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	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/30074?offset=440</link>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/news/view/40204/iitm-tokyo-tech-joint-symposium</guid>
	<pubDate>Thu, 24 Oct 2019 10:30:25 -0500</pubDate>
	<link>https://bioinformaticsonline.com/news/view/40204/iitm-tokyo-tech-joint-symposium</link>
	<title><![CDATA[IITM-Tokyo Tech Joint Symposium]]></title>
	<description><![CDATA[<p>The IITM-Tokyo Tech Joint Symposium is a biannual international symposium held in Indian Institute of Technology Madras (IITM), India in collaboration with Tokyo Institute of Technology (Tokyo-Tech), Japan. During the symposium, experts in various domains of Bioinformatics gather from India and Japan under one roof to discuss and present their works. This provides an unique opportunity to the researchers and students to learn the frontiers and interact with eminent scientists in Bioinformatics. The 5th IITM - Tokyo Tech Joint Symposium titled "Current trends in Bioinformatics: Big data analysis, machine learning and drug design", will be held on 6th - 7th March 2020 in IITM, Chennai, India.</p><p>The symposium will focus on topics in the below mentioned areas.</p><p>Topics: Algorithms for biomolecular sequences / structures Bioinformatics databases and tools Protein function Structure based drug design Machine learning Deep learning Large scale data analysis Big Data NGS Analysis Protein interactions/network Molecular modelling/docking/screening Biomolecular structure and function More</p><p>Info: https://web.iitm.ac.in/bioinfo2/symposium2020/home</p>]]></description>
	<dc:creator>Jit</dc:creator>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/34328/dfast-a-flexible-prokaryotic-genome-annotation-pipeline-for-faster-genome-publication</guid>
	<pubDate>Tue, 14 Nov 2017 10:26:16 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/34328/dfast-a-flexible-prokaryotic-genome-annotation-pipeline-for-faster-genome-publication</link>
	<title><![CDATA[DFAST: a flexible prokaryotic genome annotation pipeline for faster genome publication]]></title>
	<description><![CDATA[<p>We developed a prokaryotic genome annotation pipeline, DFAST, that also supports genome submission to public sequence databases. DFAST was originally started as an on-line annotation server, and to date, over 7,000 jobs have been processed since its first launch in 2016. Here, we present a newly implemented background annotation engine for DFAST, which is also available as a standalone command-line program. The new engine can annotate a typical-sized bacterial genome within 10 minutes, with rich information such as pseudogenes, translation exceptions, and orthologous gene assignment between given reference genomes. In addition, the modular framework of DFAST allows users to customize the annotation workflow easily and will also facilitate extensions for new functions and incorporation of new tools in the future.</p>
<div>Availability and Implementation</div>
<p>The software is implemented in Python 3 and runs in both Python 2.7 and 3.4&ndash; on Macintosh and Linux systems. It is freely available at&nbsp;<a href="https://github.com/nigyta/dfast_core/" target="">https://github.com/nigyta/dfast_core/</a>&nbsp;under the GPLv3 license with external binaries bundled in the software distribution. An on-line version is also available at&nbsp;<a href="https://dfast.nig.ac.jp/" target="">https://dfast.nig.ac.jp/</a>.</p><p>Address of the bookmark: <a href="https://dfast.nig.ac.jp/" rel="nofollow">https://dfast.nig.ac.jp/</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/37211/jbrowse-embeddable-genome-browser-built-completely-with-javascript-and-html5</guid>
	<pubDate>Fri, 29 Jun 2018 09:19:56 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/37211/jbrowse-embeddable-genome-browser-built-completely-with-javascript-and-html5</link>
	<title><![CDATA[JBrowse: Embeddable genome browser built completely with JavaScript and HTML5]]></title>
	<description><![CDATA[JBrowse is a fast, embeddable genome browser built completely with JavaScript and HTML5, with optional run-once data formatting tools written in Perl.

Headline Features:
Fast, smooth scrolling and zooming. Explore your genome with unparalleled speed.
Scales easily to multi-gigabase genomes and deep-coverage sequencing.
Quickly open and view data files on your computer without uploading them to any server.
Supports GFF3, BED, FASTA, Wiggle, BigWig, BAM, VCF (with either .tbi or .idx index), REST, and more.  BAM, BigBed, BigWig, and VCF data are displayed directly from chunks of the compressed binary files, no conversion needed.
Includes an optional “faceted” track selector (see demo) suitable for large installations with thousands of tracks.
Very light server resource requirements. In fact, JBrowse has no back-end server code, just tools for formatting data files to be read directly over HTTP. Serve huge datasets from a single low-cost cloud instance.
Can run as a stand-alone app on OSX and Windows using the Electron platform
Highly extensible plugin architecture, with a large plugin registry of existing examples here https://gmod.github.io/jbrowse-registry

https://jbrowse.org/<p>Address of the bookmark: <a href="https://github.com/GMOD/jbrowse" rel="nofollow">https://github.com/GMOD/jbrowse</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/5574/srfjrfra-university-of-hyderabad</guid>
  <pubDate>Mon, 14 Oct 2013 07:49:11 -0500</pubDate>
  <link></link>
  <title><![CDATA[SRF/JRF/RA @ UNIVERSITY OF HYDERABAD]]></title>
  <description><![CDATA[
<p>SCHOOL OF CHEMISTRY, UNIVERSITY OF HYDERABAD</p>

