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	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/32465?offset=1210</link>
	<atom:link href="https://bioinformaticsonline.com/related/32465?offset=1210" rel="self" type="application/rss+xml" />
	<description><![CDATA[]]></description>
	
	
<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/researchlabs/view/5747/dbbrowser-attwood-lab</guid>
  <pubDate>Fri, 18 Oct 2013 10:48:19 -0500</pubDate>
  <link></link>
  <title><![CDATA[DbBrowser: Attwood Lab]]></title>
  <description><![CDATA[
<p>DbBrowser: Attwood Lab research concerns protein sequence analysis, primarily using the method of protein 'fingerprinting'. DbBrowser: Attwood Lab maintain a diagnostic fingerprint database (PRINTS), one of the founding partner of InterPro. We also design software to display sequence and structural data in visually-striking ways (e.g., Ambrosia, CINEMA); DbBrowser: Attwood Lab are building re-usable software components to create semantically integrated bioinformatics applications through UTOPIA, including a 'smart' PDF reader that links bioinformatics databases and tools directly with scientific articles (Utopia Documents); and have developed a number of tools for automatic annotation and text mining (e.g., MINOTAUR, PRECIS, METIS). </p>

<p>More @ http://www.bioinf.manchester.ac.uk/dbbrowser/index.php</p>
]]></description>
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<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/36456/alpaca-a-hybrid-strategy-for-assembly-of-genomic-dna-shotgun-sequencing-reads</guid>
	<pubDate>Mon, 30 Apr 2018 04:38:40 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/36456/alpaca-a-hybrid-strategy-for-assembly-of-genomic-dna-shotgun-sequencing-reads</link>
	<title><![CDATA[ALPACA: A hybrid strategy for assembly of genomic DNA shotgun sequencing reads.]]></title>
	<description><![CDATA[<p><span>ALPACA requires Celera Assembler 8.3 or later. It is recommended to build Celera Assembler from source. (Why? The pre-built binaries CA_8.3rc1 and CA8.3rc2 will work for any large data set.&nbsp;</span></p>
<p><span>Detail paper at&nbsp;https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-017-3927-8</span></p><p>Address of the bookmark: <a href="https://github.com/VicugnaPacos/ALPACA" rel="nofollow">https://github.com/VicugnaPacos/ALPACA</a></p>]]></description>
	<dc:creator>Seema Singh</dc:creator>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/5946/bioinformatics-tata-memorial-centre-navi-mumbai</guid>
  <pubDate>Mon, 28 Oct 2013 10:40:25 -0500</pubDate>
  <link></link>
  <title><![CDATA[Bioinformatics @ TATA MEMORIAL CENTRE, NAVI MUMBAI]]></title>
  <description><![CDATA[
<p>TATA MEMORIAL CENTRE<br />ADVANCED CENTRE FOR TREATMENT, RESEARCH AND EDUCATION IN CANCER<br />KHARGHAR, NAVI MUMBAI – 410210</p>

<p>No. ACTREC/Advt./ 72 /2013</p>

<p>WALK IN INTERVIEW</p>

<p>1. JRF*<br />Genome-wide RNAi screen with human pooled tyrosine kinase shRNA libraries in head and neck squamous call carcinoma (HNSCC) cell lines<br />DBT A/C No. 3071, Dr. Amit Dutt</p>

<p>2. JRF<br />IRB Project ACTREC Funds<br />Dr. Amit Dutt</p>

<p>3. RA<br />Defining the cancer genome of Head and Neck Squamous Cell Carcinoma (HNSCC) with SNP arrays and next generation sequencing technology<br />A/C No. 2895, Dr. Amit Dutt</p>

<p>Duration of the Project: One year from the date of appointment, or as and when project terminates.</p>

<p>Consolidated Salary: RA : Rs. 40,000/- p.m.<br />JRF* (DBT): Rs. 20,800/- p.m.<br />JRF: Rs. 16,000/- p.m.<br />Date &amp; Time: 6th November, 2013, at 10.00 a.m.</p>

<p>Venue: Conference Room</p>

<p>Minimum Qualifications and Experience:</p>

<p>RA: The ideal applicant should have a PhD in a relevant field. He/she should have a strong computational biology background, with demonstrated experience in coding using Perl, Python, Java or C++. He/she should be familiar with working in unix enviromnent, devising computational algorithms for data analysis, statistical data analysis in R and matlab and database programming using MySQL. Hands on experience in analyzing high throughput data would be an added advantage.</p>

