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. Featured RNA-Seq Jobs. 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).
The candidate will be required to plan, execute, and clearly document experiments in support of RNA-Seq technology development. Candidates should have a solid educational background in molecular biology or biochemistry as well as some laboratory experience working with nucleic acid isolation and purification. Experience with RT-PCR, siRNA, nucleic acid amplification, or next generation sequencing is a plus. 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.
Genetic screens – RNA-seq into the toolkit. Pacific Biosciences Posts Q4, FY2012 Revenue Decline – Expects 2013 Uptick. 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. 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.
Hello from a new RNAseq user. SEQanswers Home. Bioinformatics challenges in de novo transcriptome assembly using short read sequences in the absence of a reference genome sequence. 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.
High-Grade Serous Ovarian Adenocarcinoma Transcriptome Sequencing. Genome-Wide Discovery of Small RNAs in Mycobacterium tuberculosis. Scientists at Raffaele Scientific Institute, Italy report a genome-wide characterization of sRNAs in M. tuberculosis integrating experimental and computational analyses. Global RNA-seq analysis of exponentially growing cultures of M. tuberculosis H37Rv had previously identified 1373 sRNA species. In the present report they show that 258 (19%) of these were also identified by microarray expression. This set included 22 intergenic sRNAs, 84 sRNAs mapping within 5′/3′ UTRs, and 152 antisense sRNAs. Expression profiles of mRNAs and lncRNAs from RNA-Seq data across 22 human tissues.
Analysis of RNA-Seq Data with R/Bioconductor. 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.
Whether it’s a need for more accurate data, better resolution, pressure from granting agencies, or just plain fear of being left behind the technology forefront, it’s clear that the demand for revolutionary sequencing technologies that deliver fast, inexpensive, and accurate genomic information has never been greater. Time to Make The Switch? RNAmapper – RNA-Seq based mapping and candidate identification of mutations from forward genetic screens. Forward genetic screens have elucidated molecular pathways required for innumerable aspects of life, however identifying the causal mutations from such screens has long been the bottleneck in the process, particularly in vertebrates.
Now, researchers at Fred Hutchinson Cancer Research Center have developed an RNA-seq based approach that identifies both the region of the genome linked to a mutation and candidate lesions that may be causal for the phenotype of interest. They show that their method successfully identifies zebrafish mutations that cause nonsense or missense changes to codons, alter transcript splicing, or alter gene expression levels. Furthermore, they have developed an online accessible or downloadable bioinformatics pipeline allowing for easy implementation of all steps of the method. Overall, they show that RNA-seq is a fast, reliable, and cost effective method to map and identify mutations that will greatly facilitate the power of forward genetics in vertebrate models.
LenzLab / RNA-seq-scripts – a collection of small scripts built by the Lenz lab to make RNA sequencing tasks more efficient. PARSES – A Pipeline for Analysis of RNA-Seq. Roche introduces new GS FLX+ software for improved long-read sequencing performance. First high-throughput sequencing platform to deliver one million reads with read lengths of up to 1000 bp and beyond.
Roche announced today the launch and immediate availability of a new software package (v2.8) that significantly improves long-read shotgun sequencing performance on its GS FLX+ System. This system is the first high-throughput sequencing platform to deliver one million reads with accuracy and length that are comparable to traditional Sanger-based methods. The improvements will allow researchers to discover more novel complex genetic variants and uncover the hidden biology in difficult-to-sequence regions of genomes, transcriptomes, and metagenomic samples. The GS FLX+ System and software will be presented today at the American Society for Human Genetics Annual Meeting in San Francisco. “We have experienced excellent results in our laboratory using the latest GS FLX+ software. About Roche. RNA-Seq Interest Over Time. Presentation – Introduction to RNA-Seq. Bioinformatics – Next Gen Sequencing – Virtual Issue.
Bioinformatics has published a Next-Gen Sequencing “Virtual Issue” covering all the sequencing tools that appeared in the journal.
RNA-Seq Blog – Poll Results. Genetic Engineering & Biotechnology News - Biotech from Bench to Business. New Methods for HLA typing from RNA-Seq Data. The Human Leukocyte Antigen (HLA) is key to many aspects of human physiology and medicine. All current sequence-based HLA typing methodologies are targeted approaches requiring the amplification of specific HLA gene segments. Whole genome, exome and transcriptome shotgun sequencing can generate prodigious data but due to the complexity of HLA loci these data have not been immediately informative regarding HLA genotype. USC Team to Use Patch-Clamp, RNA-seq to Study Gene Expression Variability in Single Neurons. RNA-Seq data release for 1000 genomes samples. Pacific Biosciences Delivers Enhanced DNA Sequencing Chemistry and Software to Help Solve Complex Genetic Problems. Average Read Lengths of 5,000 Bases and Reads as Long as 20,000; PacBio Hosting Workshop at ASHG Annual Meeting MENLO PARK, Calif., Nov. 6, 2012 (GLOBE NEWSWIRE) — Pacific Biosciences of California, Inc.
