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	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/38765?offset=360</link>
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	<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/43690/ucsc-sars-cov-2-genome-browser</guid>
	<pubDate>Thu, 06 Jan 2022 06:48:40 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/43690/ucsc-sars-cov-2-genome-browser</link>
	<title><![CDATA[UCSC SARS-CoV-2 Genome Browser]]></title>
	<description><![CDATA[<p><span>The UCSC SARS-CoV-2 Genome Browser (</span><a href="https://genome.ucsc.edu/covid19.html">https://genome.ucsc.edu/covid19.html</a><span>) is an adaptation of our popular genome-browser visualization tool for this virus, containing many annotation tracks and new features, including conservation with similar viruses, immune epitopes, RT&ndash;PCR and sequencing primers and CRISPR guides. We invite all investigators to contribute to this resource to accelerate research and development activities globally.</span></p><p>Address of the bookmark: <a href="https://www.nature.com/articles/s41588-020-0700-8" rel="nofollow">https://www.nature.com/articles/s41588-020-0700-8</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/43859/mumco-is-a-simple-bash-script-that-uses-whole-genome-alignment-information-provided-by-mummer-v4-to-detect-variants</guid>
	<pubDate>Wed, 27 Apr 2022 04:34:12 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/43859/mumco-is-a-simple-bash-script-that-uses-whole-genome-alignment-information-provided-by-mummer-v4-to-detect-variants</link>
	<title><![CDATA[MUM&amp;Co is a simple bash script that uses Whole Genome Alignment information provided by MUMmer (v4) to detect variants.]]></title>
	<description><![CDATA[<p dir="auto">MUM&amp;Co is able to detect:<br>Deletions, insertions, tandem duplications and tandem contractions (&gt;=50bp &amp; &lt;=150kb)<br>Inversions (&gt;=1kb) and translocations (&gt;=10kb)</p><p>Address of the bookmark: <a href="https://github.com/SAMtoBAM/MUMandCo" rel="nofollow">https://github.com/SAMtoBAM/MUMandCo</a></p>]]></description>
	<dc:creator>Rahul Nayak</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/44322/genome-context-viewer-gcv</guid>
	<pubDate>Sun, 21 May 2023 19:33:43 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/44322/genome-context-viewer-gcv</link>
	<title><![CDATA[Genome Context Viewer (GCV)]]></title>
	<description><![CDATA[<p><span>The Genome Context Viewer (GCV) is a web-app that visualizes genomic context data provided by third party services. Specifically, it uses functional annotations as a unit of search and comparison. By adopting a common set of annotations, data-store operators can deploy federated instances of GCV, allowing users to compare genomes from different providers in a single interface.</span></p><p>Address of the bookmark: <a href="https://github.com/legumeinfo/gcv" rel="nofollow">https://github.com/legumeinfo/gcv</a></p>]]></description>
	<dc:creator>LEGE</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/pages/view/44637/tools-to-access-the-quality-of-your-assembled-genome</guid>
	<pubDate>Thu, 08 Aug 2024 23:31:18 -0500</pubDate>
	<link>https://bioinformaticsonline.com/pages/view/44637/tools-to-access-the-quality-of-your-assembled-genome</link>
	<title><![CDATA[Tools to access the quality of your assembled genome !]]></title>
	<description><![CDATA[<ul dir="auto">
<li><a href="https://github.com/linsalrob/fasta_validator">FASTA VALIDATOR</a>&nbsp;+&nbsp;<a href="https://github.com/shenwei356/seqkit">SEQKIT RMDUP</a>: FASTA validation</li>
<li><a href="https://genometools.org/tools/gt_gff3validator.html">GENOMETOOLS GT GFF3VALIDATOR</a>: GFF3 validation</li>
<li><a href="https://github.com/PlantandFoodResearch/assemblathon2-analysis/blob/a93cba25d847434f7eadc04e63b58c567c46a56d/assemblathon_stats.pl">ASSEMBLATHON STATS</a>: Assembly statistics</li>
<li><a href="https://genometools.org/tools/gt_stat.html">GENOMETOOLS GT STAT</a>: Annotation statistics</li>