<p>JRF* (DBT project): M.Sc. in Life Sciences or M.Tech in Biotechnology with good academic record (Minimum of 60% aggregate). Valid UGC-CSIR/DBT/ICMR JRF qualification and laboratory experience in molecular biology. Previous experience in molecular biology and animal tissue culture with high throughput platforms and ability to work with a large team would be desirable.</p>

<p>JRF (ACTREC project): M.Sc. in Life Sciences or M.Tech in Biotechnology with good academic record (Minimum of 60% aggregate). Minimum 2 yrs experience in molecular biology and animal tissue culture with high throughput platforms and ability to work with a large team is essential.</p>

<p>*M.Sc. degree obtained after a one year course will not be considered.</p>

<p>Candidates fulfilling above requirements should send their application by e-mail to<br />‘careers.duttlab@gmail.com. in the format given below so as to reach on or before<br />4th November, 2013.</p>

<p>Advertisement:</p>

<p>http://www.actrec.gov.in/data%20files/2013/AD-RA-JR-TECHN-6-NOV.pdf</p>
]]></description>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/37915/dna-nucleotide-counter</guid>
	<pubDate>Fri, 12 Oct 2018 04:37:01 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/37915/dna-nucleotide-counter</link>
	<title><![CDATA[DNA Nucleotide Counter]]></title>
	<description><![CDATA[<p style="margin: 2px 5px 4px 6px; color: #000011; font-size: 12px; font-style: normal; font-weight: 400; text-align: justify;">DNA Nucleotide Counter is delivered in a DNA Baser package together with other free molecular biology tools.<span>&nbsp;</span><a href="http://www.dnabaser.com/download/biology-tools-package-download-count.html">Download</a><span>&nbsp;</span>the package and double click it. The programs inside the package will be extracted to the destination folder (specified by you). Go to the destination folder&nbsp;and double click the program you want to use.</p>
<p style="margin: 2px 5px 4px 6px; color: #000011; font-size: 12px; font-style: normal; font-weight: 400; text-align: justify;">It<span>&nbsp;</span><a href="http://www.dnabaser.com/download/install-anywhere.html">installs in any computer</a><span>&nbsp;</span>even if you don't have administrator rights!</p><p>Address of the bookmark: <a href="http://www.dnabaser.com/download/DNA-Counter/index.html" rel="nofollow">http://www.dnabaser.com/download/DNA-Counter/index.html</a></p>]]></description>
	<dc:creator>Neel</dc:creator>
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<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/6012/project-junior-research-fellow-ccmb</guid>
  <pubDate>Fri, 01 Nov 2013 10:38:22 -0500</pubDate>
  <link></link>
  <title><![CDATA[Project Junior Research Fellow @ CCMB]]></title>
  <description><![CDATA[
<p>Temporary Project positions available purely on temporary basis - Oct/2013</p>

<p>1. Project Junior Research Fellow / Project Assistant</p>

<p>Last Date: 11th Nov 2013</p>

<p>Qualification B.Tech (Comp. Sci.), B.Tech/M.Tech (Bioinformatics), MCA,  M.Sc. (Mathematics/Statistics)</p>

<p>Desirable Qualifications: Programming in FORTRAN/ C /PERL, Web application technologies</p>

<p>Upper Age limit 28</p>

<p>Rs.12000 / Rs.16000 (as sanctioned by the funding agency)</p>

<p>General terms and conditions:</p>

<p>    Positions are purely temporary and co-terminus with the project.</p>

<p>    HRDG (CSIR) prevailing guidelines are applicable these positions.</p>

<p>    All categories of applicants are required to submit online application.</p>

<p>    Enhancement of stipend to Project JRF to Project SRF will be with the due recommendation of Principal Investigator and approval of the Director on the evaluation of the 3 member Standing Committee consisting of Chairperson at the level of Chief Scientist, Coordinator of the JRFs/RAs/PDFs and the Principal Investigator of the Project.</p>

<p>    The age relaxation as per HRDG (CSIR) norms: SC/ST/OBC/Women/Physically Handicapped persons – five years.</p>

<p>    The Stipend normally be fixed at Rs.22000/- for Research Associates/Post Doc. Fellows. However, a selected RA/PDF may be placed in the higher start of stipend if there is ample justification and such recommendation is made by the Selection Committee. Based on the recommendation with justification by the PI and approval of the Director, person getting stipend at lower rate may be elevated to higher rate subject to availability of the funds in the project.</p>

