<div dir="ltr"><div class="gmail_quote"><div style="word-wrap:break-word;line-break:after-white-space"><span id="m_8605845347086637579gmail-docs-internal-guid-4da0754f-b6a0-9f69-57c7-344674e125be" style="color:rgb(34,34,34);font-family:arial,sans-serif;font-variant-ligatures:normal"><h1 dir="ltr" style="line-height:1.38;margin-top:20pt;margin-bottom:6pt"><span style="font-family:Arial;color:rgb(0,0,0);font-variant-ligatures:normal;font-variant-east-asian:normal;vertical-align:baseline;white-space:pre-wrap;font-size:14px">BioSB Course: Algorithms for Biological Networks (5th edition)</span><span id="m_8605845347086637579gmail-docs-internal-guid-4da0754f-b6a0-9f69-57c7-344674e125be" style="font-size:small;font-weight:normal"></span></h1><h1 dir="ltr" style="font-size:small;line-height:1.38;margin-top:20pt;margin-bottom:6pt;display:inline!important"><span style="font-size:10pt;font-family:Arial;color:rgb(0,0,0);font-variant-ligatures:normal;font-variant-east-asian:normal;vertical-align:baseline;white-space:pre-wrap">Course coordinators:</span><span style="font-size:10pt;font-family:Arial;color:rgb(0,0,0);font-weight:400;font-variant-ligatures:normal;font-variant-east-asian:normal;vertical-align:baseline;white-space:pre-wrap"> dr. Maria Suarez Diez (WUR), prof. dr. Dick de Ridder (WUR), dr. Jeroen de Ridder (UMCU)</span></h1><div style="font-size:small;line-height:1.38;margin-top:0pt;margin-bottom:0pt"><span style="font-size:10pt;font-family:Arial;color:rgb(0,0,0);font-variant-ligatures:normal;font-variant-east-asian:normal;vertical-align:baseline;white-space:pre-wrap"><br></span></div><div style="font-size:small;line-height:1.38;margin-top:0pt;margin-bottom:0pt"><span style="font-size:10pt;font-family:Arial;color:rgb(0,0,0);font-variant-ligatures:normal;font-variant-east-asian:normal;vertical-align:baseline;white-space:pre-wrap"><b>Date:</b></span><span style="font-size:10pt;font-family:Arial;color:rgb(0,0,0);font-variant-ligatures:normal;font-variant-east-asian:normal;vertical-align:baseline;white-space:pre-wrap"><span class="m_8605845347086637579gmail-Apple-tab-span" style="white-space:pre-wrap">        </span></span><span style="font-size:10pt;font-family:Arial;color:rgb(0,0,0);font-variant-ligatures:normal;font-variant-east-asian:normal;vertical-align:baseline;white-space:pre-wrap"><span class="m_8605845347086637579gmail-Apple-tab-span" style="white-space:pre-wrap">        </span></span><span style="font-size:10pt;font-family:Arial;color:rgb(0,0,0);font-variant-ligatures:normal;font-variant-east-asian:normal;vertical-align:baseline;white-space:pre-wrap">June 25-29, 2018</span></div><div style="font-size:small;line-height:1.38;margin-top:0pt;margin-bottom:0pt"><span style="font-size:10pt;font-family:Arial;color:rgb(0,0,0);font-variant-ligatures:normal;font-variant-east-asian:normal;vertical-align:baseline;white-space:pre-wrap"><b>Location:</b></span><span style="font-size:10pt;font-family:Arial;color:rgb(0,0,0);font-variant-ligatures:normal;font-variant-east-asian:normal;vertical-align:baseline;white-space:pre-wrap"><span class="m_8605845347086637579gmail-Apple-tab-span" style="white-space:pre-wrap"><b>        </b></span></span><span style="font-size:10pt;font-family:Arial;color:rgb(0,0,0);font-variant-ligatures:normal;font-variant-east-asian:normal;vertical-align:baseline;white-space:pre-wrap">Wageningen University &amp; Research</span></div><div style="font-size:small;line-height:1.38;margin-top:0pt;margin-bottom:0pt"><span style="font-size:10pt;font-family:Arial;color:rgb(0,0,0);font-variant-ligatures:normal;font-variant-east-asian:normal;vertical-align:baseline;white-space:pre-wrap"><b>Website:</b></span><span style="font-size:10pt;font-family:Arial;color:rgb(0,0,0);font-variant-ligatures:normal;font-variant-east-asian:normal;vertical-align:baseline;white-space:pre-wrap"><span class="m_8605845347086637579gmail-Apple-tab-span" style="white-space:pre-wrap">        </span></span><span style="font-size:10pt;font-family:Arial;color:rgb(0,0,0);font-variant-ligatures:normal;font-variant-east-asian:normal;vertical-align:baseline;white-space:pre-wrap"><span class="m_8605845347086637579gmail-Apple-tab-span" style="white-space:pre-wrap">        </span></span><a href="https://www.biosb.nl/education/course-portfolio/course-algorithms-for-biological-networks/" style="color:rgb(17,85,204);text-decoration:none" target="_blank"><span