{"id":373631,"date":"2017-03-28T06:00:49","date_gmt":"2017-03-28T13:00:49","guid":{"rendered":"https:\/\/www.microsoft.com\/en-us\/research\/?p=373631"},"modified":"2017-05-17T15:06:57","modified_gmt":"2017-05-17T22:06:57","slug":"cancer-crop-genomics-using-research-service","status":"publish","type":"post","link":"https:\/\/www.microsoft.com\/en-us\/research\/blog\/cancer-crop-genomics-using-research-service\/","title":{"rendered":"From cancer to crop genomics \u2014 using Research as a Service at the intersection of computers and biology"},"content":{"rendered":"<p>By <a class=\"msr-external-link glyph-append glyph-append-open-in-new-tab glyph-append-xsmall\" rel=\"noopener noreferrer\" href=\"http:\/\/research.microsoft.com\/en-us\/people\/kenjitak\/\" target=\"_blank\"><em>Kenji Takeda<\/em><span class=\"sr-only\"> (opens in new tab)<\/span><\/a><em>, Director, Azure for Research, AI and Research<\/em><\/p>\n<div id=\"attachment_373637\" style=\"width: 1034px\" class=\"wp-caption aligncenter\"><img loading=\"lazy\" decoding=\"async\" aria-describedby=\"caption-attachment-373637\" class=\"wp-image-373637 size-large\" src=\"https:\/\/www.microsoft.com\/en-us\/research\/wp-content\/uploads\/2017\/03\/Nicola_3_header-1024x384.jpg\" alt=\"Nicola Bonzanni, Co-Founder of ENPICOM\" width=\"1024\" height=\"384\" srcset=\"https:\/\/www.microsoft.com\/en-us\/research\/wp-content\/uploads\/2017\/03\/Nicola_3_header-1024x384.jpg 1024w, https:\/\/www.microsoft.com\/en-us\/research\/wp-content\/uploads\/2017\/03\/Nicola_3_header-300x113.jpg 300w, https:\/\/www.microsoft.com\/en-us\/research\/wp-content\/uploads\/2017\/03\/Nicola_3_header-768x288.jpg 768w, https:\/\/www.microsoft.com\/en-us\/research\/wp-content\/uploads\/2017\/03\/Nicola_3_header.jpg 1920w\" sizes=\"auto, (max-width: 1024px) 100vw, 1024px\" \/><p id=\"caption-attachment-373637\" class=\"wp-caption-text\">Nicola Bonzanni, Co-Founder, ENPICOM<\/p><\/div>\n<p>Ever since Nicola Bonzanni was a little boy playing in the tiny Italian village of Bonate Sotto, just north of Milan, he was fascinated by nature and by building things. As he grew up, he wondered how computing and nature might be intertwined. \u201cWhile I was studying computer science I was inspired by nature in building new algorithms. But then I thought perhaps you could do it the other way around, basically taking things that are being developed in computer science and apply them to biological problems.\u201d<\/p>\n<p>After finishing his master\u2019s thesis, he looked for opportunities to pursue his dream. He met a Dutch researcher while at a workshop in the south of France. The team at Vrije Universiteit Amsterdam was looking for a PhD student, so they interviewed Nicola. Despite his fears about his English proficiency, his passion for combining computer science and biology came across. Professor Jakob (Jaap) Heringa was impressed. \u201cThe fact that he already seemed to be able to combine computer science and life sciences was a very good sign to us, and we decided to hire him based on that.\u201d So Nicola packed his bags and moved to Amsterdam, even though he had never been there before.<\/p>\n<p>The next stop on Nicola\u2019s path was developing novel methods for analyzing sequences of genes to look at how they evolve through a process known as phylogenetic fingerprinting. He teamed up with Professor Berthold G\u00f6ttgens at the University of Cambridge to apply computer science to better understand leukemia, particularly how different genes in blood cells interact with each other.<\/p>\n<div class=\"yt-consent-placeholder\" role=\"region\" aria-label=\"Video playback requires cookie consent\" data-video-id=\"WqYEJhdKVBs\" data-poster=\"https:\/\/img.youtube.com\/vi\/WqYEJhdKVBs\/maxresdefault.jpg\"><iframe aria-hidden=\"true\" tabindex=\"-1\" title=\"From cancer to crop genomics\u2014using Research as a Service at the intersection of computers & biology\" width=\"500\" height=\"281\" data-src=\"https:\/\/www.youtube-nocookie.com\/embed\/WqYEJhdKVBs?feature=oembed&rel=0&enablejsapi=1\" frameborder=\"0\" allow=\"accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share\" referrerpolicy=\"strict-origin-when-cross-origin\" allowfullscreen><\/iframe><\/p>\n<div