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	<guid isPermaLink="true">https://bioinformaticsonline.com/blog/view/34326/list-of-research-institutes-in-india-biological-sciences-biotechnology</guid>
	<pubDate>Tue, 14 Nov 2017 09:46:16 -0600</pubDate>
	<link>https://bioinformaticsonline.com/blog/view/34326/list-of-research-institutes-in-india-biological-sciences-biotechnology</link>
	<title><![CDATA[List of Research Institutes in India (Biological Sciences/ Biotechnology)]]></title>
	<description><![CDATA[<p>A laboratory (normally lab) is a facility that provides controlled conditions in which scientific or technological research, experiments, and measurement may be performed.</p><p>The aims of bio/medical research are also broad, including:<br />&bull; Understanding mechanism of disease<br />&bull; Understanding the impact of genetic and external factors on human health<br />&bull; Designing and evaluating new therapeutic interventions<br />&bull; Health genomics</p><p>List of Research Institutes in India (Biological Sciences)</p><p>BANGALORE <br />Ashoka Trust for Ecology and the Environment<br />Royal Enclave, Srirampura, Jakkur Post, Bangalore-560064<br />Email: info@atree.org<br />Web: www.atree.org/<br />Research: ATREE deals with issues relating to the environmental, social and economic dimensions, and implications of, biological resources and natural ecosystems</p><p>Indian Institute of Science<br />Indian Institute of Science, Bangalore 560 012, Karnataka<br />Email:regr@admin.iisc.ernet.in<br />Web: www.iisc.ernet.in/<br />Research Areas: Biochemistry, ecological sciences, microbiology &amp; cell biology, molecular biophysics, molecular reproduction, development &amp; genetics.</p><p><br />Jawaharlal Nehru Centre for Advanced Scientific Research<br />Jakkur, Bangalore 560 064, Karnataka<br />Email: academic@jncasr.ac.in<br />Web: www.jncasr.ac.in/<br />Research Areas: Evolutionary and organismal biology, molecular biology and genetics.</p><p><br />National Centre for Biological Science<br />GKVK, Bellary Road,<br />Email: dean@ncbs.res.in<br />Web: www.ncbs.res.in<br />Research Areas: The research interests of the faculty range from single molecules to systems biology.</p><p><br />National Institute of Mental Health and Neurosciences<br />Bangalore 560029, Karnataka<br />Email: info@nimhans.kar.nic.in<br />Web: nimhans.kar.nic.in/<br />Research Areas: Biophysics, biostatistics, clinical psychology, epidemiology, human genetics, mental health education, neuroanaesthesia, neurochemistry, neuro imaging and interventional radiology, neurology, neuromicrobiology, neuropathology, neurophysiology, neurosurgery, neurovirology.</p><p><br />Stem Cell Institute<br />NCBS, GKVK, Bellary Road,<br />Email: ramas@ncbs.res.in<br />Web: underconstruction</p><p><br />University of Agricultural Sciences<br />GKVK, Bangalore 5600065, Karnataka<br />Email: root@uas.kar.nic.in<br />Web: uasbng.kar.nic.in/Default.htm<br />BARODA</p><p>Maharaja Sayajirao University of Baroda<br />Fatehgunj, Vadodara 390 002, Gujarat<br />Web: msubaroda.ac.in/</p><p>BHOPAL <br />Indian Institute of Science Education and Research&ndash;Bhopal<br />Govindpura, Bhopal - 23<br />E-mail: director@iiserbhopal.ac.in<br />Web: www.iiserbhopal.ac.in/<br />Research Areas: All areas of basic sciences &ndash; Biology, chemistry, math and physics<br />BHUBANESHWAR <br />Institute of Life Sciences<br />Bhubaneswar 751 023, Orissa<br />Web: www.ils.res.in<br />Research Areas: Cancer, malaria, age diseases, stress biology, ecophysiology, plant molecular physiology, filariasis, tuberculosis, bio-perspecitve, agricultural biotechnology, bio-informatics.</p><p><br />National Institute of Science Education and Research &ndash; Bhubaneshwar<br />Institute of Physics Campus, Bhubaneswar, Orissa - 751 005,<br />e-mail : director@niser.ac.in<br />Web: www.niser.ac.in/<br />Research Areas: All areas of basic sciences &ndash; Biology, chemistry, math and physics.</p><p><br />Regional Research Laboratory<br />Bhubaneswar 751 013, Orissa<br />Email: root@csrrlbhu.ren.nic.in<br />Web: www.icast.org.in/csir/rrl_bhu.html<br />Research Areas: Survey &amp; cultivation of aromatic, medicinal and other economic plants.</p><p><br />Utkal University<br />Vani Vihar, Bhubaneswar 751 004, Orissa<br />Web: www.utkaluniversity.org/<br />CHANDIGARH <br />Indian Institute of Science Education and Research &ndash;Mohali<br />Chandigarh<br />Email: webmaster@iisermohali.ac.in<br />Web: www.iisermohali.ac.in/<br />Research Areas: All areas of basic sciences &ndash; Biology,<br />chemistry, math and physics</p><p><br />Institute of Microbial Technology<br />Sector 39&ndash;A, Chandigarh 160 036<br />Email: raghava@imtech.res.in<br />Web: www.imtech.res.in/<br />Research Areas: Molecular biology and microbial genetics,<br />animal cell/tissue culture and protein engineering.</p><p><br />Panjab University<br />Chandigarh 160 014<br />Email: pulib@puchd.ren.nic.in<br />Web: www.puchd.ac.in/</p><p><br />Postgraduate institute of Medical Education and Research<br />Sector-12, Chandigarh, 160 012<br />Email: pgimer@chd.nic.in<br />Web: pgimer.nic.in/<br />Research Areas: Obstetrics and gynaecology, psychiatry,<br />biochemistry, haematology, clinical parasitology etc.<br />CHENNAI <br />Indian Institute of Technology Madras<br />Chennai 600 036, Tamil Nadu<br />Email: tppro@acer.iitm.ernet.in<br />Web: www.iitm.ac.in<br />Research Areas: Engineering: Biotechnology.</p><p><br />University of Madras<br />University Centenary Building, Chepauk, Chennai 600 005, Tamil Nadu<br />Email: webmaster@unom.ac.in<br />Web: www.unom.ac.in/ <br />DARJEELING <br />University of North Bengal<br />Raja Rammohunpur, Darjeeling 734 430, West Bengal<br />Email:(Registrar): regnbu@dte.vsnl.net.in<br />Web: www.nbu.ac.in/<br />DELHI <br />All India Institute of Medical Sciences<br />New Delhi<br />Email: webmastr@aiims.ac.in<br />Web: www.aiims.ac.in/</p><p><br />Institute of Genomics and Integrative Biology<br />Delhi University Campus, Mall Road, Delhi 110 007<br />Email: info@igib.res.in<br />Web: www.igib.res.in/<br />Research Areas: Allergy and immunology, diagnostics, genetic engineering, bio-organics and high-tech reagents.</p><p><br />Indian Institute of Technology Delhi<br />Hauz Khas, New Delhi 110 016<br />Email: malhotra@admin.iitd.ernet.in<br />Web: www.iitd.ac.in<br />Research Areas: Engineering: Biochemical engineering &amp; biotechnology.<br />International Centre for Genetic Engineering and Biotechnology</p><p><br />ICGEB Campus, Aruna Asaf Ali Marg,<br />New Delhi 110 067<br />Web: www.icgeb.trieste.it/<br />Research Areas: Mammalian biology:<br />Virology immunology, malaria,<br />recombinant gene products,<br />Plant molecular biology, plant transformation,<br />insect resistance, plant resistance.</p><p><br />Jawaharlal Nehru University<br />New Delhi<br />Email: webmaster@mail.jnu.ac.in<br />Web: www.jnu.ac.in</p><p><br />National Centre for Plant Genome Research<br />JNU Campus, New Delhi<br />Email: tapas_s3@yahoo.co.in<br />Web: ncpgr.nic.in/<br />Research Areas: Nutritional, structural, and functional genomics of various plant systems.</p><p><br />National Institute of Immunology<br />Aruna Asaf Ali Marg, New Delhi 110 067<br />Web: www.nii.res.in/<br />Research Areas: Gene regulation, immunity &amp; infection, molecular design, reproduction &amp; development.