<?xml version='1.0'?><rss version="2.0" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:georss="http://www.georss.org/georss" xmlns:atom="http://www.w3.org/2005/Atom" >
<channel>
	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/44718?offset=0</link>
	<atom:link href="https://bioinformaticsonline.com/related/44718?offset=0" rel="self" type="application/rss+xml" />
	<description><![CDATA[]]></description>
	
	
<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/43272/bioinformatics-head-bioinformatics-manager-iii-cancer-genomics-research-laboratory-at-frederick-national-laboratory</guid>
  <pubDate>Wed, 18 Aug 2021 00:19:48 -0500</pubDate>
  <link></link>
  <title><![CDATA[Bioinformatics Head (Bioinformatics Manager III), Cancer Genomics Research Laboratory at  Frederick National Laboratory]]></title>
  <description><![CDATA[
<p>Frederick National Laboratory seeking an enthusiastic, creative, and seasoned bioinformatics professional to join our leadership team and direct the exceptional Bioinformatics Group at the Cancer Genomics Research Laboratory (CGR).  CGR has a diverse team of bioinformatics and computational scientists that support all areas of bioinformatics and data analysis (infrastructure, data QC, pipeline development and maintenance, data curation and sharing, methodology development, statistical analyses, machine learning approaches, and scientific interpretation).</p>

<p>More at https://leidosbiomed.csod.com/ats/careersite/jobdetails.aspx?site=4&amp;c=leidosbiomed&amp;id=2040</p>
]]></description>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/researchlabs/view/26828/bioinfolab</guid>
  <pubDate>Fri, 25 Mar 2016 11:05:35 -0500</pubDate>
  <link></link>
  <title><![CDATA[BioinfoLab]]></title>
  <description><![CDATA[
<p>Laboratory of Statistics and Computational tools for Bioinformatics</p>

<p>The Laboratory of Statistics and Computational tools for Bioinformatics (BioinfoLab) is hosted at the Istituto per le Applicazioni del Calcolo "Mauro Picone" - CNR . The laboratory has been officially opened in 2012 with the support of Programma Operativo Nazionale "Ricerca e Competitività" 2007-2013 (PON "R&amp;C"), and it incorporates several expertise and research activities started since 2007, and supported by several CNR projects. Main interest of BioinfoLab is to develop novel statistical methods and computational tools for the analysis of high dimensional data arising from "Multi-omics" applications. In particular, current activities involve the analysis of ChIP-seq and RNA-seq experiments. </p>