class=\"yt-consent-placeholder__overlay\"><button class=\"yt-consent-placeholder__play\"><svg width=\"42\" height=\"42\" xmlns=\"http:\/\/www.w3.org\/2000\/svg\" aria-hidden=\"true\" focusable=\"false\"><g fill=\"none\" fill-rule=\"evenodd\"><circle fill=\"#000\" opacity=\".556\" cx=\"21\" cy=\"21\" r=\"21\"\/><path stroke=\"#FFF\" d=\"M27.5 22l-12 8.5v-17z\"\/><\/g><\/svg><span class=\"yt-consent-placeholder__label\">Video playback requires cookie consent<\/span><\/button><\/div>\n<\/div>\n<p>Nicola wanted to share his work and was inspired to build a web-based tool called <a class=\"msr-external-link glyph-append glyph-append-open-in-new-tab glyph-append-xsmall\" rel=\"noopener noreferrer\" href=\"http:\/\/www.conbind.org\" target=\"_blank\">ConBind.org<span class=\"sr-only\"> (opens in new tab)<\/span><\/a> to help others around the world studying the same thing, delivering it as Research as a Service (RaaS). He chose this model of delivery so that researchers without access to powerful computers could still do the computationally intensive work. The idea for deploying his bioinformatics service in the cloud came to Nicola after he attended a <a class=\"msr-external-link glyph-append glyph-append-open-in-new-tab glyph-append-xsmall\" rel=\"noopener noreferrer\" href=\"http:\/\/www.azure4research.com\" target=\"_blank\">Microsoft Azure for Research<span class=\"sr-only\"> (opens in new tab)<\/span><\/a> training session in Amsterdam and successfully <a class=\"msr-external-link glyph-append glyph-append-open-in-new-tab glyph-append-xsmall\" rel=\"noopener noreferrer\" href=\"https:\/\/azure4research.azurewebsites.net\/proposal\/\" target=\"_blank\">applied for an award for his project<span class=\"sr-only\"> (opens in new tab)<\/span><\/a>. The cloud provides the on-demand scalability needed for running his complex bioinformatic queries, and he\u2019s now using the <a class=\"msr-external-link glyph-append glyph-append-open-in-new-tab glyph-append-xsmall\" rel=\"noopener noreferrer\" href=\"https:\/\/azure.microsoft.com\/en-us\/services\/batch\/\" target=\"_blank\">Azure Batch<span class=\"sr-only\"> (opens in new tab)<\/span><\/a> service to make it even easier.<\/p>\n<p>While his research originally focused on understanding cancer, the techniques are equally applicable to all living things: viruses, bacteria, plants and animals. That led Nicola to see if his tool could help farmers achieve such benefits as creating drought-resistant plants, or increasing crop yields. So, he contacted KeyGene, one of the world\u2019s leading AgBioTech companies.<\/p>\n<p>\u201cKeyGene\u2019s passion is crop innovation, getting new and improved crops or actually making the technology that we provide to plant-breeding companies and food industry,\u201d explained Jan van Oeveren, program scientist lead discovery at KeyGene. Genomics is being used to identify key traits that are of interest to the plant breeder, for example disease resistance or shelf life. \u201cWe\u2019re excited to work with Nicola to see if the ConBind tool can be applied to plant genomics. Currently we\u2019re only looking at genes themselves. With ConBind, we\u2019re also looking outside the genes to see how other parts of the genome of the DNA affect a certain trait.\u201d<\/p>\n<p>Nicola isn\u2019t stopping there. His next project, in collaboration with a friend, Alvise Trevisan, is a startup called ENPICOM, supported by the <a class=\"msr-external-link glyph-append glyph-append-open-in-new-tab glyph-append-xsmall\" rel=\"noopener noreferrer\" href=\"https:\/\/bizspark.microsoft.com\/\" target=\"_blank\">Microsoft BizSpark program<span class=\"sr-only\"> (opens in new tab)<\/span><\/a>. This company combines their expertise in software engineering and life sciences to build the \u201cInternet of Living Things.\u201d This project aims to connect individuals with their environment, their health and their genomics, using Azure IoT Suite. Said Nicola, \u201cThe next step in the Internet of Living Things is using AI and Cortana Intelligence to make complex decisions using a multitude of different data sources.