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	<title><![CDATA[BOL: Related items]]></title>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/pages/view/7674/useful-publications-and-websites-for-deep-sequencing-data-analysis</guid>
	<pubDate>Sun, 29 Dec 2013 22:30:45 -0600</pubDate>
	<link>https://bioinformaticsonline.com/pages/view/7674/useful-publications-and-websites-for-deep-sequencing-data-analysis</link>
	<title><![CDATA[Useful Publications and Websites for Deep Sequencing Data Analysis]]></title>
	<description><![CDATA[<h3>Global overview papers</h3><p>Next generation quantitative genetics in plants. Jim&eacute;nez-G&oacute;mez, Frontiers in Plant Science 2:77, 2011 <span style="text-decoration: underline;"><a href="http://www.frontiersin.org/Plant_Physiology/10.3389/fpls.2011.00077/full">Full Text</a> </span><em>[equally relevant to animal and microbial systems]</em></p><p>Sense from sequence reads: methods for alignment and assembly. Flicek &amp; Birney, Nat Methods 6(11 Suppl):S6-S12, 2009. <a href="http://www.nature.com/nmeth/journal/v6/n11s/full/nmeth.1376.html"><span style="text-decoration: underline;">Full Text</span></a></p><h3>Library construction and experimental design</h3><p>Statistical design and analysis of RNA sequencing data. Auer &amp; Doerge, Genetics 185(2):405-16, 2010. <a href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2881125"><span style="text-decoration: underline;">PubMedCentral</span></a></p><p>Biases in Illumina transcriptome sequencing caused by random hexamer priming. Hansen et al., Nucleic Acids Res. 38(12): e131, 2010. <a href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2896536"><span style="text-decoration: underline;">PubMedCentral</span></a></p><p>Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries. Aird et al, Genome Biology 12:R18, 2011 <a href="http://genomebiology.com/2011/12/2/R18"><span style="text-decoration: underline;">Full Text</span></a></p><p>Amplification-free Illumina sequencing-library preparation facilitates improved mapping and assembly of GC-biased genomes. Kozarewa et al, Nature Methods 6(4):291-5, 2009 <a href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2664327/"><span style="text-decoration: underline;">PubMedCentral</span></a></p><p>Cost-effective, high-throughput DNA sequencing libraries for multiplexed target capture. Rohland &amp; Reich, Genome Research 22(5): 939&ndash;946. <a href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3337438/"><span style="text-decoration: underline;">PubMedCentral</span></a></p><h3>Data formats, data management, and alignment software tools<span style="text-decoration: underline;"> </span></h3><p>The Sequence Alignment/Map format and SAMtools. Li et al, Bioinformatics 25(16):2078-9, 2009 <a href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2723002"><span style="text-decoration: underline;">PubMedCentral</span></a></p><p>SAM format specification <a href="http://samtools.sourceforge.net/SAM1.pdf"><span style="text-decoration: underline;">file</span></a></p><p>Efficient storage of high throughput sequencing data using reference-based compression. Fritz et al, Genome Res 21(5):734-40, 2011. <a href="http://genome.cshlp.org/content/21/5/734.long"><span style="text-decoration: underline;">Full Text</span></a></p><p>Compression of DNA sequence reads in FASTQ format. Deorowicz &amp; Grabowski, Bioinformatics 27(6):860-2, 2011. <a href="http://www.ncbi.nlm.nih.gov/pubmed/21252073"><span style="text-decoration: underline;">PubMed</span></a></p><p>Fast and accurate short read alignment with Burrows-Wheeler transform. Li &amp; Durbin, Bioinformatics 25(14):1754-60, 2009. <a href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2705234"><span style="text-decoration: underline;">PubMedCentral</span></a></p><p>Improving SNP discovery by base alignment quality. Li H, Bioinformatics 27(8):1157-8, 2011. <a href="http://www.ncbi.nlm.nih.gov/pubmed/21320865"><span style="text-decoration: underline;">PubMed</span></a></p><p>BEDTools: a flexible suite of utilities for comparing genomic features. Quinlan and Hall, Bioinformatics 26:841-842, 2010. <a href="http://bioinformatics.oxfordjournals.org/content/26/6/841.full.pdf+html"><span style="text-decoration: underline;">Publisher Website</span></a></p><h3>Data quality assessment, filtering, and correction</h3><p>SolexaQA: At-a-glance quality assessment of Illumina second-generation sequencing data. Cox et al, BMC Bioinformatics 11:485, 2010. <a href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2956736"><span style="text-decoration: underline;">PubMedCentral</span></a></p><p>TileQC: a system for tile-based quality control of Solexa data. Dolan &amp; Denver, BMC Bioinformatics 9:250, 2008 <a href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2443380"><span style="text-decoration: underline;">PubMedCentral</span></a> <em>[requires a reference sequence]</em></p><p>Quake: quality-aware detection and correction of sequencing errors. Kelley et al, Genome Biol 11(11):R116, 2010. <a href="http://www.ncbi.nlm.nih.gov/pubmed/21114842"> <span style="text-decoration: underline;">PubMed</span></a></p><p>FastQC: a quality control tool for high-throughput sequence data. <a href="http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/"><span style="text-decoration: underline;">Home Page</span></a></p><p>FASTX-toolkit: FASTQ/A short-reads pre-processing tools <a href="http://hannonlab.cshl.edu/fastx_toolkit/"><span style="text-decoration: underline;">Home Page</span></a></p><p>Reference-free validation of short read data. Schr&ouml;der et al, PLoS One 5(9):e12681, 2010. <a href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2943903"> <span style="text-decoration: underline;">PubMedCentral</span></a></p><p>Correction of sequencing errors in a mixed set of reads. Salmela, Bioinformatics 26(10):1284, 2010. <a href="http://bioinformatics.oxfordjournals.org/content/26/10/1284.long"><span style="text-decoration: underline;">Full Text</span></a> <em>[includes error correction of SOLiD reads in colorspace]</em></p><p>Repeat-aware modeling and correction of short read errors. Yang et al, BMC Bioinformatics 12(Supp1):S52, 2011 <a href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3044310"> <span style="text-decoration: underline;">PubMedCentral</span></a> <em>[requires a reference sequence]</em></p><p>HiTEC: accurate error correction in high-throughput sequencing data. Ilie et al, Bioinformatics 27(3):295, 2011 <a href="http://bioinformatics.oxfordjournals.org/content/27/3/295.long"><span style="text-decoration: underline;">Full Text</span></a></p><p>Error correction of high-throughput sequencing datasets with non-uniform coverage. Medvedev et al., Bioinformatics 27(13):i137-41, 2011. <a href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3117386"><span style="text-decoration: underline;">PubMedCentral</span></a></p><h3>De novo assembly<span style="text-decoration: underline;"> </span></h3><p>Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Zerbino &amp; Birney, Genome