{"id":293570,"date":"2016-09-22T16:19:44","date_gmt":"2016-09-22T23:19:44","guid":{"rendered":"https:\/\/www.microsoft.com\/en-us\/research\/?post_type=msr-event&#038;p=293570"},"modified":"2025-08-06T11:59:12","modified_gmt":"2025-08-06T18:59:12","slug":"computational-aspects-biological-information-2016","status":"publish","type":"msr-event","link":"https:\/\/www.microsoft.com\/en-us\/research\/event\/computational-aspects-biological-information-2016\/","title":{"rendered":"Computational Aspects of Biological Information 2016"},"content":{"rendered":"\n\n<p><strong>Venue:<\/strong> <a href=\"https:\/\/www.microsoft.com\/en-us\/research\/lab\/microsoft-research-new-england\/\" target=\"_blank\" rel=\"noopener noreferrer\">Microsoft Research New England<\/a><br \/>\nHorace Mann Conference Room<br \/>\nFirst Floor Conference Center<br \/>\nOne Memorial Drive, Cambridge, MA<\/p>\n<p><strong>Contact:<\/strong> Please email the conference organizers at\u00a0<a href=\"mailto:cabi2016@microsoft.com\">cabi2016@microsoft.com<\/a>.<span id=\"label-external-link\" class=\"sr-only\" aria-hidden=\"true\">Opens in a new tab<\/span><\/p>\n<p><img loading=\"lazy\" decoding=\"async\" class=\"size-medium wp-image-293573 alignright\" src=\"https:\/\/www.microsoft.com\/en-us\/research\/wp-content\/uploads\/2016\/09\/cabi2016_top_badge-artwork-300x228.png\" alt=\"Computational Aspects of Biological Information 2016\" width=\"300\" height=\"228\" srcset=\"https:\/\/www.microsoft.com\/en-us\/research\/wp-content\/uploads\/2016\/09\/cabi2016_top_badge-artwork-300x228.png 300w, https:\/\/www.microsoft.com\/en-us\/research\/wp-content\/uploads\/2016\/09\/cabi2016_top_badge-artwork-768x583.png 768w, https:\/\/www.microsoft.com\/en-us\/research\/wp-content\/uploads\/2016\/09\/cabi2016_top_badge-artwork-1024x777.png 1024w, https:\/\/www.microsoft.com\/en-us\/research\/wp-content\/uploads\/2016\/09\/cabi2016_top_badge-artwork-80x60.png 80w, https:\/\/www.microsoft.com\/en-us\/research\/wp-content\/uploads\/2016\/09\/cabi2016_top_badge-artwork.png 2018w\" sizes=\"auto, (max-width: 300px) 100vw, 300px\" \/>Computational Aspects of Biological Information (CABI) 2016 is the fourth one-day symposium\u00a0on challenges and successes in computational biology. CABI 2016 will be held at Microsoft Research New England on November 30, 2016 and will\u00a0bring together experts in the Boston\/Cambridge area to discuss computational solutions to problems in biology, including systems biology, genomics, and related areas. The symposium\u00a0is open to everyone and registration is free of charge. Lunch will be served.<\/p>\n<h2>Symposium Speakers<\/h2>\n<p>Confirmed speakers include:<\/p>\n<ul>\n<li><a class=\"msr-external-link glyph-append glyph-append-open-in-new-tab glyph-append-xsmall\" href=\"http:\/\/imes.mit.edu\/people\/faculty\/brown-emery\/\" target=\"_blank\" rel=\"noopener noreferrer\">Emery Brown<span class=\"sr-only\"> (opens in new tab)<\/span><\/a>, Massachusetts Institute of Technology<\/li>\n<li><a class=\"msr-external-link glyph-append glyph-append-open-in-new-tab glyph-append-xsmall\" href=\"http:\/\/the_brain.bwh.harvard.edu\/\" target=\"_blank\" rel=\"noopener noreferrer\">Martha Bulyk<span class=\"sr-only\"> (opens in new tab)<\/span><\/a>, Harvard\u00a0University<\/li>\n<li><a class=\"msr-external-link glyph-append glyph-append-open-in-new-tab glyph-append-xsmall\" href=\"http:\/\/arep.med.harvard.edu\/gmc\/\" target=\"_blank\" rel=\"noopener noreferrer\">George Church<span class=\"sr-only\"> (opens in new tab)<\/span><\/a>, Harvard\u00a0University<\/li>\n<li><a class=\"msr-external-link glyph-append glyph-append-open-in-new-tab glyph-append-xsmall\" href=\"http:\/\/churchman.med.harvard.edu\/\" target=\"_blank\" rel=\"noopener noreferrer\">Stirling Churchman<span class=\"sr-only\"> (opens in new tab)<\/span><\/a>, Harvard\u00a0University<\/li>\n<li><a class=\"msr-external-link glyph-append glyph-append-open-in-new-tab glyph-append-xsmall\" href=\"http:\/\/cgs.csail.mit.edu\/\" target=\"_blank\" rel=\"noopener noreferrer\">David Gifford<span class=\"sr-only\"> (opens in new tab)<\/span><\/a>,\u00a0Massachusetts Institute of Technology<\/li>\n<li><a class=\"msr-external-link glyph-append glyph-append-open-in-new-tab glyph-append-xsmall\" href=\"http:\/\/hahnlab.dana-farber.org\/\" target=\"_blank\" rel=\"noopener noreferrer\">William Hahn<span class=\"sr-only\"> (opens in new tab)<\/span><\/a>, Dana-Farber Cancer Institute<\/li>\n<li><a class=\"msr-external-link glyph-append glyph-append-open-in-new-tab glyph-append-xsmall\" href=\"https:\/\/www.atgu.mgh.harvard.edu\/people\/benjamin_neale\" target=\"_blank\" rel=\"noopener noreferrer\">Benjamin Neale<span class=\"sr-only\"> (opens in new tab)<\/span><\/a>,\u00a0Harvard Medical School<\/li>\n<li><a class=\"msr-external-link glyph-append glyph-append-open-in-new-tab glyph-append-xsmall\" href=\"http:\/\/paulsson.med.harvard.edu\/\" target=\"_blank\" rel=\"noopener noreferrer\">Johan Paulsson<span class=\"sr-only\"> (opens in new tab)<\/span><\/a>, Harvard\u00a0University<\/li>\n<li><a class=\"msr-external-link glyph-append glyph-append-open-in-new-tab glyph-append-xsmall\" href=\"http:\/\/compbio.cs.brown.edu\/research\/\" target=\"_blank\" rel=\"noopener noreferrer\">Ben Raphael<span class=\"sr-only\"> (opens in new tab)<\/span><\/a>, Princeton\u00a0University<\/li>\n<li><a class=\"msr-external-link glyph-append glyph-append-open-in-new-tab glyph-append-xsmall\" href=\"https:\/\/people.seas.harvard.edu\/~valiant\/\" target=\"_blank\" rel=\"noopener noreferrer\">Les Valiant<span class=\"sr-only\"> (opens in new tab)<\/span><\/a>, Harvard\u00a0University<\/li>\n<\/ul>\n<h2>Organizing committee<\/h2>\n<ul>\n<li><a class=\"msr-external-link glyph-append glyph-append-open-in-new-tab glyph-append-xsmall\" href=\"http:\/\/nicolofusi.com\/\" target=\"_blank\" rel=\"noopener noreferrer\">Nicolo Fusi<span class=\"sr-only\"> (opens in new tab)<\/span><\/a>,\u00a0Microsoft Research<\/li>\n<li><a class=\"msr-external-link glyph-append glyph-append-open-in-new-tab glyph-append-xsmall\" href=\"http:\/\/maxleiserson.com\/\" target=\"_blank\" rel=\"noopener noreferrer\">Max Leiserson<span class=\"sr-only\"> (opens in new tab)<\/span><\/a>,\u00a0Microsoft Research<\/li>\n<li><a class=\"msr-external-link glyph-append glyph-append-open-in-new-tab glyph-append-xsmall\" href=\"http:\/\/research.microsoft.com\/en-us\/um\/people\/jennl\/\" target=\"_blank\" rel=\"noopener noreferrer\">Jennifer Listgarten<span class=\"sr-only\"> (opens in new tab)<\/span><\/a>,\u00a0Microsoft Research<\/li>\n<\/ul>\n<h2>Poster Session<\/h2>\n<p>There will be a poster session in the afternoon. Poster submissions are now closed.<\/p>\n<p><strong>Hospitality Notice for University and Government Employees: <\/strong>Microsoft Research is providing hospitality at this event. Please consult with your institution to determine whether you can accept meals and other hospitality under your institution&#8217;s ethics rules and any other laws that might apply. By accepting our invitation, you confirm that this invitation is compliant with your institution&#8217;s policies.<\/p>\n<p><strong>Arrival Guidance<\/strong><\/p>\n<p>Upon arrival, be prepared to show a picture ID and sign the Building Visitor Log when approaching the Lobby Floor Security Desk. Alert them to the name of the event you are attending and ask them to direct you to the appropriate floor. The talks will be held the First Floor Conference Center, Horace Mann Conference Room.<span id=\"label-external-link\" class=\"sr-only\" aria-hidden=\"true\">Opens in a new tab<\/span><\/p>\n<p><strong>Poster submissions are now closed.<\/strong><\/p>\n<p>To be considered for the CABI 2016 poster session, please submit the following information to <a href=\"mailto:CABI2016posters@microsoft.com\">CABI2016posters@microsoft.com<\/a>\u00a0by October 31st. Submissions will be evaluated on a rolling basis, and acceptance notifications will be sent by November 9th. Space is limited, and preference will be given to early submissions.<\/p>\n<p>Posters may be up to 48\u201dW X 36\u201dH.<\/p>\n<ul>\n<li>Presenting author name<\/li>\n<li>Presenting author affiliation\/institution<\/li>\n<li>Presenting author email address<\/li>\n<li>Title<\/li>\n<li>Complete list of authors (first name last name).\u00a0 Please do not list author affiliations.<\/li>\n<li>Abstract (250 words maximum)<\/li>\n<\/ul>\n<p>Please email the conference organizers at <a href=\"mailto:cabi2016@microsoft.com\">cabi2016@microsoft.com<\/a> if you have any questions.