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	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/4196?offset=490</link>
	<atom:link href="https://bioinformaticsonline.com/related/4196?offset=490" rel="self" type="application/rss+xml" />
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/41996/wgd%E2%80%94simple-command-line-tools-for-the-analysis-of-ancient-whole-genome-duplications</guid>
	<pubDate>Thu, 23 Jul 2020 05:49:45 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/41996/wgd%E2%80%94simple-command-line-tools-for-the-analysis-of-ancient-whole-genome-duplications</link>
	<title><![CDATA[wgd—simple command line tools for the analysis of ancient whole-genome duplications]]></title>
	<description><![CDATA[<p><span>wgd is a easy to use command-line tool for<span>&nbsp;</span></span><em>K</em><sub>S</sub><span><span>&nbsp;</span>distribution construction named wgd. The wgd suite provides commonly used<span>&nbsp;</span></span><em>K</em><sub>S</sub><span><span>&nbsp;</span>and colinearity analysis workflows together with tools for modeling and visualization, rendering these analyses accessible to genomics researchers in a convenient manner.</span></p>
<p><a href="https://academic.oup.com/bioinformatics/article/35/12/2153/5162749">https://academic.oup.com/bioinformatics/article/35/12/2153/5162749</a></p><p>Address of the bookmark: <a href="https://github.com/arzwa/wgd" rel="nofollow">https://github.com/arzwa/wgd</a></p>]]></description>
	<dc:creator>LEGE</dc:creator>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/videolist/watch/19555/a-3d-map-of-the-human-genome</guid>
	<pubDate>Fri, 12 Dec 2014 22:27:55 -0600</pubDate>
	<link>https://bioinformaticsonline.com/videolist/watch/19555/a-3d-map-of-the-human-genome</link>
	<title><![CDATA[A 3D Map of the Human Genome]]></title>
	<description><![CDATA[<iframe width="" height="" src="https://www.youtube-nocookie.com/embed/dES-ozV65u4" frameborder="0" allowfullscreen></iframe>Suhas Rao and Miriam Huntley (of the Aiden Lab) describe a 3D map of the human genome at kilobase resolution, revealing the principles of chromatin looping. Guest Origami Folding: Sarah Nyquist.

Suhas S.P. Rao*, Miriam H. Huntley*, Neva C. Durand, Elena K. Stamenova, Ivan D. Bochkov, James T. Robinson, Adrian L. Sanborn, Ido Machol, Arina D. Omer, Eric S. Lander, Erez Lieberman Aiden. (2014). A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping. Cell.]]></description>
	