Res 18(5):821-9, 2008. <a href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2336801">u&gt;PubMedCentral</a></p><p>Assembly of large genomes using second-generation sequencing. Schatz et al, Genome Res 20(9):1165-73, 2010. <a href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2928494"><span style="text-decoration: underline;">PubMedCentral</span></a></p><p>High-quality draft assemblies of mammalian genomes from massively parallel sequence data. Gnerre et al, PNAS 108(4): 1513-18, 2011 <a href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3029755"><span style="text-decoration: underline;">PubMedCentral</span></a></p><p>Genome assembly has a major impact on gene content: a comparison of annotation in two <em>Bos taurus </em> assemblies. Florea&nbsp; et al., PLoS One 6(6):e21400, 2011. <a href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3120881/"><span style="text-decoration: underline;">PubMedCentral</span></a></p><p>Artemis: an integrated platform for visualization and analysis of high-throughput sequence-based experimental data. Carver et al, Bioinformatics 28(4):464 - 469, 2012 <span style="text-decoration: underline;"><a href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3278759/">PubMedCentral</a></span></p><p>Efficient de novo assembly of large genomes using compressed data structures. Simpson &amp; Durbin, Genome Research 22:549-556, 2012 <span style="text-decoration: underline;"><a href="http://genome.cshlp.org/content/22/3/549.full">Full Text</a></span> <em>[Describes the String Graph Assembler (SGA), which assembled a human genome in less than 6 days using 54 Gb of RAM and a 123-processor compute cluster for calculation of an FM-index of the 1.2 billion reads]</em></p><p>Readjoiner: a fast and memory efficient string graph-based sequence assembler. Gonnella &amp; Kurtz, BMC Bioinformatics 13: 82, 2012 <a href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3507659"><span style="text-decoration: underline;">PubMedCentral</span></a></p><p>Assemblathon 1: A competitive assessment of de novo short read assembly methods. Earl et al, Genome Research 21:2224-2241, 2011 <span style="text-decoration: underline;"><a href="http://genome.cshlp.org/content/early/2011/09/16/gr.126599.111.full.pdf+html">Full Text</a></span></p><h3>Chromatin immunoprecipation analysis: ChIP-seq</h3><p>ChIP-seq: advantages and challenges of a maturing technology. Park, Nat Rev Genet. 10:669-80, 2009 <a href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3191340/"><span style="text-decoration: underline;">PubMed</span></a></p><p>ChIP-seq and Beyond: new and improved methodologies to detect and characterize protein-DNA interactions. Furey, Nat Rev Genet 13: 840&ndash;852, 2012 <a href="http://www.nature.com/nrg/journal/v13/n12/full/nrg3306.html"> <span style="text-decoration: underline;">Publisher Web Site</span></a></p><p>MuMoD: a Bayesian approach to detect multiple modes of protein&ndash;DNA binding from genome-wide ChIP data. Narlikar, Nucleic Acids Res 41:21&ndash;32, 2013 <a href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3592440/"><span style="text-decoration: underline;">PubMed</span></a></p><h3>Transcriptome analysis</h3><h3>Assembly and comparison to genome</h3><p>Full-length transcriptome assembly from RNA-Seq data without a reference genome. Grabherr et al, Nature Biotechnology 29:644 - 652, 2011. <a href="http://www.ncbi.nlm.nih.gov/pubmed/21572440"><span style="text-decoration: underline;">PubMed</span></a> <em>[The software is called <a href="http://trinityrnaseq.sourceforge.net/"><span style="text-decoration: underline;">Trinity</span></a>, and is available on Sourceforge.]</em></p><p>Comprehensive analysis of RNA-Seq data reveals extensive RNA editing in a human transcriptome. Peng et al, Nature Biotechnology 30:253 - 260, 2012. <span style="text-decoration: underline;"><a href="http://www.ncbi.nlm.nih.gov/pubmed/22327324">PubMed</a></span> <em>[Several comments on this paper question whether the reported differences are in fact evidence of editing or are simply sequencing errors - the authors stand by their conclusions, but the controversy demonstrates the importance of robust data analysis methods.] </em></p><p>Optimization of de novo transcriptome assembly from next-generation sequencing data. Surget-Groba &amp; Montoya-Burgos, Genome Res 20(10):1432-40, 2010. <a href="http://genome.cshlp.org/content/20/10/1432.long"><span style="text-decoration: underline;">Full Text</span></a></p><p>Rnnotator: an automated <em>de novo</em> transcriptome assembly pipeline from stranded RNA-Seq reads. Martin et al, BMC Genomics 11:663, 2010 <a href="http://www.biomedcentral.com/1471-2164/11/663"><span style="text-decoration: underline;">Full Text</span></a></p><p><em>De novo</em> assembly and analysis of RNA-seq data. Robertson et al, Nature Methods 7:909-912, 2010 <a href="http://www.nature.com/nmeth/journal/v7/n11/full/nmeth.1517.html"><span style="text-decoration: underline;">Full Text</span></a> <em>[describes Trans-ABySS, a pipeline to use the ABySS parallel assembler for de novo transcriptome analysis]</em></p><h3>Differential expression analysis</h3><p>R-SAP: a multi-threading computational pipeline for the characterization of high-throughput RNA-sequencing data. Mittal &amp; McDonald, Nucleic Acids Res, 2012 <span style="text-decoration: underline;"><a href="http://nar.oxfordjournals.org/content/early/2012/01/28/nar.gks047.long">Full Text</a></span></p><p>Targeted RNA sequencing reveals the deep complexity of the human transcriptome. Mercer et al, Nature Biotechnology 30:99 - 104, 2012 <span style="text-decoration: underline;"><a href="http://www.nature.com/nbt/journal/v30/n1/full/nbt.2024.html"> Publisher Website</a></span></p><p>Differential gene and transcript expression analysis of RNA-Seq experiments with TopHat and Cufflinks. Trapnell et al, Nature Protocols 7:562 - 578, 2012 <span style="text-decoration: underline;"><a href="http://www.nature.com/nprot/journal/v7/n3/full/nprot.2012.016.html"> Publisher Website</a></span></p><p>Characterization and improvement of RNA-Seq precision in quantitative transcript expression profiling. Łabaj et al, Bioinformatics 27:i383 - i391, 2011 <span style="text-decoration: underline;"><a href="http://bioinformatics.oxfordjournals.org/content/27/13/i383.full.pdf+html"> Full Text</a></span></p><p>Improving RNA-Seq expression estimates by correcting for fragment bias. Roberts et al, Genome Biol 12:R22, 2011 <span style="text-decoration: underline;"><a href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3129672/">PubMed Central</a></span></p><p>Cloud-scale RNA-sequencing differential expression analysis with Myrna. Langmead et al, Genome Biol 11:R83, 2010 <a href="http://genomebiology.com/2010/11/8/R83"><span style="text-decoration: underline;">Full Text</span></a></p><p>From RNA-seq reads to differential expression results. Oshlack et al, Genome Biol 11(12):220, 2010 <a href="http://genomebiology.com/content/11/12/220"><span style="text-decoration: underline;">Full Text</span></a></p><p>DEGseq: an R package for identifying differentially expressed genes from RNA-seq data. Wang et al., Bioinformatics. 