january 3-7, 2018 big island of hawaii program book · 2020-02-12 · pacific symposium on...

Pacific Symposium on Biocomputing 2018 January 3-7, 2018

Big Island of Hawaii

Program Book

PACIFIC SYMPOSIUM ON BIOCOMPUTING 2018 Big Island of Hawaii, January 3-7, 2018

Welcome to PSB 2018!

We have prepared this program book to give you quick access to information you need for PSB 2018.

Enclosed you will find

• Logistics information• Menus for PSB hosted meals• Full conference schedule• Call for Session and Workshop Proposals for PSB 2019• Poster/abstract titles and authors• Participant List

Conference materials are also available online at http://psb.stanford.edu/conference-materials/.

PSB 2018 gratefully acknowledges the support the Institute for Computational Biology, a collaborative effort of Case Western Reserve University, the Cleveland Clinic Foundation, and University Hospitals; Pfizer; the Institute for Informatics (I2), Washington University School of Medicine; the National Institutes of Health (NIH); and the International Society for Computational Biology (ISCB). If you or your institution are interested in sponsoring, PSB, please contact Tiffany Murray at [email protected]

If you have any questions, the PSB registration staff (Tiffany Murray, Kasey Miller, BJ Morrison-McKay, and Cindy Paulazzo) are happy to help you.

Aloha!

Russ Altman Keith Dunker Larry Hunter Teri Klein Maryln Ritchie

The PSB 2018 Organizers

PSB 2018 Program Book 1


SPEAKER INFORMATION Oral presentations of accepted proceedings papers will take place in Salon 2 & 3. Speakers are allotted 10 minutes for presentation and 5 minutes for questions for a total of 15 minutes. Instructions for uploading talks were sent to authors with oral presentations. If you need assistance with this, please see Tiffany Murray or another PSB staff member.

POSTER INFORMATION Please set up your poster upon arrival. Please use the easel marked with the same number that your poster abstract has been assigned in abstract book (e.g., if your abstract is on page 50 of the book, use the easel marked #50). Once your poster is displayed, please make sure that the number is still visible. Please remove your poster by 8:00pm, Saturday, January 6.

The poster session is on Friday, January 5 12:00-2:30. 12:30-1:30: Posters on ODD numbered boards presented. 1:30-2:30: Posters on EVEN numbered boards presented.

The poster session is centered around lunch. Please eat, talk, and network.

INTERNET CONNECTIVITY Please help keep the PSB wireless network stable: Do not download large data files due to limited bandwidth.

PSB is connected to the Internet via a secure wireless network for the conference. For transferring your data/presentations or technical difficulties with the network, please see PSB IT/AV staff members Al Conde, Ryan Whaley, or Paul Murray.

To connect to the PSB wireless network, you will need to explicitly join the “PSB” SSID, and use the passphrase “orcpsb123” with WPA2-Personal security type and AES encryption.

PSB’s wireless Internet access (802.11b/g/n) is available in the Salons 1, 2, 3, the Plaza Ballroom, and the Ballroom Courtyard of the Fairmont Orchid.



PSB 2018 HOSTED RECEPTIONS & MEALS

Wednesday, January 3 7:30-8:30pm 23rd Anniversary Reception, Kilohana Room (near Concierge)

Sponsored by Case Western Reserve University, the Cleveland Clinic Foundation, and University Hospitals

Thursday, January 4 7:30-8:30am Continental Breakfast, Ballroom Courtyard 11:45-1:00pm PSB Hosted Lunch, Ballroom Courtyard

Friday, January 5 7:30-8:30am Continental Breakfast, Ballroom Courtyard 12:00-2:30pm Poster Session with Lunch, Salon 1 and Ballroom Courtyard

Saturday, January 6 7:30-8:30am Continental Breakfast, Ballroom Courtyard 5:30-7:30pm Hawaii Loa Luau, Plantation Estate

Sunday, January 7 7:30-8:30am Continental Breakfast, Ballroom Courtyard

Please remember to wear your PSB nametag & lanyard at all PSB functions.

Enjoy the conference!


Pacific Symposium on Biocomputing 2018 Hosted Meal Menus

Wednesday, January 3

23rd Anniversary Reception (7:30-8:30pm, Kilohana Room) Wine, beer, champagne, soft drinks, coffee & tea service Chocolate Chantilly Cake, Coconut Whipped Cream, Hawaiian Sea Salt Caramel Island Pineapple Crumble Tart, Koloa Rum Sauce Local Seasonal Tropical Fruits

Thursday, January 4

Breakfast (7:30am-8:30am, Ballroom Courtyard) Orange Juice, Guava Juice & Pineapple Juice Selection of Sliced Seasonal Fruits Island Breakfast Scones: Papaya Ginger, Pineapple Vanilla & Kabocha Pumpkin Sweet Cream Butter & Tropical Fruit Preserves Selection of Dry Cereals, Muesli, with Fat Free Milk, Soy & Almond Milk, Raisins, Brown Sugar Kohala Muffin: Sausage, Egg, American Cheese, English Muffin (vegetarian option available) Coffee, Decaffeinated Coffee & Fairmont Signature Teas

Lunch (11:45am-1:00pm, Ballroom Courtyard) Island Field Green Salad: Crisp Cucumber, Vine Ripened Tomato, Shaved Maui Onion Papaya Seed Dressing, Yuzu Soy Vinaigrette Waimea Tomato, Marinated Artichoke Salad

Dim Sum Station: Char Siu Bao, Island Style Chicken Pot stickers, Edamame Pot Stickers, Pork Siu Mai, Shrimp Siu Mai Micro Steam Buns & Hoisin Kalua Pork Island Seafood Skewers with Shrimp, Scallops, Fresh Catch, Thai Basil-Curry Sauce Herb-Garlic Marinated Beef Tenderloin Medallions, Ali’i Mushroom-Red Wine Jus Roasted Kabocha, Grilled Asparagus Tips, Olive Oil Roasted Tomatoes, Mac Nut Pesto Kim Chee & Vegetable Fried Rice

Dark Chocolate Brownies Angel Food Cake, Waimea Strawberries Mango Ginger Crumble Freshly Brewed Iced Tea and Lemonade

Friday, January 5

Breakfast (7:30am-8:30am, Ballroom Courtyard) Orange Juice, Guava Juice & Pineapple Juice Island Fruit Breads, Freshly Baked Croissants, Danishes, Muffins Assorted Sliced Bread, Bagels, Cream Cheese Tropical Fruit Preserves, Butter Selection of Sliced Seasonal Fruits Selection of Dry Cereals, Muesli, with Fat Free Milk, Soy & Almond Milk, Raisins, Brown Sugar Yogurt Bar with Assorted Fruit Yogurts, Mango, Strawberries, Bananas, Mac Nut Granola Macadamia Nut Pancakes Chicken Sausage Cherrywood Smoked Bacon Coffee, Decaffeinated Coffee & Fairmont Signature Teas

Lunch (12:00pm-2:30pm, Ballroom Courtyard) Island Romaine, Croutons, Shaved Parmesan, Caesar Dressing Seasonal Tropical Fruit Display Waimea Green Bean, Roasted Pepper Salad Pineapple, Cabbage Slaw Roasted Onion, Bacon, Sweet Potato Salad Cheddar Cheese Corn Muffins, Butter


Pacific Symposium on Biocomputing 2018 Hosted Meal Menus

Kiawe Smoked Brisket, Lilikoi Barbeque Sauce, Lime Cilantro Wasabi Cream Huli Huli Chicken, Mango Glaze, Scallions Teriyaki Glazed Grilled Island Catch, Edamame, Grilled Pineapple Salsa Warm Soba Noodles, Charred Brussel Sprouts, Pickled Hamakua Mushrooms, Crispy Tofu Paniolo Braised Beans, Portuguese Sausage, Molasses Double Stuffed Baked Potato, Cheddar Cheese, Green Onions Grilled Seasonal Vegetables

Assorted Haagen Dazs Ice Cream Bars and Frozen Fruit Bars Freshly Brewed Iced Tea & Lemonade Beer and wine

Saturday, January 6

Breakfast (7:30am-8:30am, Ballroom Courtyard) Orange Juice, Guava Juice & Pineapple Juice Selection of Sliced Seasonal Fruits Malasadas: Plain, Guava, Chocolate Sweet Cream Butter & Tropical Fruit Preserves Selection of Dry Cereals, Muesli, with Fat Free Milk, Soy Milk & Almond Milk, Raisins, Brown Sugar Hilo Sunrise Wrap: Egg, Chorizo, Cheddar Cheese & Cilantro served with Mango-Pineapple Salsa (vegetarian option available) Coffee, Decaffeinated Coffee & Fairmont Signature Teas

Keynote Refreshments (11-11:30am in Salon 2&3) Mimosas Crispy Chips, Mango-Pineapple Salsa & Pico de Gallo Salsa

Hawaii Loa Luau (5:30-7:30pm, Plantation Estate)

Sample Menu Green Papaya Salad, Cilantro Chili Vinaigrette Oka - Marinated Ono in a Coconut Lime Sauce Seafood Lu'au: Medley of Seafood with Taro Leaves, Roasted Taro and a Coconut Sauce Poisson Cru - Sesame Lime marlin, Oyster Sauce Tuna, Wasabi Tuna Papaya Ginger Roast Chicken, Charred Papaya and Onions with a Mango Glaze Kalua Pork - Shredded Hawaiian Style Roast Pork Fresh Traditional Kauai Poi, Pounded Hanalei Taro Root Marinated Mushroom Salad, Artichokes & Tarragon Vinaigrette Macadamia Nut Crusted Mahi-Mahi, Caramelized Banana Emulsion Taste of Polynesia Dessert Buffet Molten Chocolate Lava Cake, Warm Hilo Vanilla sauce

Sunday, January 7

Breakfast (7:30am-8:30am, Ballroom Courtyard) Fresh Orange Juice, Guava Juice, Pineapple Juice Selection of Sliced Seasonal Fruits Island Fruit Breads, Freshly Baked Croissants, Danishes, Muffins Assorted Sliced Bread, Bagels, Cream Cheese Tropical Fruit Preserves, Butter Selection of Dry Cereals, Muesli, Raisins, Brown Sugar, Skim Milk, 2% Milk, Soy Milk Yogurt Bar with Assorted Fruit Yogurts, Mango, Strawberries, Bananas, Macadamia Nut Granola Scrambled Eggs Waimea Vegetarian Egg Scramble Cherrywood Smoked Bacon Portuguese Sausage Artichoke & Red Bliss Potato Regular, Decaffeinated Coffee & Fairmont Signature Teas


Pacific Symposium on Biocomputing (PSB) 2018 Schedule January 3-7, 2018, Big Island of Hawaii

Please wear your PSB name tag and lanyard for admission to all events and hosted meals.

