Bioinformatics Core | Gladstone Institutes

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data-drupal-messages-fallback class="hidden"></div> <div id="block-showcase-lite-page-title" class="clearfix block block-core block-page-title-block"> <div class="content"> <h1 class="title page-title"><span class="field field--name-title field--type-string field--label-hidden">Bioinformatics Core</span> </h1> </div> </div> </div> </div> </div> </div> </div> </div> </div> <div class="clearfix main-content region--dark-typography region--white-background region--no-separator"> <div class="landing-page-container" > <div class="clearfix main-content__container"> <div class="row"> <section> <div class="clearfix main-content__section" > <div class="region region-content"> <div id="block-showcase-lite-content" class="clearfix block block-system block-system-main-block"> <div class="content"> <article data-history-node-id="3268" class="node node--type-core-mini-sites node--promoted node--view-mode-full clearfix"> <div class="node__container"> <div class="node__main-content clearfix"> <header class="node__header"> </header> <div class="row"> <div id="subtabs" class="subtabs"> <ul class="sudonav"> <li class="tab"><a href="#overview"><span>Overview</span></a></li> <li class="tab"><a href="#capabilities"><span>Capabilities</span></a></li> <li class="tab"><a href="#fees-and-scheduling"><span>Fees and Scheduling</span></a></li> <li class="tab"><a href="#publications"><span>Publications</span></a></li> <li class="tab"><a href="#faqs"><span>FAQs</span></a></li> </ul> <div class="content-wrap"> <section id="overview"> <div id="intro"> <div class="container"> <p class="large">The Bioinformatics Core provides expertise on experimental design and analysis of complex data sets, with a specialization on large-scale data sets acquired from various cutting-edge technologies. Make the core part of your team for experimental design, sequence analysis, pathway and network analysis, training, and grant proposals.</p> </div> </div> <div id="manager"> <div class="container"> <h2>Contact</h2> <div class="user__compact"> <p><b>Bioinformatics Core Staff</b><br> <a href="mailto:bioinformatics@gladstone.ucsf.edu">Email</a> <br> </p> </div> </div> </div> <div class="corebk1">   </div> <div class="services"> <div class="container"> <h2>Services Provided</h2> <ul> <li>Consultation on various topics, including experimental design, power analysis, bioinformatics, and statistical analysis</li> <li>Collaboration, grant writing, and publications</li> <li class="contact-genomics">Analysis of bulk RNA-seq, single-cell RNA-seq, ChIP-seq, ATAC-seq, and other epigenetics analysis. For sample preparation, library preparation and sequencing,</li> <li>Integrated analysis including various data modalities</li> <li>Network and pathway analysis, modeling, and data visualization</li> <li>Training and workshops on topics in bioinformatics, statistics, and data science</li> </ul> </div> </div>  <div class="core-members"> <div class="container"> <h2>Core Members</h2> <div class="views-element-container"><div class="view view-user-admin-people view-id-user_admin_people view-display-id-bioinformatics_members js-view-dom-id-9270888f91044ce60c9376f85866aad176d8c920911daa17f934bb0bfa5d3676"> <div class="view-content"> <div class="views-view-grid horizontal cols-2 clearfix"> <div class="views-row clearfix row-1"> <div class="views-col col-1" style="width: 50%;"><article class="user user--compnomail"> <div class="user__compact"> <p><b>Ayushi Agrawal</b><br>Bioinformatician III<br></p> </div> </article> </div> <div class="views-col col-2" style="width: 50%;"><article class="user user--compnomail"> <div class="user__compact"> <p><b>Natalie Elphick</b><br>Bioinformatician I<br></p> </div> </article> </div> </div> <div class="views-row clearfix row-2"> <div class="views-col col-1" style="width: 50%;"><article class="user user--compnomail"> <div class="user__compact"> <p><b>Kristina Hanspers</b><br>Senior Research Associate<br></p> </div> </article> </div> <div class="views-col col-2" style="width: 50%;"><article class="user user--compnomail"> <div class="user__compact"> <p><b>Alex Pico</b><br>Core Director/Research Investigator<br></p> </div> </article> </div> </div> <div class="views-row clearfix row-3"> <div class="views-col col-1" style="width: 50%;"><article class="user user--compnomail"> <div class="user__compact"> <p><b>Min-gyoung Shin</b><br>Bioinformatician III<br></p> </div> </article> </div> <div class="views-col col-2" style="width: 50%;"><article class="user user--compnomail"> <div class="user__compact"> <p><b>Reuben Thomas</b><br>Associate Core Director<br></p> </div> </article> </div> </div> <div class="views-row clearfix row-4"> <div class="views-col col-1" style="width: 50%;"><article class="user user--compnomail"> <div