibacterial agents, she asks questions like, What structural features of the molecule inhibit growth, and How can we modify and make a better antifungal [agent]?

“By applying knowledge gained from understanding the biosynthetic pathway, and the genes involved in that pathway, one can learn from nature and perhaps make the next new therapeutic drug based on that knowledge,” she said. “Learning from nature is really cool!”

Lipsett describes herself as “jumping” into mitochondrial DNA. Her mitochondrial genomic studies began with looking at genomic variations in mitochondrial DNA, some of which have been identified as causing mitochondrial myopathies.

Plucking Patent

This past January, Lipsett received some exciting news: A letter notifying her that she was issued a United States patent for the “Isolation and Characterization of a Single Mitochondron.”

Lipsett explained that one characteristic of mitochondria is that it contains multiple copies of the mitochondrial genome, and each cell can contain many mitochondria.

“If there is a mutation in one copy of the genome, and there are 100 copies total, the other 99 copies are fine,” she said. “So why should one copy interfere with the cell?” Her questions led to studies to learn more about how that one modified copy becomes the predominant version, and therefore, causative of mitochondrial disease symptoms.

She and her colleagues at the National Institute of Standards and Technology designed a technique using what is described as “optical tweezers” that can trap and then isolate a single mitochodrion using an infrared laser.  

Lipsett decided to apply for the patent after speaking with one of her former research students.

“Christian Bauer ’97, a biochemistry and molecular biology major, went to get his master’s in forensic science,” said Lipsett. Bauer continued his education and became a patent attorney. “He was visiting to speak with students for a career panel, and he said, ‘apply for a patent—that’s intellectual property!’”

Lipsett switched gears and began examining nuclear—as opposed to the mitochondrial—genomic variations. During a sabbatical at the National Cancer Institute in Frederick, her research path transitioned to examining pedigrees of large mammals in order to identify the gene responsible for a specific disease.

“I like learning new tools for finding that needle in the haystack, that Eureka moment,” she said. “We haven’t found it yet in the deafness project, but we’ve gathered enough information from this deaf horse study to think it’s more complex than just one gene.”


          Research Technician I - Cold Spring Harbor Laboratory - Cold Spring Harbor, NY   
The core will collaborate with CSHL and other regional investigators to design, execute, and interpret single-cell genomics experiments, as well as develop...
From Cold Spring Harbor Laboratory - Wed, 21 Jun 2017 19:55:00 GMT - View all Cold Spring Harbor, NY jobs
          Rethink Big and Europe?s Position in Big Data   

I will here take a break from core database and talk a bit about EU policies for research funding.

I had lunch with Stefan Manegold of CWI last week, where we talked about where European research should go. Stefan is involved in RETHINK big, a European research project for compiling policy advice regarding big data for EC funding agencies. As part of this, he is interviewing various stakeholders such as end user organizations and developers of technology.

RETHINK big wants to come up with a research agenda primarily for hardware, anything from faster networks to greener data centers. CWI represents software expertise in the consortium.

So, we went through a regular questionnaire about how we see the landscape. I will summarize this below, as this is anyway informative.

Core competence

My own core competence is in core database functionality, specifically in high performance query processing, scale-out, and managing schema-less data. Most of the Virtuoso installed base is in the RDF space, but most potential applications are in fact outside of this niche.

User challenges

The life sciences vertical is the one in which I have the most application insight, from going to Open PHACTS meetings and holding extensive conversations with domain specialists. We have users in many other verticals, from manufacturing to financial services, but there I do not have as much exposure to the actual applications.

Having said this, the challenges throughout tend to be in diversity of data. Every researcher has their MySQL database or spreadsheet, and there may not even be a top level catalogue of everything. Data formats are diverse. Some people use linked data (most commonly RDF) as a top level metadata format. The application data, such as gene sequences or microarray assays, reside in their native file formats and there is little point in RDF-izing these.

There are also public data resources that are published in RDF serializations as vendor-neutral, self-describing format. Having everything as triples, without a priori schema, makes things easier to integrate and in some cases easier to describe and query.

So, the challenge is in the labor intensive nature of data integration. Data comes with different levels of quantity and quality, from hand-curated to NLP extractions. Querying in the single- or double-digit terabyte range with RDF is quite possible, as we have shown many times on this blog, but most use cases do not even go that far. Anyway, what we see on the field is primarily a data diversity game. The scenario is data integration; the technology we provide is database. The data transformation proper, data cleansing, units of measure, entity de-duplication, and such core data-integration functions are performed using diverse, user-specific means.

Jerven Bolleman of the Swiss Institute of Bioinformatics is a user of ours with whom we have long standing discussions on the virtues of federated data and querying. I advised Stefan to go talk to him; he has fresh views about the volume challenges with unexpected usage patterns. Designing for performance is tough if the usage pattern is out of the blue, like correlating air humidity on the day of measurement with the presence of some genomic patterns. Building a warehouse just for that might not be the preferred choice, so the problem field is not exhausted. Generally, I’d go for warehousing though.

What technology would you like to have? Network or power efficiency?

OK. Even a fast network is a network. A set of processes on a single shared-memory box is also a kind of network. InfiniBand is maybe half the throughput and 3x the latency of single threaded interprocess communication within one box. The operative word is latency. Making large systems always involves a network or something very much like one in large scale-up scenarios.

On the software side, next to nobody understands latency and contention; yet these are the one core factor in any pursuit of scalability. Because of this situation, paradigms like MapReduce and bulk synchronous parallel (BSP) processing have become popular because these take the communication out of the program flow, so the programmer cannot muck this up, as otherwise would happen with the inevitability of destiny. Of course, our beloved SQL or declarative query in general does give scalability in many tasks without programmer participation. Datalog has also been used as a means of shipping computation around, as in the the work of Hellerstein.

There are no easy solutions. We have built scale-out conscious, vectorized extensions to SQL procedures where one can express complex parallel, distributed flows, but people do not use or understand these. These are very useful, even indispensable, but only on the inside, not as a programmer-facing construct. MapReduce and BSP are the limit of what a development culture will absorb. MapReduce and BSP do not hide the fact of distributed processing. What about things that do? Parallel, partitioned extensions to Fortran arrays? Functional languages? I think that all the obvious aids to parallel/distributed programming have been conceived of. No silver bullet; just hard work. And above all the discernment of what paradigm fits what problem. Since these are always changing, there is no finite set of rules, and no substitute for understanding and insight, and the latter are vanishingly scarce. "Paradigmatism," i.e., the belief that one particular programming model is a panacea outside of its original niche, is a common source of complexity and inefficiency. This is a common form of enthusiastic naïveté.

If you look at power efficiency, the clusters that are the easiest to program consist of relatively few high power machines and a fast network. A typical node size is 16+ cores and 256G or more RAM. Amazon has these in entirely workable configurations, as documented earlier on this blog. The leading edge in power efficiency is in larger number of smaller units, which makes life again harder. This exacerbates latency and forces one to partition the data more often, whereas one can play with replication of key parts of data more freely if the node size is larger.

One very specific item where research might help without having to rebuild the hardware stack would be better, lower-latency exposure of networks to software. Lightweight threads and user-space access, bypassing slow protocol stacks, etc. MPI has some of this, but maybe more could be done.

So, I will take a cluster of such 16-core, 256GB machines on a faster network, over a cluster of 1024 x 4G mobile phones connected via USB. Very selfish and unecological, but one has to stay alive and life is tough enough as is.

Are there pressures to adapt business models based on big data?

The transition from capex to opex may be approaching maturity, as there have been workable cloud configurations for the past couple of years. The EC2 from way back, with at best a 4 core 16G VM and a horrible network for $2/hr, is long gone. It remains the case that 4 months of 24x7 rent in the cloud equals the purchase price of physical hardware. So, for this to be economical long-term at scale, the average utilization should be about 10% of the peak, and peaks should not be on for more than 10% of the time.

So, database software should be rented by the hour. A 100-150% markup for the $2.80 a large EC2 instance costs would be reasonable. Consider that 70% of the cost in TPC benchmarks is database software.

There will be different pricing models combining different up-front and per-usage costs, just as there are for clouds now. If the platform business goes that way and the market accepts this, then systems software will follow. Price/performance quotes should probably be expressed as speed/price/hour instead of speed/price.

The above is rather uncontroversial but there is no harm restating these facts. Reinforce often.

Well, the question is raised, what should Europe do that would have tangible impact in the next 5 years?

This is a harder question. There is some European business in wide area and mobile infrastructures. Competing against Huawei will keep them busy. Intel and Mellanox will continue making faster networks regardless of European policies. Intel will continue building denser compute nodes, e.g., integrated Knight’s Corner with dual IB network and 16G fast RAM on chip. Clouds will continue making these available on demand once the technology is in mass production.

What’s the next big innovation? Neuromorphic computing? Quantum computing? Maybe. For now, I’d just do more engineering along the core competence discussed above, with emphasis on good marketing and scalable execution. By this I mean trained people who know something about deployment. There is a huge training gap. In the would-be "Age of Data," knowledge of how things actually work and scale is near-absent. I have offered to do some courses on this to partners and public alike, but I need somebody to drive this show; I have other things to do.

I have been to many, many project review meetings, mostly as a project partner but also as reviewer. For the past year, the EC has used an innovation questionnaire at the end of the meetings. It is quite vague, and I don’t think it delivers much actionable intelligence.

What would deliver this would be a venture capital type activity, with well-developed networks and active participation in developing a business. The EC is not now set up to perform this role, though. But the EC is a fairly large and wealthy entity, so it could invest some money via this type of channel. Also there should be higher individual incentives and rewards for speed and excellence. Getting the next Horizon 2020 research grant may be good, but better exists. The grants are competitive enough and the calls are not bad; they follow the times.

In the projects I have seen, productization does get some attention, e.g., the LOD2 stack, but it is not something that is really ongoing or with dedicated commercial backing. It may also be that there is no market to justify such dedicated backing. Much of the RDF work has been "me, too" — let’s do what the real database and data integration people do, but let’s just do this with triples. Innovation? Well, I took the best of the real DB world and adapted this to RDF, which did produce a competent piece of work with broad applicability, extending outside RDF. Is there better than this? Well, some of the data integration work (e.g., LIMES) is not bad, and it might be picked up by some of the players that do this sort of thing in the broader world, e.g., Informatica, the DI suites of big DB vendors, Tamr, etc. I would not know if this in fact adds value to the non-RDF equivalents; I do not know the field well enough, but there could be a possibility.

The recent emphasis for benchmarking, spearheaded by Stefano Bertolo is good, as exemplified by the LDBC FP7. There should probably be one or two projects of this sort going at all times. These make challenges known and are an effective means of guiding research, with a large multiplier: Once a benchmark gets adopted, infinitely more work goes into solving the problem than in stating it in the first place.

The aims and calls are good. The execution by projects is variable. For 1% of excellence, there apparently must be 99% of so-and-so, but this is just a fact of life and not specific to this context. The projects are rather diffuse. There is not a single outcome that gets all the effort. In this, the level of engagement of participants is less and focus is much more scattered than in startups. A really hungry, go-getter mood is mostly absent. I am a believer in core competence. Well, most people will agree that core competence is nice. But the projects I have seen do not drive for it hard enough.

It is hard to say exactly what kinds of incentives could be offered to encourage truly exceptional work. The American startup scene does offer high rewards and something of this could be transplanted into the EC project world. I would not know exactly what form this could take, though.


          Master Grower - Horticulture - Fox D Consulting - Greater Toronto Area, ON   
Understanding of biotechnology, molecular biology and genomics preferred. NIAGARA ONTARIO, CHATHAM ONTARIO, MUSKOKA REGION, BRANT REGION, GTA.... $50,000 - $100,000 a year
From Indeed - Wed, 28 Jun 2017 12:14:28 GMT - View all Greater Toronto Area, ON jobs
          IT Deskside Support - Bilingual - Eurofins Canada - Toronto, ON   
We are also number one in the field of environmental laboratory services and one of the global market leaders in agroscience, genomics, discovery pharmacology,...
From Indeed - Fri, 09 Jun 2017 12:58:51 GMT - View all Toronto, ON jobs
          Laboratory Analyst I - Food Microbiology - Eurofins-Experchem Inc. - Toronto, ON   
It is also number one in the field of environmental laboratory services and one of the global market leaders in agro science, genomics, discovery pharmacology,...
From Indeed - Thu, 11 May 2017 23:32:46 GMT - View all Toronto, ON jobs
          Pooled-DNA sequencing identifies genomic regions of selection in Nigerian isolates of Plasmodium falciparum.   

Pooled-DNA sequencing identifies genomic regions of selection in Nigerian isolates of Plasmodium falciparum.