</p><p><br />TERI University<br />Vasant Kunj, New Delhi - 110 070 / India<br />E-mail: registrar@teri.res.in<br />Web: www.teriuniversity.ac.in<br />Research Areas: Environmental Studies, Natural Resources Management, Climate Science and Policy, Plant Biotechnology</p><p><br />University of Delhi<br />University Road, Delhi 110 007<br />Email: webmaster@du.ac.in<br />Web: www.du.ac.in/<br />GOA <br />National Centre for Antarctic and Ocean Research<br />Headland Sada, Vasco-da-Gama 403 804, Goa<br />Email: info@ncaor.org<br />Research Areas: Co&ndash;ordination and implementation of the Indian Antarctic Programme.<br /> <br /> <br />National Institute of Oceanography<br />Dona Paula 403 004, Goa<br />Email: webmaster@darya.nio.org<br />Web: www.nio.org/<br />Research Areas: International geosphere-bio-sphere programme, marine biotechnology.<br />GURGAON <br />National Brain Research Centre<br />Near NSG Campus, Nainwal Mode, Manesar, Gurgaon, Haryana<br />Email: info@nbrc.ac.in<br />Web: www.nbrc.ac.in/<br />Research Areas: Brain research.<br />GUWAHATI <br />Indian Institute of Technology Guwahati<br />North Guwahati, Guwahati 781 039, Assam<br />Email: mcb@iitg.ernet.in<br />Web: www.iitg.ernet.in<br />Research Areas: Engineering: Biotechnology.<br /> <br /> <br />Gauhati University<br />Gopinath Bordoloi Nagar, Guwahati 781 014, Assam<br />Web: http://www.gauhati.ac.in/.<br />HYDERABAD <br />Centre for Cellular &amp; Molecular Biology<br />Uppal Road, Hyderabad 500 007, Andhra Pradesh<br />Email: (Director): lalji@ccmb.res.in<br />Web: www.ccmb.res.in/<br />Research Areas: Biophysics &amp; biochemistry, molecular biology, genetics &amp; evolution, biomedicines &amp; biotechnology.<br /> <br /> <br />Centre for DNA Fingerprinting and Diagnostics<br />CDFD, Bldg. 7, Gruhakalpa, 5-4-399/B, Nampally, Hyderabad - 500 001.<br />Email: director@cdfd.org.in<br />Web: www.cdfd.org.in/<br />Research Areas: Automated genome analysis, bacterial genetics, cancer biology, cell biology &amp; gene expression, computational biology, computational &amp; functional genomics, immunology, mammalian genetics, molecular genetics, molecular oncology, molecular virology, structural biology, transcription, developmental neuroscience and drosophila genetics.<br /> <br /> <br />Indian Institute of Chemical Technology<br />Uppal Road, Hyderabad 500 007, Andhra Pradesh<br />Email: kvr@iict.ap.nic.in, sampath@iict.ap.nic.in<br />Web: www.iictindia.org/<br />Research Areas: Pesticides, drugs, organic intermediates and fine chemicals.<br /> <br /> <br />LV Prasad Eye Intstitute<br />Hyderabad, Andhra Pradesh, India<br />Email: communications@lvpei.org<br />Web: www.lvpei.org/<br />LVPEI is a World Health Organization Collaborating Center for Prevention of Blindness. Equipped with cutting-edge technology and distinguished professionals in the field of Eye care<br /> <br /> <br />University of Hyderabad<br />P.O. Central University, Gachibowli, Hyderabad 500 046, Andhra Pradesh<br />Email: trctcs@uohyd.ernet.in<br />Web: www.uohyd.ernet.in/<br />IMPHAL <br />Institute of Bioresources and Sustainable Development<br />Takyelpat, Imphal 795 001, Manipur<br />Email: ibsd_imp@sancharnet.in, ibsd-imphal@man.nic.in<br />Web: ibsd-imphal.nic.in/<br />Research Areas: Conservation of biodiversity and sustainable utilisation of biodiversity.<br />ITANAGAR <br />North Eastern Regional Institute of Science and Technology<br />Itanagar, Nirjuli, Papumpare 791 109, Arunachal Pradesh<br />Email: dir@nerist.ernet.in<br />Web: www.nerist.ac.in/<br />Research Areas: Agricultural engineering, forestry.<br />JAIPUR <br />University of Rajasthan<br />Jaipur 320 004, Rajasthan<br />Email: info@uniraj.org<br />Web: www.uniraj.org/<br />JAMMU and KASHMIR <br />Regional Research Laboratory<br />Canal Road, Jammu 130 001, Jammu &amp; Kashmir<br />Email: (Director): qazi_gn@yahoo.com, root@csrrljm.ren.nic.in<br />Web: www.rrljammu.org/<br />Research Areas: Natural products &amp; organic chemistry, improvement &amp; cultivation of medicinal and aromatic plants, post harvest technology and applied microbiology &amp; mutation genetics.<br /> <br />University of Jammu<br />Jammu 180 006, Jammu &amp; Kashmir<br />Web: www.jammuuniversity.org/<br /> <br />University of Kashmir<br />Hazratbal,Srinagar-190006,Jammu and Kashmir<br />Email: info@kashmiruniversity.net<br />Web: http://www.kashmiruniversity.net/<br /> <br />Sher-i-Kashmir Institute of Medical Science (SKIMS)<br />Srinagar, Jammu and Kashmir<br />Email: skimsweb@gmail.com<br />Web: http://www.skims.ac.in/<br /> <br />Sher-e-Kashmir University of Agricultural Sciences and Technology (SKUAST)<br />Shalimar Campus, Srinagar - 191121 Jammu and Kashmir<br />Email: skuastkashmir@gmail.com<br />Web: http://www.skuastkashmir.ac.in/<br />Research Areas: Agricultural Sciences, fisheries and veterinary sciences.<br />JORHAT <br />Regional Research Laboratory<br />Jorhat 785 006, Assam<br />Email: drrljt@csir.res.in, inform@csir.res.in<br />Web: jorhat.nic.in/rrl.htm<br />Research Areas: Agrochemicals, drugs and drug intermediates, organic chemistry, biochemistry.<br />KANPUR <br />Indian Institute of Technology Kanpur<br />GT Road, Kalyanpur, Kanpur 208 016, Uttar Pradesh<br />Email: infocell@iitk.ac.in<br />Web: www.iitk.ac.in/<br />Research Areas: Engineering: Biological sciences &amp; bioengineering.<br />KHARAGPUR <br />Indian Institute of Technology Kharagpur<br />Kharagpur 721 302, West Bengal<br />Email: (PRO): ashok@hijli.iitkgp.ernet.in<br />Web: www.iitkgp.ernet.in/<br />Research Areas: Engineering: Biotechnology.<br />KOCHI <br />Cochin University of Science and Technology<br />South Kalamessery, Kochi 682 022, Kerala<br />Email: webmaster@cusat.ac.in<br />Web: www.cusat.ac.in/.<br />KOLKATA <br />Bose Institute<br />93/1, Acharya Prafulla Chandra Road, Kolkata 700 009, West Bengal<br />Email: sidroy@bic.boseinst.ernet.in<br />Web: www.boseinstitute.org/<br />Research Areas: Bioinformatics &amp; computational biology, structure and functional dynamics of biomolecules, drug modeling, molecular genetics of microbes, transgenic plants etc.<br /> <br /> <br />Indian Institute of Chemical Biology<br />4, Raja S.C. Mullick Road, Jadavpur, Kolkata 700 032, West Bengal<br />Email: (Director): director@iicb.res.in<br />Web: www.iicb.res.in/<br />Research Areas: Natural products of medicinal, biological and industrial value, immunoassay techniques, tissue-targeted drug-delivery system.<br /> <br /> <br />Indian Institute of Science Education and Research &ndash;Kolkata<br />Mohanpur, Nadia, West Bengal<br />Web: www.iiserkol.ac.in/<br />Research Areas: All areas of basic sciences &ndash; Biology, chemistry, math and physics<br /> <br /> <br />Indian Statistical Institute, Kolkata<br />203 Barrackpore Trunk Road, Kolkata 700 108, West Bengal<br />Email: postmaster@isical.ac.in<br />Web: www.isical.ac.in/<br />Research Areas: Agricultural and ecological research, biological anthropology, human genetics.<br /> <br /> <br />Jadavpur University<br />188 Raja S.C. Mallik Road, Kolkata 700 032, West Bengal<br />Email: registrar@jdvu.ac.in<br />Web: www.jadavpur.edu/<br /> <br /> <br />University of Calcutta<br />Kolkata 700 009, West Bengal<br />Web: www.kolkata.org/cu/<br />KURUKSHETRA <br />Kurukshetra University<br />Kurukshetra 136 119, Haryana<br />Email: jskadian@rediffmail.com<br />Web: kuk.ernet.in/<br />LUCKNOW <br />Birbal Sahni Institute of Palaeobotany<br />53 University Road, Lucknow, Uttar Pradesh<br />Email: director@bsip.res.in<br />Web: www.bsip-india.org/index.htm<br />Research Areas: Botanical palaeobotany: Morphotaxonomy, palaeoecology, palaeogeography, phylogeny and evolution.