<p>    Recruitment will be based on initial screening based on qualifications and experience criteria and also based on suitability of the candidates to the nature of research project. This screening will be followed by written test followed / interview. After completing this process, candidates will be shortlisted and appointed in specific project subjects as and when appropriate positions become available. The pool of selected candidates will be valid for six months.</p>

<p>    Remunerations indicate are maximum admissible and will depend upon the availability of funds and subject to conditions applicable to projects from different funding agencies at the time of recruitment.</p>

<p>Apply : http://www.ccmb.res.in/positions/projects/temp_positions.php</p>

<p>Form download : http://www.ccmb.res.in/positions/projects/oct-2013/pdf_download.php</p>
]]></description>
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<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/40566/the-el-sherif-group-chair-of-developmental-biology-department-of-biology-phd-position</guid>
  <pubDate>Sun, 19 Jan 2020 10:06:37 -0600</pubDate>
  <link></link>
  <title><![CDATA[The El-Sherif Group, Chair of Developmental Biology, Department of Biology - PhD Position]]></title>
  <description><![CDATA[
<p>El-Sherif lab studies how genes are regulated to mediate patterning in Development. We use live and super-resolution imaging in addition to computational modeling to understand transcription dynamics at the single-cell level in three model systems: the fruit fly Drosophila melanogaster, the beetle Tribolium castaneum, and embryonic bodies derived from embryonic mouse stem cells.</p>

<p>In this project, you will use single-molecule techniques to label mRNA and DNA in (live and fixed) Drosophila embryos and fixed embryonic bodies. You will also use super-resolution microscopy to visualize protein condensates. Co-localization dynamics reflecting DNA-protein bindings and DNA looping events will be detected, analyzed, and used to test computational models of gene transcription.</p>

<p>Qualification:<br />MSc degree (or equivalent) in Biology, Biophysics, or Bioengineering</p>

<p>Experience in one or more of these areas: (1) molecular cloning, (2) imaging, (3) image analysis (using Matlab/Python/Java), (4) microfluidics, and (5) computational modeling.</p>

<p>How to Apply?<br />Send (1) your CV, (2) summary of research experience, and (3) email addresses of at least 2 references to ezzat.el-sherif@fau.de. Title your email ‘Transcription PhD Position’.</p>

<p>salary Grade.: E13<br />Total Time: 3 Jahre<br />Start: 01.01.2020.<br />End: 31.3.2020.</p>

<p>Address:<br />Dr. El-Sherif, Ezzat<br />Department Biologie<br />Professur für Zoologie (Entwicklungsbiologie) (Prof. Dr. Klingler)<br />Telefon 09131/85-28068, Fax 09131/85-28040, E-Mail: ezzat.el-sherif@fau.de</p>
]]></description>
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<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/researchlabs/view/6233/edwards-lab</guid>
  <pubDate>Sun, 10 Nov 2013 15:07:08 -0600</pubDate>
  <link></link>
  <title><![CDATA[Edwards Lab]]></title>
  <description><![CDATA[
<p>We study the evolutionary biology of birds and relatives, combining field, museum and genomics approaches to understand the basis of avian diversity, evolution and behavior. Our guiding approaches include population genetics, which provides a quantitative framework for studying speciation, geographic variation and genome evolution; systematics, which acknowledges that the focal species of any study has relatives that are behaviorally and ecologically no less interesting; and natural history, which gives meaning to the genes and genomic patterns we study.</p>