<p>More at http://bioinfo.na.iac.cnr.it/BioinfoLab/index.html</p>
]]></description>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/news/view/35257/india-and-germany-to-begin-joint-research-in-the-area-of-bioinformatics-in-health-research</guid>
	<pubDate>Wed, 17 Jan 2018 14:10:36 -0600</pubDate>
	<link>https://bioinformaticsonline.com/news/view/35257/india-and-germany-to-begin-joint-research-in-the-area-of-bioinformatics-in-health-research</link>
	<title><![CDATA[India and Germany to begin joint research in the area of 'Bioinformatics in Health Research']]></title>
	<description><![CDATA[<p><span>To facilitate bilateral cooperation in biotechnology between the scientific communities of India and Germany, the Department of Biotechnology (DBT) will soon begin collaborative research in the identified priority area of 'Bioinformatics in Health Research' under the programme of Indo-German Cooperation in Health Research.&nbsp;</span><br /><br /><span>The purpose of the programme is to stimulate new collaborations, e.g. the preparation of joint projects under national funding programmes. The programme facilitates bilateral cooperation in biotechnology between the scientific communities of India and Germany by way of joint research projects which will encompass bilateral workshops/seminar and exchange visits of scientists.&nbsp;</span><br /><br /><span>The programme is being implemented within the agreement of Indo-German cooperation in S&amp;T of 1974, under which the Department of Biotechnology, Government of India and Forschungszentrum Julich BMBH (FZJ), Federal Republic of Germany, have agreed for cooperative programme in biotechnology.</span><br /><br /><span>DBT of the Ministry of Science &amp; Technology, Government of India and the Project Management Agency at the German Aerospace Center (DLR-PT, European and International Cooperation), Bonn are the nodal implementing agencies from the Indian and German side respectively.</span><br /><br /><span>Through this programme, it is expected that the funded cooperation enables the partners to develop applicable scientific results which can be published and/ or could be commercialised and may lead to formation of joint ventures. All publications, patents coming out of these projects, need to be jointly authored by both Indian and German scientists. All necessary approvals like ethical clearance, HMSC approval from Indian point of view as well as EU, if applicable, from German point of view, e.g. before conducting animal experimentation if any needs to be obtained by PIs before undertaking the project.&nbsp;</span><br /><br /><span>Now, both the nodal agencies have invited research proposals in identified priority area of 'Bioinformatics in Health Research' from eligible scientists.&nbsp; Joint research projects are required to be submitted to both the nodal agencies by 15 January 2018. Scientists/faculty members working in regular capacity in universities, national R&amp;D laboratories/institutes and private R&amp;D institutes can be part of this joint research programme.&nbsp;&nbsp; For the private sector, partners from all kind of private sectors are eligible, but financing is limited. For Indian scientists from the private sector, only local hospitality in Germany as part of the exchange visit is available from the German side.&nbsp; For German scientists from the private sector, only travel costs are available for small and medium size enterprises (for definition of SME ref. to 2003/361/EC) as well as local hospitality in India will be borne by themselves.</span></p>]]></description>
	<dc:creator>Rahul Nayak</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/news/view/24264/cancer-research-database</guid>
	<pubDate>Tue, 01 Sep 2015 17:36:31 -0500</pubDate>
	<link>https://bioinformaticsonline.com/news/view/24264/cancer-research-database</link>
	<title><![CDATA[Cancer research database]]></title>
	<description><![CDATA[<p>Researchers in Andhra Pradesh have developed a database to identify genes that are common in tumours to provide their colleagues with easy access to insights into the genetic alterations in cancer.<br /> &nbsp;<br /> The database, hosted at the Sri Venkateswara University (SVU) in Tirupati, will integrate information on cancer genes and markers with experimental data.<br /> &nbsp;<br /> The <a href="http://cgmd.in/" target="_blank">Cancer Gene Markers Database</a> (CGMD) is meant to help scientists better understand tumour genes and markers at a molecular level by combining data with literature on treatment regimen and recent advances in cancer therapy.<br /> <br /> The database is free to access, and already includes 309 genes and 206 markers that correspond to 40 different human cancers. Accompanying literature comes from databases such as the United States&rsquo; <a href="http://www.ncbi.nlm.nih.gov/" target="_blank">National Center for Biotechnology Information</a> and the <a href="http://www.genome.jp/kegg/" target="_blank">Kyoto Encyclopedia of Genes and Genomes</a>. It also includes experimental data from <a href="http://www.ncbi.nlm.nih.gov/pubmed" target="_blank">PubMed</a>.<br /> <br /> In a paper <a href="http://dx.doi.org/10.1038/srep12035" target="_blank">published</a> last month in <em>Nature Scientific Reports</em>, the researchers from SVU&rsquo;s department of animal biotechnology, describes the need for a database for different genes and markers along with their molecular characteristics and pathway associations.</p>]]></description>
	<dc:creator>Neel</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/pages/view/8265/list-of-generic-simulation-softwaretoolsresource-with-brief-description-and-homepage</guid>
	<pubDate>Mon, 10 Feb 2014 05:57:29 -0600</pubDate>
	<link>https://bioinformaticsonline.com/pages/view/8265/list-of-generic-simulation-softwaretoolsresource-with-brief-description-and-homepage</link>
	<title><![CDATA[List of generic simulation software/tools/resource with brief description and homepage !!!]]></title>
	<description><![CDATA[<p>List of generic simulation software/tools/resource with brief description and homepage</p><p><img src="http://www.evolution-of-life.com/fileadmin/images/carousel/genetic.PNG" alt="image" style="border: 0px;"></p><p>ALF <br />A Simulation Framework for Genome Evolution <br />http://www.cbrg.ethz.ch/alf<br /><br />Bayesian Serial SimCoal <br />Bayesian Serial SimCoal, (BayeSSC) is a modification of SIMCOAL 1.0, a program written by Laurent Excoffier, John Novembre, and Stefan Schneider. <br />http://www.stanford.edu/group/hadlylab/ssc/index.html<br /><br />BEERS <br />BEERS was designed to benchmark RNA-Seq alignment algorithms and also algorithms that aim to reconstruct different isoforms and alternate splicing from RNA-Seq data <br />http://cbil.upenn.edu/beers/<br /><br />BOTTLENECK <br />Bottleneck is a program for detecting recent effective population size reductions from allele data frequencies <br />http://www.ensam.inra.fr/urlb/bottleneck/bottleneck.html<br /><br />BottleSim <br />BottleSim is a computer simulation program for simulating the process of population bottlenecks <br />http://chkuo.name/software/bottlesim.html<br /><br />CASS <br />Protein Sequence Simulation <br />http://www.wyomingbioinformatics.org/liberlesgroup/cass/<br /><br />CDPOP <br />CDPOP is a landscape genetics tool for simulating the emergence of spatial genetic structure in populations resulting from specified landscape processes governing organism movement behavior. <br />http://cel.dbs.umt.edu/cdpop<br /><br />CoalFace <br />CoalFace is a simulation of the coalescent process with the visual display of gene genealogies. <br />http://web.up.ac.za/default.asp?ipkcategoryid=3283<br /><br />CoaSim <br />CoaSim is a tool for simulating the coalescent process with recombination and geneconversion under various demographic models. <br />http://users-birc.au.dk/mailund/coasim/index.html<br /><br />cosi <br />The cosi package is written in C and is available as a tar file. <br />http://www.broadinstitute.org/~sfs/cosi/<br /><br />CS-PSeq-Gen <br />A program to simulate the evolution of protein sequences under the constraints of the information of a particular reconstructed phylogeny <br />http://bioserv.rpbs.univ-paris-diderot.fr/software/cs-pseq-gen.html<br /><br />DAWG <br />An application designed to simulate the evolution of recombinant DNA sequences in continuous time <br />http://scit.us/projects/dawg<br /><br />Easypop <br />EASYPOP is an individual based model intended to simulate datasets under a very broad range of conditions <br />http://www.unil.ch/dee/page36926_fr.html<br /><br />EggLib <br />EggLib is a C++/Python library and program package for evolutionary genetics and genomics. <br />http://egglib.sourceforge.net/<br /><br />EvolSimulator <br />A simulation test bed for hypotheses of genome evolution <br />http://acb.qfab.org/acb/evolsim/<br /><br />EvolveAGene <br />A realistic coding sequence simulation program that separates mutation from selection and allows the user to set selection conditions <br />http://bellinghamresearchinstitute.com/software/index.html<br /><br />fastsimcoal <br />A continuous-&not;‐time coalescent simulator of genomic diversity under arbitrarily complex evolutionary scenarios <br />http://cmpg.unibe.ch/software/fastsimcoal/<br /><br />FastSLINK <br />Simulation of Marker and Phenotype Data in Pedigrees <br />http://watson.hgen.pitt.edu/<br /><br />FFPopSim <br />C++/Python library for population genetics. <br />http://webdav.tuebingen.mpg.de/ffpopsim/<br /><br />FLUX SIMULATOR <br />The Flux Simulator aims at providing a deterministic in silico reproduction of the experimental pipelines for RNA-Seq, employing a minimal set of parameters. <br />http://flux.sammeth.net/simulator.html<br /><br />ForSim <br />ForSim: A Forward Evolutionary Computer Simulation <br />http://www.anthro.psu.edu/weiss_lab/research.shtml<br /><br />ForwSim <br />The program given below is based on the algorithm described in Padhukasahasram et al. 2008 to simulate genetic drift in a standard Wright-Fisher process. <br />http://badri-populationgeneticsimulators.blogspot.com/<br /><br />FPG <br />Forward Population Genetic simulation <br />http://genfaculty.rutgers.edu/hey/software#fpg<br /><br />FREGENE <br />FREGENE is a C++ program that simulates sequence-like data over large genomic regions in large diploid populations. <br />http://www.ebi.ac.uk/projects/bargen/download/fregen/documentation_html.html<br /><br />GAMETES <br />Genetic Architecture Model Emulator for Testing and Evaluating Software: Simulates complex SNP models with pure, strict epistatic interactions with n-loci. <br />http://sourceforge.net/projects/gametes/?source=navbar<br /><br />GASP <br />Genometric Analysis Simulation Program. A software tool for testing and investigating methods in statistical genetics by generating samples of family data based on user specified models. <br />http://research.nhgri.nih.gov/gasp/<br /><br />GemSIM <br />Next generation sequencing read simulator <br />http://sourceforge.net/projects/gemsim/<br /><br />GeneArtisan <br />Simulation of Markers in Case-Control Study Designs <br />http://www.rannala.org/?page_id=241<br /><br />GENOME <br />A rapid coalescent-based whole genome simulator <br />http://www.sph.umich.edu/csg/liang/genome/<br /><br />GenomePop2 <br />GenomePop2 is a specialization of the program GenomePop just to manage SNPs under more flexible and useful settings. If you need models with more than 2 alleles please use the GenomePop program version. <br />http://webs.uvigo.es/acraaj/genomepop2.htm<br /><br />GenomeSimla <br />GenomeSIMLA is currently under development- however, we have a beta release that we are asking to be tested <br />http://chgr.mc.vanderbilt.edu/genomesimla/<br /><br />GENS2 <br />Simulates interactions among two genetic and one environmental factor and also allows for epistatic interactions. <br />https://sourceforge.net/projects/gensim/<br /><br />GWAsimulator <br />A rapid whole genome simulation program <br />http://biostat.mc.vanderbilt.edu/wiki/main/gwasimulator<br /><br />HAP-SAMPLE <br />An association simulator for candidate regions or genome scans <br />http://www.hapsample.org/<br /><br />HAPGEN <br />A simulator for the simulation of case control datasets at SNP markers <br />https://mathgen.stats.ox.ac.uk/genetics_software/hapgen/hapgen2.html<br /><br />HapSim <br />A simulation tool for generating haplotype data with pre-specified allele frequencies and LD coefficients <br />http://cran.r-project.org/web/packages/hapsim/index.html<br /><br />HAPSIMU <br />A program that simulates heterogeneous populations with various known and controllable structures under the continuous migration model or the discrete model <br />http://l.web.umkc.edu/liujian/<br /><br />IBDsim <br />IBDSim is a computer package for the simulation of genotypic data under general isolation by distance models. <br />http://raphael.leblois.free.fr/<br /><br />indel-Seq-Gen <br />A biological sequence simulation program that simulates highly divergent DNA sequences and protein superfamilies <br />http://bioinfolab.unl.edu/~cstrope/isg/<br /><br />Indelible <br />A powerful and flexible simulator of biological evolution <br />http://abacus.gene.ucl.ac.uk/software/indelible/<br /><br />invertFREGENE <br />InvertFREGENE is a forward-in-time simulator of inversions in population genetic data <br />http://www.ebi.ac.uk/projects/bargen/<br /><br />kernalPop <br />A spatially explicit population genetic simulation engine <br />http://cran.r-project.org/src/contrib/archive/kernelpop/<br /><br />MaCS <br />Markovian Coalescent Simulator <br />http://www-hsc.usc.edu/~garykche/<br /><br />Mason <br />A package for the simulation of nucleotide data. <br />http://www.seqan.de/projects/mason/<br /><br />mbs <br />modifying Hudson's ms software to generate samples of DNA sequences with a biallelic site under selection <br />http://www.sendou.soken.ac.jp/esb/innan/innanlab/software.html<br /><br />Mendel's Accountant <br />Mendel's Accountant (MENDEL) is an advanced numerical simulation program for modeling genetic change over time and was developed collaboratively by Sanford, Baumgardner, Brewer, Gibson and ReMine <br />http://mendelsaccount.sourceforge.net/<br /><br />MetaSim <br />A tool to generate collections of synthetic reads that reflect the diverse taxonomical composition of typical metagenome data sets <br />http://ab.inf.uni-tuebingen.de/software/metasim/<br /><br />mlcoalsim <br />Multilocus Coalescent Simulations <br />http://code.google.com/p/mlcoalsim-v1/<br /><br />ms <br />The purpose of this program is to allow one to investigate the statistical properties of such samples, to evaluate estimators or statistical tests, and generally to aid in the interpretation of polymorphism data sets. <br />http://home.uchicago.edu/~rhudson1/source/mksamples.html<br /><br />msHOT <br />The purpose of this program is to allow one to investigate the statistical properties of such samples, to evaluate estimators or statistical tests, and