December 13, 2017

Wednesday,January3,2018Registration 7:30-9:30 Registration Ballroom Prefunction 12:00-2:00 Registration Ballroom Prefunction 7:30-8:30 Registration Kilohana Workshops 9:00-12:00 Machine Learning and Deep Analytics for Biocomputing: Call Salon 2&3 for Better Explainability Organizers: Dragutin Petkovic, Lester Kobzik, Christopher Re Break 12:00-1:30 Lunch on own Workshop 1:30-4:30 Integrating Community-level Data Resources for Precision Salon 2&3 Medicine Research Organizers: Dana C. Crawford, William S. Bush 1:30-4:30 Methods for Examining Data Quality in Healthcare Integrated Plaza Data Repositories Organizers: Vojtech Huser, Michael Kahn, and Jeffrey Brown Break 4:30-7:30 Dinner on own Reception Kilohana 7:30-8:30 23rd Anniversary Reception




December 13, 2017

Thursday,January4,2018Registration 7:30-9:00 Registration Ballroom Prefunction 10:30-11:30 Registration Ballroom Prefunction 12:00-1:00 Registration Ballroom Prefunction Breakfast Ballroom Courtyard 7:30-8:30 PSB Breakfast Welcome Salon 2&3 8:30-8:40 Welcome Session 1: Applications of Genetics, Genomics and Bioinformatics in Salon 2&3 Drug Discovery Co-chairs: Richard Bourgon, Rick Dewey, Zhengyan Kan, Dan Li 8:40-8:50 Introduction 8:50-9:10 Invited Talk: Rick Dewey 9:10-9:25 Large-scale integration of heterogeneous pharmacogenomic data for

identifying drug mechanism of action Yunan Luo, Sheng Wang, Jinfeng Xiao, Jian Peng

9:25-9:40 Cell-specific prediction and application of drug-induced gene expression profiles Rachel Hodos, Ping Zhang, Hao-Chih Lee, Qiaonan Duan, Zichen Wang, Neil R. Clark, Avi Ma’ayan, Fei Wang, Brian Kidd, Jianying Hu, David Sontag, Joel Dudley

9:40-9:55 Characterization of drug-induced splicing complexity in prostate cancer cell line using long read technology Xintong Chen, Sander Houten, Kimaada Allette, Robert P. Sebra, Gustavo Stolovitzky, Bojan Losic

9:55-10:10 Chemical Reaction Vector Embeddings: Towards Predicting Drug Metabolism in the Human Gut Microbiome Emily K. Mallory, Ambika Acharya, Stefano E. Rensi, Peter J Turnbaugh, Roselie A. Bright, Russ B. Altman

10:10-10:25 Extracting a Biologically Relevant Latent Space from Cancer Transcriptomes with Variational Autoencoders Gregory P. Way, Casey S. Greene

Break 10:25-10:45 Keynote Salon 2&3 10:45-11:45 Improving Healthcare through Biomedical Data Science Carlos Bustamante with introduction by Russ Altman Lunch Ballroom Courtyard 11:45-1:00 PSB Hosted Lunch




December 13, 2017

Thursday,January4,2018continued Session 2: Imaging Genomics Salon 2&3 Co-chairs: Heng Huang, Junzhou Huang, Kun Huang, Li Shen, Paul M.

Thompson, Lin Yang 1:00-1:10 Introduction 1:10-1:30 Invited Talk: Mert Sabuncu 1:30-1:45 Codon Bias Among Synonymous Rare Variants Is Associated with

Alzheimer’s Disease Imaging Biomarker Jason E. Miller, Manu K. Shivakumar, Shannon L. Risacher, Andrew J. Saykin, Seunggeun Lee, Kwangsik Nho, Dokyoon Kim

1:45-2:00 Deep Integrative Analysis for Survival Prediction Chenglong Huang, Albert Zhang, Guanghua Xiao

2:00-2:15 Discriminative Bag-of-Cells for Imaging-Genomics Benjamin Chidester, Minh N. Do, Jian Ma

2:15-2:30 Genotype-Phenotype Association Study via New Multi-Task Learning Model Zhouyuan Huo, Dinggang Shen, Heng Huang

Special Topics 2:30-3:00 Parasite & Symbiont Awards Salon 2&3 Discussion Sessions 3:00-4:00 Imaging Genomics Salon 2&3 4:00-5:00 Applications of Genetics, Genomics and Bioinformatics in Salon 2&3 Drug Discovery Meeting 5:00-5:30 ISCB Meeting Salon 2&3 Break 5:30 Dinner on own




December 13, 2017

Friday,January5,2018Registration Ballroom Prefunction 7:30-8:30 Registration Breakfast Ballroom Courtyard 7:30-8:30 PSB Breakfast Announcements Salon 2&3 8:30-8:40 Morning Announcements Session 3 Precision Medicine: from diplotypes to disparities towards Salon 2&3 improved health and therapies

Co-chairs: Bruce Aronow, Steven E. Brenner, Dana C. Crawford, Joshua C. Denny, Alexander A. Morgan

8:40-8:45 Introduction 8:45-9:05 Invited Talk: Vence Bonham 9:05-9:20 Considerations for automated machine learning in clinical metabolic

profiling: altered homocysteine plasma concentration associated with metformin exposure Alena Orlenko, Jason H. Moore, Patryk Orzechowski, Randal S. Olson, Junmei Cairns, Pedro J. Caraballo, Richard M. Weinshilboum, Liewei Wang, Matthew K. Breitenstein

9:20-9:35 Analyzing metabolomics data for association with genotypes using two-component gaussian mixture distributions Jason Westra, Nicholas Hartman, Bethany Lake, Gregory Shearer, Nathan Tintle

9:35-9:50 Single subject transcriptome analysis to identify functionally signed gene set or pathway activity Joanne Berghout, Qike Li, Nima Pouladi, Jianrong Li, Yves A Lussier

9:50-10:05 Emergence of pathway-level composite biomarkers from converging gene set signals of heterogeneous transcriptomic responses Samir Rachid Zaim, Qike Li, A. Grant Schissler, Yves A. Lussier

10:05-10:20 Coalitional game theory as a promising approach to identify candidate autism genes Anika Gupta, Min Woo Sun, Kelley M. Paskov, Nate T. Stockham, Jae-Yoon Jung, Dennis P. Wall

10:20-10:35 Using simulation and optimization approach to improve outcome through warfarin precision treatment Chih-Lin Chi, Lu He, Kourosh Ravvaz, John Weissert, Peter J. Tonellato

10:35-10:50 Addressing vital sign alarm fatigue using personalized alarm thresholds Sarah Poole, Nigam Shah

Discussion Session Salon 2&3 11:00-12:00 Precision Medicine: from diplotypes to disparities towards improved health and therapies phenotypes




December 13, 2017

Friday,January5,2018continuedPoster Session Lunch Salon 1 and Ballroom Courtyard 12:00-2:30 Poster Session with Lunch (Posters on ODD numbered boards presented from 12:30-1:30) (Posters on EVEN numbered boards presented from 1:30-2:30) Session 4 Democratizing Health Data for Translational Research Salon 2&3

Co-chairs: Philip Payne, Nigam Shah, Jessie Tenenbaum, Lara Mangravite

2:30-2:40 Introduction 2:40-3:00 Invited Talk: Joe Corkery 3:00-3:20 Invited Talk: John Wilbanks 3:20-3:35 ClinGen Cancer Somatic Working Group – Standardizing and

Democratizing Access to Cancer Molecular Diagnostic Data to Drive Translational Research Subha Madhavan, Deborah Ritter, Christine Micheel, Shruti Rao, Angshumoy Roy, Dmitriy Sonkin, Matthew McCoy, Malachi Griffith, Obi L Griffith, Peter Mcgarvey, Shashikant Kulkarni on Behalf of the ClinGen Somatic Working Group

3:35-3:50 Best Practices and Lessons Learned from Reuse of 4 Patientderived Metabolomics Datasets in Alzheimer’s Disease Jessica D. Tenenbaum, Colette Blach

3:50-4:05 A Heuristic Method for Simulating Open-Data of Arbitrary Complexity that Can Be Used to Compare and Evaluate Machine Learning Methods Jason H. Moore, Maksim Shestov, Peter Schmitt, Randal S. Olson

Discussion Session Salon 2&3 4:10-5:10 Democratizing Health Data for Translational Research Break 5:10- Dinner & Evening on own




December 13, 2017

Saturday,January6,2018Breakfast Ballroom Courtyard 7:30-8:30 PSB Breakfast Announcements Salon 2&3 8:30-8:40 Morning Announcements Session 5: Challenges of Pattern Recognition in Biomedical Data Salon 2&3

Co-chairs: Anurag Verma, Anna Basile, Marta Byrska-Bishop, Christian Darabos, Shefali Setia Verma

8:40-8:50 Introduction 8:50-9:10 Invited Talk: Larry Smarr 9:10-9:25 Functional Network Community Detection Can Disaggregate and Filter

Multiple Underlying Pathways in Enrichment Analyses Lia X. Harrington, Gregory P. Way, Jennifer A. Doherty, Casey S. Greene

9:25-9:40 Large-Scale Analysis of Disease Pathways in the Human Interactome Monica Agrawal, Marinka Zitnik, Jure Leskovec

9:40-9:55 Data-driven Advice for Applying Machine Learning to Bioinformatics Problems Randal S. Olson, William La Cava, Zairah Mustahsan, Akshay Varik, Jason H. Moore

9:55-10:10 Automated disease cohort selection using word embeddings from Electronic Health Records

Benjamin S. Glicksberg, Riccardo Miotto, Kipp W. Johnson, Khader Shameer, Li Li, Rong Chen, Joel T. Dudley

10:10-10:25 Mapping Patient Trajectories using Longitudinal Extraction and Deep Learning in the MIMIC-III Critical Care Database Brett K. Beaulieu-Jones, Patryk Orzechowski, Jason H. Moore

10:25-10:40 Causal Inference on Electronic Health Records to Assess Blood Pressure Treatment Targets: An Application of the Parametric G Formula Kipp W. Johnson, Benjamin S. Glicksberg, Rachel Hodos, Khader Shameer, Joel T. Dudley

10:40-10:55 How Powerful Are Summary-Based Methods for Identifying Expression-Trait Associations Under Different Genetic Architectures? Yogasudha Veturi, Marylyn D. Ritchie

Keynote: Salon 2&3 11:00-12:15 Data Disparities: Discrimination & Equity in Big Data

Jennifer Wagner with introduction by Marylyn Ritchie Break 12:15-1:30 Lunch on Own Workshop Salon 2&3 1:30-4:30 Diversity and Disparity in Biomedical Informatics

Organizers: Philip R.O. Payne, William M. Southerland, S. Joshua Swamidass, Laura Wiley, and ClarLynda Williams-DeVane




December 13, 2017

Saturday,January6,2018continuedDiscussion Session Salon 2&3 4:30-5:30 Challenges of Pattern Recognition in Biomedical Data Dinner Plantation Estate 5:30-7:30 Hawaii Loa Luau PSB’s dinner will be held at the Fairmont’s Hawaii Loa Luau this year. Luau Schedule:

5:30 pm Check-In & Seating Begins 6:00 pm Luau Dinner Buffet

7:00 pm Performance Begins / Bar Closed




December 13, 2017

Sunday,January7,2018Breakfast Ballroom Courtyard 7:30-8:30 Breakfast Closing Salon 2&3 8:30-8:40 Closing Announcements Session 6: Advances in Text Mining and Visualization for Precision Salon 2&3 Medicine Co-chairs: Graciela Gonzalez, Casey Greene, Hongfang Liu, Abeed Sarker 8:40-8:50 Introduction 8:50-9:10 Invited Talk: Jason Moore 9:10-9:30 Invited Talk: Sophia Ananiadou 9:30-9:45 VisAGE: Integrating External Knowledge into Electronic Medical Record

Visualization Edward W. Huang, Sheng Wang, ChengXiang Zhai

9:45-10:00 Annotating gene sets by mining large literature collections with protein networks Sheng Wang, Jianzhu Ma, Michael Ku Yu, Fan Zheng, Edward W Huang, Jiawei Han, Jian Peng,Trey Ideker

10:00-10:15 Improving Precision in Concept Normalization Mayla Boguslav, K. Bretonnel Cohen, William A. Baumgartner Jr., Lawrence E. Hunter

Session 7: Reading Between the Genes: Computational Models to Salon 2&3 Discover Function and/or Clinical Utility from Noncoding DNA Co-chairs: Yves Lussier, Maricel Kann, Jason Moore, Kenneth Ramos, Joanne Berghout, Francesca Vitali

10:20-10:30 Introduction 10:30-10:50 Invited Talk: Martha Bulyk 10:50-11:05 Network analysis of pseudogene-gene relationships: from pseudogene

evolution to their functional potentials Travis S Johnson, Sihong Li, Johnathan R Kho, Kun Huang, Yan Zhang

11:05-11:20 Convergent downstream candidate mechanisms of independent intergenic polymorphisms between co-classified diseases implicate epistasis among noncoding elements Jiali Han, Jianrong Li, Ikbel Achour, Lorenzo Pesce, Ian Foster, Haiquan Li, Yves A. Lussier

11:20-11:35 Leveraging putative enhancer-promoter interactions to investigate two-way epistasis in type 2 diabetes GWAS Elisabetta Manduchi, Alessandra Chesi, Molly A. Hall, Struan F. A. Grant, Jason H. Moore

Discussion Sessions 11:40-12:40 Reading Between the Genes: Computational Models to Salon 2&3 Discover Function and/or Clinical Utility from Noncoding DNA 11:40-12:40 Text Mining and Visualization for Precision Medicine Kilohana

PSB over--see you next year!


