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	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/26332?offset=1190</link>
	<atom:link href="https://bioinformaticsonline.com/related/26332?offset=1190" rel="self" type="application/rss+xml" />
	<description><![CDATA[]]></description>
	
	
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/42165/bioinformatics-scientistresearch-software-engineer-at-university-of-dundee-dundee-united-kingdom</guid>
  <pubDate>Wed, 26 Aug 2020 10:31:25 -0500</pubDate>
  <link></link>
  <title><![CDATA[Bioinformatics Scientist/Research Software Engineer at University of Dundee Dundee, United Kingdom]]></title>
  <description><![CDATA[
<p>We are recruiting for an exceptional individual to join us as a computational scientist, bioinformatician, or (research) software engineer with an interest in interactive data analysis platforms for biology and medicine within our Jalview (www.jalview.org) research software engineering team.</p>

<p>More at https://www.jobs.dundee.ac.uk/fe/tpl_uod01.asp?s=4A515F4E5A565B1A&amp;jobid=104342,2382988671&amp;key=147934117&amp;c=99413415238921&amp;pagestamp=sesxbbuyifokdsfygf</p>

<p>Last date: 30th August 2020</p>

<p>Informal enquiries about this position may be made to Prof. Geoff Barton (gjbarton@dundee.ac.uk) or Dr Jim Procter (jprocter@dundee.ac.uk). To find out more about Jalview research software engineering team please visit www.jalview.org and www.compbio.dundee.ac.uk</p>
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/researchlabs/view/864/the-laboratoire-de-genomique-fonctionelle</guid>
  <pubDate>Sun, 14 Jul 2013 13:03:18 -0500</pubDate>
  <link></link>
  <title><![CDATA[The Laboratoire de genomique fonctionelle]]></title>
  <description><![CDATA[
<p>One persistent challenge of post genome biology remains the determination of the functions of all potential genes. In mammals this task is formidable given that a single gene can produce numerous protein isoforms through alternative pre-mRNA splicing. Protein isoforms from a single gene can have diverse, and in some cases antagonistic, functions. AS plays a pivotal biological role in protein diversity and developmental regulation. It is now believed that AS occurs in up to 74% of human genes, making it more of a rule than an exception.</p>

<p>Link @ http://lgfus.ca/public/</p>
]]></description>
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/42227/two-faculty-positions-at-national-taiwan-university-taipei-taiwan</guid>
  <pubDate>Thu, 22 Oct 2020 04:53:12 -0500</pubDate>
  <link></link>
  <title><![CDATA[Two Faculty Positions at National Taiwan University, Taipei, Taiwan]]></title>
  <description><![CDATA[
<p>The Department of Agronomy at National Taiwan University, Taipei, Taiwan,<br />invites applications for two full-time faculty positions beginning August<br />1, 2021 at the rank of Assistant Professor, Associate Professor or<br />Professor in Biometry and Bioinformatics and Plant Breeding and Genetics,<br />respectively.</p>

<p>A qualified candidate should hold a Ph.D. in a relevant field including<br />Agronomy, Statistics, Bioinformatics, Plant Breeding, Plant Genetics or<br />Quantitative Genetics. For the position in Biometry and Bioinformatics, the<br />applicants capable of teaching fundamental statistics/bioinformatics<br />courses or with experience in crop science are preferable; for Plant<br />Breeding and Genetics, the applicants capable of teaching fundamental plant<br />breeding courses, with experience in crop breeding, or training in<br />quantitative genetics are preferred.</p>

<p>The application package should include two letters of reference and five<br />printed copies of the following documents (1) curriculum vitae, (2)<br />publication list, (3) undergraduate and graduate transcripts if applying<br />for the Assistant Professorship, (4) a photocopy of the Ph.D. diploma, (5)<br />teaching plan and course outline or syllabus (6) research proposal, (7) a<br />cover letter indicating the rank to apply, and one representative original<br />research article which was published by the applicant being the 1st or<br />corresponding author in an SCI peer-reviewed journal within 5 years (after<br />August 1, 2016); a copy of doctoral dissertation can be the representative<br />article if applying for the Assistant Professorship; (8) reprints of the<br />selected publications published within 7 years (after August 1, 2014).</p>