26(1):136-8. 2010 <a href="http://www.ncbi.nlm.nih.gov/pubmed/19855105"><span style="text-decoration: underline;"> PubMed</span></a></p><p>DEseq: Differential expression analysis for sequence count data. Anders and Huber, Genome Biology 11:R106, 2010 <a href="http://genomebiology.com/2010/11/10/R106"><span style="text-decoration: underline;">Full Text</span></a></p><p>edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Robinson et al., Bioinformatics 26(1):139-40 2010 <a href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2796818"> <span style="text-decoration: underline;">PubMedCentral</span></a></p><p>Two-stage Poisson model for testing RNA-seq data. Auer and Doerge, SAGMB 10(1), article 26 <a href="http://www.bepress.com/sagmb/vol10/iss1/art26/"><span style="text-decoration: underline;">Full Text</span></a></p><p>Experimental design, preprocessing, normalization and differential expression analysis of small RNA sequencing experiments. McCormick et al., Silence2(1):2, 2011 <a href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3055805"><span style="text-decoration: underline;">PubMedCentral</span></a></p><p>RNA-Seq gene expression estimation with read mapping uncertainty. Li et al, Bioinformatics 26:493-500, 2010 <a href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2820677">PubMedCentral</a> <em>[describes the RSEM software package]</em></p><h3>Comparing genomes and assemblies; variant detection<span style="text-decoration: underline;"> </span></h3><p>Versatile and open software for comparing large genomes. Kurtz et al, Genome Biol (5(2):R12, 2004. <a href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC395750"><span style="text-decoration: underline;">PubMedCentral</span></a> <em>[describes the MUMmer software for full-genome alignment &amp; comparisons]</em></p><p>Searching for SNPs with cloud computing. Langmead et al, Genome Biol 10(11):R134, 2009 <a href="http://genomebiology.com/content/10/11/R134"><span style="text-decoration: underline;">Full Text</span></a></p><p>Calling SNPs without a reference sequence. Ratan et al, BMC Bioinformatics 11:130, 2010 <a href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2851604"><span style="text-decoration: underline;">PubMedCentral</span></a></p><p>Microindel detection in short-read sequence data. Krawitz et al, Bioinformatics 26(6):722-9, 2010. <a href="http://bioinformatics.oxfordjournals.org/content/26/6/722.long"><span style="text-decoration: underline;">Full Text</span></a></p><p>vipR: variant identification in pooled DNA using R. Altmann et al., Bioinformatics 27: i77-i84, 2011. <a href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3117388"><span style="text-decoration: underline;">PubMedCentral</span></a></p><p>Geoseq: a tool for dissecting deep-sequencing datasets. Gurtowski et al, BMC Bioinformatics 11:506, 2010. <a href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2972303/"><span style="text-decoration: underline;">PubMedCentral</span></a> <em>[Geoseq is a web service that allows searching deep sequencing datasets with a reference sequence of a gene of interest]</em></p><p>Detecting and annotating genetic variations using the HugeSeq pipeline. Lam et al, Nature Biotechnology 30:226 - 229, 2012 <span style="text-decoration: underline;"><a href="http://www.nature.com/nbt/journal/v30/n3/full/nbt.2134.html">Publisher Website</a></span>, <span style="text-decoration: underline;"><a href="http://hugeseq.snyderlab.org/">Home Page</a></span></p><p>Genome-wide LORE1 retrotransposon mutagenesis and high-throughput insertion detection in <em>Lotus japonicus</em>. Urbański et al, Plant J 64:731-741, 2012. <span style="text-decoration: underline;"><a href="http://onlinelibrary.wiley.com/doi/10.1111/j.1365-313X.2011.04827.x/abstract">Publisher Website</a></span> <em>[This paper describes a 2-dimensional pooling strategy with barcoding to allow use of Illumina sequencing to screen for retrotransposon insertion mutations, and includes a software package called FSTpoolit for analysis of the resulting sequence reads.]</em></p><h3>Genotyping by sequencing</h3><p>Genome-wide genetic marker discovery and genotyping using next-generation sequencing. Davey et al., Nat Rev Genet 12(7):499-510, 2011 <a href="http://www.ncbi.nlm.nih.gov/pubmed/21681211"><span style="text-decoration: underline;">PubMed</span></a> <em>[A review of methods available at the time]</em></p><p>A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. Elshire et al., PLoS One 6(5):e19379, 2011. <a href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3087801"><span style="text-decoration: underline;">Full Text</span></a></p><p>Development of high-density genetic maps for barley and wheat using a novel two-enzyme genotyping-by-sequencing approach. Poland et al., PLoS One 7(2): e32253, 2012. <a href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3289635/"><span style="text-decoration: underline;">Full Text</span></a></p><p>Double digest RADseq: an inexpensive method for de novo SNP discovery and genotyping in model and non-model species. Peterson et al, PLoS One 7(5):e37135, . 2012. <a href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3365034/"><span style="text-decoration: underline;">Full Text</span></a></p><p>Imputation of unordered markers and the impact on genomic selection accuracy. Rutkowski et al, G3 3(3):427-39, 2013. <a href="http://www.g3journal.org/content/3/3/427.long"><span style="text-decoration: underline;">Full Text</span></a></p><p>Diversity Arrays Technology (DArT) and next-generation sequencing combined: genome-wide, high-throughput, highly informative genotyping for molecular breeding of <em>Eucalyptus</em>. Sansaloni et al., BMC Proceedings 5(Suppl 7):P54, 2011 <span style="text-decoration: underline;"><a href="http://www.biomedcentral.com/1753-6561/5/S7/P54">Full Text</a></span></p><p>High-throughput genotyping by whole-genome resequencing. Huang et al., Genome Res 19(6):1068-76, 2009. <a href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2694477"><span style="text-decoration: underline;">Full Text</span></a></p><p>Multiplexed shotgun genotyping for rapid and efficient genetic mapping. Andolfatto et al. Genome Res 21(4):610-7, 2011. <a href="http://genome.cshlp.org/content/21/4/610.long"><span style="text-decoration: underline;">Full Text</span></a></p><h3>Restriction-site Associated DNA (RAD) markers</h3><p>Rapid SNP discovery and genetic mapping using sequenced RAD markers. Baird et al, PLoS One 3(10):e3376, 2008 <span style="text-decoration: underline;"><a href="http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0003376">Full Text</a></span></p><p>Linkage mapping and comparative genomics using next-generation RAD sequencing of a non-model organism. Baxter et al., PLoS One 6(4):e19315, 2011. <a href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3082572"><span style="text-decoration: underline;">Full Text</span></a></p><p>Genome evolution