<span id=\"label-external-link\" class=\"sr-only\" aria-hidden=\"true\">Opens in a new tab<\/span><\/p>\n<table class=\"msr-table-schedule\">\n<thead class=\"thead\">\n<tr class=\"tr\">\n<th class=\"th\">Time<\/th>\n<th class=\"th\">Session<\/th>\n<th class=\"th\">Speaker<\/th>\n<\/tr>\n<\/thead>\n<tbody class=\"tbody\">\n<tr class=\"tr\">\n<td class=\"td-1-3\">\n<div class=\"msr-table-schedule-cell\">9:00 AM<\/div>\n<\/td>\n<td>\n<div class=\"msr-table-schedule-cell\">Registration and coffee service<\/div>\n<\/td>\n<td><\/td>\n<\/tr>\n<tr class=\"tr\">\n<td class=\"td-1-3\">\n<div class=\"msr-table-schedule-cell\">9:50 AM<\/div>\n<\/td>\n<td>Opening remarks<\/td>\n<td>Jennifer Chayes<\/td>\n<\/tr>\n<tr class=\"tr\">\n<td class=\"td-1-3\">\n<div class=\"msr-table-schedule-cell\">10:00 AM<\/div>\n<\/td>\n<td>The role of fluctuations in individual cells<\/td>\n<td>\n<div class=\"msr-table-schedule-cell\">Johan Paulsson<\/div>\n<\/td>\n<\/tr>\n<tr class=\"tr\">\n<td class=\"td-1-3\">\n<div class=\"msr-table-schedule-cell\">10:30 AM<\/div>\n<\/td>\n<td>Visualizing transcription at nucleotide resolution with NET-seq<\/td>\n<td>\n<div class=\"msr-table-schedule-cell\">Stirling Churchman<\/div>\n<\/td>\n<\/tr>\n<tr class=\"tr\">\n<td class=\"td-1-3\">\n<div class=\"msr-table-schedule-cell\">11:00 AM<\/div>\n<\/td>\n<td>\n<div class=\"msr-table-schedule-cell\">Coffee break<\/div>\n<\/td>\n<td><\/td>\n<\/tr>\n<tr class=\"tr\">\n<td class=\"td-1-3\">\n<div class=\"msr-table-schedule-cell\">11:15 AM<\/div>\n<\/td>\n<td>Systematic identification of cancer targets<\/td>\n<td>Bill Hahn<\/td>\n<\/tr>\n<tr class=\"tr\">\n<td class=\"td-1-3\">\n<div class=\"msr-table-schedule-cell\">11:45 AM<\/div>\n<\/td>\n<td>Cancer Genome Evolution<\/td>\n<td>Ben Raphael<\/td>\n<\/tr>\n<tr class=\"tr\">\n<td class=\"td-1-3\">\n<div class=\"msr-table-schedule-cell\">12:15 PM<\/div>\n<\/td>\n<td>\n<div class=\"msr-table-schedule-cell\">Lunch<\/div>\n<\/td>\n<td><\/td>\n<\/tr>\n<tr class=\"tr\">\n<td class=\"td-1-3\">\n<div class=\"msr-table-schedule-cell\">1:00 PM<\/div>\n<\/td>\n<td>\n<div class=\"msr-table-schedule-cell\">Poster session<\/div>\n<\/td>\n<td><\/td>\n<\/tr>\n<tr class=\"tr\">\n<td class=\"td-1-3\">\n<div class=\"msr-table-schedule-cell\">1:30 PM<\/div>\n<\/td>\n<td>Reading & Writing Omni Omics In Situ<\/td>\n<td>George Church<\/td>\n<\/tr>\n<tr class=\"tr\">\n<td class=\"td-1-3\">\n<div class=\"msr-table-schedule-cell\">2:00 PM<\/div>\n<\/td>\n<td>Darwinian Evolution as Learning<\/td>\n<td>Leslie Valiant<\/td>\n<\/tr>\n<tr class=\"tr\">\n<td class=\"td-1-3\">\n<div class=\"msr-table-schedule-cell\">2:30 PM<\/div>\n<\/td>\n<td>Measuring and Controlling the Dynamics of the Anesthetized Brain<\/td>\n<td>Emery Brown<\/td>\n<\/tr>\n<tr class=\"tr\">\n<td class=\"td-1-3\">\n<div class=\"msr-table-schedule-cell\">3:00 PM<\/div>\n<\/td>\n<td>\n<div class=\"msr-table-schedule-cell\">Coffee break\/poster session<\/div>\n<\/td>\n<td><\/td>\n<\/tr>\n<tr class=\"tr\">\n<td class=\"td-1-3\">\n<div class=\"msr-table-schedule-cell\">3:45 PM<\/div>\n<\/td>\n<td>Mapping the regulatory genome<\/td>\n<td>David Gifford<\/td>\n<\/tr>\n<tr class=\"tr\">\n<td class=\"td-1-3\">\n<div class=\"msr-table-schedule-cell\">4:15 PM<\/div>\n<\/td>\n<td>Genetic variation in human transcription factors<\/td>\n<td>Martha Bulyk<\/td>\n<\/tr>\n<tr class=\"tr\">\n<td class=\"td-1-3\">\n<div class=\"msr-table-schedule-cell\">4:45 PM<\/div>\n<\/td>\n<td>Scaling up genetic analysis<\/td>\n<td>Benjamin Neale<\/td>\n<\/tr>\n<tr class=\"tr\">\n<td class=\"td-1-3\">\n<div class=\"msr-table-schedule-cell\">5:15 PM<\/div>\n<\/td>\n<td>Closing remarks<\/td>\n<td><\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<p><span id=\"label-external-link\" class=\"sr-only\" aria-hidden=\"true\">Opens in a new tab<\/span><\/p>\n<p>\t<div data-wp-context='{\"items\":[]}' data-wp-interactive=\"msr\/accordion\">\n\t\t\t\t\t<div class=\"clearfix\">\n\t\t\t\t<div\n\t\t\t\t\tclass=\"btn-group align-items-center mb-g float-sm-right\"\n\t\t\t\t\tdata-bi-aN=\"accordion-collapse-controls\"\n\t\t\t\t>\n\t\t\t\t\t<button\n\t\t\t\t\t\tclass=\"btn btn-link m-0\"\n\t\t\t\t\t\tdata-bi-cN=\"Expand all\"\n\t\t\t\t\t\tdata-wp-bind--aria-controls=\"state.ariaControls\"\n\t\t\t\t\t\tdata-wp-bind--aria-expanded=\"state.ariaExpanded\"\n\t\t\t\t\t\tdata-wp-bind--disabled=\"state.isAllExpanded\"\n\t\t\t\t\t\tdata-wp-class--inactive=\"state.isAllExpanded\"\n\t\t\t\t\t\tdata-wp-on--click=\"actions.onExpandAll\"\n\t\t\t\t\t\ttype=\"button\"\n\t\t\t\t\t>\n\t\t\t\t\t\tExpand all\t\t\t\t\t<\/button>\n\t\t\t\t\t<span aria-hidden=\"true\"> | <\/span>\n\t\t\t\t\t<button\n\t\t\t\t\t\tclass=\"btn btn-link m-0\"\n\t\t\t\t\t\tdata-bi-cN=\"Collapse all\"\n\t\t\t\t\t\tdata-wp-bind--aria-controls=\"state.ariaControls\"\n\t\t\t\t\t\tdata-wp-bind--aria-expanded=\"state.ariaExpanded\"\n\t\t\t\t\t\tdata-wp-bind--disabled=\"state.isAllCollapsed\"\n\t\t\t\t\t\tdata-wp-class--inactive=\"state.isAllCollapsed\"\n\t\t\t\t\t\tdata-wp-on--click=\"actions.onCollapseAll\"\n\t\t\t\t\t\ttype=\"button\"\n\t\t\t\t\t>\n\t\t\t\t\t\tCollapse all\t\t\t\t\t<\/button>\n\t\t\t\t<\/div>\n\t\t\t<\/div>\n\t\t\t\t<ul class=\"msr-accordion\">\n\t\t\t\t\t\t\t\t<li class=\"m-0\" data-wp-context='{\"id\":\"accordion-content-2652\"}' data-wp-init=\"callbacks.init\">\n\t\t<div class=\"accordion-header\">\n\t\t\t<button\n\t\t\t\taria-controls=\"accordion-content-2652\"\n\t\t\t\tclass=\"btn btn-collapse\"\n\t\t\t\tdata-wp-bind--aria-expanded=\"state.isExpanded\"\n\t\t\t\tdata-wp-on--click=\"actions.onClick\"\n\t\t\t\tid=\"accordion-button-2651\"\n\t\t\t\ttype=\"button\"\n\t\t\t>\n\t\t\t\tThe role of fluctuations in individual cells\t\t\t<\/button>\n\t\t<\/div>\n\t\t<div\n\t\t\taria-labelledby=\"accordion-button-2651\"\n\t\t\tclass=\"msr-accordion__content\"\n\t\t\tdata-wp-bind--inert=\"!state.isExpanded\"\n\t\t\tdata-wp-run=\"callbacks.run\"\n\t\t\tid=\"accordion-content-2652\"\n\t\t>\n\t\t\t<div class=\"msr-accordion__body\">\n\t\t\t\t<p><strong>Speaker:<\/strong>\u00a0Johan Paulsson<\/p>\n<p>All processes in single cells involve components present in low numbers, creating spontaneous fluctuations that in turn can enslave the components present in high numbers. In the first half of the talk I will discuss some mathematical frameworks we developed to analytically predict and analyze random fluctuations in complex processes. The second half of the talk will focus on experimental methods to quantify dynamics in cells, as well as examples of microbial systems where fluctuations play a large role, including feedback control of replication, cell fate decisions, epigenetic oscillations and DNA repair.<\/p>\n<p><span id=\"label-external-link\" class=\"sr-only\" aria-hidden=\"true\">Opens in a new tab<\/span><\/p>\n\t\t\t<\/div>\n\t\t<\/div>\n\t<\/li>\n\t\t<li class=\"m-0\" data-wp-context='{\"id\":\"accordion-content-2654\"}' data-wp-init=\"callbacks.init\">\n\t\t<div class=\"accordion-header\">\n\t\t\t<button\n\t\t\t\taria-controls=\"accordion-content-2654\"\n\t\t\t\tclass=\"btn btn-collapse\"\n\t\t\t\tdata-wp-bind--aria-expanded=\"state.isExpanded\"\n\t\t\t\tdata-wp-on--click=\"actions.onClick\"\n\t\t\t\tid=\"accordion-button-2653\"\n\t\t\t\ttype=\"button\"\n\t\t\t>\n\t\t\t\tSystematic identification of cancer targets\t\t\t<\/button>\n\t\t<\/div>\n\t\t<div\n\t\t\taria-labelledby=\"accordion-button-2653\"\n\t\t\tclass=\"msr-accordion__content\"\n\t\t\tdata-wp-bind--inert=\"!state.isExpanded\"\n\t\t\tdata-wp-run=\"callbacks.run\"\n\t\t\tid=\"accordion-content-2654\"\n\t\t>\n\t\t\t<div class=\"msr-accordion__body\">\n\t\t\t\t<p><strong>Speaker:<\/strong>\u00a0Bill Hahn<\/p>\n<p>Although we now have a draft view of the genetic alterations that occur in human cancer, the number of mutations found at low frequency and the molecular heterogeneity of most cancers makes identifying genes that contribute to cancer phenotypes challenging. Determining the function of genes altered in cancer genomes is essential to develop new therapeutic approaches. To complement these genome characterization studies, we have used genome scale gain and loss of function approaches to identify genes required for cell survival and transformation. Specifically, we have performed systematic studies to interrogate rare alleles found altered in cancer genomes and used advances in synthetic gene synthesis to prospectively interrogate all possible alleles of known cancer genes. In parallel, we have performed both genome scale RNAi and CRISRP-Cas9 screens in more than 500 cell lines to identify differentially essential genes and the context that specifies gene dependency. This approach now permits us to identify and classify cancer dependencies. These studies allow us to begin to define a global cancer dependencies map.<\/p>\n<p><span id=\"label-external-link\" class=\"sr-only\" aria-hidden=\"true\">Opens in a new tab<\/span><\/p>\n\t\t\t<\/div>\n\t\t<\/div>\n\t<\/li>\n\t\t<li class=\"m-0\" data-wp-context='{\"id\":\"accordion-content-2656\"}' data-wp-init=\"callbacks.init\">\n\t\t<div class=\"accordion-header\">\n\t\t\t<button\n\t\t\t\taria-controls=\"accordion-content-2656\"\n\t\t\t\tclass=\"btn btn-collapse\"\n\t\t\t\tdata-wp-bind--aria-expanded=\"state.isExpanded\"\n\t\t\t\tdata-wp-on--click=\"actions.onClick\"\n\t\t\t\tid=\"accordion-button-2655\"\n\t\t\t\ttype=\"button\"\n\t\t\t>\n\t\t\t\tCancer Genome Evolution\t\t\t<\/button>\n\t\t<\/div>\n\t\t<div\n\t\t\taria-labelledby=\"accordion-button-2655\"\n\t\t\tclass=\"msr-accordion__content\"\n\t\t\tdata-wp-bind--inert=\"!state.isExpanded\"\n\t\t\tdata-wp-run=\"callbacks.run\"\n\t\t\tid=\"accordion-content-2656\"\n\t\t>\n\t\t\t<div class=\"msr-accordion__body\">\n\t\t\t\t<p><strong>Speaker:<\/strong>\u00a0Ben Raphael<\/p>\n<p>Cancer is an evolutionary process driven by somatic mutations that accumulate in a population of cells. In this talk, I will describe several algorithms to reconstruct this process from DNA sequencing data of tumor samples. These algorithms address challenges that distinguish the cancer genome phylogeny problem from classical phylogenetic tree reconstruction. I will demonstrate the application of these algorithms to sequencing data from multiple cancer types.<\/p>\n<p><span id=\"label-external-link\" class=\"sr-only\" aria-hidden=\"true\">Opens in a new tab<\/span><\/p>\n\t\t\t<\/div>\n\t\t<\/div>\n\t<\/li>\n\t\t<li class=\"m-0\" data-wp-context='{\"id\":\"accordion-content-2658\"}' data-wp-init=\"callbacks.init\">\n\t\t<div class=\"accordion-header\">\n\t\t\t<button\n\t\t\t\taria-controls=\"accordion-content-2658\"\n\t\t\t\tclass=\"btn btn-collapse\"\n\t\t\t\tdata-wp-bind--aria-expanded=\"state.isExpanded\"\n\t\t\t\tdata-wp-on--click=\"actions.onClick\"\n\t\t\t\tid=\"accordion-button-2657\"\n\t\t\t\ttype=\"button\"\n\t\t\t>\n\t\t\t\tReading & Writing Omni Omics In Situ\t\t\t<\/button>\n\t\t<\/div>\n\t\t<div\n\t\t\taria-labelledby=\"accordion-button-2657\"\n\t\t\tclass=\"msr-accordion__content\"\n\t\t\tdata-wp-bind--inert=\"!state.isExpanded\"\n\t\t\tdata-wp-run=\"callbacks.run\"\n\t\t\tid=\"accordion-content-2658\"\n\t\t>\n\t\t\t<div class=\"msr-accordion__body\">\n\t\t\t\t<p><strong>Speaker:<\/strong> George Church<\/p>\n<p>Exponential technologies such as Expansion Fluorescent In Situ Sequencing (FISSeq\/ExSeq) enable computational analysis of multicellular organs including synapse-level-resolution of connectome and transcriptome plus nucleosome-level-resolution chromosome chain tracing in situ (via Oligopaints).