Parasit Vectors. 2017 Jun 29;10(1):320

Authors: Oyebola KM, Idowu ET, Olukosi YA, Awolola TS, Amambua-Ngwa A

Abstract
BACKGROUND: The burden of falciparum malaria is especially high in sub-Saharan Africa. Differences in pressure from host immunity and antimalarial drugs lead to adaptive changes responsible for high level of genetic variations within and between the parasite populations. Population-specific genetic studies to survey for genes under positive or balancing selection resulting from drug pressure or host immunity will allow for refinement of interventions.
METHODS: We performed a pooled sequencing (pool-seq) of the genomes of 100 Plasmodium falciparum isolates from Nigeria. We explored allele-frequency based neutrality test (Tajima's D) and integrated haplotype score (iHS) to identify genes under selection.
RESULTS: Fourteen shared iHS regions that had at least 2 SNPs with a score > 2.5 were identified. These regions code for genes that were likely to have been under strong directional selection. Two of these genes were the chloroquine resistance transporter (CRT) on chromosome 7 and the multidrug resistance 1 (MDR1) on chromosome 5. There was a weak signature of selection in the dihydrofolate reductase (DHFR) gene on chromosome 4 and MDR5 genes on chromosome 13, with only 2 and 3 SNPs respectively identified within the iHS window. We observed strong selection pressure attributable to continued chloroquine and sulfadoxine-pyrimethamine use despite their official proscription for the treatment of uncomplicated malaria. There was also a major selective sweep on chromosome 6 which had 32 SNPs within the shared iHS region. Tajima's D of circumsporozoite protein (CSP), erythrocyte-binding antigen (EBA-175), merozoite surface proteins - MSP3 and MSP7, merozoite surface protein duffy binding-like (MSPDBL2) and serine repeat antigen (SERA-5) were 1.38, 1.29, 0.73, 0.84 and 0.21, respectively.
CONCLUSION: We have demonstrated the use of pool-seq to understand genomic patterns of selection and variability in P. falciparum from Nigeria, which bears the highest burden of infections. This investigation identified known genomic signatures of selection from drug pressure and host immunity. This is evidence that P. falciparum populations explore common adaptive strategies that can be targeted for the development of new interventions.

PMID: 28662682 [PubMed - in process]


          Stage-Specific Transcriptome and Proteome Analyses of the Filarial Parasite Onchocerca volvulus and Its Wolbachia Endosymbiont.   
Related Articles

Stage-Specific Transcriptome and Proteome Analyses of the Filarial Parasite Onchocerca volvulus and Its Wolbachia Endosymbiont.

MBio. 2016 Nov 23;7(6):

Authors: Bennuru S, Cotton JA, Ribeiro JM, Grote A, Harsha B, Holroyd N, Mhashilkar A, Molina DM, Randall AZ, Shandling AD, Unnasch TR, Ghedin E, Berriman M, Lustigman S, Nutman TB

Abstract
Onchocerciasis (river blindness) is a neglected tropical disease that has been successfully targeted by mass drug treatment programs in the Americas and small parts of Africa. Achieving the long-term goal of elimination of onchocerciasis, however, requires additional tools, including drugs, vaccines, and biomarkers of infection. Here, we describe the transcriptome and proteome profiles of the major vector and the human host stages (L1, L2, L3, molting L3, L4, adult male, and adult female) of Onchocerca volvulus along with the proteome of each parasitic stage and of its Wolbachia endosymbiont (wOv). In so doing, we have identified stage-specific pathways important to the parasite's adaptation to its human host during its early development. Further, we generated a protein array that, when screened with well-characterized human samples, identified novel diagnostic biomarkers of O. volvulus infection and new potential vaccine candidates. This immunomic approach not only demonstrates the power of this postgenomic discovery platform but also provides additional tools for onchocerciasis control programs.
IMPORTANCE: The global onchocerciasis (river blindness) elimination program will have to rely on the development of new tools (drugs, vaccines, biomarkers) to achieve its goals by 2025. As an adjunct to the completed genomic sequencing of O. volvulus, we used a comprehensive proteomic and transcriptomic profiling strategy to gain a comprehensive understanding of both the vector-derived and human host-derived parasite stages. In so doing, we have identified proteins and pathways that enable novel drug targeting studies and the discovery of novel vaccine candidates, as well as useful biomarkers of active infection.

PMID: 27881553 [PubMed - indexed for MEDLINE]


          Recurrent hormone-binding domain truncated ESR1 amplifications in primary endometrial cancers suggest their implication in hormone independent growth   
Recurrent hormone-binding domain truncated ESR1 amplifications in primary endometrial cancers suggest their implication in hormone independent growth Holst, Frederik; Hoivik, Erling A.; Taylor-Weiner, Amaro; Schumacher, Steven E.; Asmann, Yan W.; Grossmann, Patrick; Trovik, Jone; Necela, Brian M.; Thompson, E. Aubrey; Salvesen, Helga B.; Cherniack, Andrew D.; Gibson, William J; Meyerson, Matthew L; Beroukhim, Rameen The estrogen receptor alpha (ERα) is highly expressed in both endometrial and breast cancers, and represents the most prevalent therapeutic target in breast cancer. However, anti-estrogen therapy has not been shown to be effective in endometrial cancer. Recently it has been shown that hormone-binding domain alterations of ERα in breast cancer contribute to acquired resistance to anti-estrogen therapy. In analyses of genomic data from The Cancer Genome Atlas (TCGA), we observe that endometrial carcinomas manifest recurrent ESR1 gene amplifications that truncate the hormone-binding domain encoding region of ESR1 and are associated with reduced mRNA expression of exons encoding the hormone-binding domain. These findings support a role for hormone-binding alterations of ERα in primary endometrial cancer, with potentially important therapeutic implications.
          Project Interlinking Blockchain and Genomics Raises $824k Ahead of ICO Closure   

A blockchain project aiming to push the perimeters of ownership and protection of genomics data has raised around $824,000 in an ongoing ICO round. Gene-Chain, as the project is titled, demonstrates a blockchain which a) secures personal genomic data from cloud breaches, and b) enables the sharing of genomic data among researchers and medical practitioners. […]

The post Project Interlinking Blockchain and Genomics Raises $824k Ahead of ICO Closure appeared first on The Bitcoin News - Leading Bitcoin and Crypto News since 2012.


          Encrypgen Announces New Bonus Structure for Its Ongoing ICO   

Encrypgen, the company behind Gene Chain, a blockchain solution for the genomics industry has announced a new bonus structure for its ongoing ICO. With another 17 days, the Gene Chain Coin ICO will now have weekly bonus slabs starting June 29, 2017. As per the new bonus structure, investors purchasing the Gene-Chain tokens during this […]

The post Encrypgen Announces New Bonus Structure for Its Ongoing ICO appeared first on The Bitcoin News - Leading Bitcoin and Crypto News since 2012.


          Research Technician I - Cold Spring Harbor Laboratory - Cold Spring Harbor, NY   
The core will collaborate with CSHL and other regional investigators to design, execute, and interpret single-cell genomics experiments, as well as develop...
From Cold Spring Harbor Laboratory - Wed, 21 Jun 2017 19:55:00 GMT - View all Cold Spring Harbor, NY jobs
          Precipio Diagnostics And Transgenomic, Inc. Complete Merger    
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          Genoptix, Inc. And BioNano Genomics Announce Strategic Alliance    
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          Veracyte Announces Publication Of Study Supporting The Development Of Envisia Genomic Classifier For IPF In    
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          FDA, NCI to study cancer proteogenomics together   
The FDA and the National Cancer Institute will collaborate on clinical proteogenomics cancer research, including "statistical -More

          Mammoth task: billionaire Peter Thiel funded effort to resurrect woolly beast   

Mammoth task: billionaire Peter Thiel funded effort to resurrect woolly beastPayPal billionaire and Gawker war-wager Peter Thiel has invested $100,000 in a research effort to resurrect the woolly mammoth. Thiel, who believes that viewing death as inevitable is a sign of “complacency of the western world”, gave the money to Harvard University genomics professor George Church, whose laboratory is attempting to revive the extinct pachyderm. The donation, detailed for the first time in a new book by Ben Mezrich called Woolly: The True Story of the Quest to Revive One of History’s Most Iconic Extinct Creatures, was made in 2015.



          Research Technician I - Cold Spring Harbor Laboratory - Cold Spring Harbor, NY   
The core will collaborate with CSHL and other regional investigators to design, execute, and interpret single-cell genomics experiments, as well as develop...
From Cold Spring Harbor Laboratory - Wed, 21 Jun 2017 19:55:00 GMT - View all Cold Spring Harbor, NY jobs
          EDITORIALE: Pensiero forestale   
Negli ultimi decenni la capacità di crescita scientifica del settore forestale appare del tutto straordinaria, in grado di cambiare rapidamente qualsiasi quadro di riferimento e di aprirsi concretamente ai temi emergenti collegati alla genomica, alle biotecnologie, alle nanotecnologie, alle tecnologie spaziali e a quelle informatiche. Al contempo, da più parti viene, però, spesso evidenziata una certa carenza di cultura selvicolturale, condizione non di rado ostativa per una diffusione realmente efficace dei risultati della ricerca e per un adeguato trasferimento delle conoscenze scientifiche anche laddove è possibile fare riferimento a soluzioni innovative.
          alikhan4312 posted a blog post   
alikhan4312 posted a blog post

Ni-NTA resin column

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          Master Grower - Horticulture - Fox D Consulting - Greater Toronto Area, ON   
Understanding of biotechnology, molecular biology and genomics preferred. NIAGARA ONTARIO, CHATHAM ONTARIO, MUSKOKA REGION, BRANT REGION, GTA.... $50,000 - $100,000 a year
From Indeed - Wed, 28 Jun 2017 12:14:28 GMT - View all Greater Toronto Area, ON jobs
          CPTS Program   
The major objectives of this Master's Degree program are to provide training in conceptual/theoretical frameworks, research methodologies, and statistical methods essential to the design and conduct of clinical and epidemiologic research; to provide training in the fundamentals of molecular biology, genetics/genomics and genetic epidemiology; and to provide training in the basic skills of grant and manuscript preparation.
          Bioinformatics Specialist-Metagenomics/Proteomics - Signature Science, LLC - Austin, TX   
Travel to project and business development meetings as needed. Familiarity with machine learning, Git, and agile software development is a plus;... $90,000 a year
From Signature Science, LLC - Tue, 06 Jun 2017 09:05:50 GMT - View all Austin, TX jobs
          Il futuro della ricerca oncologica nei sei progetti tra Cro e imprese regionali finanziati con 900 mila euro   
L’Istituto Nazionale Tumori di Aviano è l’assegnatario di sei progetti inseriti nei bandi di finanziamento Por-Fesr 2016. I coordinatori dei gruppi di lavoro sono Roberta Maestro e Alessandra Viel (Oncogenetica e Oncogenomica Funzionale), Federico Polo ed Erika Cecchin (Farmacologia Sperimentale e Clinica) e Vincenzo Canzonieri di Anatomia Patologica a indirizzo Oncologico
          Master Grower - Horticulture - Fox D Consulting - Greater Toronto Area, ON   
Understanding of biotechnology, molecular biology and genomics preferred. NIAGARA ONTARIO, CHATHAM ONTARIO, MUSKOKA REGION, BRANT REGION, GTA.... $50,000 - $100,000 a year
From Indeed - Wed, 28 Jun 2017 12:14:28 GMT - View all Greater Toronto Area, ON jobs
          Front End Developer SD2 (Environmental Genomics & Systems Biology) - Lawrence Berkeley National Laboratory - Berkeley, CA   
Berkeley Lab’s Environmental Genomics & Systems Biology Division has an opening for a Front End Developer. As part of the KBase implementation team, you will
From Lawrence Berkeley National Laboratory - Tue, 30 May 2017 19:54:31 GMT - View all Berkeley, CA jobs
          Research Technician I - Cold Spring Harbor Laboratory - Cold Spring Harbor, NY   
The core will collaborate with CSHL and other regional investigators to design, execute, and interpret single-cell genomics experiments, as well as develop...
From Cold Spring Harbor Laboratory - Wed, 21 Jun 2017 19:55:00 GMT - View all Cold Spring Harbor, NY jobs
           Characterization of drug-resistant neuroblastoma cell lines by comparative genomic hybridization.    
Bedrnicek, J. and Vicha, A. and Jarosova, M. and Holzerova, M. and Cinatl, Jindrich and Michaelis, Martin and Cinatl, Jaroslav and Eckschlager, T. (2005) Characterization of drug-resistant neuroblastoma cell lines by comparative genomic hybridization. Neoplasma, 52 (5). pp. 415-9. ISSN 0028-2685. (The full text of this publication is not currently available from this repository. You may be able to access a copy if URLs are provided)
          Post Doc Computational - Cold Spring Harbor Laboratory - Cold Spring Harbor, NY   
Ancient gene flow from early modern humans into Eastern Neanderthals. Postdoctoral Positions in Computational Genomics....
From Cold Spring Harbor Laboratory - Wed, 29 Mar 2017 17:25:11 GMT - View all Cold Spring Harbor, NY jobs
          Envisioning the scientific community as One Big Lab   
The blogosphere has been abuzz recently, or, at least, it seems that way if you've only been checking up on it sporadically the last few weeks. Jennifer Rohn's post about lab notebooks has spurred over 100 lively comments spanning electronic lab notebooks, peer-review, openness in science, and the reward system in science, making for an engrossing peek at the social science of science. Cameron's own musings on that discussion. Pawel Szczesny writes about what it means to be a freelancing scientist. All of this is fascinating and it is exciting to contemplate both what the future of science holds and the obstacles we will need to overcome; the fact that there are indeed stubborn obstacles (technological as well as cultural) and potentially tremendous rewards makes the anticipation of that future all the more heightened.

Emboldened by the collective fervor, I would like to propose an idea - an idea with the same name as this blog. But first, the back story.

