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	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/42141?offset=60</link>
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	<description><![CDATA[]]></description>
	
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	<guid isPermaLink="true">https://bioinformaticsonline.com/file/view/39262/biotechnology-eligibility-test-bet-answer-set</guid>
	<pubDate>Wed, 17 Apr 2019 04:57:58 -0500</pubDate>
	<link>https://bioinformaticsonline.com/file/view/39262/biotechnology-eligibility-test-bet-answer-set</link>
	<title><![CDATA[Biotechnology Eligibility Test (BET) Answer set !]]></title>
	<description><![CDATA[<p>DBT-BET JRF 2019 Exam was held successfully on 14th April 2019. Official Question Paper &amp; Answer key of&nbsp;DBT-BET 2019 Exam has been released.</p><p>The best part about the DBT-BET Exam is both the question paper &amp; answer key is released immediately after the exam so you get the upper hand here to check how well you did in the DBT-BET exam, how much you are going to score and if you can pass the Exam with good score. This helps you in planning your career ahead.</p><p>DBT Exam is held once in a year by Department of Biotechnology &ndash; Govt of India.&nbsp;Candidates willing to get DBT-Junior Research Fellowship &ndash; DBT JRF fellowship should take up the&nbsp; DBT-BET Exam, DBT &ndash; Biotechnology Eligibility Test (BET) 2020 to be held on somewhere in the month of April. Official Notification for DBT-BET 2020 will be released in Feb 2020.</p><p>Question at&nbsp;<a href="https://bioinformaticsonline.com/file/view/39260/biotechnology-eligibility-test-bet-question-paper">https://bioinformaticsonline.com/file/view/39260/biotechnology-eligibility-test-bet-question-paper</a></p>]]></description>
	<dc:creator>Abhimanyu Singh</dc:creator>
	<enclosure url="https://bioinformaticsonline.com/file/download/39262" length="88016" type="application/pdf" />
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<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/1216/project-assistant-in-serb-dst-sponsored-project</guid>
  <pubDate>Fri, 02 Aug 2013 10:31:11 -0500</pubDate>
  <link></link>
  <title><![CDATA[Project Assistant in SERB-DST sponsored project]]></title>
  <description><![CDATA[
<p>Advertisement for post of Project Assistant in SERB-DST sponsored project @ Bioinformatics, Karunya University</p>

<p>Applications are invited for the post of Project Assistant to work in the following<br />project.</p>

<p>• Title of the project: "A novel approach for the identification of key  regulatory molecules and their pathways for Rheumatoid Arthritis" funded by Department of Science and Technology, New Delhi, Government of India.</p>

<p>• Project Assistant</p>

<p>• Essential Qualification: The minimum essential qualification would be M.Sc/B.Tech. in Bioinformatics/ Computer Science /Biotechnology.</p>

<p>• Salary : Rs. 8,000/month for a period of 3 years</p>

<p>Application in plain paper with following details: Name, Address, Date of Birth and Educational Qualifications and details of research experience with publications if any, may be sent to:</p>

<p>Mr. Sachidanand Singh,<br />Principal Investigator,<br />Department of Bioinformatics, School of Biotechnology and Health Sciences<br />Karunya University,<br />Karunya Nagar, Coimbatore- 641114</p>