<p>The application package should mail to the Chair, Dr. Li-yu Daisy Liu<br />(lyliu@ntu.edu.tw), in the Department of Agronomy, National Taiwan<br />University, No. 1, Section 4, Roosevelt Road, Taipei 10617, Taiwan, before<br />December 15, 2020 for full consideration.</p>
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/researchlabs/view/42326/edanchin-lab</guid>
  <pubDate>Thu, 19 Nov 2020 08:00:07 -0600</pubDate>
  <link></link>
  <title><![CDATA[Edanchin Lab]]></title>
  <description><![CDATA[
<p>My main topics of interest are:</p>

<p>The impact of non tree-like evolution such as horizontal gene transfers and hybridization on species biology<br />Evolution and adaptation of animals in the absence of sexual reproduction and the underlying mechanisms<br />Genomic signatures of adaptation to a parasitic life-style</p>

<p>More at https://edanchin.org/</p>
]]></description>
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/1149/system-biologist-at-millennium-software-productions-india-private-limited</guid>
  <pubDate>Fri, 19 Jul 2013 09:43:53 -0500</pubDate>
  <link></link>
  <title><![CDATA[System Biologist at Millennium Software productions India Private Limited]]></title>
  <description><![CDATA[
<p>Millennium Software productions India Private Limited</p>

<p>www.cytosolve.com</p>

<p>Post - System Biologist</p>

<p>Job Description: Role of system biology is to design quantitative models of bimolecular networks and to study interactions between the components of biological systems, and how these interactions give rise to the function and behavior of that system (Enzyme, metabolites and pathway).</p>

<p>Qualification : B.Tech or M.Sc in Bioinformatics</p>

<p>Required Skills:</p>

<p>1) Basic knowledge of cell signaling pathways, chemical/enzyme kinetics, and differential equation based modeling approach.<br />2) Previous laboratory experience could be an advantage<br />3) Good Communication skills.</p>