<br /> <br /> <br />Central Drug Research Institute<br />Chattar Manzil Palace, Post Box No. 173, Lucknow 226 001, Uttar Pradesh<br />Email: info@cdriindia.org<br />Web: www.cdriindia.org/<br />Research Areas: Development of contraceptives, new drugs for tropical diseases (malaria, filariasis, leishmaniasis), cardio-vascular and central nervous system disorders.<br /> <br /> <br />Indian Institute of Science Education and Research &ndash;Kolkata<br />Mohanpur, Nadia, West Bengal<br />Web: www.iiserkol.ac.in/<br />Research Areas: All areas of basic sciences &ndash; Biology, chemistry, math and physics<br /> <br /> <br />Indian Statistical Institute, Kolkata<br />203 Barrackpore Trunk Road, Kolkata 700 108, West Bengal<br />Email: postmaster@isical.ac.in<br />Web: www.isical.ac.in/<br />Research Areas: Agricultural and ecological research, biological anthropology, human genetics.<br /> <br /> <br />Central Institute of Medicinal and Aromatic Plants<br />Lucknow 226 015, Uttar Pradesh<br />Email: director@cimap.res.in<br />Web: www.cimap.res.in/<br />Research Areas: Agrotechnologies for medicinal and aromatic plants, phytochemistry, plant physiology and biochemistry, pathology, genetics, entomology and pharmacognosy.<br /> <br /> <br />Industrial Toxicology Research Centre<br />Mahatma Gandhi Marg, P.O. Box No. 80, Lucknow 226 001, Uttar Pradesh<br />Email: info@itrcindia.org<br />Web: www.itrcindia.org/<br />Research Areas: Neurotoxicology, environmental health, immunotoxicology and environmental biotechnology.<br /> <br /> <br />National Botanical Research Institute<br />Rana Pratap Marg, Lucknow 226 001, Uttar Pradesh<br />Email: p.pushpangadan@nbri.res.in<br />Web: www.nbri-lko.org/<br />Research Areas: Plant biotechnology, environmental sciences, taxonomy and ethnobotany, plant molecular biology.<br />MUMBAI <br />Advanced Centre for Treatment, Research and Education in Cancer (ACTREC)<br />Tata Memorial Centre, Navi Mumbai - 410 210<br />Web: www.actrec.gov.in/<br />Research Areas: Research investigations currently focus on molecular mechanisms of cancer, drug development and emerging therapies for treatment and prevention of cancer.<br /> <br /> <br />Bhabha Atomic Research Centre<br />Trombay, Mumbai 400 085, Maharashtra<br />Email: webmaster@magnum.barc.ernet.in<br />Web: www.barc.ernet.in/<br />Research Areas: Chemical and life sciences, nuclear agriculture.<br /> <br /> <br />Bombay Natural History Society<br />Hornbill House, Shaheed Bhagat Singh Road, Mumbai 400 023, Maharashtra<br />Email: bnhs@bom4.vsnl.net.in<br />Web: www.bnhs.org/<br /> <br /> <br />Indian Institute of Technology Bombay<br />Powai, Mumbai 400 076, Maharashtra<br />Email: registrar@iitb.ac.in<br />Web: www.iitb.ac.in/<br />Research Areas: Earth sciences; Science: Biology, chemistry, mathematics, physics.<br /> <br /> <br />Tata Institute of Fundamental Research<br />Homi Bhabha Road, Navy Nagar, Colaba, Mumbai 400 005.<br />Web: www.tifr.res.in/<br />Department of Biological Sciences: www.tifr.res.in/~dbs<br />Research Areas: TIFR is a multidisciplinary research organisation working in the area of Natural Sciences (Biology, Chemistry, and Physics), Mathematics and Computer Science.<br /> <br /> <br />University of Mumbai<br />Vidyanagari, Kalina, Santa Cruz (W), Mumbai 400 098, Maharashtra<br />Web: www.mu.ac.in/<br /> <br /> <br />National Botanical Research Institute<br />Rana Pratap Marg, Lucknow 226 001, Uttar Pradesh<br />Email: p.pushpangadan@nbri.res.in<br />Web: www.nbri-lko.org/<br />Research Areas: Plant biotechnology, environmental sciences, taxonomy and ethnobotany, plant molecular biology.<br />NAGPUR <br />National Environmental Engineering Research Institute<br />Nehru Marg, Nagpur 440 020, Maharashtra<br />Email: dirneeri@nagpur.dot.net.in<br />Web: www.neeri.nic.in/<br />Research Areas: Environmental biotechnology.<br />PUNE <br />Agharkar Research Institute<br />G.G. Agarkar Road, Pune 411 004, Maharashtra<br />Web: www.aripune.org/<br />Research Areas: Animal sciences, microbial sciences, plant sciences.<br /> <br /> <br />Indian Institute of Science Education and Research&ndash;Pune<br />Email: director@iiserpune.ac.in<br />Web: www.iiserpune.ac.in/<br />Research Areas: All areas of basic sciences &ndash; Biology, chemistry, math and physics.<br /> <br /> <br />National Chemical Laboratory<br />Dr. Homi Bhabha Road, Pune 411 008, Maharashtra<br />Email: director@ems.ncl.res.in<br />Web: www.ncl-india.org/<br />Research Areas: biotechnology, biochemistry.&gt;<br /> <br /> <br />National Centre for Cell Sciences<br />NCCS Complex, Ganeshkhind, Pune 411 007, Maharashtra<br />Email: infonccs@giaspn01.vsnl.net.in<br />Web: www.nccs.res.in/<br />Research Areas: Cell biology, molecular biology, immunology, parasitology, hybridoma technology, tissue banking &amp; tissue engineering, regenerative biology, virology (HIV), cancer biology, diabetes, cryobiology transplantation, gene therapy.<br /> <br /> <br />University of Pune<br />Ganeshkhind Road, Pune 411 007, Maharashtra Telephone: 020-5601305<br />Email: Registrar): regis@unipune.ernet.in<br />Web: www.unipune.ernet.in/<br />PALAMPUR <br />Institute of Himalayan Bioresource Technology<br />Post Box No. 6, Palampur 176 061, Himachal Pradesh<br />Email: root@csihbt.ren.nic.in, director@ihbt.csir.res.in<br />Web: www.icast.org.in/csir/ihbt.html<br />Research Areas: Floriculture, tea sciences, biotechnology and natural plant products.<br />PATIALA <br />Punjabi University<br />Patiala 147 002, Punjab<br />Email: ucc@pbi.ac.in<br />Web: www.universitypunjabi.org/<br />PILANI <br />Birla Institute of Technology and Science<br />Vidhya Vihar Campus, Pilani, 333 031, Rajasthan<br />Email: mmsanand@bits-pilani.ac.in<br />Web: www.bits-pilani.ac.in/<br />ROORKEE <br />Indian Institute of Technology Roorkee<br />Roorkee 247 667, Uttaranchal<br />Email: (Registrar): regis@iitr.ernet.in<br />Web: www.iitr.ernet.in/<br />Research Areas: Engineering: Biotechnology.<br />SHANTINIKETAN <br />Visva-Bharati University<br />Santiniketan, Birbhum 731 235, West Bengal<br />Email: Root@vbharat.ernet.in<br />Web: www.visva-bharati.ac.in/<br />SHILLONG <br />North-Eastern Hill University<br />Umshing, Shillong 793 022, Meghalaya<br />Email: admin@nehu.ac.in<br />Web: www.nehu.ac.in/<br />SILCHAR <br />Assam University<br />P.O. Box 63, Silchar 788 011, Assam<br />Email: auliba@sancharnet.in, asokesen@sancharnet.in<br />Web: assamuniversity.nic.in/<br />TRIVANDUM <br />Indian Institute of Science Education and Research&ndash;Trivandum<br />Trivandrum, Kerala,India.<br />Web: www.iisertvm.ac.in/<br />Research Areas: All areas of basic sciences &ndash; Biology, chemistry, math and physics<br /> <br /> <br />Rajiv Gandhi Centre for Biotechnology<br />Thycaud P.O., Thiruvananthapuram 695 , Kerala<br />Email: info@rgcb.res.in<br />Web: rgcb.res.in/<br />Research Areas: Disease biology and molecular medicine, Plant biotechnology<br /> <br /> <br />Regional Research Laboratory<br />Industrial Estate P.O., Pappanamcode, Thiruvananthapuram 695 019, Kerala<br />Email: root@csrrltrd.ren.nic.in<br />Web: w3rrlt.csir.res.in/<br />Research Areas: Chemistry of natural products, agroprocessing, photochemical systems including solar energy conversion, analysis of pollutants and waste-water technology.