<li><a href="https://github.com/ncbi/fcs">NCBI FCS ADAPTOR</a>: Adaptor contamination pass/fail</li>
<li><a href="https://github.com/ncbi/fcs">NCBI FCS GX</a>: Foreign organism contamination pass/fail</li>
<li><a href="https://gitlab.com/ezlab/busco">BUSCO</a>: Gene-space completeness estimation</li>
<li><a href="https://github.com/tolkit/telomeric-identifier">TIDK</a>: Telomere repeat identification</li>
<li><a href="https://github.com/oushujun/LTR_retriever/blob/master/LAI">LAI</a>: Continuity of repetitive sequences</li>
<li><a href="https://github.com/DerrickWood/kraken2">KRAKEN2</a>: Taxonomy classification</li>
<li><a href="https://github.com/igvteam/juicebox.js">HIC CONTACT MAP</a>: Alignment and visualisation of HiC data</li>
<li><a href="https://github.com/mummer4/mummer">MUMMER</a>&nbsp;&rarr;&nbsp;<a href="http://circos.ca/documentation/">CIRCOS</a>&nbsp;+&nbsp;<a href="https://plotly.com/">DOTPLOT</a>&nbsp;&amp;&nbsp;<a href="https://github.com/lh3/minimap2">MINIMAP2</a>&nbsp;&rarr;&nbsp;<a href="https://github.com/schneebergerlab/plotsr">PLOTSR</a>: Synteny analysis</li>
<li><a href="https://github.com/marbl/merqury">MERQURY</a>: K-mer completeness, consensus quality and phasing assessment</li>
</ul>]]></description>
	<dc:creator>LEGE</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/blog/view/44754/early-genome-screening-the-new-health-horoscope</guid>
	<pubDate>Thu, 02 Jan 2025 19:44:36 -0600</pubDate>
	<link>https://bioinformaticsonline.com/blog/view/44754/early-genome-screening-the-new-health-horoscope</link>
	<title><![CDATA[Early Genome Screening: The New Health Horoscope!]]></title>
	<description><![CDATA[<p>In an era where precision medicine is reshaping healthcare, genome screening is emerging as the modern equivalent of a health horoscope. It offers insights into our biological "stars," unraveling predispositions to various conditions and empowering individuals with knowledge to navigate their health journeys proactively. But how reliable is this "horoscope," and how does it impact our lives?</p><h3>Understanding Genome Screening</h3><p>Genome screening involves analyzing an individual's DNA to identify genetic variations that may influence health and disease susceptibility. This can range from simple single-gene tests to comprehensive whole-genome sequencing. By peering into our genetic blueprint, we can uncover risks for conditions like cancer, diabetes, cardiovascular diseases, and even rare genetic disorders.</p><p>The process is straightforward: a saliva or blood sample is collected, and advanced sequencing technologies decipher the genetic code. The results provide a personalized health map, guiding lifestyle modifications, preventive measures, or medical interventions.</p><h3>A Shift from Reactive to Proactive Healthcare</h3><p>Traditional healthcare often focuses on treating diseases after they manifest. Genome screening flips this model on its head, enabling a shift toward prevention and early intervention. For instance:</p><ul>
<li>
<p><strong>Cancer Risk Management</strong>: Individuals with BRCA1 or BRCA2 gene mutations can opt for enhanced screening programs or preventive surgeries to mitigate their risk of breast and ovarian cancers.</p>
</li>
<li>
<p><strong>Cardiovascular Health</strong>: Genetic predispositions to conditions like familial hypercholesterolemia can prompt early cholesterol monitoring and lifestyle adjustments.</p>
</li>
<li>
<p><strong>Rare Diseases</strong>: Identifying carriers of genetic disorders can aid in family planning and reduce the incidence of inherited conditions.</p>
</li>
</ul><h3>The Ethical and Practical Concerns</h3><p>While genome screening offers incredible promise, it is not without challenges:</p><ol>
<li>
<p><strong>Accuracy and Interpretation</strong>: Genetic predisposition does not guarantee disease. Misinterpretation of results can lead to unnecessary anxiety or unwarranted medical interventions.</p>
</li>
<li>