<p>Ph.no: 09489677764, 09047654981</p>

<p>E-mail: sachidanand@karunya.edu</p>

<p>http://www.karunya.edu/bioinformatics/people/faculty/</p>

<p>Deadline : 25th August 2013</p>

<p>Advertisement: www.karunya.edu/bioinformatics/Project%20Assistant%20in%20SERB.pdf</p>
]]></description>
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<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/news/view/39025/binc-exam-merged-with-dbt-bet-jrf-exam</guid>
	<pubDate>Thu, 21 Feb 2019 09:37:36 -0600</pubDate>
	<link>https://bioinformaticsonline.com/news/view/39025/binc-exam-merged-with-dbt-bet-jrf-exam</link>
	<title><![CDATA[BINC Exam merged with DBT- BET JRF Exam]]></title>
	<description><![CDATA[<p>Another breaking news received has been received from the Department of biotechnology &ndash; DBT. As per a notification released by DBT, Bioinformatics National Certification (BINC) Exam conducted once per year by DBT has been now merged with DBT- BET JRF Exam.</p><p>Also, Bioinformatics Industrial Training Program (BIITP) is merged with the HRD Biotechnology Industrial Training Programme (BITP).</p><p>While this comes as a surprise for a lot of participants. We believe this is a good attempt to unify and create a national benchmark for talent. And we appreciate this endeavor from Department of biotechnology.</p><p>However, such last-minute announcements can create confusion. Thus candidates are advised to go through the complete notification DBT-BET JRF 2019 via the link below.If you have any kind of doubts, you must contact DBT JRF or Biotecnika for any kind of help &amp; assistance.</p><p><br />Attention:-Bioinformatics Programs (BINC and BIITP)</p><p>1. Bioinformatics National Certification (BINC) has been merged with DBT-Junior<br />Research Fellow (BET Exam)</p><p>2. Bioinformatics Industrial Training Program (BIITP) is merged with HRDBiotechnology Industrial Training Programme (BITP).</p><p>Students of Bioinformatics, who are interested to apply for Fellowship or Industrial<br />Training may keep track of the advertisement of DBT-JRF (BET Exam) and BITP<br />of DBT.</p><p>&nbsp;More at&nbsp;http://www.bcil.nic.in/files/Attention_Bioinformatics_Programs_(BINC_and_BIITP).pdf</p>]]></description>
	<dc:creator>Jit</dc:creator>
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<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/42172/sr-scientist-bioinformatics-vacancies-at-indian-institute-of-toxicology-research-india</guid>
  <pubDate>Tue, 01 Sep 2020 07:21:04 -0500</pubDate>
  <link></link>
  <title><![CDATA[Sr. Scientist Bioinformatics Vacancies at Indian Institute of Toxicology Research, India]]></title>
  <description><![CDATA[
<p>Start date of online Registration: Wednesday August 19, 2020 11:00 Hrs IST<br />Last date for Registration: Monday September 21, 2020 17:30 Hrs IST<br />Last date for submission of online application: Monday September 21, 2020 17:30 Hrs IST<br />Last date of Receipt of physical copy of application at CSIR-IITR: Tuesday October 05, 2020 17:30 Hrs IST</p>

<p>Pay Matrix Level-12<br />No. of Post-01<br />(UR)<br />Post – Sr. Scientist<br />Area Bioinformatics<br />Age limit : 37 years<br />PhD in Computational Biology/Bioinformatics with 2 years experience in desired area<br />Or<br />ME/M.Tech in Bioinformatics or Genome Informatics or Genetic Engineering with 3 years experience in desired area<br />Experience of understanding fundamental science behind Artificial Intelligence, machine learning, novel Artificial Intelligence algorithms and architectures, software engineering principles for Artificial Intelligence, natural language processing with proficiency in programming as evident by publications in SCI journals with high impact factor. To be part a group of scientists working in the area of genomics, running the central<br />bioinformatics facility, developing independent projects and providing bioinformatics support to the user scientists of the Institute.</p>

<p>More at </p>

<p>http://14.139.62.50/CSIR-IITR%20Scientist%20Recruitment%20Adv%202020.pdf</p>
]]></description>
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<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/researchlabs/view/4657/giovanni-parmigiani-lab</guid>
  <pubDate>Fri, 20 Sep 2013 13:21:41 -0500</pubDate>
  <link></link>
  <title><![CDATA[Giovanni Parmigiani Lab]]></title>
  <description><![CDATA[
<p>Scientific Interests:</p>

