17th Annual Biomedical Computation at StanfordSymposium

BCATS2017

Stanford University

April 10, 2017

2017 Sponsors

Corporate Sponsors

Genentech

SynTest Technologies

2017 BCATS Schedule

8:15 AM Badge Pickup and Breakfast

8:45 AM Opening Remarks

Session 1

9:00 AM Keynote Address: Michael Snyder, PhDUsing Big Data to Manage Health and Disease

9:45 AM Peyton GreensideGenomics-specific deep learning architectures reveal mechanisms of gene regulation

10:00 AM Ethan FastIris: A Natural Language Platform for Biomedical Data Analysis

10:15 AM Coffee Break

Session 2

10:30 AM Keynote Address: Olga Vitek, MS, PhDStatistical methods for quantitative proteomics

11:15 AM Michael SharpnackProteogenomic analysis of surgically resected lung adenocarcinoma

11:30 AM Anna ScherbinaDeep learning approaches for functional variant prioritization

11:45 AM Lunch

Session 3

1:00 PM Keynote Address: Nicholas Tatonetti, PhDEstimating disease heritability using 13 million patients records

1:45 PM Robin BetzSimulating the binding of opioid antagonists using adaptively sampled molecular dynamics simulation

2:15 PM Keynote Address: Ron Dror, MPhil, PhDDiscovering how drugs and their targets work through simulation and machine learning

3:00 PM Snack Break

Session 4

3:15 PM Industry Panel: Brendan Faherty, Carlo Artieri, Grace Zheng, Christine Lo

4:00 PM Closing Remarks

4:15 PM Poster Session with Happy Hour

5:15 PM Symposium End

About Us

Alice YuBiomedical Informatics

Plevritis Lab

Alice Yu received her B.S. in Bioengineering:

Bioinformatics from UC San Diego and is currently a

2nd year PhD student in the Stanford Biomedical

Informatics training program. She is now developing

an informatics method to understand the complexity

of cancer in Dr. Sylvia Plevritis’ lab. Her current

work involves infering the cell signaling networks in

non-small cell lung carcinoma (NSCLC).

Kristin MuenchNeurosciencePalmer Lab

Kristin studied Cognitive Science with an emphasis in

Neuroscience at UC San Diego. She subsequently

research language development at Emory University

before joining Stanford’s Neurosciences Ph.D.

program. Now in her fourth year of graduate school,

Kristin studies the transcriptional consequences of

maternal illness during pregnancy on the developing

fetal brain.

Hunter BoyceBiomedical Informatics

Mallick Lab

Hunter Boyce received his B.S. in Bioinformatics from

UC San Diego and is currently a 2nd year PhD

student in the Stanford Biomedical Informatics

training program. He is now working with Dr. Parag

Mallick on using integrative, multi-omic approaches to

model the processes that govern proteome dynamics

and to use those models to discover cancer biomarkers

and mechanisms.

Christine YehBiomedical InformaticsPitteri Lab, Snyder Lab

Christine Yeh is a co-terminal masters student in the

Biomedical Informatics Program at Stanford

University. She is working on a collaborative effort

between the Snyder and Pitteri labs to model and

predict human disease using integrative, longitudinal

multi-omics.

Organizer RemarksWe are proud to host and have you here at the 17th annual conference forbiomedical computation at Stanford, or what we call as BCATS. Every year, we asmembers of the organizing committee, including the departments of ComputerScience, Neuroscience, and Biomedical Informatics provide a platform for scientificinteraction between students, faculty and members of the industry involved insolving computational problems in biology, healthcare and biomedicine. In thepast, our affiliates and attendees have been involved in some of the most cuttingedge discoveries and technologies that continue to drive great breakthroughs inthese fields and beyond. This year, our participants include students and facultyfrom Stanford University, UC San Francisco, UC San Diego, UC Santa Cruz, andSan Francisco State. Our keynote speakers will be speaking on topics such asGenomics, Proteomics, Machine Learning, and Translational Informatics. Ourindustry panel includes esteemed speakers from some of the hottest companies inthe Bay Area including Guardant Health, Counsyl, Genentech, and 10X Genomics.Our attendees also include researchers from Roche and IBM. We are generouslysupported by various departments within Stanford, the Li Ka Shing Center forLearning and Knowledge and also our industry affiliates in the Bay Area.

Your organizing committee,

Hunter Boyce, Kristin Muench, Christine Yeh, Alice Yu

Keynote Speakers

Michael Snyder, PhDProfessor and Chair, Department of GeneticsStanford UniversityTalk Title: Using Big Data to Manage Health and Disease

Dr. Mike Snyder is a leader in functional genomics andproteomics. His lab develops methods to analyze genomesand regulatory networks, such as proteome chips, highresolution tiling arrays for the entire human genome, andmethods for global mapping of transcription factor binding sites (ChIP-chip nowreplaced by ChIP-seq) in organisms, such as yeast and human.