<p>Applications on plain paper along with details of CV (relevant photocopies of their<br />qualifications/experience and reprints of published work to be attached) are invited from qualified candidates for Research Fellowship in CSIR- sponsored research project.</p>

<p>JRF/SRF/RA (one vacancy)</p>

<p>CSIR sponsored “In silico design, identification and in vitro validation of lead molecule inhibitors to Bcr-Abl kinase”</p>

<p>JRF: M.Sc in Chemistry/ Bioinformatics/ Biotechnology with I division and NET or GATE qualified</p>

<p>SRF: M.Sc in chemistry/ Bioinformatics/ Biotechnology with at least two years of post- M.Sc research experience as evidenced from published papers in standard refereed journals in relevant area</p>

<p>RA: PhD in chemistry/ Bioinformatics/ Biotechnology with research experience in<br />relevant area.</p>

<p>As per CSIR guidelines</p>

<p>Notes:<br />1) You may visit the University of Hyderabad website www.uohyd.ernet.in to learn more about the University of Hyderabad.<br />2) Applicants should note that the appointment to be made is purely temporary and there is no right for claiming for any regular appointment in the University.<br />3) No TA/DA will be paid for attending the interview or at the time of joining the post, if selected.<br />4) The application should be submitted by post/courier/in-person to the address given below on or before November 1st 2013.</p>

<p>Prof. Lalitha Guruprasad<br />W-103, Gurbakhsh Singh Building<br />School of Chemistry<br />University of Hyderabad<br />Hyderabad- 500 046<br />5) Short-listed candidates will be called for interview at a short notice.</p>

<p>Advertisement: http://www.uohyd.ac.in/images/recruitment/chemisry_advt_101013.pdf</p>
]]></description>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/38672/ltr-retriever-accurately-identifies-and-annotates-ltr-retrotransposons-and-use-lai-to-evaluates-the-continuity-of-genome-assemblies</guid>
	<pubDate>Sun, 13 Jan 2019 07:14:31 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/38672/ltr-retriever-accurately-identifies-and-annotates-ltr-retrotransposons-and-use-lai-to-evaluates-the-continuity-of-genome-assemblies</link>
	<title><![CDATA[LTR_retriever: accurately identifies and annotates LTR retrotransposons and use LAI to evaluates the continuity of genome assemblies.]]></title>
	<description><![CDATA[<p>LTR_retriever is a command line program (in Perl) for accurate identification of LTR retrotransposons (LTR-RTs) from outputs of LTRharvest, LTR_FINDER, and/or MGEScan-LTR and generating non-redundant LTR-RT library for genome annotations.</p>
<p>By default, the program will generate whole-genome LTR-RT annotation and the LTR Assembly Index (LAI) for evaluations of the assembly continuity of the input genome. Users can also run LAI separately (see&nbsp;<code>Usage</code>).</p><p>Address of the bookmark: <a href="https://github.com/oushujun/LTR_retriever" rel="nofollow">https://github.com/oushujun/LTR_retriever</a></p>]]></description>
	<dc:creator>Neel</dc:creator>
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/5702/research-fellow-in-bioinformatics-queens-university-belfast-institute-for-global-food-security-school-of-biological-sciences</guid>
  <pubDate>Thu, 17 Oct 2013 04:33:02 -0500</pubDate>
  <link></link>
  <title><![CDATA[Research Fellow in Bioinformatics @  Queen's University Belfast -Institute for Global Food Security, School of Biological Sciences]]></title>
  <description><![CDATA[
<p>Ref: 13/102900</p>

<p>Available immediately until 30th November 2015, to work on the development of bioinformatics approaches to aid analysis of data derived from the metabolomic profiling of biological matrices. The successful applicant will lead research activities on an FP7 funded EU-wide collaborative project aimed at establishing biomarker-based strategies for high throughput diagnostic screening. Key tasks will involve multivariate analysis of large datasets, bioinformatic-based selection and validation of identified markers, construction of metabolomic spectral profile databases and development of machine learning/database searching approaches amenable to analytical screening techniques. This position will offer the opportunity to travel and undertake work with project collaborators based in the Republic of Ireland and Europe.</p>