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

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

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

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

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

<p>http://scholar.google.com/citations?user=OlpYP3UAAAAJ&amp;hl=en</p>
]]></description>
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<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/43292/bioinformatics-scientist-production-bioinformatics-south-san-francisco-ca</guid>
  <pubDate>Thu, 19 Aug 2021 08:45:24 -0500</pubDate>
  <link></link>
  <title><![CDATA[Bioinformatics Scientist, Production Bioinformatics @ South San Francisco, CA]]></title>
  <description><![CDATA[
<p>wist is looking for a Bioinformatics Scientist to join our Production Bioinformatics Team. You will work alongside research scientists, software engineers and data scientists to further deliver on our mission to expand access to best-in-class synthetic biology and next-generation sequencing applications. You will be developing and engineering tools to better evaluate and build hardened, production quality pipelines, optimize data quality, and automate lab and bioinformatics processes. Our ideal candidate is an organized problem solver with a background in developing and building novel production-quality bioinformatics tools and packages. Equally excellent communication skills and a proven ability to work independently are required.</p>

<p>More at https://boards.greenhouse.io/twistbioscience/jobs/3135495?gh_src=9ecc0b941us</p>
]]></description>
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<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/4728/3-days-intensive-course-on-understanding-omics-data-in-basel-switzerland-19-21st-november</guid>
  <pubDate>Mon, 23 Sep 2013 10:46:57 -0500</pubDate>
  <link></link>
  <title><![CDATA[3 days intensive course on Understanding 'omics data in Basel, Switzerland, 19-21st November]]></title>
  <description><![CDATA[
<p>Benefits for the participants</p>

<p>- Plan more efficient experiments<br />- Correctly interpret results<br />- Communicate results in publications more effectively</p>

<p>The course focus is on methodologies, not on particular software tools. After the course participants should be able to apply the methods in their respective environment. However, during the course, hands-on sessions will be performed using the Genedata Expressionist® software, which enables participants to quickly apply the discussed methods and visualize results. No previous knowledge on Expressionist® is required; access to the software is free of charge during the course.</p>