Olga Vitek, MS, PhDSy and Laurie Sternberg Interdisciplinary AssociateProfessor, Science; Computer and Information ScienceNortheasten UniversityTalk Title: Statistical methods for quantitativeproteomics

Dr. Olga Vitek’s group works with high-throughputinvestigations in multi-omics to characterize the

components of biological systems, functional interactions, and disease relevance withthe goal of providing methods and software for experimental design and accuracyimprovement.

Nicholas Tatonetti, PhDAssistant Professor, Departmentof Biomedical Informatics and Systems BiologyColumbia UniversityTalk Title: Estimatingdisease heritability using 13 million patients records

Dr. Nicholas Tatonetti’s lab focuses on multi-omics data integration, such astranscriptome sequencing, metabolomics, proteomics, and electronic medicalrecords. Some of his exciting translational projects include understanding how touse venom for drug development and finding deadly drug interactions using clinicalinformatics approach.

Ron Dror, MPhil, PhDAssociate Professor of Computer Science, Molecular andCellular PhysiologyStanford UniversityTalk Title: Discovering how drugs and their targets workthrough simulation and machine learning

Dr. Ron Dror’s lab is multidisciplinary and works withvarying areas ranging from high-performance computing

to drug discovery. Specifically, the group focuses on understanding the spatialorganization and dynamics of biomolecules to answer questions about our livingsystems and improve precision medicine.

Bio-X is Stanford’s pioneering initiative in the interdisciplinary movement at Stanford

University. Over the past 18 years, Bio-X has developed into an impactful institute that brings together biomedical and life science researchers, clinicians, engineers, physicists, and computational scientists to unlock the secrets of the human body. Over 800 Stanford faculty from all 7 Stanford schools and 65+ departments are affiliated with Bio-X,

and participating in the following Core Programs: Interdisciplinary Initiatives Seed Grant

Program (IIP)

Ventures

Graduate Student Fellowships and Bio-X Stanford Interdisciplinary Graduate Fellowships

Undergraduate Research Awards

Travel Awards In addition, Bio-X establishes numerous collaborations between the Stanford scientists and large corporations

by being a networking portal and providing opportunities for companies to join and participate in

symposia/seminars/mixers and customized technical summits, developing faculty liaisons, and more.

The James H. Clark Center is the hub of Bio-X, comprising the equipment, resources, and utilities required to conduct breakthrough research at the cutting edge of engineering, science, and medicine.

STANFORD BIO-X

To learn more about Bio-X,

visit our website:

biox.stanford.edu

Stanford BiomedicalInformatics

TrainingProgram TheBiomedicalInformaticsTrainingProgram(BMI)isaninterdisciplinarygraduateandpostdoctoraltrainingprogram,partoftheBiosciencesProgramatStanfordUniversity’sSchoolofMedicine.WeofferMSandPhDdegrees,andothercourseworkandresearchoptions.

Full-TimeGraduatePrograms: •PhDinBiomedicalInformatics •ResearchMSdegree(primarily,butnotexclusively,forthosewithPhDand/orMD)

Part-TimeDistanceEducationPrograms: •Professional/HonorsCooperativeProgramMSdegree•CertificateinBiomedicalInformatics•Non-degreeoptionforindividualclasses

ForStanfordStudents:•CoterminalMSdegreeinBiomedicalInformaticsinadditiontoBA/BS •PhDMinorinBiomedicalInformaticsforStanfordgraduatestudents

ForStanfordMedicalStudents: •CourseworkandresearchopportunitiesthroughScholarlyConcentrationandMedicalScholarsprograms

AlldegreeprogramsrequirerigorouscourseworkinBiomedicalInformaticscorecourses,acoherentsetofelectivesfromComputerScience,Statistics,Mathand/orandEngineering,andtraininginSocial,LegalandEthicalissues.

Formoreinformation,contact:StudentServicesOfficer StanfordBiomedicalInformaticsTrainingProgram Phone:(650)723-1398MedicalSchoolOfficeBuilding,RoomX-215 Fax:(650)725-7944 1265WelchRoad,MailCode:5479 email:bmi-contact@lists.stanford.edu Stanford,CA94305-5479 http://bmi.stanford.edu

SupportedbyNationalLibraryofMedicineTrainingGrantLM007033

Student SpeakersAnna ShcherbinaTalk Title: Deep learning approaches for functional variant prioritization

Ethan FastTalk Title: Iris: Analyzing Biomedical Data through Natural Language

Michael SharpnackTalk Title: Proteogenomic analysis of surgically resected lung adenocarcinoma

Peyton GreensideTalk Title: Interpretable deep learning approaches to decipher context-specificusage of regulatory DNA sequence

Robin BetzTalk Title: Simulating the binding of opioid antagonists using adaptively sampledmolecular dynamics simulation

Industry PanelChristine Lo, MS, PhDCounsyl, Software Engineer

Carlo Artieri, MS, PhDGuardant Health, Senior Bioninformatics Scientist

Grace Zheng, PhD10X Genomics, Senior Scientist

Brendan Faherty, MBA, PhDGenentech, Protein Sciences Consultant

We aim to understand how the brain gives rise to mental life and behavior, both in health and in disease. Our research community draws from multiple disciplines, including neuroscience, medicine, engineering, psychology, education and law.