\u201d<\/p>\n<p>It\u2019s been an amazing journey for Nicola, starting in Bonate Sotto, where his passion for nature and technology was born, to his exciting new startup ENPICOM. \u201cI think that the challenge of this century is transforming life science in an engineering process and to do that you need to bring engineering into life science. And although probably I will not see the end of this journey, I would like to participate in it.\u201d<\/p>\n<p><strong>Learn more <\/strong><\/p>\n<ul>\n<li><a class=\"msr-external-link glyph-append glyph-append-open-in-new-tab glyph-append-xsmall\" rel=\"noopener noreferrer\" target=\"_blank\" href=\"http:\/\/www.conbind.org\/\">Conbind.org<span class=\"sr-only\"> (opens in new tab)<\/span><\/a><\/li>\n<li><a class=\"msr-external-link glyph-append glyph-append-open-in-new-tab glyph-append-xsmall\" rel=\"noopener noreferrer\" target=\"_blank\" href=\"https:\/\/www.enpicom.com\/\">ENPICOM<span class=\"sr-only\"> (opens in new tab)<\/span><\/a><\/li>\n<li><a class=\"msr-external-link glyph-append glyph-append-open-in-new-tab glyph-append-xsmall\" rel=\"noopener noreferrer\" target=\"_blank\" href=\"http:\/\/www.keygene.com\/\">KeyGene<span class=\"sr-only\"> (opens in new tab)<\/span><\/a><\/li>\n<li><a class=\"msr-external-link glyph-append glyph-append-open-in-new-tab glyph-append-xsmall\" rel=\"noopener noreferrer\" target=\"_blank\" href=\"http:\/\/www.vu.nl\/nl\/index.aspx\">Vrije Universiteit Amsterdam<span class=\"sr-only\"> (opens in new tab)<\/span><\/a><\/li>\n<li><a class=\"msr-external-link glyph-append glyph-append-open-in-new-tab glyph-append-xsmall\" rel=\"noopener noreferrer\" target=\"_blank\" href=\"https:\/\/azure.microsoft.com\/en-us\/services\/batch\/\">Azure Batch<span class=\"sr-only\"> (opens in new tab)<\/span><\/a><\/li>\n<li><a href=\"https:\/\/www.microsoft.com\/en-us\/server-cloud\/cortana-intelligence-suite\/overview.aspx\">Cortana Intelligence Suite<\/a><\/li>\n<li><a class=\"msr-external-link glyph-append glyph-append-open-in-new-tab glyph-append-xsmall\" rel=\"noopener noreferrer\" target=\"_blank\" href=\"https:\/\/azure.microsoft.com\/en-us\/suites\/iot-suite\/\">Azure IoT Suite<span class=\"sr-only\"> (opens in new tab)<\/span><\/a><\/li>\n<li><a class=\"msr-external-link glyph-append glyph-append-open-in-new-tab glyph-append-xsmall\" rel=\"noopener noreferrer\" target=\"_blank\" href=\"https:\/\/enterprise.microsoft.com\/en-us\/industries\/health\/genomics\/\">Microsoft Genomics<span class=\"sr-only\"> (opens in new tab)<\/span><\/a><\/li>\n<li><a class=\"msr-external-link glyph-append glyph-append-open-in-new-tab glyph-append-xsmall\" rel=\"noopener noreferrer\" target=\"_blank\" href=\"http:\/\/research.microsoft.com\/en-us\/projects\/azure\/default.aspx\">Microsoft Azure for Research<span class=\"sr-only\"> (opens in new tab)<\/span><\/a><\/li>\n<li><a class=\"msr-external-link glyph-append glyph-append-open-in-new-tab glyph-append-xsmall\" rel=\"noopener noreferrer\" target=\"_blank\" href=\"https:\/\/azure.microsoft.com\/en-us\/\">Microsoft Azure<span class=\"sr-only\"> (opens in new tab)<\/span><\/a><\/li>\n<\/ul>\n","protected":false},"excerpt":{"rendered":"<p>By Kenji Takeda, Director, Azure for Research, AI and Research Ever since Nicola Bonzanni was a little boy playing in the tiny Italian village of Bonate Sotto, just north of Milan, he was fascinated by nature and by building things. As he grew up, he wondered how computing and nature might be intertwined. \u201cWhile I [&hellip;]<\/p>\n","protected":false},"author":39507,"featured_media":373637,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"msr-url-field":"","msr-podcast-episode":"","msrModifiedDate":"","msrModifiedDateEnabled":false,"ep_exclude_from_search":false,"_classifai_error":"","msr-author-ordering":[],"msr_hide_image_in_river":0,"footnotes":""},"categories":[205399,197938,194484],"tags":[233960,194896,233954,195367,233969,195664,233966,196385,233963,233951,233972,233957],"research-area":[13553],"msr-region":[256048],"msr-event-type":[],"msr-locale":[268875],"msr-post-option":[],"msr-impact-theme":[],"msr-promo-type":[],"msr-podcast-series":[],"class_list":["post-373631","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-azure","category-case-studies","category-medical-health-and-genomics","tag-azure-batch","tag-cancer","tag-conbind-org","tag-dna","tag-enpicom","tag-genome","tag-keygene","tag-microsoft-azure-for-research","tag-microsoft-bizspark","tag-nicola-bonzanni","tag-phylogenetic-fingerprinting","tag-research-as-a-service","msr-research-area-medical-health-genomics","msr-region-global","msr-locale-en_us"],"msr_event_details":{"start":"","end":"","location":""},"podcast_url":"","podcast_episode":"","msr_research_lab":[199561],"msr_impact_theme":[],"related-publications":[],"related-downloads":[],"related-videos":[],"related-academic-programs":[204065,204068],"related-groups":[],"related-projects":[],"related-events":[],"related-researchers":[],"msr_type":"Post","featured_image_thumbnail":"<img