<br /> <br />VARANASI <br />Banaras Hindu University<br />Varanasi 221 005, Uttar Pradesh<br />Email: webmaster@bhu.ac.in<br />Web: www.bhu.ac.in/index.html<br /> <br />Rajiv Gandhi Centre for Biotechnology<br />Thycaud P.O., Thiruvananthapuram 695 , Kerala<br />Email: info@rgcb.res.in<br />Web: rgcb.res.in/<br />Research Areas: Disease biology and molecular medicine, Plant biotechnology<br /> <br /> <br />Indian Council for Agricultural Research<br />Main Web site: www.icar.org.in/<br />Research Institutes under ICAR: www.icar.org.in/icar15.html<br /> <br /> <br />CSIR Laboratories<br />Main CSIR website&ndash;www.csir.res.in/</p><p>-------------------------------</p><p>Department of Atomic Energy<br />Main CSIR website&ndash;www.barc.ernet.in/<br /> <br /> <br />Department of Biotechnology<br />Main CSIR website&ndash;dbtindia.nic.in/index.asp</p><p>&nbsp;</p><p>Dept. of Science &amp; Technology<br />Main Website: Main Website: www.dst.gov.in/<br /> <br /> <br />Indian Council for Medical Research<br />Main Web site: icmr.nic.in/<br />Research Institutes under ICMR: icmr.nic.in/institute.htm#Permanent%20Institutes/Centres</p><p>Ministry of Environment and Forest<br />Main Web site: envfor.nic.in/<br />Research Institutes under ICAR: cyberjournalist.org.in/linksr.html</p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/blog/view/41455/coronavirus-covid-%E2%80%9019-testing-sites-in-india</guid>
	<pubDate>Mon, 16 Mar 2020 16:13:41 -0500</pubDate>
	<link>https://bioinformaticsonline.com/blog/view/41455/coronavirus-covid-%E2%80%9019-testing-sites-in-india</link>
	<title><![CDATA[Coronavirus COVID ‐19 Testing Sites In India]]></title>
	<description><![CDATA[<p>COVID-19 is a new illness that can affect your lungs and airways. It's caused by a virus called coronavirus.</p><h2>Stay at home if you have coronavirus symptoms</h2><p>Stay at home if you have either:</p><ul>
<li>a high temperature &ndash; you feel hot to touch on your chest or back</li>
<li>a new, continuous cough &ndash; this means you've started coughing repeatedly</li>
</ul><h2>DO NOT TAKE</h2><p><em>Ibrufen</em></p><p><em>https://amp.theguardian.com/world/2020/mar/14/anti-inflammatory-drugs-may-aggravate-coronavirus-infection</em></p><h2>How to avoid catching and spreading coronavirus (social distancing)</h2><p>Everyone should do what they can to stop coronavirus spreading.</p><p>It is particularly important for people who:</p><ul>
<li>are 70 or over</li>
<li>have a long-term condition</li>
<li>are pregnant</li>
<li>have a weakened immune system</li>
</ul><p><img src="https://www.hindustantimes.com/rf/image_size_960x540/HT/p2/2020/03/16/Pictures/_c0c377e0-6789-11ea-8a5c-cb364e4c5304.png" alt="image" width="960" height="543" style="border: 0px; border: 0px;"></p><p><strong>Below are the 52 Coronavirus COVID-19 Testing sites/locations in India.</strong></p><p>State:&nbsp;Andhra Pradesh&nbsp; &nbsp; &nbsp; &nbsp;</p><ol>
<li>Sri Venkateswara Institute of Medical Sciences, Tirupati</li>
<li>Andhra Medical College, Visakhapatnam, Andhra Pradesh</li>
<li>GMC, Anantapur, AP</li>
</ol><p>State:&nbsp;Andaman &amp; Nicobar islands</p><ol>
<li>Regional Medical Research Centre, Port Blair, Andaman, and Nicobar</li>
</ol><p>State:&nbsp;Assam</p><ol>
<li>Gauhati Medical College, Guwahati</li>
<li>&nbsp;Regional Medical Research Center, Dibrugarh</li>
</ol><p>State:&nbsp;Bihar</p><ol>
<li>Rajendra Memorial Research Institute of Medical Sciences, Patna</li>
</ol><p>State: Chandigarh</p><ol>
<li>Post Graduate Institute of Medical Education &amp; Research, Chandigarh</li>
</ol><p>State: Chhattisgarh</p><ol>
<li>All India Institute Medical Sciences, Raipur</li>
</ol><p>Union Territory: Delhi-NCT&nbsp;</p><ol>
<li>All India Institute Medical Sciences, Delhi</li>
<li>National Centre for Disease Control, Delhi</li>
</ol><p>State: Gujarat</p><ol>
<li>BJ Medical College, Ahmedabad</li>
<li>M.P.Shah Government Medical College, Jamnagar</li>
</ol><p>State: Haryana</p><ol>
<li>Pt. B.D. Sharma Post Graduate Inst. of Med. Sciences, Rohtak, Haryana</li>
<li>BPS Govt Medical College, Sonipat</li>
</ol><p>State: Himachal Pradesh</p><ol>
<li>Indira Gandhi Medical College, Shimla, Himachal Pradesh</li>
<li>Dr.Rajendra Prasad Govt. Med. College, Kangra, Tanda, HP</li>
</ol><p>Union Territory: Jammu and Kashmir</p><ol>
<li>Sher‐e‐ Kashmir Institute of Medical Sciences, Srinagar</li>
<li>Government Medical College, Jammu</li>
</ol><p>State: Jharkhand</p><ol>
<li>MGM Medical College, Jamshedpur</li>
</ol><p>State: Karnataka</p><ol>
<li>Bangalore Medical College &amp; Research Institute, Bangalore</li>
<li>National Institute of Virology Field Unit Bangalore</li>
<li>Mysore Medical College &amp; Research Institute, Mysore</li>
<li>Hassan Inst. of Med. Sciences, Hassan, Karnataka</li>
<li>Shimoga Inst. of Med. Sciences, Shivamogga, Karnataka</li>
</ol><p>State: Kerala</p><ol>
<li>National Institute of Virology Field Unit, Kerala</li>
<li>Govt. Medical College, Thiruvananthapuram, Kerala</li>
<li>Govt. Medical College, Kozhikode, Kerala</li>
</ol><p>State: Madhya Pradesh</p><ol>
<li>All India Institute Medical Sciences, Bhopal</li>
<li>National Institute of Research in Tribal Health (NIRTH), Jabalpur</li>
</ol><p>State: Meghalaya</p><ol>
<li>NEIGRI of Health and Medical Sciences, Shillong, Meghalaya</li>
</ol><p>State: Maharashtra</p><ol>
<li>Indira Gandhi Government Medical College, Nagpur</li>
<li>Kasturba Hospital for Infectious Diseases, Mumbai</li>
</ol><p>State: Manipur</p><ol>
<li>J N Inst. of Med. Sciences Hospital, Imphal‐East, Manipur</li>
</ol><p>State: Odisha</p><ol>
<li>Regional Medical Research Center, Bhubaneswar</li>
</ol><p>Union Territory: Puducherry</p><ol>
<li>Jawaharlal Institute of Postgraduate Medical Education &amp; Research, Puducherry</li>
</ol><p>State: Punjab</p><ol>
<li>Government Medical College, Patiala, Punjab</li>
<li>Government Medical College, Amritsar</li>
</ol><p>State: Rajasthan</p><ol>
<li>Sawai Man Singh, Jaipur</li>
<li>Dr. S.N Medical College, Jodhpur</li>
<li>Jhalawar Medical College, Jhalawar, Rajasthan</li>
<li>SP Med. College, Bikaner, Rajasthan</li>
</ol><p>State: Tamil Nadu</p><ol>
<li>King&rsquo;s Institute of Preventive Medicine &amp; Research, Chennai</li>
<li>Government Medical College, Theni</li>
</ol><p>State: Tripura</p><ol>
<li>Government Medical College, Agartala</li>
</ol><p>State: Telangana</p><ol>
<li>Gandhi Medical College, Secunderabad</li>
</ol><p>State: Uttar Pradesh</p><ol>
<li>King&rsquo;s George Medical University, Lucknow</li>
<li>Institute of Medical Sciences, Banaras, Hindu University, Varanasi</li>
<li>Jawaharlal Nehru Medical College, Aligarh</li>
</ol><p>State: Uttarakhand</p><ol>
<li>Government Medical College, Haldwani</li>
</ol><p>State: West Bengal</p><ol>
<li>National Institute of Cholera and Enteric Diseases, Kolkata</li>
<li>IPGMER, Kolkata</li>
</ol>]]></description>
	<dc:creator>Neel</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/pages/view/11313/linux-sort-commands-for-bioinformatics</guid>
	<pubDate>Sat, 31 May 2014 15:41:16 -0500</pubDate>
	<link>https://bioinformaticsonline.com/pages/view/11313/linux-sort-commands-for-bioinformatics</link>
	<title><![CDATA[Linux Sort Commands for Bioinformatics]]></title>
