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	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/41991?offset=510</link>
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	<description><![CDATA[]]></description>
	
	
<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/4314/postdocs-positions-in-computer-science-in-helsinki-finland</guid>
  <pubDate>Fri, 06 Sep 2013 10:11:19 -0500</pubDate>
  <link></link>
  <title><![CDATA[PostDocs positions in computer science in HELSINKI, FINLAND]]></title>
  <description><![CDATA[
<p>Several university departments in the Helsinki region, Finland, are looking for postdoctoral researchers in the field of computer science and information technology. Jobs are available at:<br />·       Helsinki Institute for Information Technology HIIT, Aalto University and University of Helsinki, http://www.hiit.fi<br />·       Department of Computer Science, University of Helsinki, http://www.cs.helsinki.fi<br />·       Department of Information and Computer Science, Aalto University, http://ics.aalto.fi<br />·       Department of Computer Science and Engineering, Aalto University, http://cse.aalto.fi<br />·       Department of Mathematics and Statistics, University of Helsinki, http://mathstat.helsinki.fi/english/<br /> <br />Why Helsinki?<br />The collaborating Aalto University and University of Helsinki form a leading hub of computer science and modelling, including Machine learning, Data mining, Algorithms, Computational Logic, Cloud computing, Distributed computing, Human-centric ubiquitous ICT, Bioinformatics, etc.<br />Helsinki region is a safe, pleasant and attractive place to live in, with well-functioning services such as public transport etc. Finland has a comprehensive social security and health care system, including exceptionally good parental leaves, and children's day care services.<br /> <br />Positions are offered in:<br />Algorithm engineering (String Algorithms group)<br />Algorithmic bioinformatics (Genome-Scale Algorithmics group)<br />Automated reasoning and search, especially propositional logic (Computational Logic group)<br />Computational astrophysics and/or data analysis (Computational Methods and Data Analysis for Astrophysics group)<br />Computational biology and statistical methods in bioinformatics (Computational Systems Biology group)<br />Computational creativity and data mining (Discovery group)<br />Dynamic and large-scale networked systems (Data Communications Software group)<br />Intelligent multimodal information access (Content-Based Image and Information Retrieval Group)<br />Machine learning and neuroscience (Statistical Machine Learning group)<br />Machine learning for structured data (Kernel Machines, Pattern Analysis and Computational Biology group)<br />Machine learning methods for infectious disease epidemiology (Bayesian Statistics Group)<br />Probabilistic modeling and machine learning (Complex Systems Computation group)<br />Statistical machine learning (Statistical Machine Learning group)<br />Analysing ubiquitous sensor data (HIIT-Wide Focus Area)<br />Interactive visualization (HIIT-Wide Focus Area)<br />Affective computing and BCI (HIIT-Wide Focus Area)<br />Intelligent user interfaces and/or recommender systems (HIIT-Wide Focus Area)<br />Information retrieval and HCI (HIIT-Wide Focus Area)<br />Machine learning and data analysis, especially information retrieval, HCI, text and context data (HIIT-Wide Focus Area)<br />Probabilistic modeling and data analysis for bioinformatics (HIIT-Wide Focus Area)</p>

<p>More at http://www.hiit.fi/postdoc-call-2013</p>
]]></description>
</item>

<item>
  <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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<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/4351/cpcri-kasaragod-bioinformatics-pa</guid>
  <pubDate>Sat, 07 Sep 2013 14:15:53 -0500</pubDate>
  <link></link>
  <title><![CDATA[CPCRI Kasaragod Bioinformatics PA]]></title>
  <description><![CDATA[
<p>CENTRAL PLANTATION CROPS RESEARCH INSTITUTE<br />(Indian Council of Agricultural Research)<br />KASARAGOD -671 124, KERALA</p>

<p>WALK-IN-INTERVIEW</p>

<p>Walk-in-test cum interview for selection to the following temporary assignments sanctioned under the DBT sponsored adhoc time bound research scheme entitled "Establishment of a Sub-DIC" will be held at CPCRl, Kudlu PO, Kasaragod District, Kerala -6711 24 on the date and time indicated against each:</p>

<p>Project Assistant</p>

<p>    Qualification: Essential: Masters Degree in Bioinformatics / B.Tech Degree in Bioinformatics</p>

<p>    Desirable: 1. Experience in the field of bioinformatics<br />    2. M.Phil / Doctoral degree in the field</p>

<p>    Date of interview 24.09.2013 at 10.00 a.m.</p>

<p>Trainee – 2 Posts</p>

<p>    Essential: Masters Degree in Bioinformatics or B.Tech Degree in Bioinformatics.</p>

<p>    Date of interview 25.09.2013 at 10.00 a.m.</p>

<p>Studentship – 2 Posts</p>

<p>    Essential Final Year/Semester students of MSc Bioinformatics or B.Tech Bioinformatics</p>

