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	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/27818?offset=520</link>
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/42374/postdoc-in-comparative-genomics</guid>
  <pubDate>Tue, 08 Dec 2020 09:26:40 -0600</pubDate>
  <link></link>
  <title><![CDATA[Postdoc in comparative genomics]]></title>
  <description><![CDATA[
<p>We are looking for a highly motivated researcher for an 18 month postdoctoral position collaborating in an exciting project on comparative genomics of marine fish and shellfish species. In the project, we use genome resequencing data from a range of species to reconstruct the demographic history and characterize genomic signals associated with population divergence and local adaptation in high gene flow scenarios. The work will improve our understanding of interacting evolutionary processes and provide valuable data for securing sustainable management and conservation of exploited resources. Applicants are encouraged to develop their own research ideas within this framework.</p>

<p>The fellowship is part of a larger Nordic collaborative project, MarGen_II, financed by the EU Interreg Öresund-Kattegat-Skagerrak Programme, the Danish Rod and Net License Funds and the National Institute of Aquatic Resources (DTU Aqua). The project will primarily be carried out in the population genetics group, Section for Marine Living Resources, situated in Silkeborg, Denmark. DTU Aqua is an institute at the Technical University of Denmark. In addition, the position offers many opportunities for collaborating with Nordic and other European colleagues in the field.</p>

<p>Application:<br />Apply online at<br />https://www.dtu.dk/english/About/JOB-and-CAREER/vacant-positions/job?id=d198fd80-4856-4a56-943d-485106026504.<br />The deadline is 4 January 2021. For further information, please contact<br />Senior Researcher Jakob Hemmer-Hansen, jhh@aqua.dtu.dk.</p>

<p>You can read more about DTU Aqua at www.aqua.dtu.dk<br />and the population genetics group at<br />https://www.aqua.dtu.dk/english/research/population_genetics.</p>

<p>All interested candidates irrespective of age, gender, race, disability,<br />religion or ethnic background are encouraged to apply.</p>