<p>More @ http://www.dixa-fp7.eu/dixa-training/dixa-training-agenda/genedata-academy#!</p>
]]></description>
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<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/blog/view/43670/useful-bioinformatics-analysis-tools</guid>
	<pubDate>Thu, 23 Dec 2021 23:10:02 -0600</pubDate>
	<link>https://bioinformaticsonline.com/blog/view/43670/useful-bioinformatics-analysis-tools</link>
	<title><![CDATA[Useful Bioinformatics Analysis Tools !]]></title>
	<description><![CDATA[<h3><a href="http://sun.aei.polsl.pl/REFRESH/index.php?page=projects&amp;project=cometa&amp;subpage=about">CoMeta</a></h3><p><strong>Classificier of reads from metagenomic sequencing experiments.</strong></p><p><span>&bull;&nbsp;&nbsp;Kawulok, J., Deorowicz, S.,&nbsp;</span><em>CoMeta: Classification of Metagenomes Using k-mers</em><span>,&nbsp;</span><a href="http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0121453">PLOS ONE,&nbsp;</a><span>2015; 10(4):1&ndash;23,</span></p><h3><a href="http://sun.aei.polsl.pl/REFRESH/index.php?page=projects&amp;project=CoMSA&amp;subpage=about">CoMSA</a></h3><p><strong>Compressor of multiple sequence alignments of proteins.</strong></p><p><span>&bull;&nbsp;&nbsp;Deorowicz, S., Walczyszyn, J., Debudaj-Grabysz, A.,&nbsp;</span><em>CoMSA: compression of protein multiple sequence alignment files</em><span>,&nbsp;</span><a href="https://doi.org/10.1093/bioinformatics/bty619">Bioinformatics,&nbsp;</a><span>2019; 35(2):22&ndash;234,</span></p><h3><a href="http://sun.aei.polsl.pl/REFRESH/index.php?page=projects&amp;project=dsrc&amp;subpage=about">DSRC</a></h3><p><strong>Compressor of sequencing reads.</strong></p><p><span>&bull;&nbsp;&nbsp;Roguski, L., Deorowicz, S.,&nbsp;</span><em>DSRC 2: Industry-oriented compression of FASTQ files</em><span>,&nbsp;</span><a href="http://bioinformatics.oxfordjournals.org/content/30/15/2213">Bioinformatics,&nbsp;</a><span>2014; 30(15):2213&ndash;2215,</span><br /><span>&bull;&nbsp;&nbsp;Deorowicz, S., Grabowski, Sz.,&nbsp;</span><em>Compression of DNA sequences in FASTQ format</em><span>,&nbsp;</span><a href="http://bioinformatics.oxfordjournals.org/">Bioinformatics,&nbsp;</a><span>2011; 27(6):860&ndash;862,</span></p><h3><a href="http://sun.aei.polsl.pl/REFRESH/index.php?page=projects&amp;project=famsa&amp;subpage=about">FAMSA</a></h3><p><strong>Multiple sequence alignment designed for huge families of proteins (even containing hundreds of thousands of sequences).</strong></p><p><span>&bull;&nbsp;&nbsp;Deorowicz, S., Debudaj-Grabysz, A., Gudys, A.,&nbsp;</span><em>FAMSA: Fast and accurate multiple sequence alignment of huge protein families</em><span>,&nbsp;</span><a href="http://www.nature.com/articles/srep33964">Scientific Reports,&nbsp;</a><span>2016; 6(33964):</span></p><h3><a href="http://sun.aei.polsl.pl/REFRESH/index.php?page=projects&amp;project=fastore&amp;subpage=about">FaStore</a></h3><p><strong>Compressor of FASTQ files.</strong></p><p><span>&bull;&nbsp;&nbsp;Roguski, L., Ochoa, I., Hernaez, M., Deorowicz, S.,&nbsp;</span><em>FaStore - a space-saving solution for raw sequencing data</em><span>,&nbsp;</span><a href="https://doi.org/10.1093/bioinformatics/bty205">Bioinformatics,&nbsp;</a><span>2018; 34(16):2748&ndash;2756,</span></p><h3><a href="http://sun.aei.polsl.pl/REFRESH/index.php?page=projects&amp;project=fqsqueezer&amp;subpage=about">FQSqueezer</a></h3><p><strong>Experimental high-end compressor of FASTQ files.</strong></p><p><span>&bull;&nbsp;&nbsp;Deorowicz, S.,&nbsp;</span><em>FQSqueezer: k-mer-based compression of sequencing data</em><span>,&nbsp;</span><a href="https://www.nature.com/articles/s41598-020-57452-6">Scientific Reports,&nbsp;</a><span>2020; 10(578):</span></p><h3><a href="http://sun.aei.polsl.pl/REFRESH/index.php?page=projects&amp;project=gdc&amp;subpage=about">GDC</a></h3><p><strong>Compressor of collections of genome sequences.