\u00a0 We can also computationally design and build whole genomes (via synthesis and recombination) and epigenomes (via comprehensive transcription factor libraries).\u00a0 Data from the IARPA MICrONS BRAIN project is aimed at new insights into visual machine learning strategies.<\/p>\n<p><span id=\"label-external-link\" class=\"sr-only\" aria-hidden=\"true\">Opens in a new tab<\/span><\/p>\n\t\t\t<\/div>\n\t\t<\/div>\n\t<\/li>\n\t\t<li class=\"m-0\" data-wp-context='{\"id\":\"accordion-content-2660\"}' data-wp-init=\"callbacks.init\">\n\t\t<div class=\"accordion-header\">\n\t\t\t<button\n\t\t\t\taria-controls=\"accordion-content-2660\"\n\t\t\t\tclass=\"btn btn-collapse\"\n\t\t\t\tdata-wp-bind--aria-expanded=\"state.isExpanded\"\n\t\t\t\tdata-wp-on--click=\"actions.onClick\"\n\t\t\t\tid=\"accordion-button-2659\"\n\t\t\t\ttype=\"button\"\n\t\t\t>\n\t\t\t\tDarwinian Evolution as Learning\t\t\t<\/button>\n\t\t<\/div>\n\t\t<div\n\t\t\taria-labelledby=\"accordion-button-2659\"\n\t\t\tclass=\"msr-accordion__content\"\n\t\t\tdata-wp-bind--inert=\"!state.isExpanded\"\n\t\t\tdata-wp-run=\"callbacks.run\"\n\t\t\tid=\"accordion-content-2660\"\n\t\t>\n\t\t\t<div class=\"msr-accordion__body\">\n\t\t\t\t<p><strong>Speaker:<\/strong>\u00a0Leslie Valiant<\/p>\n<p>Living organisms function according to protein circuits. Darwin&#8217;s theory of evolution suggests that these circuits have evolved through variation guided by natural selection. However, the question of which kinds of circuits can so evolve in realistic population sizes and within realistic numbers of generations has remained essentially unaddressed.<\/p>\n<p>We suggest that computational learning theory offers the framework for investigating this question, of how circuits can come into existence adaptively from experience, without a designer, or be then maintained. We formulate evolution as a form of learning from examples. The targets of the learning process are the functions of highest fitness. The examples are the experiences. The learning process is constrained so that the feedback from the experiences is Darwinian. We formulate a notion of evolvability that distinguishes function classes that are evolvable with polynomially bounded resources from those that are not. The dilemma is that if the function class, in particualr of the expression levels of proteins in terms of each other, is too restrictive, then it will not support biology, while if it is too expressive then no evolution algorithm will exist to navigate it. We shall review current work in this area.<\/p>\n<p><span id=\"label-external-link\" class=\"sr-only\" aria-hidden=\"true\">Opens in a new tab<\/span><\/p>\n\t\t\t<\/div>\n\t\t<\/div>\n\t<\/li>\n\t\t<li class=\"m-0\" data-wp-context='{\"id\":\"accordion-content-2662\"}' data-wp-init=\"callbacks.init\">\n\t\t<div class=\"accordion-header\">\n\t\t\t<button\n\t\t\t\taria-controls=\"accordion-content-2662\"\n\t\t\t\tclass=\"btn btn-collapse\"\n\t\t\t\tdata-wp-bind--aria-expanded=\"state.isExpanded\"\n\t\t\t\tdata-wp-on--click=\"actions.onClick\"\n\t\t\t\tid=\"accordion-button-2661\"\n\t\t\t\ttype=\"button\"\n\t\t\t>\n\t\t\t\tScaling up genetic analysis\t\t\t<\/button>\n\t\t<\/div>\n\t\t<div\n\t\t\taria-labelledby=\"accordion-button-2661\"\n\t\t\tclass=\"msr-accordion__content\"\n\t\t\tdata-wp-bind--inert=\"!state.isExpanded\"\n\t\t\tdata-wp-run=\"callbacks.run\"\n\t\t\tid=\"accordion-content-2662\"\n\t\t>\n\t\t\t<div class=\"msr-accordion__body\">\n\t\t\t\t<p><strong>Speaker:<\/strong>\u00a0Ben Neale<\/p>\n<p>With the advent of sequencing technology and ever increasing genome-wide association datasets, we tools to meet the challenges of scale. Here I will describe our efforts to develop a software package, hail, that is built using spark and scala. Hail leverages a distributed model of computing to perform scalable sequence data quality control and analysis. In doing so, we can perform primary quality control analyses on whole genome sequencing datasets of ~5,000 individuals in under an hour. Using hail, we have performed analyses of education attainment on a sample of over 14,000 individuals, identifying a clear role of ultra-rare disruptive mutations in the genetic architecture. We further explored the consequences of this class of variation across a wide range of traits and demonstrate that neuropsychiatric traits appear to have a directional burden effect in contrast to later onset systemic disease.<\/p>\n<p><span id=\"label-external-link\" class=\"sr-only\" aria-hidden=\"true\">Opens in a new tab<\/span><\/p>\n\t\t\t<\/div>\n\t\t<\/div>\n\t<\/li>\n\t\t<li class=\"m-0\" data-wp-context='{\"id\":\"accordion-content-2664\"}' data-wp-init=\"callbacks.init\">\n\t\t<div class=\"accordion-header\">\n\t\t\t<button\n\t\t\t\taria-controls=\"accordion-content-2664\"\n\t\t\t\tclass=\"btn btn-collapse\"\n\t\t\t\tdata-wp-bind--aria-expanded=\"state.isExpanded\"\n\t\t\t\tdata-wp-on--click=\"actions.onClick\"\n\t\t\t\tid=\"accordion-button-2663\"\n\t\t\t\ttype=\"button\"\n\t\t\t>\n\t\t\t\tMapping the regulatory genome\t\t\t<\/button>\n\t\t<\/div>\n\t\t<div\n\t\t\taria-labelledby=\"accordion-button-2663\"\n\t\t\tclass=\"msr-accordion__content\"\n\t\t\tdata-wp-bind--inert=\"!state.isExpanded\"\n\t\t\tdata-wp-run=\"callbacks.run\"\n\t\t\tid=\"accordion-content-2664\"\n\t\t>\n\t\t\t<div class=\"msr-accordion__body\">\n\t\t\t\t<p><strong>Speaker:<\/strong>\u00a0David Gifford<\/p>\n<p>With the advent of multiplexed DNA oligo synthesis, CRISPR genome editing, and high-throughput sequencing it is now possible to characterize genome function with experiments that directly observe the effect of sequence variants.\u00a0\u00a0 We will discuss the computational design and analysis of sequence variants that have a causal effect on the binding of DNA regulatory proteins and proximal gene expression.\u00a0\u00a0\u00a0 New results include the observation of regulatory elements in regions of the genome with no observed epigenetic marks.<\/p>\n<p><span id=\"label-external-link\" class=\"sr-only\" aria-hidden=\"true\">Opens in a new tab<\/span><\/p>\n\t\t\t<\/div>\n\t\t<\/div>\n\t<\/li>\n\t\t<li class=\"m-0\" data-wp-context='{\"id\":\"accordion-content-2666\"}' data-wp-init=\"callbacks.init\">\n\t\t<div class=\"accordion-header\">\n\t\t\t<button\n\t\t\t\taria-controls=\"accordion-content-2666\"\n\t\t\t\tclass=\"btn btn-collapse\"\n\t\t\t\tdata-wp-bind--aria-expanded=\"state.isExpanded\"\n\t\t\t\tdata-wp-on--click=\"actions.onClick\"\n\t\t\t\tid=\"accordion-button-2665\"\n\t\t\t\ttype=\"button\"\n\t\t\t>\n\t\t\t\tGenetic variation in human transcription factors\t\t\t<\/button>\n\t\t<\/div>\n\t\t<div\n\t\t\taria-labelledby=\"accordion-button-2665\"\n\t\t\tclass=\"msr-accordion__content\"\n\t\t\tdata-wp-bind--inert=\"!state.isExpanded\"\n\t\t\tdata-wp-run=\"callbacks.run\"\n\t\t\tid=\"accordion-content-2666\"\n\t\t>\n\t\t\t<div class=\"msr-accordion__body\">\n\t\t\t\t<p><strong>Speaker:<\/strong>\u00a0Martha Bulyk<\/p>\n<p>Sequencing of exomes and genomes has revealed abundant genetic variation affecting the coding sequences of human transcription factors (TFs), but the consequences of such variation remain largely unexplored. We developed a computational, structure-based approach to evaluate TF variants for their impact on DNA-binding activity and used universal protein binding microarrays to assay sequence-specific DNA-binding activity across 41 reference and 117 variant alleles found in individuals of diverse ancestries and families with Mendelian diseases. We found 77 variants in 28 genes that affect DNA-binding affinity or specificity and identified thousands of rare alleles likely to alter the DNA-binding activity of human sequence-specific TFs. Our results suggest that most individuals have unique repertoires of TF DNA-binding activities, which may contribute to phenotypic variation.<\/p>\n<p><span id=\"label-external-link\" class=\"sr-only\" aria-hidden=\"true\">Opens in a new tab<\/span><\/p>\n\t\t\t<\/div>\n\t\t<\/div>\n\t<\/li>\n\t\t\t\t\t\t<\/ul>\n\t<\/div>\n\t<span id=\"label-external-link\" class=\"sr-only\" aria-hidden=\"true\">Opens in a new tab<\/span><\/p>\n","protected":false},"excerpt":{"rendered":"<p>Computational Aspects of Biological Information (CABI) 2016 is the fourth one-day symposium on challenges and successes in computational biology. CABI 2016 will be held at Microsoft Research New England on November 30, 2016 and will bring together experts in the Boston\/Cambridge area to discuss computational solutions to problems in biology, including systems biology, genomics, and related areas. The symposium is open to everyone and registration is free of charge.<\/p>\n","protected":false},"featured_media":381725,"template":"","meta":{"msr-url-field":"","msr-podcast-episode":"","msrModifiedDate":"","msrModifiedDateEnabled":false,"ep_exclude_from_search":false,"_classifai_error":"","msr_startdate":"2016-11-30","msr_enddate":"2016-11-30","msr_location":"Cambridge, MA, USA","msr_expirationdate":"","msr_event_recording_link":"","msr_event_link":"","msr_event_link_redirect":false,"msr_event_time":"9:00 AM \u2013 5:30 PM","msr_hide_region":true,"msr_private_event":false,"msr_hide_image_in_river":0,"footnotes":""},"research-area":[13553],"msr-region":[197900],"msr-event-type":[197944],"msr-video-type":[],"msr-locale":[268875],"msr-program-audience":[],"msr-post-option":[],"msr-impact-theme":[],"class_list":["post-293570","msr-event","type-msr-event","status-publish","has-post-thumbnail","hentry","msr-research-area-medical-health-genomics","msr-region-north-america","msr-event-type-hosted-by-microsoft","msr-locale-en_us"],"msr_about":"<!