class="user__compact"> <p><b>Michela Traglia</b><br>Senior Statistician<br></p> </div> </article> </div> <div class="views-col col-2" style="width: 50%;"><article class="user user--compnomail"> <div class="user__compact"> <p><b>Yihang Xin</b><br>Software Engineer III<br></p> </div> </article> </div> </div> <div class="views-row clearfix row-5"> <div class="views-col col-1" style="width: 50%;"><article class="user user--compnomail"> <div class="user__compact"> <p><b>Zainab Yusuf-Sada</b><br>Senior Executive Administrator<br></p> </div> </article> </div> </div> </div> </div> </div> </div> </div> </div> <div id="events"> <div class="container"> <h2 class="text-align-center">Events</h2> <p class="text-align-center large">The Gladstone Data Science Training Program was started in 2018 to provide trainees with learning opportunities and hands-on workshops to improve their skills in bioinformatics and computational analysis.</p> <p class="text-align-center"><a class="button magenta" href="/events?series=data-science-training-program">Upcoming Events</a></p> </div> </div> <div id="related-news"> <div class="container"> <h2>Related News</h2> <div class="owl-carousel" id="news-carousel"> <a href="/news/gladstone-expand-stem-cell-research-capabilities-multi-million-dollar-regenerative-medicine" title="Read more" target="_self"><div class="item"><img alt="Sam Hu prepares induced pluripotent stem cells." class="owl-lazy" data-src="/sites/default/files/styles/news_card/public/news-events/_aaa1066_1.jpg?itok=IrGOuDA_ " /><div class="blowpic">Gladstone to Expand Stem Cell Research Capabilities with Multi-Million Dollar Regenerative Medicine Grant<br><div class="summy">Funds from the California Institute for Regenerative Medicine will allow Gladstone to bolster its disease-modeling technologies, add robust CRISPR screening capabilities, and educate young…</div><div class="authored"><time datetime="2024-03-11T09:34:32-07:00" class="datetime">March 11, 2024</time> </div></div></div></a><a href="/news/where-biology-and-open-source-coding-converge" title="Read more" target="_self"><div class="item"><img alt="Alex Pico and Kristina Hanspers sitting at a desk discussing something over a laptop" class="owl-lazy" data-src="/sites/default/files/styles/news_card/public/news-events/_dsc6977.jpg?itok=csGoPrYe " /><div class="blowpic">Where Biology and Open-Source Coding Converge<br><div class="summy">Software developers and their mentors at Gladstone help advance research through Google Summer of Code</div><div class="authored"><time datetime="2023-10-16T07:37:48-07:00" class="datetime">October 16, 2023</time> </div></div></div></a><a href="/news/meet-gladstone-leandro-lima" title="Read more" target="_self"><div class="item"><img alt="Gif of Leandro Lima talking with his hands" class="owl-lazy" data-src="/sites/default/files/styles/news_card/public/news-events/leandro_lima_meet_gladstone_hero.gif?itok=zkltjRVI " /><div class="blowpic">Meet Gladstone: Leandro Lima<br><div class="summy">Learn how a Gladstone bioinformatician is spending his days during shelter-in-place</div><div class="authored"><time datetime="2020-10-13T01:00:00-07:00" class="datetime">October 13, 2020</time> </div></div></div></a><a href="/news/finding-covid-19-treatments-fda-approved-drugs-rapid-repurposing" title="Read more" target="_self"><div class="item"><img alt="Discovering Protein Interaction to Identify Drugs to Repurpose" class="owl-lazy" data-src="/sites/default/files/styles/news_card/public/news-events/drug-target.jpg?itok=mH4VFGvM " /><div class="blowpic">Finding COVID-19 Treatments in FDA-Approved Drugs for Rapid Repurposing<br><div class="summy">There are thousands of prescription drugs already approved by the FDA for treating diseases. Can one of them work for COVID-19?</div><div class="authored"><time datetime="2020-04-29T04:36:00-07:00" class="datetime">April 29, 2020</time> </div></div></div></a><a href="/news/data-driven-discovery" title="Read more" target="_self"><div class="item"><img alt="Illustration of computer with representations of data" class="owl-lazy" data-src="/sites/default/files/styles/news_card/public/news-events/datasciencestory-banner.jpg?itok=6kXzbvEO " /><div class="blowpic">Data-Driven Discovery<br><div class="summy">Many Gladstone researchers rely on computational approaches, machine learning, and innovative software to make biomedical discoveries.