Maq Featured RNA-Seq Job – Computational Biologist The Opportunity: The Morgridge Institute for Research seeks a Computational Biologist to provide bioinformatics support to researchers studying gene expression, epigenomics, proteomics and transcriptional regulation in embryonic stem cells and their differentiated derivatives. This position is part of the bioinformatics team within stem cell pioneer James Thomson’s Regenerative Biology Laboratory of the Morgridge Institute for Research. The following are core responsibilities of this position: Candidate Requirements: We are seeking candidates who have a master’s degree (or a bachelor’s degree plus equivalent experience and education) in computer science, mathematics, bioinformatics, or biological sciences, Ph.D is preferred. The Organization: The Morgridge Institute for Research benefits the University of Wisconsin–Madison and the citizens of Wisconsin by advancing breakthrough biomedical discoveries to solve important global health challenges and by educating the public about science.
services:dbfetch | EBI Web Services WSDbfetch allows you to retrieve entries from various up-to-date biological databases using entry identifiers or accession numbers. This is equivalent to the CGI based dbfetch service. Like the CGI service a request can return a maximum of 200 entries. For more information see: Web services registry entries: Sample clients are provided for a number of programming languages. There are three interfaces to the WSDbfetch ( SOAP ) service, each with its own WSDL : Fetch a set of entries in a defined format and style. db : the name of the database to obtain the entries from. query : a string containing a comma separated list of entry identifiers. format : the name of the format required. style : the name of the style required. The format of the response depends on the interface to the service used: WSDBFetchServerService and WSDBFetchDoclitServerService: the entries as a string. WSDBFetchServerLegacyService: an array of strings containing the entries. Fetch an entry in a defined format and style.
Master thesis – Bioinformatics – RNA-Seq analysis Development of a RNA-seq analysis pipeline for bacterial transcriptomics Introduction/framework ** Recent developments in new high-throughput technologies have revolutionized molecular biology. This technological progress has led to an explosive growth of the biological information (e.g. via DNA sequencing, RNA microarrays, proteomics), creating new opportunities in the field of bioinformatics in order to computationally deal with the dramatic increase of data. More specifically, the recent availability of next-generation sequencing (NGS) methods has opened up new horizons at the level of gene expression analysis. However, these high-throughput sequencing methods produce a massive amount of data. Objectives of the project ** The objective of this PhD research is the development of a bioinformatics pipeline able to analyze microbial RNA-seq data based on the next-generation DNA-sequencing technologies.
Pacific Biosciences’ Software Upgrade Enhances De Novo Genome Assembly, Variant Calling and cDNA Transcript Analysis MENLO PARK, Calif., Jan. 29, 2013 (GLOBE NEWSWIRE) — Pacific Biosciences of California, Inc. (Nasdaq:PACB) provider of the PacBio® RS High Resolution Genetic Analyzer, today announced it is releasing a new software upgrade that provides higher quality genome assemblies with near perfect base level accuracy in addition to other key features. The software upgrade extends the range of projects that uniquely benefit from the company’s Single Molecule, Real-Time (SMRT®) DNA Sequencing method, and will be available to customers for download on January 31st. SMRT Analysis 1.4 includes a new hierarchical de novo genome assembly process (HGAP), which allows researchers to assemble entire microbial and fungal genomes solely using PacBio long reads. As a result, users can generate better assemblies with a single library preparation and fewer SMRT® Cells than previous approaches that also required short-read sequencing technologies or circular consensus sequencing. About Pacific Biosciences
Internship Available – Product Development – RNA-Seq Intern Product Development Job Location: Austin, TX The successful candidate will support product development activities for gene expression analysis through next generation sequencing (NGS). Throughout the course of the internship, the candidate will be trained in nucleic acid sample preparation and extraction techniques from different biological matrices, PCR, nucleic acid characterization, and library preparation for NGS, and . RequirementsIntern candidates must be enrolled at an accredited college or university pursuing a Bachelor’s, Master’s, or PhD degree. Typical LocationsAustin, TX The CompanyAt Life Technologies, we believe in the power of science to transform life and the power of people to make it happen. Job ID: 12987BR