(Nasdaq:PACB) provider of the PacBio® RS High Resolution Genetic Analyzer, today announced the latest enhancements to its DNA sequencing system, the XL release featuring new chemistry and software for extraordinarily long read lengths that average 5,000 bases. Pacific Biosciences’ Single Molecule, Real-Time (SMRT®) sequencing generates reads an order of magnitude longer than other leading DNA sequencing technologies. With the latest advance, the average read length increases 67 percent from 3,000 to 5,000 bases, with some reads as long as 20,000 bases. The new XL release provides increased read lengths through a combination of chemistry and software.
Dr. Transcriptomic analysis of ‘Suli’ pear by RNA-Seq. Bud dormancy is a critical developmental process that allows perennial plants to survive unfavorable environmental conditions. Pear is one of the most important deciduous fruit trees in the world, but the mechanisms regulating bud dormancy in this species are unknown. Because genomic information for pear is currently unavailable, transcriptome and digital gene expression data for this species would be valuable resources to better understand the molecular and biological mechanisms regulating its bud dormancy.
The diverse applications of RNA-seq for functional genomic studies in Aspergillus fumigatus. The deep sequencing of an mRNA population, RNA-seq, is a very successful application of next-generation sequencing technologies (NGSTs). RNA-seq takes advantage of two key NGST features: (1) samples can be mixtures of different DNA pieces, and (2) sequencing provides both qualitative and quantitative information about each DNA piece analyzed. A team led by researchers at Vanderbilt University recently used RNA-seq to study the transcriptome of Aspergillus fumigatus, a deadly human fungal pathogen. Transcriptomics: From Microarrays to RNA-Seq. By Josh P. Roberts at Biocompare When next-gen sequencing exploded onto the scene, it brought in its wake a host of innovations. Among these is the deep-sequencing of RNA (RNA-Seq), which is giving unprecedented breadth and depth to our understanding of the way cells develop, regulate themselves and each other, and respond to their environment.
Although the study of cellular RNA is not new, the scale on which researchers are now undertaking transcriptomic investigations and many of the questions they are now able to ask, would not have been possible with earlier technologies. The transcriptome is commonly defined as “the complete set of transcripts in a cell, and their quantity, for a specific developmental stage or physiological condition.”[1] Transcriptomics can address all or a segment of the transcriptome, from normal or diseased single cells or tissues. Featured Job Listing – Senior Application Scientist – Ingenuity Systems. RNA-Seq Blog – Poll Results. RNA-Seq Blog Poll Results. Industry News. From GenomeWeb Illumina Battles BGI Over Purchase of Complete Genomics Illumina confirmed that it made a competing unsolicited bid for Complete Genomics at about 5 percent above BGI-Shenzhen’s offer for the Mountain View, Calif.
Fluidigm Completes C1™ Single-Cell Auto Prep System Early Access Program. Oversubscribed Program Includes World’s Leading Research Centers SOUTH SAN FRANCISCO, Calif. – Jan. 2, 2013 – Fluidigm Corporation (NASDAQ:FLDM) announced that its C1™ Single-Cell Auto Prep system Early Access Program (EAP) has concluded. The EAP originally targeted 25 customers that would gain early access to the new platform, protocols and consumables. RNA-Seq Analysis Survey. RNA-Seq Blog. Seqnews.net – discover and share news on next-generation sequencing, genomics and biological data analysis. Featured Job Listing – Global Lead – NGS Core. News – Illumina Announces Sequencing Technology Innovations. SAN DIEGO–(BUSINESS WIRE)–Jan. 8, 2013– Illumina (NASDAQ: ILMN) today announced a series of product and technology innovations for its powerful sequencing ecosystem – from sample preparation to system enhancements to data analysis –– that will enable the next breakthroughs in understanding the genome.
“Illumina has consistently led the market in conceptualizing, developing, and executing on industry-changing sequencing technology, and we continue to provide scientific advances that facilitate fully integrated and highly economical sequencing with very rapid turnaround,” said Jay Flatley, President and Chief Executive Officer of Illumina. “These capabilities allow us to continue to meet the evolving needs of our customers, as they develop an ever-increasing range of applications, in new and emerging markets from agrigenomics to molecular diagnostics.” Sample Prep Evolution Core Technology Enhancements Informatics Advances About Illumina Forward-Looking Statements Source: Illumina, Inc. Available PhD Research Project – RNA-Seq. Analysts Increase Valuations, Upgrade Illumina. Complex RNA-Seq experiment analysis with SeqMonk. Transcriptomics in the RNA-Seq Era. RNA-SEQ Workshop – Life Technologies.
Combinational Usage of Next Generation Sequencing and qPCR for the analysis of tumour samples. EBI: Next Generation Sequencing Practical Course – RNA-Seq Ensembl gene build. The Latest RNA-Seq Application – Degradome Sequencing. GitHub – Shared RNA-Seq Analysis Code. GitHub helps people build software together. 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. Statistics for Genomics – Introduction to RNAseq.