About 8 months ago, one of my lab mates was writing up a short paper for submission to a translational bioinformatics conference. The work she was submitting revolved around a powerful literature-search tool tailored for pharmacogenomics called Pharmspresso. Although Pharmspresso had features lacking in existing search methods and was thus useful, the intent was for it to recognize genes, drugs and polymorphisms in free text, and so she needed a way to evaluate its performance. The evaluation task would be straightforward: given a set of pharmacogenomics papers, what percentage of the mentions of genes, drugs, and polymorphisms does Pharmspresso capture? Getting the list of recognized entities from Pharmspresso would be easy, just give it the documents and set it running. But what would be the gold standard?

Typically, gold standards are created by humans. In this case, it would be the list of entities recognized by human readers with the appropriate knowledge to make the distinctions, in the same set of papers. To get her gold standard then, she essentially asked favors of her colleagues in the lab and the department, which translated to a number of them reading papers and doing data entry during free time (or during faculty talks) at a departmental retreat in early fall - not exactly fun, but done out of a sense of duty to science and the goodness of their hearts.

Afterwards, while socializing during one of the poster sessions, this task came up, and the discussion (in which Samuel Flores, Magda Jonikas, Yael Garten, Alain Laederach, and Bernie Daigle all participated) quickly turned to alternative solutions for tackling this and similar problems in science - those requiring knowledge and resources external to your own. As another example, many bioinformaticians work on problems that produce predictions of functions which would benefit from experimental tests of their validity. Conversely, a wet lab may benefit greatly from someone with computational expertise guiding or leading the data analysis, or even providing the hypotheses for experimental studies (in the form of predictions). This is the stuff from which many collaborations are born, but it may be difficult to find the right people in the first place, or the task at hand might seem not quite collaboration-worthy.

In essence, the problem boils down to this: you or your lab possesses a certain collection of skills, knowledge, and resources (hereafter referred to as simply resources), but your needs may not be fully addressed by what you possess. The solution lies in this simple proposition: some other person or lab has what you're looking for.

While it makes sense for a lab or individual to grow their resources and be mostly self-sufficient, at some point it becomes more economical to outsource certain tasks - to companies for antibody development, software for data analysis, supercomputers for high-throughput computing, etc. In some cases, the exchange takes place directly at the academic level, for example, with some labs maintaining and sharing specific cell lines or mouse strains for use by other researchers, or less directly through the use of published and available tools for all sorts of tasks in bioinformatics. So it would seem that outsourcing is common and accepted. But aside from these sorts of established avenues, what other needs do scientists have in conducting their research that are not easily solved? How often is a line of inquiry abandoned or slowed because of a lack of necessary skills, knowledge, or material resources?

The idea behind One Big Lab is that the scientific community should act as, well, one big lab, sharing resources when it makes sense, and everyone, especially the community as a whole, benefits.

During that discussion at the departmental retreat, the solution boiled down to some form of online transaction service built around a credit system. Scientist X would like 5 gold standard outputs for a certain task, so she posts a description of the task along with some credit attached. Other users can then sign up to complete the task, after which they receive the stated number of credits. Of course, in order to post tasks, you need to have a balance of credits you can draw from - which you earn by doing other people's tasks. Getting credits into the system to start needs to be figured out (give everyone N credits? Money for credits?), but assuming there's some baseline of credit floating around amongst the various users, an equilibrium should eventually be reached (at least, that's the hope).

Variations on this theme are natural - have a peer rating system, have the final credit payment be subject to a bidding system (based somehow on user ratings, e.g. highly rated users can ask for more credits to complete a task and the task-poster may select which user to "hire" based on the user ratings as well as how much each user is asking), have some kind of mechanism for taking transactions "offline" into serious collaborations, etc. Tasks may run the gamut from routine and rote to intellectually stimulating and scientifically rewarding. Obviously, guidelines will have to be set for what transactions may be appropriate for this forum and which ones might be more suited for formal, collaborative relationships - but even here, a forum such as this could be very useful for finding collaborators.

In addition to the scientific transaction system, there could be other features that build on the community aspect, such as journal clubs, informal manuscript review, resources for students, and discussion forums. There could be repositories for knowledge or links to existing ones, informal or formal consulting, and casual exchange of ideas which could stimulate research or professional development. All of this should reinforce the idea that science is strengthened by community and the scientific community should not be held back by insufficient allocation of resources.

Although there are a number of websites out there that tackle some of these aspects, especially the community-building ones, I haven't really seen much resembling the transaction system, which is really the core of the idea. Pawel's freelance science comes close, and what I'd like to see is a formalized community-wide online service for essentially that. Maybe this is technically infeasible right now right the way grants work (it may be difficult to justify spending time or resources on other people's research) or with the way scientists work, but I would like to think that the basic premise - bringing together people with complementary skills and resources - makes sense and balances out in everyone's favor. (Whether this premise actually pans out in practice is up for debate - if we offered credits for cash, would anyone ever do someone else's tasks, or would demand outpace supply? By the same token, there could be "freelance" scientists like Pawel who primarily complete tasks, and could then have the option of "cashing out".) I'm sure there are a ton of tricky legal, IP, financial, organizational, etc not to mention social and cultural issues (would you trust someone you don't know to do work for you?), but I think the idea of having One Big Lab is worth exploring.

If I had the time, skills, and business acumen I would throw together a prototype and work out a business plan, but at the moment the most I can do is outsource it to the closest thing we have to One Big Lab - the blogosphere. ;)

Incidentally, Alain Laederach had come up with a similar idea about a year earlier and we thought about naming it "Experitrade" - an online system for trading experiments, essentially, but the name sounded too corporate and the grant he wrote never got off the ground. But the idea has persisted and inspired One Big Lab.

So, I'd welcome any thoughts, logical extensions, deal-makers or deal-breakers, important issues to consider, "prior art"... does anyone think this idea has legs? Will it work if it is completely altruistic? Does adding money into the equation detract from its mission or the science? What sorts of technical and organizational roadblocks are there? Clearly it makes the most sense, if any prototype is developed, to start small - with a couple participating labs or within a school or university, which helps with the trust issue as well. But I'd like to make sure I'm not completely missing the picture!
          AMIA Summit on Translational Bioinformatics   





Hundreds of clinical scientists, biologists, bioinformaticians, and policy gurus descended on the swanky Intercontinental Mark Hopkins hotel for the first AMIA-sponsored Summit on Translational Bioinformatics last week. Stanford's Atul Butte rallied impressive troops for this inaugural meeting, including the leaders of all of the National Centers for Biomedical Computation (NCBCs, 7 or so total). Since translational bioinformatics is not simply about research, but about translating research into tangible benefits (clinical diagnostics, therapeutics, and standard of care), this meant a many faceted conversation involving basic researchers, large-scale integrative projects (e.g. caBIG, the NCBCs), clinical scientists, informaticians, and government agencies. This was reflected by the structure of the meeting, which consisted of tutorials; policy, technology, and organization panels; primary paper sessions; and posters covering topics ranging from how to establish collaborative projects to ontologies and phenomics.

Given the breadth of the audience, I'm sure the highlights of the conference vary from person to person. Below are some of mine:

Eitan Rubin from Ben Gurion University, Israel (Talk highlight). "Reverse translational bioinformatics: a bioinformatics assay of age, gender and clinical biomarker." A self-proclaimed biologist, Eitan presented some intriguing work in what he called "reverse translational bioinformatics" - using clinical/medical data to make useful discoveries about biology. As an additional aim, he strove to show that existing bioinformatics tools could be applied to clinical data with little modification. To do this, he took an immense data set - thousands of variables collected for tens of thousands of individuals (part of a nutrition and lifestyle survey that was epidemiological in nature), including laboratory tests, questionnaire answers, and medication data - and essentially turned it into a microarray after binning by age. Note that this was a proxy for clinical data since no such data is currently publicly available. He then subjected this array to the same kinds of analyses one would perform on an array of molecular biological data: normalization, calculation of median values, clustering by age and variable. The results encompassed both the expected and the surprising. For example, when he clustered by age, he found distinct boundaries between somewhat intuitive ages - at 12 yrs and 16 yrs for both sexes, at 40 yrs for women and again around 49, and around 45 for men; these could point to interesting biological changes going on at these age boundaries. He also plotted the median values for variables like serum lead level vs age and found distinct patterns. At this point, he has only begun to analyze the enormous amounts of data, and more interesting patterns are sure to emerge. In the meantime, it helps drive home the potential behind open data and data (and methods!) re-use.

Yael Garten from Stanford University (talk highlight). "Pharmspresso: a text analysis tool for linking pharmacogenomic concepts." [Disclaimer: Yael and I are colleagues in the same lab and I helped to critique her presentation.] Yael's work on a semantic, scoped search engine for pharmacogenomics is worth mentioning because of its immediate and potential utility. Pharmspresso allows a user to query a corpus of documents (currently about a thousand pharmacogenomic-related articles previously curated by the PharmGKB team) for keywords, genes, drugs, and/or polymorphisms occurring in the same sentences. Based on the Textpresso ontology created for mining the C.elegans literature, Pharmspresso includes semantic support for human genes, drugs, and genetic polymorphisms and additionally improves upon more general search engines such as Google and PubMed by limiting the scope of the hits to the sentence-level and returning hits color-coded within each sentence for easy evaluation of search results. Pharmspresso has already helped the PharmGKB curators and in the future will be incorporated into an automatic curation pipeline.

Selected papers to be published in BMC Bioinformatics. At the close of the conference, the surprise announcement was made that 15 of the 27 presented papers had been selected to be published in a summer issue of BMC Bioinformatics as a joint agreement between the Open Access journal and AMIA, who would foot the bill. The papers would need to be expanded and updated for submission but the peer review process had happened for the conference and so they were already considered accepted for the journal. A couple of big conferences already do something similar - ISMB/ECCB and RECOMB - but it would be great if every major conference had some kind of arrangement like this with a journal. It seems like it would be a win-win for everyone - peer-review already taken care of, an increased audience for that issue of the journal, and a nice CV boost for the authors (and no more hard decisions between presenting at a conference vs publishing in a journal). Given the fact that this was the very first meeting for this conference, it was a very nice surprise indeed.

Thoughtful A/V setup. This is simply a logistical highlight. We've all sat through our share of technical difficulties, but this conference (at least in the main room) was astonishingly free of them. A large part of this was due to the presence of dedicated A/V staff who knew just when to dim and raise the lights, cue mood music, and put up the "transition screen" - a screen blank except for the AMIA logo. This screen went up whenever a presenter's slides were NOT up, and prevented those awkward moments when the audience could see the desktop of the presenter's laptop or the view of the Powerpoint application. It was also nice not to have to see the blue or black screens when video input was changed. All in all, it imparted a much-appreciated professional touch to the conference which other meetings would do well to emulate.

In summary, there were some informative panels on various policies and the NCBCs, interesting research, and nice extras that made this first Summit on Translational Bioinformatics a big success!
          Front End Developer SD2 (Environmental Genomics & Systems Biology) - Lawrence Berkeley National Laboratory - Berkeley, CA   
Berkeley Lab’s Environmental Genomics & Systems Biology Division has an opening for a Front End Developer. As part of the KBase implementation team, you will
From Lawrence Berkeley National Laboratory - Tue, 30 May 2017 19:54:31 GMT - View all Berkeley, CA jobs
          Bacteria Laden Meat in Question, But Don't Eat Fish Instead   

A study conducted by the Arizona-based Translational Genomics Research Institute (TGRI) and released last Friday found that nearly half of all meat products sampled contained high levels of bacteria and some strains were resistant to multiple types of antibiotics. The research team examined 136 meat samples from 26 grocery stores in Illinois, Florida, California, Arizona […]

The post Bacteria Laden Meat in Question, But Don't Eat Fish Instead appeared first on Organic Authority.