style="font-size:10pt;font-family:Arial;font-variant-ligatures:normal;font-variant-east-asian:normal;text-decoration:underline;vertical-align:baseline;white-space:pre-wrap">link to course page</span></a></div><div style="font-size:small;line-height:1.38;margin-top:0pt;margin-bottom:0pt"><span style="font-size:10pt;font-family:Arial;color:rgb(0,0,0);font-variant-ligatures:normal;font-variant-east-asian:normal;vertical-align:baseline;white-space:pre-wrap"><b>Registration:</b></span><span style="font-size:10pt;font-family:Arial;color:rgb(0,0,0);font-variant-ligatures:normal;font-variant-east-asian:normal;vertical-align:baseline;white-space:pre-wrap"><span class="m_8605845347086637579gmail-Apple-tab-span" style="white-space:pre-wrap">        </span></span><a href="https://www.biosb.nl/education/course-portfolio/course-algorithms-for-biological-networks/enrollment-afbn-course-5th-edition/" style="color:rgb(17,85,204);text-decoration:none" target="_blank"><span style="font-size:10pt;font-family:Arial;font-variant-ligatures:normal;font-variant-east-asian:normal;text-decoration:underline;vertical-align:baseline;white-space:pre-wrap">link to registration form</span></a></div><br><div style="font-size:small;line-height:1.38;margin-top:0pt;margin-bottom:0pt"><span style="font-size:10pt;font-family:Arial;color:rgb(0,0,0);font-weight:700;font-variant-ligatures:normal;font-variant-east-asian:normal;vertical-align:baseline;white-space:pre-wrap">Course description</span></div><div style="font-size:small;line-height:1.38;margin-top:0pt;margin-bottom:0pt"><span style="font-size:10pt;font-family:Arial;color:rgb(0,0,0);font-variant-ligatures:normal;font-variant-east-asian:normal;vertical-align:baseline;white-space:pre-wrap">Molecular biology is concerned with the study of the presence of and interactions between molecules, at the cellular and sub-cellular level. In bioinformatics and systems biology, algorithms and tools are developed to model these interactions, with various goals: predicting yet unobserved interactions, assigning functions to yet unknown molecules through their relations with known molecules; predicting certain phenotypes such as diseases; or just to build up biological knowledge in a structured way. </span><span style="color:rgb(0,0,0);font-family:Arial;font-size:10pt;white-space:pre-wrap">Such interaction models are often best modelled as networks or graphs, which opens up the possibility of using a large number of readily available algorithms for inferring networks, performing simulations of biology, optimising paths or flows through networks, graph-based data integration and graph mining. Many of these algorithms can be applied (sometimes with slight alterations) to solve a particular biological problem, such as modeling transcriptional regulation or predicting protein interaction/complex formation, but also to derive systems behaviour by breaking down networks into modules or motifs with certain characteristics.</span></div><br><div style="font-size:small;line-height:1.38;margin-top:0pt;margin-bottom:0pt"><span style="font-size:10pt;font-family:Arial;color:rgb(0,0,0);font-variant-ligatures:normal;font-variant-east-asian:normal;vertical-align:baseline;white-space:pre-wrap">In this course, we will first give a brief overview of molecular biology, the advent of high-throughput measurement techniques and large databases containing biological knowledge, and the importance of networks to model all this. We will highlight a number of peculiar features of biological networks. Next, a number of basic network models (linear, Boolean, Bayesian) will be discussed, as well as methods of inferring these from observed measurement data. A number of alternative network models more suited for high-level simulation of cellular behaviour will also be introduced. Building on the network inference methods, a number of ways of integrating various data sources and databases to refine biological networks will be discussed, with specific attention to the use of sequence information to refine interaction and transcription regulation networks. Finally, we will give some examples of algorithms exploiting the networks found to learn about biology, specifically for inspecting protein interaction networks.