<p>Lab page: http://www.oeb.harvard.edu/faculty/edwards/index.html</p>
]]></description>
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<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/41825/hnadock-a-nucleic-acid-docking-server-for-modeling-rnadna%E2%80%93rnadna-3d-complex-structures</guid>
	<pubDate>Thu, 04 Jun 2020 23:19:07 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/41825/hnadock-a-nucleic-acid-docking-server-for-modeling-rnadna%E2%80%93rnadna-3d-complex-structures</link>
	<title><![CDATA[HNADOCK: a nucleic acid docking server for modeling RNA/DNA–RNA/DNA 3D complex structures]]></title>
	<description><![CDATA[<p><span>The HNADOCK server is to predict the binding complex structure between two nucleic acid molecules through a hierarchical docking algorihtm of an FFT-based global search strategy and an intrinsic scoring function for nucleic acid interactions. Users are required to provide the three-dimensional (3D) structures of the two molecules to be docked.&nbsp;</span></p><p>Address of the bookmark: <a href="http://huanglab.phys.hust.edu.cn/hnadock/" rel="nofollow">http://huanglab.phys.hust.edu.cn/hnadock/</a></p>]]></description>
	<dc:creator>Poonam Mahapatra</dc:creator>
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<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/6559/ai-cadd-project-kerela-university</guid>
  <pubDate>Tue, 19 Nov 2013 17:48:15 -0600</pubDate>
  <link></link>
  <title><![CDATA[Ai-CADD Project @ Kerela University]]></title>
  <description><![CDATA[
<p>Applications are invited for the following Positions in the AiCADD project funded by MHRD Govt of India</p>

<p>Last Date for Submitting Application: 25th November 2013</p>

<p>1. Senior Scientist: (01 position)<br />Pay Scale: Rs.40, 000/-<br />Qualifications:  PhD/ Post Doctoral with Experience in CADD</p>

<p>2. Junior Scientist (10 positions)<br />Pay Scale: Rs. 22,000/-<br />Qualifications: MPhil / Masters Degree in Bioinformatics / Computational Biology / CADD / Ayurveda</p>

<p>3. Technical Assistant (01+01 positions)<br />Pay Scale: Rs.12,000/-<br />Qualifications: 1. BSc Computer Science/ MCA<br />Qualifications: 2. MSc Biotechnology / MSc Microbiology </p>

<p>4. Programmer (01 position)<br />Pay Scale: Rs.20,000/-<br />Qualifications: MSc Computer Science/ MCA / B Tech (Experience in MATLAB, C, C++) Industrial experience is desirable</p>

<p>5. Teaching Assistant (03 positions)<br />Pay Scale: Rs.10,000/-<br />Qualifications: MSc in Bioinformatics </p>

<p>6. Administration Assistant (02 positions)<br />Pay Scale: Rs.8,000/-<br />Qualifications: Degree + PGDCA</p>

<p>The Selection process comprises of written test and interview. Positions are purely temporary (initially for the period of one year) and co-terminus with the project. For more details mail to: cbi.uok [at] gmail.com</p>

<p>More detail @ https://sites.google.com/site/centreforbioinformatics/announcements/applicationsinvitedforapplicationforai-caddproject</p>
]]></description>
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<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/44495/exrec-exclusion-of-recombined-dna</guid>
	<pubDate>Wed, 27 Mar 2024 20:48:26 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/44495/exrec-exclusion-of-recombined-dna</link>
	<title><![CDATA[ExRec: Exclusion of Recombined DNA]]></title>
	<description><![CDATA[<p><span>ExRec (Exclusion of Recombined DNA) is a Python pipeline that implements the four-gamete test to filter out recombined DNA sites from up to thousands of DNA sequence loci. The pipeline consists of five standalone applications: the first two convert folders of NEXUS or PHYLIP files into the standard input file for the main program that conducts the four-gamete filtering procedures. The pipeline outputs recombination-filtered data in concatenated NEXUS and PHYLIP formats and a tab-delimited table containing descriptive statistics for all loci and the results. This software also allows the user to output the longest non-recombined sequence blocks from loci (current best practice) or randomly select non-recombined blocks from loci (a newer approach). Two other applications in the package convert the recombination-filtered data into single-locus NEXUS or PHYLIP files. The ExRec package can thus facilitate species delimitation, species tree, and historical demography studies by providing loci that better meet the no-recombination assumption in coalescent-based analyses.</span></p>
<p><span>Link to the article:&nbsp;</span><a href="https://academic.oup.com/bioinformaticsadvances/article/3/1/vbad174/7455250?searchresult=1" target="_blank">https://academic.oup.com/bioinformaticsadvances/article/3/1/vbad174/7455250?searchresult=1</a><br><br><span>Link to the software:</span><br><a href="https://github.com/Sammccarthypotter/ExRec" target="_blank">https://github.com/Sammccarthypotter/ExRec</a></p><p>Address of the bookmark: <a href="https://github.com/Sammccarthypotter/ExRec" rel="nofollow">https://github.com/Sammccarthypotter/ExRec</a></p>]]></description>
	<dc:creator>LEGE</dc:creator>
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