<p>Jakob Hemmer Hansen</p>
]]></description>
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<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/pages/view/920/bioinformatics-algorithms</guid>
	<pubDate>Tue, 16 Jul 2013 03:35:15 -0500</pubDate>
	<link>https://bioinformaticsonline.com/pages/view/920/bioinformatics-algorithms</link>
	<title><![CDATA[Bioinformatics Algorithms]]></title>
	<description><![CDATA[<p>An algorithm is a computable set of steps to achieve a desired result.</p><p>We use algorithms every day. For example, a recipe for baking a cake is an algorithm. Most programs, with the exception of some artificial intelligence applications, consist of algorithms. Inventing elegant algorithms -- algorithms that are simple and require the fewest steps possible -- is one of the principal challenges in programming. An algorithm is a description of a procedure which terminates with a result. In other words an algorithm is a set of instructions, sometimes called a procedure or a function, that is used to perform a certain task. This can be a simple process, such as adding two numbers together, or a complex function, such as adding effects to an image. For example, in order to sharpen a digital photo, the algorithm would need to process each pixel in the image and determine which ones to change and how much to change them in order to make the image look sharper.</p><p>In mathematics, computer science, and related subjects, an algorithm is an effective method for solving a problem using a finite sequence of instructions. Algorithms are used for calculation, data processing, and many other fields.<br />Each algorithm is a list of well-defined instructions for completing a task. Starting from an initial state, the instructions describe a computation that proceeds through a well-defined series of successive states, eventually terminating in a final ending state. The transition from one state to the next is not necessarily deterministic; some algorithms, known as randomized algorithms, incorporate randomness.</p><p><strong>History</strong></p><p>The origin of the term comes from the ancients. The concept becomes more precise with the use of variables in mathematics. Algorithm in the sense of what is now used by computers appeared as soon as first mechanical engines were invented.<br />The word algorithm comes from the name of the 9th century Persian Muslim mathematician Abu Abdullah Muhammad ibn Musa Al-Khwarizmi. The word algorism originally referred only to the rules of performing arithmetic using Hindu-Arabic numerals but evolved via European Latin translation of Al-Khwarizmi's name into algorithm by the 18th century. The use of the word evolved to include all definite procedures for solving problems or performing tasks.<br />The algorithm of Archimedes gives an approximation of the Pi number.<br />Eratosthenes has defined an algorithim for retrieving prime numbers.<br />Averro&egrave;s (1126-1198) was using algorithmic methods for calculations.<br />Adelard de Bath (12 th) introduces the algorismus term, from Al-Khwarizmi.<br />During the 1800's up to the mid-1900's:<br /><br />- George Boole (1847) has invented the binary algebra, the basis of computers. Actually he has unified logic and calculation in a common symbolism.<br /><br />- Gottlob Frege (1879) formula language's, that is a lingua characterica, a language written with special symbols, "for pure thought", that is free from rhetorical embellishments... constructed from specific symbols that are manipulated according to definite rules.<br /><br />- Giuseppe Peano (1888) It's The principles of arithmetic, presented by a new method was the first attempt at an axiomatization of mathematics in a symbolic language.<br /><br />- Alfred North Whitehead and Bertrand Russell in their Principia Mathematica (1910-1913) has further simplified and amplified the work of Frege.<br /><br />- Kurt Go&euml;del (1931) cites the paradox of the liar that completely reduces rules of recursion to numbers.<br /><br />The concept of algorithm was formalized in 1936 through Alan Turing's Turing machines and Alonzo Church's lambda calculus, which in turn formed the foundation of computer science.<br />Stephen C. Kleene (1943) defined his now-famous thesis known as the "Church-Turing Thesis". In this context:<br /><br />" Algorithmic theories... In setting up a complete algorithmic theory, what we do is to describe a procedure, performable for each set of values of the independent variables, which procedure necessarily terminates and in such manner that from the outcome we can read a definite answer, "yes" or "no," to the question, "is the predicate value true?"</p><p><strong>Classification</strong></p><p><strong>Classification by purpose</strong></p><p>Each algorithm has a goal, for example, the purpose of the Quick Sort algorithm is to sort data in ascending or descending order. But the number of goals is infinite, and we have to group them by kind of purposes:</p><p><strong>Classification by implementation</strong></p><p>An algorithm may be implemeted according to different basical principles.</p><ul>
<li>Recursive or iterative</li>
</ul><p>A recursive algorithm is one that calls itself repeatedly until a certain condition matches. It is a method common to functional programming.&nbsp;<br />Iterative algorithms use repetitive constructs like loops.<br />Some problems are better suited for one implementation or the other. For example, the towers of hanoi problem is well understood in recursive implementation. Every recursive version has an iterative equivalent iterative, and vice versa.</p><ul>
<li>Logical or procedural</li>
