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	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/31300?offset=670</link>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/news/view/39612/bioclues-and-pine-biotech-join-forces-to-advance-bioinformatics-in-india</guid>
	<pubDate>Fri, 14 Jun 2019 10:20:47 -0500</pubDate>
	<link>https://bioinformaticsonline.com/news/view/39612/bioclues-and-pine-biotech-join-forces-to-advance-bioinformatics-in-india</link>
	<title><![CDATA[Bioclues and Pine Biotech join forces to advance Bioinformatics in India]]></title>
	<description><![CDATA[<p><img src="https://edu.t-bio.info/wp-content/uploads/2019/06/PineBio-Bioclues.jpg" alt="Bioclues and Pine Biotech join forces" width="1280" height="720" style="border: 0px; border: 0px;">&nbsp;As a collaborative effort, the two organizations will help implement best practices in bioinformatics education across universities in Inida that have little to no experience in bioinformatics. The collaboration comes as Pine Biotech starts registrations for it's pilot program at Amity University in Kolkata, India.</p><p>To read more about this collaboration, visit:&nbsp;https://edu.t-bio.info/pine-biotech-joins-forces-with-the-bioclues-organization-to-promote-bioinformatics/</p>]]></description>
	<dc:creator>eliabrodsky</dc:creator>
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/researchlabs/view/4108/tijana-milenkovic-lab</guid>
  <pubDate>Fri, 30 Aug 2013 06:45:20 -0500</pubDate>
  <link></link>
  <title><![CDATA[Tijana Milenkovic Lab]]></title>
  <description><![CDATA[
<p>Complex networks and network mining: developing graph theoretic, mathematical, and computational algorithms for efficient extraction of function from topology of complex real-world networks, such as biological, social, and technological networks.</p>

<p>Computational and systems biology: studying the interplay between network topology and biological function, disease, and evolution in molecular (e.g., protein-protein interaction) networks.</p>

<p>Computational chemistry: protein folding; computational drug discovery and design.</p>

<p>Synthetic biology.</p>

<p>More at http://www.cse.nd.edu/~tmilenko/index.html</p>
]]></description>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/videolist/watch/4234/ncbi-psi-blast-tutorial</guid>
	<pubDate>Wed, 04 Sep 2013 11:46:06 -0500</pubDate>
	<link>https://bioinformaticsonline.com/videolist/watch/4234/ncbi-psi-blast-tutorial</link>
	<title><![CDATA[NCBI PSI-BLAST Tutorial]]></title>
	<description><![CDATA[<iframe width="" height="" src="https://www.youtube-nocookie.com/embed/T3kHEieyylk" frameborder="0" allowfullscreen></iframe>http:--www.biotechnology.jhu.edu-
Tutorial for PSI-BLAST, an extension of BLAST that uses matrix algebra. BLAST is a cornerstone bioinformatics tool at NCBI. BLAST is the
Basic Local Alignment Search tool and will protein and DNA sequences that
are related to a sequence that the user provides.]]></description>
	
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/41394/ngsymposium-in-computational-biology</guid>
  <pubDate>Mon, 09 Mar 2020 06:00:30 -0500</pubDate>
  <link></link>
  <title><![CDATA[NGSymposium in Computational Biology]]></title>
  <description><![CDATA[
<p>We have a great pleasure to invite you to the NGSymposium in Computational Biology to celebrate the 5th anniversary of the NGSchool Summer Schools. This international conference will make way for exchanging knowledge and experiences between experienced and early-stage researchers as well as bioinformaticians. The meeting will be held on 31.07 - 1.08.2020 in Warsaw. It will be a satellite event to the #NGSchool2020: Statistical Learning in Genomics. It will cover a wide range of topics from basic and applied biomedical sciences: bioinformatics, genomics, transcriptomics, computational biology, Machine Learning.</p>

<p>Registration of active participants will be open from February, 27 12 PM CET to April 17, 23:59 CET. In registration forms you will be asked for providing us with some basic information about yourself. You will also be able to submit your abstract. You can save your registration form after filling it partially and come back later to supply more data e.g. upload an abstract. Your registration will be completed only with the payment of the registration fee reaching our accounts - please make sure to transfer the money in advance!</p>

<p>Registration of passive participants will be open after closing of registration of active participants.</p>