generally to aid in the interpretation of polymorphism data sets. <br />http://home.uchicago.edu/~rhudson1/<br /><br />msms <br />A coalescent Simlation tool with selection. <br />http://www.mabs.at/ewing/msms/index.shtml<br /><br />MySSP <br />A program for the simulation of DNA sequence evolution across a phylogenetic tree <br />http://www.rosenberglab.net/software.php<br /><br />Nemo <br />A forward-time, individual-based, genetically explicit, and stochastic simulation program designed to study the evolution of genetic markers, life history traits, and phenotypic traits in a flexible (meta-)population framework. <br />http://nemo2.sourceforge.net/<br /><br />NetRecodon <br />Coalescent simulation of coding DNA sequences with recombination (inter and intracodon), migration and demography <br />http://code.google.com/p/netrecodon/<br /><br />PEDAGOG <br />Software for simulating eco-evolutionary population dynamics <br />https://bcrc.bio.umass.edu/pedigreesoftware/node/5<br /><br />phenosim <br />A tool to add phenotypes to simulated genotypes <br />http://evoplant.uni-hohenheim.de/doku.php?id=software:software<br /><br />PhyloSim <br />An R package for the Monte Carlo simulation of sequence evolution <br />http://bit.ly/rlsim-git<br /><br />pIRS <br />Profile-based Illumina pair-end reads simulator <br />https://code.google.com/p/pirs/<br /><br />ProteinEvolver <br />Simulation of protein evolution along phylogenies under structure-based substitution models <br />http://code.google.com/p/proteinevolver/<br /><br />QMSim <br />QTL and Marker Simulator <br />http://www.aps.uoguelph.ca/~msargol/qmsim/<br /><br />quantiNEMO <br />An individual-based program for the analysis of quantitative traits with explicit genetic architecture potentially under selection in a structured population <br />http://www2.unil.ch/popgen/softwares/quantinemo/<br /><br />RECOAL <br />Simulates new haplotype data from a reference population of haplotypes. <br />ftp://popgen.usc.edu/<br /><br />Recodon <br />Coalescent simulation of coding DNA sequences with recombination, migration and demography <br />http://code.google.com/p/recodon/<br /><br />rlsim <br />A package for simulating RNA-seq library preparation with parameter estimation <br />http://bit.ly/rlsim-git<br /><br />Rmetasim <br />Rmetasim is a front-end for the metasim engine that is implemented as a package that runs in the statistical computing environment R <br />http://linum.cofc.edu/software.html#metasim<br /><br />RNA Seq Simulator <br />RSS takes SAM alignment files from RNA-Seq data and simulates over dispersed, multiple replica, differential, non-stranded RNA-Seq datasets. <br />http://useq.sourceforge.net/cmdlnmenus.html#rnaseqsimulator<br /><br />Rose <br />Random model of sequence evolution <br />http://bibiserv.techfak.uni-bielefeld.de/rose/<br /><br />SelSim <br />SelSim is a program for Monte Carlo simulation of DNA polymorphism data for a recom- bining region within which a single bi-allelic site has experienced natural selection <br />http://www.well.ox.ac.uk/~spencer/selsim/<br /><br />Seq-Gen <br />An application for the Monte Carlo simulation of molecular sequence evolution along phylogenetic trees. <br />http://tree.bio.ed.ac.uk/software/seqgen/<br /><br />SEQPower <br />Statistical power analysis for sequence-based association studies <br />http://bioinformatics.org/spower/<br /><br />SeqSIMLA <br />SeqSIMLA can simulate sequence data with user-specified disease and quantitative trait models. Family or unrelated case-control data can be simulated. <br />http://seqsimla.sourceforge.net/<br /><br />Serial NetEvolve <br />A flexible utility for generating serially-sampled sequences along a tree or recombinant network <br />http://biorg.cis.fiu.edu/sne/<br /><br />SFS_CODE <br />SFS_CODE can perform forward population genetic simulations under a general Wright-Fisher model with arbitrary migration, demographic, selective, and mutational effects. <br />http://sfscode.sourceforge.net/sfs_code/index/index.html<br /><br />SIBSIM <br />Quantitative phenotype simulation in extended pedigrees <br />http://sourceforge.net/projects/sibsim/<br /><br />SIMCOAL2 <br />A coalescent program for the simulation of complex recombination patterns over large genomic regions under various demographic models <br />http://cmpg.unibe.ch/software/simcoal2/<br /><br />SimCopy <br />An R package simulating the evolution of copy number profiles along a tree. <br />http://bit.ly/simcopy<br /><br />SIMLA <br />SIMLA is a SIMuLAtion program that generates data sets of families for use in Linkage and Association studies. <br />http://www.chg.duke.edu/research/simla.html<br /><br />SimPed <br />A Simulation Program to Generate Haplotype and Genotype Data for Pedigree Structures <br />http://www.hgsc.bcm.tmc.edu/content/simped<br /><br />Simprot <br />A program to simulate protein evolution by substitution, insertion and deletion <br />http://www.uhnresearch.ca/labs/tillier/software.htm#3<br /><br />SimRare <br />Rare variant simulation and analysis tool <br />http://code.google.com/p/simrare/<br /><br />simuGWAS <br />A forward-time simulator that simulates realistic samples for genome-wide association studies. <br />http://simupop.sourceforge.net/cookbook/simucomplexdisease<br /><br />simuPOP <br />simuPOP is a general-purpose individual-based forward-time population genetics simulation environment. <br />http://simupop.sourceforge.net/<br /><br />SISSI <br />A software tool to generate data of related sequences along a given phylogeny, taking into account user defined system of neighbourhoods and instantaneous rate matrices. <br />http://www.cibiv.at/software/sissi/<br /><br />SNPsim <br />Coalescent simulation of hotspot recombination <br />http://code.google.com/p/phylosoftware/<br /><br />SPIP <br />SPIP simulates the transmission of genes from parents to offspring in a population having demographic structure defined by the user <br />http://swfsc.noaa.gov/textblock.aspx?division=fed&amp;id=3434<br /><br />Splatche <br />Spatial and Temporal Coalescences in Heterogeneous Environment <br />http://www.splatche.com/<br /><br />srv <br />Simulator of Rare Varaints (srv) is a simulator for the simulation of the introduction and evolution of (rare) genetic variants. <br />http://simupop.sourceforge.net/cookbook/simurarevariants<br /><br />SUP <br />SLINK/FastSLINK utility program <br />http://mlemire.freeshell.org/software.html<br /><br />TreesimJ <br />A flexible, forward-time population genetic simulator <br />http://code.google.com/p/treesimj/<br /><br />Vortex <br />VORTEX is an individual-based simulation model for population viability analysis (PVA). <br />http://www.vortex9.org/vortex.html<br /><br />References:</p><p>Image www.evolution-of-life.com</p><p>www.cancer.gov</p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/researchlabs/view/40882/troyanskaya-lab</guid>
  <pubDate>Tue, 04 Feb 2020 06:40:36 -0600</pubDate>
  <link></link>
  <title><![CDATA[Troyanskaya Lab]]></title>
  <description><![CDATA[
<p>The goal of our research is to interpret and distill this complexity through accurate analysis and modeling of molecular pathways, particularly those in which malfunctions lead to the manifestation of disease. We are inventing integrative methods for systems-level pathway modeling through integrative analysis of genome-scale datasets. We apply these approaches in studying challenging biological problems, such as how pathways function in diverse cell types and how they change dynamically.</p>