          17-0031 Bioanalytical Scientist - USA-CA-La Jolla   
At Synthetic Genomics, Inc., we are dedicated to developing and commercializing genomic-driven solutions to address global challenges. We are currently seeking a Bioanalytical Scientist within our Ana...
          Master Grower - Horticulture - Fox D Consulting - Greater Toronto Area, ON   
Understanding of biotechnology, molecular biology and genomics preferred. NIAGARA ONTARIO, CHATHAM ONTARIO, MUSKOKA REGION, BRANT REGION, GTA.... $50,000 - $100,000 a year
From Indeed - Wed, 28 Jun 2017 12:14:28 GMT - View all Greater Toronto Area, ON jobs
          Post Doc Computational - Cold Spring Harbor Laboratory - Cold Spring Harbor, NY   
Familiarity with UNIX. Professor McCombie is seeking highly motivated Postdoctoral Fellows in Statistical Genomics and Human Genetics for his group at the...
From Cold Spring Harbor Laboratory - Wed, 12 Apr 2017 05:15:08 GMT - View all Cold Spring Harbor, NY jobs
          Post-doctoral Fellow - Functional & Chemical Genomics - Oklahoma Medical Research Foundation - Oklahoma City, OK   
*Posting Number: * 0001040 *Working Title: * Post-doctoral Fellow *Classification* : On-going *Status* : Full-Time *Department: * Functional &...
From Indeed - Tue, 27 Jun 2017 19:39:34 GMT - View all Oklahoma City, OK jobs
          Post Doc Computational - Cold Spring Harbor Laboratory - Cold Spring Harbor, NY   
Gronau I, Arbiza L, Mohammed J, Siepel A. Kuhlwilm M, Gronau I, Hubisz MJ, de Filippo C, Prado J, et al. Postdoctoral Positions in Computational Genomics....
From Cold Spring Harbor Laboratory - Wed, 29 Mar 2017 17:25:11 GMT - View all Cold Spring Harbor, NY jobs
          Front End Developer SD2 (Environmental Genomics & Systems Biology) - Lawrence Berkeley National Laboratory - Berkeley, CA   
Berkeley Lab’s Environmental Genomics & Systems Biology Division has an opening for a Front End Developer. As part of the KBase implementation team, you will
From Lawrence Berkeley National Laboratory - Tue, 30 May 2017 19:54:31 GMT - View all Berkeley, CA jobs
          Research Technician I - Cold Spring Harbor Laboratory - Cold Spring Harbor, NY   
The core will collaborate with CSHL and other regional investigators to design, execute, and interpret single-cell genomics experiments, as well as develop...
From Cold Spring Harbor Laboratory - Wed, 21 Jun 2017 19:55:00 GMT - View all Cold Spring Harbor, NY jobs
          Post Doc Computational - Cold Spring Harbor Laboratory - Cold Spring Harbor, NY   
Ancient gene flow from early modern humans into Eastern Neanderthals. Postdoctoral Positions in Computational Genomics....
From Cold Spring Harbor Laboratory - Wed, 29 Mar 2017 17:25:11 GMT - View all Cold Spring Harbor, NY jobs
          Technical Officer   
NSW-Dubbo, Working for NSW Health Pathology NSW Health Pathology is a government agency that operates for the good of NSW's health and justice systems and the well-being of the community. The organisation invests in its people as well as the technologies that ensure staff can deliver the answers customers need when they need them. NSW Health Pathology is at the forefront of emerging fields such as genomics,
          Master Grower - Horticulture - Fox D Consulting - Greater Toronto Area, ON   
Understanding of biotechnology, molecular biology and genomics preferred. NIAGARA ONTARIO, CHATHAM ONTARIO, MUSKOKA REGION, BRANT REGION, GTA.... $50,000 - $100,000 a year
From Indeed - Wed, 28 Jun 2017 12:14:28 GMT - View all Greater Toronto Area, ON jobs
          Master Grower - Horticulture - Fox D Consulting - Greater Toronto Area, ON   
Understanding of biotechnology, molecular biology and genomics preferred. NIAGARA ONTARIO, CHATHAM ONTARIO, MUSKOKA REGION, BRANT REGION, GTA.... $50,000 - $100,000 a year
From Indeed - Wed, 28 Jun 2017 12:14:28 GMT - View all Greater Toronto Area, ON jobs
          Molecular and FISH analyses of a 53-kbp intact DNA fragment inserted by biolistics in wheat (Triticum aestivum L.) genome.   

Molecular and FISH analyses of a 53-kbp intact DNA fragment inserted by biolistics in wheat (Triticum aestivum L.) genome.

Plant Cell Rep. 2017 Jun 30;:

Authors: Partier A, Gay G, Tassy C, Beckert M, Feuillet C, Barret P

Abstract
KEY MESSAGE: A large, 53-kbp, intact DNA fragment was inserted into the wheat ( Triticum aestivum L.) genome. FISH analyses of individual transgenic events revealed multiple insertions of intact fragments. Transferring large intact DNA fragments containing clusters of resistance genes or complete metabolic pathways into the wheat genome remains a challenge. In a previous work, we showed that the use of dephosphorylated cassettes for wheat transformation enabled the production of simple integration patterns. Here, we used the same technology to produce a cassette containing a 44-kb Arabidopsis thaliana BAC, flanked by one selection gene and one reporter gene. This 53-kb linear cassette was integrated in the bread wheat (Triticum aestivum L.) genome by biolistic transformation. Our results showed that transgenic plants harboring the entire cassette were generated. The inheritability of the cassette was demonstrated in the T1 and T2 generation. Surprisingly, FISH analysis performed on T1 progeny of independent events identified double genomic insertions of intact fragments in non-homoeologous positions. Inheritability of these double insertions was demonstrated by FISH analysis of the T1 generation. Relative conclusions that can be drawn from molecular or FISH analysis are discussed along with future prospects of the engineering of large fragments for wheat transformation or genome editing.

PMID: 28667403 [PubMed - as supplied by publisher]


          Data Scientist   
San Francisco, Data Scientist Company: Ancestry DNA Location: San Francisco, CA Position Type: Full Time Experience: 1 year Education: Master's Degree Data Scientist: Dvlp comp. methods/models to analyze genomic data from genomic samples. Anlze big data from high-throughput sequencing tech platforms. Dvlp & validate machine learning. Req: MSCS & 1 yr. exp. w/ sequencing data, predictive modeling, visualization,
          Second-generation PLINK: rising to the challenge of larger and richer datasets.   

PLINK 1 is a widely used open-source C/C++ toolset for genome-wide association studies and research in population genetics. However, the steady accumulation of data from imputation and whole-genome sequencing studies has exposed a strong need for faster and scalable implementations of key functions, such as logistic regression, linkage disequilibrium estimation, and genomic distance evaluation.


          Research Technician I - Cold Spring Harbor Laboratory - Cold Spring Harbor, NY   
The core will collaborate with CSHL and other regional investigators to design, execute, and interpret single-cell genomics experiments, as well as develop...
From Cold Spring Harbor Laboratory - Wed, 21 Jun 2017 19:55:00 GMT - View all Cold Spring Harbor, NY jobs
          Senior Systems Engineer - Linux/Virtualization/RAID   
San Diego, Located in beautiful San Diego, CA, we deliver on the promise of precision medicine today. Through daily re-computation of individual member clinical and full-sequence genomic data, our analytics provides a prospective clinical interpretation that enables true personalization of therapy, and prevents clinical gaps before they occur. Top Reasons to Work with Us - HUGE Room for Growth - Great Work/L
          Senior Systems Engineer - Linux/Virtualization/RAID   
San Diego, Located in beautiful San Diego, CA, we deliver on the promise of precision medicine today. Through daily re-computation of individual member clinical and full-sequence genomic data, our analytics provides a prospective clinical interpretation that enables true personalization of therapy, and prevents clinical gaps before they occur. Top Reasons to Work with Us - HUGE Room for Growth - Great Work/L
          Manager of Software Development   
Bellevue, If you are a "Hands On" Manager of Software Development with experience, please read on! Located in beautiful Bellevue, WA, we are a rapidly growing SaaS company that is making precision medicine a reality for thousands of physicians every day. We are looking for a Director of Software Development to build the team that will make genomic medicine an integral part of the global health systems. The
          Epigenomics » Übernahmefrist für China-Offerte läuft Freitag ab   
von Klaus Schachinger, €uro am Sonntag

Das Unternehmen hat auf Anfrage von €uro am Sonntag noch einmal für die Annahme der Offerte geworben, wollte aber keine weiteren Details nennen.

Aktionäre halten die ...
          Genomic Signal Processing   

          Introduction to Computational Genomics: A Case Studies Approach   

          ‘Biological Teleportation’ Edges Closer With Craig Venter’s Digital-to-Biological Converter   
The year is 2030. In a high-security containment lab, scientists gathered around a towering machine, eagerly awaiting the first look at a newly discovered bacterium on Mars. With a series of beeps, the machine—a digital-to-biological converter, or DBC—signaled that it had successfully received the bacterium’s digitized genomic file. Using a chemical cocktail comprised of the […]
          Post-doctoral Fellow - Functional & Chemical Genomics - Oklahoma Medical Research Foundation - Oklahoma City, OK   
*Posting Number: * 0001040 *Working Title: * Post-doctoral Fellow *Classification* : On-going *Status* : Full-Time *Department: * Functional &...
From Indeed - Tue, 27 Jun 2017 19:39:34 GMT - View all Oklahoma City, OK jobs
          Post Doc Computational - Cold Spring Harbor Laboratory - Cold Spring Harbor, NY   
Gronau I, Arbiza L, Mohammed J, Siepel A. Kuhlwilm M, Gronau I, Hubisz MJ, de Filippo C, Prado J, et al. Postdoctoral Positions in Computational Genomics....
From Cold Spring Harbor Laboratory - Wed, 29 Mar 2017 17:25:11 GMT - View all Cold Spring Harbor, NY jobs
          Fulltime tenure-track position in the field of nutrition and human intestinal microbiome   
Universite Laval - School of Nutrition - Laval, QC - Quebec City, QC - nutrition or biochemistry or microbiology or a related discipline; 2) Have a recognized expertise in the field of the human intestinal microbiome; 3..., grants or awards; 4) Have demonstrated skills for laboratory work in microbiology, metagenomics, molecular biology and nutritional biochemistry...
          IT Deskside Support - Bilingual - Eurofins Canada - Toronto, ON   
We are also number one in the field of environmental laboratory services and one of the global market leaders in agroscience, genomics, discovery pharmacology,...
From Indeed - Fri, 09 Jun 2017 12:58:51 GMT - View all Toronto, ON jobs
          Laboratory Analyst I - Food Microbiology - Eurofins-Experchem Inc. - Toronto, ON   
It is also number one in the field of environmental laboratory services and one of the global market leaders in agro science, genomics, discovery pharmacology,...
From Indeed - Thu, 11 May 2017 23:32:46 GMT - View all Toronto, ON jobs
          Openwashing   

          Post Doc Computational - Cold Spring Harbor Laboratory - Cold Spring Harbor, NY   
The applicant will be expected to integrate with others at the Stanley Institute and analyze family and population based genomic data of neurological and...
From Cold Spring Harbor Laboratory - Wed, 12 Apr 2017 05:15:08 GMT - View all Cold Spring Harbor, NY jobs
          Bioinformatics Specialist-Metagenomics/Proteomics - Signature Science, LLC - Austin, TX   
Travel to project and business development meetings as needed. Familiarity with machine learning, Git, and agile software development is a plus;... $90,000 a year
From Signature Science, LLC - Tue, 06 Jun 2017 09:05:50 GMT - View all Austin, TX jobs
          Post Doc Computational - Cold Spring Harbor Laboratory - Cold Spring Harbor, NY   
The applicant will be expected to integrate with others at the Stanley Institute and analyze family and population based genomic data of neurological and...
From Cold Spring Harbor Laboratory - Wed, 12 Apr 2017 05:15:08 GMT - View all Cold Spring Harbor, NY jobs
          Buzzword bingo   

Game brings entertainment to genetics meeting

On the Scene

Science is serious business, but some geneticists have found a way to make sitting through scientific lectures a little more fun.

Dozens of researchers attending the American Society of Human Genetics annual meeting are playing buzzword bingo during presentations. The game is played with randomly generated bingo cards on the Interpretome.com web site. Players listen for speakers to spout certain overused words or phrases or flash slides bearing oft-seen images, and then tap the corresponding box on the bingo card. Some of the phrases are ones audiences could hear at any symposium, such as asking if the laser pointer is working or the classic “How am I doing for time?” Others are only-at-genetics-conference entries, including “metagenomics,” “exome chip,” “$1,000 genome” and “missing heritability.” Mentions of a little boy from Wisconsin named Nicholas Volker, whose doctors used analysis of his genetic instruction book as part of his care, or of famous scientists like National Institutes of Health director Francis Collins or father of the personal genetics movement George Church could also earn players a square.

No one is shouting “bingo” in the middle of talks. That would be rude. Game master Konrad Karczewski, a graduate student at Stanford University, says the perfect way to win would be to ask a question of the speaker and incorporate “bingo” into the question. That also hasn’t happened yet as far as he knows. Instead, players who get bingo can submit their scorecard online, and the winners are announced on Twitter.

Karczewski admits his bingo game isn’t just for fun. It’s a type of viral marketing for Interpretome, which aims to help people explore their own genetic makeup (provided they have already paid a company such as 23andMe or Lumigenix to decipher their genomes). The site was created as part of a Stanford course on personalized medicine and genomics.

Whether the marketing scheme is successful remains to be seen, but providing a little levity to genetics, well, that’s a bingo.