<p>    Date of Interview 25.09.2013 at 10.00 a.m.</p>

<p>The candidates fulfilling the above eligibility criteria for Item No.1 &amp; II shall apply online and walk-in for a written test and interview at CPCRI, Kasaragod on the respective dates at 10.00 a.m. The candidates for Studentship should submit the application through their Head of the Department. They shall also bring with them a set of bio data and original certificates in proof of age, educational qualifications, experience etc. Candidates who fail to produce the original of the Degree/PO certificates OR provisional certificate will not be allowed to attend the test / interview. Those who are qualified in written test will only be permitted to attend the interview.</p>

<p>No TA will be paid for the journey for attending the interview.</p>

<p>Advertisement: http://www.cpcri.gov.in/images/images/opportunity/sep4_opp.pdf</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/opportunity/view/4654/la-trobe-university-melbourne-australia</guid>
  <pubDate>Fri, 20 Sep 2013 13:05:14 -0500</pubDate>
  <link></link>
  <title><![CDATA[La Trobe University, Melbourne, Australia]]></title>
  <description><![CDATA[
<p>La Trobe University, Melbourne, Australia</p>

<p>An exciting opportunity exists for a highly motivated and enthusiastic bioinformatics researcher to work in the Exosome, Secretome and Systems Biology laboratory of Dr Suresh Mathivanan. This position is funded through the National Institutes of Health (NIH) USA, to study the role of extracellular RNA or ExRNA in intercellular communication.</p>

<p>The successful applicant will be involved in collaborative bioinformatics research with more than 30 American Universities/Institutes.  The ExRNA consortium is a multi-institute USD 17 million funded program which has 5 primary aims: to understand the biogenesis of ExRNA (vesicles and non-vesicles), to explore the use of ExRNA in biomarker research, to establish a reference profile of ExRNA in various disease conditions, to explore the role of ExRNA in therapeutic purposes and to manage the generated data through a reference portal.  The bioinformatics component is critical in managing and analysing the data generated by the entire consortium.  The researcher is required to contribute to the management and perform the analysis of ExRNA data.</p>

<p>The candidate to succeed, you will possess:</p>

<p>Experience in the analysis and modelling of data, including the capacity to integrate data from a range of sources and of uneven quality.</p>

<p>Evidence of experience in research and of the ability to work effectively under limited supervision or independently.</p>

<p>A record of contribution to publications, conference papers and/or reports, or professional or technical contributions which provide evidence of research potential.</p>

<p>Completion of a doctoral degree in bioinformatics or biostatistics with a focus on transcriptomic data will be highly regarded.</p>

<p>Preference will be given to applicants with competence in programming (JavaScript, Perl/Python), any web-based applications (PHP, ZOPE) and relational databases (MySQL).</p>

<p>Closing date:  30 September 2013</p>

<p>Position Enquiries: Dr Suresh Mathivanan (s.mathivanan@latrobe.edu.au)</p>

<p>More at http://www.mathivananlab.org/</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>
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<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/researchlabs/view/4656/pandey-lab</guid>
  <pubDate>Fri, 20 Sep 2013 13:19:18 -0500</pubDate>
  <link></link>
  <title><![CDATA[Pandey Lab]]></title>
  <description><![CDATA[
<p>The Pandey Lab at Johns Hopkins University is a Systems Biology lab that combines molecular biology, analytical chemistry and computational biology with various "Omics" technologies including genomics and proteomics to understand signaling pathways and to identify therapeutic targets and biomarkers in a number of cancers.</p>

<p>More at http://pandeylab.igm.jhmi.edu/</p>

<p>http://scholar.google.com/citations?user=OhuG0FcAAAAJ&amp;hl=en</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/4873/vveks-lab</guid>
  <pubDate>Thu, 26 Sep 2013 11:11:39 -0500</pubDate>
  <link></link>
  <title><![CDATA[Vvek's Lab]]></title>
  <description><![CDATA[
<p>Broad Area of Research: RNA biology (microRNA, lncRNA), Stem cells, Functional genomics, Epigenomics and Cancer</p>

<p>RNAs, especially non-coding RNAs (such as microRNA, long ncRNAs) are recently identified to be very abundant in mammalian organisms and play some key roles in gene expression regulation, gene silencing, and also implicated in disease progression, stem cell pluripotency etc. Current research activities of our lab include analysis of expression pattern of ncRNAs by microarray and next-gen sequencing data and understanding the role of miRNAs or other regulatory RNAs in various diseases, especially cancer and validation by reporter assays (renilla/luciferase) and other experimental tools.</p>

<p>More @ http://vvekslab.in/index.html</p>
]]></description>
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<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>
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