<p>https://function.princeton.edu/</p>
]]></description>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/41905/research-associate-bioinformatics-in-iisc-recruitment-2020</guid>
  <pubDate>Tue, 23 Jun 2020 21:53:34 -0500</pubDate>
  <link></link>
  <title><![CDATA[Research Associate Bioinformatics in IISc Recruitment 2020]]></title>
  <description><![CDATA[
<p>Research Associate Bioinformatics in IISc Recruitment 2020</p>

<p>Essential Qualifications: Ph.D. (Bioinformatics/ Biophysics/ Biotechnology or any other stream of biological/ physical sciences) with a minimum of two publications in reputed peer reviewed journals in the area of structural bioinformatics or biophysics or biomolecular modeling/ simulation.</p>

<p>Job description: Development of bioinformatics tools and algorithms/software for structure based analysis of biomolecular systems. Programmatic access to major biomolecular databases using APIs Knowledge based prediction and analysis of biomolecular structure, function and interactions. Docking/simulations for inhibitor design.</p>

<p>Desirable Qualifications (Research Associate/s): i)  Strong computer programming skills (in Python/PERL/PHP or C++ or object oriented database management systems like MySQL etc or scripting languages under LINUX/UNIX environment). </p>

<p>ii) Extensive experience in computational analysis of biomolecular structure/interactions and usage of advanced biomolecular simulation softwares. iii) Adequate knowledge of major databases, webservers and softwares in the area of biomolecular structure/function and drug design. iv)  Familiarity with Parallel Programming environments and experience in usage of high-end HPC clusters.</p>

<p>The candidates must highlight their experience in above mentioned fields/topics in their CV. Initial appointment will be for a period of 1 year, subject to extension after review of performance.</p>

