<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/20454?offset=70 https://bioinformaticsonline.com/bookmarks/view/19636/google-genomics Thu, 18 Dec 2014 11:05:42 -0600 https://bioinformaticsonline.com/bookmarks/view/19636/google-genomics <![CDATA[Google Genomics]]>

  • Explore genetic variation interactively. Compare entire cohorts in seconds with SQL-like queries. Compute transition/transversion ratios, genome-wide association, allelic frequency and more.

  • Process big genomic data easily. Run batch analyses like principal component analysis and Hardy-Weinberg equilibrium on as many samples as you like, in minutes or hours, with just a little code.

  • Use Google's infrastructure and big data expertise. Store one genome or a million using Google Genomics and take advantage of the same infrastructure that powers Search, Maps, YouTube, Gmail and Drive.

  • Support emerging global standards. Google Genomics is implementing the API defined by the Global Alliance for Genomics and Health for visualization, analysis and more. Compliant software can access Google Genomics, local servers, or any other implementation.

    • Address of the bookmark: https://cloud.google.com/genomics/

    ]]>     Tenzin Paul     https://bioinformaticsonline.com/bookmarks/view/26325/crossmap Mon, 08 Feb 2016 15:47:00 -0600 https://bioinformaticsonline.com/bookmarks/view/26325/crossmap <![CDATA[CrossMap]]> CrossMap is a program for convenient conversion of genome coordinates (or annotation files) between different assemblies (such as Human hg18 (NCBI36) <> hg19 (GRCh37), Mouse mm9 (MGSCv37) <> mm10 (GRCm38)).

    It supports most commonly used file formats including SAM/BAM, Wiggle/BigWig, BED, GFF/GTF, VCF.

    CrossMap is designed to liftover genome coordinates between assemblies. It’s not a program for aligning sequences to reference genome.

    We do not recommend using CrossMap to convert genome coordinates between species.

    More at http://crossmap.sourceforge.net/

    Address of the bookmark: http://crossmap.sourceforge.net/

    ]]>     Jitendra Narayan     https://bioinformaticsonline.com/bookmarks/view/27333/satsuma-highly-sensitive-whole-genome-synteny-alignments Fri, 13 May 2016 05:25:26 -0500 https://bioinformaticsonline.com/bookmarks/view/27333/satsuma-highly-sensitive-whole-genome-synteny-alignments <![CDATA[SATSUMA : Highly sensitive whole-genome synteny alignments.]]> Satsuma is a whole-genome synteny alignment program. It takes two genomes, computes alignments, and then keeps only the parts that are orthologous, i.e. following the conserved order and orientation of features, such as protein coding genes, non-coding genes, or neutral sequences. Satsuma does not require any pre-processing, such as repeat masking, since it will automatically detect ambiguous mappings.

    Satsuma has parallelization built-in and is designed to run on multi-core architectures. The run-time for aligning two bird-size genomes (~1.2 Gb) is around two days on 24 CPUs.

    You can find the manual here.
    Download the latest source code from here.
    Stable versions can also be downloaded from the Broad Institute's web site.

    An incomplete list of questions and answers (yes, these have really been asked by our users! Please feel free to add your own by e-mailing us) is here.

    If you use Satsuma in your research, please cite:
    Grabherr, M. G., Russell, P., Meyer, M., Mauceli, E., Alföldi, J., Di Palma, F., & Lindblad-Toh, K. (2010). Genome-wide synteny through highly sensitive sequence alignment: Satsuma. Bioinformatics, 26(9), 1145-51.

    Tutorial at http://evomics.org/learning/genomics/satsuma/

    Address of the bookmark: http://satsuma.sourceforge.net/

    ]]>     Jit     https://bioinformaticsonline.com/bookmarks/view/30102/prism Sat, 10 Dec 2016 15:19:40 -0600 https://bioinformaticsonline.com/bookmarks/view/30102/prism <![CDATA[PRISM]]> PRISM is a software for split read (reads which span across a structrual variant -- SV ) mapping and SV calling from the mapping result. PRISM is able to detect small insertions and abitrary size deletions, inversions and tandom duplications with the direction of discordant read pairs. PRISM_CTX is a tool for detecting inter-chromosome trans-location events. 

    PRISM and PRISM_CTX were originally designed and written by Michael Brudno and Yue Jiang, The original PRISM publication can be found here. 

    The authors may be contacted via e-mail at: prism at cs.toronto.edu. 

    Additional information is available in the PRISM README file and PRISM_CTX README file. 

    http://compbio.cs.toronto.edu/prism/

    Address of the bookmark: http://compbio.cs.toronto.edu/prism/

    ]]>     Jit     https://bioinformaticsonline.com/pages/view/1514/list-of-pharmacogenomics-companies-worldwide Fri, 09 Aug 2013 13:24:47 -0500 https://bioinformaticsonline.com/pages/view/1514/list-of-pharmacogenomics-companies-worldwide <![CDATA[List of pharmacogenomics companies worldwide]]>

    Pharmacogenomics are the most promising area of research. Here is the list of some Pharmacogenomics companies worldwide. Feel free to add more pharmacogenomics companies if not mentioned in here.