</div><div class="authored"><time datetime="2020-04-22T14:17:22-07:00" class="datetime">April 22, 2020</time> </div></div></div></a><a href="/news/help-gladstone-bioinformatics-cores-effort-tackle-covid-19" title="Read more" target="_self"><div class="item"><img alt="Alex Pico with his arms crossed outside the Gladstone building" class="owl-lazy" data-src="/sites/default/files/styles/news_card/public/news-events/alex-pico-2020.jpg?itok=cm4Ae_Ai " /><div class="blowpic">Help the Gladstone Bioinformatics Core’s Effort to Tackle COVID-19<br><div class="summy">You can help advance research on COVID-19</div><div class="authored"><time datetime="2020-03-25T13:53:55-07:00" class="datetime">March 25, 2020</time> </div></div></div></a><a href="/news/measuring-research-impact" title="Read more" target="_self"><div class="item"><img alt="Headshot of Alex Pico outside the Gladstone building" class="owl-lazy" data-src="/sites/default/files/styles/news_card/public/news-events/alex.pico_.jpg?itok=jfWOlu7x " /><div class="blowpic">Measuring Research Impact<br><div class="summy">Gladstone researcher Alex Pico helped develop a new way to measure the difference one discovery can make on science around the world.</div><div class="authored"><time datetime="2020-01-16T16:01:00-08:00" class="datetime">January 16, 2020</time> </div></div></div></a><a href="/news/students-use-their-computer-skills-help-advance-biology" title="Read more" target="_self"><div class="item"><img alt="Alex Pico in the lab" class="owl-lazy" data-src="/sites/default/files/styles/news_card/public/news-events/alexpico-inthelab.jpeg?itok=D6io5PQx " /><div class="blowpic">Students Use Their Computer Skills to Help Advance Biology<br><div class="summy">An ongoing collaboration with Google Summer of Code</div><div class="authored"><time datetime="2018-05-31T20:47:00-07:00" class="datetime">May 31, 2018</time> </div></div></div></a><a href="/news/big-data-introduces-new-era-discovery-science" title="Read more" target="_self"><div class="item"><img alt="Bioinformatics Lab" class="owl-lazy" data-src="/sites/default/files/styles/news_card/public/news-events/bioinformatics-lab.jpg?itok=fpN7w48b " /><div class="blowpic">Big Data Introduces a New Era of Discovery in Science<br><div class="summy">Gladstone’s Bioinformatics Core is dedicated to providing expertise in data analysis and visualization to answer complex biological questions with Big Data. </div><div class="authored"><time datetime="2017-03-14T23:55:00-07:00" class="datetime">March 14, 2017</time> </div></div></div></a> </div> </div> </div> </section> <section id="capabilities"> <div id="capab-intro"> <div class="container"> <p class="large">Our team consists of several individuals with formal training in statistics, bioinformatics, and computer science, and should be able handle almost any question that involves experimental design, bioinformatics, statistical analysis, programming, or figure generation.</p> </div></div> <div class="alt-rows odd ar-1"> <div class="container"> <div class="row"> <div class="col-sm-6 capspacer">   </div> <div class="col-sm-6"> <p class="large">We offer consulting on experimental design, analysis planning and statistical methodology, as well as on training and software development.</p> </div> </div> </div> </div> <div class="alt-rows even ar-2"> <div class="container"> <div class="row"> <div class="col-sm-6"> <p class="large">We also team up in analyzing your primary data. We have broad and deep experience with most forms of sequencing data and omics data. We also regularly work with genotype and phenotype data in multivariate analysis.</p> </div> <div class="col-sm-6 capspacer">   </div> </div> </div> </div> <div class="alt-rows odd ar-3"> <div class="container"> <div class="row"> <div class="col-sm-6 capspacer">   </div> <div class="col-sm-6"> <p class="large">We can assist with Integrating data across batches and types or with publicly available data. Our methods include customized statistical modeling and network analysis.</p> </div> </div> </div> </div> <div class="alt-rows even ar-4"> <div class="container"> <div class="row"> <div class="col-sm-6"> <p class="large">We have expertise in visualizing data for both exploratory and publication-ready applications. In addition to figures, we routinely generate detailed pathway models and interactive web displays.</p> </div> <div class="col-sm-6 capspacer">   </div> </div> </div> </div> <div class="alt-rows odd ar-5"> <div class="container"> <div class="row"> <div class="col-sm-6 capspacer">   </div> <div class="col-sm-6"> <p class="large">Our team has over a decade of experience developing open source software and methods, including algorithms, pipelines and custom scripts, along with software packages and applications with global usage.</p> </div> </div> </div> </div> <div class="alt-rows even ar-6"> <div class="container"> <div class="row"> <div class="col-sm-6"> <p class="large">We are committed to training researchers in the ways of bioinformatic analysis, statistics and programming. We conduct multiple campus-wide workshops each month as well as tailored training events for individual labs.