<p>Informal enquiries may be directed to Dr Terry McGrath, email: terry.mcgrath@qub.ac.uk.</p>

<p>Anticipated interview date: Thursday 31st October 2013<br />Salary scale: £30,424 – £39,649 per annum (including contribution points)<br />Closing date: Monday 21st October 2013  </p>

<p>Telephone (028) 90973044 FAX: (028) 90971040 or e-mail on personnel@qub.ac.uk</p>

<p>The University is committed to equality of opportunity and to selection on merit.  It therefore welcomes applications from all sections of society and particularly welcomes applications from people with a disability. </p>

<p>Fixed term contract posts are available for the stated period in the first instance but in particular circumstances may be renewed or made permanent subject to availability of funding.</p>

<p>More @ https://hrwebapp.qub.ac.uk/tlive_webrecruitment/wrd/run/ETREC107GF.open?VACANCY_ID=5616943npO&amp;WVID=6273090Lgx&amp;LANG=USA</p>
]]></description>
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/5947/jrf-national-jalma-institute-of-leprosy-and-other-mycobacterial-diseases</guid>
  <pubDate>Mon, 28 Oct 2013 10:42:48 -0500</pubDate>
  <link></link>
  <title><![CDATA[JRF @ NATIONAL JALMA INSTITUTE OF LEPROSY AND OTHER MYCOBACTERIAL DISEASES]]></title>
  <description><![CDATA[
<p>NATIONAL JALMA INSTITUTE OF LEPROSY AND OTHER MYCOBACTERIAL DISEASES</p>

<p>(INDIAN COUNCIL OF MEDICAL RESEARCH)</p>

<p>P.O BOX 101,<br />Dr. M. Miyazaki Marg,<br />Tajganj, Agra - 282001</p>

<p>Applications are invited for a walk-in interview to be held in the Seminar Hall of the on 15th November, 2013, 9:30 am for temporary positions of JRF, Lab Technician and Field attendant in a ICMR funded project entitled "Elucidating the strain differentiation and transmission dynamics of M. leprae through simple sequence repeats ISSR-PCR marker"</p>

<p>1. JRF (one Post)</p>

<p>    Essential qualification: Candidates with M.Sc/IVI.Tech or equivalent degree in any life science related subjects with UGC-CSIR/ICMR/DBT-Net qualified</p>

<p>    Desirable qualification: Experience in Molecular Biology/Computational Biology will be preferred.</p>

<p>    Age. Maximum 28 years as on 11.11.2013. Age relaxation as per GOI rules.</p>

<p>    Emoluments: Rs. 6,000 + 20% HRA per Month</p>

<p>2. Lab Technician (One Post)</p>

<p>    Essential Qualification: 12th with DMLT/B.SCA4.SC in Life sciences</p>

<p>    Desirable qualification: Experience in Molecular Biology/Computational Biology will be preferred.</p>

<p>    Age: Maximum 30 years as on 11.11.2013. Age relaxation as per GOI rules.</p>

<p>    Emoluments: Rs13,760/ Per Month</p>

<p>3. Field Attendant (One Post)</p>

<p>Essential Qualification: 10th Pass</p>

<p>Desirable Qualification: Experience in field work</p>

<p>Age: Maximum 28 years as on 11.11.2013. Age relaxation as per GOI rules.</p>

<p>Emoluments: Rsl2,040l Per Month</p>

<p>Terms: posts are purely temporary. Appointment will be initially made for a period of one (01) year and may be extended further based on the performance of the candidate up to completion of the project.</p>

<p>Application &amp; Selection procedure: candidates have to appear in the walk-in-interview in person along with an application/CV on plain paper giving details of at educational qualificationq experience and submit photocopies of relevant documents at the time of interview. Selection will be based on the performance of the candidate in the interview' Candidates will not be sent any interview call letter separately. No TA/DA will be paid to the candidate for appearing in the interview. selection is not possible without appearing in the interview. All candidates must report by 9:00am on the date of interview. Advance copy of CV may be sent to m.sarathipartha@gmail.com</p>