<p>Emoluments: As per DST, GOI norms and commensurate with experience.</p>

<p>More at https://www.iisc.ac.in/positions-open/</p>
]]></description>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/blog/view/44914/predicting-pathogen-virulence-using-bioinformatics-tools</guid>
	<pubDate>Tue, 04 Nov 2025 07:55:53 -0600</pubDate>
	<link>https://bioinformaticsonline.com/blog/view/44914/predicting-pathogen-virulence-using-bioinformatics-tools</link>
	<title><![CDATA[Predicting Pathogen Virulence Using Bioinformatics Tools]]></title>
	<description><![CDATA[<p>In the genomic era, the ability to predict the virulence potential of pathogens has become an indispensable part of infectious disease research. With the exponential growth of microbial genome data, bioinformatics tools now enable scientists to identify virulence factors, model pathogen behavior, and even forecast outbreak risks &mdash; all from sequence data.</p><p>In an age where pathogens continue to evolve and cross boundaries, understanding <strong>what makes them virulent</strong>&mdash;that is, capable of causing disease&mdash;has become a critical focus in modern microbiology and genomics. <strong>Virulence prediction</strong> bridges computational biology, genomics, and machine learning to forecast the pathogenic potential of microbes before they strike.</p><h3>What Is Virulence?</h3><p><em>Virulence</em> refers to the degree of damage a pathogen can inflict on its host. It is determined by a combination of genetic factors&mdash;called <strong>virulence factors (VFs)</strong>&mdash;that allow the organism to attach, invade, evade, and harm the host. These include genes coding for toxins, secretion systems, adhesins, and enzymes that disrupt host defenses.</p><p>Understanding virulence factors not only helps in deciphering the mechanisms of infection but also provides early warning signs for emerging threats.</p><h3>Why Predict Virulence?</h3><p>Traditional virulence studies relied heavily on experimental infection models, which, although accurate, are <strong>time-consuming, expensive, and ethically constrained</strong>.<br /> Today, the availability of whole-genome sequences and large-scale pathogen databases has paved the way for <strong>in silico virulence prediction</strong>&mdash;a computational approach that can screen thousands of genomes within hours.</p><p>This approach enables researchers to:</p><ul>
<li>
<p>Rapidly identify potential <strong>high-risk strains</strong>.</p>
</li>
<li>
<p>Prioritize pathogens for <strong>containment, surveillance, or further study</strong>.</p>
</li>
<li>
<p>Guide <strong>vaccine development</strong> and <strong>drug target discovery</strong>.</p>
</li>
<li>
<p>Support <strong>One Health frameworks</strong>, linking animal, human, and environmental health data.</p>
</li>
</ul><h3>How Is Virulence Predicted?</h3><p>Virulence prediction combines <strong>bioinformatics pipelines</strong> with <strong>machine learning</strong> and <strong>comparative genomics</strong>. The process generally involves:</p><ol>
<li>
<p><strong>Genome Annotation:</strong> Identifying genes and coding sequences in microbial genomes.</p>
</li>
<li>
<p><strong>Feature Extraction:</strong> Comparing sequences with curated databases like <strong>VFDB (Virulence Factor Database)</strong>, <strong>PATRIC</strong>, or <strong>Victors</strong>.</p>
</li>
<li>
<p><strong>Pattern Recognition:</strong> Using algorithms (e.g., Random Forest, SVM, or deep learning models) to classify genes or strains as virulent or non-virulent based on sequence patterns, motifs, and protein domains.</p>
</li>
<li>
<p><strong>Scoring and Visualization:</strong> Assigning a virulence score or confidence level and visualizing it through heatmaps or genome maps.</p>
</li>
</ol><h3>Tools and Resources for Virulence Prediction</h3><p>A number of tools and databases make virulence prediction accessible to the scientific community:</p><ul>
<li>
<p><strong>VFanalyzer</strong> &ndash; For identifying virulence genes based on VFDB.</p>
</li>
<li>
<p><strong>PathoFact</strong> &ndash; Predicts virulence, antimicrobial resistance (AMR), and toxin genes from metagenomic data.</p>
</li>
<li>
<p><strong>Pangenome-based models</strong> &ndash; Identify virulence-associated gene clusters across strains.</p>
</li>
<li>
<p><strong>Machine learning models</strong> &ndash; Use features like GC content, codon usage bias, or protein domains to predict pathogenicity.</p>
</li>
</ul><p>Emerging tools now integrate <strong>multi-omic data</strong>&mdash;including transcriptomics, proteomics, and metabolomics&mdash;to understand virulence in a systems biology framework.</p><h3>Applications in the Real World</h3><p>Virulence prediction has major implications across public health and research sectors:</p><ul>
<li>
<p><strong>Epidemic preparedness:</strong> Early identification of virulent strains in outbreak samples.</p>
</li>
<li>
<p><strong>AMR surveillance:</strong> Linking virulence profiles with antibiotic resistance determinants.</p>
</li>
<li>
<p><strong>Environmental monitoring:</strong> Predicting pathogenic potential of soil or waterborne microbes.</p>
</li>
<li>
<p><strong>Clinical diagnostics:</strong> Supporting personalized treatment through pathogen profiling.</p>
</li>
</ul><p>For instance, integrating virulence prediction pipelines into <strong>national surveillance networks</strong> could enable faster risk assessment and response to infectious outbreaks.</p><h3>The Road Ahead</h3><p>As machine learning and genomics advance, virulence prediction will evolve from simple gene-based detection to <strong>dynamic, context-aware models</strong> that account for host&ndash;pathogen interactions, environmental signals, and evolutionary adaptation.</p><p>Future tools may predict <strong>not just if a strain is virulent</strong>, but <strong>under what conditions</strong> it expresses that virulence&mdash;bridging the gap between genotype and phenotype.</p><h3>In Summary</h3><p>Virulence prediction is redefining how we understand and anticipate infectious diseases. By coupling <strong>genomic insights</strong> with <strong>computational intelligence</strong>, researchers can identify potential threats earlier, design smarter interventions, and ultimately, strengthen our preparedness against emerging pathogens.</p>]]></description>
	<dc:creator>BioStar</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/pages/view/7986/list-of-bioinformatics-open-source-projectssoftware</guid>
	<pubDate>Tue, 21 Jan 2014 14:28:37 -0600</pubDate>
	<link>https://bioinformaticsonline.com/pages/view/7986/list-of-bioinformatics-open-source-projectssoftware</link>
	<title><![CDATA[List of bioinformatics open source projects/software.]]></title>