<p>Details an registration: https://ngschool.eu/conference/</p>
]]></description>
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/4352/jrf-bharathidasan-university</guid>
  <pubDate>Sat, 07 Sep 2013 14:20:03 -0500</pubDate>
  <link></link>
  <title><![CDATA[JRF @ BHARATHIDASAN UNIVERSITY]]></title>
  <description><![CDATA[
<p>Department of Bioinformatics<br />School of Life Sciences<br />BHARATHIDASAN UNIVERSITY,<br />TIRUCHIRAPPALLI-620 024</p>

<p>WALK-IN-INTERVIEW FOR JUNIOR RESEARCH FELLOWSHIP</p>

<p>Project title: Structural and Functional Evolution of Bacterial ADP-ribosylation Superfamily–A Special Emphasis for Engineering Immunotoxins from Binary toxin A Funding Agency: Life Science Research Board, Defence Research and Development Organization, New Delhi</p>

<p>Tenure of the project: Three years or till the end of the project period.</p>

<p>Position: Junior Research Fellow (1 no.)</p>

<p>Essential qualification: First class in M.Sc. in Genomics/Biotechnology/ Microbiology/ Biochemistry/Life Sciences</p>

<p>Desirable qualification: Experience in an area relevant (Molecular Microbiology, Protein engineering and Structural Bioinformatics) to the project.</p>

<p>Fellowship: Rs. 16, 000 per month plus HRA as per University rule.</p>

<p>Upper age limit: 28 years</p>

<p>Date of interview: 16-09-2013</p>

<p>Venue of interview: Department of Bioinformatics, Bharathidasan University, Tiruchirappalli -620 024, Tamil Nadu</p>

<p>The above post is purely temporary and will be terminated with three month notice. The Terms and the condition of the appointment shall be governed according to DRDO, Govt. of India. The eligible candidates will bring their original certificates and documents at the time of interview. No TA/DA will be paid for attending the interview.</p>

<p>Dr. P. CHELLAPANDI<br />Principal Investigator,<br />Department of Bioinformatics,<br />Bharathidasan University,<br />Tiruchirappalli -620 024, Tamil Nadu</p>