          Epigenomics: „Eine Übernahmeprämie von rund 50 Prozent erhält man nicht alle Tage“   
Cathay Fortune will Epigenomics übernehmen. Bis zum 7. Juli können Aktionäre das Angebot der Asiaten annehmen. Geboten werden 7,52 Euro je Aktie. Im Exklusivinterview mit der Redaktion von ...
          Post-dengue acute disseminated encephalomyelitis: A case report and meta-analysis   
by Mohamed Gomaa Kamel, Nguyen Tran Nam, Nguyen Huu Bao Han, Abd-Elaziz El-Shabouny, Abd-ElRahman Mohamed Makram, Fatma Abd-Elshahed Abd-Elhay, Tran Ngoc Dang, Nguyen Le Trung Hieu, Vu Thi Que Huong, Trinh Huu Tung, Kenji Hirayama, Nguyen Tien Huy Background Dengue is one of the most common infectious diseases. The aim of this study was to … Continua la lettura di Post-dengue acute disseminated encephalomyelitis: A case report and meta-analysis
          Transcriptomes of six mutants in the Sen1 pathway reveal combinatorial control of transcription termination across the Saccharomyces cerevisiae genome   
by Xin Chen, Kunal Poorey, Melissa N. Carver, Ulrika Müller, Stefan Bekiranov, David T. Auble, David A. Brow Transcriptome studies on eukaryotic cells have revealed an unexpected abundance and diversity of noncoding RNAs synthesized by RNA polymerase II (Pol II), some of which influence the expression of protein-coding genes. Yet, much less is known about … Continua la lettura di Transcriptomes of six mutants in the Sen1 pathway reveal combinatorial control of transcription termination across the <i>Saccharomyces cerevisiae</i> genome
          2017 ISCB Accomplishment by a Senior Scientist Award given to Pavel Pevzner   
by Christiana N. Fogg, Diane E. Kovats, Bonnie Berger Tratto da: www.plos.org. All site content, except where otherwise noted, is licensed under a Creative Commons Attribution (CC BY) license.
          2017 Outstanding Contributions to ISCB Award: Fran Lewitter   
by Christiana N. Fogg, Diane E. Kovats, Bonnie Berger Tratto da: www.plos.org. All site content, except where otherwise noted, is licensed under a Creative Commons Attribution (CC BY) license.
          2017 ISCB Overton Prize awarded to Christoph Bock   
by Christiana N. Fogg, Diane E. Kovats, Bonnie Berger Tratto da: www.plos.org. All site content, except where otherwise noted, is licensed under a Creative Commons Attribution (CC BY) license.
          2017 ISCB Innovator Award: Aviv Regev   
by Christiana N. Fogg, Diane E. Kovats, Bonnie Berger Tratto da: www.plos.org. All site content, except where otherwise noted, is licensed under a Creative Commons Attribution (CC BY) license.
          Essential multimeric enzymes in kinetoplastid parasites: A host of potentially druggable protein-protein interactions   
by Leah M. Wachsmuth, Meredith G. Johnson, Jason Gavenonis Parasitic diseases caused by kinetoplastid parasites of the genera Trypanosoma and Leishmania are an urgent public health crisis in the developing world. These closely related species possess a number of multimeric enzymes in highly conserved pathways involved in vital functions, such as redox homeostasis and nucleotide … Continua la lettura di Essential multimeric enzymes in kinetoplastid parasites: A host of potentially druggable protein-protein interactions
          Efficacy and safety of available treatments for visceral leishmaniasis in Brazil: A multicenter, randomized, open label trial   
by Gustavo Adolfo Sierra Romero, Dorcas Lamounier Costa, Carlos Henrique Nery Costa, Roque Pacheco de Almeida, Enaldo Viera de Melo, Sílvio Fernando Guimarães de Carvalho, Ana Rabello, Andréa Lucchesi de Carvalho, Anastácio de Queiroz Sousa, Robério Dias Leite, Simone Soares Lima, Thais Alves Amaral, Fabiana Piovesan Alves, Joelle Rode, the Collaborative LVBrasil Group Background There … Continua la lettura di Efficacy and safety of available treatments for visceral leishmaniasis in Brazil: A multicenter, randomized, open label trial
          Cryptococcal meningitis: A neglected NTD?   
by Síle F. Molloy, Tom Chiller, Gregory S. Greene, Jessica Burry, Nelesh P. Govender, Cecilia Kanyama, Sayoki Mfinanga, Sokoine Lesikari, Yacouba N. Mapoure, Charles Kouanfack, Victor Sini, Elvis Temfack, David R. Boulware, Francoise Dromer, David W. Denning, Jeremy Day, Neil R. H. Stone, Tihana Bicanic, Joseph N. Jarvis, Olivier Lortholary, Thomas S. Harrison, Shabbar Jaffar, … Continua la lettura di Cryptococcal meningitis: A neglected NTD?
          Can cancer researchers accurately judge whether preclinical reports will reproduce?   
by Daniel Benjamin, David R. Mandel, Jonathan Kimmelman There is vigorous debate about the reproducibility of research findings in cancer biology. Whether scientists can accurately assess which experiments will reproduce original findings is important to determining the pace at which science self-corrects. We collected forecasts from basic and preclinical cancer researchers on the first 6 … Continua la lettura di Can cancer researchers accurately judge whether preclinical reports will reproduce?
          Landscape and variation of novel retroduplications in 26 human populations   
by Yan Zhang, Shantao Li, Alexej Abyzov, Mark B. Gerstein Retroduplications come from reverse transcription of mRNAs and their insertion back into the genome. Here, we performed comprehensive discovery and analysis of retroduplications in a large cohort of 2,535 individuals from 26 human populations, as part of 1000 Genomes Phase 3. We developed an integrated … Continua la lettura di Landscape and variation of novel retroduplications in 26 human populations
          Genome-scale analysis of the genes that contribute to Burkholderia pseudomallei biofilm formation identifies a crucial exopolysaccharide biosynthesis gene cluster   
by Grace I. Borlee, Brooke A. Plumley, Kevin H. Martin, Nawarat Somprasong, Mihnea R. Mangalea, M. Nurul Islam, Mary N. Burtnick, Paul J. Brett, Ivo Steinmetz, David P. AuCoin, John T. Belisle, Dean C. Crick, Herbert P. Schweizer, Bradley R. Borlee Burkholderia pseudomallei, the causative agent of melioidosis, is an important public health threat due … Continua la lettura di Genome-scale analysis of the genes that contribute to <i>Burkholderia pseudomallei</i> biofilm formation identifies a crucial exopolysaccharide biosynthesis gene cluster
          Sequential sampling of visual objects during sustained attention   
by Jianrong Jia, Ling Liu, Fang Fang, Huan Luo In a crowded visual scene, attention must be distributed efficiently and flexibly over time and space to accommodate different contexts. It is well established that selective attention enhances the corresponding neural responses, presumably implying that attention would persistently dwell on the task-relevant item. Meanwhile, recent studies, … Continua la lettura di Sequential sampling of visual objects during sustained attention
          Environmental change drives accelerated adaptation through stimulated copy number variation   
by Ryan M. Hull, Cristina Cruz, Carmen V. Jack, Jonathan Houseley Copy number variation (CNV) is rife in eukaryotic genomes and has been implicated in many human disorders, particularly cancer, in which CNV promotes both tumorigenesis and chemotherapy resistance. CNVs are considered random mutations but often arise through replication defects; transcription can interfere with replication … Continua la lettura di Environmental change drives accelerated adaptation through stimulated copy number variation
          Low-intensity cognitive-behaviour therapy interventions for obsessive-compulsive disorder compared to waiting list for therapist-led cognitive-behaviour therapy: 3-arm randomised controlled trial of clinical effectiveness   
by Karina Lovell, Peter Bower, Judith Gellatly, Sarah Byford, Penny Bee, Dean McMillan, Catherine Arundel, Simon Gilbody, Lina Gega, Gillian Hardy, Shirley Reynolds, Michael Barkham, Patricia Mottram, Nicola Lidbetter, Rebecca Pedley, Jo Molle, Emily Peckham, Jasmin Knopp-Hoffer, Owen Price, Janice Connell, Margaret Heslin, Christopher Foley, Faye Plummer, Christopher Roberts Background Obsessive-compulsive disorder (OCD) is prevalent … Continua la lettura di Low-intensity cognitive-behaviour therapy interventions for obsessive-compulsive disorder compared to waiting list for therapist-led cognitive-behaviour therapy: 3-arm randomised controlled trial of clinical effectiveness
          A Collection on the prevention, diagnosis, and treatment of sexually transmitted infections: Call for research papers   
by Nicola Low, Nathalie Broutet, Richard Turner Nicola Low and colleagues announce a call for research papers on sexually transmitted infections, to accompany a Collection on the topic. Tratto da: www.plos.org. All site content, except where otherwise noted, is licensed under a Creative Commons Attribution (CC BY) license.
          Effectiveness and equity of sugar-sweetened beverage taxation   
by Sanjay Basu, Kristine Madsen Sanjay Basu and Kristine Madsen discuss the effects of taxes on sugar-sweetened beverages in both Australia and Berkeley, USA. Tratto da: www.plos.org. All site content, except where otherwise noted, is licensed under a Creative Commons Attribution (CC BY) license.
          Vaccination to prevent human papillomavirus infections: From promise to practice   
by Paul Bloem, Ikechukwu Ogbuanu In an essay, Paul Bloem and Ikechukwu Ogbuanu discuss the public health implications of HPV vaccination. Tratto da: www.plos.org. All site content, except where otherwise noted, is licensed under a Creative Commons Attribution (CC BY) license.
          Is This Exxon’s Secret Weapon Against Electric Cars?   
Every now and then, an oil supermajor comes up with what they tout as a breakthrough in scientific research of renewable energy sources. This month, it was ExxonMobil’s turn to report a breakthrough in advanced biofuels. Exxon said that it had found a way to make algae ‘fatter’, and those algae could become part of the (distant) future energy mix, could cut carbon dioxide emissions, and would not compete with food crops like other biofuel sources. Exxon and Synthetic Genomics have been partners since 2009 in researching and developing…
          Bioinformatics Specialist-Metagenomics/Proteomics - Signature Science, LLC - Austin, TX   
Travel to project and business development meetings as needed. Familiarity with machine learning, Git, and agile software development is a plus;... $90,000 a year
From Signature Science, LLC - Tue, 06 Jun 2017 09:05:50 GMT - View all Austin, TX jobs
          In the recurrence club now   

My CT scan this week (done in response to a spike in my CA-125) showed multiple nodules in both lungs and a mass on the outside of my colon. My medical oncologist is calling it a systemic recurrence and says that there's now no chance of a cure or long-term NED. I'm having a biopsy this week for genomic testing; that should help identify the best chemo or immunotherapies. While that is being done, I will probably have two rounds of chemo--probably Carbo and Taxotere (can't have Taxol again because of my neuropathy)--and another CT scan.

What is especially scary is that a scan three months ago showed no cause for concern, so this has come back quite ferociously. I've had a pain in my right side for about a week and I'm sure that's the tumor. My abdomen is not too swollen but I can tell there is more fluid there. This is the first time I've dealt with physical discomfort from the cancer itself, rather than from the treatments. When I think about dying from cancer I've always thought about the suffering caused by all the interventions that come at the end, not pain from the disease itself.

So this is serious now. I've had several days to process the news and am largely used to the idea that my life is not going to be what I hoped it would be, even when I was in treatment. My family and friends have been so supportive; with my family, it's understood that every day we have together is precious, and no one has to say it.

My question for ladies who've been in similar situations is whether anyone has seen significant reduction of tumors like these from additional chemo or from other treatments.

While my oncologist was talking to me, she kept saying "You're not there yet," meaning that there are still treatments that we can try. But in her accent it sounded more like "You're not dead yet." I still laugh when I think about that.

I'm so glad I have the people on this board to talk to now.

Discussion boards: 

          (USA-MI-Ann Arbor) Software Developer   
h2Software Developer/h2 Ann Arbor, MI h4Job Overview/h4 We're looking for a senior full-stack software engineer who can take direction and run with it in building out new products and new product features. This role will be involved in our entire stack, and will take ownership of the services they build. You'll be working directly with our CTO, who built several startups (the last of which was acquired by Edmunds.com), and who authors and contributes to many open source projects, including as a member of the Ruby on Rails core team. h4What We're Looking For:/h4 A highly energetic "A" player who thrives in a fast-paced software development environment and has had a range of experience working full-stack on web-based applications, as well as back-end data processing applications and pipelines handling large amounts of textual, genomic, or similar data. Our ideal candidate will fully engage in the company by contributing great ideas, design, architecture and code development to help us build the next bio-informatics success stories. This is a full-time position working at our Ann Arbor headquarters. h4Position Responsibilities:/h4 liWork directly with CTO and VP of Product Strategy to develop new products product features for our current products./li liDev-Ops, Server Management, AWS and other VPS/li liAutomated Testing, Code Reviews, Team Reviews/li liStaging and Production Releases/li liDatabase Management, High Throughput Data Processing/li liPerform other duties as required to help the Genomenon team achieve its objectives/li /ul Required Skills and Background: liSoftware Languages / Frameworks / Libraries: Ruby and Python (or similar object-oriented languages), Ruby on Rails (or similar MVC frameworks)/li liDatabases and Queues: Postgres (or other SQL), queue and messaging systems, text indexing and search software/li liFront-end Technologies: HTML (obviously), CSS (including pre-processors like SCSS or LESS), JavaScript, DOM frameworks/libraries such as Angular.js and React/li liOS: Linux and OS X (Bash and command-line things)/li liVersion Control: Git (or Mercurial or similar distributed VCS)/li liDemonstrated ability to work in a team environment/li liStrong verbal and written communications skills, able to work independently/li liSelf motivator with strong work ethic with a "can-do" positive attitude/li liDesire to be a part of the fast-paced, high-energy entrepreneurial experience/li /ul Compensation Competitive base salary, health insurance, PTO and holidays, a great work environment, and equity participation opportunities If you are interested in this position, please send your resume with salary requirements to [careers @ genomenon.com]
          Molybdenum-based diazotrophy in a Sphagnum peatland in northern Minnesota.   

Molybdenum-based diazotrophy in a Sphagnum peatland in northern Minnesota.