</p> </div> <div class="col-sm-6 capspacer">   </div> </div> </div> </div> </section> <section id="fees-and-scheduling"> <div class="container"> <p>All service projects are coordinated through the iLabs system. <a href="https://gladstone.corefacilities.org/account/signup/34">Register for an account</a> and then log in to iLabs to <a href="https://gladstone.corefacilities.org/service_center/2998/?tab=services">initiate your request.</a> You can contact us with a brief description of your project at <a href="mailto:bioinformatics@gladstone.ucsf.edu">bioinformatics@gladstone.ucsf.edu.</a> In addition to fee-for-service work, we also routinely work as collaborators by percent effort on grant subawards.</p><h2>Fees</h2><table style="width:500px;" border="1" cellpadding="1" cellspacing="1"><tbody><tr><td>Gladstone</td><td>$120 per hour</td></tr><tr><td>UCSF</td><td>$200 per hour</td></tr><tr><td>External</td><td>$240 per hour</td></tr></tbody></table> </div> </section> <section id="publications"> <div class="container"> <h3>Publications</h3> <ul id="datalist"> <p>Our core staff are career scientists too! We often make substantial contributions to projects leading to co-authorship and collaborations on grant applications. For basic routine analysis, we request acknowledgement in publications, e.g. “We thank Dr. XYZ of the Gladstone Bioinformatics Core for their assistance with statistical and bioinformatics analysis.”</p><p><a href="https://scholar.google.com/citations?hl=en&user=0SojVdYAAAAJ&view_op=list_works&authuser=1&sortby=pubdate">Check out our latest co-authored and acknowledged publications on Google Scholar.</a></p> </ul> </div> </section> <section id="faqs"> <div class="accordion-wrapper"> <div class="container"> <h2>FAQs</h2> <div class="accordion accord1"><h3>How Do I Schedule an Initial Meeting?</h3></div> <div class="panel"> <p><a href="https://gladstone.corefacilities.org/service_center/2998/?tab=services">Initiate a consultation request in iLabs</a> or simply <a href="mailto:bioinformatics@gladstone.ucsf.edu">email us at bioinformatics@gladstone.ucsf.edu.</a></p> </div> <div class="accordion"><h3>What If I Just Have a Quick Question?</h3></div> <div class="panel"> <p><a href="https://gladstoneinstitutes.slack.com/archives/C0145F1L7QS">Join our Gladstone Slack channel #questionsforbioinformaticscore</a> to ask and follow questions at any time, or <a href="mailto:bioinformatics@gladstone.ucsf.edu">email us at bioinformatics@gladstone.ucsf.edu.</a></p> </div> <div class="accordion"><h3>Does the Bioinformatics Core Have Suggested Pipelines to Process, Run Quality Control Checks Etc. on Sequencing Data of Different Kinds (RNA-seq, Chip-seq, Atac-seq)?</h3></div> <div class="panel"> <p>We recommend Nextflow pipelines, which we have configured to run on the <a href="https://github.com/ucsf-wynton/tutorials/wiki">UCSF-Wynton compute cluster.</a></p> </div> <div class="accordion"><h3>How Should I Acknowledge Minor Contributions to a Paper?</h3></div> <div class="panel"> <p>We commonly contribute at the level of co-authors, but for minor contributions an acknowledgement is much appreciated, e.g., <em>We thank Dr. XYZ of the Gladstone Bioinformatics Core for their assistance with statistical and bioinformatics analysis.</em></p> </div> </div> </div> </section> </div> </div> </div> <script src="/libraries/easytabs/jquery-1.7.1.min.js" type="text/javascript"></script> <script src="/libraries/easytabs/jquery.hashchange.min.js" type="text/javascript"></script> <script src="/libraries/easytabs/jquery.easytabs.min.js" type="text/javascript"></script> <script type="text/javascript"> $(function( $ ){ $('#subtabs').easytabs(); }); </script> <script src="//ajax.googleapis.com/ajax/libs/jquery/1.11.0/jquery.min.js"></script> <script src="/libraries/owl-carousel2/owl.carousel.js"></script> <script> var owl = $('.owl-carousel'); owl.owlCarousel({ margin: 10, lazyLoad:true, lazyLoadEager: 1, loop: true, dots: false, responsive: { 0: { items: 1 }, 600: { items: 2 }, 1000: { items: 3, nav: true } } }) // disable scroll owl.on('drag.owl.carousel', function(event) { document.ontouchmove = function (e) { e.preventDefault() } }) // enable scroll owl.on('dragged.owl.carousel', function(event) { document.ontouchmove = function (e) { return true } }) </script> <script> var acc = document.getElementsByClassName("accordion"); var i; for (i = 0; i < acc.length; i++) { acc[i].addEventListener("click", function() { this.classList.toggle("active"); var panel = this.nextElementSibling; if (panel.style.maxHeight){ panel.style.maxHeight = null; } else { panel.style.maxHeight = panel.scrollHeight + "px"; } }); } </script> <script> // This prevents the page from scrolling down to where it was previously. if ('scrollRestoration' in history) { history.scrollRestoration = 'manual'; } // This is needed if the user scrolls down during page load and you want to make sure the page is scrolled to the top once it's fully loaded. 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