and meiotic maps by massively parallel DNA sequencing: spotted gar, an outgroup for the teleost genome duplication. Amores et al, Genetics 188(4):799-808, 2011. <a href="http://www.ncbi.nlm.nih.gov/pubmed/21828280"><span style="text-decoration: underline;"> PubMed</span></a></p><p>Construction and application for QTL analysis of a Restriction-site Associated DNA (RAD) linkage map in barley. Chutimanitsakun et al, BMC Genomics 4; 12:4, 2011. <a href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3023751"><span style="text-decoration: underline;">Full Text</span></a></p><p>RAD tag sequencing as a source of SNP markers in <em>Cynara cardunculus </em>L. Scaglione et al., BMC Genomics 13:3, 2012. <span style="text-decoration: underline;"><a href="http://www.biomedcentral.com/1471-2164/13/3">Full Text</a></span></p><p>Paired-end RAD-seq for de novo assembly and marker design without available reference. Willing et al., Bioinformatics 27(16):2187-93, 2011. <a href="http://bioinformatics.oxfordjournals.org/content/27/16/2187.long"><span style="text-decoration: underline;">Publisher Website</span></a></p><p>Local de novo assembly of RAD paired-end contigs using short sequencing reads. Etter et al., PLOS ONE 6(4): e18561, 2011. <a href="http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0018561"><span style="text-decoration: underline;">Full Text</span></a></p><p>Stacks: building and genotyping loci de novo from short-read sequences. Catchen et al., G3: Genes, Genomes, Genetics, 1:171-182, 2011. <span style="text-decoration: underline;"> Full Text</span>, <a href="http://creskolab.uoregon.edu/stacks/"><span style="text-decoration: underline;">Home Page</span></a></p><p>Rainbow: an integrated tool for efficient clustering and assembling RAD-seq reads. Chong et al, Bioinformatics 28(21):2732-7, 2012. <a href="http://bioinformatics.oxfordjournals.org/content/28/21/2732.long"> <span style="text-decoration: underline;">Publisher Website</span></a></p><p>UK RAD Sequencing Wiki page, with bibliography and RADTools software download <a href="https://www.wiki.ed.ac.uk/display/RADSequencing/Home"><span style="text-decoration: underline;">Home Page</span></a></p><h3>Workspace environments</h3><p><span style="text-decoration: underline;">Papers</span></p><p>Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Goecks et al, Genome Biol 11(8):R86, 2010 <a href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2945788"><span style="text-decoration: underline;">PubMedCentral</span></a></p><p>Galaxy Cloudman: Delivering compute clusters. BMC Bioinformatics 11(Suppl. 12):S4, 2010 <a href="http://www.biomedcentral.com/content/pdf/1471-2105-11-S12-S4.pdf"><span style="text-decoration: underline;">Full Text</span></a></p><p><a href="http://www.broadinstitute.org/gsa/wiki/index.php/The_Genome_Analysis_Toolkit"><span style="text-decoration: underline;">The Genome Analysis Toolkit</span></a>: a MapReduce framework for analyzing next-generation DNA sequencing data. McKenna et al, Genome Res 20(9):1297-303, 2010. <a href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2928508"><span style="text-decoration: underline;">PubMedCentral</span></a></p><p>A framework for variation discovery and genotyping using next-generation DNA sequencing data. DePristo et al., Nat Genet 43(5):491-8, 2011. <a href="http://www.ncbi.nlm.nih.gov/pubmed/21478889"><span style="text-decoration: underline;"> PubMed</span></a></p><p><span style="text-decoration: underline;">Online resources</span></p><p>The <a href="http://cran.r-project.org/"><span style="text-decoration: underline;">R statistical computing</span></a> environment includes<a href="http://www.bioconductor.org/"><span style="text-decoration: underline;"> Bioconductor</span></a>, a specialized set of tools for analysis of microarray and high-throughput sequencing data. Introductory materials from on-line or short workshops are widely available online; examples are <span style="text-decoration: underline;"><a href="http://bioconductor.org/help/course-materials/2012/Evomics2012/Bioconductor-tutorial.pdf">Evomics2012 Bioconductor-tutorial.pdf</a></span>, and <a href="http://bcb.dfci.harvard.edu/%7Eaedin/courses/Bioconductor/"><span style="text-decoration: underline;">Intro to Bioconductor</span></a>. Materials from an advanced course on high-throughput genetic data analysis are at <span style="text-decoration: underline;"><a href="http://bioconductor.org/help/course-materials/2012/SeattleFeb2012/">Seattle 2012 materials</a></span>. Thomas Girke of UC-Riverside has written a very complete set of manuals describing the use of R and Bioconductor for analysis of genomic datasets, available at <a href="http://manuals.bioinformatics.ucr.edu/home/R_BioCondManual">R and Bioconductor Manuals</a>. <br /> <a href="http://cran.r-project.org/manuals.html"><span style="text-decoration: underline;">Manuals</span></a> and contributed <a href="http://cran.r-project.org/other-docs.html"><span style="text-decoration: underline;">documentation</span></a> for R are available at the R-project.org website, and video tutorials are also available on Youtube; those posted by Tutorlol are brief, clear, and to the point. <br /> Materials from a series of mini-courses in R taught in 2010 at UCLA are available:</p><ul>
<li><a href="http://scc.stat.ucla.edu/page_attachments/0000/0141/10S-basicR.pdf">Intro to programming and graphics</a></li>
<li><a href="http://scc.stat.ucla.edu/page_attachments/0000/0143/S10_RProgII.pdf">Data manipulation and functions</a></li>
<li><a href="http://scc.stat.ucla.edu/page_attachments/0000/0185/Graphics_course.pdf">Graphics for exploratory data analysis</a></li>
<li><a href="http://scc.stat.ucla.edu/page_attachments/0000/0147/20100503_IntroStats.pdf">Introductory statistics</a></li>
<li><a href="http://scc.stat.ucla.edu/page_attachments/0000/0188/reg_R_1_09S_slides.pdf">Linear regression</a></li>
</ul><p><a href="http://a-little-book-of-r-for-bioinformatics.readthedocs.org/en/latest/"> <span style="text-decoration: underline;">A Little Book of R for Bioinformatics</span></a> is an on-line resource with information and exercises to provide practice in bioinformatics analysis of DNA sequences and other biological data in R. <br /> Many books on specific topics in R programming are also available through Amazon or other vendors.</p><h3>Cloud computing resources</h3><p>The case for cloud computing in genome informatics. Lincoln Stein, Genome Biol. 11(5):207, 2010 <a href="http://www.ncbi.nlm.nih.gov/pubmed/20441614"><span style="text-decoration: underline;">Pubmed</span></a></p><p>Galaxy Cloudman: delivering cloud compute clusters. Afgan et al, BMC Bioinformatics <span style="text-decoration: underline;">11</span>(Suppl 12):S4, 2010 <a href="http://www.biomedcentral.com/1471-2105/11/S12/S4"><span style="text-decoration: underline;">Full Text</span></a></p><p><a href="http://cloudbiolinux.com/">CloudBioLinux</a> is an open-source project that provides a bioinformatics Linux system for cloud computing, pre-configured with a variety of software tools installed and ready to use.