Call for Session Proposals Pacific Symposium on Biocomputing

The Big Island of Hawaii, January 3-7, 2019

http://psb.stanford.edu/callfor/sessionproposals/

This is an invitation to submit proposals for sessions in the 24th Pacific Symposium on Biocomputing (PSB), to be held January 3-7, 2019 on the Kohala Coast, the Big Island of Hawaii. PSB will bring together top researchers from the US, the Asian Pacific nations and around the world to exchange research for the presentation of work in databases, algorithms, interfaces, natural language processing, modeling and other computational methods, as applied to biological problems, with emphasis on applications in data-rich areas of molecular biology. PSB has been designed to be responsive to the need for critical mass in sub-disciplines within biocomputing. For that reason, it is the only meeting whose sessions are defined dynamically each year in response to specific proposals. PSB sessions are organized by leaders in the emerging areas, and targeted to provide a forum for publication and discussion of research in biocomputing's "hot topics." In this way, PSB provides an early forum for serious examination of emerging methods and approaches in this rapidly changing field. Proposals for such sessions are hereby solicited. A proposal should identify a coherent topic that can be addressed by 3 to 12 papers. For example, a session might bring together papers on alternative approaches to a particular biological question or it might examine the applications of a particular technology in a variety of biological areas. A sample of more than 20 different decisions at previous PSB meetings have included:

• Applications of Genetics, Genomics and Bioinformatics in Drug Discovery • Challenges of Pattern Recognition in Biomedical Data • Democratizing Health Data for Translational Research • Imaging Genomics • Precision Medicine: from diplotypes to disparities towards improved health and therapies • Reading Between the Genes: Computational Models to Discover Function and/or

Clinical Utility from Noncoding DNA • Text Mining and Visualization for Precision Medicine

A major goal of PSB is to create productive interaction among the rather different research cultures of computer science and biology. Recognizing that many in the computational community believe the value of a meeting depends on the quality of its review process, every full manuscript submitted to PSB is reviewed by at least two anonymous reviewers, as well as the session organizers and meeting chairs. Accepted papers are distributed in a proceedings volume at the meeting, and are indexed in Medline and other bibliographic databases. However, we also recognize that many potential participants, particularly from the biological community, do not choose to submit full papers to conferences, even with assurance of availability and broad indexing. Therefore, PSB also includes a separate open submission abstract book and open poster presentations in which any registrant can present research. Responsibilities of a session chair As a proposer of an accepted session, you will become the session chair. The chair's primary responsibility is to solicit high quality papers for the session, oversee the review, and write a tutorial introduction to your session. You are to solicit manuscripts, have them refereed, collaborate with the conference chairs in determining which manuscripts are to be accepted and structure presentation time in your session. Please contact us at the address below if you have any questions about the obligations entailed in becoming a session organizer.


Call for Session Proposals Pacific Symposium on Biocomputing


http://psb.stanford.edu/callfor/sessionproposals/

Procedure for submitting proposals Session proposals can be as short as a single page and should in no case be more than 6 pages. The proposal should:

• Define a specific technical area to be covered. • Justify why the proposed area is appropriate for PSB. Discuss why the topic is timely

and important, and how the topic has been addressed in other conferences or recent publications.

• Argue that there is likely to be sufficient high quality, unpublished material to fill the session, e.g., a list of researchers you intend to solicit for papers. If there are unlikely to be adequate paper submissions, consider applying for a PSB workshop instead.

• Provide a short autobiographical sketch and an explicit statement that your organization endorses your involvement.

• Proposals must be submitted online at http://psb.wufoo.com/forms/psb-session-proposal-submission-form/.

Important Dates February 9, 2018 Proposals Due March 9, 2018 Notification Regarding the Proposals Each proposal will be evaluated by the organizing committee. We look forward to your submissions. Questions? Please send email to Lawrence Hunter, Ph.D. Director, Center for Computational Pharmacology & Computational Bioscience Program Professor of Pharmacology (Denver) & Computer Science (Boulder) E-mail: [email protected]


Call for Workshop Proposals Pacific Symposium on Biocomputing


http://psb.stanford.edu/callfor/workshopproposals/

This is an invitation to submit proposals for workshops at the 24th Pacific Symposium on Biocomputing (PSB), to be held January 3-7, 2019 on the Kohala Coast, the Big Island of Hawaii. PSB will bring together top researchers from the US, the Asian Pacific nations and around the world to exchange research for the presentation of work in databases, algorithms, interfaces, natural language processing, modeling and other computational methods, as applied to biological problems, with emphasis on applications in data-rich areas of molecular biology.

We are soliciting proposals for three hour workshops appropriate to the diverse PSB conference community. Workshops can include: panels of experts on emerging areas of computational biology that are not likely to attract the number of paper submissions required for a session; open discussions of topics important to the computational biology community; or other topics and formats. Workshops at previous PSB meetings have included:

• The Future of Genome-Based Medicine • Modeling Cell Heterogeneity: from Single-Cell Variations to Mixed Cells Populations • Training the Next Generation of Quantitative Biologists • Uncovering the Etiology of Autism Spectrum Disorders: Genomics, Bioinformatics,

Environment, Data Collection and Exploration, and Future Possibilities • Diversity and Disparity in Biomedical Informatics • Integrating Community-level Data Resources for Precision Medicine Research • Machine Learning and Deep Analytics for Biocomputing: Call for Better Explainability • Methods for Examining Data Quality in Healthcare Integrated Data Repositories

Responsibilities of a workshop chair As a proposer of an accepted workshop, you will become the workshop chair. The chair's primary responsibility is to organize and preside over the presentations related to your workshop. Procedure for submitting proposals Proposals can be as short as a single page and should in no case be more than 6 pages. The proposal should:

• Define a specific technical area to be covered, and a format for the workshop. • Justify why the proposed area is appropriate for PSB. Discuss why the topic is timely

and important, and how the topic has been addressed in other conferences or recent publications. Describe why the proposed format is appropriate for the workshop.

• If the workshop proposes invited experts, provide evidence that the experts will attend the workshop. Participants are required to register for the conference, and, unlike sessions, no financial support from the conference is offered to workshop organizers. Emails from potential participants are sufficient.

• Provide a short autobiographical sketch and an explicit statement that your organization endorses your involvement.

• Proposals must be submitted online at https://psb.wufoo.com/forms/psb-workshop-proposal-submission-form/.


Call for Workshop Proposals Pacific Symposium on Biocomputing


http://psb.stanford.edu/callfor/workshopproposals/

Important Dates February 9, 2018 Proposals Due March 9, 2018 Notification Regarding the Proposals Each proposal will be evaluated by the organizing committee. We look forward to your submissions. Questions? Please send email to Lawrence Hunter, Ph.D. Director, Center for Computational Pharmacology & Computational Bioscience Program Professor of Pharmacology (Denver) & Computer Science (Boulder) E-mail: [email protected]


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TABLEOFCONTENTS

PROCEEDINGSPAPERSWITHORALPRESENTATIONAPPLICATIONSOFGENETICS,GENOMICSANDBIOINFORMATICSINDRUGDISCOVERY......................................................................................................................................................................1CHARACTERIZATIONOFDRUG-INDUCEDSPLICINGCOMPLEXITYINPROSTATECANCERCELLLINEUSINGLONGREADTECHNOLOGY........................................................................................2XintongChen,SanderHouten,KimaadaAllette,RobertP.Sebra,GustavoStolovitzky,BojanLosic

CELL-SPECIFICPREDICTIONANDAPPLICATIONOFDRUG-INDUCEDGENEEXPRESSIONPROFILES.................................................................................................................................................................3RachelHodos,PingZhang,Hao-ChihLee,QiaonanDuan,ZichenWang,NeilR.Clark,AviMa’ayan,FeiWang,BrianKidd,JianyingHu,DavidSontag,JoelT.Dudley

LARGE-SCALEINTEGRATIONOFHETEROGENEOUSPHARMACOGENOMICDATAFORIDENTIFYINGDRUGMECHANISMOFACTION.......................................................................................4YunanLuo,ShengWang,JinfengXiao,JianPeng

CHEMICALREACTIONVECTOREMBEDDINGS:TOWARDSPREDICTINGDRUGMETABOLISMINTHEHUMANGUTMICROBIOME...............................................................................5EmilyK.Mallory,AmbikaAcharya,StefanoE.Rensi,PeterJ.Turnbaugh,RoselieA.Bright,RussB.Altman

EXTRACTINGABIOLOGICALLYRELEVANTLATENTSPACEFROMCANCERTRANSCRIPTOMESWITHVARIATIONALAUTOENCODERS.............................................................6GregoryP.Way,CaseyS.Greene

CHALLENGESOFPATTERNRECOGNITIONINBIOMEDICALDATAORALPRESENTATION......................................................................................................................................7LARGE-SCALEANALYSISOFDISEASEPATHWAYSINTHEHUMANINTERACTOME...........8MonicaAgrawal,MarinkaZitnik,JureLeskovec

MAPPINGPATIENTTRAJECTORIESUSINGLONGITUDINALEXTRACTIONANDDEEPLEARNINGINTHEMIMIC-IIICRITICALCAREDATABASE................................................................9BrettK.Beaulieu-Jones,PatrykOrzechowski,JasonH.Moore

AUTOMATEDDISEASECOHORTSELECTIONUSINGWORDEMBEDDINGSFROMELECTRONICHEALTHRECORDS...............................................................................................................10BenjaminS.Glicksberg,RiccardoMiotto,KippW.Johnson,KhaderShameer,LiLi,RongChen,JoelT.Dudley

FUNCTIONALNETWORKCOMMUNITYDETECTIONCANDISAGGREGATEANDFILTERMULTIPLEUNDERLYINGPATHWAYSINENRICHMENTANALYSES.........................................11LiaX.Harrington,GregoryP.Way,JenniferA.Doherty,CaseyS.Greene