<p>Advertisement: http://www.bdu.ac.in/tender_list.php</p>
]]></description>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/pages/view/42275/frequent-parameters-for-bioinformatics-tools</guid>
	<pubDate>Tue, 27 Oct 2020 19:42:32 -0500</pubDate>
	<link>https://bioinformaticsonline.com/pages/view/42275/frequent-parameters-for-bioinformatics-tools</link>
	<title><![CDATA[Frequent parameters for bioinformatics tools !]]></title>
	<description><![CDATA[<div><div>Third party executable parameters and options.</div><div>&nbsp;</div><div>Trimmomatic</div><div>&nbsp;</div><div>&ldquo;ILLUMINACLIP:...:2:30:10&rdquo;</div><div>&ldquo;LEADING:15&rdquo;</div><div>&ldquo;TRAILING:15&rdquo;</div><div>&ldquo;SLIDINGWINDOW:4:20&rdquo;</div><div>&ldquo;MINLEN:20&rdquo;</div><div>&ldquo;TOPHRED33&rdquo;</div><div>&nbsp;</div><div>Filtlong</div><div>--min_length 500</div><div>--min_mean_q 85</div><div>--min_window_q 65</div><div>&nbsp;</div><div>FastQ Screen</div><div>--aligner bowtie2' (bwa for PacBio)</div><div>--subset 1000 (for PacBio)</div><div>&nbsp;</div><div>SPAdes</div><div>--careful</div><div>--disable-gzip-output</div><div>--cov-cutoff auto</div><div>--phred-offset 33</div><div>&nbsp;</div><div>HGAP</div><div>Pbalign.task_options.min_accuracy: 70</div><div>Pbalign.task_options.no_split_subreads: false</div><div>Genomic_consensus.task_options.min_confidence: 40</div><div>falcon_ns.task_options.HGAP_GenomeLength_str:</div><div>6000000</div><div>Pbcoretools.task_options.read_length: 0</div><div>Genomic_consensus.task_options.use_score: 0</div><div>Pbalign.task_options.min_length: 50</div><div>Pbalign.task_options.algorithm_options: --minMatch 12</div><div>--bestn 10 --minPctSimilarity 70.0</div><div>Pbalign.task_options.hit_policy: randombest</div><div>Pbcoretools.task_options.other_filters: rq &gt;= 0.7</div><div>Pbalign.task_options.concordant: false</div><div>Genomic_consensus.task_options.min_coverage: 5</div><div>falcon_ns.task_options.HGAP_SeedCoverage_str: 30</div><div>falcon_ns.task_options.HGAP_AggressiveAsm_bool: false</div><div>Genomic_consensus.task_options.algorithm: best</div><div>falcon_ns.task_options.HGAP_SeedLengthCutoff_str: -1</div><div>Genomic_consensus.task_options.diploid: false</div><div>&nbsp;</div><div>MeDuSa</div><div>-random 100</div><div>&nbsp;</div><div>Prokka</div><div>--usegenus</div><div>--force</div><div>--addgenes</div><div>--rfam</div><div>--rawproduct</div><div>&nbsp;</div><div>cmsearch (taxonomy, 16S)</div><div>--rfam</div><div>--noali</div><div>&nbsp;</div><div>blastn (taxonomy, 16S)</div><div>-evalue 1E-10</div><div>&nbsp;</div><div>blastn (MLST)</div><div>-ungapped</div></div><div><div>-dust no</div><div>-evalue 1E-20</div><div>-word_size 32</div><div>-culling_limit 2</div><div>-perc_identity 95</div><div>&nbsp;</div><div>blastp (VF)</div><div>-culling_limit 2</div><div>&nbsp;</div><div>RGI (ABR)</div><div>--input_type contig</div><div>&nbsp;</div><div>bowtie2 (mapping)</div><div>--sensitive</div><div>&nbsp;</div><div>minimap2 (mapping)</div><div>-a</div><div>-x map-ont</div><div>&nbsp;</div><div>samtools mpileup (SNP&nbsp;detection)</div><div>-uRI</div><div>&nbsp;</div><div>bcftools call (SNP detection)</div><div>--variants-only</div><div>--skip-variants indels</div><div>--output-type v</div><div>--ploidy 1</div><div>-c</div><div>&nbsp;</div><div>SNPsift filter (SNP detection)</div><div>"( QUAL &gt;= 30 ) &amp; (( na FILTER ) | (FILTER = 'PASS')) &amp;</div><div>( DP &gt;= 20 ) &amp; ( MQ &gt;= 20 )"</div><div>&nbsp;</div><div>SNPeff ann (SNP detection)</div><div>-nodownload</div><div>-no-intron</div><div>-no-downstream</div><div>-no SPLICE_SITE_REGION</div><div>-upDownStreamLen 250</div><div>&nbsp;</div><div>bcftools consensus</div><div>(phylogenetic tree)</div><div>--haplotype 1</div><div>&nbsp;</div><div>fasttreemp</div><div>-nt</div><div>-boot 100</div><div>&nbsp;</div><div>roary</div><div>-e</div><div>-n</div><div>-cd 100</div><div>-g 100000</div></div>]]></description>
	<dc:creator>BioStar</dc:creator>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/file/view/4482/bioinformatics-definitions-and-applications</guid>
	<pubDate>Thu, 12 Sep 2013 15:04:36 -0500</pubDate>
	<link>https://bioinformaticsonline.com/file/view/4482/bioinformatics-definitions-and-applications</link>
	<title><![CDATA[Bioinformatics definitions and applications !!!]]></title>
	<description><![CDATA[<p>There have been long discussion amongst several specialized/expert educator regarding bioinformatics arena, but everyone explain bioinformatics with their own view. I tried to explain it with a cartoon. Hope you all will like it.</p>]]></description>
	<dc:creator>Jit</dc:creator>
	<enclosure url="https://bioinformaticsonline.com/file/download/4482" length="49464" type="image/gif" />
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	<guid isPermaLink="true">https://bioinformaticsonline.com/blog/view/42664/common-bioinformatics-interview-questions</guid>
	<pubDate>Sat, 23 Jan 2021 06:07:50 -0600</pubDate>
	<link>https://bioinformaticsonline.com/blog/view/42664/common-bioinformatics-interview-questions</link>