The Neurosciences Institute is shaping the future of neuroscience in three interdisciplinary areas as reflect-ed in the few examples below:

Stanford Neurosciences Institute

The Big Idea, NeuroChoice, probes how the brain makes decisions and expands that to influence public policy and economic decisions.

The Big Idea, Stanford NeuroTechnology Initiative, creates an incubator for next-generation neural interface platforms.

The Big Idea, Brain Rejuvenation, creates a center for neurodegeneration research focusing on brain maintenance and regeneration, and the role of the immune system in these processes.

NeuroDiscovery - probing the inner workings of the brain

NeuroEngineering - creating innovative new technologies for interfacing with the brain

NeuroHealth - translating neuroscience discoveries into treatments

The institute awarded a seed grant to develop and validate a new PET ligand for imaging microglial inflammation in Alzhei-mer’s Disease.

SIGF student, Tatiana Glozman, focuces her research on devel-oping tools for shape analysis of brain structures.

Postdoctoral Scholar, Alan Ceaser, aims to better understand the neural mechanisms of complex cognition.

OpportunitiesInterdisciplinary ResearchBig Ideas in NeuroscienceSeed GrantsStanford Program in Neurosciences and SocietyVisiting Scholars

TrainingInterdisciplinary Postdoctoral AwardsStanford Interdisciplinary Graduate FellowshipsSoftware Carpentry Workshops

Engaging our CommunityWeekly Seminar SeriesAnnual SymposiumBrain Broadcast NewsletterRetreat - coming soon!

Get Involvedhttp://neuroscience.stanford.edu

Poster TitlesAditya Rao, TE Sweeney, P KhatriA robust host-based gene expression diagnostic for malaria versus other infectiousdiseases

Alex WilliamsDimensionality Reduction of Neural Dynamics Within and Across Trials By TensorDecomposition

Erika BongenProfiling immune system sex differences in the healthy human transcriptome

Gautam MachirajuMathematical Model of Cancer Heterogeneity & Biomarker Shedding Kinetics

Greg McInnesGlobal Biobank Engine: An Online Tool for the Statistical Exploration of LargeGenomic Datasets

Idit KostiMeta Analysis of Microbiome Data and Electronic Medical Data Provides NewInsights On Preterm Births

Jessica TorresCharacterization of Hypertrophic Cardiomyopathy using Wearable Sensors

Shubham Chandak, Kedar TatwawadiCompression of genomic sequencing reads with and without preserving the order

Kelly ZalocuskyThe 10,000 Immunomes Project: A Data Resource for Human Immunology

Michael GloudemansWhole genome sequencing of diverse human populations resolves causal regulatoryvariants

Nandita Bhaskhar and Pulkit TandonAutomated methods for detection of axon bundle activation in Epiretinal Prostheses

Oliver Bear Don’t Walk IV, Sandeep Ayyar, Manuel RivasTagging Patient Notes With ICD-9 Codes

Pratibha JagannathaThe Role of Alternative Splicing Regulation in the Innate Immune Response

The Stanford Computer Forum is a cooperative venture that encourages collaboration between the Computer Science and the Electrical Engineering Departments at Stanford, and 100+ companies located in Silicon Valley, the rest of the U.S., Asia, and Europe. The Forum provides a mechanism for developing interaction with industrial researchers and their academic counterparts, promoting the exchange of the most advanced technological ideas in fields of computer science and electrical engineering. The Computer Forum also offers industry the opportunity to become familiar with the professional abilities and interests of Stanford students through its active recruiting program.

For further information please visit http://www.forum.stanford.edu or e-mail forumstaff@cs.stanford.edu

Department of Genetics - Ranked #1 in Genetics, Genomics and

Bioinformatics fifth year in a row!

We provide training through laboratory rotations, dissertation research, seminar series, didactic and interactive coursework, and an

annual three-day retreat of nearly 200 students, faculty, postdoctoral fellows, and research staff.

Join us and be part of leading department in the world for Genetics research!

Thank YouKiran Malladi

Linny Le

Ayla Akgul

Michelle Kibby-Parra

Joy Morimoto

LKSC Staff