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	<guid isPermaLink="true">https://bioinformaticsonline.com/blog/view/43260/bioinformatics-tools-for-telomere-to-telomere-assembly</guid>
	<pubDate>Tue, 17 Aug 2021 13:17:09 -0500</pubDate>
	<link>https://bioinformaticsonline.com/blog/view/43260/bioinformatics-tools-for-telomere-to-telomere-assembly</link>
	<title><![CDATA[Bioinformatics tools for telomere to telomere assembly !]]></title>
	<description><![CDATA[<p>●&nbsp;<a href="https://github.com/arangrhie/merfin" target="_blank">Merfin</a>&nbsp;&ndash; k-mer-based assembly and variant calling evaluation for improved consensus accuracy (Arang Rhie)<br />●&nbsp;<a href="https://www.biorxiv.org/content/10.1101/2020.11.11.378133v1" target="_blank">PanGenie</a>&nbsp;&ndash; algorithm that leverages a pangenome reference built from haplotype-resolved genome assemblies in conjunction with k-mer count information from raw, short-read sequencing data to genotype a wide spectrum of genetic variation (Tobias Marschall)<br />●&nbsp;<a href="https://github.com/ConesaLab/SQANTI3" target="_blank">SQANTI3</a>&nbsp;&ndash; an automated pipeline for the classification of long-read transcripts that can assess the quality of data and the preprocessing pipeline (Roc&iacute;o Amor&iacute;n de Heged&uuml;s&nbsp;<a href="https://twitter.com/rocioadh" target="_blank">@rocioadh</a>)<br />●&nbsp;<a href="https://github.com/GenomeRIK/tama" target="_blank">tama</a>&nbsp;(Transcriptome Annotation by Modular Algorithms) &ndash; software designed for processing Iso-Seq data and other long-read transcriptome data (Richard Kuo&nbsp;<a href="https://twitter.com/GenomeRIK" target="_blank">@GenomeRIK</a>)<br />●&nbsp;<a href="https://github.com/PacificBiosciences/pbAA" target="_blank">pbaa</a>&nbsp;(PacBio Amplicon Analysis) &ndash; separates complex mixtures of amplicon targets from genomic samples to cluster and generate high-quality consensus sequences from HiFi reads (Zev Kronenberg&nbsp;<a href="https://twitter.com/zevkronenberg" target="_blank">@zevkronenberg</a>)<br />●&nbsp;<a href="https://github.com/yuanyuan929/bellerophon" target="_blank">bellerophon</a>&nbsp;&ndash; analyzes MHC typing and other low-complexity gene amplicon data; performs allele calling while detecting polymorphic sites within the sequences and removing potential chimeric sequence variants (Yuanyuan Cheng&nbsp;<a href="https://twitter.com/Yuanyuan929" target="_blank">@Yuanyuan929</a>)<br />●&nbsp;<a href="https://github.com/amwenger/svpack" target="_blank">svpack</a>&nbsp;&ndash; tools for filtering, comparing, and annotating structural variant (SV) calls in VCF format (Aaron Wenger)<br />●&nbsp;<a href="https://github.com/AntonBankevich/jumboDB" target="_blank">JumboDB</a>&nbsp;&ndash; tool for de Bruijn graph construction (Anton Bankevich&nbsp;<a href="https://twitter.com/AntonBankevich" target="_blank">@AntonBankevich</a>)<br />●&nbsp;<a href="https://github.com/ksahlin/ultra" target="_blank">uLTRA</a>&nbsp;&ndash; tool for splice alignment of long transcriptomic reads to a genome, guided by a database of exon annotations. (Kristoffer Sahlin&nbsp;<a href="https://twitter.com/krsahlin" target="_blank">@krsahlin</a>)<br />●&nbsp;<a href="https://www.biorxiv.org/content/10.1101/2021.01.25.428044v1.full.pdf" target="_blank">LeafGo</a>&nbsp;&ndash; workflow to rapidly produce high-quality de novo plant genomes (Luca Ermini&nbsp;<a href="https://twitter.com/ermini_luca" target="_blank">@ermini_luca</a>)</p><p>Reference:</p><p>https://www.pacb.com/blog/young-investigators-share-stellar-science-career-advice-and-bioinformatics-tools-at-smrt-leiden-2021/</p><p>&nbsp;</p>]]></description>
	<dc:creator>BioStar</dc:creator>
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/19544/sau-bioinformaticsplant-biotech-jrf-vacancy</guid>
  <pubDate>Fri, 12 Dec 2014 21:27:12 -0600</pubDate>
  <link></link>
  <title><![CDATA[SAU Bioinformatics/Plant Biotech JRF Vacancy]]></title>
  <description><![CDATA[
<p>Applications are invited for the post of Junior Research Fellow (JRF) to work on SERB, DST funded project entitled “Genome wide analysis of ascorbate oxidase multi-gene family and elucidating its role in negative regulation of stress response in rice” under the supervision of Dr. Ananda Mustafiz, Faculty of Life Sciences and Biotechnology, South Asian University.</p>

<p>Qualification: Highly motivated M.Sc. (Bioinformatics/ Biotechnology/ Life Sciences/ Botany/ Agriculture) students are encouraged to apply. Prior experience in Bioinformatics/Plant tissue culture work is preferable. Preferences would be given to DBT/ CSIR / UGC NET qualified students.</p>

<p>Application Procedure: A detailed CV indicating name, date of birth, address, contact number, e-mail address, educational qualifications, NET qualified or not, research experiences if any, should be e-mailed to This email address is being protected from spambots. You need JavaScript enabled to view it. on or before 24th December 2014.</p>