<p><strong>Privacy and Data Security</strong>: Genetic data is highly sensitive. Ensuring robust data protection measures is crucial to prevent misuse.</p>
</li>
<li>
<p><strong>Accessibility and Equity</strong>: High costs and limited availability may restrict access to genome screening, exacerbating health disparities.</p>
</li>
</ol><h3>Balancing Science and Pseudoscience</h3><p>The comparison of genome screening to horoscopes isn&rsquo;t entirely unfounded. Both offer predictive insights, but the scientific foundation of genome screening distinguishes it from astrology. Unlike the alignment of celestial bodies, genetic predictions are based on rigorous data and evidence. However, the probabilistic nature of genetic predispositions underscores the importance of interpreting results in conjunction with clinical and lifestyle factors.</p><h3>The Road Ahead</h3><p>As genome screening becomes more affordable and integrated into routine healthcare, its potential to transform lives is immense. Policymakers, healthcare providers, and genetic counselors must collaborate to ensure ethical implementation, public awareness, and equitable access.</p><p>Imagine a future where your genetic "horoscope" is a trusted guide, not just a prediction. Early genome screening could help chart a healthier path for generations, making it a cornerstone of personalized medicine. After all, our genes might just hold the key to unlocking a future of better health and well-being.</p><p>&nbsp;</p>]]></description>
	<dc:creator>LEGE</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/44902/hite-a-fast-and-accurate-dynamic-boundary-adjustment-approach-for-full-length-transposable-elements-detection-and-annotation-in-genome-assemblies</guid>
	<pubDate>Sat, 20 Sep 2025 09:34:04 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/44902/hite-a-fast-and-accurate-dynamic-boundary-adjustment-approach-for-full-length-transposable-elements-detection-and-annotation-in-genome-assemblies</link>
	<title><![CDATA[HiTE: a fast and accurate dynamic boundary adjustment approach for full-length Transposable Elements detection and annotation in Genome Assemblies]]></title>
	<description><![CDATA[<p dir="auto"><code>HiTE</code>&nbsp;is a Python software that uses a dynamic boundary adjustment approach to detect and annotate full-length Transposable Elements in Genome Assemblies. In comparison to other tools, HiTE demonstrates superior performance in detecting a greater number of full-length TEs.</p>
<div dir="auto">
<h2 dir="auto">panHiTE</h2>
<a href="https://github.com/CSU-KangHu/HiTE#panhite"></a></div>
<p dir="auto">We have developed panHiTE, a comprehensive and accurate pipeline for TE detection in large-scale population genomes. It has been successfully applied to hundreds of plant population genomes, demonstrating its effectiveness and scalability.</p>
<p dir="auto">For detailed instructions, please refer to the&nbsp;<a href="https://github.com/CSU-KangHu/HiTE/wiki/panHiTE-tutorial">panHiTE tutorial</a>.</p><p>Address of the bookmark: <a href="https://github.com/CSU-KangHu/HiTE" rel="nofollow">https://github.com/CSU-KangHu/HiTE</a></p>]]></description>
	<dc:creator>LEGE</dc:creator>
</item>
<item>
	<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>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/41009/genomics-public-data-links</guid>
	<pubDate>Thu, 13 Feb 2020 00:20:00 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/41009/genomics-public-data-links</link>
	<title><![CDATA[genomics public data links !]]></title>
	<description><![CDATA[<p>List of publically available databases on google server.</p>
<p>More at <a href="https://software.broadinstitute.org/gatk/download/bundle">https://software.broadinstitute.org/gatk/download/bundle</a></p>
<p><a href="ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606/VCF/GATK/">ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606/VCF/GATK/</a>.</p>