<p>santhiya.ram@mproductions.com and 044-42946555.</p>
]]></description>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/pages/view/42809/bioinformatics-in-africa-part2-kenya</guid>
	<pubDate>Sat, 06 Feb 2021 13:23:54 -0600</pubDate>
	<link>https://bioinformaticsonline.com/pages/view/42809/bioinformatics-in-africa-part2-kenya</link>
	<title><![CDATA[Bioinformatics in Africa: Part2 - Kenya]]></title>
	<description><![CDATA[<p>International Livestock Research Institute (ILRI):</p><p>Under&nbsp; &nbsp;a&nbsp; &nbsp;NEPAD&nbsp; &nbsp;initiative,&nbsp; &nbsp;the&nbsp; &nbsp;Biosciences&nbsp; &nbsp;Eastern&nbsp; &nbsp;and&nbsp; &nbsp;Central&nbsp; &nbsp;Africa&nbsp; &nbsp;(BECA)&nbsp; (www.biosciencesafrica.org) was established at ILRI. BECA consists of a hub, regional nodes, and&nbsp; other affiliated laboratories and partner institutes. A state of the art joint Bioinformatics Platform&nbsp; (www.becabioinfo.org), whose overall goal is to provide a coherent and powerful bioinformatics&nbsp; infrastructure for use by all scientists in East and central Africa. The Platform goal requires both&nbsp; physical and intellectual developments that together provide researchers with access to diverse&nbsp; infrastructure in a wide&shy;area network, thereby addressing four important aspects of bioinformatics:&nbsp;</p><p>1) Science: bioinformatics tools for data integration and visualization, standardization of data&nbsp; formats and data analysis strategies, and distribution of analysis tasks over local&shy; and widearea networks are in development;&nbsp;</p><p>2)&nbsp; Bioinformatics Support Facility: provides assistance and custom programming to projects&nbsp; and those unable to establish a bioinformatics support function intrinsic to their project due&nbsp; to shortage of qualified personnel or lack of funding;&nbsp;</p><p>3) Hardware Platform: provide a powerful high performance computing platform capable of&nbsp; handling the largest analysis needs for projects;&nbsp;</p><p>4) Bioinformatics Training for East and central African scientists: While many Web&shy;based&nbsp; tools are available to the wet&shy;lab researcher, the Web is not well suited for tasks beyond&nbsp; single&shy;sequence annotation. Researchers need to become productive in a server&shy;based Unix&nbsp; environment with its wealth of scripting and automation tools. Even at an entry&shy;level, this&nbsp; can be an intimidating task if proper guidance is not available.</p><p>International&nbsp;Centre&nbsp;of&nbsp;Insect&nbsp;Physiology&nbsp;and&nbsp;Ecology&nbsp;(ICIPE): ICIPE&rsquo;s&nbsp;research&nbsp;focus&nbsp;is&nbsp;on&nbsp;insect&nbsp;biology,&nbsp;in&nbsp;order&nbsp;to&nbsp;improve&nbsp;the&nbsp;wellbeing&nbsp;of&nbsp;the&nbsp;peoples&nbsp;of&nbsp;the&nbsp; tropics&nbsp;through&nbsp;insect&nbsp;science.&nbsp;There&nbsp;is&nbsp;a&nbsp;commitment&nbsp;to&nbsp;utilise&nbsp;contemporary&nbsp;science&nbsp;in&nbsp;order&nbsp;to&nbsp; limit&nbsp;the&nbsp;impact&nbsp;of&nbsp;disease&nbsp;vectors,&nbsp;and&nbsp;agricultural&nbsp;pests.&nbsp;The&nbsp;understanding&nbsp;of&nbsp;the&nbsp;mechanisms&nbsp; associated&nbsp;with&nbsp;behaviour&nbsp;(e.g.&nbsp;attraction&nbsp;and&nbsp;repellency)&nbsp;is&nbsp;crucial.&nbsp;ICIPE&nbsp;seeks&nbsp;to&nbsp;enhance&nbsp;its&nbsp; bioinformatics&nbsp;capacity&nbsp;in&nbsp;order&nbsp;to&nbsp;support&nbsp;data&nbsp;from&nbsp;various&nbsp;EST&nbsp;projects&nbsp;designed&nbsp;to&nbsp;gain&nbsp;insights&nbsp; into&nbsp;the&nbsp;insect&nbsp;ecology&nbsp;and&nbsp;plant&nbsp;pathogen&nbsp;interactions&nbsp;though&nbsp;studies&nbsp;of&nbsp;metabolic&nbsp;pathways&nbsp; associated&nbsp;with&nbsp;production&nbsp;of&nbsp;all&nbsp;elochemicals.&nbsp;</p><p>Long&shy;term training activities:</p><p>Kenyatta University: An introductory course in Bioinformatics is offers to MSc Biotechnology&nbsp; students. This comprises of 35 hours of lectures and practicals.</p><p>University of Nairobi: A centre for Biotechnology and Bioinformatics (CEBIB), which will offer&nbsp; postgraduate training (diplomas, MSc and PhD) in areas of biotechnology and bioinformatics has&nbsp; recently been launched. Other universities in Kenya, including Egerton, Maseno and the Jomo Kenyatta University of&nbsp; Agriculture and Technology offer introductory courses to undergraduates in biomedical sciences. In addition, under the BECA platform MSc and PhD fellowships are being made available for&nbsp; Bioinformatics students. ILRI is forging links with Universities in South Africa and the United&nbsp; Kingdom to provide access to courses and training material.&nbsp;</p><p>Research Interest and Activities:</p><p>The following are the present areas of research interest: 1. EST clustering 2. Genome sequencing and annotation 3. Functional genomics and proteomics (including key tropical pathogens) 4. Structural bioinformatics 5. Development of Bioinformatics Data Management Systems 6. Gene Mining 7. High Throughput Genotyping 8. Microarray data management and analysis 9. Metagenomics 10. Immunoinformatics 11. Host&shy;pathogen interaction 12. High performance computing and grid development 13. Parasite transfection technologies 14. Cell cycle regulation 15. Population genetics 16. Vector genomics 17. Drug, vaccine and diagnostic target discovery</p><p>More at&nbsp;Web&nbsp;site&nbsp;and&nbsp;links:</p><p>http://www.ilri.cgiar.org/</p><p>http://www.icipe.org/ &nbsp; &nbsp;</p><p>http://www.uonbi.ac.ke/cebib</p>]]></description>
	<dc:creator>BioStar</dc:creator>
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/1217/studentship-at-bioinformatics-infrastructure-facility-bif-department-of-biotechnology-alagappa-university</guid>
  <pubDate>Fri, 02 Aug 2013 10:33:54 -0500</pubDate>
  <link></link>
  <title><![CDATA[Studentship at Bioinformatics Infrastructure Facility (BIF), Department of Biotechnology, Alagappa University]]></title>
  <description><![CDATA[
<p>WALK IN INTERVIEW</p>