</strong></p><p><span>&bull;&nbsp;&nbsp;Deorowicz, S., Danek, A., Niemiec, M.,&nbsp;</span><em>GDC 2: Compression of large collections of genomes</em><span>,&nbsp;</span><a href="http://www.nature.com/srep/2015/150625/srep11565/full/srep11565.html">Scientific Reports,&nbsp;</a><span>2015; 5(11565):1&ndash;12,</span><br /><span>&bull;&nbsp;&nbsp;Deorowicz, S., Grabowski, Sz.,&nbsp;</span><em>Robust relative compression of genomes with random access</em><span>,&nbsp;</span><a href="http://sun.aei.polsl.pl/REFRESH/bioinformatics.oxfordjournals.org/content/27/21/2979.abstract">Bioinformatics,&nbsp;</a><span>2011; 27(21):2979&ndash;2986,</span></p><h3><a href="http://sun.aei.polsl.pl/REFRESH/index.php?page=projects&amp;project=gtc&amp;subpage=about">GTC</a></h3><p><strong>Genotype databases compressor with support for fast queries.</strong></p><p><span>&bull;&nbsp;&nbsp;Danek, A., Deorowicz, S.,&nbsp;</span><em>GTC: how to maintain huge genotype collections in a compressed form</em><span>,&nbsp;</span><a href="https://doi.org/10.1093/bioinformatics/bty023">Bioinformatics,&nbsp;</a><span>2018; 34(11):1834&ndash;1840,</span></p><h3><a href="http://sun.aei.polsl.pl/REFRESH/index.php?page=projects&amp;project=gtshark&amp;subpage=about">GTShark</a></h3><p><strong>Genotypes compressor.</strong></p><p><span>&bull;&nbsp;&nbsp;Deorowicz, S., Danek, A.,&nbsp;</span><em>GTShark: Genotype compression in large projects</em><span>,&nbsp;</span><a href="https://doi.org/10.1093/bioinformatics/btz508">Bioinformatics,&nbsp;</a><span>2019; 35(22):4791&ndash;4793,</span></p><h3><a href="http://sun.aei.polsl.pl/REFRESH/index.php?page=projects&amp;project=kmc&amp;subpage=about">KMC</a></h3><p><strong>Memory frugal&nbsp;<em>k</em>-mer counter.</strong></p><p><span>&bull;&nbsp;&nbsp;Kokot, M., Długosz, M., Deorowicz, S.,&nbsp;</span><em>KMC 3: counting and manipulating k -mer statistics</em><span>,&nbsp;</span><a href="https://doi.org/10.1093/bioinformatics/btx304">Bioinformatics,&nbsp;</a><span>2017; 33(17):2759&ndash;2761,</span><br /><span>&bull;&nbsp;&nbsp;Deorowicz, S., Kokot, M., Grabowski, Sz., Debudaj-Grabysz, A.,&nbsp;</span><em>KMC 2: Fast and resource-frugal k-mer counting</em><span>,&nbsp;</span><a href="https://doi.org/10.1093/bioinformatics/btv022">Bioinformatics,&nbsp;</a><span>2015; 31(10):1569&ndash;1576,</span><br /><span>&bull;&nbsp;&nbsp;Deorowicz, S., Debudaj-Grabysz, A., Grabowski, Sz.,&nbsp;</span><em>Disk-based k-mer counting on a PC</em><span>,&nbsp;</span><a href="http://www.biomedcentral.com/1471-2105/14/160">BMC Bioinformatics,&nbsp;</a><span>2013; 14():Article no. 160,</span></p><h3><a href="http://sun.aei.polsl.pl/REFRESH/index.php?page=projects&amp;project=kmer-db&amp;subpage=about">Kmer-db</a></h3><p><strong>Tool for estimation of evolutionary distances in a collection of genomes.</strong></p><p><span>&bull;&nbsp;&nbsp;Deorowicz, S., Gudys, A., Dlugosz, M., Kokot, M., Danek, A.,&nbsp;</span><em>Kmer-db: instant evolutionary distance estimation</em><span>,&nbsp;</span><a href="https://doi.org/10.1093/bioinformatics/bty610">Bioinformatics,&nbsp;</a><span>2019; 35(1):133&ndash;136,</span></p><h3><a href="http://sun.aei.polsl.pl/REFRESH/index.php?page=projects&amp;project=mugi&amp;subpage=about">MuGI</a></h3><p><strong>Index allowing queries for a collection of multiple genome sequences.</strong></p><p><span>&bull;&nbsp;&nbsp;Danek, A., Deorowicz, S., Grabowski, Sz.,&nbsp;</span><em>Indexes of Large Genome Collections on a PC</em><span>,&nbsp;</span><a href="http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0109384">PLOS ONE,&nbsp;</a><span>2014; 9(10):e109384,</span></p><h3><a href="http://sun.aei.polsl.pl/REFRESH/index.php?page=projects&amp;project=orcom&amp;subpage=about">ORCOM</a></h3><p><strong>Experimental compressor of sequencing reads.</strong></p><p><span>&bull;&nbsp;&nbsp;Grabowski, Sz., Deorowicz, S., Roguski, L.,&nbsp;</span><em>Disk-based compression of data from genome sequencing</em><span>,&nbsp;</span><a href="http://bioinformatics.oxfordjournals.org/content/early/2014/12/22/bioinformatics.btu844.abstract">Bioinformatics,&nbsp;</a><span>2014; 31(9):1389&ndash;1395,</span></p><h3><a href="http://sun.aei.polsl.pl/REFRESH/index.php?page=projects&amp;project=pgsa&amp;subpage=about">PgSA</a></h3><p><strong>Index allowing queries for a collection of sequencing reads.