<p><a href="ftp://ftp.broadinstitute.org/bundle/hg38/hg38bundle/">ftp://ftp.broadinstitute.org/bundle/hg38/hg38bundle/</a></p><p>Address of the bookmark: <a href="https://console.cloud.google.com/storage/browser/genomics-public-data/resources/broad/hg38/v0?pli=1" rel="nofollow">https://console.cloud.google.com/storage/browser/genomics-public-data/resources/broad/hg38/v0?pli=1</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/7387/bioinformatics-software-for-biologists-in-the-genomics-era</guid>
	<pubDate>Sun, 22 Dec 2013 17:31:05 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/7387/bioinformatics-software-for-biologists-in-the-genomics-era</link>
	<title><![CDATA[Bioinformatics software for biologists in the genomics era]]></title>
	<description><![CDATA[<p>The genome sequencing revolution is approaching a landmark figure of 1000 completely sequenced genomes. Coupled with fast-declining, per-base sequencing costs, this influx of DNA sequence data has encouraged laboratory scientists to engage large datasets in comparative sequence analyses for making evolutionary, functional and translational inferences. However, the majority of the scientists at the forefront of experimental research are not bioinformaticians, so a gap exists between the user-friendly software needed and the scripting/programming infrastructure often employed for the analysis of large numbers of genes, long genomic segments and groups of sequences. We see an urgent need for the expansion of the fundamental paradigms under which biologist-friendly software tools are designed and developed to fulfill the needs of biologists to analyze large datasets by using sophisticated computational methods. We argue that the design principles need to be sensitive to the reality that comparatively small teams of biologists have historically developed some of the most popular biological software packages in molecular evolutionary analysis. Furthermore, biological intuitiveness and investigator empowerment need to take precedence over the current supposition that biologists should re-tool and become programmers when analyzing genome scale datasets.</p><p>Address of the bookmark: <a href="http://bioinformatics.oxfordjournals.org/content/23/14/1713.full" rel="nofollow">http://bioinformatics.oxfordjournals.org/content/23/14/1713.full</a></p>]]></description>
	<dc:creator>Poonam Mahapatra</dc:creator>
</item>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/17924/software-developed-in-pevsner-lab</guid>
	<pubDate>Mon, 06 Oct 2014 12:41:26 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/17924/software-developed-in-pevsner-lab</link>
	<title><![CDATA[Software developed in pevsner lab]]></title>
	<description><![CDATA[<div>
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<p><a href="http://pevsnerlab.kennedykrieger.org/dragon.htm">DRAGON</a>: Database Referencing of Array Genes Online</p>
<p><a href="http://pevsnerlab.kennedykrieger.org/php/node/96">SNOMAD</a>: Standardization and Normalization of Microarray Data</p>
<p><a href="http://pevsnerlab.kennedykrieger.org/php/node/70">SNPduo</a>: SNP Analysis Between Two Individuals</p>
<p><a href="http://pevsnerlab.kennedykrieger.org/php/node/71">SNPtrio</a>: Analyzing and Visualizing and Inheritance Patterns in Trios</p>
<p><a href="http://pevsnerlab.kennedykrieger.org/php/node/64">SNPscan</a>: Data Analysis and Visualization of SNP Data</p>
<p><a href="http://pevsnerlab.kennedykrieger.org/php/node/64">pediSNP</a>: Analyze SNP Data From a Pedigree of Two Generations</p>
<p><a href="http://pevsnerlab.kennedykrieger.org/php/node/73">kcoeff</a>: Calculate Cotterman Coefficients of SNP Genotype Data</p>
<p><a href="http://pevsnerlab.kennedykrieger.org/php/node/113">triPOD:</a> Detects chromosomal abnormalities in parent-child trio-based microarray data</p>
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</div><p>Address of the bookmark: <a href="http://pevsnerlab.kennedykrieger.org/php/?q=software" rel="nofollow">http://pevsnerlab.kennedykrieger.org/php/?q=software</a></p>]]></description>
	<dc:creator>Robert M Willioms</dc:creator>
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