Abstract is missing.
- Session IntroductionRichard Bourgon, Frederick E. Dewey, Zhengyan Kan, Shuyu D. Li. 1-7 [doi]
- Characterization of drug-induced splicing complexity in prostate cancer cell line using long read technologyXintong Chen, Sander M. Houten, Kimaada Allette, Robert P. Sebra, Gustavo Stolovitzky, Bojan Losic. 8-19 [doi]
- Prediction of protein-ligand interactions from paired protein sequence motifs and ligand substructuresPeyton Greenside, Maureen Hillenmeyer, Anshul Kundaje. 20-31 [doi]
- Cell-specific prediction and application of drug-induced gene expression Rachel Hodos, Ping Zhang, Hao-Chih Lee, Qiaonan Duan, Zichen Wang, Neil R. Clark, Avi Ma'ayan, Fei Wang, Brian A. Kidd, Jianying Hu, David Sontag, Joel Dudley. 32-43 [doi]
- Large-scale integration of heterogeneous pharmacogenomic data for identifying drug mechanism of actionYunan Luo, Sheng Wang, Jinfeng Xiao, Jian Peng 0001. 44-55 [doi]
- Chemical reaction vector embeddings: towards predicting drug metabolism in the human gut microbiomeEmily K. Mallory, Ambika Acharya, Stefano E. Rensi, Peter J Turnbaugh, Roselie A. Bright, Russ B. Altman. 56-67 [doi]
- Loss-of-function of neuroplasticity-related genes confers risk for human neurodevelopmental disordersMilo R. Smith, Benjamin S. Glicksberg, Li Li, Rong Chen, Hirofumi Morishita, Joel T. Dudley. 68-79 [doi]
- Extracting a biologically relevant latent space from cancer transcriptomes with variational autoencodersGregory P. Way, Casey S. Greene. 80-91 [doi]
- Diffusion mapping of drug targets on disease signaling network elements reveals drug combination strategiesJielin Xu, Kelly Regan-Fendt, Siyuan Deng, William E. Carson III, Philip R. O. Payne, Fuhai Li. 92-103 [doi]
- Session IntroductionShefali Setia Verma, Anurag Verma, Anna Okula Basile, Marta Byrska-Bishop, Christian Darabos. 104-110 [doi]
- Large-scale analysis of disease pathways in the human interactomeMonica Agrawal, Marinka Zitnik, Jure Leskovec. 111-122 [doi]
- Mapping patient trajectories using longitudinal extraction and deep learning in the MIMIC-III Critical Care DatabaseBrett K. Beaulieu-Jones, Patryk Orzechowski, Jason H. Moore. 123-132 [doi]
- OWL-NETS: Transforming OWL representations for improved network inferenceTiffany J. Callahan, William A. Baumgartner Jr., Michael Bada, Adrianne L. Stefanski, Ignacio Tripodi, Elizabeth K. White, Lawrence E. Hunter. 133-144 [doi]
- Automated disease cohort selection using word embeddings from Electronic Health RecordsBenjamin S. Glicksberg, Riccardo Miotto, Kipp W. Johnson, Khader Shameer, Li Li, Rong Chen, Joel T. Dudley. 145-156 [doi]
- Functional network community detection can disaggregate and filter multiple underlying pathways in enrichment analysesLia X. Harrington, Gregory P. Way, Jennifer A. Doherty, Casey S. Greene. 157-167 [doi]
- An ultra-fast and scalable quantification pipeline for transposable elements from next generation sequencing dataHyun-hwan Jeong, Hari Krishna Yalamanchili, Caiwei Guo, Joshua M. Shulman, Zhandong Liu. 168-179 [doi]
- Causal inference on electronic health records to assess blood pressure treatment targets: An application of the parametric g formulaKipp W. Johnson, Benjamin S. Glicksberg, Rachel Hodos, Khader Shameer, Joel T. Dudley. 180-191 [doi]
- Data-driven advice for applying machine learning to bioinformatics problemsRandal S. Olson, William La Cava, Zairah Mustahsan, Akshay Varik, Jason H. Moore. 192-203 [doi]