CAUSALINFERENCEONELECTRONICHEALTHRECORDSTOASSESSBLOODPRESSURETREATMENTTARGETS:ANAPPLICATIONOFTHEPARAMETRICGFORMULA..................12KippW.Johnson,BenjaminS.Glicksberg,RachelHodos,KhaderShameer,JoelT.Dudley


ii

DATA-DRIVENADVICEFORAPPLYINGMACHINELEARNINGTOBIOINFORMATICSPROBLEMS............................................................................................................................................................13RandalS.Olson,WilliamLaCava,ZairahMustahsan,AkshayVarik,JasonH.Moore

HOWPOWERFULARESUMMARY-BASEDMETHODSFORIDENTIFYINGEXPRESSION-TRAITASSOCIATIONSUNDERDIFFERENTGENETICARCHITECTURES?...............................14YogasudhaC.Veturi,MarylynD.Ritchie

DEMOCRATIZINGHEALTHDATAFORTRANSLATIONALRESEARCH................................15CLINGENCANCERSOMATICWORKINGGROUP–STANDARDIZINGANDDEMOCRATIZINGACCESSTOCANCERMOLECULARDIAGNOSTICDATATODRIVETRANSLATIONALRESEARCH......................................................................................................................16SubhaMadhavan,DeborahRitter,ChristineMicheel,ShrutiRao,AngshumoyRoy,DmitriySonkin,MatthewMcCoy,MalachiGriffith,ObiL.Griffith,PeterMcGarvey,ShashikantKulkarni,onbehalfoftheClingenSomaticWorkingGroup

AHEURISTICMETHODFORSIMULATINGOPEN-DATAOFARBITRARYCOMPLEXITYTHATCANBEUSEDTOCOMPAREANDEVALUATEMACHINELEARNINGMETHODS....17JasonH.Moore,MaksimShestov,PeterSchmitt,RandalS.Olson

BESTPRACTICESANDLESSONSLEARNEDFROMREUSEOF4PATIENT-DERIVEDMETABOLOMICSDATASETSINALZHEIMER'SDISEASE................................................................18JessicaD.Tenenbaum,ColetteBlach

IMAGINGGENOMICS...........................................................................................................................19DISCRIMINATIVEBAG-OF-CELLSFORIMAGING-GENOMICS.......................................................20BenjaminChidester,MinhN.Do,JianMa

DEEPINTEGRATIVEANALYSISFORSURVIVALPREDICTION......................................................21ChenglongHuang,AlbertZhang,GuanghuaXiao

GENOTYPE-PHENOTYPEASSOCIATIONSTUDYVIANEWMULTI-TASKLEARNINGMODEL....................................................................................................................................................................22ZhouyuanHuo,DinggangShen,HengHuang

CODONBIASAMONGSYNONYMOUSRAREVARIANTSISASSOCIATEDWITHALZHEIMER’SDISEASEIMAGINGBIOMARKER..................................................................................23JasonE.Miller,ManuK.Shivakumar,ShannonL.Risacher,AndrewJ.Saykin,SeunggeunLee,KwangsikNho,DokyoonKim

PRECISIONMEDICINE:FROMDIPLOTYPESTODISPARITIESTOWARDSIMPROVEDHEALTHANDTHERAPIES.................................................................................................................24SINGLESUBJECTTRANSCRIPTOMEANALYSISREPRODUCESSIGNEDGENESETFUNCTIONALACTIVATIONSIGNALSFROMCOHORTANALYSISOFMURINERESPONSETOHIGHFATDIET............................................................................................................................................25JoanneBerghout,QikeLi,NimaPouladi,JianrongLi,YvesA.Lussier

USINGSIMULATIONANDOPTIMIZATIONAPPROACHTOIMPROVEOUTCOMETHROUGHWARFARINPRECISIONTREATMENT...............................................................................26Chih-LinChi,LuHe,KouroshRavvaz,JohnWeissert,PeterJ.Tonellato


iii

COALITIONALGAMETHEORYASAPROMISINGAPPROACHTOIDENTIFYCANDIDATEAUTISMGENES...................................................................................................................................................27AnikaGupta,MinWooSun,KelleyM.Paskov,NateT.Stockham,Jae-YoonJung,DennisP.Wall

CONSIDERATIONSFORAUTOMATEDMACHINELEARNINGINCLINICALMETABOLICPROFILING:ALTEREDHOMOCYSTEINEPLASMACONCENTRATIONASSOCIATEDWITHMETFORMINEXPOSURE................................................................................................................................28AlenaOrlenko,JasonH.Moore,PatrykOrzechowski,RandalS.Olson,JunmeiCairns,PedroJ.Caraballo,RichardM.Weinshilboum,LieweiWang,MatthewK.Breitenstein

ADDRESSINGVITALSIGNALARMFATIGUEUSINGPERSONALIZEDALARMTHRESHOLDS......................................................................................................................................................29SarahPoole,NigamShah

EMERGENCEOFPATHWAY-LEVELCOMPOSITEBIOMARKERSFROMCONVERGINGGENESETSIGNALSOFHETEROGENEOUSTRANSCRIPTOMICRESPONSES.........................30SamirRachidZaim,QikeLi,A.GrantSchissler,YvesA.Lussier

ANALYZINGMETABOLOMICSDATAFORASSOCIATIONWITHGENOTYPESUSINGTWO-COMPONENTGAUSSIANMIXTUREDISTRIBUTIONS.......................................................................31JasonWestra,NicholasHartman,BethanyLake,GregoryShearer,NathanTintle

READINGBETWEENTHEGENES:COMPUTATIONALMODELSTODISCOVERFUNCTIONAND/ORCLINICALUTILITYFROMNONCODINGDNA..............................................................32CONVERGENTDOWNSTREAMCANDIDATEMECHANISMSOFINDEPENDENTINTERGENICPOLYMORPHISMSBETWEENCO-CLASSIFIEDDISEASESIMPLICATEEPISTASISAMONGNONCODINGELEMENTS.......................................................................................33JialiHan,JianrongLi,IkbelAchour,LorenzoPesce,IanFoster,HaiquanLi,YvesA.Lussier

NETWORKANALYSISOFPSEUDOGENE-GENERELATIONSHIPS:FROMPSEUDOGENEEVOLUTIONTOTHEIRFUNCTIONALPOTENTIALS.........................................................................34TravisS.Johnson,SihongLi,JohnathanR.Kho,KunHuang,YanZhang

LEVERAGINGPUTATIVEENHANCER-PROMOTERINTERACTIONSTOINVESTIGATETWO-WAYEPISTASISINTYPE2DIABETESGWAS...........................................................................35ElisabettaManduchi,AlessandraChesi,MollyA.Hall,StruanF.A.Grant,JasonH.Moore

TEXTMININGANDVISUALIZATIONFORPRECISIONMEDICINE..........................................36IMPROVINGPRECISIONINCONCEPTNORMALIZATION...............................................................37MaylaBoguslav,K.BretonnelCohen,WilliamA.BaumgartnerJr.,LawrenceE.Hunter

VISAGE:INTEGRATINGEXTERNALKNOWLEDGEINTOELECTRONICMEDICALRECORDVISUALIZATION.................................................................................................................................................38EdwardW.Huang,ShengWang,ChengXiangZhai

ANNOTATINGGENESETSBYMININGLARGELITERATURECOLLECTIONSWITHPROTEINNETWORKS.....................................................................................................................................39ShengWang,JianzhuMa,MichaelKuYu,FanZheng,EdwardW.Huang,JiaweiHan,JianPeng,TreyIdeker


iv

PROCEEDINGSPAPERSWITHPOSTERPRESENTATIONSAPPLICATIONSOFGENETICS,GENOMICSANDBIOINFORMATICSINDRUGDISCOVERY...................................................................................................................................................................40PREDICTIONOFPROTEIN-LIGANDINTERACTIONSFROMPAIREDPROTEINSEQUENCEMOTIFSANDLIGANDSUBSTRUCTURES................................................................................................41PeytonGreenside,MaureenHillenmeyer,AnshulKundaje

LOSS-OF-FUNCTIONOFNEUROPLASTICITY-RELATEDGENESCONFERSRISKFORHUMANNEURODEVELOPMENTALDISORDERS.................................................................................42MiloR.Smith,BenjaminS.Glicksberg,LiLi,RongChen,HirofumiMorishita,JoelT.Dudley

DIFFUSIONMAPPINGOFDRUGTARGETSONDISEASESIGNALINGNETWORKELEMENTSREVEALSDRUGCOMBINATIONSTRATEGIES.............................................................43JielinXu,KellyRegan,SiyuanDeng,WilliamE.CarsonIII,PhilipR.O.Payne,FuhaiLi

CHALLENGESOFPATTERNRECOGNITIONINBIOMEDICALDATA.....................................44OWL-NETS:TRANSFORMINGOWLREPRESENTATIONSFORIMPROVEDNETWORKINFERENCE..........................................................................................................................................................45TiffanyJ.Callahan,WilliamA.BaumgartnerJr.,MichaelBada,AdrianneL.Stefanski,IgnacioTripodi,ElizabethK.White,LawrenceE.Hunter

ANULTRA-FASTANDSCALABLEQUANTIFICATIONPIPELINEFORTRANSPOSABLEELEMENTSFROMNEXTGENERATIONSEQUENCINGDATA........................................................46Hyun-HwanJeong,HariKrishnaYalamanchili,CaiweiGuo,Joshua,M.Shulman,ZhandongLiu

IMPROVINGTHEEXPLAINABILITYOFRANDOMFORESTCLASSIFIER–USERCENTEREDAPPROACH...........................................................................................................................................................47DragutinPetkovic,RussB.Altman,MikeWong,ArthurVigil

TREE-BASEDMETHODSFORCHARACTERIZINGTUMORDENSITYHETEROGENEITY...48KatherineShoemaker,BrianP.Hobbs,KarthikBharath,ChaanS.Ng,VeerabhadranBaladandayuthapani

DEMOCRATIZINGHEALTHDATAFORTRANSLATIONALRESEARCH................................49IDENTIFYINGNATURALHEALTHPRODUCTANDDIETARYSUPPLEMENTINFORMATIONWITHINADVERSEEVENTREPORTINGSYSTEMS.............................................50VivekanandSharma,IndraNeilSarkar

DEMOCRATIZINGDATASCIENCETHROUGHDATASCIENCETRAINING...............................51JohnDarrellVanHorn,LilyFierro,JeanaKamdar,JonathanGordon,CrystalStewart,AvnishBhattrai,SumikoAbe,XiaoxiaoLei,CarolineO’Driscoll,AakanchhaSinha,PriyambadaJain,GullyBurns,KristinaLerman,JoséLuisAmbite

IMAGINGGENOMICS...........................................................................................................................52HERITABILITYESTIMATESONRESTINGSTATEFMRIDATAUSINGTHEENIGMAANALYSISPIPELINE.........................................................................................................................................53BhimM.Adhikari,NedaJahanshad,DineshShukla,DavidC.Glahn,JohnBlangero,RichardC.Reynolds,RobertW.Cox,ElsFieremans,JelleVeraart,DmitryS.Novikov,ThomasE.Nichols,L.ElliotHong,PaulM.Thompson,PeterKochunov


v

MRITOMGMT:PREDICTINGMETHYLATIONSTATUSINGLIOBLASTOMAPATIENTSUSINGCONVOLUTIONALRECURRENTNEURALNETWORKS......................................................54LichyHan,MaulikR.Kamdar