	<title><![CDATA[Common Bioinformatics Interview Questions !]]></title>
	<description><![CDATA[<p>The possibility of an interview for a bioinformatics position in the life sciences may be very disquieting, but the same concerns emerge time and again in my experience. So, it is exceedingly worthwhile to plan for future bioinformatics interview questions. Doing this will really give you the advantage in obtaining the position.</p><p>The following 5 questions are those that I have heard many times during the job-search process. There is no reason for not planning responses in such situations.</p><p><strong>1. Tell Us About Yourself</strong><br />This is a very typical opener in interviews. It's a perfect question to ask, and getting something planned will really help you concentrate and ease in the conversation. However, you need to make sure that your response is applicable to the job you're interviewing.<br />It's probably better to keep your answer professional. Try to include these in the answer as well: where did your love of science and bioinformatics come from? How the heck did you end up in this field? Why programming and scripting ?</p><p><strong>2. What is your plan for your bioinformatics career? / How do you look at yourself in five years? / How are your personal objectives to accomplish these goals / What are the plan for your research fundings ?</strong></p><p>Your CV/resume has already impressed the selection panel if you have been invited for an interview. The questions from the bioinformatics interview team provide an incentive for you to market yourself and illustrate the work in question with the most appropriate knowledge.</p><p><strong>3. What do you understand about the job description/What would your suggested research path be if you were a successful candidate?</strong><br />Summarize the specifics of the advertised bioinformatics position in your own words. Follow on with some suggestions of how you want to extend your research and create your own projects within the community.</p><p><strong>4. Will you work as a group or do you want to work on your own?</strong><br />This requirement can vary from jobs to job, so when addressing, be alert. A company/research PI may need a bioinformatician that is able to work on a single project autonomously, or they may need a person who can help direct and organize a team. In your response, refer to the job description.</p><p><strong>5. What particular methods have you used to date with your experiments?</strong><br />You might have experience with all the laboratory techniques described in the job description, but stress the ones you highly experienced with. Highlight your professional abilities and stress that you are extremely capable of mastering new techniques with others ...</p><p>At the end of the day, remember that you're questioning the jury as well as they're interviewing you. You will ought to think of any questions you would like the interview panel to pose. This indicates that you have done your homework and serious about the position.</p><p>All the best for your future job interview.</p>]]></description>
	<dc:creator>Jit</dc:creator>
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/4575/hiv-phd-and-msc-research-positions</guid>
  <pubDate>Mon, 16 Sep 2013 18:55:44 -0500</pubDate>
  <link></link>
  <title><![CDATA[HIV PhD and MSc Research Positions]]></title>
  <description><![CDATA[
<p>SANBI are looking to recruit two MSc students and a PhD student who are interested in implementing a computational biology approach to explore HIV’s glycan shield. Successful candidates for the MSc should hold an honours degree in physics, computer science or biological sciences while PhD applicants should hold an honours degree and a MSc in one or more of physics, computer science or biological sciences.</p>

<p>As these positions are funded by the South African National Research Foundation (NRF) priority will be given to South African citizens and permanent residents however exceptional applicants who do not fulfil these criteria may be considered.</p>

<p>Applications including a CV outlining your experience together with a cover letter detailing why you are a suitable candidate should be sent to simon_at_sanbi.ac.za by 30th September 2013.</p>

<p>More @ http://www.sanbi.ac.za/hiv-phd-and-msc-research-positions/</p>
]]></description>
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/researchlabs/view/43044/kanthida-lab</guid>
  <pubDate>Wed, 28 Apr 2021 02:27:22 -0500</pubDate>
  <link></link>
  <title><![CDATA[Kanthida Lab !]]></title>
  <description><![CDATA[
<p>Research Interest: </p>

<p>Bioinformatics </p>

<p>High-throughput and high-dimensional data analysis</p>

<p>Microbiome data analysis (Main focus)</p>

<p>Next-generation and third-generation sequencing data analysis for genomics</p>

<p>Gene expression data analysis</p>

<p>Machine learning for biological data</p>

<p>Biomarkers identification </p>

<p>Database and web-application for biological data</p>

<p>More at <br />https://sites.google.com/mail.kmutt.ac.th/kanthida-k/home?authuser=0</p>
]]></description>
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