</strong></p><p><span>&bull;&nbsp;&nbsp;Kowalski, T., Grabowski, Sz., Deorowicz, S.,&nbsp;</span><em>Indexing arbitrary-length k-mers in sequencing reads</em><span>,&nbsp;</span><a href="http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0133198">PLOS ONE,&nbsp;</a><span>2015; 10(7):1&ndash;16,</span></p><h3><a href="http://sun.aei.polsl.pl/REFRESH/index.php?page=projects&amp;project=quickprobs&amp;subpage=about">QuickProbs</a></h3><p><strong>Multiple sequence alignment designed especially for GPU.</strong></p><p><span>&bull;&nbsp;&nbsp;Gudys, A., Deorowicz, S.,&nbsp;</span><em>QuickProbs 2: towards rapid construction of high-quality alignments of large protein families</em><span>,&nbsp;</span><a href="http://www.nature.com/articles/srep41553">Scientific Reports,&nbsp;</a><span>2017; 7(41553):</span><br /><span>&bull;&nbsp;&nbsp;Gudys, A., Deorowicz, S.,&nbsp;</span><em>QuickProbs &ndash; A Fast Multiple Sequence Alignment Algorithm Designed for Graphics Processors</em><span>,&nbsp;</span><a href="http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0088901">PLOS ONE,&nbsp;</a><span>2014; 9(2):e88901,</span></p><h3><a href="http://sun.aei.polsl.pl/REFRESH/index.php?page=projects&amp;project=reckoner&amp;subpage=about">RECKONER</a></h3><p><strong>Read error corrector.</strong></p><p><span>&bull;&nbsp;&nbsp;Maciej Długosz, M., Deorowicz, S.,&nbsp;</span><em>RECKONER: read error corrector based on KMC</em><span>,&nbsp;</span><a href="https://academic.oup.com/bioinformatics/article-abstract/33/7/1086/2843893/RECKONER-read-error-corrector-based-on-KMC">Bioinformatics,&nbsp;</a><span>2017; 33(7):1086&ndash;1089,</span></p><h3><a href="http://sun.aei.polsl.pl/REFRESH/index.php?page=projects&amp;project=tgc&amp;subpage=about">TGC</a></h3><p><strong>Compressor of collections of genomes given in Variant Call Format (VCF) files.</strong></p><p><span>&bull;&nbsp;&nbsp;Deorowicz, S., Danek, A., Grabowski, Sz.,&nbsp;</span><em>Genome compression: a novel approach for large collections</em><span>,&nbsp;</span><a href="http://bioinformatics.oxfordjournals.org/content/early/2013/08/29/bioinformatics.btt460">Bioinformatics,&nbsp;</a><span>2013; 29(20):2572&ndash;2578,</span></p><h3><a href="http://sun.aei.polsl.pl/REFRESH/index.php?page=projects&amp;project=vcfshark&amp;subpage=about">VCFShark</a></h3><p><strong>Compressor of VCF files.</strong></p><p><span>&bull;&nbsp;&nbsp;Deorowicz, S., Danek, A.,&nbsp;</span><em>GTShark: Genotype compression in large projects</em><span>,&nbsp;</span><a href="https://www.biorxiv.org/content/10.1101/2020.12.18.423437v1">biorxiv.org,&nbsp;</a><span>2020; ():</span></p><h3><a href="http://sun.aei.polsl.pl/REFRESH/index.php?page=projects&amp;project=whisper&amp;subpage=about">Whisper</a></h3><p><strong>Experimental mapper of whole genome sequencing data.</strong></p><p><span>&bull;&nbsp;&nbsp;Deorowicz, S., Gudys, A.,&nbsp;</span><em>Whisper 2: indel-sensitive short read mapping</em><span>,&nbsp;</span><a href="https://doi.org/10.1101/2019.12.18.881292">bioRxiv.org,&nbsp;</a><span>2019; :</span><br /><span>&bull;&nbsp;&nbsp;Deorowicz, S., Debudaj-Grabysz, A., Gudys, A., Grabowski, Sz.,&nbsp;</span><em>Whisper: read sorting allows robust robust mapping of DNA sequencing data</em><span>,&nbsp;</span><a href="https://doi.org/10.1093/bioinformatics/bty927">Bioinformatics,&nbsp;</a><span>2019; 35(12):2043&ndash;2050,</span><br /><span>&bull;&nbsp;&nbsp;Deorowicz, S., Debudaj-Grabysz, A., Gudys, A., Grabowski, Sz.,&nbsp;</span><em>Robust mapping of whole genome sequencing data</em><span>,&nbsp;</span><a href="https://meetings.cshl.edu/abstracts.aspx?meet=GENOME&amp;year=17">Poster at The Biology of Genomes Conference,&nbsp;</a><span>2017;</span></p>]]></description>
	<dc:creator>Neel</dc:creator>
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/researchlabs/view/5209/anders-krogh-lab</guid>
  <pubDate>Mon, 30 Sep 2013 19:07:40 -0500</pubDate>
  <link></link>
  <title><![CDATA[Anders Krogh Lab]]></title>
  <description><![CDATA[
<p>In a lot of my work in bioinformatics, I have been using hidden Markov models (HMMs). As a postdoc with David Haussler at UCSC we developed the so-called profile HMMs (refs). Since then I have applied HMMs to membrane proteins (refs) and gene identification (refs) and have worked on methods for such things as discriminative estimation of HMMs (refs) and alternative decoding algorithms etc. (refs).</p>