BUILDINGTRANS-OMICSEVIDENCE:USINGIMAGINGAND‘OMICS’TOCHARACTERIZECANCERPROFILES............................................................................................................................................55ArunimaSrivastava,ChaitanyaKulkarni,ParagMallick,KunHuang,RaghuMachiraju

PRECISIONMEDICINE:FROMDIPLOTYPESTODISPARITIESTOWARDSIMPROVEDHEALTHANDTHERAPIES.................................................................................................................56LOCALANCESTRYTRANSITIONSMODIFYSNP-TRAITASSOCIATIONS..................................57AlexandraE.Fish,DanaC.Crawford,JohnA.Capra,WilliamS.Bush

EVALUATIONOFPREDIXCANFORPRIORITIZINGGWASASSOCIATIONSANDPREDICTINGGENEEXPRESSION...........................................................................................................................................58BinglanLi,ShefaliS.Verma,YogasudhaC.Veturi,AnuragVerma,YukiBradford,DavidW.Haas,MarylynD.Ritchie

READINGBETWEENTHEGENES:COMPUTATIONALMODELSTODISCOVERFUNCTIONAND/ORCLINICALUTILITYFROMNONCODINGDNA.............................................................59PAN-CANCERANALYSISOFEXPRESSEDSOMATICNUCLEOTIDEVARIANTSINLONGINTERGENICNON-CODINGRNA................................................................................................................60TraversChing,LanaX.Garmire

TEXTMININGANDVISUALIZATIONFORPRECISIONMEDICINE.........................................61GENEDIVE:AGENEINTERACTIONSEARCHANDVISUALIZATIONTOOLTOFACILITATEPRECISIONMEDICINE.....................................................................................................................................62PaulPrevide,BrookThomas,MikeWong,EmilyK.Mallory,DragutinPetkovic,RussB.Altman,AnaghaKulkarni

POSTERPRESENTATIONSAPPLICATIONSOFGENETICS,GENOMICSANDBIOINFORMATICSINDRUGDISCOVERY...................................................................................................................................................................63CELL-SPECIFICPREDICTIONANDAPPLICATIONOFDRUG-INDUCEDGENEEXPRESSIONPROFILES..............................................................................................................................................................64RachelHodos,PingZhang,Hao-ChihLee,QiaonanDuan,ZichenWang,NeilR.Clark,AviMa’ayan,FeiWang,BrianKidd,JianyingHu,DavidSontag,JoelT.Dudley

SYSTEMATICDISCOVERYOFGENOMICMARKERSFORCLINICALOUTCOMESTHROUGHCOMBINEDANALYSISOFCLINICALANDGENOMICDATA...........................................................65JinhoKim,HonguiCha,Hyun-TaeShin,BoramLee,JaeWonYun,JoonHoKang,Woong-YangPark

IDENTIFICATIONOFAPREDICTIVEGENESIGNATUREFORDIFFERENTIATINGTHEEFFECTSOFCIGARETTESMOKING..........................................................................................................66GangLiu,JustinLi,G.L.Prasad

THEEXTREMEMEMORY®CHALLENGE:ASEARCHFORTHEHERITABLEFOUNDATIONSOFEXCEPTIONALMEMORY........................................................................................67MaryA.Pyc,DouglasFenger,PhilipCheung,J.StevendeBelle,TimTully


vi

EXTRACTINGABIOLOGICALLYRELEVANTLATENTSPACEFROMCANCERTRANSCRIPTOMESWITHVARIATIONALAUTOENCODERS..........................................................68GregoryP.Way,CaseyS.Greene

CHALLENGESOFPATTERNRECOGNITIONINBIOMEDICALDATAORALPRESENTATION...................................................................................................................................69LARGE-SCALEANALYSISOFDISEASEPATHWAYSINTHEHUMANINTERACTOME........70MonicaAgrawal,MarinkaZitnik,JureLeskovec

PROFILINGOFSOMATICALTERATIONSINBRCA1-LIKEBREASTTUMORS.........................71YoudinghuanChen,YueWang,LucasA.Salas,ToddW.Miller,JonathanD.Marotti,NicoleP.Jenkins,ArminjaN.Kettenbach,ChaoCheng,BrockC.Christensen

USINGARTIFICIALINTELLIGENCEINDIGITALPATHOLOGYTOCLASSIFYMELANOCYTICLESIONS................................................................................................................................72StevenN.Hart,W.Flotte,A.P.Norgan,K.K.Shah,Z.R.Buchan,K.B.Geiersbach,T.Mounajjed,T.J.Flotte

AMACHINELEARNINGAPPROACHTOSTUDYCOMMONGENEEXPRESSIONPATTERNS...................................................................................................................................................................................73MingzeHe,CarolynJ.Lawrence-Dill

GENERAL................................................................................................................................................74DATABASE-FREEMETAGENOMICANALYSISWITHAKRONYMER............................................75GabrielAl-Ghalith,AbigailJohnson,PajauVangay,DanKnights

SOFTWARECOMPARISONFORPREPROCESSINGGC/LC-MS-BASEDMETABOLOMICSDATA.......................................................................................................................................................................76JulianAldana,MonicaCalaMolina,MarthaZuluaga

GATEKEEPER:ANEWHARDWAREARCHITECTUREFORACCELERATINGPRE-ALIGNMENTINDNASHORTREADMAPPING......................................................................................77MohammedAlser,HasanHassan,HongyiXin,OğuzErgin,OnurMutlu,CanAlkan

MODELINGTHEENHANCERACTIVITYTHROUGHTHECOMBINATIONOFEPIGENETICFACTORS...............................................................................................................................................................78MinGyunBae,TaeyeopLee,JaehoOh,JunHyeongLee,JungKyoonChoi

FREQUENCYANDPROPERTIESOFMOSAICSOMATICMUTATIONSINANORMALDEVELOPINGBRAIN........................................................................................................................................79TaejeongBae,JessicaMariani,LiviaTomasini,BoZhou,AlexanderE.Urban,AlexejAbyzov,FloraM.Vaccarino

CYCLONOVO:DENOVOSEQUENCINGALGORITHMDISCOVERSNOVELCYCLICPEPTIDENATURALPRODUCTSINSUNFLOWERANDCYANOBACTERIAUSINGTANDEMMASSSPECTROMETRYDATA...................................................................................................................................80BaharBehsaz,HoseinMohimani,AlexeyGurevich,AndreyPrjibelski,MarkF.Fisher,LarrySmarr,PieterC.Dorrestein,JoshuaS.Mylne,PavelA.Pevzner

FUNCTIONALANNOTATIONOFGENOMICVARIANTSINSTUDIESOFLATE-ONSETALZHEIMER’SDISEASE...................................................................................................................................81MariuszButkiewicz,JonathanL.Haines,WilliamS.Bush


vii

OCTAD:ANOPENCANCERTHERAPEUTICDISCOVERYWORKSPACEINTHEERAOFPRECISIONMEDICINE.....................................................................................................................................82BinChen,BenjaminS.Glicksberg,WilliamZeng,YuyingChen,KeLiu

DEEPLEARNINGPREDICTSTUBERCULOSISDRUGRESISTANCESTATUSFROMWHOLE-GENOMESEQUENCINGDATA......................................................................................................................83MichaelL.Chen,IsaacS.Kohane,AndrewL.Beam,MahaFarhat

DESIGNINGPREDICTIONMODELFORHYPERURICEMIAWITHVARIOUSMACHINELEARNINGTOOLSUSINGHEALTHCHECK-UPEHRDATABASE..................................................84EunKyungChoe,SangWooLee

RICK:RNAINTERACTIVECOMPUTINGKIT..........................................................................................85GalinaA.Erikson,LingHuang,MaximShokhirev

PRIVATEINFORMATIONLEAKAGEINFUNCTIONALGENOMICSEXPERIMENTS:QUANTIFICATIONANDLINKING...............................................................................................................86GamzeGursoy,MarkGerstein

CARPED.I.E.M:ADATAINTEGRATIONEXPECTATIONMAPFORTHEPOTENTIALOFMULTI-`OMICSINTEGRATIONINCOMPLEXDISEASE.....................................................................87TiaTateHudson,ClarLyndaWilliams-DeVane

IMPROVINGGENEFUSIONDETECTIONACCURACYWITHFUSIONCONTIGREALIGNMENTINTARGETEDTUMORSEQUENCING......................................................................88JinHyunJu,XiaoChen,JuneSnedecor,Han-YuChuang,BenMishkanian,SvenBilke

SPARSEREGRESSIONFORNETWORKGRAPHSANDITSAPPLICATIONTOGENENETWORKSOFTHEBRAIN..........................................................................................................................89HidekoKawakubo,YusukeMatsui,TeppeiShimamura

GRIM-FILTER:FASTSEEDLOCATIONFILTERINGINDNAREADMAPPINGUSINGPROCESSING-IN-MEMORYTECHNOLOGIES.........................................................................................90JeremieS.Kim,DamlaS.Cali,HongyiXin,DonghyukLee,SaugataGhose,MohammedAlser,HasanHassan,OğuzErgin,CanAlkan,OnurMutlu

MULTI-CLASSCLASSIFICATIONSTRATEGYFORSUPPORTVECTORMACHINESUSINGWEIGHTEDVOTINGANDVOTINGDROP...............................................................................................91SunghoKim,TaehunKim

GENOME-WIDEANALYSISOFTRANSCRIPTIONALANDCYTOKINERESPONSEVARIABILITYINACTIVATEDHUMANIMMUNECELLS...................................................................92SarahKim-Hellmuth,MatthiasBechheim,BennoPütz,PejmanMohammadi,JohannesSchumacher,VeitHornung,BertramMüller-Myhsok,TuuliLappalainen

PREDICTINGFATIGUESEVERITYINONCOLOGYPATIENTSONEWEEKFOLLOWINGCHEMOTHERAPY...............................................................................................................................................93KordM.Kober,XiaoHu,BruceA.Cooper,StevenM.Paul,ChristineMiaskowski

SINGLE-MOLECULEPROTEINIDENTIFICATIONBYSUB-NANOPORESENSORS.................94MikhailKolmogorov,EamonnKennedy,ZhuxinDong,GregoryTimp,PavelA.Pevzner

GENEEXPRESSIONPROFILEOFOSTEOARTHRITISAFFECTEDFINGERJOINTS................95MilicaKrunic,KlausBobacz,ArndtvonHaeseler


viii

DISCOVERYANDPRIORITIZATIONOFDENOVOMUTATIONSINAUTISMSPECTRUMDISORDER.............................................................................................................................................................96TaeyeopLee,JaehoOh,MinGyunBae,JunHyeongLee,JungKyoonChoi

CROSSTALKER:ANOPENNETWORKANDPATHWAYANALYSISPLATFORM.....................97SeanMaxwell,MarkR.Chance

SIGNATURESOFNON–SMALL-CELLLUNGCANCERRELAPSEPATIENTS:DIFFERENTIALEXPRESSIONANALYSISANDGENENETWORKANALYSIS............................................................98AbigailE.Moore,BrandonZheng,PatriciaM.Watson,RobertC.Wilson,DennisK.Watson,PaulE.Anderson