	<description><![CDATA[<p>Almost all the scripting languages such as Perl, Python etc have built-in sort, but unfortunately none of them are as flexible as sort command. But one when it come to space efficiency GNU sort stands at the top. It can sort a 20Gb file with less than 2Gb memory. It is not trivial to implement so powerful a sort by yourself.</p><p>sort a space-delimited file based on its first column, then the second if the first is the same, and so on:<br />sort input.txt</p><p>sort a huge file (GNU sort ONLY):<br />sort -S 1500M -t $HOME/tmp input.txt &gt; sorted.txt</p><p>sort starting from the third column, skipping the first two columns:<br />sort +2 input.txt</p><p>sort the second column as numbers, descending order; if identical, sort the 3rd as strings, ascending order:<br />sort -k2,2nr -k3,3 input.txt</p><p>sort starting from the 4th character at column 2, as numbers:<br />sort -k2.4n input.txt</p><p>More Linxu sort command information<br /><br />If you have any sort commands you'd like to share, please add them to our comments section below. For more help, you can also type:<br /><br />man sort<br /><br />or<br /><br />sort --help<br /><br />on your Unix/Linux system.</p>]]></description>
	<dc:creator>Rahul Nayak</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/pages/view/11399/next-generation-sequencing-in-r-or-bioconductor-environment</guid>
	<pubDate>Mon, 02 Jun 2014 18:03:09 -0500</pubDate>
	<link>https://bioinformaticsonline.com/pages/view/11399/next-generation-sequencing-in-r-or-bioconductor-environment</link>
	<title><![CDATA[Next generation sequencing in R or bioconductor environment]]></title>
	<description><![CDATA[<p>There are many R software and bioconductor packages for NGS data analysis, some of them are as follows</p><h3><a name="TOC-Biostrings" id="TOC-Biostrings"></a>Biostrings</h3><p>The Biostrings package from Bioconductor provides an advanced environment for efficient sequence management and analysis in R. It contains many speed and memory effective string containers, string matching algorithms, and other utilities, for fast manipulation of large sets of biological sequences. The objects and functions provided by Biostrings form the basis for many other sequence analysis packages. <a href="http://bioconductor.org/packages/release/bioc/html/Biostrings.html">Documentation</a></p><div><div style="text-align: left;"><div style="color: #000000;"><h4><a name="TOC-IRanges-Overview" id="TOC-IRanges-Overview"></a>IRanges Overview</h4><p>IRanges provides the low-level infrastructure and containers for handling sets of integer ranges within Bioconductor's BioC-Seq domain. Its classes and methods provide support for many more high-level packages like GenomicRanges, ShortRead, Rsamtools, etc. <a href="http://bioconductor.org/packages/release/bioc/html/IRanges.html">Documentation</a></p><div style="text-align: right;"><div style="text-align: left;"><h4><a name="TOC-GenomicRanges-Overview" id="TOC-GenomicRanges-Overview"></a>GenomicRanges Overview</h4><p>The <em>GenomicRanges</em> package serves as the foundation for representing genomic locations within the Bioconductor project. It is built upon the <em>IRanges</em> infrastructure and defines three major data containers - <em>GRanges, GRangesList</em> and <em>GappedAlignments</em> - which are supporting other important BioC-Seq packages including <em>ShortRead, Rsamtools, rtracklayer, GenomicFeatures</em> and <em>BSgenome</em>.&nbsp; Compared to the IRanges container, the GRanges/<em>GRangesList</em> classes are more flexible and extensible to store additional information about sequence ranges, such as chromosome identifiers (sequence space), strand information and annotation data. <a href="http://bioconductor.org/packages/release/bioc/html/GenomicRanges.html">Documentation</a></p></div></div></div></div><h3><a name="TOC-Motif-Discovery" id="TOC-Motif-Discovery"></a>Motif Discovery</h3><h4><a name="TOC-cosmo" id="TOC-cosmo"></a>cosmo</h4><p>The cosmo package allows to search a set of unaligned DNA sequences for a shared motif that may function as transcription factor binding site. The algorithm extends the popular motif discovery tool MEME (Bailey and Elkan, 1995) in that it allows the search to be supervised by specifying a set of constraints that the motif to be discovered must satisfy. <a href="http://bioconductor.org/packages/release/bioc/html/cosmo.html">Documentation</a></p></div><div>
<p><span></span><span></span></p>
<div style="color: #0000ff;"><h4><a name="TOC-BCRANK" id="TOC-BCRANK"></a>BCRANK</h4><p>BCRANK is a method that takes a ranked list of genomic regions as input and outputs short DNA sequences that are overrepresented in some part of the list. The algorithm was developed for detecting transcription factor (TF) binding sites in a large number of enriched regions from high-throughput ChIP-chip or ChIP-seq experiments, but it can be applied to any ranked list of DNA sequences. Documentation</p>
<p><a href="http://bioconductor.org/packages/release/bioc/html/BCRANK.html"></a></p>
<p>rGADEM: <a href="http://bioconductor.org/packages/devel/bioc/html/rGADEM.html">Documentation</a></p><p>MotIV: <a href="http://bioconductor.org/packages/devel/bioc/html/MotIV.html">Documentation</a></p></div><h3><a name="TOC-ShortRead" id="TOC-ShortRead"></a>ShortRead</h3><p>The ShortRead package provides input, quality control, filtering, parsing, and manipulation functionality for short read sequences produced by high throughput sequencing technologies. While support is provided for many sequencing technologies, this package is primairly focused on Solexa/Illumina reads. <a href="http://bioconductor.org/packages/release/bioc/html/ShortRead.html">Documentation</a></p><h3><a name="TOC-Rsamtools" id="TOC-Rsamtools"></a>Rsamtools</h3><p>Rsamtools provides functions for parsing and inspecting samtools BAM formatted binary alignment data. SAM/BAM is quickly becoming a universal standard alignment format, and is now supported by a wide variety of alignment tools. <a href="http://bioconductor.org/help/bioc-views/2.7/bioc/html/Rsamtools.html">Documentation</a></p>
<p><a href="http://samtools.sourceforge.net/">Samtools Website</a><br /> <a href="http://bio-bwa.sourceforge.net/">BWA (Burrows-Wheeler Alignment) Website</a><br /><span style="color: #0000ff;"></span></p>
<div style="color: #000000;">&nbsp;</div></div><div>
<p><span style="color: #000000;">Additional tools for SNP analysis:&nbsp;</span></p>
<p><a href="http://bioconductor.org/help/bioc-views/release/bioc/html/snpMatrix.html">snpMatrix</a></p><h3><a name="TOC-BSgenome" id="TOC-BSgenome"></a>BSgenome</h3><p>BSgenome provides an object oriented infrastructure for interacting with a Biostring based genome sequence. BSgenome packages exist for many common genomes, and can be created to represent custom genomes. See the "How to forge a BSgenome data package" Vignette for instructions to create a new BSgenome package if a prebuilt package does not exist for your organism. <a href="http://bioconductor.org/packages/release/bioc/html/BSgenome.html">Documentation</a></p><h3><a name="TOC-rtracklayer" id="TOC-rtracklayer"></a>rtracklayer</h3><p>rtracklayer provides an interface for exporting annotation feature data to various genome browsers and file formats (such as GFF). See the Small RNA Profiling exercise for an example of using rtracklayer to visualize alignment coverage. <a href="http://bioconductor.org/packages/release/bioc/html/rtracklayer.html">Documentation</a></p><h3><a name="TOC-biomaRt" id="TOC-biomaRt"></a>biomaRt</h3><p>The biomaRt package, provides an interface to a growing collection of databases implementing the BioMart software suite (http:// www.biomart.org). The package enables online retrieval of large amounts of data in a uniform way without the need to know the underlying database schemas. This data is retrieved automatically via the Internet, so it's recommended that you cache the data locally, or check versions if your code will be adversely affected by updates to these data. <a href="http://bioconductor.org/packages/release/bioc/html/biomaRt.html">Documentation</a></p><h3><a name="TOC-ChIP-Seq-Analysis-Packages" id="TOC-ChIP-Seq-Analysis-Packages"></a>ChIP-Seq Analysis Packages</h3><p>Bioconductor provides various packages for analyzing and visualizing ChIP-Seq data. Only a small selection of these packages is introduced here. Additional useful introductions to this topic are: <a href="http://www.bioconductor.org/workshops/2009/SeattleJan09/ChIP-seq/">BioC ChIP-seq Case Study</a> and BioC <a href="http://www.bioconductor.org/help/course-materials/2009/SeattleNov09/ChIP-seq/">ChIP-Seq</a>.