	<description><![CDATA[<p>Open source software is software that can be freely used, changed, and shared (in modified or unmodified form) by anyone. Open source software is made by many people, and distributed under licenses that comply with the Open Source Definition.The Open Source Initiative (OSI) is a global non-profit that supports and promotes the open source movement. Followings are the OS bioinformatics projects/software :</p><p><strong>.NET Bio</strong></p><p>http://blogs.msdn.com/b/msr_er/archive/2011/10/18/microsoft-biology-foundation-evolves-into-new-toolkit-net-bio.aspx</p><p>A language-neutral bioinformatics toolkit built using the Microsoft 4.0 .NET Framework to help developers, researchers, and scientists.</p><p><strong>AMPHORA</strong> ("AutoMated Phylogenomic infeRence Application")</p><p>http://wolbachia.biology.virginia.edu/WuLab/Software.html</p><p><a href="http://en.wikipedia.org/wiki/Metagenomics" title="Metagenomics">Metagenomics</a> analysis software</p><p><strong>Anduril</strong></p><p>http://www.anduril.org/anduril/site/</p><p>Component-based <a href="http://en.wikipedia.org/wiki/Workflow" title="Workflow">workflow</a> framework for data analysis</p><p>Armadillo workflow platform</p><p>Tool for designing and executing phylogenetic workflows</p><p><strong>AutoDock</strong></p><p>http://autodock.scripps.edu/</p><p>suite of automated docking tools</p><p><strong>Biochemical Algorithms Library (BALL)</strong></p><p>http://www.ball-project.org/</p><p>C++ library and framework for molecular modeling and visualization designed for rapid prototyping</p><p><strong>Bio4j</strong></p><p>http://bio4j.com/</p><p>Bio4j is a <a href="http://en.wikipedia.org/wiki/Bioinformatics" title="Bioinformatics">bioinformatics</a> platform and <a href="http://en.wikipedia.org/wiki/Chart" title="Chart">graph</a> based <a href="http://en.wikipedia.org/wiki/Database" title="Database">database</a> built around most data available in <a href="http://en.wikipedia.org/wiki/UniProt" title="UniProt">UniProt</a> KB(<a href="http://en.wikipedia.org/wiki/Swiss-Prot" title="Swiss-Prot">Swiss-Prot</a> + <a href="http://en.wikipedia.org/wiki/TrEMBL" title="TrEMBL">TrEMBL</a>), <a href="http://en.wikipedia.org/wiki/Gene_Ontology" title="Gene Ontology">Gene Ontology</a> (GO), <a href="http://en.wikipedia.org/w/index.php?title=UniRef&amp;action=edit&amp;redlink=1" title="UniRef (page does not exist)">UniRef</a> (50,90,100), <a href="http://en.wikipedia.org/wiki/RefSeq" title="RefSeq">RefSeq</a>, <a href="http://en.wikipedia.org/wiki/National_Center_for_Biotechnology_Information" title="National Center for Biotechnology Information">NCBI</a> taxonomy, and Expasy Enzyme DB</p><p><strong>Bioclipse</strong></p><p>www.bioclipse.net</p><p>Visual platform for <a href="http://en.wikipedia.org/wiki/Cheminformatics" title="Cheminformatics">chemo</a>- and <a href="http://en.wikipedia.org/wiki/Bioinformatics" title="Bioinformatics">bioinformatics</a> based on the <a href="http://en.wikipedia.org/wiki/Eclipse_%28software%29" title="Eclipse (software)">Eclipse</a> Rich Client Platform (RCP).</p><p><strong>Bioconductor</strong></p><p>http://www.bioconductor.org/</p><p><a href="http://en.wikipedia.org/wiki/R_%28programming_language%29" title="R (programming language)">R (programming language)</a> language toolkit</p><p><strong>Bioinformatics Learning Tutorial (BLT)</strong></p><p>http://sourceforge.net/projects/biotutorial/</p><p>Educational <a href="http://en.wikipedia.org/wiki/Interactive_tutorials" title="Interactive tutorials">interactive tutorials</a> and 3D animations for Replication, Transcription, and Translation</p><p><strong>BioHaskell</strong></p><p>http://biohaskell.org/</p><p><a href="http://en.wikipedia.org/wiki/Haskell_%28programming_language%29" title="Haskell (programming language)">Haskell (programming language)</a></p><p><strong>BioJava</strong></p><p>http://biojava.org/wiki/Main_Page</p><p><a href="http://en.wikipedia.org/wiki/Java_%28programming_language%29" title="Java (programming language)">Java (programming language)</a></p><p><strong>BioMOBY</strong></p><p>http://biomoby.org/</p><p>registry of <a href="http://en.wikipedia.org/wiki/Web_services" title="Web services">web services</a></p><p><strong>BioPerl</strong></p><p>http://www.bioperl.org/wiki/Main_Page</p><p><a href="http://en.wikipedia.org/wiki/Perl" title="Perl">Perl</a> language toolkit</p><p><strong>BioPHP</strong></p><p>http://www.biophp.org/</p><p><a href="http://en.wikipedia.org/wiki/PHP" title="PHP">PHP</a> language toolkit</p><p><strong>Biopython</strong></p><p>http://biopython.org/wiki/Main_Page</p><p><a href="http://en.wikipedia.org/wiki/Python_%28programming_language%29" title="Python (programming language)">Python</a> language toolkit</p><p><strong>BioRails</strong></p><p>https://github.com/biorails</p><p>a <a href="http://en.wikipedia.org/wiki/Data_management_system" title="Data management system">data management system</a> designed to support researchers in <a href="http://en.wikipedia.org/wiki/Drug_discovery" title="Drug discovery">drug discovery</a></p><p><strong>BioRuby</strong></p><p>http://bioruby.org/</p><p><a href="http://en.wikipedia.org/wiki/Ruby_%28programming_language%29" title="Ruby (programming language)">Ruby</a> language toolkit</p><p><strong>BioSmalltalk</strong></p><p>https://code.google.com/p/biosmalltalk/</p><p><a href="http://en.wikipedia.org/wiki/Smalltalk_%28programming_language%29" title="Smalltalk (programming language)">Smalltalk</a> language toolkit</p><p><strong>BioUno</strong></p><p>http://www.biouno.org/</p><p><a href="http://en.wikipedia.org/w/index.php?title=BioUno&amp;action=edit&amp;redlink=1" title="BioUno (page does not exist)">BioUno</a> is a project that applies <a href="http://en.wikipedia.org/wiki/Continuous_Integration" title="Continuous Integration">Continuous Integration</a> tools and techniques in <a href="http://en.wikipedia.org/wiki/Bioinformatics" title="Bioinformatics">Bioinformatics</a>. It uses <a href="http://en.wikipedia.org/wiki/Jenkins_%28software%29" title="Jenkins (software)">Jenkins</a> and its plug-in API to create <a href="http://en.wikipedia.org/wiki/Bioinformatics_workflow_management_system" title="Bioinformatics workflow management system">biology workflows</a> and manage <a href="http://en.wikipedia.org/wiki/Computer_clusters" title="Computer clusters">computer clusters</a>.</p><p><strong>caCORE</strong></p><p>&nbsp;</p><p>ontologic representation environment</p><p><strong>caArray</strong></p><p>https://cabig-stage.nci.nih.gov/community/tools/caArray</p><p>ontologic representation environment</p><p><strong>EMBOSS</strong></p><p>http://emboss.sourceforge.net/</p><p>Suite of packages for sequencing, searching, etc.