</p><p>A <a href="https://github.com/chapmanb/cloudbiolinux/blob/master/doc/intro/gettingStarted_CloudBioLinux.pdf?raw=true"><span style="text-decoration: underline;">tutorial</span></a> on getting started with CloudBioLinux on the Amazon Web Services Elastic Compute Cloud (EC2)</p><p><a href="http://userwww.service.emory.edu/%7Eeafgan/content/ppt/EnisAfgan_BOSC_2010.pdf"><span style="text-decoration: underline;">Deploying Galaxy on the Cloud</span></a>  slides from a presentation by Enis Afgan (Emory University) at the <br /> &nbsp;Bioinformatics Open Source Conference in Boston, July 2010</p><p>A <a href="http://screencast.g2.bx.psu.edu/cloud/"><span style="text-decoration: underline;"> screencast</span></a> that provides a step-by-step guide to starting a Galaxy cluster in the EC2 environment</p><p>A <a href="https://bitbucket.org/galaxy/galaxy-central/wiki/cloud"><span style="text-decoration: underline;">webpage</span></a> that has the same information in text form, and is the basis for the screencast</p><p>The iPlant Collaborative, an NSF-funded project to create computational resources for plant biology research, provides access to cloud computing resources through <span style="text-decoration: underline;"><a href="http://www.iplantcollaborative.org/discover/atmosphere">Atmosphere</a></span></p><p>SeqWare Query Engine: storing and searching sequence data in the cloud. OConnor et al, BMC Bioinformatics <strong>11</strong>(Suppl 12)<strong>:</strong>S2, 2010 <a href="http://www.biomedcentral.com/1471-2105/11/S12/S2"><span style="text-decoration: underline;">Full Text</span></a></p><p>An overview of the Hadoop/MapReduce/HBase framework and its current applications in bioinformatics. Taylor, BMC Bioinformatics <strong>11</strong>(Suppl 12)<strong>:</strong>S1, 2010 <a href="http://www.biomedcentral.com/1471-2105/11/S12/S1"><span style="text-decoration: underline;">Full Text</span></a></p><h3>Links to Linux command-line tutorials and resources</h3><p>Tutorials for AWK, a powerful tool for handling data tables</p><ul>
<li>A set of <a href="http://people.bu.edu/scottm/AWK.NOTES"><span style="text-decoration: underline;">awk notes</span></a> from Boston University</li>
<li>Bruce Barnett's <a href="http://www.grymoire.com/Unix/Awk.html"><span style="text-decoration: underline;">awk tutorial</span></a></li>
<li>Greg Goebel's <a href="http://www.vectorsite.net/tsawk.html"><span style="text-decoration: underline;">awk tutorial</span></a></li>
<li><a href="http://teaching.software-carpentry.org/2013/01/16/1433/"><span style="text-decoration: underline;">Executing an awk command from R</span></a> to simplify data exploratory analysis, from Lex Nederbragt</li>
</ul><p>Tutorials for bash shell scripting</p><ul>
<li>A <a href="http://www.linuxconfig.org/bash-scripting-tutorial"><span style="text-decoration: underline;">tutorial</span></a> at linuxconfig.org</li>
<li>A <a href="http://www.hypexr.org/bash_tutorial.php"><span style="text-decoration: underline;">Getting Started With Bash</span></a> tutorial at hypexr.org</li>
<li>Mendel Cooper's <a href="http://tldp.org/LDP/abs/html/"><span style="text-decoration: underline;">Advanced Bash Shell-Scripting Guide</span></a></li>
</ul><p>Tutorials for sed, the command-line stream editor</p><ul>
<li>A <a href="http://www.panix.com/%7Eelflord/unix/sed.html"><span style="text-decoration: underline;">tutorial</span></a> at Rutgers</li>
<li>Peteris Krumins claims to have the <a href="http://www.catonmat.net/blog/worlds-best-introduction-to-sed/"><span style="text-decoration: underline;"> World's Best Introduction to Sed</span></a>; take a look and judge for yourself.</li>
<li>Bruce Barnett's <a href="http://www.grymoire.com/Unix/Sed.html"><span style="text-decoration: underline;">sed tutorial</span></a>.</li>
</ul><h3>Links to other useful sites</h3><p>The<a href="http://seqanswers.com/"><span style="text-decoration: underline;"> SEQanswers</span></a> online community has forums on several topics related to sequencing; the bioinformatics forum is the most active.</p><p>The SEQanswers <span style="text-decoration: underline;"><a href="http://seqanswers.com/wiki/Software">Software Wiki</a></span> is a list of software for analysis of sequencing data</p><p><a href="http://biostar.stackexchange.com/">Biostar</a> is another online community for questions and answers on bioinformatics and computational genomics.</p><p>Information on file formats used by the University of California - Santa Cruz Genome Browser is on the <a href="http://genome.ucsc.edu/FAQ/FAQformat"><span style="text-decoration: underline;"> FAQ list</span></a></p><p>A manual for the Integrated Genome Browser visualization tool is <a href="http://wiki.transvar.org/confluence/display/igbman/Home"><span style="text-decoration: underline;">here</span></a></p><p>Course materials for a short course entitled <a href="http://bioconductor.org/help/course-materials/2010/SeattleIntro/"><span style="text-decoration: underline;">Introduction to R and Bioconductor</span></a>, held in Seattle in Dec 2010</p><p><a href="http://great.stanford.edu/"><span style="text-decoration: underline;">Genomic Regions Enrichment of Annotations Tool</span></a> - A web service to test for over-representation of specific ontology categories among genes near ChIP-seq peaks</p><p><a href="http://www.animalgenome.org/bioinfo/resources/nextgensoft.html"><span style="text-decoration: underline;">Next-gen-seq software</span></a> - a list of software packages, both commercial and open-source, related to analysis of deep sequencing datasets</p><p><a href="http://www.cbcb.umd.edu/software/"><span style="text-decoration: underline;">Software</span></a> from the Center for Bioinformatics and Computational Biology, University of Maryland - many useful programs, all open-source</p><p><a href="http://bioinformatics.psb.ugent.be/plaza/"><span style="text-decoration: underline;"> PLAZA</span></a>: a comparative genomics resource to study gene and genome evolution in plants; described by Proost et al, Plant Cell 21:3718, 2010 <a href="http://www.plantcell.org/content/21/12/3718.full"><span style="text-decoration: underline;">Full Text</span></a></p><p>The European Bioinformatics Institute provides tools <a href="http://www.ebi.ac.uk/Tools/rcloud/"><span style="text-decoration: underline;">ArrayExpressHTS</span><span style="text-decoration: underline;"> and R-Cloud</span></a> for analysis of transcriptome data</p>]]></description>
	<dc:creator>Rahul Nayak</dc:creator>
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/20508/15-highly-motivated-early-stage-researchers-esrsphd-positions</guid>
  <pubDate>Sun, 25 Jan 2015 05:23:53 -0600</pubDate>
  <link></link>
  <title><![CDATA[15 highly motivated Early Stage Researchers (ESRs)/PhD positions]]></title>
  <description><![CDATA[
<p>The MiND programme  looking for 15 highly motivated Early Stage Researchers (ESRs), researchers with a BSc or MSc degree within the first four years (full-time equivalent) of their research career</p>

