BOL: Related items

CrossMap

Jitendra Narayan — Mon, 08 Feb 2016 15:47:00 -0600

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/

List of pharmacogenomics companies worldwide

Jitendra Narayan — Fri, 09 Aug 2013 13:24:47 -0500

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

Cancer's origins revealed

Jitendra Narayan — Thu, 15 Aug 2013 13:06:56 -0500

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

Bioinformatics Head (Bioinformatics Manager III), Cancer Genomics Research Laboratory at Frederick National Laboratory

Wed, 18 Aug 2021 00:19:48 -0500

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

Shendure Lab

Wed, 09 Oct 2013 14:21:58 -0500

The Shendure Lab is part of the Department of Genome Sciences at the University of Washington (Seattle, WA). The mission of the lab is to develop and apply new technologies in genomics and molecular biology. Most projects in the lab exploit new DNA sequencing technologies (Shendure et al., Nature Reviews Genetics 2004; Shendure & Ji, Nature Biotechnology 2008; Shendure & Lieberman Aiden, Nature Biotechnology 2012), and generally fall into one of six areas: 1) next-generation human genetics; 2) genome contiguity & completeness; 3) massively parallel functional analysis; 4) molecular tagging; 5) synthetic biology; 6) translational genomics. Our interests in each of these areas are outlined briefly below, and a full list of publications is available via PubMed. http://www.ncbi.nlm.nih.gov/pubmed?cmd=search&term=shendure
More http://krishna.gs.washington.edu/research.html

Lab page @ http://krishna.gs.washington.edu/index.html

Shankar Lab

Wed, 16 Oct 2013 07:02:22 -0500

Research Interest:

(A) Regulatory System Analysis with respect to microRNAs

(B) Computational Epigenomics & Regulomics:

Department of Biotechnology,
Institute of Himalyan Bioresources Technology
CSIR, Palampur(Himachal Pradesh), India.
Email: ravishihbt.res.in; ravish9gmail.com

More @ http://scbb.ihbt.res.in/SCBB_dept/Lab_Member.php

DbBrowser: Attwood Lab

Fri, 18 Oct 2013 10:48:19 -0500

DbBrowser: Attwood Lab research concerns protein sequence analysis, primarily using the method of protein 'fingerprinting'. DbBrowser: Attwood Lab maintain a diagnostic fingerprint database (PRINTS), one of the founding partner of InterPro. We also design software to display sequence and structural data in visually-striking ways (e.g., Ambrosia, CINEMA); DbBrowser: Attwood Lab are building re-usable software components to create semantically integrated bioinformatics applications through UTOPIA, including a 'smart' PDF reader that links bioinformatics databases and tools directly with scientific articles (Utopia Documents); and have developed a number of tools for automatic annotation and text mining (e.g., MINOTAUR, PRECIS, METIS).

More @ http://www.bioinf.manchester.ac.uk/dbbrowser/index.php

Edwards Lab

Sun, 10 Nov 2013 15:07:08 -0600

We study the evolutionary biology of birds and relatives, combining field, museum and genomics approaches to understand the basis of avian diversity, evolution and behavior. Our guiding approaches include population genetics, which provides a quantitative framework for studying speciation, geographic variation and genome evolution; systematics, which acknowledges that the focal species of any study has relatives that are behaviorally and ecologically no less interesting; and natural history, which gives meaning to the genes and genomic patterns we study.

Lab page: http://www.oeb.harvard.edu/faculty/edwards/index.html

Bioinformatics course and lectures

Rahul Agarwal — Tue, 03 Sep 2013 16:41:02 -0500

http://openwetware.org/wiki/User:Jarle_Pahr/Bioinformatics

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

Key Bioinformatics Scientists

Rahul Agarwal — Wed, 09 Oct 2013 13:37:07 -0500

Address of the bookmark: http://www.iscb.org/iscb-leadership-a-staff-/officers-and-board-directors