-- wp:msr\/event-details {\"title\":\"Computational Aspects of Biological Information 2016\",\"backgroundColor\":\"grey\",\"image\":{\"id\":381725,\"url\":\"https:\/\/www.microsoft.com\/en-us\/research\/wp-content\/uploads\/2016\/09\/MSR-CABI-Hero_1920x720-v1.jpg\",\"alt\":\"\"}} \/-->\n\n<!-- wp:msr\/content-tabs --><!-- wp:msr\/content-tab {\"title\":\"About\"} --><!-- wp:freeform --><p><strong>Venue:<\/strong> <a href=\"https:\/\/www.microsoft.com\/en-us\/research\/lab\/microsoft-research-new-england\/\" target=\"_blank\" rel=\"noopener noreferrer\">Microsoft Research New England<\/a><br \/>\nHorace Mann Conference Room<br \/>\nFirst Floor Conference Center<br \/>\nOne Memorial Drive, Cambridge, MA<\/p>\n<p><strong>Contact:<\/strong> Please email the conference organizers at\u00a0<a href=\"mailto:cabi2016@microsoft.com\">cabi2016@microsoft.com<\/a>.<span id=\"label-external-link\" class=\"sr-only\" aria-hidden=\"true\">Opens in a new tab<\/span><\/p>\n<p><img loading=\"lazy\" decoding=\"async\" class=\"size-medium wp-image-293573 alignright\" src=\"https:\/\/www.microsoft.com\/en-us\/research\/wp-content\/uploads\/2016\/09\/cabi2016_top_badge-artwork-300x228.png\" alt=\"Computational Aspects of Biological Information 2016\" width=\"300\" height=\"228\" srcset=\"https:\/\/www.microsoft.com\/en-us\/research\/wp-content\/uploads\/2016\/09\/cabi2016_top_badge-artwork-300x228.png 300w, https:\/\/www.microsoft.com\/en-us\/research\/wp-content\/uploads\/2016\/09\/cabi2016_top_badge-artwork-768x583.png 768w, https:\/\/www.microsoft.com\/en-us\/research\/wp-content\/uploads\/2016\/09\/cabi2016_top_badge-artwork-1024x777.png 1024w, https:\/\/www.microsoft.com\/en-us\/research\/wp-content\/uploads\/2016\/09\/cabi2016_top_badge-artwork-80x60.png 80w, https:\/\/www.microsoft.com\/en-us\/research\/wp-content\/uploads\/2016\/09\/cabi2016_top_badge-artwork.png 2018w\" sizes=\"auto, (max-width: 300px) 100vw, 300px\" \/>Computational Aspects of Biological Information (CABI) 2016 is the fourth one-day symposium\u00a0on challenges and successes in computational biology. CABI 2016 will be held at Microsoft Research New England on November 30, 2016 and will\u00a0bring together experts in the Boston\/Cambridge area to discuss computational solutions to problems in biology, including systems biology, genomics, and related areas. The symposium\u00a0is open to everyone and registration is free of charge. Lunch will be served.<\/p>\n<h2>Symposium Speakers<\/h2>\n<p>Confirmed speakers include:<\/p>\n<ul>\n<li><a class=\"msr-external-link glyph-append glyph-append-open-in-new-tab glyph-append-xsmall\" href=\"http:\/\/imes.mit.edu\/people\/faculty\/brown-emery\/\" target=\"_blank\" rel=\"noopener noreferrer\">Emery Brown<span class=\"sr-only\"> (opens in new tab)<\/span><\/a>, Massachusetts Institute of Technology<\/li>\n<li><a class=\"msr-external-link glyph-append glyph-append-open-in-new-tab glyph-append-xsmall\" href=\"http:\/\/the_brain.bwh.harvard.edu\/\" target=\"_blank\" rel=\"noopener noreferrer\">Martha Bulyk<span class=\"sr-only\"> (opens in new tab)<\/span><\/a>, Harvard\u00a0University<\/li>\n<li><a class=\"msr-external-link glyph-append glyph-append-open-in-new-tab glyph-append-xsmall\" href=\"http:\/\/arep.med.harvard.edu\/gmc\/\" target=\"_blank\" rel=\"noopener noreferrer\">George Church<span class=\"sr-only\"> (opens in new tab)<\/span><\/a>, Harvard\u00a0University<\/li>\n<li><a class=\"msr-external-link glyph-append glyph-append-open-in-new-tab glyph-append-xsmall\" href=\"http:\/\/churchman.med.harvard.edu\/\" target=\"_blank\" rel=\"noopener noreferrer\">Stirling Churchman<span class=\"sr-only\"> (opens in new tab)<\/span><\/a>, Harvard\u00a0University<\/li>\n<li><a class=\"msr-external-link glyph-append glyph-append-open-in-new-tab glyph-append-xsmall\" href=\"http:\/\/cgs.csail.mit.edu\/\" target=\"_blank\" rel=\"noopener noreferrer\">David Gifford<span class=\"sr-only\"> (opens in new tab)<\/span><\/a>,\u00a0Massachusetts Institute of Technology<\/li>\n<li><a class=\"msr-external-link glyph-append glyph-append-open-in-new-tab glyph-append-xsmall\" href=\"http:\/\/hahnlab.dana-farber.org\/\" target=\"_blank\" rel=\"noopener noreferrer\">William Hahn<span class=\"sr-only\"> (opens in new tab)<\/span><\/a>, Dana-Farber Cancer Institute<\/li>\n<li><a class=\"msr-external-link glyph-append glyph-append-open-in-new-tab glyph-append-xsmall\" href=\"https:\/\/www.atgu.mgh.harvard.edu\/people\/benjamin_neale\" target=\"_blank\" rel=\"noopener noreferrer\">Benjamin Neale<span class=\"sr-only\"> (opens in new tab)<\/span><\/a>,\u00a0Harvard Medical School<\/li>\n<li><a class=\"msr-external-link glyph-append glyph-append-open-in-new-tab glyph-append-xsmall\" href=\"http:\/\/paulsson.med.harvard.edu\/\" target=\"_blank\" rel=\"noopener noreferrer\">Johan Paulsson<span class=\"sr-only\"> (opens in new tab)<\/span><\/a>, Harvard\u00a0University<\/li>\n<li><a class=\"msr-external-link glyph-append glyph-append-open-in-new-tab glyph-append-xsmall\" href=\"http:\/\/compbio.cs.brown.edu\/research\/\" target=\"_blank\" rel=\"noopener noreferrer\">Ben Raphael<span class=\"sr-only\"> (opens in new tab)<\/span><\/a>, Princeton\u00a0University<\/li>\n<li><a class=\"msr-external-link glyph-append glyph-append-open-in-new-tab glyph-append-xsmall\" href=\"https:\/\/people.seas.harvard.edu\/~valiant\/\" target=\"_blank\" rel=\"noopener noreferrer\">Les Valiant<span class=\"sr-only\"> (opens in new tab)<\/span><\/a>, Harvard\u00a0University<\/li>\n<\/ul>\n<h2>Organizing committee<\/h2>\n<ul>\n<li><a class=\"msr-external-link glyph-append glyph-append-open-in-new-tab glyph-append-xsmall\" href=\"http:\/\/nicolofusi.com\/\" target=\"_blank\" rel=\"noopener noreferrer\">Nicolo Fusi<span class=\"sr-only\"> (opens in new tab)<\/span><\/a>,\u00a0Microsoft Research<\/li>\n<li><a class=\"msr-external-link glyph-append glyph-append-open-in-new-tab glyph-append-xsmall\" href=\"http:\/\/maxleiserson.com\/\" target=\"_blank\" rel=\"noopener noreferrer\">Max Leiserson<span class=\"sr-only\"> (opens in new tab)<\/span><\/a>,\u00a0Microsoft Research<\/li>\n<li><a class=\"msr-external-link glyph-append glyph-append-open-in-new-tab glyph-append-xsmall\" href=\"http:\/\/research.microsoft.com\/en-us\/um\/people\/jennl\/\" target=\"_blank\" rel=\"noopener noreferrer\">Jennifer Listgarten<span class=\"sr-only\"> (opens in new tab)<\/span><\/a>,\u00a0Microsoft Research<\/li>\n<\/ul>\n<h2>Poster Session<\/h2>\n<p>There will be a poster session in the afternoon. Poster submissions are now closed.<\/p>\n<p><strong>Hospitality Notice for University and Government Employees: <\/strong>Microsoft Research is providing hospitality at this event. Please consult with your institution to determine whether you can accept meals and other hospitality under your institution&#8217;s ethics rules and any other laws that might apply. By accepting our invitation, you confirm that this invitation is compliant with your institution&#8217;s policies.<\/p>\n<p><strong>Arrival Guidance<\/strong><\/p>\n<p>Upon arrival, be prepared to show a picture ID and sign the Building Visitor Log when approaching the Lobby Floor Security Desk. Alert them to the name of the event you are attending and ask them to direct you to the appropriate floor. The talks will be held the First Floor Conference Center, Horace Mann Conference Room.<span id=\"label-external-link\" class=\"sr-only\" aria-hidden=\"true\">Opens in a new tab<\/span><\/p>\n<!-- \/wp:freeform --><!-- \/wp:msr\/content-tab --><!-- wp:msr\/content-tab {\"title\":\"Poster Submissions\"} --><!-- wp:freeform --><p><strong>Poster submissions are now closed.<\/strong><\/p>\n<p>To be considered for the CABI 2016 poster session, please submit the following information to <a href=\"mailto:CABI2016posters@microsoft.com\">CABI2016posters@microsoft.com<\/a>\u00a0by October 31st. Submissions will be evaluated on a rolling basis, and acceptance notifications will be sent by November 9th. Space is limited, and preference will be given to early submissions.<\/p>\n<p>Posters may be up to 48\u201dW X 36\u201dH.<\/p>\n<ul>\n<li>Presenting author name<\/li>\n<li>Presenting author affiliation\/institution<\/li>\n<li>Presenting author email address<\/li>\n<li>Title<\/li>\n<li>Complete list of authors (first name last name).\u00a0 Please do not list author affiliations.<\/li>\n<li>Abstract (250 words maximum)<\/li>\n<\/ul>\n<p>Please email the conference organizers at <a href=\"mailto:cabi2016@microsoft.com\">cabi2016@microsoft.com<\/a> if you have any questions.<span id=\"label-external-link\" class=\"sr-only\" aria-hidden=\"true\">Opens in a new tab<\/span><\/p>\n<!-- \/wp:freeform --><!-- \/wp:msr\/content-tab --><!-- wp:msr\/content-tab {\"title\":\"Agenda\"} --><!