<p> All applications sent before  2nd of February 2015.</p>

<p>http://www.mind-project.eu/career</p>
]]></description>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/2457/rdataminingcom-r-and-data-mining</guid>
	<pubDate>Thu, 15 Aug 2013 18:37:23 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/2457/rdataminingcom-r-and-data-mining</link>
	<title><![CDATA[Rdatamining.com : R and Data Mining]]></title>
	<description><![CDATA[<p>This website presents examples, documents and resources on data mining with R. <br>Documents on using R for data mining are available to download for non-commercial personal use, including&nbsp;R Reference card for Data Mining, R and Data Mining: Examples and Case Studies and Time Series Analysis and Mining with R.</p><p>Address of the bookmark: <a href="http://www.rdatamining.com/" rel="nofollow">http://www.rdatamining.com/</a></p>]]></description>
	<dc:creator>Poonam Mahapatra</dc:creator>
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/22891/17-marie-curie-phd-position-available-immediately</guid>
  <pubDate>Tue, 23 Jun 2015 06:52:06 -0500</pubDate>
  <link></link>
  <title><![CDATA[17 Marie Curie PhD position available immediately]]></title>
  <description><![CDATA[
<p>Kindly look into following webpage:<br />http://medhealth.leeds.ac.uk/info/1450/scholarships/1795/marie_curie_phd_training_network</p>