- Improving the explainability of Random Forest classifier - user centered approachDragutin Petkovic, Russ B. Altman, Mike Wong, Arthur Vigil. 204-215 [doi]
- Tree-based methods for characterizing tumor density heterogeneityKatherine Shoemaker, Brian P. Hobbs, Karthik Bharath, Chaan S. Ng, Veerabhadran Baladandayuthapani. 216-227 [doi]
- How powerful are summary-based methods for identifying expression-trait associations under different genetic architectures?Yogasudha Veturi, Marylyn D. Ritchie. 228-239 [doi]
- Session introductionPhilip R. O. Payne, Nigam H. Shah, Jessica D. Tenenbaum, Lara Mangravite. 240-246 [doi]
- ClinGen Cancer Somatic Working Group - Standardizing and democratizing access to cancer molecular diagnostic data to drive translational researchSubha Madhavan, Deborah Ritter, Christine Micheel, Shruti Rao, Angshumoy Roy, Dmitriy Sonkin, Matthew McCoy, Malachi Griffith, Obi L. Griffith, Peter B. McGarvey, Shashikant Kulkarni. 247-258 [doi]
- A heuristic method for simulating open-data of arbitrary complexity that can be used to compare and evaluate machine learning methodsJason H. Moore, Maksim Shestov, Peter Schmitt, Randal S. Olson. 259-267 [doi]
- Identifying natural health product and dietary supplement information within adverse event reporting systemsVivekanand Sharma, Indra Neil Sarkar. 268-279 [doi]
- Best practices and lessons learned from reuse of 4 patient-derived metabolomics datasets in Alzheimer's diseaseJessica D. Tenenbaum, Colette Blach. 280-291 [doi]
- Democratizing data science through data science trainingJohn Darrell Van Horn, Lily Fierro, Jeana Kamdar, Jonathan Gordon 0001, Crystal Stewart, Avnish Bhattrai, Sumiko Abe, Xiaoxiao Lei, Caroline O'Driscoll, Aakanchha Sinha, Priyambada Jain, Gully Burns, Kristina Lerman, José Luis Ambite. 292-303 [doi]
- Session introductionHeng Huang, Li Shen, Paul M. Thompson, Kun Huang 0001, JunZhou Huang, Lin Yang. 304-306 [doi]
- Heritability estimates on resting state fMRI data using the ENIGMA analysis pipelineBhim M. Adhikari, Neda Jahanshad, Dinesh Shukla, David C. Glahn, John Blangero, Richard C. Reynolds, Robert W. Cox, Els Fieremans, Jelle Veraart, Dmitry S. Novikov, Thomas E. Nichols, L. Elliot Hong, Paul M. Thompson, Peter V. Kochunov. 307-318 [doi]
- Discriminative bag-of-cells for imaging-genomicsBenjamin Chidester, Minh N. Do, Jian Ma 0004. 319-330 [doi]
- MRI to MGMT: Predicting methylation status in glioblastoma patients using convolutional recurrent neural networksLichy Han, Maulik R. Kamdar. 331-342 [doi]
- Deep integrative analysis for survival predictionChenglong Huang, Albert Zhang, Guanghua Xiao. 343-352 [doi]
- Genotype-Phenotype association study via new multi-task learning modelZhouyuan Huo, Dinggang Shen, Heng Huang. 353-364 [doi]
- Codon bias among synonymous rare variants is associated with Alzheimer's disease imaging biomarkerJason E. Miller, Manu K. Shivakumar, Shannon L. Risacher, Andrew J. Saykin, SeungGeun Lee, Kwangsik Nho, Dokyoon Kim. 365-376 [doi]
- Building trans-omics evidence: using imaging and 'omics' to characterize cancer profilesArunima Srivastava, Chaitanya Kulkarni, Parag Mallick, Kun Huang 0001, Raghu Machiraju. 377-388 [doi]
- Session IntroductionDana C. Crawford, Alexander A. Morgan, Joshua C. Denny, Bruce J. Aronow, Steven E. Brenner. 389-399 [doi]
