<?xml version='1.0'?><rss version="2.0" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:georss="http://www.georss.org/georss" xmlns:atom="http://www.w3.org/2005/Atom" >
<channel>
	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/17176?offset=1280</link>
	<atom:link href="https://bioinformaticsonline.com/related/17176?offset=1280" rel="self" type="application/rss+xml" />
	<description><![CDATA[]]></description>
	
	<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/videolist/watch/4043/what-is-bioinformatics</guid>
	<pubDate>Wed, 28 Aug 2013 06:53:05 -0500</pubDate>
	<link>https://bioinformaticsonline.com/videolist/watch/4043/what-is-bioinformatics</link>
	<title><![CDATA[What is Bioinformatics?]]></title>
	<description><![CDATA[<iframe src="http://player.vimeo.com/video/71581534?byline=0" width="" height="" frameborder="0" webkitAllowFullScreen allowFullScreen></iframe>Illustration and Animation: Rachel Robinson Script: Tiffany Trent Voice-over: Kris Monger Sound: Glisten Carefully by Guennadi Malyshevski]]></description>
	
</item>
<item>
	<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>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/researchlabs/view/40881/liu-lab</guid>
  <pubDate>Tue, 04 Feb 2020 06:27:02 -0600</pubDate>
  <link></link>
  <title><![CDATA[Liu Lab]]></title>
  <description><![CDATA[
<p>Shirley is a computational biologist with expertise in cancer epigenetics. Her research focuses on algorithm development and integrative mining from big data generated on microarrays, massively parallel sequencing, and other high throughput techniques to model the specificity and function of transcription factors, chromatin regulators and lncRNAs in tumor development, progression, drug response and resistance.</p>

<p>https://liulab-dfci.github.io/software/</p>
]]></description>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/videolist/watch/4271/may-17-2013-differential-network-analysis</guid>
	<pubDate>Wed, 04 Sep 2013 16:22:28 -0500</pubDate>
	<link>https://bioinformaticsonline.com/videolist/watch/4271/may-17-2013-differential-network-analysis</link>
	<title><![CDATA[May 17, 2013 - Differential Network Analysis]]></title>
	<description><![CDATA[<iframe width="" height="" src="https://www.youtube-nocookie.com/embed/BvD6SkZRw9w" frameborder="0" allowfullscreen></iframe>Steve Horvath presents Differential Network Analysis at the UCLA Human Genetics/Biostatistics Network Course]]></description>
	
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/4353/project-fellow-alagappa-university</guid>
  <pubDate>Sat, 07 Sep 2013 14:24:13 -0500</pubDate>
  <link></link>
  <title><![CDATA[Project Fellow @ Alagappa University]]></title>
  <description><![CDATA[
<p>Advertisement for the post of project Fellow in UGC project</p>

<p>Project Fellow – One Post</p>

<p>Duration: Three Years</p>

<p>Fellowship : Rs.14, 000/- per month + HRA</p>

<p>Walk-in-interview: 16th Sept, 2013 at 10.00 am</p>

<p>Venue : Department of Bioinformatics, Alagappa University</p>

<p>Eligible candidates can attend walk in interview for the post of Project Fellow in UGC supported project entitled “Shape and chemical feature based 3D- Pharmacophore Model generation, Virtual Screening and MESP studies to identify Potential Leads for Antifungal Azoles”</p>

<p>Interested candidates may apply to Dr. Sanjeev Kumar Singh, Principal Investigator, Department of Bioinformatics, Karaikudi with their Curriculum Vitae along with the copies of the certificates in proof of their educational qualification and experience at skysanjeev@gmail.com</p>

<p>Qualification:</p>

<p>PG Degree in Bioinformatics / Chemistry/ Molecular Biology/ Biotechnology / Biophysics / Biochemistry / Life Sciences/ Pharmacy with minimum of 55% marks in the PG examinations</p>

<p>Desirable:</p>

<p>Research experience in Molecular modeling and CADD will be given preference. UGC-NET/ CSIR-JRF qualified candidates will get preference.</p>

<p>The posts are purely on temporary basis. No TA/DA will be paid for attending the interview.</p>