<p>The closing date for application will be 26 June 2015.</p>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/pages/view/2573/most-commonly-used-awk-by-bioinformatician</guid>
	<pubDate>Mon, 19 Aug 2013 01:12:38 -0500</pubDate>
	<link>https://bioinformaticsonline.com/pages/view/2573/most-commonly-used-awk-by-bioinformatician</link>
	<title><![CDATA[Most Commonly used Awk by Bioinformatician]]></title>
	<description><![CDATA[<p style="text-align: center;">&nbsp;</p><p>Awk is a programming language that is specifically designed for quickly manipulating space delimited data. Although you can achieve all its functionality with Perl, awk is simpler in many practical cases.</p><p>Why awk? You can replace a pipeline of 'stuff | grep | sed | cut...' with a single call to awk. For a simple script, most of the timelag is in loading these apps into memory, and it's much faster to do it all with one. This is ideal for something like an openbox pipe menu where you want to generate something on the fly. You can use awk to make a neat one-liner for some quick job in the terminal, or build an awk section into a shell script. You can find a lot of online tutorials, but here I will only show a few examples which cover most of bioinformatician daily uses of awk.</p><p>choose rows where column 3 is larger than column 5:</p><p>awk '$3&gt;$5' input.txt &gt; output.txt</p><p>extract column 2,4,5:</p><p>awk '{print $2,$4,$5}' input.txt &gt; output.txt</p><p>awk 'BEGIN{OFS="\t"}{print $2,$4,$5}' input.txt</p><p>show rows between 20th and 80th:</p><p>awk 'NR&gt;=20&amp;&amp;NR&lt;=80' input.txt &gt; output.txt</p><p>calculate the average of column 2:</p><p>awk '{x+=$2}END{print x/NR}' input.txt</p><p>regex (egrep):</p><p>awk '/^test[0-9]+/' input.txt</p><p>calculate the sum of column 2 and 3 and put it at the end of a row or replace the first column:</p><p>awk '{print $0,$2+$3}' input.txt</p><p>awk '{$1=$2+$3;print}' input.txt</p><p>join two files on column 1:</p><p>awk 'BEGIN{while((getline&lt;"file1.txt")&gt;0)l[$1]=$0}$1 in l{print $0"\t"l[$1]}' file2.txt &gt; output.txt</p><p>count number of occurrence of column 2 (uniq -c):</p><p>awk '{l[$2]++}END{for (x in l) print x,l[x]}' input.txt</p><p>apply "uniq" on column 2, only printing the first occurrence (uniq):</p><p>awk '!($2 in l){print;l[$2]=1}' input.txt</p><p>count different words (wc):</p><p>awk '{for(i=1;i!=NF;++i)c[$i]++}END{for (x in c) print x,c[x]}' input.txt</p><p>deal with simple CSV:</p><p>awk -F, '{print $1,$2}'</p><p>substitution (sed is simpler in this case):</p><p>awk '{sub(/test/, "no", $0);print}' input.txt</p><p>&nbsp;</p><p>OK now here's where to read this stuff properly explained. roll</p><p>Two thorough tutorials:</p><p>http://www.gnu.org/software/gawk/manual/gawk.html</p><p>http://www.grymoire.com/Unix/Awk.html</p><p>A famous list of useful one-liners - though they're short, many are quite tricky:</p><p>http://www.pement.org/awk/awk1line.txt</p><p>And some nice explanations of those one-liners. After reading this you'll have a pretty good grasp!</p><p>http://www.catonmat.net/blog/awk-one-li &hellip; -part-one/</p><p>http://www.catonmat.net/blog/ten-awk-ti &hellip; -pitfalls/</p>]]></description>
	<dc:creator>Neel</dc:creator>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/blog/view/34727/letter-of-motivation-for-bioinformatics-applicants</guid>
	<pubDate>Thu, 21 Dec 2017 03:43:04 -0600</pubDate>
	<link>https://bioinformaticsonline.com/blog/view/34727/letter-of-motivation-for-bioinformatics-applicants</link>
	<title><![CDATA[Letter of motivation for bioinformatics applicants !]]></title>
	<description><![CDATA[<p>A motivation letter, or sometimes called letter of motivation or motivational letter, is actually a letter being send together with your professional resume to support your application for job, University admission or internship. The motivational letter is actually a personal statement which should persuade selection panel, or human resource clerk that you are perfect candidate for a position. Writing a impressive &lsquo;Letter of Motivation&rsquo; might help you to get the post with an ease.&nbsp;</p><p>Usually when you apply anywhere you need to fulfill some specific kind of requirements which usually include writing a formal application, letter of motivation, research proposal etc. Usually it is hard for grad students to write a crisp, clean and clear letter of motivation. To be honest, you may find several posts on the internet which do tell you how to write professionally. They are good enough to clearly tell you what points should be included, what not and many other things to learn about professional writing. Still, when I look back at my graduation days, I know even after reading many instructions I was not able to write &lsquo;to-the-point&rsquo;. According to me , writing skill is not something that you can part in binary like- &lsquo;I write perfectly&rsquo; or &lsquo;I can not write even a word&rsquo;. It is something that you learn and get better with the the time. So, I am not going to pin-point the suggestions because you can get it many where but some &lsquo;to-the-point&rsquo; things which you may use directly in your letter.</p><h5>Ideas and main points</h5><p>Start with writing down some of the main ideas, important points you would like to approach in your letter and later build around them, enrich their content; an example would be :</p><ol>
<li>Make your goal clear; provide a short preview of the rest of the letter;</li>
<li>Why do you think that the university and the Master's program are interesting and suitable for you? ;</li>
<li>Focus on some of your strongest qualifications, past experiences (international experiences are always relevant) and qualities; organise the middle paragraphs in terms of the qualifications most relevant to the programme, you can also refer to your CV for more details;</li>
<li>Conclude by restating your interest and show appreciation for the chance to prove yourself in the letter (in some cases you can ask for a personal interview)</li>
</ol><p>How to start- <br />Your very first line should not be just a line but an impression and reference. None would want to read you unless he knows what it is about. Just like this post. If I would not have written that it is about writing a motivation-letter, you probably would not get annoyed. So start by writing what your letter is about. It could seem like this-</p><h5>Letter Of Application</h5><p>Your Address And Contact Details</p><p>Receiver&rsquo;s Address</p><p>Dear XYZ</p><p>I would like to apply for the&hellip;..</p><p>or</p><p>I am writing here to apply for the&hellip;</p><p>or</p><p>This is regarding your advert. published&hellip;.</p><p>Then Tell Background like-<br />As my resume reveals, I have Bachelor`s degree from XYZ University and currently, I am&hellip;..</p><p>Be sure to signify your institution/University like-<br />I am privileged to obtain my postgraduate education in Bioinformatics at XXX which is known for its enriching academic ambiance where learning and research complement each other.</p><p>Then tell about your professional experience like-<br />Being taught by eminent faculty, I have developed a big interest and passion towards Bioinformatics and managed to have a strong foundation in &hellip;&hellip;</p><p>After that tell how this position would help you, like-<br />The opportunity to participate in this study would foster&hellip;.</p><p>Assure them that you will make use of whatever you learn there, like-<br />I plan to ensure the further dissemination of the knowledge and experience gained by this opportunity in&hellip;</p><p>Close the letter with usual formality, like-<br />I, hereby enclose a copy of my CV/Resume (whatever it is, there is a difference we all know it) with the hope of consideration. Looking forward to hearing from you.</p><p><br />All the things written above is just my view. You still should see and learn which can be done by one thing and that is -reading about it. Then , please try to write yourself, do not copy /paste. Whatever is written in the post is just to have an idea about the things that should be included in the letter of motivation. You need to write accordingly with a wise choice of words.<br />Hope this was helpful. You may comment or ask anything if you want to.</p>]]></description>
	<dc:creator>Neel</dc:creator>
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/4106/phd-at-national-institute-for-research-in-reproductive-health</guid>
  <pubDate>Fri, 30 Aug 2013 04:50:35 -0500</pubDate>
  <link></link>
  <title><![CDATA[PhD at National Institute for Research in Reproductive Health]]></title>
  <description><![CDATA[
<p>National Institute for Research in Reproductive Health</p>