</p><p><strong>Gaggle</strong></p><p>https://www.gaggle.net/</p><p>A framework for interoperability between systems biology software</p><p><strong>Galaxy</strong></p><p>http://galaxyproject.org/</p><p><a href="http://en.wikipedia.org/wiki/Scientific_workflow_system" title="Scientific workflow system">Scientific workflow</a> and <a href="http://en.wikipedia.org/wiki/Data_integration" title="Data integration">data integration</a> system</p><p><strong>GenePattern</strong></p><p>http://www.broadinstitute.org/cancer/software/genepattern/</p><p><a href="http://en.wikipedia.org/wiki/Scientific_workflow_system" title="Scientific workflow system">Scientific workflow system</a> that provides access to more than 150 genomic analysis tools</p><p><strong>GeWorkbench</strong></p><p>http://wiki.c2b2.columbia.edu/workbench/index.php/Home</p><p>Genomic <a href="http://en.wikipedia.org/wiki/Data_integration" title="Data integration">data integration</a> platform</p><p><strong>GMOD</strong></p><p>http://www.gmod.org/wiki/Main_Page</p><p>Toolkit for addressing many common challenges at biological databases.</p><p><strong>GeneProf</strong></p><p>http://www.geneprof.org/GeneProf/</p><p>A web-based, bioinformatics software suite for the analysis of functional genomics experiments, e.g. RNA-seq or ChIP-seq.</p><p><strong>GeneTalk</strong></p><p>http://www.gene-talk.de/</p><p>Tool for filtering sequence variants in <a href="http://en.wikipedia.org/wiki/Variant_Call_Format" title="Variant Call Format">VCF</a> files. Network for scientists and clinicians for expertise and knowledge exchange. Database of annotations aboute sequence variants with clinically relevant information.</p><p><strong>GenGIS</strong></p><p>http://kiwi.cs.dal.ca/GenGIS/Main_Page</p><p>Application that allows users to combine digital map data with information about biological sequences collected from the environment.</p><p><strong>GenomeSpace</strong></p><p>http://www.genomespace.org/</p><p>Centralized web application that provides data format transformations and facilitates connections with other bioinformatics tools</p><p><strong>GENtle</strong></p><p>http://directory.fsf.org/wiki/GENtle</p><p>An equivalent to the proprietary <a href="http://en.wikipedia.org/wiki/Vector_NTI" title="Vector NTI">Vector NTI</a>, a tool to analyze and edit <a href="http://en.wikipedia.org/wiki/DNA" title="DNA">DNA</a> sequence files</p><p><strong>Integrated Genome Browser</strong></p><p>http://bioviz.org/igb/</p><p><a href="http://en.wikipedia.org/wiki/Java_%28software_platform%29" title="Java (software platform)">Java</a>-based desktop <a href="http://en.wikipedia.org/wiki/Genome_browser" title="Genome browser">genome browser</a></p><p><strong>Integrative Genomics Viewer (IGV)</strong></p><p>http://www.broadinstitute.org/igv/</p><p>High-performance desktop tool for interactive visual exploration of diverse genomic data</p><p><strong>IntAct</strong></p><p>http://www.ebi.ac.uk/intact/</p><p>molecular interaction database</p><p><strong>InterMine</strong></p><p>http://intermine.github.io/intermine.org/</p><p>Extensive data warehouse system for the analysis and integration of biological datasets</p><p><strong>Java Treeview</strong></p><p>http://jtreeview.sourceforge.net/</p><p>microarray data viewer</p><p><strong>LabKey Server</strong></p><p>http://labkey.com/</p><p>platform for integrating, analyzing and sharing data</p><p><strong>OpenClinica</strong></p><p>https://www.openclinica.com/</p><p>software for capturing and managing data in clinical trials</p><p><a href="http://www.biomedcentral.com/1471-2164/13/512">PromKappa</a></p><p>http://xbioinformatics.wordpress.com/tag/promkappa/</p><p>PromKappa (Promoter analysis by Kappa) software program used for promoter pattern generation and promoter analysis.</p><p><strong>MeV: Multi-Experiment Viewer</strong></p><p>http://www.tm4.org/mev.html</p><p>a desktop application for the analysis, visualization and data-mining of large-scale genomic data</p><p><strong>PathVisio</strong></p><p>http://www.pathvisio.org/</p><p>a desktop software for drawing, analysis and visualization of biological pathways</p><p>REDCRAFT</p><p>software for determining tertiary protein structure given assigned Residual Dipolar Coupling data</p><p>SAM Tools</p><p>Data format (SAM) and accompanying tool suite, for storing large nucleotide sequence alignments</p><p><a href="http://en.wikipedia.org/wiki/Staden_Package" title="Staden Package">Staden Package</a></p><p>Sequence assembly, editing and analysis, primarily consisting of gap4, gap5 and spin.</p><p><a href="http://en.wikipedia.org/wiki/STAMP" title="STAMP">STAMP</a></p><p>Software package for analyzing metagenomic profiles that promotes &lsquo;best practices&rsquo; in choosing appropriate statistical techniques and reporting results.</p><p><a href="http://supfam.org/supraHex">supraHex</a></p><p>An open-source R/Bioconductor package for omics data analysis using a supra-hexagonal map</p><p><a href="http://en.wikipedia.org/wiki/Taverna_workbench" title="Taverna workbench">Taverna workbench</a></p><p>Tool for designing and executing workflows</p><p>TGAC Browser</p><p>Genome Browser, visualisation solutions for big data in the genomic era</p><p>T-REX WebServer</p><p>Bioinformatics and phylogenetics webserver (NJ, PhyML, RAxML, MAFFT, MUSCLE, Newick viewer, <a href="http://en.wikipedia.org/wiki/Horizontal_gene_transfer" title="Horizontal gene transfer">Horizontal gene transfer</a> detection, Reticulograms, Substitution models)</p><p><a href="http://en.wikipedia.org/wiki/UGENE" title="UGENE">UGENE</a></p><p>integrated bioinformatics tools</p><p>Visomics</p><p>bioinformatics tools for omics data</p><p>Genome Analysis Toolkit 1.0 (GATK 1.0)</p><p>a software package to analyse next-generation resequencing data</p>]]></description>
	<dc:creator>Rahul Nayak</dc:creator>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/23122/candidates-required-in-bioinformatics-and-genomics-uk-only</guid>
  <pubDate>Fri, 03 Jul 2015 08:22:41 -0500</pubDate>
  <link></link>
  <title><![CDATA[Candidates required in Bioinformatics and Genomics UK ONLY]]></title>
  <description><![CDATA[
<p>I have various permanent positions available based in London, Manchester, Herftfordshire, Oxford and Belfast, as well as other areas throughout the UK.</p>

<p>If you are looking for a new opportunity and have skills within any sector of Bioinformatics with an IT skill then I would love to hear from you.  I have various exciting opportunities from programmers to researchers to scientists.</p>

<p>Call me now on 01772 278050 or email me your cv and requirements and I will call you back dareen.evans@itworkshealth.co.uk</p>
]]></description>
</item>

</channel>
</rss>