</p><h4><a name="TOC-chipseq" id="TOC-chipseq"></a>chipseq</h4><p>The chipseq package combines a variety of HT-Seq packages to a pipeline for ChIP-Seq data analysis. <a href="http://bioconductor.org/packages/release/bioc/html/chipseq.html">Documentation</a></p><h4><a name="TOC-BayesPeak" id="TOC-BayesPeak"></a>BayesPeak</h4><p>BayesPeak is a peak calling package for identifying DNA binding sites of proteins in ChIP-Seq experiments. Its algorithm uses hidden Markov models (HMM) and Bayesian statistical methods. The following sample code introduces the identification of peaks with the BayesPeak package as well as the incorporation of read coverage information obtained by the chipseq package. <a href="http://bioconductor.org/packages/release/bioc/html/BayesPeak.html">Documentation</a> [ <a href="http://www.biomedcentral.com/1471-2105/10/299">Publication</a> ]</p><h4><a name="TOC-PICS" id="TOC-PICS"></a>PICS</h4><p>The PICS package applies probabilistic inference to aligned-read ChIP-Seq data in order to identify regions bound by transcription factors. PICS identifies enriched regions by modeling local concentrations of directional reads, and uses DNA fragment length prior information to discriminate closely adjacent binding events via a Bayesian hierarchical t-mixture model. The following sample code uses the test data set from the above BayesPeak package in order to compare the results from both methods by identifying their consensus peak set. <a href="http://www.bioconductor.org/packages/release/bioc/html/PICS.html">Documentation</a> [ <a href="http://www.hubmed.org/display.cgi?uids=20528864">Publication</a> ]</p><h4><a name="TOC-ChIPpeakAnno" id="TOC-ChIPpeakAnno"></a>ChIPpeakAnno</h4><p>The ChIPpeakAnno package provides. batch annotation of the peaks identified from either ChIP-seq or ChIP-chip experiments. It includes functions to retrieve the sequences around peaks, obtain enriched Gene Ontology (GO) terms, find the nearest gene, exon, miRNA or custom features such as most conserved elements and other transcription factor binding sites supplied by users. The package leverages the biomaRt, IRanges, Biostrings, BSgenome, GO.db, multtest and stat packages. <a href="http://bioconductor.org/packages/release/bioc/html/ChIPpeakAnno.html">Documentation</a></p><h4><a name="TOC-Additional-ChIP-Seq-Packages" id="TOC-Additional-ChIP-Seq-Packages"></a>Additional ChIP-Seq Packages</h4><p>DiffBind: <a href="http://www.bioconductor.org/packages/release/bioc/html/DiffBind.html">Documentation</a></p><p>MOSAICS: <a href="http://bioconductor.org/packages/devel/bioc/html/mosaics.html">Documentation</a></p><p>iSeq: <a href="http://bioconductor.org/packages/release/bioc/html/iSeq.html">Documentation</a></p><p>ChIPseqR: <a href="http://bioconductor.org/packages/release/bioc/html/ChIPseqR.html">Documentation</a></p><p>ChiPsim: <a href="http://bioconductor.org/packages/release/bioc/html/ChIPsim.html">Documentation</a></p><p>CSAR: <a href="http://www.bioconductor.org/packages/devel/bioc/html/CSAR.html">Documentation</a></p><p>ChIP-Seq Pipeline: <a href="http://www.bioconductor.org/packages/release/bioc/html/PICS.html">PICS</a>, rGADEM and MotIV (<a href="http://www.rglab.org/pics-and-bioconductor/">developer web site</a>)</p><p>SPP: <a href="http://compbio.med.harvard.edu/Supplements/ChIP-seq/">ChIP-seq processing pipeline</a></p><p><a href="http://compbio.med.harvard.edu/Supplements/ChIP-seq/tutorial.html">SPP Tutorial</a></p><p><a href="http://liulab.dfci.harvard.edu/MACS/index.html">MACS</a></p><p><a href="http://gmdd.shgmo.org/Computational-Biology/ChIP-Seq/download/SIPeS">SIPeS</a></p><h3><a name="TOC-RNA-Seq-Analysis" id="TOC-RNA-Seq-Analysis"></a>RNA-Seq Analysis</h3><h4><a name="TOC-Counting-Reads-that-Overlap-with-Annotation-Ranges-" id="TOC-Counting-Reads-that-Overlap-with-Annotation-Ranges-"></a>Counting Reads that Overlap with Annotation Ranges&nbsp;</h4><p>The GenomicRanges package provides support for importing into R short read alignment data in BAM format (via Rsamtools) and associating them with genomic feature ranges, such as exons or genes. This way one can quantify the number of reads aligning to annotated genomic regions. The package defines general purpose containers for storing genomic intervals as well as more specialized containers for storing alignments against a reference genome. The two main functions for read counting provided by this infrastructure are <span>countOverlaps <span style="color: #000000;"><span>and</span></span> summarizeOverlaps</span>. For their proper usage, it is important to read the corresponding <a href="http://www.bioconductor.org/packages/devel/bioc/vignettes/GenomicRanges/inst/doc/summarizeOverlaps.pdf">PDF manual</a>. <a href="http://bioconductor.org/packages/release/bioc/html/GenomicRanges.html">Documentation</a></p><h4><a name="TOC-Differential-Gene-Expression-Analysis-with-DESeq" id="TOC-Differential-Gene-Expression-Analysis-with-DESeq"></a>Differential Gene Expression Analysis with DESeq</h4><p>The DESeq package contains functions to call differentially expressed genes (DEGs) in count tables based on a model using the negative binomial distribution. It expects as input a data frame with the raw read counts per region/gene of interest (rows) for each test sample (columns).&nbsp; Such a count table can be imported into R or generated from BAM alignment files using the <span>countOverlaps</span> function as introduced above. <a href="http://www.bioconductor.org/packages/release/bioc/html/DESeq.html">Documentation</a></p><h4><a name="TOC-Differential-Gene-Expression-Analysis-with-edgeR" id="TOC-Differential-Gene-Expression-Analysis-with-edgeR"></a>Differential Gene Expression Analysis with edgeR</h4><p>The edgeR package uses empirical Bayes estimation and exact tests based on the negative binomial distribution to call differentially expressed genes (DEGs) in count data.&nbsp;</p>
<p><a href="http://www.bioconductor.org/packages/release/bioc/html/edgeR.html">Documentation</a></p>