</ul><p>An algorithm may be viewed as controlled logical deduction.&nbsp;<br />A logic component expresses the axioms which may be used in the computation and a control component determines the way in which deduction is applied to the axioms.&nbsp;<br />This is the basis of the logic programming. In pure logic programming languages the control component is fixed and algorithms are specified by supplying only the logic component.</p><ul>
<li>Serial or parallel</li>
</ul><p>Algorithms are usually discussed with the assumption that computers execute one instruction of an algorithm at a time. This is a serial algorithm, as opposed to parallel algorithms, which take advantage of computer architectures to process several instructions at once. They divide the problem into sub-problems and pass them to several processors. Iterative algorithms are generally parallelizable. Sorting algorithms can be parallelized efficiently.</p><ul>
<li>Deterministic or non-deterministic</li>
</ul><p>Deterministic algorithms solve the problem with a predefined process whereas non-deterministic algorithm must perform guesses of best solution at each step through the use of heuristics.<br /><br /><strong>Classification by design paradigm</strong></p><p>A design paradigm is a domain in research or class of problems that requires a dedicated kind of algorithm:</p><ul>
<li>Divide and conquer</li>
</ul><p>A divide and conquer algorithm repeatedly reduces an instance of a problem to one or more smaller instances of the same problem (usually recursively), until the instances are small enough to solve easily. One such example of divide and conquer is merge sorting. Sorting can be done on each segment of data after dividing data into segments and sorting of entire data can be obtained in conquer phase by merging them.<br />The binary search algorithm is an example of a variant of divide and conquer called decrease and conquer algorithm, that solves an identical subproblem and uses the solution of this subproblem to solve the bigger problem.</p><ul>
<li>Dynamic programming</li>
</ul><p>The shortest path in a weighted graph can be found by using the shortest path to the goal from all adjacent vertices.&nbsp;<br />When the optimal solution to a problem can be constructed from optimal solutions to subproblems, using dynamic programming avoids recomputing solutions that have already been computed.&nbsp;<br />- The main difference with the "divide and conquer" approach is, subproblems are independent in divide and conquer, where as the overlap of subproblems occur in dynamic programming.&nbsp;<br />- Dynamic programming and memoization go together. The difference with straightforward recursion is in caching or memoization of recursive calls. Where subproblems are independent, this is useless. By using memoization or maintaining a table of subproblems already solved, dynamic programming reduces the exponential nature of many problems to polynomial complexity.</p><ul>
<li>The greedy method</li>
</ul><p>A greedy algorithm is similar to a dynamic programming algorithm, but the difference is that solutions to the subproblems do not have to be known at each stage. Instead a "greedy" choice can be made of what looks the best solution for the moment.&nbsp;<br />The most popular greedy algorithm is finding the minimal spanning tree as given by Kruskal.</p><ul>
<li>Linear programming</li>
</ul><p>The problem is expressed as a set of linear inequalities and then an attempt is made to maximize or minimize the inputs. This can solve many problems such as the maximum flow for directed graphs, notably by using the simplex algorithm.&nbsp;<br />A complex variant of linear programming is called integer programming, where the solution space is restricted to all integers.</p><ul>
<li>Reduction also called transform and conquer</li>
</ul><p>Solve a problem by transforming it into another problem. A simple example: finding the median in an unsorted list is first translating this problem into sorting problem and finding the middle element in sorted list. The main goal of reduction is finding the simplest transformation possible.</p><ul>
<li>Using graphs</li>
</ul><p>Many problems, such as playing chess, can be modeled as problems on graphs. A graph exploration algorithms are used.&nbsp;<br />This category also includes the search algorithms and backtracking.<br /><br /><strong>The probabilistic and heuristic paradigm</strong></p><ul>
<li>Probabilistic</li>
</ul><p>Those that make some choices randomly.</p><ul>
<li>Genetic</li>
</ul><p>Attempt to find solutions to problems by mimicking biological evolutionary processes, with a cycle of random mutations yielding successive generations of "solutions". Thus, they emulate reproduction and "survival of the fittest".</p><ul>
<li>Heuristic</li>
</ul><p>Whose general purpose is not to find an optimal solution, but an approximate solution where the time or resources to find a perfect solution are not practical.</p><p><strong>Classification by complexity</strong></p><p>Some algorithms complete in linear time, and some complete in exponential amount of time, and some never complete.</p><p><strong>Algorithms resources on net.</strong></p><p><a href="http://www.cs.uga.edu/~cai/courses/compbio/2008fall/bookchapters/Chapter08/Ch08_GraphsDNAseq.pdf">Graph Algorithms in Bioinformatics</a></p><p><a href="http://zikuladevs.com/notes/Part%20II%20Revision/Bio_Alg_Descriptions[1].pdf">Bioinformatics Algorithms Description</a></p><p><a href="http://users.aims.ac.za/~marshall/BioinformaticsCourse.html">Bioinformatics Algorithms Course Page</a></p><p><a href="http://www.cybertory.org/downloads/bae/BioinformaticsAlgorithmsExcelDoc.pdf">Bioinformatics Algorithm Demonstrations</a></p><p><a href="http://www.cse.sc.edu/~maxal/csce590b/Lect01-02.pdf">Introduction to Bioinformatics Algorithms Lectures 1-2 by Dr. Max Alekseyev USC, 2009</a></p><p><a href="http://lectures.molgen.mpg.de/online_lectures.html">Online Lectures on Bioinformatics</a></p><p><a href="http://www.ks.uiuc.edu/Training/Tutorials/science/bioinformatics-tutorial/bioinformatics.pdf.bak">Sequence Alignment Algorithms</a></p><p><a href="http://www.avatar.se/molbioinfo2001/seqali-dyn.html">Algorithm for sequence alignment: dynamic programming</a></p><p><a href="http://www.4tphi.net/~awalters/PI/pi.pdf">Network Protocol Analysis using Bioinformatics Algorithms</a></p><p><strong>Bioinformatics Algorithms Links</strong></p><p><strong>Dynamic Programming</strong></p><p>Particularly good sites...