-- wp:freeform --><table class=\"msr-table-schedule\">\n<thead class=\"thead\">\n<tr class=\"tr\">\n<th class=\"th\">Time<\/th>\n<th class=\"th\">Session<\/th>\n<th class=\"th\">Speaker<\/th>\n<\/tr>\n<\/thead>\n<tbody class=\"tbody\">\n<tr class=\"tr\">\n<td class=\"td-1-3\">\n<div class=\"msr-table-schedule-cell\">9:00 AM<\/div>\n<\/td>\n<td>\n<div class=\"msr-table-schedule-cell\">Registration and coffee service<\/div>\n<\/td>\n<td><\/td>\n<\/tr>\n<tr class=\"tr\">\n<td class=\"td-1-3\">\n<div class=\"msr-table-schedule-cell\">9:50 AM<\/div>\n<\/td>\n<td>Opening remarks<\/td>\n<td>Jennifer Chayes<\/td>\n<\/tr>\n<tr class=\"tr\">\n<td class=\"td-1-3\">\n<div class=\"msr-table-schedule-cell\">10:00 AM<\/div>\n<\/td>\n<td>The role of fluctuations in individual cells<\/td>\n<td>\n<div class=\"msr-table-schedule-cell\">Johan Paulsson<\/div>\n<\/td>\n<\/tr>\n<tr class=\"tr\">\n<td class=\"td-1-3\">\n<div class=\"msr-table-schedule-cell\">10:30 AM<\/div>\n<\/td>\n<td>Visualizing transcription at nucleotide resolution with NET-seq<\/td>\n<td>\n<div class=\"msr-table-schedule-cell\">Stirling Churchman<\/div>\n<\/td>\n<\/tr>\n<tr class=\"tr\">\n<td class=\"td-1-3\">\n<div class=\"msr-table-schedule-cell\">11:00 AM<\/div>\n<\/td>\n<td>\n<div class=\"msr-table-schedule-cell\">Coffee break<\/div>\n<\/td>\n<td><\/td>\n<\/tr>\n<tr class=\"tr\">\n<td class=\"td-1-3\">\n<div class=\"msr-table-schedule-cell\">11:15 AM<\/div>\n<\/td>\n<td>Systematic identification of cancer targets<\/td>\n<td>Bill Hahn<\/td>\n<\/tr>\n<tr class=\"tr\">\n<td class=\"td-1-3\">\n<div class=\"msr-table-schedule-cell\">11:45 AM<\/div>\n<\/td>\n<td>Cancer Genome Evolution<\/td>\n<td>Ben Raphael<\/td>\n<\/tr>\n<tr class=\"tr\">\n<td class=\"td-1-3\">\n<div class=\"msr-table-schedule-cell\">12:15 PM<\/div>\n<\/td>\n<td>\n<div class=\"msr-table-schedule-cell\">Lunch<\/div>\n<\/td>\n<td><\/td>\n<\/tr>\n<tr class=\"tr\">\n<td class=\"td-1-3\">\n<div class=\"msr-table-schedule-cell\">1:00 PM<\/div>\n<\/td>\n<td>\n<div class=\"msr-table-schedule-cell\">Poster session<\/div>\n<\/td>\n<td><\/td>\n<\/tr>\n<tr class=\"tr\">\n<td class=\"td-1-3\">\n<div class=\"msr-table-schedule-cell\">1:30 PM<\/div>\n<\/td>\n<td>Reading &amp; Writing Omni Omics In Situ<\/td>\n<td>George Church<\/td>\n<\/tr>\n<tr class=\"tr\">\n<td class=\"td-1-3\">\n<div class=\"msr-table-schedule-cell\">2:00 PM<\/div>\n<\/td>\n<td>Darwinian Evolution as Learning<\/td>\n<td>Leslie Valiant<\/td>\n<\/tr>\n<tr class=\"tr\">\n<td class=\"td-1-3\">\n<div class=\"msr-table-schedule-cell\">2:30 PM<\/div>\n<\/td>\n<td>Measuring and Controlling the Dynamics of the Anesthetized Brain<\/td>\n<td>Emery Brown<\/td>\n<\/tr>\n<tr class=\"tr\">\n<td class=\"td-1-3\">\n<div class=\"msr-table-schedule-cell\">3:00 PM<\/div>\n<\/td>\n<td>\n<div class=\"msr-table-schedule-cell\">Coffee break\/poster session<\/div>\n<\/td>\n<td><\/td>\n<\/tr>\n<tr class=\"tr\">\n<td class=\"td-1-3\">\n<div class=\"msr-table-schedule-cell\">3:45 PM<\/div>\n<\/td>\n<td>Mapping the regulatory genome<\/td>\n<td>David Gifford<\/td>\n<\/tr>\n<tr class=\"tr\">\n<td class=\"td-1-3\">\n<div class=\"msr-table-schedule-cell\">4:15 PM<\/div>\n<\/td>\n<td>Genetic variation in human transcription factors<\/td>\n<td>Martha Bulyk<\/td>\n<\/tr>\n<tr class=\"tr\">\n<td class=\"td-1-3\">\n<div class=\"msr-table-schedule-cell\">4:45 PM<\/div>\n<\/td>\n<td>Scaling up genetic analysis<\/td>\n<td>Benjamin Neale<\/td>\n<\/tr>\n<tr class=\"tr\">\n<td class=\"td-1-3\">\n<div class=\"msr-table-schedule-cell\">5:15 PM<\/div>\n<\/td>\n<td>Closing remarks<\/td>\n<td><\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<p><span id=\"label-external-link\" class=\"sr-only\" aria-hidden=\"true\">Opens in a new tab<\/span><\/p>\n<!-- \/wp:freeform --><!-- \/wp:msr\/content-tab --><!-- wp:msr\/content-tab {\"title\":\"Abstracts\"} --><!-- wp:freeform --><p>\t<div data-wp-context='{\"items\":[]}' data-wp-interactive=\"msr\/accordion\">\n\t\t\t\t\t<div class=\"clearfix\">\n\t\t\t\t<div\n\t\t\t\t\tclass=\"btn-group align-items-center mb-g float-sm-right\"\n\t\t\t\t\tdata-bi-aN=\"accordion-collapse-controls\"\n\t\t\t\t>\n\t\t\t\t\t<button\n\t\t\t\t\t\tclass=\"btn btn-link m-0\"\n\t\t\t\t\t\tdata-bi-cN=\"Expand all\"\n\t\t\t\t\t\tdata-wp-bind--aria-controls=\"state.ariaControls\"\n\t\t\t\t\t\tdata-wp-bind--aria-expanded=\"state.ariaExpanded\"\n\t\t\t\t\t\tdata-wp-bind--disabled=\"state.isAllExpanded\"\n\t\t\t\t\t\tdata-wp-class--inactive=\"state.isAllExpanded\"\n\t\t\t\t\t\tdata-wp-on--click=\"actions.onExpandAll\"\n\t\t\t\t\t\ttype=\"button\"\n\t\t\t\t\t>\n\t\t\t\t\t\tExpand all\t\t\t\t\t<\/button>\n\t\t\t\t\t<span aria-hidden=\"true\"> | <\/span>\n\t\t\t\t\t<button\n\t\t\t\t\t\tclass=\"btn btn-link m-0\"\n\t\t\t\t\t\tdata-bi-cN=\"Collapse all\"\n\t\t\t\t\t\tdata-wp-bind--aria-controls=\"state.ariaControls\"\n\t\t\t\t\t\tdata-wp-bind--aria-expanded=\"state.ariaExpanded\"\n\t\t\t\t\t\tdata-wp-bind--disabled=\"state.isAllCollapsed\"\n\t\t\t\t\t\tdata-wp-class--inactive=\"state.isAllCollapsed\"\n\t\t\t\t\t\tdata-wp-on--click=\"actions.onCollapseAll\"\n\t\t\t\t\t\ttype=\"button\"\n\t\t\t\t\t>\n\t\t\t\t\t\tCollapse all\t\t\t\t\t<\/button>\n\t\t\t\t<\/div>\n\t\t\t<\/div>\n\t\t\t\t<ul class=\"msr-accordion\">\n\t\t\t\t\t\t\t\t<li class=\"m-0\" data-wp-context='{\"id\":\"accordion-content-2652\"}' data-wp-init=\"callbacks.init\">\n\t\t<div class=\"accordion-header\">\n\t\t\t<button\n\t\t\t\taria-controls=\"accordion-content-2652\"\n\t\t\t\tclass=\"btn btn-collapse\"\n\t\t\t\tdata-wp-bind--aria-expanded=\"state.isExpanded\"\n\t\t\t\tdata-wp-on--click=\"actions.onClick\"\n\t\t\t\tid=\"accordion-button-2651\"\n\t\t\t\ttype=\"button\"\n\t\t\t>\n\t\t\t\tThe role of fluctuations in individual cells\t\t\t<\/button>\n\t\t<\/div>\n\t\t<div\n\t\t\taria-labelledby=\"accordion-button-2651\"\n\t\t\tclass=\"msr-accordion__content\"\n\t\t\tdata-wp-bind--inert=\"!state.isExpanded\"\n\t\t\tdata-wp-run=\"callbacks.run\"\n\t\t\tid=\"accordion-content-2652\"\n\t\t>\n\t\t\t<div class=\"msr-accordion__body\">\n\t\t\t\t<p><strong>Speaker:<\/strong>\u00a0Johan Paulsson<\/p>\n<p>All processes in single cells involve components present in low numbers, creating spontaneous fluctuations that in turn can enslave the components present in high numbers. In the first half of the talk I will discuss some mathematical frameworks we developed to analytically predict and analyze random fluctuations in complex processes. The second half of the talk will focus on experimental methods to quantify dynamics in cells, as well as examples of microbial systems where fluctuations play a large role, including feedback control of replication, cell fate decisions, epigenetic oscillations and DNA repair.<\/p>\n<p><span id=\"label-external-link\" class=\"sr-only\" aria-hidden=\"true\">Opens in a new tab<\/span><\/p>\n\t\t\t<\/div>\n\t\t<\/div>\n\t<\/li>\n\t\t<li class=\"m-0\" data-wp-context='{\"id\":\"accordion-content-2654\"}' data-wp-init=\"callbacks.init\">\n\t\t<div class=\"accordion-header\">\n\t\t\t<button\n\t\t\t\taria-controls=\"accordion-content-2654\"\n\t\t\t\tclass=\"btn btn-collapse\"\n\t\t\t\tdata-wp-bind--aria-expanded=\"state.isExpanded\"\n\t\t\t\tdata-wp-on--click=\"actions.onClick\"\n\t\t\t\tid=\"accordion-button-2653\"\n\t\t\t\ttype=\"button\"\n\t\t\t>\n\t\t\t\tSystematic identification of cancer targets\t\t\t<\/button>\n\t\t<\/div>\n\t\t<div\n\t\t\taria-labelledby=\"accordion-button-2653\"\n\t\t\tclass=\"msr-accordion__content\"\n\t\t\tdata-wp-bind--inert=\"!state.isExpanded\"\n\t\t\tdata-wp-run=\"callbacks.run\"\n\t\t\tid=\"accordion-content-2654\"\n\t\t>\n\t\t\t<div class=\"msr-accordion__body\">\n\t\t\t\t<p><strong>Speaker:<\/strong>\u00a0Bill Hahn<\/p>\n<p>Although we now have a draft view of the genetic alterations that occur in human cancer, the number of mutations found at low frequency and the molecular heterogeneity of most cancers makes identifying genes that contribute to cancer phenotypes challenging. Determining the function of genes altered in cancer genomes is essential to develop new therapeutic approaches. To complement these genome characterization studies, we have used genome scale gain and loss of function approaches to identify genes required for cell survival and transformation. Specifically, we have performed systematic studies to interrogate rare alleles found altered in cancer genomes and used advances in synthetic gene synthesis to prospectively interrogate all possible alleles of known cancer genes. In parallel, we have performed both genome scale RNAi and CRISRP-Cas9 screens in more than 500 cell lines to identify differentially essential genes and the context that specifies gene dependency. This approach now permits us to identify and classify cancer dependencies. These studies allow us to begin to define a global cancer dependencies map.<\/p>\n<p><span id=\"label-external-link\" class=\"sr-only\" aria-hidden=\"true\">Opens in a new tab<\/span><\/p>\n\t\t\t<\/div>\n\t\t<\/div>\n\t<\/li>\n\t\t<li class=\"m-0\" data-wp-context='{\"id\":\"accordion-content-2656\"}' data-wp-init=\"callbacks.init\">\n\t\t<div class=\"accordion-header\">\n\t\t\t<button\n\t\t\t\taria-controls=\"accordion-content-2656\"\n\t\t\t\tclass=\"btn btn-collapse\"\n\t\t\t\tdata-wp-bind--aria-expanded=\"state.isExpanded\"\n\t\t\t\tdata-wp-on--click=\"actions.onClick\"\n\t\t\t\tid=\"accordion-button-2655\"\n\t\t\t\ttype=\"button\"\n\t\t\t>\n\t\t\t\tCancer Genome Evolution\t\t\t<\/button>\n\t\t<\/div>\n\t\t<div\n\t\t\taria-labelledby=\"accordion-button-2655\"\n\t\t\tclass=\"msr-accordion__content\"\n\t\t\tdata-wp-bind--inert=\"!state.isExpanded\"\n\t\t\tdata-wp-run=\"callbacks.run\"\n\t\t\tid=\"accordion-content-2656\"\n\t\t>\n\t\t\t<div class=\"msr-accordion__body\">\n\t\t\t\t<p><strong>Speaker:<\/strong>\u00a0Ben Raphael<\/p>\n<p>Cancer is an evolutionary process driven by somatic mutations that accumulate in a population of cells. In this talk, I will describe several algorithms to reconstruct this process from DNA sequencing data of tumor samples. These algorithms address challenges that distinguish the cancer genome phylogeny problem from classical phylogenetic tree reconstruction. I will demonstrate the application of these algorithms to sequencing data from multiple cancer types.