<p><span style="color: #000000;">A variety of additional R packages are available for normalizing RNA-Seq read count data and identifying differentially expressed genes (DEG): <br /> </span></p><p><a href="http://bioconductor.org/packages/devel/bioc/html/easyRNASeq.html">easyRNASeq</a> (simplifies read counting per genome feature)</p><p><a href="http://www.bioconductor.org/packages/release/bioc/html/DEXSeq.html">DEXSeq</a> (Inference of differential exon usage);&nbsp;<a href="http://www.bioconductor.org/packages/release/data/experiment/html/parathyroidSE.html">parathyroidSE</a> explains how to generate exon read counts in R</p><p><a href="http://bioconductor.org/packages/release/bioc/html/DEGseq.html">DEGseq</a></p><p><a href="http://www.bioconductor.org/packages/release/bioc/html/baySeq.html">baySeq</a> (also see: <a href="http://www.bioconductor.org/packages/release/bioc/html/segmentSeq.html">segmentSeq</a>)</p><p><a href="http://bioconductor.org/packages/release/bioc/html/Genominator.html">Genominator</a> (<a href="http://www.hubmed.org/display.cgi?uids=20167110">Bullard et al. 2010</a>)</p><div style="text-align: right;"><div style="text-align: left;"><h4><a name="TOC-Detection-of-Alternative-Splice-Junctions" id="TOC-Detection-of-Alternative-Splice-Junctions"></a>Detection of Alternative Splice Junctions</h4>
<p><span style="color: #000000;">Another utility of RNA-Seq experiments is the analysis of splice junctions. The following software suggestions provide this utility:</span></p>
<p><a href="http://woldlab.caltech.edu/rnaseq/">ERANGE<br /> </a><a href="http://tophat.cbcb.umd.edu/">TopHat</a></p><p><a href="http://biogibbs.stanford.edu/%7Ekinfai/SpliceMap/">SpliceMap</a></p><p><a href="http://solidsoftwaretools.com/gf/project/splitseek/">SplitSeek</a></p><h3><a name="TOC-DNA-Methylation-Data-Analysis" id="TOC-DNA-Methylation-Data-Analysis"></a>DNA-Methylation Data Analysis</h3><div><ul>
<li><span style="font-size: 10pt;"><a href="http://www.bioconductor.org/help/course-materials/2012/BiocEurope2012/mattia_pelizzola_methylPipe.pdf">methylPipe</a></span></li>
<li><span style="font-size: 10pt;"><a href="http://www.bioconductor.org/packages/devel/bioc/html/bsseq.html">bsseq</a></span></li>
<li><a href="http://www.bioconductor.org/packages/devel/bioc/html/BiSeq.html">BiSeq</a></li>
<li>Much more under <a href="http://www.bioconductor.org/packages/devel/BiocViews.html#___DNAMethylation">BiocViews</a></li>
</ul></div></div></div><h3><a name="TOC-HT-Seq-Data-Visualization" id="TOC-HT-Seq-Data-Visualization"></a>HT-Seq Data Visualization</h3>
<p><a href="http://www.bioconductor.org/packages/release/bioc/html/ggbio.html">ggbio</a>: ggplot2 extension for genomics data (<a href="http://tengfei.github.com/ggbio/">online manual</a>) <a href="http://www.bioconductor.org/packages/devel/bioc/html/Gviz.html">Gviz</a>:&nbsp;Plotting data and annotation information along genomic coordinates <a href="http://bioconductor.org/packages/release/bioc/html/HilbertVis.html">HilbertVis</a>: Hilbert genome plots</p>
<p><a href="http://bioconductor.org/packages/release/bioc/html/GenomeGraphs.html">GenomeGraphs</a>: Plotting genomic information from Ensembl</p><p><a href="http://www.hubmed.org/display.cgi?uids=18507856">TileQC</a>: Flow Cell Quality Visualization</p><p><a href="http://bioconductor.org/packages/release/bioc/html/rtracklayer.html">rtracklayer</a>: R interface to genome browsers</p><p><a href="http://genoplotr.r-forge.r-project.org/">genoPlotR</a>: Plotting maps of genes and genomes</p><p><a href="http://bioconductor.org/packages/release/bioc/html/Genominator.html">Genominator</a>: Tools for storing, accessing, analyzing and visualizing genomic data.</p><p>&nbsp;</p><p>To install all packages</p><blockquote><p>source("http://bioconductor.org/biocLite.R")<br />biocLite()<br />biocLite(c("ShortRead", "Biostrings", "IRanges", "BSgenome", "rtracklayer", "biomaRt", "chipseq", "ChIPpeakAnno", "Rsamtools", "BayesPeak", "PICS", "GenomicRanges", "DESeq", "edgeR", "leeBamViews", "GenomicFeatures", "BSgenome.Celegans.UCSC.ce2"))</p></blockquote></div>]]></description>
	<dc:creator>John Parker</dc:creator>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/11494/postdoc-position-at-centre-mediterraneen-de-medecine-moleculaire-nice-france</guid>
  <pubDate>Wed, 04 Jun 2014 07:20:57 -0500</pubDate>
  <link></link>
  <title><![CDATA[Postdoc position at Centre Méditerranéen de Médecine Moléculaire - Nice - France]]></title>
  <description><![CDATA[
<p>The research group of Dr. Michele Trabucchi at the Centre Méditerranéen de Médecine Moléculaire (C3M) at INSERM U1065 (University of Nice Sophia-Antipolis, France) is seeking candidates for a Postdoctoral fellow position to start on October 2014 for 3 years funded by FRM (Fondation pour la Recherche Médicale).<br />The broad interest of the lab is in understanding the expression control and function of small RNAs in activated myeloid cells (visit our webpage to check research interests and publications of the group : http://www.unice.fr/c3m/EN/Equipe10.html ). </p>

<p>The work will focus on the functional studies of small RNAs by using next-generation sequencing approaches.<br /> <br />Candidates should hold a Ph.D. degree and have strong background in bioinformatics.<br />The University of Nice Sophia-Antipolis provides a wide range of facilities and training essential for biomedical research.</p>

<p>Interested applicants should send a PDF with a cover letter stating research interests and qualifications, an updated CV, a summary of previous research experience and contact information for two references to Michele Trabucchi ( mtrabucchi@unice.fr )</p>

<p>Homepage: http://www.unice.fr/c3m/EN/Equipe10.html</p>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/11611/ten-recommendations-for-creating-usable-bioinformatics-command-line-software</guid>
	<pubDate>Sun, 08 Jun 2014 10:06:26 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/11611/ten-recommendations-for-creating-usable-bioinformatics-command-line-software</link>
	<title><![CDATA[Ten recommendations for creating usable bioinformatics command line software]]></title>
	<description><![CDATA[<p><span>Bioinformatics software varies greatly in quality. In terms of usability, the command line interface is the first experience a user will have of a tool. Unfortunately, this is often also the last time a tool will be used. Here I present ten recommendations for command line software author&rsquo;s tools to follow, which I believe would greatly improve the uptake and usability of their products, waste less user&rsquo;s time, and improve the quality of scientific analyses.</span></p><p>Address of the bookmark: <a href="http://www.gigasciencejournal.com/content/2/1/15?utm_content=buffer25ee0&amp;utm_medium=social&amp;utm_source=twitter.com&amp;utm_campaign=buffer" rel="nofollow">http://www.gigasciencejournal.com/content/2/1/15?utm_content=buffer25ee0&amp;utm_medium=social&amp;utm_source=twitter.com&amp;utm_campaign=buffer</a></p>]]></description>
	<dc:creator>RAJESH DETROJA</dc:creator>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/12206/bioinformatics-algorithms-tutorials</guid>
	<pubDate>Tue, 24 Jun 2014 00:10:45 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/12206/bioinformatics-algorithms-tutorials</link>
	<title><![CDATA[Bioinformatics algorithms tutorials]]></title>
	<description><![CDATA[<p>Useful bioinformatics tutorial, such as</p>
<p>De Bruijn Graphs for NGS Assembly<br>Algorithms for PacBio Reads<br>Software and Hardware Concepts for Bioinformatics<br>Finding us in Homolog.us (Search Algorithms)<br>NGS Genome and RNAseq Assembly - a Hands on Primer<br>Introduction to PERL, Python, R and C/C++ for Bioinformatics</p><p>Address of the bookmark: <a href="http://www.homolog.us/Tutorials/" rel="nofollow">http://www.homolog.us/Tutorials/</a></p>]]></description>
	<dc:creator>John Parker</dc:creator>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/12944/orione-%E2%80%93-a-web-based-framework-for-ngs-analysis-in-microbiology</guid>