Appl Environ Microbiol. 2017 Jun 30;:

Authors: Warren MJ, Lin X, Gaby JC, Kretz CB, Kolton M, Morton PL, Pett-Ridge J, Weston DJ, Schadt CW, Kostka JE, Glass JB

Abstract
Microbial N2 fixation (diazotrophy) represents an important nitrogen source to oligotrophic peatland ecosystems, which are important sinks for atmospheric CO2 and susceptible to changing climate. The objectives of this study were: (i) to determine the active microbial group and type of nitrogenase mediating diazotrophy in a ombrotrophic Sphagnum-dominated peat bog (the S1 peat bog, Marcell Experimental Forest, Minnesota, USA); and (ii) to determine the effect of environmental parameters (light, O2, CO2, CH4) on potential rates of diazotrophy measured by acetylene (C2H2) reduction and (15)N2 incorporation. Molecular analysis of metabolically active microbial communities suggested that diazotrophy in surface peat was primarily mediated by Alphaproteobacteria (Bradyrhizobiaceae and Beijerinckiaceae). Despite higher dissolved vanadium (V; 11 nM) than molybdenum (Mo; 3 nM) in surface peat, a combination of metagenomic, amplicon sequencing and activity measurements indicated that Mo-containing nitrogenases dominate over the V-containing form. Acetylene reduction was only detected in surface peat exposed to light, with the highest rates observed in peat collected from hollows with the highest water content. Incorporation of (15)N2 was suppressed 90% by O2 and 55% by C2H2, and was unaffected by CH4 and CO2 amendments. These results suggest that peatland diazotrophy is mediated by a combination of C2H2-sensitive and C2H2-insensitive microbes that are more active at low O2 and show similar activity at high and low CH4Importance Previous studies indicate that diazotrophy provides an important nitrogen source and is linked to methanotrophy in Sphagnum-dominated peatlands. However, the environmental controls and enzymatic pathways of peatland diazotrophy, as well as the metabolically active microbial populations that catalyze this process remain in question. Our findings indicate that oxygen levels and photosynthetic activity override low nutrient availability in limiting diazotrophy, and that members of the Alphaproteobacteria (Rhizobiales) catalyze this process at the bog surface using the molybdenum-based form of the nitrogenase enzyme.

PMID: 28667112 [PubMed - as supplied by publisher]


          Response of microbial community function to fluctuating geochemical conditions within a legacy radioactive waste trench environment.   

Response of microbial community function to fluctuating geochemical conditions within a legacy radioactive waste trench environment.

Appl Environ Microbiol. 2017 Jun 30;:

Authors: Vázquez-Campos X, Kinsela AS, Bligh MW, Harrison JJ, Payne TE, Waite TD

Abstract
During the 1960s, small quantities of radioactive materials were co-disposed with chemical waste at the Little Forest Legacy Site (Sydney, Australia) in three-metre-deep, unlined trenches. Chemical and microbial analyses, including functional and taxonomic information derived from shotgun metagenomics, were collected across a six-week period immediately after a prolonged rainfall event to assess how changing water levels impact upon the microbial ecology and contaminant mobility. Collectively, results demonstrated that oxygen-laden rainwater rapidly altered the redox balance in the trench water, strongly impacting microbial functioning as well as the radiochemistry. Two contaminants of concern, plutonium and americium, were shown to transition from solid-iron-associated species immediately after the initial rainwater pulse, to progressively more soluble moieties as reducing conditions were enhanced. Functional metagenomics revealed the potentially important role that the taxonomically-diverse microbial community played in this transition. In particular, aerobes dominated in the first day followed by an increase of facultative anaerobes/denitrifiers at day four. Towards the mid-end of the sampling period, the functional and taxonomic profiles depicted an anaerobic community distinguished by a higher representation of dissimilatory sulfate reduction and methanogenesis pathways. Our results have important implications to similar near-surface environmental systems in which redox cycling occurs.Importance The role of chemical and microbiological factors in mediating the biogeochemistry of groundwaters from trenches used to dispose of radioactive materials during the 1960s is examined in this study. Specifically, chemical and microbial analyses, including functional and taxonomic information derived from shotgun metagenomics, were collected across a six-week period immediately after a prolonged rainfall event to assess how changing water levels influence microbial ecology and contaminant mobility.Results demonstrate that oxygen-laden rainwater rapidly altered the redox balance in the trench water, strongly impacting microbial functioning as well as the radiochemistry. Two contaminants of concern, plutonium and americium, were shown to transition from solid-iron-associated species immediately after the initial rainwater pulse, to progressively more soluble moieties as reducing conditions were enhanced. Functional metagenomics revealed the important role that the taxonomically-diverse microbial community played in this transition. Our results have important implications to similar near-surface environmental systems in which redox cycling occurs.

PMID: 28667104 [PubMed - as supplied by publisher]


          Comentario en ¿Qué Es La Carragenina?¿Es Segura? ¿Dónde Se Encuentra? por José Arrunategui Rivero   
Esto no es novedad incluso la Leche materna tiene más elementos químicos que muchos productos que se venden en el mercado por poner un ejemplo la leche materna contiene taurina y creatina que son compuestos químicos en estado natural pero para saber si algo es dañino o no, no interesa si es natural o artificial lo que interesa es la dosis que ingieres la toxicidad está en la dosis si consumes Glutamato Monosodico una vez a la semana quizás no te haga daño a que si lo consumes a diario, si te pica una Abeja no te mueres a pesar que te inyecto veneno pero si te pican 100 Abejas te puedes morir porque la dosis de veneno es mayor si te expones a los rayos ultravioletas durante pocos minutos al día no te hará daño pero si te expones horas y horas todos los días el riesgo de degeneración celular es alto no sólo el Sol emite rayos Ionisantes si no también las Frutas así es los plátanos son Radiactivos pero en una escala ínfima contienen potasio 40 que es un isotopo radiactivo otros alimentos que son naturalmente radiactivos son las zanahorias y las papas, hablando de radiación los rayos x son 100 mil veces más radiactivos que el plátano así que nesecitarias comer millones de plátanos de una sola vez para morir por radiación recuerda que el daño está en la dosis muchas gente dice que las Ondas electromagnéticas del teléfono producen Cancer o incluso Esterilidad eso no es verdad, porque las Ondas del celular no son Ionizantes no destruyen tejidos las únicas Ondas que destruyen tejidos son los rayos ultravioletas los rayos x, en cambio las demás Ondas no destruyen tejidos porque no son Ionizantes las Ondas del celular Tienen una frecuencia tan baja como las Ondas del horno microondas las ondas de radio y las ondas del Wii Fii, quiero resaltar que las ondas de radio y televisión están en todas partes la humanidad ha vivido décadas con esas ondas y no se ha asociado ningún caso de degeneración de células o Cáncer, hablando de Cáncer existen mitos sobre eso muchas gente afirma que la Carragenina una causan cancer pero lo cierto es que para que un elemento químico produzca Cancer puede generar un ambiente inospido, para las células del cuerpo y no basta con eso! debe provocar también que las células se vuelvan mutantes me explicó el cuerpo humano esta compuesto por órganos que a su vez se componen por tejidos y estos a su vez por células! las células contienen tu ADN esta programadas para adaptarse al ambiente en el que se encuentran y también están programadas para crecer multiplicarse y producir nuevas células llas células mueren y cada cierto periodo se forman nuevas eso es normal de esta manera los tejidos del cuerpo se regeneran siempre por eso la materia que en este momento compone tu cuerpo no es la materia que componía tu cuerpo hace diez años, sin embargo hay células que no se regeneran nunca así como hay células que se regeneran a diario si expones tus células a los rayos x de manera frecuente y excesiva llegarán un momento en que los genes de tu células comenzarán a mutar y porque mutan, mutan, para sobrevivir tus células actúan de acuerdo al ambiente en el que están si las expones a ambientes Inospitos tratarán de sobrevivir y las manera de sobrevivir es alterando su código genético, una célula puede modificar su ADN varias veces hasta obtener una inesestabilidad genomica y convertirse en una célula neoplasica esto provoca que la célula ya no cumpla con las características de una célula normal como por ejemplo morir, las células mutadas no mueren cuando deberían morir y encima se multiplican sin control esa reproduccion masiva de células neoplasicas hace que se generen tejidos extras los cuales requieren espacios y así se originan los tumores, hay tumores benignos y tumores malignos, los tumores malignos son los tumores que invaden otras partes del cuerpo, las células neoplasicas que lo provocan son llamadas células Cancerígenas ósea el tumor maligno es el mismo Cáncer el adjetivo cancerígeno sólo se aplica a las células si alguien quiere referirse a los agentes que causan Cancer como la Nicotina o los rayos ultravioletas, deberá usar el término Calcinogeno por ejemplo: la Nicotina no es Cancerígena es Calcinogeno las sustancias que pueden causar cáncer son conocidos como Calcinogenos en proceso de desarrollo del Cáncer se llama Calcinogenesis si se determina que un Tumor fue causado por Células Cancerígenas se dice que el Tumor es Canceroso en conclusión a menos que se demuestre que la Carragenina sea capaz de provocar mutación del ADN no se puede decir que es Calcinogena aún así no esta demás ser prevenidos y evitar aquello que este cuestionado mientras sea así No olvide que la peligrosidad está en cantidad de la Dosis muchas gracias....
          Sr. / Research Technician / Research Assistant - Oklahoma Medical Research Foundation - Oklahoma City, OK   
We utilize both animal and cellular models, and cutting edge technologies in functional genomics, bioinformatics, genetics, molecular and cell biology, and...
From Indeed - Fri, 26 May 2017 13:59:53 GMT - View all Oklahoma City, OK jobs
          Multiple Testing Procedures: R multtest Package and Applications to Genomics   

The Bioconductor R package multtest implements widely applicable resampling-based single-step and stepwise multiple testing procedures (MTP) for controlling a broad class of Type I error rates, in testing problems involving general data generating distributions (with arbitrary dependence structures among variables), null hypotheses, and test statistics. The current version of multtest provides MTPs for tests concerning means, differences in means, and regression parameters in linear and Cox proportional hazards models. Procedures are provided to control Type I error rates defined as tail probabilities for arbitrary functions of the numbers of false positives and rejected hypotheses. These error rates include tail probabilities for the number of false positives (generalized family-wise error rate, gFWER) and the proportion of false positives among the rejected hypotheses (TPPFP). Single-step and step-down common-cut-off (maxT) and common-quantile (minP) procedures, that take into account the joint distribution of the test statistics, are proposed to control the family-wise error rate (FWER), or chance of at least one Type I error. In addition, augmentation multiple testing procedures are provided to control the gFWER and TPPFP, based on any initial FWER-controlling procedure. The results of a multiple testing procedure can be summarized using rejection regions for the test statistics, confidence regions for the parameters of interest, or adjusted p-values. A key ingredient of our proposed MTPs is the test statistics null distribution (and estimator thereof) used to derive rejection regions and corresponding confidence regions and adjusted p-values. Both bootstrap and permutation estimators of the test statistics null distribution are available. The S4 class/method object-oriented programming approach was adopted to summarize the results of a MTP. The modular design of multtest allows interested users to readily extend the package's functionality. Typical testing scenarios are illustrated by applying various MTPs implemented in multtest to the Acute Lymphoblastic Leukemia (ALL) dataset of Chiaretti et al. (2004), with the aim of identifying genes whose expression measures are associated with (possibly censored) biological and clinical outcomes.


          Master Grower - Horticulture - Fox D Consulting - Greater Toronto Area, ON   
Understanding of biotechnology, molecular biology and genomics preferred. NIAGARA ONTARIO, CHATHAM ONTARIO, MUSKOKA REGION, BRANT REGION, GTA.... $50,000 - $100,000 a year
From Indeed - Wed, 28 Jun 2017 12:14:28 GMT - View all Greater Toronto Area, ON jobs
          Post-doctoral Fellow - Functional & Chemical Genomics - Oklahoma Medical Research Foundation - Oklahoma City, OK   
A postdoctoral fellow position is available immediately in the laboratory of Dr. Functional &amp; Chemical Genomics - Yoon....
From Indeed - Tue, 27 Jun 2017 19:39:34 GMT - View all Oklahoma City, OK jobs
          TWiV 448: Mavis the Structure Maven   

From ASV 2017 in Madison, Wisconsin, the complete TWiV team speaks with Mavis Agbandje-McKenna about her career and her work solving virus structures by x-ray crystallography and cryo-electron microscopy.

Hosts: Vincent Racaniello, Dickson DespommierAlan Dove, Rich Condit, and Kathy Spindler

Guest: Mavis Agbandje-McKenna

 

Become a patron of TWiV!

This episode of TWiV is sponsored by Promega Corporation.  Promega is a leader in providing innovative solutions and technical support to the life science industry. The company’s 3,500 products support scientists’ worldwide to advance their knowledge in genomics, proteomics, cellular analysis, drug discovery and human identification. Founded in 1978, the company is headquartered in Madison, WI with branches in 16 countries and over 50 global distributors.

Promega products are used by life scientists who are asking fundamental questions about biological processes applying their knowledge to diagnose and treat diseases or discover new therapeutics.

For more information about Promega, visit www.promega.com/ASV

Weekly Science Picks

Kathy - Doktor Kaboom!
Dickson - 
Mars as you've never seen it before
Alan
- Eclipse 2017
Rich - Sirens of Titan by Kurt Vonnegut
Vincent - Research!America

Intro music is by Ronald Jenkees.