<\/p>\n<p><span id=\"label-external-link\" class=\"sr-only\" aria-hidden=\"true\">Opens in a new tab<\/span><\/p>\n\t\t\t<\/div>\n\t\t<\/div>\n\t<\/li>\n\t\t<li class=\"m-0\" data-wp-context='{\"id\":\"accordion-content-2658\"}' data-wp-init=\"callbacks.init\">\n\t\t<div class=\"accordion-header\">\n\t\t\t<button\n\t\t\t\taria-controls=\"accordion-content-2658\"\n\t\t\t\tclass=\"btn btn-collapse\"\n\t\t\t\tdata-wp-bind--aria-expanded=\"state.isExpanded\"\n\t\t\t\tdata-wp-on--click=\"actions.onClick\"\n\t\t\t\tid=\"accordion-button-2657\"\n\t\t\t\ttype=\"button\"\n\t\t\t>\n\t\t\t\tReading &amp; Writing Omni Omics In Situ\t\t\t<\/button>\n\t\t<\/div>\n\t\t<div\n\t\t\taria-labelledby=\"accordion-button-2657\"\n\t\t\tclass=\"msr-accordion__content\"\n\t\t\tdata-wp-bind--inert=\"!state.isExpanded\"\n\t\t\tdata-wp-run=\"callbacks.run\"\n\t\t\tid=\"accordion-content-2658\"\n\t\t>\n\t\t\t<div class=\"msr-accordion__body\">\n\t\t\t\t<p><strong>Speaker:<\/strong> George Church<\/p>\n<p>Exponential technologies such as Expansion Fluorescent In Situ Sequencing (FISSeq\/ExSeq) enable computational analysis of multicellular organs including synapse-level-resolution of connectome and transcriptome plus nucleosome-level-resolution chromosome chain tracing in situ (via Oligopaints).\u00a0 We can also computationally design and build whole genomes (via synthesis and recombination) and epigenomes (via comprehensive transcription factor libraries).\u00a0 Data from the IARPA MICrONS BRAIN project is aimed at new insights into visual machine learning strategies.<\/p>\n<p><span id=\"label-external-link\" class=\"sr-only\" aria-hidden=\"true\">Opens in a new tab<\/span><\/p>\n\t\t\t<\/div>\n\t\t<\/div>\n\t<\/li>\n\t\t<li class=\"m-0\" data-wp-context='{\"id\":\"accordion-content-2660\"}' data-wp-init=\"callbacks.init\">\n\t\t<div class=\"accordion-header\">\n\t\t\t<button\n\t\t\t\taria-controls=\"accordion-content-2660\"\n\t\t\t\tclass=\"btn btn-collapse\"\n\t\t\t\tdata-wp-bind--aria-expanded=\"state.isExpanded\"\n\t\t\t\tdata-wp-on--click=\"actions.onClick\"\n\t\t\t\tid=\"accordion-button-2659\"\n\t\t\t\ttype=\"button\"\n\t\t\t>\n\t\t\t\tDarwinian Evolution as Learning\t\t\t<\/button>\n\t\t<\/div>\n\t\t<div\n\t\t\taria-labelledby=\"accordion-button-2659\"\n\t\t\tclass=\"msr-accordion__content\"\n\t\t\tdata-wp-bind--inert=\"!state.isExpanded\"\n\t\t\tdata-wp-run=\"callbacks.run\"\n\t\t\tid=\"accordion-content-2660\"\n\t\t>\n\t\t\t<div class=\"msr-accordion__body\">\n\t\t\t\t<p><strong>Speaker:<\/strong>\u00a0Leslie Valiant<\/p>\n<p>Living organisms function according to protein circuits. Darwin&#8217;s theory of evolution suggests that these circuits have evolved through variation guided by natural selection. However, the question of which kinds of circuits can so evolve in realistic population sizes and within realistic numbers of generations has remained essentially unaddressed.<\/p>\n<p>We suggest that computational learning theory offers the framework for investigating this question, of how circuits can come into existence adaptively from experience, without a designer, or be then maintained. We formulate evolution as a form of learning from examples. The targets of the learning process are the functions of highest fitness. The examples are the experiences. The learning process is constrained so that the feedback from the experiences is Darwinian. We formulate a notion of evolvability that distinguishes function classes that are evolvable with polynomially bounded resources from those that are not. The dilemma is that if the function class, in particualr of the expression levels of proteins in terms of each other, is too restrictive, then it will not support biology, while if it is too expressive then no evolution algorithm will exist to navigate it. We shall review current work in this area.<\/p>\n<p><span id=\"label-external-link\" class=\"sr-only\" aria-hidden=\"true\">Opens in a new tab<\/span><\/p>\n\t\t\t<\/div>\n\t\t<\/div>\n\t<\/li>\n\t\t<li class=\"m-0\" data-wp-context='{\"id\":\"accordion-content-2662\"}' data-wp-init=\"callbacks.init\">\n\t\t<div class=\"accordion-header\">\n\t\t\t<button\n\t\t\t\taria-controls=\"accordion-content-2662\"\n\t\t\t\tclass=\"btn btn-collapse\"\n\t\t\t\tdata-wp-bind--aria-expanded=\"state.isExpanded\"\n\t\t\t\tdata-wp-on--click=\"actions.onClick\"\n\t\t\t\tid=\"accordion-button-2661\"\n\t\t\t\ttype=\"button\"\n\t\t\t>\n\t\t\t\tScaling up genetic analysis\t\t\t<\/button>\n\t\t<\/div>\n\t\t<div\n\t\t\taria-labelledby=\"accordion-button-2661\"\n\t\t\tclass=\"msr-accordion__content\"\n\t\t\tdata-wp-bind--inert=\"!state.isExpanded\"\n\t\t\tdata-wp-run=\"callbacks.run\"\n\t\t\tid=\"accordion-content-2662\"\n\t\t>\n\t\t\t<div class=\"msr-accordion__body\">\n\t\t\t\t<p><strong>Speaker:<\/strong>\u00a0Ben Neale<\/p>\n<p>With the advent of sequencing technology and ever increasing genome-wide association datasets, we tools to meet the challenges of scale. Here I will describe our efforts to develop a software package, hail, that is built using spark and scala. Hail leverages a distributed model of computing to perform scalable sequence data quality control and analysis. In doing so, we can perform primary quality control analyses on whole genome sequencing datasets of ~5,000 individuals in under an hour. Using hail, we have performed analyses of education attainment on a sample of over 14,000 individuals, identifying a clear role of ultra-rare disruptive mutations in the genetic architecture. We further explored the consequences of this class of variation across a wide range of traits and demonstrate that neuropsychiatric traits appear to have a directional burden effect in contrast to later onset systemic disease.<\/p>\n<p><span id=\"label-external-link\" class=\"sr-only\" aria-hidden=\"true\">Opens in a new tab<\/span><\/p>\n\t\t\t<\/div>\n\t\t<\/div>\n\t<\/li>\n\t\t<li class=\"m-0\" data-wp-context='{\"id\":\"accordion-content-2664\"}' data-wp-init=\"callbacks.init\">\n\t\t<div class=\"accordion-header\">\n\t\t\t<button\n\t\t\t\taria-controls=\"accordion-content-2664\"\n\t\t\t\tclass=\"btn btn-collapse\"\n\t\t\t\tdata-wp-bind--aria-expanded=\"state.isExpanded\"\n\t\t\t\tdata-wp-on--click=\"actions.onClick\"\n\t\t\t\tid=\"accordion-button-2663\"\n\t\t\t\ttype=\"button\"\n\t\t\t>\n\t\t\t\tMapping the regulatory genome\t\t\t<\/button>\n\t\t<\/div>\n\t\t<div\n\t\t\taria-labelledby=\"accordion-button-2663\"\n\t\t\tclass=\"msr-accordion__content\"\n\t\t\tdata-wp-bind--inert=\"!state.isExpanded\"\n\t\t\tdata-wp-run=\"callbacks.run\"\n\t\t\tid=\"accordion-content-2664\"\n\t\t>\n\t\t\t<div class=\"msr-accordion__body\">\n\t\t\t\t<p><strong>Speaker:<\/strong>\u00a0David Gifford<\/p>\n<p>With the advent of multiplexed DNA oligo synthesis, CRISPR genome editing, and high-throughput sequencing it is now possible to characterize genome function with experiments that directly observe the effect of sequence variants.\u00a0\u00a0 We will discuss the computational design and analysis of sequence variants that have a causal effect on the binding of DNA regulatory proteins and proximal gene expression.\u00a0\u00a0\u00a0 New results include the observation of regulatory elements in regions of the genome with no observed epigenetic marks.<\/p>\n<p><span id=\"label-external-link\" class=\"sr-only\" aria-hidden=\"true\">Opens in a new tab<\/span><\/p>\n\t\t\t<\/div>\n\t\t<\/div>\n\t<\/li>\n\t\t<li class=\"m-0\" data-wp-context='{\"id\":\"accordion-content-2666\"}' data-wp-init=\"callbacks.init\">\n\t\t<div class=\"accordion-header\">\n\t\t\t<button\n\t\t\t\taria-controls=\"accordion-content-2666\"\n\t\t\t\tclass=\"btn btn-collapse\"\n\t\t\t\tdata-wp-bind--aria-expanded=\"state.isExpanded\"\n\t\t\t\tdata-wp-on--click=\"actions.onClick\"\n\t\t\t\tid=\"accordion-button-2665\"\n\t\t\t\ttype=\"button\"\n\t\t\t>\n\t\t\t\tGenetic variation in human transcription factors\t\t\t<\/button>\n\t\t<\/div>\n\t\t<div\n\t\t\taria-labelledby=\"accordion-button-2665\"\n\t\t\tclass=\"msr-accordion__content\"\n\t\t\tdata-wp-bind--inert=\"!state.isExpanded\"\n\t\t\tdata-wp-run=\"callbacks.run\"\n\t\t\tid=\"accordion-content-2666\"\n\t\t>\n\t\t\t<div class=\"msr-accordion__body\">\n\t\t\t\t<p><strong>Speaker:<\/strong>\u00a0Martha Bulyk<\/p>\n<p>Sequencing of exomes and genomes has revealed abundant genetic variation affecting the coding sequences of human transcription factors (TFs), but the consequences of such variation remain largely unexplored. We developed a computational, structure-based approach to evaluate TF variants for their impact on DNA-binding activity and used universal protein binding microarrays to assay sequence-specific DNA-binding activity across 41 reference and 117 variant alleles found in individuals of diverse ancestries and families with Mendelian diseases. We found 77 variants in 28 genes that affect DNA-binding affinity or specificity and identified thousands of rare alleles likely to alter the DNA-binding activity of human sequence-specific TFs. Our results suggest that most individuals have unique repertoires of TF DNA-binding activities, which may contribute to phenotypic variation.<\/p>\n<p><span id=\"label-external-link\" class=\"sr-only\" aria-hidden=\"true\">Opens in a new tab<\/span><\/p>\n\t\t\t<\/div>\n\t\t<\/div>\n\t<\/li>\n\t\t\t\t\t\t<\/ul>\n\t<\/div>\n\t<span id=\"label-external-link\" class=\"sr-only\" aria-hidden=\"true\">Opens in a new tab<\/span><\/p>\n<!-- \/wp:freeform --><!-- \/wp:msr\/content-tab --><!-- \/wp:msr\/content-tabs -->","tab-content":[{"id":0,"name":"About","content":"<img class=\"size-medium wp-image-293573 alignright\" src=\"https:\/\/www.microsoft.com\/en-us\/research\/wp-content\/uploads\/2016\/09\/cabi2016_top_badge-artwork-300x228.png\" alt=\"Computational Aspects of Biological Information 2016\" width=\"300\" height=\"228\" \/>Computational Aspects of Biological Information (CABI) 2016 is the fourth one-day symposium\u00a0on challenges and successes in computational biology. CABI 2016 will be held at Microsoft Research New England on November 30, 2016 and will\u00a0bring together experts in the Boston\/Cambridge area to discuss computational solutions to problems in biology, including systems biology, genomics, and related areas. The symposium\u00a0is open to everyone and registration is free of charge. Lunch will be served.