	<pubDate>Wed, 23 Jul 2014 06:43:03 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/12944/orione-%E2%80%93-a-web-based-framework-for-ngs-analysis-in-microbiology</link>
	<title><![CDATA[Orione – a web-based framework for NGS analysis in microbiology]]></title>
	<description><![CDATA[<p>End-to-end NGS microbiology data analysis requires a diversity of tools covering bacterial resequencing, de novo assembly, scaffolding, bacterial RNA-Seq, gene annotation and metagenomics. However, the construction of computational pipelines that use different software packages is difficult due to a lack of interoperability, reproducibility, and transparency. To overcome these limitations researchers at <a href="http://www.crs4.it/" target="_blank">CRS4</a>, Italy have developed Orione, a Galaxy-based framework consisting of publicly available research software and specifically designed pipelines to build complex, reproducible workflows for NGS microbiology data analysis. Enabling microbiology researchers to conduct their own custom analysis and data manipulation without software installation or programming, Orione provides new opportunities for data-intensive computational analyses in microbiology and metagenomics.</p>
<p>Reference</p>
<p>Cuccuru G1, Orsini M, Pinna A, Sbardellati A, Soranzo N, Travaglione A, Uva P, Zanetti G, Fotia G. (2014)<strong> Orione, a web-based framework for NGS analysis in microbiology.</strong> <em>Bioinformatics</em> [Epub ahead of print]. [<a href="http://bioinformatics.oxfordjournals.org/content/early/2014/03/10/bioinformatics.btu135.long" target="_blank">article</a>]</p><p>Address of the bookmark: <a href="http://orione.crs4.it/" rel="nofollow">http://orione.crs4.it/</a></p>]]></description>
	<dc:creator>Martin Jones</dc:creator>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/news/view/12883/breaking-chromosomes-to-study-cancer</guid>
	<pubDate>Fri, 18 Jul 2014 05:42:09 -0500</pubDate>
	<link>https://bioinformaticsonline.com/news/view/12883/breaking-chromosomes-to-study-cancer</link>
	<title><![CDATA[Breaking chromosomes to study cancer !!!]]></title>
	<description><![CDATA[<p>Chromosomes are present in every cell of our body and they contain the information the body needs to develop and function properly. This information is carried in genes that are arranged along the chromosomes. There are usually 46 chromosomes in every cell. These chromosomes come in pairs, one from our mother and one from our father. The chromosomes can be sorted into 23 pairs by looking at them down a microscope.</p><p>Most people who have a balanced translocation have the right amount of chromosome material but it has been rearranged in some way. This may happen if two chromosomes swap pieces (a reciprocal translocation). In other cases two whole chromosomes may become stuck together (a Robertsonian translocation). This page describes what happens when someone has a reciprocal translocation. <br /><br />Reciprocal chromosomal translocations occur following double-strand breaks (DSBs) in DNA when a section of one chromosome is exchanged with that of another, non-homologous chromosome. These exchanges may produce a dysfunctional fusion gene that disrupts cell growth and survival pathways, such as the translocations seen in leukemia and childhood sarcomas. <br /><br />Chromosomal translocations have been well studied in cancer cell lines which are associated with two types of cancer, acute myeloid leukemia and Ewing's sarcoma, but determining how they contribute to cancer development is complicated by additional mutations and altered gene expression profiles in these cultured cells. Now, Juan Carlos Ramirez, head of the Viral Vector Facility at the Fundacion Centro Nacional de Investigaciones Cardiovasculares (CNIC) and his colleagues Raul Torres at CNIC and Sandra Rodriguez-Peralez at the Spanish National Cancer Center (CNIO) in Madrid, Spain have used a new genome editing tool, CRISPR-Cas9, to induce chromosomal translocations for the first time in a human cell line and in primary cells. The study's authors conclude by stating that the use of this technology will allow for the clarification of how and why chromosomal translocation occurs, which without doubt will allow new anti-cancer therapeutic strategies to be tackled.</p><p>Using RNA-Guided Endonuclease (RGEN) technology or CRISPR/Cas9 genome engineering technology, CNIO and CNIC researchers have shown that it is possible to obtain such chromosomal translocations. The CRISPR-Cas9 system is extremely simple to introduce a cut at the desired locus, easier to design, and cheaper than many other systems. Using the CRISPR-Cas9 system, Ramirez and his colleagues reproduced the translocations observed in Ewing&rsquo;s Sarcoma (ES) and Acute Myeloid Leukemia (AML) patient cell lines in HEK293 cells and also generated the ES translocation in human mesenchymal stem cells and the AML translocation in umbilical cord blood cells.</p><p>By focusing on chromosomal translocation without the confounding characteristics of established cell lines, these new cells lines should help answer the fundamental question of what causes a cell to become cancerous. Ramirez and his team now look forward to modeling other chromosome translocations in a variety of cell types.</p><p>Reference:</p><p>http://en.wikipedia.org/wiki/Chromosomal_translocation</p><p>http://www.nature.com/ncomms/2014/140603/ncomms4964/abs/ncomms4964.html<br /><br /></p>]]></description>
	<dc:creator>Jit</dc:creator>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/news/view/13226/you-and-your-friend-have-similar-dna</guid>
	<pubDate>Sun, 27 Jul 2014 20:44:05 -0500</pubDate>
	<link>https://bioinformaticsonline.com/news/view/13226/you-and-your-friend-have-similar-dna</link>
	<title><![CDATA[You and your friend have similar DNA !!!]]></title>
	<description><![CDATA[<p>New research out of Massachusetts claims that people often choose friends that are similar to them in genetics and they are more accurate than you might suppose. A study published on PNAS&nbsp;http://www.pnas.org/content/111/Supplement_3/10796.full found that people are apt to pick friends who are genetically similar to themselves - so much so that friends tend to be as alike at the genetic level as a person's fourth cousin.</p><div style="text-align: center;"><img src="http://i.kinja-img.com/gawker-media/image/upload/s--CwLwHa43--/18fbmlokxcmqcjpg.jpg" alt="image" width="300" height="271" style="border: 0px; border: 0px;"></div><p>Scientists with a long-running Framingham Heart Study looked at 1,932 people (examination of about 1.5 million markers of genetic variations), comparing unrelated friends to unrelated strangers. They found that friends shared about 1% of their genes &mdash; a percentage much higher than those shared with strangers.This new findings made it clear that people have more DNA in common with those who are selected as friends than with strangers in the same population.&nbsp;</p><p>The genes that lined up the most were olfactory genes, which deal with smell. The ones that lined up the least were immune system genes. The researchers weren't sure why that happened :/. Olfactory genes might be a straightforward explanation: People who like the same smells tend to be drawn to similar environments, where they meet others with the same tendencies.</p><p>Reference:</p><p>http://www.pnas.org/content/111/Supplement_3/10796.full</p><p>Image : http://i.kinja-img.com</p>]]></description>
	<dc:creator>Jit</dc:creator>
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