<p>Important Note: Only short listed candidates will be called for interview at Akbar Bhawan, Chanakyapuri, New Delhi. No TA/DA will be paid for attending the interview. SAU Selection Committee reserves the rights to relax any of the qualifications in case the candidate is found otherwise well qualified. The above- mentioned post is temporary and will be initially offered for a period of one year, which can be extended to one more year.</p>

<p>Advertisement:  www.sau.ac.in/recruitment/vacancy.html</p>
]]></description>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/44288/upset-plots</guid>
	<pubDate>Fri, 24 Mar 2023 22:30:23 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/44288/upset-plots</link>
	<title><![CDATA[Upset plots !]]></title>
	<description><![CDATA[<p>Upset plots are a type of visualization used to analyze the intersection of sets or categories. They are particularly useful for displaying data with multiple categories and analyzing their overlaps.</p>
<p>In an upset plot, each row represents a category or set, and each column represents a data point. The length of the bar for each category indicates the number of data points that belong to that category. The plot also shows the intersections between categories, represented by overlapping bars.</p>
<p>Upset plots are useful for visualizing complex data with multiple categories and intersections, and can help identify patterns and relationships between categories. They are often used in fields such as bioinformatics, where they can be used to analyze gene expression data or to compare the results of different experimental conditions.</p>
<p>https://jokergoo.github.io/ComplexHeatmap-reference/book/upset-plot.html#example-with-the-genomic-regions</p><p>Address of the bookmark: <a href="https://jokergoo.github.io/ComplexHeatmap-reference/book/upset-plot.html#example-with-the-genomic-regions" rel="nofollow">https://jokergoo.github.io/ComplexHeatmap-reference/book/upset-plot.html#example-with-the-genomic-regions</a></p>]]></description>
	<dc:creator>BioStar</dc:creator>
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/19635/walk-in-interview-for-research-associate-studentship-and-traineeship-at-bif-nehu-tura-campus</guid>
  <pubDate>Thu, 18 Dec 2014 11:02:05 -0600</pubDate>
  <link></link>
  <title><![CDATA[Walk in interview for Research Associate, Studentship and Traineeship at BIF, NEHU, Tura Campus]]></title>
  <description><![CDATA[
<p>BIOINFORMATICS INFRASTRUCTURE FACILITY (BIF)<br />Department of RDAP<br />North-Eastern Hil University, Tura Campus<br />Tura-79402, Meghalaya</p>

<p>Walk in interview for Research Associate, Studentship and Traineeship at BIF</p>

<p>Applications are invited for the Post of Research Associate, Traineeship and Studentship in the DBT sponsored Bioinformatics Infrastructure Facility (BIF) at the Bioinformatics Centre, Department of RDAP, North-Eastern Hil University, Tura Campus, Tura-79402, Meghalaya. The Posts are purely temporary and terminable at any time without prior notice or assigning any reason thereof. The person engaged, shall not be entailed for any claim implicit or explicit for permanent absorption in the University.</p>

<p>Research Associate- 01</p>

<p>Essential Qualification: M.Sc. in Bioinformatics/Biotechnology from a recognized University/ institute.</p>

<p>Desirable: PhD or Pursuing PhD in the relevant subject(s) or equivalent published work in reputed peer reviewed journals or Advance PG diploma in Bioinformatics courses.</p>

<p>Duties: Creation of database, web designing, maintenance of internet, training of students in Bioinformatics, handling and knowledge of Bioinformatics software tools and technique, conducting Bioinformatics based research and other day to day laboratory work, writing report and scientific papers.</p>

<p>Pay:Rs. 2,00/- + Admissible 10% HRA per month</p>

<p>Age: Below 35 years</p>

<p>Traineeship- 02</p>

<p>Students who have completed Masters Degree in Bioinformatics/Biotechnology or any branch of Life Sciences/Agricultural Sciences/Computer Science to cary out a project work in Bioinformatics.</p>

<p>Desirable: Prior Knowledge of programming languages such as C, JAVA, MySQL is preferable.</p>

<p>Stipend: Rs. 800/- p.m. fixed. Purely temporary for a period of six months.</p>