    Great Pharmacogenomics companies
    www.aruplab.com
    www.clarientinc.com
    www.cns-hts.com
    www.dnanow.com
    www.dnavision.be
    www.dnavision.com
    www.dxsdiagnostics.com
    www.entrogen.com
    www.exiqon.com
    www.gene.com
    www.genomichealth.com
    www.genoptix.com
    www.genpathdiagnostics.com
    www.gentris.com
    www.immunicon.com
    www.ingenuity.com
    www.lab21.com
    www.labcorp.com
    www.lion-ag.de
    www.lynxgen.com
    www.mayoclinic.com
    www.mesoscale.com
    www.microcide.com
    www.mitokor.com
    www.monarchlifesciences.com
    www.mplnet.com
    www.orchidbio.com
    www.pebio.com
    www.phenomenome.com
    www.phenopath.com
    www.ppgx.com
    www.prometheuslabs.com
    www.protogene.com
    www.questdiagnostics.com
    www.rigelinc.com
    www.rii.com
    www.saladax.com
    www.tmdlab.com
    www.transgenomic.com
    www.twt.com
    www.uslabs.net
    www.variagenics.com

    Great Equipment Companies for Genomics
    www.affymetrix.com
    www.illumina.com
    www.iontorrent.com
    www.sequenom.com
    www.appliedbiosystems.com
    www.454.com
    www.appliedbiosystems.com

    Genomics in India
    www.ganitlabs.in
    www.sandor.co.in
    www.igib.res.in
    www.genotypic.co.in
    www.ocimumbio.com
    www.abcgenomics.com
    www.xcelrisgenomics.com
    www.ayugen.com
    www.geneombiotech.com

    Large Global Whole Genome Companies
    www.decode.com
    www.23andme.com
    www.navigenics.com
    www.pathway.com

    Global companies offering genomics services
    www.asuragen.com
    www.baseclear.com
    www.agtcenter.com
    www.ambrygen.com
    www.arosab.com
    www.agrf.org.au
    www.beckmangenomics.com
    www.genomics.cn
    www.bsf.a-star.edu.sg
    www.cbm.fvg.it
    www.cincinnatichildrens.org
    www.cofactorgenomics.com
    www.covance.com
    www.dnalandmarks.ca
    www.dnavision.com
    www.expressionanalysis.com
    www.fasteris.com
    www.gatc-biotech.com
    www.genesdiffusion.com
    www.geneseek.com
    www.geneticvisions.com
    www.geneworks.com.au
    www.genizon.com
    www.genoskan.dk/uk
    www.gpbio.jp
    www.igatechnology.com
    www.igenixinc.com
    www.auxologico.it
    www.lifeandbrain.com
    www.macrogen.co.kr/eng
    www.gqinnovationcenter.com
    www.mftservices.de
    www.ncgr.org
    www.ramaciotti.unsw.edu.au
    www.rikengenesis.jp
    www.SABiosciences.com
    www.sequensysbio.com
    www.servicexs.com
    www.snp-genetics.com
    www.takara-bio.com
    www.gen-probe.com
    www.traitgenetics.com

    ]]>     Jitendra Narayan     https://bioinformaticsonline.com/news/view/2423/cancers-origins-revealed Thu, 15 Aug 2013 13:06:56 -0500 https://bioinformaticsonline.com/news/view/2423/cancers-origins-revealed <![CDATA[Cancer's origins revealed]]> Researchers have provided the first comprehensive compendium of mutational processes that drive tumour development. Together, these mutational processes explain most mutations found in 30 of the most common cancer types. This new understanding of cancer development could help to treat and prevent a wide-range of cancers.

    More at >> http://www.sanger.ac.uk/about/press/2013/130814.html

    ]]>     Jitendra Narayan     https://bioinformaticsonline.com/researchlabs/view/4657/giovanni-parmigiani-lab Fri, 20 Sep 2013 13:21:41 -0500 <![CDATA[Giovanni Parmigiani Lab]]> Scientific Interests:

    Models and software for predicting who is at risk of carrying genetic variants that confer susceptibility to cancer. Application to breast, ovarian, colorectal, pancreatic and skin cancer.

    Statistical methods for the analysis of high throughput genomic data: analysis of cancer genome sequencing projects; integration of genomic information across technologies; cross-study validation of genomics results.

    Statistical methods for comparative effectiveness research: comprehensive models for lifetime history of chronic disease outcomes; Bayesian meta-analysis; Bayesian causal inference; decision analysis.

    Bayesian modeling and computation: multilevel models; decision theoretic approaches to inference; sequential experimental design and their application to adaptive and multistage studies in clinical and epidemiological research.

    http://bcb.dfci.harvard.edu/~gp/index.html

    http://scholar.google.com/citations?user=OlpYP3UAAAAJ&hl=en

    ]]>         https://bioinformaticsonline.com/opportunity/view/43272/bioinformatics-head-bioinformatics-manager-iii-cancer-genomics-research-laboratory-at-frederick-national-laboratory Wed, 18 Aug 2021 00:19:48 -0500 <![CDATA[Bioinformatics Head (Bioinformatics Manager III), Cancer Genomics Research Laboratory at Frederick National Laboratory]]> 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).

    More at https://leidosbiomed.csod.com/ats/careersite/jobdetails.aspx?site=4&c=leidosbiomed&id=2040

    ]]>         https://bioinformaticsonline.com/bookmarks/view/4197/bioinformatics-course-and-lectures Tue, 03 Sep 2013 16:41:02 -0500 https://bioinformaticsonline.com/bookmarks/view/4197/bioinformatics-course-and-lectures <![CDATA[Bioinformatics course and lectures]]> http://openwetware.org/wiki/User:Jarle_Pahr/Bioinformatics

    Address of the bookmark: http://gtpb.igc.gulbenkian.pt/bicourses/index.html

    ]]>     Rahul Agarwal     https://bioinformaticsonline.com/researchlabs/view/7088/gabi Fri, 06 Dec 2013 16:43:01 -0600 <![CDATA[GABi]]> GABi Research
    The major researching fields defined as the GABi scope are described next:
    Sequence Analysis
    Protein Structure Prediction
    Comparative Genomics
    Functional Analysis of Residues on Protein Families
    Gene/Protein Networks
    Genome structure & base composition
    Highthroughput data analysis from NGS

    Lab Page http://gabi.cidbio.org/index/

    ]]>