RANKINGBIOLOGICALFEATURESBYDIFFERENTIALABUNDANCE.......................................99SoumyashantNayak,NicholasLahens,EunJiKim,GregoryGrant

SYSTEMATICANALYSISOFOBESITYASSOCIATEDVARIATIONSTHROUGHMACHINELEARNINGBASEDONGENOMICSANDEPIGENOMICS..................................................................100JaehoOh,JunHyeongLee,TaeyeopLee,MinGyunBae,JungKyoonChoi

SPARSEREGRESSIONMODELINGOFDRUGRESPONSEWITHALOCALIZEDESTIMATIONFRAMEWORK....................................................................................................................................................101TeppeiShimamura,HidekoKawakubo,HyunhaNam,YusukeMatsui

PDBMAP:APIPELINEANDDATABASEFORMAPPINGGENETICVARIATIONINTOPROTEINSTRUCTURESANDHOMOLOGYMODELS........................................................................102R. MichaelSivley,JohnA.Capra,WilliamS.Bush

REPETITIVERNAANDGENOMICINSTABILITYINHIGH-GRADESEROUSOVARIANCANCERPROGRESSIONANDDEVELOPMENT...................................................................................103JamesR.Torpy,NenadBartonicek,DavidD.L.Bowtell,MarcelE.Dinger

DIMENSIONREDUCTIONOFGENOME-WIDESEQUENCINGDATABASEDONLINKAGEDISEQUILIBRIUMSTRUCTURE.................................................................................................................104YunJooYoo,Suh-RyungKim,SunAhKim,ShelleyB.Bull

THEMULTIPLEGENEISOFORMTEST...................................................................................................105YaoYu,ChadD.Huff

IMAGINGGENOMICS.........................................................................................................................106GENETICANALYSISOFCEREBRALBLOODFLOWIMAGINGPHENOTYPESINALZHEIMER’SDISEASE.................................................................................................................................107XiaohuiYao,ShannonL.Risacher,KwangsikNho,AndrewJ.Saykin,HengHuang,ZeWang,LiShen

PBRM1MUTATIONSAREASSOCIATEDWITHTISSUEMORPHOLOGICALCHANGESINKIDNEYCANCER..............................................................................................................................................108JunCheng,JieZhang,ZhiHan,LiangCheng,QianjinFeng,KunHuang

IMAGEGENOMICSOFINTRA-TUMORHETEROGENEITYUSINGDEEPNEURALNETWORKS........................................................................................................................................................109HuiQu,SubhajyotiDe,DimitrisMetaxas

THENEUROIMAGINGINFORMATICSTOOLSANDRESOURCESCOLLABORATORY(NITRC)ANDITSIMAGINGGENOMICSDOMAIN.............................................................................110LiShen,DavidKennedy,ChristianHaselgrove,AbbyPaulson,NinaPreuss,RobertBuccigrossi,MatthewTravers,AlbertCrowley,andTheNITRCTeam


ix

IDENTIFYINGTHEGISTOFCNNS:FINDINGINTERPRETABLESIGNATURESOFHISTOLOGYIMAGEMODELSBUILTUSINGNEURALNETWORKS...........................................111ArunimaSrivastava,ChaitanyaKulkarni,KunHuang,ParagMallick,RaghuMachiraju

PRECISIONMEDICINE:FROMDIPLOTYPESTODISPARITIESTOWARDSIMPROVEDHEALTHANDTHERAPIES...............................................................................................................112EXPLORINGTHEPOTENTIALOFEXOMESEQUENCINGINNEWBORNSCREENING.......113StevenE.Brenner,AashishN.Adhikari,YaqiongWang,RobertJ.Currier,RenataC.Gallagher,RobertL.Nussbaum,YangyunZou,UmaSunderam,JosephSheih,FlaviaChen,MarkKvale,SeanD.Mooney,RajSrinivasan,BarbaraA.Koenig,PuiKwok,JenniferM.Puck,TheNBSeqProject

AMETHODFORIMPROVEDVARIANTCALLINGATHOMOPOLYMERMARGINS(ANDELSEWHERE)....................................................................................................................................................114J.Buckley,M.Hiemenz,J.Biegel,T.Triche,A.Ryutov,D.Maglinte,D.Ostrow,X.Gai

EFFICIENTSURVIVALMULTIFACTORDIMENSIONALITYREDUCTIONMETHODFORDETECTINGGENE-GENEINTERACTION..............................................................................................115JiangGui,XuemeiJi,ChristopherI.Amos

BIOINFORMATICSPROCESSINGSTRATEGIESFOREFFICIENTSEQUENCINGDATASTORAGEUSINGGVCFBANDING.............................................................................................................116NicholasB.Larson,ShannonK.McDonnell,IainF.Horton,SaurabhBaheti,JeanetteE.Eckel-Passow,StevenN.Hart

IDENTIFICATIONOFANOVELTSC2MUTATIONINAPATIENTWITHTUBEROUSSCLEROSISCOMPLEX....................................................................................................................................117Jae-HyungLee,Su-KyeongHwang,Jung-eunYang,Chae-SeokLim,Jin-ALee,KyungminLee,Bong-KiunKaang,Yong-SeokLee

CONSIDERATIONSFORAUTOMATEDMACHINELEARNINGINCLINICALMETABOLICPROFILING:ALTEREDHOMOCYSTEINEPLASMACONCENTRATIONASSOCIATEDWITHMETFORMINEXPOSURE..............................................................................................................................118AlenaOrlenko,JasonH.Moore,PatrykOrzechowski,RandalS.Olson,JunmeiCairns,PedroJ.Caraballo,RichardM.Weinshilboum,LieweiWang,MatthewK.Breitenstein

PHARMGKB:NEWWEBSITERELEASE2017........................................................................................119MichelleWhirl-Carrillo,RyanM.Whaley,MarkWoon,KatrinSangkuhi,LiGong,JuliaBarbarino,CarolineThorn,RachelHuddart,MariaAlvarellos,JillRobinson,RussB.Altman,TeriE.Klein

READINGBETWEENTHEGENES:COMPUTATIONALMODELSTODISCOVERFUNCTIONAND/ORCLINICALUTILITYFROMNONCODINGDNA...........................................................120NETWORKANALYSISOFPSEUDOGENE-GENERELATIONSHIPS:FROMPSEUDOGENEEVOLUTIONTOTHEIRFUNCTIONALPOTENTIALS........................................................................121TravisS.Johnson,SihongLi,JohnathanR.Kho,KunHuang,YanZhang

RANDOMWALKSONMUTUALMICRORNA-TARGETGENEINTERACTIONNETWORKIMPROVETHEPREDICTIONOFDISEASE-ASSOCIATEDMICRORNAS....................................122Duc-HauLe,LievenVerbeke,LeHoangSon,Dinh-ToiChu,Van-HuyPham


x

TEXTMININGANDVISUALIZATIONFORPRECISIONMEDICINE.......................................123MININGELECTRONICHEALTHRECORDSFORPATIENT-CENTEREDOUTCOMESTOGUIDETREATMENTPATHWAYDECISIONSFOLLOWINGPROSTATECANCERDIAGNOSIS..........................................................................................................................................................124SelenBozkurt,JungInPark,DanielL.Rubin,JamesD.Brooks,TinaHernandez-Boussard

GDMINER:ABIOTEXTMININGSYSTEMFORGENE-DISEASERELATIONANALYSIS.....125SooJunPark,JihyunKim,SooYoungCho,CharnyPark,YoungSeekLee

WORKSHOP.....................................................................................................................................126MACHINELEARNINGANDDEEPANALYTICSFORBIOCOMPUTING:CALLFORBETTEREXPLAINABILITY...............................................................................................................................126METHODSFOREXAMININGDATAQUALITYINHEALTHCAREINTEGRATEDDATAREPOSITORIES..................................................................................................................................................127VojtechHuser,MichaelG.Kahn,JeffreyS.Brown,RamkiranGouripeddi

MULTI-CLASSCLASSIFICATIONSTRATEGYFORSUPPORTVECTORMACHINESUSINGWEIGHTEDVOTINGANDVOTINGDROP.............................................................................................128SunghoKim,TaehunKim

ATOPOLOGY-BASEDAPPROACHTOQUANTIFYNETWORKPERTURBATIONSCORESFORASSESSMENTOFDIFFERENTTOBACCOPRODUCTCLASSES...........................................129QuynhT.Tran,LeeLarcombe,SubhashiniArimilli,G.L.Prasad

AUTHORINDEX.............................................................................................................................130


130

AUTHORINDEX

A

Abe,Sumiko·51Abyzov,Alexej·79Acharya,Ambika·5Achour,Ikbel·33Adhikari,AashishN.·113Adhikari,BhimM.·53Agrawal,Monica·8,70Aldana,Julian·76Al-Ghalith,Gabriel·75Alkan,Can·77,90Allette,Kimaada·2Alser,Mohammed·77,90Altman,RussB.·5,47,62,119Alvarellos,Maria·119Ambite,JoséLuis·51Amos,ChristopherI.·115Anderson,PaulE.·98Arimilli,Subhashini·129

B

Bada,Michael·45Bae,MinGyun·78,96,100Bae,Taejeong·79Baheti,Saurabh·116Baladandayuthapani,Veerabhadran·48Barbarino,Julia·119Bartonicek,Nenad·103BaumgartnerJr.,WilliamA.·37,45Beam,AndrewL.·83Beaulieu-Jones,BrettK.·9Bechheim,Matthias·92Behsaz,Bahar·80Berghout,Joanne·25Bharath,Karthik·48Bhattrai,Avnish·51Biegel,J.·114Bilke,Sven·88Blach,Colette·18Blangero,John·53Bobacz,Klaus·95Boguslav,Mayla·37Bowtell,DavidD.L.·103Bozkurt,Selen·124Bradford,Yuki·58Breitenstein,MatthewK.·28,118Brenner,StevenE.·113Bright,RoselieA.·5Brooks,JamesD.·124Brown,JeffreyS.·127Buccigrossi,Robert·110

Buchan,Z.R.·72Buckley,J.·114Bull,ShelleyB.·104Burns,Gully·51Bush,WilliamS.·57,81,102Butkiewicz,Mariusz·81

C

Cairns,Junmei·28,118Cali,DamlaS.·90Callahan,TiffanyJ.·45Capra,JohnA.·57,102Caraballo,PedroJ.·28,118CarsonIII,WilliamE.·43Cha,Hongui·65Chance,MarkR.·97Chen,Bin·82Chen,Flavia·113Chen,MichaelL.·83Chen,Rong·10,42Chen,Xiao·88Chen,Xintong·2Chen,Youdinghuan·71Chen,Yuying·82Cheng,Chao·71Cheng,Jun·108Cheng,Liang·108Chesi,Alessandra·35Cheung,Philip·67Chi,Chih-Lin·26Chidester,Benjamin·20Ching,Travers·60Cho,SooYoung·125Choe,EunKyung·84Choi,JungKyoon·78,96,100Christensen,BrockC.·71Chu,Dinh-Toi·122Chuang,Han-Yu·88Clark,NeilR.·3,64Cohen,K.Bretonnel·37Cooper,BruceA.·93Cox,RobertW.·53Crawford,DanaC.·57Crowley,Albert·110Currier,RobertJ.·113

D

deBelle,J.Steven·67De,Subhajyoti·109Deng,Siyuan·43Dinger,MarcelE.·103Do,MinhN.·20