<p>Now my main interests are in gene regulation, where we work on promoter analysis; non-coding RNA, where miRNAs and structure prediction are the main areas; and protein structure, where the group is working on methods for structure prediction from sequence. To read more about these topics, please see the research pages. </p>

<p>Lab page @ http://wiki.binf.ku.dk/User:Krogh</p>
]]></description>
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/43993/phd-positions-on-integrative-omics-and-phylogenomics</guid>
  <pubDate>Wed, 19 Oct 2022 05:11:11 -0500</pubDate>
  <link></link>
  <title><![CDATA[PhD positions on integrative omics and phylogenomics]]></title>
  <description><![CDATA[
<p>Would you like to participate in an exciting interdisciplinary research project to discover the hidden chemistry of plants and its evolution using computational omics approaches? Do you enjoy collaboration and teamwork while being at the cutting edge of scientific progress? We are looking for two PhD candidates with complementary skills to pioneer new technologies to analyze, explore and leverage the diversity of plant chemistry hidden in plant genomes.</p>

<p>Plants represent an untapped resource of natural bioactive compounds that significantly contribute to plant resilience to pathogens, herbivores, and abiotic stresses, and may be applied for medicine or crop protection. In this project, you will design and/or apply innovative omics integration strategies for genomics, transcriptomics, and metabolomics data, to discover plant specialized metabolite biosynthetic pathways and study their evolution. You will work together with the other PhD candidate in this project, which will entail a combination of algorithm development, greenhouse experiments, integrative omics analysis, and evolutionary genomics. Extensive local and international collaboration is foreseen, including possibilities for a foreign research visit as part of your PhD project.</p>

<p>The research is embedded within the chairs of Bioinformatics and Biosystematics. The projects will be (co-)supervised by Dr. Marnix Medema, Dr. Justin van der Hooft, Dr. Klaas Bouwmeester and Prof. Dr. Eric Schranz.</p>

<p>We ask</p>

<p>We are looking for two enthusiastic and complementary team players with all or a subset of the following skills:</p>

<p>a solid academic record (MSc) in bioinformatics, biology, or biotechnology<br />experience in computational omics analysis and proficiency in programming (in, e.g., Python)<br />at least basic to intermediate statistical and mathematical skills<br />demonstrable experience in working with next-generation sequencing data or with greenhouse experiments with plants<br />affinity with plant science, metabolism and/or biosynthetic pathways<br />you meet all the entry requirements of the  WUR PhD programme.<br />More information</p>

<p>For more information about this position, please contact Marnix Medema, Associate Professor Bioinformatics, by email (marnix.medema@wur.nl).<br />For more information about the procedure, please contact vacaturemeldingen.psg@wur.nl.</p>
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