Featured Job – Senior Scientist – Pfizer Org Marketing Statement All over the world, Pfizer colleagues are working together to positively impact health for everyone, everywhere. Each position at Pfizer touches and contributes to the success of our business and our world. That’s why, as one of the global leaders in the biopharmaceutical industry, Pfizer is committed to seeking out inspired new talent who share our core values and mission of making the world a healthier place. Role Description We seek an highly motivated immunologist to work with members of the Immunoregulation Group within the Immunology and Autoimmunity Research Unit. The primary focus of the position will be to participate in the identification, evaluation and development of the next generation of novel therapies for autoimmune disease. Apply Now
Softberry Releases 80 Free Bioinformatics Programs for Immediate Download by Academic Users MOUNT KISCO, N.Y.–(BUSINESS WIRE)–Softberry, Inc. announces release of a comprehensive set of biomedical research-oriented software applications for academic users to install and run locally on a limited basis. The programs, already cited in thousands of scientific publications, are available for Linux and Mac OS platforms and focus primarily on genomic and proteomic research. Another group of programs facilitates analysis of genomic sequences: alignment of genomes, bacterial and eukaryotic promoter prediction, discovery of functional/regulatory motifs, splice sites identification and gene prediction. Software for protein sequence and structure analysis includes tools for identification of sub-cellular protein location, prosite pattern search, 3D structure comparison, protein structure modeling using molecular dynamic approach and homology modeling. About Softberry Softberry, Inc. is a leading developer of research oriented software tools for genomic and proteomic research.
The Latest RNA-Seq Application – Degradome Sequencing Degradome sequencing for identification of miRNA targets in plants MicroRNAs (miRNAs) are endogenous regulators of a broad range of physiological processes and act by either degrading mRNA or blocking its translation. Mature miRNAs function within large complexes to negatively regulate specific target mRNAs. In plants, miRNAs not only post-transcriptionally regulate their own targets but also interact with each other in regulatory networks to affect many aspects of development, such as growth, development and responses to biotic and abiotic stresses. Originally, plant miRNA targets have been studied via computational prediction, which is based on either perfect or near-perfect sequence complementarity between miRNA and the target mRNA or sequence conservation among different species. Recently, a new method called degradome sequencing, which combines high-throughput RNA sequencing with bioinformatic tools, has-been successfully established to screen for miRNA targets in plants.
GitHub – Shared RNA-Seq Analysis Code GitHub helps people build software together. yarden/MISO MISO: Mixture of Isoforms model for RNA-Seq isoform quantitation jrbustosm/rna-seq rna-seq analysis utils drli/RNA-seq RNA-seq data analysis andymckenzie/RNA-Seq algorithms for analyzing rna-seq data jnhutchinson/ensembl_based_RNA_seq ensembl_based_RNA_seq vsbuffalo/rna-seq-example An analysis of Arabidopsis RNA-seq data (hy5 mutant and wt, two replicates each; SRA accession SRX029582) fatPerlHacker/rna-seq-analysis-pipeline sgivan/RNA-Seq-Toolkit Collection of scripts to facilitate the analysis of RNA-Seq data gusevfe/RnaSeqAB Tool for detecting allele bias in Genome vs. luwening/RNA-Seq-RP-Pseudogenes Lots more shared RNA-Seq Code…
Next-Generation Sequencing vs. Microarrays from genengnews.com – by Shawn C. Baker, Ph.D, CSO BlueSEQ (www.blueseq.com)- Reprinted with permission from Genetic Engineering & Biotechnology News (GEN) With recent advancements and a radical decline in sequencing costs, the popularity of next generation sequencing (NGS) has skyrocketed. As costs become less prohibitive and methods become simpler and more widespread, researchers are choosing NGS over microarrays for more of their genomic applications. Rising maturity in NGS systems and ancillary protocols such as library preparation and data analysis tools have certainly contributed to the increasing popularity among the research community. As outlined in a previous article (GEN Sep 1, 2012; Vol. 32, No. 15), NGS technologies have made great strides both economically and technically, and are gaining in popularity since first appearing on the scene less than a decade ago. Microarrays’ Proven Track Record Time to Make The Switch? Conclusion