131

Doherty,JenniferA.·11Dong,Zhuxin·94Dorrestein,PieterC.·80Duan,Qiaonan·3,64Dudley,JoelT.·3,10,12,42,64

E

Eckel-Passow,JeanetteE.·116Ergin,Oğuz·77,90Erikson,GalinaA.·85

F

Farhat,Maha·83Feng,Qianjin·108Fenger,Douglas·67Fieremans,Els·53Fierro,Lily·51Fish,AlexandraE.·57Fisher,MarkF.·80Flotte,T.J.·72Flotte,W.·72Foster,Ian·33

G

Gai,X.·114Gallagher,RenataC.·113Garmire,LanaX.·60Geiersbach,K.B.·72Gerstein,Mark·86Ghose,Saugata·90Glahn,DavidC.·53Glicksberg,BenjaminS.·10,12,42,82Gong,Li·119Gordon,Jonathan·51Gouripeddi,Ramkiran·127Grant,Gregory·99Grant,StruanF.A.·35Greene,CaseyS.·6,11,68Greenside,Peyton·41Griffith,Malachi·16Griffith,ObiL.·16Gui,Jiang·115Guo,Caiwei·46Gupta,Anika·27Gurevich,Alexey·80Gursoy,Gamze·86

H

Haas,DavidW.·58Haines,JonathanL.·81Hall,MollyA.·35

Han,Jiali·33Han,Jiawei·39Han,Lichy·54Han,Zhi·108Harrington,LiaX.·11Hart,StevenN.·72,116Hartman,Nicholas·31Haselgrove,Christian·110Hassan,Hasan·77,90He,Lu·26He,Mingze·73Hernandez-Boussard,Tina·124Hiemenz,M.·114Hillenmeyer,Maureen·41Hobbs,BrianP.·48Hodos,Rachel·3,12,64Hong,L.Elliot·53Hornung,Veit·92Horton,IainF.·116Houten,Sander·2Hu,Jianying·3,64Hu,Xiao·93Huang,Chenglong·21Huang,EdwardW.·38,39Huang,Heng·22,107Huang,Kun·34,55,108,111,121Huang,Ling·85Huddart,Rachel·119Hudson,TiaTate·87Huff,ChadD.·105Hunter,LawrenceE.·37,45Huo,Zhouyuan·22Huser,Vojtech·127Hwang,Su-Kyeong·117

I

Ideker,Trey·39

J

Jahanshad,Neda·53Jain,Priyambada·51Jenkins,NicoleP.·71Jeong,Hyun-Hwan·46Ji,Xuemei·115Johnson,Abigail·75Johnson,KippW.·10,12Johnson,TravisS.·34,121Ju,JinHyun·88Jung,Jae-Yoon·27

K

Kaang,Bong-Kiun·117Kahn,MichaelG.·127Kamdar,Jeana·51


132

Kamdar,MaulikR.·54Kang,JoonHo·65Kawakubo,Hideko·89,101Kennedy,David·110Kennedy,Eamonn·94Kettenbach,ArminjaN.·71Kho,JohnathanR.·34,121Kidd,Brian·3,64Kim,Dokyoon·23Kim,EunJi·99Kim,JeremieS.·90Kim,Jihyun·125Kim,Jinho·65Kim,Suh-Ryung·104Kim,SunAh·104Kim,Sungho·91,128Kim,Taehun·91,128Kim-Hellmuth,Sarah·92Klein,TeriE.·119Knights,Dan·75Kober,KordM.·93Kochunov,Peter·53Koenig,BarbaraA.·113Kohane,IsaacS.·83Kolmogorov,Mikhail·94Krunic,Milica·95Kulkarni,Anagha·62Kulkarni,Chaitanya·55,111Kulkarni,Shashikant·16Kundaje,Anshul·41Kvale,Mark·113Kwok,Pui·113

L

LaCava,William·13Lahens,Nicholas·99Lake,Bethany·31Lappalainen,Tuuli·92Larcombe,Lee·129Larson,NicholasB.·116Lawrence-Dill,CarolynJ.·73Le,Duc-Hau·122Lee,Boram·65Lee,Donghyuk·90Lee,Hao-Chih·3,64Lee,Jae-Hyung·117Lee,Jin-A·117Lee,JunHyeong·78,96,100Lee,Kyungmin·117Lee,SangWoo·84Lee,Seunggeun·23Lee,Taeyeop·78,96,100Lee,Yong-Seok·117Lee,YoungSeek·125Lei,Xiaoxiao·51Lerman,Kristina·51Leskovec,Jure·8,70Li,Binglan·58

Li,Fuhai·43Li,Haiquan·33Li,Jianrong·25,33Li,Justin·66Li,Li·10,42Li,Qike·25,30Li,Sihong·34,121Lim,Chae-Seok·117Liu,Gang·66Liu,Ke·82Liu,Zhandong·46Losic,Bojan·2Luo,Yunan·4Lussier,YvesA.·25,30,33

M

Ma,Jian·20Ma,Jianzhu·39Ma’ayan,Avi·3,64Machiraju,Raghu·55,111Madhavan,Subha·16Maglinte,D.·114Mallick,Parag·55,111Mallory,EmilyK.·5,62Manduchi,Elisabetta·35Mariani,Jessica·79Marotti,JonathanD.·71Matsui,Yusuke·89,101Maxwell,Sean·97McCoy,Matthew·16McDonnell,ShannonK.·116McGarvey,Peter·16Metaxas,Dimitris·109Miaskowski,Christine·93Micheel,Christine·16Miller,JasonE.·23Miller,ToddW.·71Miotto,Riccardo·10Mishkanian,Ben·88Mohammadi,Pejman·92Mohimani,Hosein·80Molina,MonicaCala·76Mooney,SeanD.·113Moore,AbigailE.·98Moore,JasonH.·9,13,17,28,35,118Morishita,Hirofumi·42Mounajjed,T.·72Müller-Myhsok,Bertram·92Mustahsan,Zairah·13Mutlu,Onur·77,90Mylne,JoshuaS.·80

N

Nam,Hyunha·101Nayak,Soumyashant·99Ng,ChaanS.·48


133

Nho,Kwangsik·23,107Nichols,ThomasE.·53Norgan,A.P.·72Novikov,DmitryS.·53Nussbaum,RobertL.·113

O

O’Driscoll,Caroline·51Oh,Jaeho·78,96,100Olson,RandalS.·13,17,28,118Orlenko,Alena·28,118Orzechowski,Patryk·9,28,118Ostrow,D.·114

P

Park,Charny·125Park,JungIn·124Park,SooJun·125Park,Woong-Yang·65Paskov,KelleyM.·27Paul,StevenM.·93Paulson,Abby·110Payne,PhilipR.O.·43Peng,Jian·4,39Pesce,Lorenzo·33Petkovic,Dragutin·47,62Pevzner,PavelA.·80,94Pham,Van-Huy·122Poole,Sarah·29Pouladi,Nima·25Prasad,G.L.·66,129Preuss,Nina·110Previde,Paul·62Prjibelski,Andrey·80Puck,JenniferM.·113Pütz,Benno·92Pyc,MaryA.·67

Q

Qu,Hui·109

R

RachidZaim,Samir·30Rao,Shruti·16Ravvaz,Kourosh·26Regan,Kelly·43Rensi,StefanoE.·5Reynolds,RichardC.·53Risacher,ShannonL.·23,107Ritchie,MarylynD.·14,58Ritter,Deborah·16

Robinson,Jill·119Roy,Angshumoy·16Rubin,DanielL.·124Ryutov,A.·114

S

Salas,LucasA.·71Sangkuhi,Katrin·119Sarkar,IndraNeil·50Saykin,AndrewJ.·23,107Schissler,A.Grant·30Schmitt,Peter·17Schumacher,Johannes·92Sebra,RobertP.·2Shah,K.K.·72Shah,Nigam·29Shameer,Khader·10,12Sharma,Vivekanand·50Shearer,Gregory·31Sheih,Joseph·113Shen,Dinggang·22Shen,Li·107,110Shestov,Maksim·17Shimamura,Teppei·89,101Shin,Hyun-Tae·65Shivakumar,ManuK.·23Shoemaker,Katherine·48Shokhirev,Maxim·85Shukla,Dinesh·53Shulman,Joshua,M.·46Sinha,Aakanchha·51Sivley,R.Michael·102Smarr,Larry·80Smith,MiloR.·42Snedecor,June·88Son,LeHoang·122Sonkin,Dmitriy·16Sontag,David·3,64Srinivasan,Raj·113Srivastava,Arunima·55,111Stefanski,AdrianneL.·45Stewart,Crystal·51Stockham,NateT.·27Stolovitzky,Gustavo·2Sun,MinWoo·27Sunderam,Uma·113

T

Tenenbaum,JessicaD.·18Thomas,Brook·62Thompson,PaulM.·53Thorn,Caroline·119Timp,Gregory·94Tintle,Nathan·31Tomasini,Livia·79Tonellato,PeterJ.·26


134

Torpy,JamesR.·103Tran,QuynhT.·129Travers,Matthew·110Triche,T.·114Tripodi,Ignacio·45Tully,Tim·67Turnbaugh,PeterJ.·5

U

Urban,AlexanderE.·79

V

Vaccarino,FloraM.·79VanHorn,JohnDarrell·51Vangay,Pajau·75Varik,Akshay·13Veraart,Jelle·53Verbeke,Lieven·122Verma,Anurag·58Verma,ShefaliS.·58Veturi,YogasudhaC.·14,58Vigil,Arthur·47vonHaeseler,Arndt·95

W

Wall,DennisP.·27Wang,Fei·3,64Wang,Liewei·28,118Wang,Sheng·4,38,39Wang,Yaqiong·113Wang,Yue·71Wang,Ze·107Wang,Zichen·3,64Watson,DennisK.·98Watson,PatriciaM.·98Way,GregoryP.·6,11,68Weinshilboum,RichardM.·28,118Weissert,John·26

Westra,Jason·31Whaley,RyanM.·119Whirl-Carrillo,Michelle·119White,ElizabethK.·45Williams-DeVane,ClarLynda·87Wilson,RobertC.·98Wong,Mike·47,62Woon,Mark·119

X

Xiao,Guanghua·21Xiao,Jinfeng·4Xin,Hongyi·77,90Xu,Jielin·43

Y

Yalamanchili,HariKrishna·46Yang,Jung-eun·117Yao,Xiaohui·107Yoo,YunJoo·104Yu,MichaelKu·39Yu,Yao·105Yun,JaeWon·65

Z

Zeng,William·82Zhai,ChengXiang·38Zhang,Albert·21Zhang,Jie·108Zhang,Ping·3,64Zhang,Yan·34,121Zheng,Brandon·98Zheng,Fan·39Zhou,Bo·79Zitnik,Marinka·8,70Zou,Yangyun·113Zuluaga,Martha·76


PacificSymposiumonBiocomputing2018ParticipantsList

(asofDecember16,2017)AlexejAbyzovMayoClinicBrianAevermannJ.CraigVenterInstituteMonicaAgrawalStanfordUniversityGabrielAl-GhalithUniversityofMinnesota-TwinCitiesJulianAldanaUniversidaddelosAndesRussAltmanStanfordUniversitySophiaAnaniadouUniversityofManchesterMingyunBaeKoreaAdvancedInstituteofScienceandTechnologyPierreBaldiUniversityofCalifornia,IrvineAnnaBasileThePennsylvaniaStateUniversityAnandBasuESACInc.BrettBeaulieu-JonesUniversityofPennsylvaniaGurkanBebekCaseWesternReserveUniversityBaharBehsazUniversityofCalifornia,SanDiego

