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	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/26375?offset=1170</link>
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	<description><![CDATA[]]></description>
	
	
<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/researchlabs/view/8385/peng-lab</guid>
  <pubDate>Tue, 18 Feb 2014 13:53:46 -0600</pubDate>
  <link></link>
  <title><![CDATA[Peng Lab]]></title>
  <description><![CDATA[
<p>Peng Lab at Janelia Farm Research Campus, Howard Hughes Medical Institute focuses on data mining for bioinformatics and computational molecular biology, particularly, bioimage data mining and informatics. These bioimages include cellular and molecular images and related medical images. </p>

<p>* Analysis of Gene Expression Pattern Images: high-performance image analysis and mining for different model organisms, such as fruitfly, C. elegans, and mouse;<br />* Feature/Model Learning: developing algorithms and software</p>

<p>Location :Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, USA.</p>

<p>http://research.janelia.org/peng/</p>
]]></description>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/news/view/40204/iitm-tokyo-tech-joint-symposium</guid>
	<pubDate>Thu, 24 Oct 2019 10:30:25 -0500</pubDate>
	<link>https://bioinformaticsonline.com/news/view/40204/iitm-tokyo-tech-joint-symposium</link>
	<title><![CDATA[IITM-Tokyo Tech Joint Symposium]]></title>
	<description><![CDATA[<p>The IITM-Tokyo Tech Joint Symposium is a biannual international symposium held in Indian Institute of Technology Madras (IITM), India in collaboration with Tokyo Institute of Technology (Tokyo-Tech), Japan. During the symposium, experts in various domains of Bioinformatics gather from India and Japan under one roof to discuss and present their works. This provides an unique opportunity to the researchers and students to learn the frontiers and interact with eminent scientists in Bioinformatics. The 5th IITM - Tokyo Tech Joint Symposium titled "Current trends in Bioinformatics: Big data analysis, machine learning and drug design", will be held on 6th - 7th March 2020 in IITM, Chennai, India.</p><p>The symposium will focus on topics in the below mentioned areas.</p><p>Topics: Algorithms for biomolecular sequences / structures Bioinformatics databases and tools Protein function Structure based drug design Machine learning Deep learning Large scale data analysis Big Data NGS Analysis Protein interactions/network Molecular modelling/docking/screening Biomolecular structure and function More</p><p>Info: https://web.iitm.ac.in/bioinfo2/symposium2020/home</p>]]></description>
	<dc:creator>Jit</dc:creator>
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/8442/assistant-professor-king-saud-university-riyadh</guid>
  <pubDate>Fri, 21 Feb 2014 05:57:18 -0600</pubDate>
  <link></link>
  <title><![CDATA[Assistant Professor @ King Saud University Riyadh]]></title>
  <description><![CDATA[
<p>Qualifications: Candidates must have a Ph.D. and a strong background in Molecular and Cellular Biology, protein expression, FACS, or computational biology, and ability to work collaboratively.</p>

<p>This position will have a significant focus on providing analytical support for next generation sequencing data analysis – Exome-sequencing, Targetted sequencing as well as high-throughput genotyping on Illumina platform.</p>

<p>Job location:</p>

<p>Genome Research Chair<br />King Saud University, Riyadh-11451<br />KSA</p>

<p>Interested candidate may forward their CV to grcksu@gmail.com</p>
]]></description>
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/researchlabs/view/40882/troyanskaya-lab</guid>
  <pubDate>Tue, 04 Feb 2020 06:40:36 -0600</pubDate>
  <link></link>
  <title><![CDATA[Troyanskaya Lab]]></title>
  <description><![CDATA[
<p>The goal of our research is to interpret and distill this complexity through accurate analysis and modeling of molecular pathways, particularly those in which malfunctions lead to the manifestation of disease. We are inventing integrative methods for systems-level pathway modeling through integrative analysis of genome-scale datasets. We apply these approaches in studying challenging biological problems, such as how pathways function in diverse cell types and how they change dynamically.</p>

<p>https://function.princeton.edu/</p>
]]></description>
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/8466/srf-position-in-computational-systems-biology-computational-biology-group-iiit-delhi</guid>
  <pubDate>Sun, 23 Feb 2014 20:56:08 -0600</pubDate>
  <link></link>
  <title><![CDATA[SRF position in Computational Systems Biology Computational biology Group, IIIT-Delhi]]></title>
  <description><![CDATA[
<p>An opportunity to perform research in DST supported project that involves building of mathematical models to understand the functional relationship between circadian rhythms and memory formation under stressful condition.  In this project, mathematical model of circadian rhythms based on gene regulatory mechanisms will be unified with the mathematical model of calcium signal transduction pathway to understand and predict the formation of fear memory under stressful conditions. The research scholar will spend full time on this project to build new models and expected to contribute significantly to prepare the results for publication and presentation, and to contribute to grant proposals. </p>

<p>Required Qualifications: Masters in physics/chemistry/mathematics (or) MTech in bioengineering, chemical (or) Masters in any traditional field of science with outstanding performance throughout the program. Candidate should have cleared GATE/UGC-CSIR examinations. Applicant should have done basic mathematics courses like calculus, differential equations, numerical analysis etc in their degree program and have obtained good grades in those courses. Knowledge of MATLAB and C or at least one traditional programming language is absolutely necessary. Strong inclination to understand biological concepts is a must for this research work as this project is about modeling biological systems.     </p>

<p>Salary: A fixed salary of Rs 18000 PM including HRA will be paid. </p>

<p>Last date for application: This advertisement is open until suitable candidate is found for the project. </p>

<p>Preferred Qualifications:  - Expertise in dynamical systems theory, bifurcation theory, numerical simulations, parameter estimation. </p>

<p>Independence and high motivation for carrying out interdisciplinary research. - Excellent communication skills and ability to work independently. - Good working habits. </p>

<p>Interested candidates should submit both curriculum vitae and statement of interest in PDF format to sriramk@iiitd.ac.in and should clearly mention in the subject "Application for SRF".</p>
]]></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/researchlabs/view/12868/landry-lab</guid>
  <pubDate>Thu, 17 Jul 2014 14:33:57 -0500</pubDate>
  <link></link>
  <title><![CDATA[Landry Lab]]></title>
  <description><![CDATA[
<p>EVOLUTIONARY AND INTEGRATIVE CELL BIOLOGY</p>

<p>Our research is at the crossroad between cell biology, ecological genomics, systems biology, molecular evolution and population genetics. We study the architecture and evolution of protein and signalling networks.</p>

<p>More at http://landrylab.ibis.ulaval.ca/</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>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/researchlabs/view/8970/j-aires-de-sousa-research-group</guid>
  <pubDate>Wed, 12 Mar 2014 09:57:25 -0500</pubDate>
  <link></link>
  <title><![CDATA[J. Aires de Sousa Research Group]]></title>
  <description><![CDATA[
<p>We are involved in the development of methods and software in chemoinformatics. Current main projects are:</p>

<p>1.automatic learning of chemical reactivity and metabolism,<br />2.simulation of NMR spectra,<br />3.modelling of properties of ionic liquids, and<br />4.representation of molecular chirality.</p>

<p>More at http://joao.airesdesousa.com/</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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