<p>Studentship: 02</p>

<p>Students pursuing postgraduate degree in Bioinformatics/biotechnology/Agricultural Sciences or any branch of Life Science</p>

<p>Desirable: Prior knowledge of bioinformatics/ programming language is preferable.</p>

<p>Stipend: 800/- p.m. fixed. Purely temporary for a period of six months.</p>

<p>Candidates must send the detailed Biodata via mail/post and bring al the relevant documents in original and one set of attested photocopies of the same at the time of interview. No TA/DA will be paid for attending the interview and candidates have to make their own arrangements.</p>

<p>Last date for receiving application by mail or by post: 16.02.2014</p>

<p>Contact Information:<br />Dr.B.K. Mishra<br />Cordinator BIF,<br />RDAP Department, NEHU, Tura Campus<br />Phone: 91-03651-23107<br />Fax: 91-03651-23953<br />E-mail: drbkm1972@yaho.co.in, birendramishra14@gmail.com</p>

<p>Advertisement: http://www.nehu.ac.in/Advertisements/BIF_TuraAdtvPV_171214.pdf</p>
]]></description>
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/19597/assistant-professor-at-gauhati-university-guwahati</guid>
  <pubDate>Tue, 16 Dec 2014 01:15:30 -0600</pubDate>
  <link></link>
  <title><![CDATA[Assistant Professor at GAUHATI UNIVERSITY, GUWAHATI]]></title>
  <description><![CDATA[
<p>Advt. No.T/2014/4</p>

<p>Ref. No. GU/Estt/T/308(VI)/2014/6451-61</p>

<p>Applications are invited from the Indian citizens for five (5) teaching posts of Assistant Professor (Contractual) under various departments of Gauhati University. Details of the advertisement, other terms and conditions and the application forms are available in the University website www.gauhati.ac.in</p>

<p>Asstt. Professor (Contractual)</p>

<p>    2. M.Sc. Microbiology Course in Botany</p>

<p>    3 1.M.Sc. Microbiology/M.Sc. Botany (Specialization in Microbiology)/M.Sc. Biochemistry (1 post). (Preference will be given to candidates having experience in Biochemistry).</p>

<p>    2.M.Sc. Microbiology/M.Sc. Botany (Specialization in Microbiology)/M.Sc. Biotechnology(1 post). (Preference will be given to candidates having experience in Bioinformatics).</p>

<p>    3.M.Sc. Microbiology/M.Sc. Botany (Specialization in Microbiology)/M.Sc.  Biotechnology(1 post). (Preference will be given to candidates having experience in Microbial Genetics).</p>

<p>As per UGC norms</p>

<p>Pay Band &amp; Academic Grade Pay : (Consolidated pay) : Rs. 21,600/- per month</p>

<p>Application Form : Prescribe application form may download from the G.U. website www.gauhati.ac.in</p>

<p>Last date of receipt of filled-in application is 08.01.2015.</p>

<p>Advertisement: www.gauhati.ac.in/openfile.php?file=Notice1258.pdf</p>
]]></description>
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/19695/china-university-of-macau-phd-position-2015-in-bioinformatics-computer-science</guid>
  <pubDate>Mon, 22 Dec 2014 00:12:49 -0600</pubDate>
  <link></link>
  <title><![CDATA[China University of Macau PhD Position 2015 in Bioinformatics, Computer Science]]></title>
  <description><![CDATA[
<p>The Computational Biology and Bioinformatics Group at the University of Macau is inviting applications for PhD Position. Applicants will work on a research project focusing on the flexible receptor protein-ligand docking algorithms for computer-aided drug design.  The candidate will be working as part of a team in developing novel metaheuristic algorithms and scoring functions for large-scale, highly flexible protein-ligand docking problems. The duration of this PhD position is 2-3 years, starting in August 2015. Remuneration paid to candidate is MOP 11000-14000/month (~USD 1375-1750/month). The applications should be submitted before March 2015.</p>

<p>Study Subject(s): PhD position is award in the field of Bioinformatics/Computer Science.<br />Course Level: Position is available for pursuing PhD degree level at the University of Macau.<br />Scholarship Provider: University of Macau<br />Scholarship can be taken at: China</p>