</p><p>&bull;<a href="http://www.cis.upenn.edu/~sahuguet/MSA/">http://www.cis.upenn.edu/~sahuguet/MSA/</a><br />&bull;<a href="http://www.blc.arizona.edu/courses/bioinformatics/align.html">http://www.blc.arizona.edu/courses/bioinformatics/align.html</a><br />&bull;<a href="http://www.cs.monash.edu.au/~lloyd/tildeStrings/Notes/DPA.html">http://www.cs.monash.edu.au/~lloyd/tildeStrings/Notes/DPA.html</a><br />&bull;<a href="http://www.cs.orst.edu/~schut/cs325/dynamic.htm">http://www.cs.orst.edu/~schut/cs325/dynamic.htm</a><br />&bull;<a href="http://www.catalase.com/dprog.htm">http://www.catalase.com/dprog.htm</a><br />&bull;<a href="http://bioweb.ncsa.uiuc.edu/~bioph490/BIOPH2.html#SEQUENCE_COMP">http://bioweb.ncsa.uiuc.edu/~bioph490/BIOPH2.html#SEQUENCE_COMP</a><br />&bull;<a href="http://www.qucis.queensu.ca/home/cisc365/javascript/dp1/index.html">http://www.qucis.queensu.ca/home/cisc365/javascript/dp1/index.html</a><br />Other sites...<br />&bull;<a href="http://bioweb.ncsa.uiuc.edu/~bioph490/dynamic_programming_demo.html">http://bioweb.ncsa.uiuc.edu/~bioph490/dynamic_programming_demo.html</a><br />&bull;<a href="http://www.qucis.queensu.ca/home/cisc365/365overheads.html">http://www.qucis.queensu.ca/home/cisc365/365overheads.html</a><br />&bull;<a href="http://www.qucis.queensu.ca/home/cisc365/dp/dp.p01.html">http://www.qucis.queensu.ca/home/cisc365/dp/dp.p01.html</a><br />&bull;<a href="http://www.dgp.toronto.edu/csc270/tut_dp.html">http://www.dgp.toronto.edu/csc270/tut_dp.html</a><br />&bull;<a href="http://queue.ieor.berkeley.edu/~jshu/knapsack/DP/dp.html">http://queue.ieor.berkeley.edu/~jshu/knapsack/DP/dp.html</a><br />&bull;<a href="http://mat.gsia.cmu.edu/classes/dynamic/dynamic.html">http://mat.gsia.cmu.edu/classes/dynamic/dynamic.html</a><br />&bull;<a href="http://www.cs.sandia.gov/~scistra/class_3">http://www.cs.sandia.gov/~scistra/class_3</a><br />&bull;<a href="http://levine.sscnet.ucla.edu/Econ101/dynamic.htm">http://levine.sscnet.ucla.edu/Econ101/dynamic.htm</a><br />&bull;<a href="http://mat.gsia.cmu.edu/classes/stoch_dynamic/stoch_dynamic.html">http://mat.gsia.cmu.edu/classes/stoch_dynamic/stoch_dynamic.html</a><br />&bull;<a href="http://mat.gsia.cmu.edu/classes/dynamic/node8.html">http://mat.gsia.cmu.edu/classes/dynamic/node8.html</a><br />&bull;<a href="http://www.maths.mu.oz.au/~moshe/dp/bibl/bibliography.html">http://www.maths.mu.oz.au/~moshe/dp/bibl/bibliography.html</a><br />&bull;<a href="http://cartan.gmd.de/PAPER/ismb95/ismb_html.html">http://cartan.gmd.de/PAPER/ismb95/ismb_html.html</a><br />&bull;<a href="http://screwdriver.bu.edu/bibliography/dynamic_programming.htm">http://screwdriver.bu.edu/bibliography/dynamic_programming.htm</a><br />&bull;<a href="http://www.norvig.com/design-patterns/">http://www.norvig.com/design-patterns/</a><br />&bull;<a href="http://tome.cbs.univ-montp1.fr/htmltxt/Doc/manual/node137.html">http://tome.cbs.univ-montp1.fr/htmltxt/Doc/manual/node137.html</a><br />&bull;<a href="http://poem.princeton.edu/~verdu/dynamic.html">http://poem.princeton.edu/~verdu/dynamic.html</a><br />&bull;<a href="http://www.orca1.com/opushelpweb/opusDynamic_Programming.html">http://www.orca1.com/opushelpweb/opusDynamic_Programming.html</a><br />&bull;<a href="http://screwdriver.bu.edu/cn760-lectures/l7/index.htm">http://screwdriver.bu.edu/cn760-lectures/l7/index.htm</a><br />&bull;<a href="http://www.ms.unimelb.edu.au/~moshe/dp/dp.html">http://www.ms.unimelb.edu.au/~moshe/dp/dp.html</a><br />&bull;<a href="http://mat.gsia.cmu.edu/ORCS/0255.html">http://mat.gsia.cmu.edu/ORCS/0255.html</a><br />&bull;<a href="http://aae.wisc.edu/e703/notes/a13dynpr.htm">http://aae.wisc.edu/e703/notes/a13dynpr.htm</a><br />&bull;<a href="http://bioweb.pasteur.fr/docs/modeller/node137.html">http://bioweb.pasteur.fr/docs/modeller/node137.html</a><br />&bull;<a href="http://www2.uwindsor.ca/~lama/my470/ddynamic.htm">http://www2.uwindsor.ca/~lama/my470/ddynamic.htm</a><br />&bull;<a href="http://students.ceid.upatras.gr/~papagel/project/ex5_6_1.htm">http://students.ceid.upatras.gr/~papagel/project/ex5_6_1.htm</a><br />&bull;<a href="http://www.cs.sunysb.edu/~algorith/lectures-good/node12.html">http://www.cs.sunysb.edu/~algorith/lectures-good/node12.html</a><br />&bull;<a href="http://www.cs.sunysb.edu/~algorith/lectures-good/node12.html">http://www.cs.sunysb.edu/~algorith/lectures-good/node12.html</a><br />&bull;<a href="http://www.utdallas.edu/~scniu/documents/7315.htm">http://www.utdallas.edu/~scniu/documents/7315.htm</a><br />&bull;<a href="http://www.ii.uib.no/~pinar/seminar/larry.html">http://www.ii.uib.no/~pinar/seminar/larry.html</a><br />&bull;<a href="http://www.deakin.edu.au/~gecole/books.html">http://www.deakin.edu.au/~gecole/books.html</a><br />&bull;<a href="http://www.cseg.engr.uark.edu/~wessels/algs/notes/dynamic.html">http://www.cseg.engr.uark.edu/~wessels/algs/notes/dynamic.html</a><br />&bull;<a href="http://www.csc.liv.ac.uk/~ped/teachadmin/algor/dyprog.html">http://www.csc.liv.ac.uk/~ped/teachadmin/algor/dyprog.html</a><br />&bull;<a