<p>Advertisement: http://www.alagappauniversity.ac.in/files/news_files/new%20advt-UGC-16sept,13.doc</p>
]]></description>
</item>
<item>
	<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>
</item>
<item>
	<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>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/blog/view/43084/frequently-used-bioinformatics-tools-for-viral-genome-analysis</guid>
	<pubDate>Wed, 23 Jun 2021 07:40:41 -0500</pubDate>
	<link>https://bioinformaticsonline.com/blog/view/43084/frequently-used-bioinformatics-tools-for-viral-genome-analysis</link>
	<title><![CDATA[Frequently used bioinformatics tools for viral genome analysis !]]></title>
	<description><![CDATA[<p><strong>IVA: accurate de novo assembly of RNA virus genomes.</strong><br /> Hunt M, Gall A, Ong SH, Brener J, Ferns B, Goulder P, Nastouli E, Keane JA, Kellam P, Otto TD.<br /> Bioinformatics. 2015 Jul 15;31(14):2374-6. doi: <a href="http://bioinformatics.oxfordjournals.org/content/31/14/2374.long">10.1093/bioinformatics/btv120</a>. Epub 2015 Feb 28.</p><p><a href="http://www.nature.com/nmeth/journal/v9/n1/full/nmeth.1814.html"><strong>Adapter sequences</strong></a>:<br /> <strong>Optimal enzymes for amplifying sequencing libraries.</strong><br /> Quail, M. a et al. Nat. Methods 9, 10-1 (2012).</p><p><a href="http://genome.cshlp.org/content/early/2012/01/12/gr.131383.111"><strong>GAGE</strong></a>:<br /> <strong>GAGE: A critical evaluation of genome assemblies and assembly algorithms.</strong><br /> Salzberg, S. L. et al. Genome Res. 22, 557-67 (2012).</p><p><a href="http://www.biomedcentral.com/1471-2105/14/160"><strong>KMC</strong></a>:<br /> <strong>Disk-based k-mer counting on a PC.</strong><br /> Deorowicz, S., Debudaj-Grabysz, A. &amp; Grabowski, S. BMC Bioinformatics 14, 160 (2013).</p><p><a href="http://genomebiology.com/2014/15/3/R46"><strong>Kraken</strong></a>:<br /> <strong>Kraken: ultrafast metagenomic sequence classification using exact alignments.</strong><br /> Wood, D. E. &amp; Salzberg, S. L. Genome Biol. 15, R46 (2014).</p><p><a href="http://genomebiology.com/2004/5/2/r12"><strong>MUMmer</strong></a>:<br /> <strong>Versatile and open software for comparing large genomes.</strong><br /> Kurtz, S. et al. Genome Biol. 5, R12 (2004).</p><p><strong>R</strong>:<br /> <strong>R: A language and environment for statistical computing.</strong><br /> R Core Team (2013). R Foundation for Statistical Computing, Vienna, Austria. URL <a href="http://www.R-project.org/">http://www.R-project.org/</a>.</p><p><a href="http://nar.oxfordjournals.org/content/39/9/e57"><strong>RATT</strong></a>:<br /> <strong>RATT: Rapid Annotation Transfer Tool.</strong><br /> Otto, T. D., Dillon, G. P., Degrave, W. S. &amp; Berriman, M. Nucleic Acids Res. 39, e57 (2011).</p><p><a href="http://bioinformatics.oxfordjournals.org/content/25/16/2078.abstract"><strong>SAMtools</strong></a>:<br /> <strong>The Sequence Alignment/Map format and SAMtools.</strong><br /> Li, H. et al. Bioinformatics 25, 2078-9 (2009).</p><p><a href="http://bioinformatics.oxfordjournals.org/content/early/2014/04/12/bioinformatics.btu170"><strong>Trimmomatic</strong></a>:<br /> <strong>Trimmomatic: A flexible trimmer for Illumina Sequence Data.</strong><br /> Bolger, A. M., Lohse, M. &amp; Usadel, B. Bioinformatics 1-7 (2014).</p>]]></description>
	<dc:creator>Neel</dc:creator>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/4706/junior-research-fellow-iit</guid>
  <pubDate>Sat, 21 Sep 2013 18:04:50 -0500</pubDate>
  <link></link>
  <title><![CDATA[Junior Research Fellow @ IIT]]></title>
  <description><![CDATA[
<p>Applications are invited from the citizens of India for filling up the following temporary position for the sponsored project undertaken in the Department of Biosciences and Bioengineering of this Institute. The position is temporary initially for a period of  1 Year  and tenable only for the duration of the project. The requisite qualification &amp; experience etc. are given below:<br /> <br />Project Code, Project Title &amp; Funding Agency<br />13DST016 : "Studies on the component of mimivirus DNA replication machinery" (Department of Science &amp; Technology)<br /> <br />Position &amp; Salary	<br />Junior Research Fellow (1 Post )<br />Consolidated salary <br /> Rs.16000/- p.m. + HRA<br />Qualification	<br />MSc or MTech or BTech or BE in one of the following branches with first class-Biochemistry, Microbiology, genetic Engineering, Biotechnology, Medical Microbiology, Bioinformatics, life sciences etc.<br />Job Profile	<br />Project involves virus culturing and purification, cloning, protein purification and measurement of helicase, primase, nuclease, translocase activities using various methods. Person should be highly motivated and some experience in cloning and protein purification is desirable. Experience in handling insect cell lines will be an added advantage.</p>