JoanneBerghoutUniversityofArizonaMaylaBoguslavUniversityofColoradoMaryReginaBolandUniversityofPennsylvaniaRichardBourgonGenentech,Inc.PhilipBourneUVADataScienceInstituteYukiBradfordUniversityofPennsylvaniaMatthewBreitensteinUniversityofPennsylvaniaStevenBrennerUniversityofCalifornia,BerkeleyJeffreyBrownHarvardMedicalSchoolSorenBrunakNovoNordiskFoundationCenterforProteinResearchJonathanBuckleyU.S.CMarthaBulykBrigham&Women’sHospitalandHarvardMedicalSchoolLegandBurgeHowardUniversityWilliamBushCaseWesternReserveUniversity



(asofDecember16,2017)CarlosBustamanteStanfordUniversityJ.BrianByrdUniversityofMichiganHealthSystemTomCaldwellTheUniversityofPennsylvaniaTiffanyCallahanUniversityofColoradoPoulamiChaudhuriTataconsultancyservices(Innovationlabs,Hyderabad)BinChenUCSFMichaelChenHarvardMedicalSchoolYongChenUniversityofPennsylvaniaYoudinghuanChenDartmouthCollegeChih-LinChiUofMinnesotaBenjaminChidesterCarnegieMellonUniversitySooYoungChoNationalCancerCenterEunKyungChoeSeoulNationalUniversityHospitalGangnamCenterSongYiChoiChungnamNationalUniversityHospital

Suh-YeonChoiAmorepacificCorp.KevinCohenUniversityofColoradoSchoolofMedicineJoeCorkeryGoogleDanaCrawfordCaseWesternReserveUniversityChristianDarabosDartmouthCollegeScottDelpStanfordUniversityValentinDinuArizonaStateUniversityScottDudekUniversityofPennsylvaniaJoelDudleyIcahnSchoolofMedicineatMountSinaiSeanDudleyArizonaStateUniversityAKeithDunkerIndianaUniversitySchoolofMedicineClaireDuvalletMassachusettsInstituteofTechnologyTaraEicherTheOhioStateUniversityJonathanEisenUCDavis



(asofDecember16,2017)GalinaEriksonSalkInstituteAndreEstevaStanfordUniversity-ArtificialIntelligenceLabAlexandraFishGenomicsPLCJamesFosterUniversityofIdahoAndreFrankeIKMB,KielUniversityAlexFraseUniversityofPennsylvaniaDarcyFreedmanCaseWesternReserveUniversityLanaGarmireUniversityofHawaiiCancerCenterRezaGhanadanGoogleInc.BenjaminGlicksbergUniversityofCalifornia,SanFranciscoGracielaGonzalezHernandezUniversityofPennsylvaniaRamGouripeddiUniversityofUtahCaseyGreeneUniversityofPennsylvaniaPeytonGreensideStanfordUniversity

JiangGuiHanoverAnikaGuptaStanfordUniversityGamzeGursoyYaleUniversityJonathanHainesCaseWesternReserveUniversityLichyHanStanfordUniversityLiaHarringtonDartmouthCollegeStevenHartMayoClinicDavidHausslerHowardHughesMedicalInstitute/UCSantaCruzMingzeHeIowastateuniversityTinaHernandez-BoussardStanfordUniversityRachelHodosIcahnSchoolofMedicineatMountSinaiJohnHolmesUniversityofPennsylvaniaPerelmanSchoolofMedicineChenglongHuangColleyvilleHeritageHighSchoolEdwardHuangUniversityofIllinoisatUrbana-Champaign



(asofDecember16,2017)HengHuangUniversityofPittsburghKunHuangIndianaUniversitySchoolofMedicineTiaHudsonNorthCarolinaCentralUniversityChadHuffTheUniversityofTexasMDAndersonCancerCenterLawrenceHunterUniversityofColoradoVojtechHuserNIH/NLMKetlyJean-PierreHowardUniversityHyun-HwanJeongBaylorCollegeofMedicineKippJohnsonIcahnSchoolofMedicineatMountSinaiTravisJohnsonOhioStateUniversityJinHyunJuIlluminaMichaelKahnUniversityofColoradoDenverMaulikKamdarStanfordUniversitySaiKanaparthiImmuneToleranceNetwork

HidekoKawakuboNagoyaUniversityGraduateSchoolofMedicinesMichaelKeiserUCSFColleenKenostTheUniversityofArizonaWarrenKibbeDukeUniversityDokyoonKimGeisingerHealthSystemHyunSeokKimYonseiUniversityCollegeofMedicineJeremieKimCarnegieMellonUniversityJihyunKimClinicalGenomicsAnalysisBranchJinhoKimSamsungMedicalCenterMinjuKimASANMedicalCenterSeonokKimASANMedicalCenterShinKimKeimyungUniversity,SchoolofMedicineSunghoKimElectronicEngineering/YeungnamUniversitySarahKim-HellmuthMax-Planck-InstituteforPsychiatry



(asofDecember16,2017)TeriKleinStanfordUniversityKordKoberUniversityofCaliforniaSanFranciscoLesterKobzikHarvardUniversityPeterKochunovMarylandPsychiatricResearchCenterMikhailKolmogorovUniversityofCalifornia,SanDiegoMilicaKrunicUniversityofViennaAnaghaKulkarniSanFranciscoStateUniversityWilliamLaCavaUniversityofPennsylvaniaNicholasLarsonMayoClinicDuc-HauLeVinmecResearchInstituteofStemCellandGeneTechnologyJae-HyungLeeKyungHeeUniversityJunHyeongLeeKoreaAdvancedInstituteofScienceandTechnology(KAIST)TaeyeopLeeKAISTYong-SeokLeeSeoulNationalUniversityCollegeofMedicine

BinglanLiThePennsylvaniaStateUniversityFuhaiLiTheOhioStateUniversityHaiquanLiUniversityofArizonaQikeLiTheUniversityofArizonaShuyuLiSema4Gang(Michael)LiuRAIServicesCompanyTianyunLiuStanfordUniversityBojanLosicIcahnSchoolofMedicine,MountSinaiYunanLuoUniversityofIllinoisatUrbana-ChampaignYvesLussierUniversityofArizonaHealthSciences&BIO5InstituteSelahLynchUniversityofPennsylvaniaJianzhuMaUniversityofCalifornia,SanDiegoSubhaMadhavanGeorgetownUniversityEmilyMalloryStanfordUniversity



(asofDecember16,2017)ElisabettaManduchiUniversityofPennsylvaniaSergheiMangulUCLAAdamMargolinOregonHealth&ScienceUniversityGaborMarthUniversityofUtahYusukeMatsuiNagoyaUniversityGraduateSchoolofMedicineMarlonMejiasHowardUniversityDimitrisMetaxasRutgersUniversityBrandonMikkelsenArizonaStateUniversityJasonMillerGeisingerHealthSystemRiccardoMiottoIcahnSchoolofMedicineatMountSinaiRobertModlinUniversityofCalifornia,LosAngelesAbigailMooreHampshireCollegeJasonMooreUniversityofPennsylvaniaAlexanderMorganKhoslaVentures

OnurMutluETHZurichMasaharuNakayamaTohokuUniversityHyunhaNamNagoyaUniversitySoumyashantNayakUniversityofPennsylvaniaEricNeumannAIDAKASoichiOgishimaToMMo,TohokuUniversityJaehoOhKoreaAdvancedInstituteofScienceandTechnologyLawrenceOloffSOARRandalOlsonUniversityofPennsylvaniaAlenaOrlenkoUniversityofPennsylvaniaAbiodunOtolotinHowardUniversityCharnyParkNationalCancerCenter,RepublicofKoreaSooJunParkElectronicsandTelecommunicationsResearchInstituteYuRangParkAsanMedicalcenter



(asofDecember16,2017)JyotishmanPathakCornellUniversityCindyPaulazzoStanfordUniversityPhilipPayneWashingtonUniversitySchoolofMedicineMatteoPellegriniUCLAJianPengUniversityofIllinoisatUrbana-ChampaignBethanyPerchaIcahnSchoolofMedicineatMountSinaiMinoliPereraNorthwesternUniversityDragutinPetkovicSanFranciscoStateUniversityStevenPitts23andMe,Inc.TherapeuticsSarahPooleStanfordUniversityAleksanderPopelJohnsHopkinsUniversityPredragRadivojacIndianaUniversityMarylynRitchieUniversityofPennsylvaniaDavidRockeUniversityofCalifornia,Davis

RichardRoettgerUniversityofSouthernDenmarkMertSabuncuCornellUniversityKatrinSangkuhlStanfordUniversityNeilSarkarBrownUniversityRichardScheuermannJ.CraigVenterInstituteGrantSchisslerUniversityofArizonaRalphSchlapbachETHZurichAbhikShahLexentBioVivekanandSharmaCenterforBiomedicalInformatics,BrownUniversityLiShenUniversityofPennsylvaniaYingShenVeracyte,Inc.TaoShiCelgeneCorp.TeppeiShimamuraNagoyaUniversityGraduateSchoolofMedicineKatherineShoemakerRiceUniversity



(asofDecember16,2017)JamesSikelaUniversityofColoradoDenverRobertSivleyVanderbiltUniversityChantelSloanBrighamYoungUniversityLarrySmarrUniversityofCaliforniaCalit2MiloSmithIcahnSchoolofMedicineatMountSinaiWilliamSoutherlandHowardUniversityArunimaSrivastavaTheOhioStateUniversityHowardSueingGoogleMinWooSunWallLab-StanfordSchoolofMedicineS.JoshuaSwamidassWashingtonUniversityinSaintLouisNicholasTatonettiColumbiaUniversityMedicalCollegeJessicaTenenbaumDukeUniversitySchoolofMedicinePascalTimshelStanfordUniversity/CZBiohub/UCPHJamesTorpyGarvanInstituteofMedicalResearch

NhuQuynhTranRAISJohnVanHornUniversityofSouthernCaliforniaAnuragVermaUniversityofPennsylvaniaShefaliVermaUniversityofPennsylvaniaYogasudhaVeturiUniversityofPennsylvaniaFrancescaVitaliUniversityofArizonaBenjaminVoightUniversityofPennsylvaniaJenniferWagnerGeisingerHealthSystemDennisWallStanfordUniversityJiguangWangHongKongUniversityofScienceandTechnologyZhengyuanWangAbbvieMichaelWatermanUniversityofSouthernCaliforniaGregoryWayUniversityofPennsylvaniaJasonWestraDordtCollege



(asofDecember16,2017)RyanWhaleyStanfordUniversityMichelleWhirl-CarrilloStanfordUniversityJohnWilbanksSageBionetworksScottWilliamsCaseWesternReserveUniversityMikeWongSanFranciscoStateUniversityXinshuXiaoUniversityofCalifornia,LosAngelesXinanHollyYangTheUniversityofChicagoYunJooYooSeoulNationalUniversityJieZhangIndianaUniversitySchoolofMedicineXiangZhangPennStateYanZhangTheOhioStateUniversityYaozhongZhangTheUniversityofTokyoYizhenZhongNorthwesternUniversityJiayuZhouMichiganStateUniversity

MarinkaZitnikStanfordUniversity


january 3-7, 2018 big island of hawaii program book · 2020-02-12 · pacific symposium on...

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