href="http://www.eli.sdsu.edu/courses/fall96/cs660/notes/dynamicProg/dynamicProg.html">http://www.eli.sdsu.edu/courses/fall96/cs660/notes/dynamicProg/dynamicProg.html</a><br />&bull;<a href="http://www.cs.indiana.edu/l/www/ftp/techreports/TR514.html">http://www.cs.indiana.edu/l/www/ftp/techreports/TR514.html</a><br />&bull;<a href="http://www.cs.brandeis.edu/~mairson/poems/node3.html">http://www.cs.brandeis.edu/~mairson/poems/node3.html</a><br />&bull;<a href="http://www.cis.tu-graz.ac.at/igi/oaich/animations/Dynamic2.html">http://www.cis.tu-graz.ac.at/igi/oaich/animations/Dynamic2.html</a><br />&bull;<a href="http://bioweb.ncsa.uiuc.edu/~workshop/">http://bioweb.ncsa.uiuc.edu/~workshop/</a></p><p><br />Smith Waterman<br />&bull;<a href="http://genome-www.stanford.edu/Saccharomyces/help/sw_alignment.html">http://genome-www.stanford.edu/Saccharomyces/help/sw_alignment.html</a><br />&bull;<a href="http://genome-www.stanford.edu/Saccharomyces/help/sw_details.html">http://genome-www.stanford.edu/Saccharomyces/help/sw_details.html</a><br />&bull;<a href="http://www.stanford.edu/~sntaylor/bioc218/final.htm">http://www.stanford.edu/~sntaylor/bioc218/final.htm</a><br />&bull;<a href="http://www.maths.tcd.ie/~lily/pres2/sld009.htm">http://www.maths.tcd.ie/~lily/pres2/sld009.htm</a><br />&bull;<a href="http://bioweb.ncsa.uiuc.edu/~workshop/Lab_3/Smith-Waterman.htm">http://bioweb.ncsa.uiuc.edu/~workshop/Lab_3/Smith-Waterman.htm</a><br />&bull;<a href="http://www.tigem.it/LOCAL/SW/threshold.html">http://www.tigem.it/LOCAL/SW/threshold.html</a><br />&bull;<a href="http://sgbcd.weizmann.ac.il/genweb/help/smith-waterman.html">http://sgbcd.weizmann.ac.il/genweb/help/smith-waterman.html</a><br />&bull;<a href="http://cbrg.ethz.ch/ServerBooklet/section2_3_5.html">http://cbrg.ethz.ch/ServerBooklet/section2_3_5.html</a><br />Needleman &amp; Wunsch<br />&bull;<a href="http://www.maths.tcd.ie/~lily/pres2/sld003.htm">http://www.maths.tcd.ie/~lily/pres2/sld003.htm</a><br />&bull;<a href="http://acer.gen.tcd.ie/~amclysag/nwswat.html">http://acer.gen.tcd.ie/~amclysag/nwswat.html</a><br />&bull;<a href="http://www.nada.kth.se/~erikw/thesis/chapter2_3.html">http://www.nada.kth.se/~erikw/thesis/chapter2_3.html</a><br />&bull;<a href="http://www.irbm.it/irbm-course95/gb/docs/amps/subsection3_6_1.html">http://www.irbm.it/irbm-course95/gb/docs/amps/subsection3_6_1.html</a><br />&bull;<a href="http://www.ibc.wustl.edu/~zuker/Bio-5495/align-html/node3.html">http://www.ibc.wustl.edu/~zuker/Bio-5495/align-html/node3.html</a></p><p><strong>General (NW vs. SW vs. HMM, etc.)</strong></p><p>&bull;<a href="http://www.maths.tcd.ie/~lily/pres2/">http://www.maths.tcd.ie/~lily/pres2/</a><br />&bull;<a href="http://acer.gen.tcd.ie/~amclysag/nwswat.html">http://acer.gen.tcd.ie/~amclysag/nwswat.html</a><br />&bull;<a href="http://laguerre.psc.edu/biomed/TUTORIALS/SEQUENCE/MULTIPLE/tutorial.html">http://laguerre.psc.edu/biomed/TUTORIALS/SEQUENCE/MULTIPLE/tutorial.html</a><br />&bull;<a href="http://www.cse.ucsc.edu/research/compbio/">http://www.cse.ucsc.edu/research/compbio/</a></p><p><strong>Hmms</strong></p><p>&bull;<a href="http://www.medmicro.mds.qmw.ac.uk/HMMER/main.html">http://www.medmicro.mds.qmw.ac.uk/HMMER/main.html</a><br />&bull;<a href="http://alfredo.wustl.edu/ismb96/abs/p02.html">http://alfredo.wustl.edu/ismb96/abs/p02.html</a><br />&bull;<a href="http://www.cse.ucsc.edu/research/compbio/html_format_papers/hughkrogh96/cabios.html">http://www.cse.ucsc.edu/research/compbio/html_format_papers/hughkrogh96/cabios.html</a><br />&bull;<a href="http://wwwsyseng.anu.edu.au/~jason/hmmlinks.html">http://wwwsyseng.anu.edu.au/~jason/hmmlinks.html</a><br />&bull;<a href="http://www.breadfan.com/markov.html">http://www.breadfan.com/markov.html</a><br />&bull;<a href="http://cslu.cse.ogi.edu/HLTsurvey/ch1node34.html">http://cslu.cse.ogi.edu/HLTsurvey/ch1node34.html</a><br />&bull;<a href="http://www.ibc.wustl.edu/service/hmmalign/glocal.html">http://www.ibc.wustl.edu/service/hmmalign/glocal.html</a><br />&bull;<a href="http://www.cse.ucsc.edu/research/compbio/html_format_papers/ismb94/node5.html">http://www.cse.ucsc.edu/research/compbio/html_format_papers/ismb94/node5.html</a><br />&bull;<a href="http://www.iscs.nus.edu.sg/~luakt/ic3222/lecture/nlp18new/index.htm">http://www.iscs.nus.edu.sg/~luakt/ic3222/lecture/nlp18new/index.htm</a><br />&bull;<a href="http://www.cse.ucsc.edu/research/compbio/sam.html">http://www.cse.ucsc.edu/research/compbio/sam.html</a>&nbsp;SAM Software for HMMs</p><p><strong>Genetic Algorithms</strong><br /><br />&bull;<a href="http://www.staff.uiuc.edu/~carroll/ga.html">http://www.staff.uiuc.edu/~carroll/ga.html</a><br />&bull;<a href="http://kal-el.ugr.es/gags.html">http://kal-el.ugr.es/gags.html</a><br />&bull;<a href="http://kal-el.ugr.es/~jmerelo/GAJS.html">http://kal-el.ugr.es/~jmerelo/GAJS.html</a><br />&bull;<a href="http://www.genetic-programming.org/">http://www.genetic-programming.org/</a><br />&bull;<a href="http://www.iitk.ac.in/kangal/deb_tut.shtml">http://www.iitk.ac.in/kangal/deb_tut.shtml</a></p>]]></description>
	<dc:creator>Jitendra Narayan</dc:creator>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/42670/icgeb-bioinformatics-job</guid>
  <pubDate>Sat, 23 Jan 2021 21:01:55 -0600</pubDate>
  <link></link>
  <title><![CDATA[ICGEB Bioinformatics Job]]></title>
  <description><![CDATA[
<p>The following vacancies are available in the various ongoing bioinformatics projects at.<br />Translational Bioinformatics Group (https://www.icgeb.org/dinesh-gupta/), ICGEB, New Delhi, India. Shortlisted candidates will be welcomed for an on-line interview at ICGEB. Only the chosen applicants will be informed individually. Preference will be given to the applicants with experience related to Bioinformatics as well as Computational area.</p>