<p>A walk-in Interview for the following position tenable at the Bioinformatics Infrastructure Facility (BIF), Department of Biotechnology, Alagappa University will be held at the Department of Biotechnology, Science Campus, Alagappa University, Karaikudi 630 004 on 03.08.2013 (Saturday) at 12:30 PM. This national facility is funded by the Department of Biotechnology, Ministry of Science and Technology, Government of India, New Delhi. The main objectives of the Centre involve teaching and research activities in bioinformatics/biotechnology.</p>

<p>1. Studentship (One Post):</p>

<p>Stipend : Rs. 5000 p.m. (consolidated)</p>

<p>Qualification: M.Sc., in Bioinformatics/Biotechnology/Biophysics/Biochemistry/<br />Life Sciences</p>

<p>Interested candidates are encouraged to send their Curriculum Vitae by email to alagappauniv.btisnet@nic.in in advance. On the day of interview, the candidates must produce original certificates in proof of their educational qualification and experience and a recommendation letter from the Head of the Department/Institution where last studied/worked. Candidates who have already passed the required Degree alone are eligible to appear for interview. No TA&amp;DA will be given for attending the interview.</p>

<p>Advertisement: http://www.alagappabiotech.org/Notification.pdf</p>
]]></description>
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/43993/phd-positions-on-integrative-omics-and-phylogenomics</guid>
  <pubDate>Wed, 19 Oct 2022 05:11:11 -0500</pubDate>
  <link></link>
  <title><![CDATA[PhD positions on integrative omics and phylogenomics]]></title>
  <description><![CDATA[
<p>Would you like to participate in an exciting interdisciplinary research project to discover the hidden chemistry of plants and its evolution using computational omics approaches? Do you enjoy collaboration and teamwork while being at the cutting edge of scientific progress? We are looking for two PhD candidates with complementary skills to pioneer new technologies to analyze, explore and leverage the diversity of plant chemistry hidden in plant genomes.</p>

<p>Plants represent an untapped resource of natural bioactive compounds that significantly contribute to plant resilience to pathogens, herbivores, and abiotic stresses, and may be applied for medicine or crop protection. In this project, you will design and/or apply innovative omics integration strategies for genomics, transcriptomics, and metabolomics data, to discover plant specialized metabolite biosynthetic pathways and study their evolution. You will work together with the other PhD candidate in this project, which will entail a combination of algorithm development, greenhouse experiments, integrative omics analysis, and evolutionary genomics. Extensive local and international collaboration is foreseen, including possibilities for a foreign research visit as part of your PhD project.</p>

<p>The research is embedded within the chairs of Bioinformatics and Biosystematics. The projects will be (co-)supervised by Dr. Marnix Medema, Dr. Justin van der Hooft, Dr. Klaas Bouwmeester and Prof. Dr. Eric Schranz.</p>

<p>We ask</p>

<p>We are looking for two enthusiastic and complementary team players with all or a subset of the following skills:</p>