<p>(Indian Council of Medical Research )<br />Jehangir Merwanji Street, Parel, Mumbai 400 012</p>

<p>Advertisement No. 1/NIRRH/Ph.D. 2013<br />Admission to Ph.D. Programme – 2013</p>

<p>National Institute for Research in Reproductive Health, Mumbai, a premier institute of the Indian Council of Medical Research, conducts basic, clinical and operational research in different areas of reproductive health. The thrust areas of research include: Fertility Regulation, Infertility and Reproductive Disorders, Reproductive Tract Infections, Maternal and Child Health, Osteoporosis, Genetic Disorders, Stem Cell Biology, Structural Biology, Bioinformatics and Reproductive Toxicology. Institute is affiliated to the University of Mumbai for the award of Ph.D. degree in Applied Biology, Biochemistry, Life Sciences and Biotechnology. The institute invites applications from young and bright students for enrollment in Ph.D. programme.</p>

<p>More at http://www.nirrh.res.in/announcements/phd_program_2013.htm</p>
]]></description>
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/35423/jrf-at-jaypee-institute-of-information-technology-jiit-noida-department-of-biotechnology</guid>
  <pubDate>Fri, 02 Feb 2018 11:26:14 -0600</pubDate>
  <link></link>
  <title><![CDATA[JRF at Jaypee Institute of Information Technology (JIIT), Noida Department of Biotechnology]]></title>
  <description><![CDATA[
<p>Lab of Dr. Rawal is supported by generous grants to build advanced applications in emerging areas of cancer genomics, network sciences, vaccine development and epidemiology. The lab has dedicated high end Xeon servers, desktops, &amp; laptops for research purpose. Currently, there are several researchers (JRFs, B. Techs, M. Tech and PhDs) working on several challenging bioinformatics projects. In addition, Dr. Rawal has collaborations with reputed national and international research teams.</p>

<p>Dr. Rawal and his US based collaborators have recently secured grant for development of vaccine against an infectious disease agent. For this project, applications are invited for the posts of Junior Research Fellow (two positions) for the following time-bound sponsored projects as per the details given below:</p>

<p>PI: Dr. Kamal Rawal, Biotechnology Department, JIIT, Noida.</p>

<p>Post: JRF (Two)</p>

<p>Job Description: Bioinformatics analysis, Software development, Programming, Text Mining, Deep Curation</p>

<p>Duration: The post is valid upto duration of the project. Continuation is subject to satisfactory performance.</p>

<p>Emoluments depends upon experience and skill sets. We will hire them on following scale:</p>

<p>Junior Scale- Level 1: Rs 22000 per month.</p>

<p>Senior Scale - Level 2: Rs 30000 per month.</p>

<p>Essential Qualification(s) for JRF post:</p>

<p>(A) A Master degree (MSc or MTech or equivalent with minimum of 55% marks) in Bioinformatics/Computer Sciences, IT, Life Sciences, Physical Sciences, Chemical Sciences, Mathematical Sciences or Statistics, Agriculture, Veterinary, Medicine, Pharmacy, Engineering &amp; Technology from a recognized University/Institute and having some experience/skills in bioinformatics, programming, computational or software development work.</p>

<p>(B) In exceptional cases, we can also consider candidates with B. Tech or equivalent with right skill sets and experience for the post of JRFs.</p>

<p>Desirable:</p>

<p>A) Preference will be given to BINC (Bioinformatics National Certification)/DBT-BET/ICMR/ CSIR /UGC/ JRF/ NET qualified candidates. However, Non- NET qualified candidates can also apply.<br />B) Candidates who have worked with programing, text mining, NGS data analysis etc are encouraged to apply.<br />Updated resume including a cover letter (preferably by E. mail) should be mailed to bioinfocvatgmaildotcom, and Dr. Kamal Rawal at kamaldotrawalatgmaildotcom. Short listed candidates would be called for interview. No TA/DA will be paid to the candidates called for interview.</p>

<p>Candidate may also fill the following form:</p>

<p>https://docs.google.com/…/1FAIpQLSdZoZ21ZoNRStEeL5…/viewform</p>

<p>Or</p>

<p>http://tinyurl.com/bioinfocv2017</p>
]]></description>
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/researchlabs/view/2742/baumbach-lab</guid>
  <pubDate>Wed, 21 Aug 2013 10:56:35 -0500</pubDate>
  <link></link>
  <title><![CDATA[Baumbach Lab]]></title>
  <description><![CDATA[
<p>The Computational Biology research group was established in October 2012 at the Department of Mathematics and Computer Science (IMADA) at the University of Southern Denmark (SDU). It emerged from the Computational Systems Biology group, founded in March 2010 at the Max Planck Institute for Informatics (MPII) and the Cluster of Excellence for Multimodel Computing and Interaction (MMCI) at Saarland University, Saarbrücken, Germany.<br />​<br />The group is headed by Prof. Dr. Jan Baumbach and currently hosts nine PhD students and one postdoctoral fellow at both, IMADA/SDU and MMCI/MPII.</p>

<p>More at &gt;&gt; http://www.baumbachlab.net/</p>
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/researchlabs/view/35868/simpson-lab</guid>
  <pubDate>Tue, 06 Mar 2018 08:59:09 -0600</pubDate>
  <link></link>
  <title><![CDATA[Simpson Lab]]></title>
  <description><![CDATA[
<p>We are the Statistical Bioinformatics group in the Institute for Adaptive and Neural Computation in the School of Informatics at the University of Edinburgh. The group is led by Dr. Ian Simpson who is a Lecturer in Biological Informatics in the School of Informatics at Edinburgh University. Details to follow....</p>

<p>http://statbio.github.io</p>
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