<p>Interested applicants must submit their complete, updated Curriculum Vitae, mentioning details of two references as well as various other details at – http://14.139.62.220/survey/index.php/2021/01/21/icgeb-dbt-project-vacancy/</p>

<p>The last date of submission of applications is January 31st, 2021.</p>

<p>Research Associate : PhD. Degree in Computational Biology/Bioinformatics.</p>

<p>Consolidated Salary: 58280/- pm (including HRA).</p>

<p>More at https://www.icgeb.org/project-positions-translational-bioinformatics-group/ and https://www.icgeb.org/category/vacancies/</p>
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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>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/pages/view/42810/bioinformatics-in-africa-part3-mali</guid>
	<pubDate>Sat, 06 Feb 2021 13:28:44 -0600</pubDate>
	<link>https://bioinformaticsonline.com/pages/view/42810/bioinformatics-in-africa-part3-mali</link>
	<title><![CDATA[Bioinformatics in Africa: Part3 - Mali]]></title>
	<description><![CDATA[<p>International&nbsp;Center&nbsp;for&nbsp;Excellence&nbsp;in&nbsp;Research&nbsp;(ICER):</p><p>The&nbsp;ICER&nbsp;is&nbsp;a&nbsp;research&nbsp;center&nbsp;composed&nbsp;of&nbsp;the&nbsp;following&nbsp;three&nbsp;programs: 1. The&nbsp;Malaria&nbsp;Research&nbsp;and&nbsp;Training&nbsp;Center&nbsp;&shy;&nbsp;Parasitology&nbsp;Group,&nbsp; 2. The&nbsp;Malaria&nbsp;Research&nbsp;and&nbsp;Training&nbsp;Center&nbsp;&shy;&nbsp;Entomology&nbsp;Group&nbsp; 3. The&nbsp;SEREFO&nbsp;Group.</p><p>The&nbsp;first&nbsp;two&nbsp;programs&nbsp;develop&nbsp;biomedical&nbsp;researches&nbsp;in&nbsp;malaria,&nbsp;Filariasis&nbsp;and&nbsp;Leishmaniasis.&nbsp;The&nbsp; third&nbsp;program&nbsp;develops&nbsp;biomedical&nbsp;researches&nbsp;in&nbsp;tuberculosis&nbsp;and&nbsp;HIV.</p><p>Bioinformatics&nbsp;was&nbsp;introduced&nbsp;recently&nbsp;to&nbsp;the&nbsp;ICER&nbsp;and&nbsp;is&nbsp;constantly&nbsp;growing.&nbsp;The&nbsp;ICER&nbsp;has&nbsp;one&nbsp; team,&nbsp;headed&nbsp;by&nbsp;Sidy&nbsp;SOUMARE,&nbsp;which&nbsp;supports&nbsp;the&nbsp;three&nbsp;programmes&nbsp;in&nbsp;all&nbsp;their&nbsp;needs&nbsp;in&nbsp; informatics&nbsp;and&nbsp;bioinformatics.&nbsp;This&nbsp;team&nbsp;can&nbsp;beneficiate&nbsp;from&nbsp;some&nbsp;computational&nbsp;facilities&nbsp;(4&nbsp; blast&nbsp;servers,&nbsp;15&nbsp;other&nbsp;servers&nbsp;and&nbsp;around&nbsp;200&nbsp;terminals),&nbsp;but&nbsp;the&nbsp;ICER&nbsp;staff&nbsp;needs&nbsp;some&nbsp;training&nbsp;in&nbsp; order&nbsp;to&nbsp;be&nbsp;able&nbsp;to&nbsp;administrate&nbsp;these&nbsp;facilities.</p><p>Research&nbsp;Interest&nbsp;and&nbsp;Activities: The&nbsp;following&nbsp;are&nbsp;the&nbsp;present&nbsp;areas&nbsp;of&nbsp;research&nbsp;interest: 1. Functional&nbsp;genomics 2. Analysis&nbsp;of&nbsp;microarray&nbsp;data 3. Interaction&nbsp;between&nbsp;the&nbsp;vector&nbsp;and&nbsp;the&nbsp;parasite.</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>
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/42907/lecturer-in-evolutionary-biology-bioinformatics-at-department-of-zoology-te-tari-matai-kararehe-division-of-sciences-te-rohe-a-ahikaroa</guid>
  <pubDate>Tue, 23 Feb 2021 02:05:15 -0600</pubDate>
  <link></link>
  <title><![CDATA[Lecturer in Evolutionary Biology (Bioinformatics) at DEPARTMENT of ZOOLOGY | TE TARI MĀTAI KARAREHE DIVISION of SCIENCES | TE ROHE A AHIKAROA]]></title>
  <description><![CDATA[
<p>DEPARTMENT of ZOOLOGY | TE TARI MĀTAI KARAREHE<br />DIVISION of SCIENCES | TE ROHE A AHIKAROA</p>

<p>Applications are invited for the position of Lecturer in Evolutionary Biology (Bioinformatics).</p>

<p>We are seeking a person with a relevant doctorate, and demonstrated potential to develop as an outstanding researcher and teacher in evolutionary bioinformatics in the Department of Zoology. The position affords an exciting opportunity for an emerging scholar to research and teach in a vibrant and diverse Department. The successful candidate will develop a transformative and collaborative research program, supporting the university's commitment to excellence in research.</p>

<p>Your skills and experience</p>

<p>A PhD with a background in analysis of high-throughput sequencing data and evolutionary biology.<br />Knowledge of and familiarity with a range of bioinformatics skills, concepts, and practices as they relate to the biology of animals, including genomic, transcriptomic and metabarcoding data analyses.<br />A strong interest, and experience, in research and teaching of bioinformatics and evolutionary genomics.<br />An ability to contribute to teaching and learning environments that support engagement of students and staff with bioinformatics and genomics.<br />Be committed to and or have established connections or track record of working with national and local bioinformaticians. <br />Be committed to being a productive collaborator with a track record of working collegially.<br />Further details</p>

<p>This is a confirmation-path (tenure track) position at the level of Lecturer. The successful candidate is expected to take up duties by 1 July 2021.</p>