width=\"960\" height=\"360\" src=\"https:\/\/www.microsoft.com\/en-us\/research\/wp-content\/uploads\/2017\/03\/Nicola_3_header.jpg\" class=\"img-object-cover\" alt=\"a man riding a bike down a dirt road\" decoding=\"async\" loading=\"lazy\" srcset=\"https:\/\/www.microsoft.com\/en-us\/research\/wp-content\/uploads\/2017\/03\/Nicola_3_header.jpg 1920w, https:\/\/www.microsoft.com\/en-us\/research\/wp-content\/uploads\/2017\/03\/Nicola_3_header-300x113.jpg 300w, https:\/\/www.microsoft.com\/en-us\/research\/wp-content\/uploads\/2017\/03\/Nicola_3_header-768x288.jpg 768w, https:\/\/www.microsoft.com\/en-us\/research\/wp-content\/uploads\/2017\/03\/Nicola_3_header-1024x384.jpg 1024w\" sizes=\"auto, (max-width: 960px) 100vw, 960px\" \/>","byline":"","formattedDate":"March 28, 2017","formattedExcerpt":"By Kenji Takeda, Director, Azure for Research, AI and Research Ever since Nicola Bonzanni was a little boy playing in the tiny Italian village of Bonate Sotto, just north of Milan, he was fascinated by nature and by building things. As he grew up, he&hellip;","locale":{"slug":"en_us","name":"English","native":"","english":"English"},"_links":{"self":[{"href":"https:\/\/www.microsoft.com\/en-us\/research\/wp-json\/wp\/v2\/posts\/373631","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.microsoft.com\/en-us\/research\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.microsoft.com\/en-us\/research\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.microsoft.com\/en-us\/research\/wp-json\/wp\/v2\/users\/39507"}],"replies":[{"embeddable":true,"href":"https:\/\/www.microsoft.com\/en-us\/research\/wp-json\/wp\/v2\/comments?post=373631"}],"version-history":[{"count":9,"href":"https:\/\/www.microsoft.com\/en-us\/research\/wp-json\/wp\/v2\/posts\/373631\/revisions"}],"predecessor-version":[{"id":375530,"href":"https:\/\/www.microsoft.com\/en-us\/research\/wp-json\/wp\/v2\/posts\/373631\/revisions\/375530"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/www.microsoft.com\/en-us\/research\/wp-json\/wp\/v2\/media\/373637"}],"wp:attachment":[{"href":"https:\/\/www.microsoft.com\/en-us\/research\/wp-json\/wp\/v2\/media?parent=373631"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.microsoft.com\/en-us\/research\/wp-json\/wp\/v2\/categories?post=373631"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.microsoft.com\/en-us\/research\/wp-json\/wp\/v2\/tags?post=373631"},{"taxonomy":"msr-research-area","embeddable":true,"href":"https:\/\/www.microsoft.com\/en-us\/research\/wp-json\/wp\/v2\/research-area?post=373631"},{"taxonomy":"msr-region","embeddable":true,"href":"https:\/\/www.microsoft.com\/en-us\/research\/wp-json\/wp\/v2\/msr-region?post=373631"},{"taxonomy":"msr-event-type","embeddable":true,"href":"https:\/\/www.microsoft.com\/en-us\/research\/wp-json\/wp\/v2\/msr-event-type?post=373631"},{"taxonomy":"msr-locale","embeddable":true,"href":"https:\/\/www.microsoft.com\/en-us\/research\/wp-json\/wp\/v2\/msr-locale?post=373631"},{"taxonomy":"msr-post-option","embeddable":true,"href":"https:\/\/www.microsoft.com\/en-us\/research\/wp-json\/wp\/v2\/msr-post-option?post=373631"},{"taxonomy":"msr-impact-theme","embeddable":true,"href":"https:\/\/www.microsoft.com\/en-us\/research\/wp-json\/wp\/v2\/msr-impact-theme?post=373631"},{"taxonomy":"msr-promo-type","embeddable":true,"href":"https:\/\/www.microsoft.com\/en-us\/research\/wp-json\/wp\/v2\/msr-promo-type?post=373631"},{"taxonomy":"msr-podcast-series","embeddable":true,"href":"https:\/\/www.microsoft.com\/en-us\/research\/wp-json\/wp\/v2\/msr-podcast-series?post=373631"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}