</span></div><br><div style="font-size:small;line-height:1.38;margin-top:0pt;margin-bottom:0pt"><span style="font-size:10pt;font-family:Arial;color:rgb(0,0,0);font-weight:700;font-variant-ligatures:normal;font-variant-east-asian:normal;vertical-align:baseline;white-space:pre-wrap">Course programme</span></div><div style="font-size:small;line-height:1.38;margin-top:0pt;margin-bottom:0pt"><span style="font-size:10pt;font-family:Arial;color:rgb(0,0,0);font-variant-ligatures:normal;font-variant-east-asian:normal;vertical-align:baseline;white-space:pre-wrap">The tentative course programme and course materials can be found <a href="http://www.bioinformatics.nl/courses/BioSB-AfBN/">here</a></span><span style="font-size:10pt;font-family:Arial;color:rgb(0,0,0);font-variant-ligatures:normal;font-variant-east-asian:normal;vertical-align:baseline;white-space:pre-wrap">.</span></div><br><div style="font-size:small;line-height:1.38;margin-top:0pt;margin-bottom:0pt"><span style="font-size:10pt;font-family:Arial;color:rgb(0,0,0);font-weight:700;font-variant-ligatures:normal;font-variant-east-asian:normal;vertical-align:baseline;white-space:pre-wrap">Target audience</span></div><div style="font-size:small;line-height:1.38;margin-top:0pt;margin-bottom:0pt"><span style="font-size:10pt;font-family:Arial;color:rgb(0,0,0);font-variant-ligatures:normal;font-variant-east-asian:normal;vertical-align:baseline;white-space:pre-wrap">The course is aimed at PhD students with a background in bioinformatics, computer science or a related field; a working knowledge of basic statistics and linear algebra is assumed. The </span><a href="https://www.biosb.nl/education/course-portfolio/pattern-recognition/" style="color:rgb(17,85,204);text-decoration:none" target="_blank"><span style="font-size:10pt;font-family:Arial;font-variant-ligatures:normal;font-variant-east-asian:normal;text-decoration:underline;vertical-align:baseline;white-space:pre-wrap">BioSB course “Pattern recognition”</span></a><span style="font-size:10pt;font-family:Arial;color:rgb(0,0,0);font-variant-ligatures:normal;font-variant-east-asian:normal;vertical-align:baseline;white-space:pre-wrap"> and the ASCI course “Advanced pattern recognition” (a1) discuss many of the tools used in this course, but it is not required to have followed these. Prior knowledge of molecular biology is a bonus, but also not strictly required.</span></div><p dir="ltr" style="font-size:small;line-height:1.2;margin-top:10pt;margin-bottom:10pt"><span style="font-size:10pt;font-family:Arial;color:rgb(0,0,0);background-color:rgb(255,255,255);font-weight:700;font-variant-ligatures:normal;font-variant-east-asian:normal;vertical-align:baseline;white-space:pre-wrap">BioSB research school</span></p><p dir="ltr" style="font-size:small;line-height:1.2;margin-top:10pt;margin-bottom:10pt"><span style="font-size:10pt;font-family:Arial;color:rgb(0,0,0);background-color:rgb(255,255,255);font-variant-ligatures:normal;font-variant-east-asian:normal;vertical-align:baseline;white-space:pre-wrap">This course is part of the</span><a href="http://biosb.nl/education/course-portfolio-2/" style="color:rgb(17,85,204);text-decoration:none" target="_blank"><span style="font-size:10pt;font-family:Arial;color:rgb(128,0,128);background-color:rgb(255,255,255);font-variant-ligatures:normal;font-variant-east-asian:normal;text-decoration:underline;vertical-align:baseline;white-space:pre-wrap"> Education Programme of BioSB</span></a><span style="font-size:10pt;font-family:Arial;color:rgb(0,0,0);background-color:rgb(255,255,255);font-variant-ligatures:normal;font-variant-east-asian:normal;vertical-align:baseline;white-space:pre-wrap">, the Netherlands Bioinformatics and Systems Biology Research School, which offers training and education for in bioinformatics and systems biology.</span></p><p dir="ltr" style="font-size:small;line-height:1.2;margin-top:10pt;margin-bottom:10pt"><span style="font-size:10pt;font-family:Arial;color:rgb(0,0,0);background-color:rgb(255,255,255);font-variant-ligatures:normal;font-variant-east-asian:normal;vertical-align:baseline;white-space:pre-wrap">More information about BioSB can be found at </span><a href="http://www.biosb.nl/" style="color:rgb(17,85,204);text-decoration:none" target="_blank"><span style="font-size:10pt;font-family:Arial;color:rgb(128,0,128);background-color:rgb(255,255,255);font-variant-ligatures:normal;font-variant-east-asian:normal;text-decoration:underline;vertical-align:baseline;white-space:pre-wrap">www.biosb.nl</span></a><span style="font-size:10pt;font-family:Arial;color:rgb(0,0,0);background-color:rgb(255,255,255);font-variant-ligatures:normal;font-variant-east-asian:normal;vertical-align:baseline;white-space:pre-wrap">.</span></p></span><div>
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