Send your virology questions and comments to twiv@microbe.tv


          IT Deskside Support - Bilingual - Eurofins Canada - Toronto, ON   
We are also number one in the field of environmental laboratory services and one of the global market leaders in agroscience, genomics, discovery pharmacology,...
From Indeed - Fri, 09 Jun 2017 12:58:51 GMT - View all Toronto, ON jobs
          Laboratory Analyst I - Food Microbiology - Eurofins-Experchem Inc. - Toronto, ON   
It is also number one in the field of environmental laboratory services and one of the global market leaders in agro science, genomics, discovery pharmacology,...
From Indeed - Thu, 11 May 2017 23:32:46 GMT - View all Toronto, ON jobs
          Sr. / Research Technician / Research Assistant - Oklahoma Medical Research Foundation - Oklahoma City, OK   
We utilize both animal and cellular models, and cutting edge technologies in functional genomics, bioinformatics, genetics, molecular and cell biology, and...
From Indeed - Fri, 26 May 2017 13:59:53 GMT - View all Oklahoma City, OK jobs
          Computational Chemogenomics   
Computational Chemogenomics

Computational Chemogenomics by Edgar Jacoby
English | 2013 | ISBN: 190479842X , 9814411396 | 264 pages | PDF | 4,4 MB

          Left Bans Scientist Who Discovered DNA   

By Professor Doom

 “Show me the man, and I’ll show you the crime.”

--Beria, head of Stalin’s Secret Police 


   Only an idiot could have thought the Left agenda of shutting down Conservative speakers on campus would stop at just those speakers. Having succeeded in making it impossible for a Conservative to show his or her (Hi Ann Coulter!) face on campus without risking violence, they now are moving on to everyone who dares to utter a word against Leftist ideas…even those who simply are pursuing knowledge and have no interest in politics.

      James Watson is one of the co-discoverers of DNA, and won a Nobel prize for the achievement. Not to put too fine a point on it, but DNA is a pretty major thing for humanity to know, and few concepts have penetrated modern society so deeply and yet can be directly attributed to only a handful at most of names.

      In short, for such a contribution to human knowledge, any legitimate university would be deeply honored to have such a towering figure speak on campus.

      Unless of course, at any point of time in the past the figure said something wrongthink:



--“backlash” is Lefist for “someone complained about being offended.”


      Before going further, I want to mention that this talk was not a general address to the students, not even remotely. It was a very technical discussion on a very tiny aspect of cancer research, intended for only for the most well trained faculty and graduate students (i.e., the only ones likely to follow such a discussion). Universities hold such seminars all the time; they don’t make the papers because they are of such narrow interest.

      Now that the Left has shut down the big speakers and big talks, it’s going after even small discussions strictly among academics.

      When the Left targets you, it combs through anything you may have said, going back a lifetime if need be, and reinterprets it in the most offensive way possible (Hi President Trump!). So, here we go again:

“…has been castigated by fellow scientists for his discredited views on race and intelligence.”

--“discredited” is Leftist for “something someone was offended by.”


      Yeah, discredited, with such discreditation being published in the same journals that’ll publish research showing the penis causes global warming. This fallacy is called ‘ad hominem,’ is irrelevant in the face of his past achievements, and unrelated to cancer research.

      At the risk of overindulging in hyperbole, the gentle reader should at least consider the possibility that what this scientist might say at his seminar might have led to the cure for cancer…but the Left doesn’t care about that risk, they need shut down everyone who doesn’t toe the party line at all times.

      So, the guy wants to give a technical talk, Leftists complain, and admin has to make a decision to either adhere to the university mission of education and research…or to cave in spinelessly. You can guess how that went:

"We considered that carefully and decided to make plans to hold that lecture,"
--Carl Woese Institute for Genomic Biology Director Robinson made the call. Do note the length of the title, not a good sign at all. And, as backward as it sounds, “hold” is Leftist for “cancel.”


     I concede Watson said some things people don’t want to hear, but to his credit, he did apologize. No apology is ever enough when the Left targets you.

Clancy said Watson, "didn't apologize for everything," 

--Kate Clancy’s tweets more or less started the protest silencing the Nobel Laureate.  “Apologize” is Leftist for “die quickly.” Those experienced in dealing with the Left advise to never apologize.  


     Literally nobody is safe from these monsterspeople, and I know simply quoting people who disagree with them on my blog means I’ll never be a talking head on TV, and probably never speak on campus in a public forum. No great loss, I imagine.
      It’s so funny to see spineless admin cower before these people:

Robinson said free speech is a concern, but "I really respect the perspectives of the faculty who raised the concern..."

--how about respecting the faculty that want to advance human knowledge? Don’t scholars get a say? Or is campus all about ideology now?


     Seriously? Spreading the latest research on cancer (something of a life-and-death issue for many people) is even remotely the same as attempting to satisfy a perpetually displeased minority? You already tried making them happy by banning Conservative speakers and that accomplished nothing. Now they’re going for more. Can you really not see the pattern here?

     The foolishness here is mighty, but the hypocrisy manages to exceed it:

"We support Dr. Watson for his discovery and work, and believe that his remorse and subsequent apology to those groups he spoke against are genuine, but the IGB's stance is unchanged — we do not condone discrimination of any form, and the respect that we give to each individual in our community is paramount."
--“each individual in our community” is Lefist for “just us.”

    
      But…you’re discriminating against him! You’re showing amazing disrespect to science, scholarly work, your students, and legitimate faculty by shutting down his speech.

      And yet, admin somehow manages to spin ending of free speech and academic freedom into a noble act on their part, one where they had to struggle with the decision.

      I began my essay with a quote from the head of Stalin’s secret police because ultimately, this is the status of academics today. The thoughtcrimes defined by the Left are so widespread (and so hypocritically defined) that at the university level, literally anyone who tries to stand up against them is pronounced guilty, and silenced.

       Why are people paying $100,000 to get anything at all from universities in this environment?




          IT Deskside Support - Bilingual - Eurofins Canada - Toronto, ON   
We are also number one in the field of environmental laboratory services and one of the global market leaders in agroscience, genomics, discovery pharmacology,...
From Indeed - Fri, 09 Jun 2017 12:58:51 GMT - View all Toronto, ON jobs
          Laboratory Analyst I - Food Microbiology - Eurofins-Experchem Inc. - Toronto, ON   
It is also number one in the field of environmental laboratory services and one of the global market leaders in agro science, genomics, discovery pharmacology,...
From Indeed - Thu, 11 May 2017 23:32:46 GMT - View all Toronto, ON jobs
          Post Doc Computational - Cold Spring Harbor Laboratory - Cold Spring Harbor, NY   
The applicant will be expected to integrate with others at the Stanley Institute and analyze family and population based genomic data of neurological and...
From Cold Spring Harbor Laboratory - Wed, 12 Apr 2017 05:15:08 GMT - View all Cold Spring Harbor, NY jobs
          Link Mining for Kernel-based Compound-Protein Interaction Predictions Using a Chemogenomics Approach. (arXiv:1705.01667v2 [q-bio.QM] UPDATED)   

Authors: Masahito Ohue, Takuro Yamazaki, Tomohiro Ban, Yutaka Akiyama

Virtual screening (VS) is widely used during computational drug discovery to reduce costs. Chemogenomics-based virtual screening (CGBVS) can be used to predict new compound-protein interactions (CPIs) from known CPI network data using several methods, including machine learning and data mining. Although CGBVS facilitates highly efficient and accurate CPI prediction, it has poor performance for prediction of new compounds for which CPIs are unknown. The pairwise kernel method (PKM) is a state-of-the-art CGBVS method and shows high accuracy for prediction of new compounds. In this study, on the basis of link mining, we improved the PKM by combining link indicator kernel (LIK) and chemical similarity and evaluated the accuracy of these methods. The proposed method obtained an average area under the precision-recall curve (AUPR) value of 0.562, which was higher than that achieved by the conventional Gaussian interaction profile (GIP) method (0.425), and the calculation time was only increased by a few percent.


          Untangling Genetic Risk for Alzheimer's Disease.   

Untangling Genetic Risk for Alzheimer's Disease.

Biol Psychiatry. 2017 May 22;:

Authors: Pimenova AA, Raj T, Goate AM

Abstract
Alzheimer's disease (AD) is a genetically heterogeneous neurodegenerative disorder caused by fully penetrant single gene mutations in a minority of cases, while the majority of cases are sporadic or show modest familial clustering. These cases are of late onset and likely result from the interaction of many genes and the environment. More than 30 loci have been implicated in AD by a combination of linkage, genome-wide association, and whole genome/exome sequencing. We have learned from these studies that perturbations in endolysosomal, lipid metabolism, and immune response pathways substantially contribute to sporadic AD pathogenesis. We review here current knowledge about functions of AD susceptibility genes, highlighting cells of the myeloid lineage as drivers of at least part of the genetic component in late-onset AD. Although targeted resequencing utilized for the identification of causal variants has discovered coding mutations in some AD-associated genes, a lot of risk variants lie in noncoding regions. Here we discuss the use of functional genomics approaches that integrate transcriptomic, epigenetic, and endophenotype traits with systems biology to annotate genetic variants, and to facilitate discovery of AD risk genes. Further validation in cell culture and mouse models will be necessary to establish causality for these genes. This knowledge will allow mechanism-based design of novel therapeutic interventions in AD and promises coherent implementation of treatment in a personalized manner.

PMID: 28666525 [PubMed - as supplied by publisher]


          Potential of gene-based testing in Thoroughbreds to reduce disease highlighted   

Horsetalk.co.nz

Full breadth of application for genetic and genomic research goes beyond that of faster horses, says expert.

Potential of gene-based testing in Thoroughbreds to reduce disease highlighted -- Horsetalk.co.nz - equine news, research, and information


          Sr. / Research Technician / Research Assistant - Oklahoma Medical Research Foundation - Oklahoma City, OK   
We utilize both animal and cellular models, and cutting edge technologies in functional genomics, bioinformatics, genetics, molecular and cell biology, and...
From Indeed - Fri, 26 May 2017 13:59:53 GMT - View all Oklahoma City, OK jobs
          We Can Now Build Biomolecules From Computer Code — No Humans Necessary   
Futurism IN BRIEF Synthetic Genomics has created a digital-to-biological converter that uses digital code to create biologics like DNA, RNA, proteins, and viral particles. This may have major implications for space colonization, fighting disease outbreaks, and personalized medicine. DIGITAL-TO-BIOLOGICAL CONVERTER People often describe DNA as the “blueprint” for life, and geneticist J. Craig Venter and his team […]
          What’s the Business Model for Artificial Intelligence in Healthcare?   
This story is part of an ongoing Xconomy series on A.I. in healthcare. These are heady times for using artificial intelligence to extract insights from healthcare data—in particular, from the tidal wave of information coming out of fields like genomics and medical imaging. Yet as innovations proliferate, some age-old business questions have come to the […]
          Post-doctoral Fellow - Functional & Chemical Genomics - Oklahoma Medical Research Foundation - Oklahoma City, OK   
A postdoctoral fellow position is available immediately in the laboratory of Dr. Functional &amp; Chemical Genomics - Yoon....
From Indeed - Tue, 27 Jun 2017 19:39:34 GMT - View all Oklahoma City, OK jobs
          Genomics not the panacea that makes breeding decent sheep easy   
OPINION: I attended the Beef and Lamb sheep breeders forum in Napier recently. It's a conference where growers listen to various talks from scientists as to where we are heading with genetic tools for breeding. You meet and discuss a lot of issues with the experts and growers alike.
          The genomic landscape of African populations in health and disease   
Abstract
A deeper appreciation of the complex architecture of African genomes is critical to the global effort to understand human history, biology, and differential distribution of disease by geography and ancestry. Here, we report on how the growing engagement of African populations in genome science is providing new insights into the forces that shaped human genomes before and after the Out-of-Africa migrations. As a result of this human evolutionary history, African ancestry populations have the greatest genomic diversity in the world, and this diversity has important ramifications for genomic research. In the case of pharmacogenomics, for instance, variants of consequence are not limited to those identified in other populations, and diversity within African ancestry populations precludes summarizing risk across different African ethnic groups. Exposure of Africans to fatal pathogens, such as Plasmodium falciparum, Lassa Virus, and Trypanosoma brucei rhodesiense, has resulted in elevated frequencies of alleles conferring survival advantages for infectious diseases, but that are maladaptive in modern-day environments. Illustrating with cardiometabolic traits, we show that while genomic research in African ancestry populations is still in early stages, there are already many examples of novel and African ancestry-specific disease loci that have been discovered. Furthermore, the shorter haplotypes in African genomes have facilitated fine-mapping of loci discovered in other human ancestry populations. Given the insights already gained from the interrogation of African genomes, it is imperative to continue and increase our efforts to describe genomic risk in and across African ancestry populations.

          VROUWELIJKE FEMbryos (Melkvee)   

Transactie: Aangeboden
Categorie: Melkvee
Aantal: 100
Soort: Embryo
Geslacht: Vrouwelijk
Kleur: Zwartbont
Prijs:
Omschrijving:

A.L.H. Genetics is wereldleider in het leveren van het beste fokmateriaal voor de melkvee-houderij. Embryo donoren van A.L.H. Genetics zijn kwalitatief van hoog niveau, zowel voor productie als exterieur. Alle embryo donoren zijn getest op genomics en geselecteerd op vruchtbaarheid, celgetal, productie, exterieur, etc. Daarbij zijn ze ook nog eens afkomstig uit bewezen koefamilie´s, dus zeer betrouwbaar. Om maximaal resultaat te behalen worden alle embryo donoren gecombineerd met de beste stieren die wereldwijd beschikbaar zijn. Zodoende weten wij zeker dat alleen het beste naar uw stal toegaat.