<p>Advertisement: http://www.jalma-icmr.org.in/P_S_M_advertisment.pdf</p>
]]></description>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/news/view/40416/5700-year-old-human-genome</guid>
	<pubDate>Thu, 19 Dec 2019 11:22:18 -0600</pubDate>
	<link>https://bioinformaticsonline.com/news/view/40416/5700-year-old-human-genome</link>
	<title><![CDATA[5700 year-old human genome !]]></title>
	<description><![CDATA[<p>A Landmark in genomics, scientists have done something that hasn't been done ever.</p><p>Scientists have reconstructed the genome of an ancient human who lived nearly 5,700 years ago in Southern Denmark from the birch pitch- an ancient tar-like substance.</p><p>By sequencing the sample, researchers not only discovered the ancient human DNA but also microbial DNA reflecting the oral microbiome of the person who chewed the pitch, along with plant and animal DNA that could be the recent<span> meal she might have consumed.</span></p><p><span style="font-size: 12.8px;">The DNA sample is comparable in quality to well-preserved teeth and skull bones. The DNA suggests that the chewer was a female, most likely with dark skin, dark brown hair and blue eyes.</span></p><div><p><a href="https://www.nature.com/articles/s41467-019-13549-9?fbclid=IwAR0FPk0Cl25YjHVdcfK4tqFhCsPx00SCSMUwlU6zNwMDNrKi1QynwtJKDfE" target="_blank">https://www.nature.com/articles/s41467-019-13549-9</a></p><p><img src="https://i.kinja-img.com/gawker-media/image/upload/c_scale,f_auto,fl_progressive,q_80,w_800/ykcvh491evenyvlrjb9r.jpg" width="800" height="450" alt="image" style="border: 0px;"></p><p>Artistic reconstruction. (Tom Bj&ouml;rklund)</p><p>More at&nbsp;<a href="https://gizmodo.com/scientists-reconstruct-lola-after-finding-her-dna-in-1840481633">https://gizmodo.com/scientists-reconstruct-lola-after-finding-her-dna-in-1840481633</a></p></div>]]></description>
	<dc:creator>Jit</dc:creator>
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/7815/post-doc-in-systems-genetics</guid>
  <pubDate>Wed, 08 Jan 2014 19:23:37 -0600</pubDate>
  <link></link>
  <title><![CDATA[Post-doc in Systems Genetics]]></title>
  <description><![CDATA[
<p>Gagneur lab at Gene Center, Ludwig-Maximilians-Universitaet, Munich, Germany</p>

<p>Deadline for applications : January 15, 2014.</p>

<p>Description :</p>

<p>We seek a talented and motivated post-doc to develop computational methods for inferring the molecular basis of genetic diseases by integration of personal omics data. Research topics include: identifying causal mutations of rare disease patients by meta-analysis; inferring disease-causing molecular pathways from genotype, human phenotypes, and omics profile of patient-derived cell lines; and causal inference from longitudinal omics studies of patients. The developed methods will be applied to analyze data from our medical collaborators.</p>

<p>Candidates must either hold a PhD in computational biology or bioinformatics, or hold a PhD in physics, statistics, or applied mathematics with practical experience with high-dimensional data analysis. Experience in quantitative genetics is a plus. Applicants must have a proven publication record and an interest for translational research.</p>

<p>The Gagneur lab is a young, lively and multidisciplinary group with a research focus on systems genetics and gene regulation. It is located at the Gene Center of the LMU (University of Munich), an interdisciplinary institution whose 16 independent research groups investigate the regulation of gene expression at all levels - from the underlying molecular mechanisms to the biological system. The institute is located on the biomedical research campus Munich-Grosshadern, offering a dynamic, interactive and internationally oriented research environment. The dynamism of Munich and the proximity of the Alps provide an excellent quality of life.</p>

<p>The salary is according to the TV-L (German academic salary scale).<br />Applications including a cover letter, CV, and references must be sent by January 15th 2014 to Julien Gagneur (gagneur@genzentrum.lmu.de)</p>

<p>About the lab: http://www.gagneur.genzentrum.lmu.de</p>
]]></description>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/news/view/40789/complete-genome-sequence-of-wuhan-seafood-market-pneumonia-virus-is-out</guid>
	<pubDate>Fri, 31 Jan 2020 02:36:59 -0600</pubDate>
	<link>https://bioinformaticsonline.com/news/view/40789/complete-genome-sequence-of-wuhan-seafood-market-pneumonia-virus-is-out</link>
	<title><![CDATA[Complete genome sequence of Wuhan seafood market pneumonia virus is out !]]></title>
	<description><![CDATA[<p>Wuhan-Hu-1 claimed at least 40 lives and infected at least 1300 others in China. Cases are now being reported from Thailand, Singapore, Malaysia, South Korea, Japan, Vietnam, Nepal, France, Australia and even as far as the US.&nbsp;On Jan 10 2020, while news of the first fatality was barely trickling in, the <a href="https://www.ncbi.nlm.nih.gov/nuccore/MN908947">29,903 letters</a> constituting the viral genome from an affected individual in Wuhan had already been elucidated (even though a few corrections were made subsequently). All the viral genome sequences from affected individuals are very very close to each other. Several are identical and none has more than 5 differences (99.983% similarity). This strongly suggests that transmission into humans came from a single pointed source and happened very recently, between Sep-Dec 2019.</p><p>Check out the detail at https://www.ncbi.nlm.nih.gov/nuccore/MN908947</p>]]></description>
	<dc:creator>Jit</dc:creator>
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