<?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/30540?offset=1440</link>
	<atom:link href="https://bioinformaticsonline.com/related/30540?offset=1440" rel="self" type="application/rss+xml" />
	<description><![CDATA[]]></description>
	
	<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/opportunity/view/6715/research-associate-school-of-computational-and-integrative-sciences-under-jawaharlal-nehru-university</guid>
  <pubDate>Fri, 22 Nov 2013 19:06:44 -0600</pubDate>
  <link></link>
  <title><![CDATA[Research Associate@ School of Computational and Integrative Sciences under Jawaharlal Nehru University]]></title>
  <description><![CDATA[
<p>School of Computational and Integrative Sciences under Jawaharlal Nehru University, New Delhi invited applications for filling up 4 posts of Research Associates (RA) and Junior Research Fellow (JRF) (2 posts each)  purely on temporary basis, liable to be terminated at any time without prior notice or ceased/withdrawn by the funding agency. The vacancies are for a Department of Biotechnology, Government of India funded project entitled "Computational Core for Plant Metabolomics" (Project ID: 632) being administered by Prof Indira Ghosh. Interested candidates should send their applications till 13 December 2013.<br />Important Dates<br />Last Date for receipt of applications: 13 December 2013<br />Vacancy Details<br />Total Vacancies: 4 posts<br />Type of recruitment: Temporary<br />Sl. No.: 01<br />Name of the Post: Research Associate<br />No of Posts: 1 post<br />Remuneration: Rs.  23000 + 30%<br />Qualifications: PhD in Bioinformatics / computational biology / Biophysics / Physical Chemistry / Computer Science. Computational experience, proven by paper published, is a necessary qualification.<br /> Sl. No.: 02<br />Name of the Post: Research Associate<br />No of Posts: 1 post<br />Remuneration: Rs. 23000 + 30%<br />Qualifications: PhD in Computational Biology / Bioinformatics &amp; related subjects. Computational experience, proven by paper published, is a necessary qualification.<br />Sl. No.: 03<br />Name of the Post: Junior Research Fellow<br />No of Posts: 1 post<br />Remuneration: Rs. 12000 + 30%<br />Qualifications: M. Sc. / B. Tech. preferably in Computational Biology /Bioinformatics and related fields with experience in Website designing &amp; maintenance of Database.<br />Sl. No.: 04<br />Name of the Post: Junior Research Fellow<br />No of Posts: 1 post<br />Remuneration: Rs.  12000 + 30%<br />Qualifications: M. Sc. / MCA / B. Tech. preferably in Computational Biology / Computer science with experience in Programming in Java / Python, C++ etc &amp; designing of Database.<br />Selection Procedure: Selection will be done on the basis of candidates’ performance in the Interview.  <br />Candidates short-listed / selected for Interview will be informed through email only.<br />How to Apply: Interested eligible candidates should send their applications, in the prescribed format, along with their current CV by post to “Prof Indira Ghosh, Project Investigator,  Hall#6, School of Computational and Integrative Sciences,  Jawaharlal Nehru University,  New Delhi-110 067” so as to reach the concerned authority by 13 December 2013.<br />Name of the post applied for’ must be superscripted on the envelope containing the application.<br />NOTE: For the post of Research Associates, only those candidates who have submitted thesis are eligible to apply. However, salary will be provided as per DBT / DST guidelines (i.e. candidates who have qualified NET /BET / BINC will have higher pay scale).<br />Candidates interested to register for PhD may not apply for JRF.<br />More @ http://www.jnu.ac.in/Career/currentjobs.htm</p>
]]></description>
</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/opportunity/view/4653/human-genome-meeting-2014-geneva-switzerland</guid>
  <pubDate>Fri, 20 Sep 2013 12:36:44 -0500</pubDate>
  <link></link>
  <title><![CDATA[Human Genome Meeting 2014, Geneva, Switzerland]]></title>
  <description><![CDATA[
<p>The spectacular advances of the last few years resulted in the rapid analysis of the genome sequence of each individual. The biomedical world is now faced with the enormous challenges of assigning pathogenicity to each genomic variant, the functional analysis of the genome of each individual, and the accurate and detailed phenotypic characterization. Advances in these challenges are likely to fundamentally change the medical practice in a global scale.</p>

<p>This 2014 HUGO Meeting in Geneva will be a Forum for discussions on innovative approaches, and proposals to tackle the anticipated challenges.</p>