<p>More at http://www.ircc.iitb.ac.in/IRCC-Webpage/rnd/RecruitmentGenerateCircular.jsp?srno=2013086</p>
]]></description>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/43329/postdoc-position-at-kiel-university-germany</guid>
  <pubDate>Sat, 28 Aug 2021 01:16:55 -0500</pubDate>
  <link></link>
  <title><![CDATA[Postdoc position at Kiel University, Germany]]></title>
  <description><![CDATA[
<p>In the Genomic Microbiology Group of Prof. Tal Dagan at the Institute<br />of Microbiology at Kiel University, Germany, a</p>

<p>Postdoc position (m/w/d)</p>

<p>in the field of computational evolutionary microbiology is available<br />for an initially limited period of 36 months at the earliest possible<br />date. The weekly working time corresponds to 100% of full employment<br />(If the legal requirements under collective bargaining law are met, the<br />tariff grouping is carried out up to pay scale 13 TV-L. The obligation<br />to teach amounts to 4 hours.</p>

<p>The Genomic Microbiology Group research interests are focused on<br />microbial genome evolution with an emphasis on the study of lateral gene<br />transfer. In our research we use both computational and experimental<br />approaches (see www.uni-kiel.de/genomik). The position offers the<br />opportunity to develop an independent research profile within the group<br />research focus. The successful applicant is expected to be involved<br />in teaching of bioinformatics and molecular evolution, including the<br />development of teaching materials (lectures/exercises/short videos).</p>

<p>Your profile:<br />· Doctoral or PhD degree in Molecular Evolution, Bioinformatics or<br />related fields.<br />· Knowledge and experience in programming (e.g., Python) and<br />biostatistical analysis (e.g., with R or MatLab).<br />· Any of the following expertise is an advantage: the analysis of<br />genomic or transcriptomic data, phylogenetic reconstruction,<br />comparative genomics.<br />· Good oral and written communication skills in English.<br />· Ability to teach in German is an advantage (alternatively, an<br />indication to do so from the 2nd year on).<br />· Skills and motivation to communicate and interact with other<br />scientists.<br /> <br />The Christian-Albrechts-University sees itself as a modern and<br />cosmopolitan employer. We welcome your application regardless of your age,<br />gender, cultural and social background, religion, ideology, disability<br />or sexual identity. We promote equality of the sexes.</p>

<p>The Christian-Albrechts-University is committed to the employment of<br />people with disabilities. Preference will be given to applications from<br />severely handicapped persons and persons of equal standing, provided<br />they are suitable.</p>

<p>We expressly welcome applications from people with a migration background.</p>

<p>For enquiries regarding the position, teaching obligations and research<br />topic please contact Prof. Tal Dagan: tdagan@ifam.uni-kiel.de.</p>

<p>Applications should be submitted by email to Mrs. Haacks<br />(dhaacks@ifam.uni-kiel.de) as a single PDF and include: (1) a letter of<br />motivation (max 1 page, Arial 11, line spacing 1.15), (2) CV, (3) PhD<br />certificate. Please use 'GMG postdoc application - [your name]'<br />as a subject.</p>

<p>Please, refrain from sending us application photos.</p>

<p>Application deadline:  August 31 2021 or until the position is<br />filled. Interviews will take place during September/October 2021. The<br />planned starting date for the position is flexible (but in 2021).</p>
]]></description>
</item>

</channel>
</rss>