\r\n<h2>Symposium Speakers<\/h2>\r\nConfirmed speakers include:\r\n<ul>\r\n \t<li><a href=\"http:\/\/imes.mit.edu\/people\/faculty\/brown-emery\/\" target=\"_blank\" rel=\"noopener noreferrer\">Emery Brown<\/a>, Massachusetts Institute of Technology<\/li>\r\n \t<li><a href=\"http:\/\/the_brain.bwh.harvard.edu\/\" target=\"_blank\" rel=\"noopener noreferrer\">Martha Bulyk<\/a>, Harvard\u00a0University<\/li>\r\n \t<li><a href=\"http:\/\/arep.med.harvard.edu\/gmc\/\" target=\"_blank\" rel=\"noopener noreferrer\">George Church<\/a>, Harvard\u00a0University<\/li>\r\n \t<li><a href=\"http:\/\/churchman.med.harvard.edu\/\" target=\"_blank\" rel=\"noopener noreferrer\">Stirling Churchman<\/a>, Harvard\u00a0University<\/li>\r\n \t<li><a href=\"http:\/\/cgs.csail.mit.edu\/\" target=\"_blank\" rel=\"noopener noreferrer\">David Gifford<\/a>,\u00a0Massachusetts Institute of Technology<\/li>\r\n \t<li><a href=\"http:\/\/hahnlab.dana-farber.org\/\" target=\"_blank\" rel=\"noopener noreferrer\">William Hahn<\/a>, Dana-Farber Cancer Institute<\/li>\r\n \t<li><a href=\"https:\/\/www.atgu.mgh.harvard.edu\/people\/benjamin_neale\" target=\"_blank\" rel=\"noopener noreferrer\">Benjamin Neale<\/a>,\u00a0Harvard Medical School<\/li>\r\n \t<li><a href=\"http:\/\/paulsson.med.harvard.edu\/\" target=\"_blank\" rel=\"noopener noreferrer\">Johan Paulsson<\/a>, Harvard\u00a0University<\/li>\r\n \t<li><a href=\"http:\/\/compbio.cs.brown.edu\/research\/\" target=\"_blank\" rel=\"noopener noreferrer\">Ben Raphael<\/a>, Princeton\u00a0University<\/li>\r\n \t<li><a href=\"https:\/\/people.seas.harvard.edu\/~valiant\/\" target=\"_blank\" rel=\"noopener noreferrer\">Les Valiant<\/a>, Harvard\u00a0University<\/li>\r\n<\/ul>\r\n<h2>Organizing committee<\/h2>\r\n<ul>\r\n \t<li><a href=\"http:\/\/nicolofusi.com\/\" target=\"_blank\" rel=\"noopener noreferrer\">Nicolo Fusi<\/a>,\u00a0Microsoft Research<\/li>\r\n \t<li><a href=\"http:\/\/maxleiserson.com\/\" target=\"_blank\" rel=\"noopener noreferrer\">Max Leiserson<\/a>,\u00a0Microsoft Research<\/li>\r\n \t<li><a href=\"http:\/\/research.microsoft.com\/en-us\/um\/people\/jennl\/\" target=\"_blank\" rel=\"noopener noreferrer\">Jennifer Listgarten<\/a>,\u00a0Microsoft Research<\/li>\r\n<\/ul>\r\n<h2>Poster Session<\/h2>\r\nThere will be a poster session in the afternoon. Poster submissions are now closed.\r\n\r\n<strong>Hospitality Notice for University and Government Employees: <\/strong>Microsoft Research is providing hospitality at this event. Please consult with your institution to determine whether you can accept meals and other hospitality under your institution's ethics rules and any other laws that might apply. By accepting our invitation, you confirm that this invitation is compliant with your institution's policies.\r\n\r\n<strong>Arrival Guidance<\/strong>\r\n\r\nUpon arrival, be prepared to show a picture ID and sign the Building Visitor Log when approaching the Lobby Floor Security Desk. Alert them to the name of the event you are attending and ask them to direct you to the appropriate floor. The talks will be held the First Floor Conference Center, Horace Mann Conference Room."},{"id":1,"name":"Poster Submissions","content":"<strong>Poster submissions are now closed.<\/strong>\r\n\r\nTo be considered for the CABI 2016 poster session, please submit the following information to <a href=\"mailto:CABI2016posters@microsoft.com\">CABI2016posters@microsoft.com<\/a>\u00a0by October 31st. Submissions will be evaluated on a rolling basis, and acceptance notifications will be sent by November 9th. Space is limited, and preference will be given to early submissions.\r\n\r\nPosters may be up to 48\u201dW X 36\u201dH.\r\n<ul>\r\n \t<li>Presenting author name<\/li>\r\n \t<li>Presenting author affiliation\/institution<\/li>\r\n \t<li>Presenting author email address<\/li>\r\n \t<li>Title<\/li>\r\n \t<li>Complete list of authors (first name last name).\u00a0 Please do not list author affiliations.<\/li>\r\n \t<li>Abstract (250 words maximum)<\/li>\r\n<\/ul>\r\nPlease email the conference organizers at <a href=\"mailto:cabi2016@microsoft.com\">cabi2016@microsoft.com<\/a> if you have any questions."},{"id":2,"name":"Agenda","content":"<table class=\"msr-table-schedule\">\r\n<thead class=\"thead\">\r\n<tr class=\"tr\">\r\n<th class=\"th\">Time<\/th>\r\n<th class=\"th\">Session<\/th>\r\n<th class=\"th\">Speaker<\/th>\r\n<\/tr>\r\n<\/thead>\r\n<tbody class=\"tbody\">\r\n<tr class=\"tr\">\r\n<td class=\"td-1-3\">\r\n<div class=\"msr-table-schedule-cell\">9:00 AM<\/div><\/td>\r\n<td>\r\n<div class=\"msr-table-schedule-cell\">Registration and coffee service<\/div><\/td>\r\n<td><\/td>\r\n<\/tr>\r\n<tr class=\"tr\">\r\n<td class=\"td-1-3\">\r\n<div class=\"msr-table-schedule-cell\">9:50 AM<\/div><\/td>\r\n<td>Opening remarks<\/td>\r\n<td>Jennifer Chayes<\/td>\r\n<\/tr>\r\n<tr class=\"tr\">\r\n<td class=\"td-1-3\">\r\n<div class=\"msr-table-schedule-cell\">10:00 AM<\/div><\/td>\r\n<td>The role of fluctuations in individual cells<\/td>\r\n<td>\r\n<div class=\"msr-table-schedule-cell\">Johan Paulsson<\/div><\/td>\r\n<\/tr>\r\n<tr class=\"tr\">\r\n<td class=\"td-1-3\">\r\n<div class=\"msr-table-schedule-cell\">10:30 AM<\/div><\/td>\r\n<td>Visualizing transcription at nucleotide resolution with NET-seq<\/td>\r\n<td>\r\n<div class=\"msr-table-schedule-cell\">Stirling Churchman<\/div><\/td>\r\n<\/tr>\r\n<tr class=\"tr\">\r\n<td class=\"td-1-3\">\r\n<div class=\"msr-table-schedule-cell\">11:00 AM<\/div><\/td>\r\n<td>\r\n<div class=\"msr-table-schedule-cell\">Coffee break<\/div><\/td>\r\n<td><\/td>\r\n<\/tr>\r\n<tr class=\"tr\">\r\n<td class=\"td-1-3\">\r\n<div class=\"msr-table-schedule-cell\">11:15 AM<\/div><\/td>\r\n<td>Systematic identification of cancer targets<\/td>\r\n<td>Bill Hahn<\/td>\r\n<\/tr>\r\n<tr class=\"tr\">\r\n<td class=\"td-1-3\">\r\n<div class=\"msr-table-schedule-cell\">11:45 AM<\/div><\/td>\r\n<td>Cancer Genome Evolution<\/td>\r\n<td>Ben Raphael<\/td>\r\n<\/tr>\r\n<tr class=\"tr\">\r\n<td class=\"td-1-3\">\r\n<div class=\"msr-table-schedule-cell\">12:15 PM<\/div><\/td>\r\n<td>\r\n<div class=\"msr-table-schedule-cell\">Lunch<\/div><\/td>\r\n<td><\/td>\r\n<\/tr>\r\n<tr class=\"tr\">\r\n<td class=\"td-1-3\">\r\n<div class=\"msr-table-schedule-cell\">1:00 PM<\/div><\/td>\r\n<td>\r\n<div class=\"msr-table-schedule-cell\">Poster session<\/div><\/td>\r\n<td><\/td>\r\n<\/tr>\r\n<tr class=\"tr\">\r\n<td class=\"td-1-3\">\r\n<div class=\"msr-table-schedule-cell\">1:30 PM<\/div><\/td>\r\n<td>Reading &amp; Writing Omni Omics In Situ<\/td>\r\n<td>George Church<\/td>\r\n<\/tr>\r\n<tr class=\"tr\">\r\n<td class=\"td-1-3\">\r\n<div class=\"msr-table-schedule-cell\">2:00 PM<\/div><\/td>\r\n<td>Darwinian Evolution as Learning<\/td>\r\n<td>Leslie Valiant<\/td>\r\n<\/tr>\r\n<tr class=\"tr\">\r\n<td class=\"td-1-3\">\r\n<div class=\"msr-table-schedule-cell\">2:30 PM<\/div><\/td>\r\n<td>Measuring and Controlling the Dynamics of the Anesthetized Brain<\/td>\r\n<td>Emery Brown<\/td>\r\n<\/tr>\r\n<tr class=\"tr\">\r\n<td class=\"td-1-3\">\r\n<div class=\"msr-table-schedule-cell\">3:00 PM<\/div><\/td>\r\n<td>\r\n<div class=\"msr-table-schedule-cell\">Coffee break\/poster session<\/div><\/td>\r\n<td><\/td>\r\n<\/tr>\r\n<tr class=\"tr\">\r\n<td class=\"td-1-3\">\r\n<div class=\"msr-table-schedule-cell\">3:45 PM<\/div><\/td>\r\n<td>Mapping the regulatory genome<\/td>\r\n<td>David Gifford<\/td>\r\n<\/tr>\r\n<tr class=\"tr\">\r\n<td class=\"td-1-3\">\r\n<div class=\"msr-table-schedule-cell\">4:15 PM<\/div><\/td>\r\n<td>Genetic variation in human transcription factors<\/td>\r\n<td>Martha Bulyk<\/td>\r\n<\/tr>\r\n<tr class=\"tr\">\r\n<td class=\"td-1-3\">\r\n<div class=\"msr-table-schedule-cell\">4:45 PM<\/div><\/td>\r\n<td>Scaling up genetic analysis<\/td>\r\n<td>Benjamin Neale<\/td>\r\n<\/tr>\r\n<tr class=\"tr\">\r\n<td class=\"td-1-3\">\r\n<div class=\"msr-table-schedule-cell\">5:15 PM<\/div><\/td>\r\n<td>Closing remarks<\/td>\r\n<td><\/td>\r\n<\/tr>\r\n<\/tbody>\r\n<\/table>"},{"id":3,"name":"Abstracts","content":"[accordion]\r\n\r\n[panel header=\"The role of fluctuations in individual cells\"]\r\n\r\n<strong>Speaker:<\/strong>\u00a0Johan Paulsson\r\n\r\nAll processes in single cells involve components present in low numbers, creating spontaneous fluctuations that in turn can enslave the components present in high numbers. In the first half of the talk I will discuss some mathematical frameworks we developed to analytically predict and analyze random fluctuations in complex processes. The second half of the talk will focus on experimental methods to quantify dynamics in cells, as well as examples of microbial systems where fluctuations play a large role, including feedback control of replication, cell fate decisions, epigenetic oscillations and DNA repair.\r\n\r\n[\/panel]\r\n\r\n[panel header=\"Systematic identification of cancer targets\"]\r\n\r\n<strong>Speaker:<\/strong>\u00a0Bill Hahn\r\n\r\nAlthough we now have a draft view of the genetic alterations that occur in human cancer, the number of mutations found at low frequency and the molecular heterogeneity of most cancers makes identifying genes that contribute to cancer phenotypes challenging. Determining the function of genes altered in cancer genomes is essential to develop new therapeutic approaches. To complement these genome characterization studies, we have used genome scale gain and loss of function approaches to identify genes required for cell survival and transformation. Specifically, we have performed systematic studies to interrogate rare alleles found altered in cancer genomes and used advances in synthetic gene synthesis to prospectively interrogate all possible alleles of known cancer genes. In parallel, we have performed both genome scale RNAi and CRISRP-Cas9 screens in more than 500 cell lines to identify differentially essential genes and the context that specifies gene dependency. This approach now permits us to identify and classify cancer dependencies. These studies allow us to begin to define a global cancer dependencies map.