<p>To see a full job description and to apply online go to: https://otago.taleo.net/careersection/2/jobdetail.ftl?job=2100342</p>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/pages/view/1332/bioinformatics-companies-in-india</guid>
	<pubDate>Mon, 05 Aug 2013 20:20:07 -0500</pubDate>
	<link>https://bioinformaticsonline.com/pages/view/1332/bioinformatics-companies-in-india</link>
	<title><![CDATA[Bioinformatics Companies in India]]></title>
	<description><![CDATA[<p>Following are the list of top 30 bioinformatics companies in India. The companies name order does not follow any specific pattern.</p><p>1. Accelrys Software Solution Pvt Ltd.<br />12th Floor, Discover, ITPL, White Field, Bangalore-65.<br /><a href="http://www.accelrys.com/">www.accelrys.com</a></p><p>2. Apticraft Systems (P) Ltd.<br />142, Electronics Complex, Pardeshipura, Indore &ndash; 452010 (M.P.), India<br /><a href="http://www.apticraft.com/">www.apticraft.com</a></p><p>3. Aptuit Informatics<br />Plot No. 100-103, Export Promotion Industrial Park, White Field, Bangalore-560066<br /><a href="http://www.aptiuit.com/">www.aptiuit.com</a></p><p>4. Bigtec<br />J. K. Towers, 8th Block, Sangam Circle,46th Cross, Bangalore-560082.<br /><a href="http://www.bigtec.org/">www.bigtec.org</a></p><p>5. Bijam Biosciences Private Limited<br />Nagarjuna Hills, Hyderabad 500 082, India<br /><a href="http://www.nagarjunagroup.com/">www.nagarjunagroup.com</a></p><p>6. Bio Base Databases India Pvt Ltd.<br />Crescent Towers, 4th Floor, No : 32/1, Crescent Road, Bnagalore &ndash; 560 001<br /><a href="http://www.biobase-international.com/">www.biobase-international.com</a></p><p>7. BioImagene India Pvt. Ltd.<br />4th floor, C-Wing, Godrej Eternia, Shivajinagar, Pune-411005<br /><a href="http://www.bioimagene.com/">www.bioimagene.com</a></p><p>8. BioInformatics Institute Of India &ndash; Noida<br />C-56 A/28, Sector -62, Noida &ndash; 201 301<br /><a href="http://www.bii.in/">www.bii.in</a></p><p>9. CLC bio India Pvt Ltd<br />#Plot No. 51, H.No. 8-3-214/51, Srinivasa Nagar (West) Ameerpet Hyderabad &ndash; 500 038<br /><a href="http://www.clcbio.com/india">www.clcbio.com/india</a></p><p>10. CytoGenomics India (P) Ltd.<br />#3004, 12A Main HAL 2nd Stage, Bangalore 560008<br /><a href="http://www.silicocyte.com/">www.silicocyte.com</a></p><p>11. Genotypic Technology<br />211, 6th Cross, 80ft Road, RMV II Stage, Bangalore 560094<br /><a href="http://www.genotypic.co.in/">www.genotypic.co.in</a></p><p>12. Genvea Biosciences<br />Dr. D. T. Singh, CSO, 53, Craig Rd. #04-01, Singapore-089691<br /><a href="http://www.genvea.com/">www.genvea.com</a></p><p>13. Helix Info Systems<br />132 A, II Floor, Sterling Towers, IV Cross Street, Sterling Road, Nungambakkam, Chennai.<br /><a href="http://www.helixinfosystems.com/">www.helixinfosystems.com</a></p><p>14. Jalaja Technologies Pvt. Ltd.,<br />21/1,Victoria Layout, Victoria Road, Bangalore-47<br /><a href="http://www.jalaja.com/">www.jalaja.com</a></p><p>15. Jubilant Biosys Ltd<br />#96, Industrial Subrub, 2nd Stage, Yeshwanthpur, Bangalore- 560022<br />Jubilant Organosys Ltd.<br />1A, Sector 16A, Noida &ndash; 201 301 (India)<br /><a href="http://www.jubl.com/">www.jubl.com</a></p><p>16. Kshema Technologies<br />#1, Global Village, Mylasandra, Mysore Road, Bangalore-560 059.<br /><a href="http://www.mphasis.com/">www.mphasis.com</a></p><p>17. LabNetworx<br />B-704, Gitanjali Apartments, Vikas Marg Extension, New Delhi &ndash; 110 092<br /><a href="http://www.labnetworx.com/">www.labnetworx.com</a></p><p>18. LabVantage Solutions Pvt. Ltd.<br />Bengal Intelligent Park, Building C, 2nd Floor, Sector V, Salt Lake Electronics Complex, Kolkata &ndash; 700 091<br /><a href="http://www.labvantage.com/">www.labvantage.com</a></p><p>19. LeadInvent,&nbsp;<br />2nd Floor, Biotech Centre, University of Delhi, South Campus, Benito Juarez Road, New Delhi 110021, India<br />Contact no: +91 11 24119241<br />Email: contact@leadinvent.com<br /><a href="http://www.leadinvent.com">www.leadinvent.com</a></p><p>20. Mascon Life Sciences<br />B &ndash; 8/ 10, Vasant Vihar, New Delhi 110057, India<br /><a href="http://www.masconlifesciences.com/">www.masconlifesciences.com</a></p><p>21. Molecular Connections P Ltd<br />Kandala Mansion, 2/2 Kariappa Road, Near Krishna Rao Park, Basavangudi, Bangalore &ndash; 4<br /><a href="http://www.molecularconnections.com/">www.molecularconnections.com</a></p><p>22.Novo Informatics Pvt. Ltd.<br />TBIU, 2nd Floor, Synergy Building, Indian Institute of Technology,&nbsp;Hauz Khas, New Delhi-16.<br />Contact: 91-11-26581524, 91-11-26581766(Extension: 28)<br />Email: info@novoinformatics.com<br /><a href="http://www.novoinformatics.com">www.novoinformatics.com</a></p><p>23. Ocimum Biosolutions (India) Ltd<br />6th Floor, Reliance Classic, Road No.1 Banjara Hills, Hyderabad 500 034, India.<br /><a href="http://www.ocimumbio.com/">www.ocimumbio.com</a></p><p>24. Scube Scientific Software Solutions<br />613, Hemkunt Chambers, 89, Nehru Place, New Delhi -110 019<br /><a href="http://www.scribeindia.com/">www.scribeindia.com</a></p><p>25. Siri Technologies Pvt Ltd.<br />38/C -23, South End Road, Basavanagudi, Bangalore-56004.<br /><a href="http://www.siritech.com/">www.siritech.com</a></p><p>26. Strand Life Sciences Pvt. Ltd.<br />#237, Sir C. V. Raman Avenue, Raj Mahal Vilas, Bangalore 560 080 INDIA<br /><a href="http://www.strandls.com/">www.strandls.com<br /></a><br />27. SooryaKiran Bioinformatics (P) Ltd<br />TBIC-13, Tejaswini Building, Technopark, Thriruvananthapuram- 695 584, Keralam, India</p><p>Ph: +91 471 4060979,+91 9895404104<br />Email:&nbsp;<a href="mailto:reachus@sooryakiran.com">reachus@sooryakiran.com</a><br /><a href="http://www.sooryakiran.com/">http://www.sooryakiran.com</a></p><p>28. Systat Software Asia Pacific<br />4th Floor, Block 1, Shankar Narayan Building, No.25, MG Road, Bangalore &ndash; 560001<br /><a href="http://www.systat.com/">www.systat.com</a></p><p>29. ABC Genomics (India) Pvt. Ltd.<br />Biotech Park, Sector G, Jankipuram, Kursi Road, Lucknow-226021, U.P., INDIA<br />Tel +91-522-4068579, Email: director@abcgenomics.com<br /><a href="http://www.abcgenomics.com/">www.abcgenomics.com</a></p><p>30. en-GENE-ier's Core Technology Services,<br />1/340, Virat Khand, Gomtinagar,&nbsp;<br />(Near Maharaja Agrasen Public School)<br />lucknow-226010, U.P., India.<br /><a href="http://www.bio.egicore.com/"></a><a href="http://www.bio.egicore.com/">http://www.bio.egicore.com/</a></p><p>&nbsp;</p><p>Best of luck for your job hunts :).</p>]]></description>
	<dc:creator>Jitendra Narayan</dc:creator>
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/43559/job-offer-for-a-postdoctoral-researcher-in-genomics-bioinformatics-2-years</guid>
  <pubDate>Fri, 22 Oct 2021 04:44:33 -0500</pubDate>
  <link></link>
  <title><![CDATA[Job offer for a postdoctoral researcher in genomics / bioinformatics (2 years)]]></title>
  <description><![CDATA[
<p>Ongoing research in the group of Karine Van Doninck involves topics at the core of<br />evolutionary biology, including the evolution of sex, genome maintenance,<br />recombination and extreme stress resistance on different eukaryotic systems,<br />including rotifers, amoeba and Corbicula clams. We are employing different tools<br />(including experimental ecology, population genetics, phylogeny, comparative<br />genomics, transcriptomics, bioinformatics, molecular and cellular biology) to study<br />evolutionary processes at the level of populations, both experimental and natural, and<br />genomes.</p>