Waarom A.L.H. kiezen?
A.L.H. Genetics werkt uitsluitend met de beste embryo implantatie en vruchtbaarheid specialisten in Nederland. Samen kunnen wij zorgen voor het maximale resultaat!

Uw voordeel:
* hogere drachtigheids percentages
* met embryo´s geen insleep van IBR, BVD, Salmonella, Para, Neospora, etc.
* embryo´s zijn belasting technisch aftrekbaar
* maximaal melken per fosfaat recht
* beste koeien verkrijgen waar u jarenlang mee kan werken en die geld opleveren!

Wij leveren:
* klasse 1 ingevroren embryo´s
* embryo´s in diverse prijsklassen 
* bewezen koefamilies 
* vrouwelijke embryo´s beschikbaar!

DIRECT EMBRYO’S KOPEN?
Dat kan op www.embryosale.com, de online embryo marktplaats van A.L.H. Genetics.

Vertrouw op de kwaliteit en bel ons gerust voor meer informatie, tel. 0511-424243.

Laat onze ruim 25 jaar fokkerij ervaring voor u werken.


          Master Grower - Horticulture - Fox D Consulting - Greater Toronto Area, ON   
Understanding of biotechnology, molecular biology and genomics preferred. NIAGARA ONTARIO, CHATHAM ONTARIO, MUSKOKA REGION, BRANT REGION, GTA.... $50,000 - $100,000 a year
From Indeed - Wed, 28 Jun 2017 12:14:28 GMT - View all Greater Toronto Area, ON jobs
          English speaking customer support engineer AK munkakörbe keresünk munkatársat. | Feladatok: Tri...   
English speaking customer support engineer AK munkakörbe keresünk munkatársat. | Feladatok: Triage level response to all technical support questions • Log Support Cases with Jira • Work as part of the Global Support Team • Work closely and collaborate with the other teams including Quality Management Team, Research & Development Team, including product testing • Assist with Workshops, on-site installation • Additional duties as required. | Mit ajánlunk: Familiarity with Salesforce, MS Office products, Google-Docs, Jira, Java, SQL • Experience with remote support e.g. TeamViewer, GoToMeeting, Skype • Experience with configuration and troubleshooting on Windows or Linux or OS X the rest can be learned on the job • Active collaboration with key stakeholders in the Europe and US offices • Willingness to learn in all fields connected to the role. | Elvárások: Bachelors or Masters degree in IT - Bio-IT field molecular biology, genomics or similar will be advantageous • 3+ years in a Technical Support role at a company with a scientific focus • Fluent English is a must • Experience with networking and command line tools • Technical/analytical mindset - strong troubleshooting skills • Ability to prioritize and work under pressure • Self-motivated, works well under minimal supervision • Confident strong communicator • High energy level; positive attitude; works well in a rapidly evolving business environment | További infó és jelentkezés itt: www.profession.hu/allas/1036992
          Front End Web Engineer   
CA-San Carlos, We are a Biotech software and services company focused on the development, refinement and advancement of genomic diagnostic technologies. We are a fully integrated organization that owns our methods; from early scientific research all the way through the execution/analysis of diagnostic tests in physicians’ offices. While we consider ourselves a leader in the DNA mapping industry, we cannot contin
          Post Doc Computational - Cold Spring Harbor Laboratory - Cold Spring Harbor, NY   
Familiarity with UNIX. Professor McCombie is seeking highly motivated Postdoctoral Fellows in Statistical Genomics and Human Genetics for his group at the...
From Cold Spring Harbor Laboratory - Wed, 12 Apr 2017 05:15:08 GMT - View all Cold Spring Harbor, NY jobs
          Post-doctoral Fellow - Functional & Chemical Genomics - Oklahoma Medical Research Foundation - Oklahoma City, OK   
*Posting Number: * 0001040 *Working Title: * Post-doctoral Fellow *Classification* : On-going *Status* : Full-Time *Department: * Functional &...
From Indeed - Tue, 27 Jun 2017 19:39:34 GMT - View all Oklahoma City, OK jobs
          Post Doc Computational - Cold Spring Harbor Laboratory - Cold Spring Harbor, NY   
Gronau I, Arbiza L, Mohammed J, Siepel A. Kuhlwilm M, Gronau I, Hubisz MJ, de Filippo C, Prado J, et al. Postdoctoral Positions in Computational Genomics....
From Cold Spring Harbor Laboratory - Wed, 29 Mar 2017 17:25:11 GMT - View all Cold Spring Harbor, NY jobs
          Post-doctoral Fellow - Functional & Chemical Genomics - Oklahoma Medical Research Foundation - Oklahoma City, OK   
A postdoctoral fellow position is available immediately in the laboratory of Dr. Functional &amp; Chemical Genomics - Yoon....
From Indeed - Tue, 27 Jun 2017 19:39:34 GMT - View all Oklahoma City, OK jobs
          Post Doc Computational - Cold Spring Harbor Laboratory - Cold Spring Harbor, NY   
The applicant will be expected to integrate with others at the Stanley Institute and analyze family and population based genomic data of neurological and...
From Cold Spring Harbor Laboratory - Wed, 12 Apr 2017 05:15:08 GMT - View all Cold Spring Harbor, NY jobs
          iCare4: Genomic Signatures With Midostaurin in Acute Myeloid Leukemia   
Condition:   Acute Myeloid Leukemia
Interventions:   Drug: Midostaurin;   Drug: Cytarabine
Sponsors:   University of Florida;   Novartis Pharmaceuticals
Not yet recruiting - verified June 2017
          Master Grower - Horticulture - Fox D Consulting - Greater Toronto Area, ON   
Understanding of biotechnology, molecular biology and genomics preferred. NIAGARA ONTARIO, CHATHAM ONTARIO, MUSKOKA REGION, BRANT REGION, GTA.... $50,000 - $100,000 a year
From Indeed - Wed, 28 Jun 2017 12:14:28 GMT - View all Greater Toronto Area, ON jobs
          Senior Systems Engineer - Linux/Virtualization/RAID   
San Diego, Located in beautiful San Diego, CA, we deliver on the promise of precision medicine today. Through daily re-computation of individual member clinical and full-sequence genomic data, our analytics provides a prospective clinical interpretation that enables true personalization of therapy, and prevents clinical gaps before they occur. Top Reasons to Work with Us - HUGE Room for Growth - Great Work/L
          Senior Systems Engineer - Linux/Virtualization/RAID   
San Diego, Located in beautiful San Diego, CA, we deliver on the promise of precision medicine today. Through daily re-computation of individual member clinical and full-sequence genomic data, our analytics provides a prospective clinical interpretation that enables true personalization of therapy, and prevents clinical gaps before they occur. Top Reasons to Work with Us - HUGE Room for Growth - Great Work/L
          Medical education in pharmacogenomics-results from a survey on pharmacogenetic knowledge in healthcare professionals within the European pharmacogenomics clinical implementation project Ubiquitous Pharmacogenomics (U-PGx).   

Medical education in pharmacogenomics-results from a survey on pharmacogenetic knowledge in healthcare professionals within the European pharmacogenomics clinical implementation project Ubiquitous Pharmacogenomics (U-PGx).

Eur J Clin Pharmacol. 2017 Jul 02;:

Authors: Just KS, Steffens M, Swen JJ, Patrinos GP, Guchelaar HJ, Stingl JC

Abstract
PURPOSE: Due to the diversity within Europe, the implementation of pharmacogenomic testing in clinical practice faces specific challenges. In the context of the European pharmacogenomics implementation project "Ubiquitous Pharmacogenomics" (U-PGx; funded by the European Commission), we studied the current educational background.
METHODS: We developed a questionnaire including 29 questions. It was spread out to healthcare professionals working at the future implementation sites (in Austria, Greece, Italy, Netherlands, Slovenia, Spain and Great Britain) of the U-PGx project in preparation of an educational programme. Aim of the survey was to analyse the current educational situation at the implementation sites.
RESULTS: In total, 70 healthcare professionals participated in the survey. Of participants, 84.3% found pharmacogenomics relevant to their current practice, but experience was still rare. More than two-thirds (65.7%) did not order nor recommend a pharmacogenomic test in the past year. This was mainly attributed to not having enough knowledge on pharmacogenomics (40.0%). Needs were identified in application of pharmacogenomics (identifying drugs 41.4%, interpreting test results 37.2%) as well as in underlining mechanisms (better knowledge on drug metabolism 67.1%, better knowledge on basic principles of pharmacogenomics 60.0%).
CONCLUSIONS: This study analysed the specific attitudes, experience and education on pharmacogenomics of future users. There was a general positive attitude and interest towards pharmacogenomic testing. However, the grade of own experience, and knowledge about application and interpretation of pharmacogenomics caused uncertainty. Thus, education and training programmes may be helpful for implementation of pharmacogenomics at a homogenous level within Europe.

PMID: 28669097 [PubMed - as supplied by publisher]


          A convenient method to pre-screen candidate guide RNAs for CRISPR/Cas9 gene editing by NHEJ-mediated integration of a ‘self-cleaving’ GFP-expression plasmid   
Abstract
The efficacies of guide RNAs (gRNAs), the short RNA molecules that bind to and determine the sequence specificity of the Streptococcus pyogenes Cas9 nuclease, to mediate DNA cleavage vary dramatically. Thus, the selection of appropriate target sites, and hence spacer sequence, is critical for most applications. Here, we describe a simple, unparalleled method for experimentally pre-testing the efficiencies of various gRNAs targeting a gene. The method explores NHEJ-cloning, genomic integration of a GFP-expressing plasmid without homologous arms and linearized in-cell. The use of ‘self-cleaving’ GFP-plasmids containing universal gRNAs and corresponding targets alleviates cloning burdens when this method is applied. These universal gRNAs mediate efficient plasmid cleavage and are designed to avoid genomic targets in several model species. The method combines the advantages of the straightforward FACS detection provided by applying fluorescent reporter systems and of the PCR-based approaches being capable of testing targets in their genomic context, without necessitating any extra cloning steps. Additionally, we show that NHEJ-cloning can also be used in mammalian cells for targeted integration of donor plasmids up to 10 kb in size, with up to 30% efficiency, without any selection or enrichment.

          [مکینتاش] دانلود iSkysoft iTube Studio v6.2.0.3 MacOSX - نرم افزار دانلود ویدئوهای آنلاین برای مک   

دانلود iSkysoft iTube Studio v6.2.0.3 MacOSX - نرم افزار دانلود ویدئوهای آنلاین برای مک

سرعت بالا در دانلود ویدئوها، تبدیل در نرم افزار به منظور اجرا در سیستم های مختلف، مدیریت و پخش آنلاین ویدئوها، امکان تهیه عکس از مراحل اجرای یک ویدئو و قابلیت های متعدد دیگر از جمله خصوصیاتی هستند که مورد ...
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          IT Deskside Support - Bilingual - Eurofins Canada - Toronto, ON   
We are also number one in the field of environmental laboratory services and one of the global market leaders in agroscience, genomics, discovery pharmacology,...
From Indeed - Fri, 09 Jun 2017 12:58:51 GMT - View all Toronto, ON jobs
          Laboratory Analyst I - Food Microbiology - Eurofins-Experchem Inc. - Toronto, ON   
It is also number one in the field of environmental laboratory services and one of the global market leaders in agro science, genomics, discovery pharmacology,...
From Indeed - Thu, 11 May 2017 23:32:46 GMT - View all Toronto, ON jobs
          QBI Neuroscience Seminar: `What do reproduction and memory have in common? The epigenetic ...   
Professor David Tremethick, The John Curtin School of Medical Research, Head of Genome Biology Department - Australian National University, Canberra ACT 2601 Title: `What do reproduction and memory have in common? The epigenetic regulator H2A.B` Abstract: It is now clearly established that the central regulator of eukaryotic gene expression is the organization of the genome into chromatin.  Chromatin performs this crucial function by partitioning the genome into domains that are either open and transcriptionally active or closed and repressed. Chromatin is built from nucleosomes (histones plus DNA), the universal repeating protein-DNA complex in all eukaryotic cells. Nucleosome function is dependent upon the composition of the underlying nucleosome. The key way the biochemical composition of the nucleosome is altered is by the substitution of one or more of the core histones with the corresponding histone variant.  Previously, we discovered a new histone variant, H2A.B that displays a unique tissue expression pattern i.e. it is expressed in the testis and the brain. In order to gain mechanistic insights into the role of H2A.B.3 in these different tissues, we took a proteomic approach to identify proteins that specifically interact with H2A.B-containing nucleosomes, analysed its pattern of organisation and expression, uncovered its genomic locations and its relationship with other epigenetic marks, analysed an unexpected interaction with RNA both in vivo and in vitro and most recently, generated a H2A.B mouse knockout. Taken together, our data thus far allows us to propose that H2A.B participates in a novel gene activation and pre-mRNA splicing mechanism that operates uniquely in the testis and brain. 
          Mugurii genomicii   
Deşi rezultatele nu par încă spectaculoase, cel puţin la nivelul masei largi a populaţiei, probabil că cele mai remarcabile progrese în domeniul sănătăţii din ultimii 25 de ani se referă la cartografierea genomului uman (finalizată în anul 2003), a genomului altor specii animale şi vegetale şi la dezvoltarea bioinformaticii.