<p>Time : 27 April 2014 - 30 April 2014 </p>

<p>For enquiries, please email hugo2014@mci-group.com or visit www.hugo-international.org</p>

<p>More at http://www.hgm2014-geneva.org/</p>
]]></description>
</item>

<item>
  <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>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/researchlabs/view/4636/molecular-and-computational-biology-research-school</guid>
  <pubDate>Fri, 20 Sep 2013 09:01:18 -0500</pubDate>
  <link></link>
  <title><![CDATA[Molecular and Computational Biology Research School]]></title>
  <description><![CDATA[
<p>The ambition of the Molecular and Computational Biology Research School (MCB) is to create an attractive and stimulating training environment for PhD students in molecular and computational biology, both to better serve the needs for relevant training in the field, and to stimulate crossdiscipline developments in the research of the parties.</p>

<p>http://www.uib.no/rs/mcb</p>
]]></description>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/43323/biostarhandbook</guid>
	<pubDate>Fri, 27 Aug 2021 01:31:01 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/43323/biostarhandbook</link>
	<title><![CDATA[biostarhandbook]]></title>
	<description><![CDATA[<p>Nice book collection for bioinformatician ... highly recommended.</p><p>Address of the bookmark: <a href="https://www.biostarhandbook.com/" rel="nofollow">https://www.biostarhandbook.com/</a></p>]]></description>
	<dc:creator>Neel</dc:creator>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/researchlabs/view/4888/murray-coxs-genomicus-lab</guid>
  <pubDate>Thu, 26 Sep 2013 16:42:42 -0500</pubDate>
  <link></link>
  <title><![CDATA[Murray Cox's Genomicus Lab]]></title>
  <description><![CDATA[
<p>This group interested in modeling genome dynamics in following topics:</p>

<p>---how genetic variation is distributed within and between individuals, <br />---determining how this diversity changes over evolutionary time.</p>

<p>Hence, Cox group work at the interface between biology, statistics and computer science to address questions of outstanding biological importance through intrepretation of large genetic datasets.</p>

<p>Profile:<br />Associate Professor Murray Cox, <br />Inaugural Rutherford Fellow of the Royal Society of New Zealand,  Principal Investigator in the BioProtection Research Center and Associate Investigator in the Allan Wilson Center for Molecular Ecology and Evolution<br />Email : m.p.cox@massey.ac.nz<br />Webpage: http://massey.genomicus.com/index.html</p>
]]></description>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/researchlabs/view/44400/pevzner-lab</guid>
  <pubDate>Thu, 02 Nov 2023 05:39:26 -0500</pubDate>
  <link></link>
  <title><![CDATA[Pevzner Lab !]]></title>
  <description><![CDATA[
<p>The laboratory works on genome sequencing, immunoproteogenomics, antibiotics sequencing, and comparative genomics - computational technologies that enabled new applications and allowed scientists to attack biological problems that remained beyond the reach of previous techniques.</p>

<p>https://bioalgorithms.ucsd.edu/research4.html</p>
]]></description>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/videolist/watch/5380/04-informatics-approach-to-cancer-interview-with-dr-joel-saltz</guid>
	<pubDate>Mon, 07 Oct 2013 14:35:43 -0500</pubDate>
	<link>https://bioinformaticsonline.com/videolist/watch/5380/04-informatics-approach-to-cancer-interview-with-dr-joel-saltz</link>
	<title><![CDATA[04- Informatics Approach to Cancer - Interview with Dr. Joel Saltz]]></title>
	<description><![CDATA[<iframe width="" height="" src="https://www.youtube-nocookie.com/embed/8Kf5EP4LY7k" frameborder="0" allowfullscreen></iframe>For additional information visit http://www.cancerquest.org/joel-saltz-interview.

Dr. Joel Saltz is a Professor in the Departments of Pathology, Biostatistics and Bioinformatics, and Mathematics and Computer Science at
Emory University. Dr. Saltz's research on bioinformatics spans several disciplines.  One project involves applying computer analysis to medical imaging to yield better results for patients.  As an example, a computer program may able to help doctors detect small cancers in a CT scan or mammogram. 

In this interview segment, Dr. Saltz  discusses the informatics approach to cancer.

To learn more about cancer and watch additional interviews, please visit the CancerQuest website at http://www.cancerquest.org.]]></description>
	
</item>

</channel>
</rss>