<p>Offer<br />We offer a full-time contract for two years. The contract starts between October 2021<br />and December 2021. The position involves no or extremely light teaching load, if the<br />candidate is interested. Salaries are competitive at the European level. The recruited<br />person will benefit from the Belgian social insurance scheme (health care, etc.) without<br />additional expenses.</p>

<p>Profile<br />Applicants are expected to show outstanding commitment to research and must have<br />obtained a PhD by the start of the position. A strong expertise in genomics is required.<br />More specifically, solid competences in bioinformatics (e.g. scripting pipelines) and in<br />genome evolution are needed. Knowledge or interest regarding recombination,<br />metazoan evolution, phylogenomics and population genomics is an added-value.</p>

<p>Application<br />Applications should be submitted via email to karine.van.doninck@ulb.be. The<br />application package should contain the following documents:<br />- A curriculum vitae with the complete list of publications<br />- A cover letter mentioning why the candidate is interested in the position<br />- Minimum 2 recommendation letters<br />Interviews: Interviews will be conducted with the selected candidates. Selected<br />candidates could also be invited to give a seminar to MBE ULB.<br />For any additional information, please contact karine.van.doninck@ulb.be</p>
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/1490/bioinformatics-jrf-at-iiser-mohali</guid>
  <pubDate>Thu, 08 Aug 2013 15:56:02 -0500</pubDate>
  <link></link>
  <title><![CDATA[Bioinformatics JRF at IISER MOHALI]]></title>
  <description><![CDATA[
<p>Applications are invited for a Junior Research Fellow (JRF) in Innovative Young Biotechnologist Award (IYBA) research project funded by Department of Biotechnology (DBT).</p>

<p>The project involves identification and characterization of transcription factors (TFs) from the Arabidopsis shoot apical meristem stem cell niche using genomic approaches and construction of a gene regulatory network for the identified TFs.</p>

<p>Positions: 1</p>

<p>Duration: 1 year but extendable up to three years based on performance and availability of funds.</p>

<p>Emoluments: As per DST rules.</p>

<p>Essential Qualifications: M.Sc. in any branch of life sciences with excellent academic record with CSIR-UGC NET or DBT-JRF. Candidate having previous work experience in the area of bioinformatics, molecular biology and genetics is preferred, but not required.</p>

<p>How to Apply: Applicants are requested to send a cover letter outlining previous research experiences and reasons for joining this position. Please send your complete bio-data including the cover letter as PDF attachment by email to Dr. Ram Yadav at ryadav@iisermohali.ac.in</p>

<p>Last date of submission is 17.00 IST, August 10, 2013.</p>

<p>Advertisement: www.iisermohali.ac.in/project_openings.html#29</p>
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