\r\n\r\n[\/panel]\r\n\r\n[panel header=\"Cancer Genome Evolution\"]\r\n\r\n<strong>Speaker:<\/strong>\u00a0Ben Raphael\r\n\r\nCancer is an evolutionary process driven by somatic mutations that accumulate in a population of cells. In this talk, I will describe several algorithms to reconstruct this process from DNA sequencing data of tumor samples. These algorithms address challenges that distinguish the cancer genome phylogeny problem from classical phylogenetic tree reconstruction. I will demonstrate the application of these algorithms to sequencing data from multiple cancer types.\r\n\r\n[\/panel]\r\n\r\n[panel header=\"Reading &amp; Writing Omni Omics In Situ\"]\r\n\r\n<strong>Speaker:<\/strong> George Church\r\n\r\nExponential technologies such as Expansion Fluorescent In Situ Sequencing (FISSeq\/ExSeq) enable computational analysis of multicellular organs including synapse-level-resolution of connectome and transcriptome plus nucleosome-level-resolution chromosome chain tracing in situ (via Oligopaints).\u00a0 We can also computationally design and build whole genomes (via synthesis and recombination) and epigenomes (via comprehensive transcription factor libraries).\u00a0 Data from the IARPA MICrONS BRAIN project is aimed at new insights into visual machine learning strategies.\r\n\r\n[\/panel]\r\n\r\n[panel header=\"Darwinian Evolution as Learning\"]\r\n\r\n<strong>Speaker:<\/strong>\u00a0Leslie Valiant\r\n\r\nLiving organisms function according to protein circuits. Darwin's theory of evolution suggests that these circuits have evolved through variation guided by natural selection. However, the question of which kinds of circuits can so evolve in realistic population sizes and within realistic numbers of generations has remained essentially unaddressed.\r\n\r\nWe suggest that computational learning theory offers the framework for investigating this question, of how circuits can come into existence adaptively from experience, without a designer, or be then maintained. We formulate evolution as a form of learning from examples. The targets of the learning process are the functions of highest fitness. The examples are the experiences. The learning process is constrained so that the feedback from the experiences is Darwinian. We formulate a notion of evolvability that distinguishes function classes that are evolvable with polynomially bounded resources from those that are not. The dilemma is that if the function class, in particualr of the expression levels of proteins in terms of each other, is too restrictive, then it will not support biology, while if it is too expressive then no evolution algorithm will exist to navigate it. We shall review current work in this area.\r\n\r\n[\/panel]\r\n\r\n[panel header=\"Scaling up genetic analysis\"]\r\n\r\n<strong>Speaker:<\/strong>\u00a0Ben Neale\r\n\r\nWith the advent of sequencing technology and ever increasing genome-wide association datasets, we tools to meet the challenges of scale. Here I will describe our efforts to develop a software package, hail, that is built using spark and scala. Hail leverages a distributed model of computing to perform scalable sequence data quality control and analysis. In doing so, we can perform primary quality control analyses on whole genome sequencing datasets of ~5,000 individuals in under an hour. Using hail, we have performed analyses of education attainment on a sample of over 14,000 individuals, identifying a clear role of ultra-rare disruptive mutations in the genetic architecture. We further explored the consequences of this class of variation across a wide range of traits and demonstrate that neuropsychiatric traits appear to have a directional burden effect in contrast to later onset systemic disease.\r\n\r\n[\/panel]\r\n\r\n[panel header=\"Mapping the regulatory genome\"]\r\n\r\n<strong>Speaker:<\/strong>\u00a0David Gifford\r\n\r\nWith the advent of multiplexed DNA oligo synthesis, CRISPR genome editing, and high-throughput sequencing it is now possible to characterize genome function with experiments that directly observe the effect of sequence variants.\u00a0\u00a0 We will discuss the computational design and analysis of sequence variants that have a causal effect on the binding of DNA regulatory proteins and proximal gene expression.\u00a0\u00a0\u00a0 New results include the observation of regulatory elements in regions of the genome with no observed epigenetic marks.\r\n\r\n[\/panel]\r\n\r\n[panel header=\"Genetic variation in human transcription factors\"]\r\n\r\n<strong>Speaker:<\/strong>\u00a0Martha Bulyk\r\n\r\nSequencing of exomes and genomes has revealed abundant genetic variation affecting the coding sequences of human transcription factors (TFs), but the consequences of such variation remain largely unexplored. We developed a computational, structure-based approach to evaluate TF variants for their impact on DNA-binding activity and used universal protein binding microarrays to assay sequence-specific DNA-binding activity across 41 reference and 117 variant alleles found in individuals of diverse ancestries and families with Mendelian diseases. We found 77 variants in 28 genes that affect DNA-binding affinity or specificity and identified thousands of rare alleles likely to alter the DNA-binding activity of human sequence-specific TFs. Our results suggest that most individuals have unique repertoires of TF DNA-binding activities, which may contribute to phenotypic variation.\r\n\r\n[\/panel]\r\n\r\n[\/accordion]"}],"msr_startdate":"2016-11-30","msr_enddate":"2016-11-30","msr_event_time":"9:00 AM \u2013 5:30 PM","msr_location":"Cambridge, MA, USA","msr_event_link":"","msr_event_recording_link":"","msr_startdate_formatted":"November 30, 2016","msr_register_text":"Watch now","msr_cta_link":"","msr_cta_text":"","msr_cta_bi_name":"","featured_image_thumbnail":"<img width=\"960\" height=\"360\" src=\"https:\/\/www.microsoft.com\/en-us\/research\/wp-content\/uploads\/2016\/09\/MSR-CABI-Hero_1920x720-v1.jpg\" class=\"img-object-cover\" alt=\"\" decoding=\"async\" loading=\"lazy\" srcset=\"https:\/\/www.microsoft.com\/en-us\/research\/wp-content\/uploads\/2016\/09\/MSR-CABI-Hero_1920x720-v1.jpg 1920w, https:\/\/www.microsoft.com\/en-us\/research\/wp-content\/uploads\/2016\/09\/MSR-CABI-Hero_1920x720-v1-300x113.jpg 300w, https:\/\/www.microsoft.com\/en-us\/research\/wp-content\/uploads\/2016\/09\/MSR-CABI-Hero_1920x720-v1-768x288.jpg 768w, https:\/\/www.microsoft.com\/en-us\/research\/wp-content\/uploads\/2016\/09\/MSR-CABI-Hero_1920x720-v1-1024x384.jpg 1024w\" sizes=\"auto, (max-width: 960px) 100vw, 960px\" \/>","event_excerpt":"Computational Aspects of Biological Information (CABI) 2016 is the fourth one-day symposium on challenges and successes in computational biology. CABI 2016 will be held at Microsoft Research New England on November 30, 2016 and will bring together experts in the Boston\/Cambridge area to discuss computational solutions to problems in biology, including systems biology, genomics, and related areas. The symposium is open to everyone and registration is free of charge.","msr_research_lab":[199563],"related-researchers":[],"msr_impact_theme":[],"related-academic-programs":[],"related-groups":[],"related-projects":[],"related-opportunities":[],"related-publications":[],"related-videos":[342035,342038,342041],"related-posts":[],"_links":{"self":[{"href":"https:\/\/www.microsoft.com\/en-us\/research\/wp-json\/wp\/v2\/msr-event\/293570","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.microsoft.com\/en-us\/research\/wp-json\/wp\/v2\/msr-event"}],"about":[{"href":"https:\/\/www.microsoft.com\/en-us\/research\/wp-json\/wp\/v2\/types\/msr-event"}],"version-history":[{"count":2,"href":"https:\/\/www.microsoft.com\/en-us\/research\/wp-json\/wp\/v2\/msr-event\/293570\/revisions"}],"predecessor-version":[{"id":1147247,"href":"https:\/\/www.microsoft.com\/en-us\/research\/wp-json\/wp\/v2\/msr-event\/293570\/revisions\/1147247"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/www.microsoft.com\/en-us\/research\/wp-json\/wp\/v2\/media\/381725"}],"wp:attachment":[{"href":"https:\/\/www.microsoft.com\/en-us\/research\/wp-json\/wp\/v2\/media?parent=293570"}],"wp:term":[{"taxonomy":"msr-research-area","embeddable":true,"href":"https:\/\/www.microsoft.com\/en-us\/research\/wp-json\/wp\/v2\/research-area?post=293570"},{"taxonomy":"msr-region","embeddable":true,"href":"https:\/\/www.microsoft.com\/en-us\/research\/wp-json\/wp\/v2\/msr-region?post=293570"},{"taxonomy":"msr-event-type","embeddable":true,"href":"https:\/\/www.microsoft.com\/en-us\/research\/wp-json\/wp\/v2\/msr-event-type?post=293570"},{"taxonomy":"msr-video-type","embeddable":true,"href":"https:\/\/www.microsoft.com\/en-us\/research\/wp-json\/wp\/v2\/msr-video-type?post=293570"},{"taxonomy":"msr-locale","embeddable":true,"href":"https:\/\/www.microsoft.com\/en-us\/research\/wp-json\/wp\/v2\/msr-locale?post=293570"},{"taxonomy":"msr-program-audience","embeddable":true,"href":"https:\/\/www.microsoft.com\/en-us\/research\/wp-json\/wp\/v2\/msr-program-audience?post=293570"},{"taxonomy":"msr-post-option","embeddable":true,"href":"https:\/\/www.microsoft.com\/en-us\/research\/wp-json\/wp\/v2\/msr-post-option?post=293570"},{"taxonomy":"msr-impact-theme","embeddable":true,"href":"https:\/\/www.microsoft.com\/en-us\/research\/wp-json\/wp\/v2\/msr-impact-theme?post=293570"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}