<p>a solid academic record (MSc) in bioinformatics, biology, or biotechnology<br />experience in computational omics analysis and proficiency in programming (in, e.g., Python)<br />at least basic to intermediate statistical and mathematical skills<br />demonstrable experience in working with next-generation sequencing data or with greenhouse experiments with plants<br />affinity with plant science, metabolism and/or biosynthetic pathways<br />you meet all the entry requirements of the  WUR PhD programme.<br />More information</p>

<p>For more information about this position, please contact Marnix Medema, Associate Professor Bioinformatics, by email (marnix.medema@wur.nl).<br />For more information about the procedure, please contact vacaturemeldingen.psg@wur.nl.</p>
]]></description>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/44254/bioinformatics-chat</guid>
	<pubDate>Mon, 13 Mar 2023 13:20:27 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/44254/bioinformatics-chat</link>
	<title><![CDATA[Bioinformatics Chat !]]></title>
	<description><![CDATA[<p>The bioinformatics chat is a podcast about computational biology, bioinformatics, and next generation sequencing.</p>
<p>The bioinformatics chat is produced by&nbsp;<a href="https://ro-che.info/">Roman&nbsp;Cheplyaka</a>&nbsp;and hosted by Roman and&nbsp;<a href="https://jmschrei.github.io/">Jacob&nbsp;Schreiber</a>.</p><p>Address of the bookmark: <a href="https://bioinformatics.chat/" rel="nofollow">https://bioinformatics.chat/</a></p>]]></description>
	<dc:creator>BioStar</dc:creator>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/pages/view/44618/important-bioinformatics-tools</guid>
	<pubDate>Tue, 30 Jul 2024 05:03:29 -0500</pubDate>
	<link>https://bioinformaticsonline.com/pages/view/44618/important-bioinformatics-tools</link>
	<title><![CDATA[Important Bioinformatics Tools !]]></title>
	<description><![CDATA[<p><span>1. Ktrim: An extra-fast, accurate adapter trimmer for sequencing data. It processes FASTQ files from multiple lanes with minimal mismatching and over-trimming of adapters.</span><span><br /></span><span><br /></span><span>2. BWA MEM: A reliable alignment tool (particularly for mapping ALT contigs and HLA genes, which are not fully addressed in BWA-MEM2).</span><span><br /></span><span><br /></span><span>3. Sambamba markdup: Quickly marks or removes duplicate reads using Picard's criteria.</span><span><br /></span><span><br /></span><span>4. ichorCNA: Estimates the tumor DNA fraction in cell-free DNA from ultra-low-pass whole genome sequencing (0.1x coverage) based on copy number alterations (CNA).</span><span><br /></span><span><br /></span><span>5. Fragle: A deep learning method for quantifying ctDNA levels from cell-free DNA fragmentomic profiles. It detects TF as low as ~1% ctDNA and works with targeted genomic panel sequencing data.</span><span><br /></span><span><br /></span><span>6. AlfredQC: A quality control tool for high-throughput sequencing data. It assesses metrics like read quality scores, GC content, and duplication rates, visualized through detailed plots and summary statistics.</span><span><br /></span><span><br /></span><span>7. Mosdepth: A fast tool for calculating sequencing coverage depth, offering a quicker alternative to samtools/sambamba depth by processing BAM and CRAM files.</span><span><br /></span><span><br /></span><span>8. Bedtools: A versatile toolkit for genomics, enabling operations like intersect, merge, count, and shuffle on genomic intervals across formats such as BAM, BED, GFF/GTF, and VCF.</span><span><br /></span><span><br /></span><span>9. Datamash: A command-line tool for basic numeric, textual, and statistical operations on input data streams. It supports operations such as grouping, sorting, transposing, and performing arithmetic calculations on tabular data.</span><span><br /></span><span><br /></span><span>10.</span><span> </span><a href="http://gwf.app/" target="_self">gwf.app</a><span>: A pragmatic alternative to Snakemake. Developed at</span><span> </span><a href="https://www.linkedin.com/company/aarhus-university-denmark-/" target="_self"><span>Aarhus University</span></a><span>, this flexible, generic workflow tool builds and runs large scientific workflows.</span></p>]]></description>
	<dc:creator>BioStar</dc:creator>
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