<p>Eligibility: The ideal candidate would be a master degree holder in Bioinformatics or related disciplines with knowledge in Medical sciences or Life sciences (with GPA of at least 3.0 on a 4-point scale or equivalent) . Knowledge in programming (C and C++) and Linux scripting are necessary; experience in molecular docking, molecular dynamics simulations or molecular modeling is an advantage. The candidate should be fluent in spoken and written English; preference will be given to applicants with good publication records in relevant areas.</p>

<p>Scholarship Open for International Students: Researchers from China can apply for this PhD position.</p>

<p>Scholarship Description:</p>

<p>The Computational Biology and Bioinformatics Group at the University of Macau is looking for a motivated PhD student in Bioinformatics or Computer Science to work on a research project focusing on the flexible receptor protein-ligand docking algorithms for computer-aided drug design.  The candidate will be working as part of a team in developing novel metaheuristic algorithms and scoring functions for large-scale, highly flexible protein-ligand docking problems.</p>

<p>Number of award(s): There is only one PhD position available.</p>

<p>Duration of award(s): The duration of this PhD position is 2-3 years.</p>

<p>What does it cover? Remuneration paid to candidate is  MOP 11000-14000/month (~USD 1375-1750/month).</p>

<p>Selection Criteria: Not Known</p>

<p>Notification: Not Known</p>

<p>How to Apply: Send your current CV, your academic transcripts, a letter of motivation and research interests, two letters of recommendations from academic faculty to Dr. Shirley Siu at shirleysiu[at]umac.mo before March 2015.</p>

<p>Scholarship Application Deadline: The applications should be submitted before March 2015.</p>
]]></description>
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/19811/jnu-neurosciencesystems-biologymathematical-modeling-jrf-vacancies</guid>
  <pubDate>Fri, 26 Dec 2014 11:22:20 -0600</pubDate>
  <link></link>
  <title><![CDATA[JNU Neuroscience/Systems Biology/Mathematical modeling JRF Vacancies]]></title>
  <description><![CDATA[
<p>School of Computational and Integrative Sciences<br />Jawaharlal Nehru University<br />New Delhi 110067</p>

<p>Recruitment for Project</p>

<p>Applications were invited from the citizens of India for filling up the following temporary position for the CSIR sponsored Fellowship in the School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067. This position is temporary for a period of two and half years or tenable only for the duration of the project. The requisite qualifications &amp; experience are given below.</p>

<p>Project Title : "Understanding Complex dynamics and Information processing in Brain Networks"<br />Funding Agency : CSIR</p>

<p>Principal Investigator : Dr. R.K. Brojen Singh</p>

<p>Position : Junior Research Fellow(One post)</p>

<p>Salary : As per CSIR rules and guidelines for JRF.</p>

<p>Qualifications &amp; Experience : M.Sc. in Physics/Mathematics/Biology/B.Tech. In Eng. Physics/Comp. Sc. and desirable CSIR-UGC NET Qualified. Candidates should also have at least one years research experience after M. Sc./B.Tech. in works related to Neuroscience/Mathematical modeling.</p>

<p>Candidates possessing requisite qualifications may apply either on plain paper stating the project title along with CV and send to the following address or send as email attachment (pdf or word format) so as to reach on or before 8 January, 2014.</p>

<p>Dr. R.K. Brojen Singh<br />School of Computational and Integrative Sciences<br />Jawharlal Nehru University<br />New Delhi 110067<br />Email: brojen@jnu.ac.in, brojen@mail.jnu.ac.in</p>
]]></description>
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/researchlabs/view/19979/zhang-lab</guid>
  <pubDate>Sun, 28 Dec 2014 12:43:08 -0600</pubDate>
  <link></link>
  <title><![CDATA[Zhang Lab]]></title>
  <description><![CDATA[
<p>We develop and use integrative bioinformatics approaches to extract biological meanings from experimental data and generate hypotheses for experimental validation. Please explore our website to learn more about our people and our research.</p>

<p>More at http://bioinfo.vanderbilt.edu/zhanglab/</p>
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