- Single subject transcriptome analysis to identify functionally signed gene set or pathway activityJoanne Berghout, Qike Li, Nima Pouladi, Jianrong Li, Yves A. Lussier. 400-411 [doi]
- Using simulation and optimization approach to improve outcome through warfarin precision treatmentChih-Lin Chi, Lu He, Kourosh Ravvaz, John Weissert, Peter J. Tonellato. 412-423 [doi]
- Local ancestry transitions modify snp-trait associationsAlexandra E. Fish, Dana C. Crawford, John A. Capra, William S. Bush. 424-435 [doi]
- Coalitional game theory as a promising approach to identify candidate autism genesAnika Gupta, Min Woo Sun, Kelley M. Paskov, Nate T. Stockham, Jae-Yoon Jung, Dennis P. Wall. 436-447 [doi]
- Evaluation of PrediXcan for prioritizing GWAS associations and predicting gene expressionBinglan Li, Shefali S. Verma, Yogasudha Veturi, Anurag Verma, Yuki Bradford, David W. Haas, Marylyn D. Ritchie. 448-459 [doi]
- Considerations for automated machine learning in clinical metabolic profiling: Altered homocysteine plasma concentration associated with metformin exposureAlena Orlenko, Jason H. Moore, Patryk Orzechowski, Randal S. Olson, Junmei Cairns, Pedro J. Caraballo, Richard M. Weinshilboum, Liewei Wang, Matthew K. Breitenstein. 460-471 [doi]
- Addressing vital sign alarm fatigue using personalized alarm thresholdsSarah Poole, Nigam Shah. 472-483 [doi]
- Emergence of pathway-level composite biomarkers from converging gene set signals of heterogeneous transcriptomic responsesSamir Rachid Zaim, Qike Li, A. Grant Schissler, Yves A. Lussier. 484-495 [doi]
- Analyzing metabolomics data for association with genotypes using two-component Gaussian mixture distributionsJason Westra, Nicholas Hartman, Bethany Lake, Gregory Shearer, Nathan L. Tintle. 496-506 [doi]
- Session IntroductionYves A. Lussier, Joanne Berghout, Francesca Vitali, Kenneth S. Ramos, Maricel G. Kann, Jason H. Moore. 507-511 [doi]
- Pan-cancer analysis of expressed somatic nucleotide variants in long intergenic non-coding RNATravers Ching, Lana X. Garmire. 512-523 [doi]
- Convergent downstream candidate mechanisms of independent intergenic polymorphisms between co-classified diseases implicate epistasis among noncoding elementsJiali Han, Jianrong Li, Ikbel Achour, Lorenzo L. Pesce, Ian T. Foster, Haiquan Li, Yves A. Lussier. 524-535 [doi]
- Network analysis of pseudogene-gene relationships: from pseudogene evolution to their functional potentialsTravis Johnson, Sihong Li, Jonathan R. Kho, Kun Huang, Yan Zhang. 536-547 [doi]
- Leveraging putative enhancer-promoter interactions to investigate two-way epistasis in Type 2 Diabetes GWASElisabetta Manduchi, Alessandra Chesi, Molly A. Hall, Struan F. A. Grant, Jason H. Moore. 548-558 [doi]
- Session IntroductionGraciela Gonzalez-Hernandez, Abeed Sarker, Karen O'Connor, Casey S. Greene, Hongfang Liu. 559-565 [doi]
- Improving precision in concept normalizationMayla Boguslav, K. Bretonnel Cohen, William A. Baumgartner Jr., Lawrence E. Hunter. 566-577 [doi]
- VisAGE: Integrating external knowledge into electronic medical record visualizationEdward W. Huang, Sheng Wang, ChengXiang Zhai. 578-589 [doi]
- GeneDive: A gene interaction search and visualization tool to facilitate precision medicinePaul Previde, Brook Thomas, Mike Wong, Emily K. Mallory, Dragutin Petkovic, Russ B. Altman, Anagha Kulkarni. 590-601 [doi]
- Annotating gene sets by mining large literature collections with protein networksSheng Wang, Jianzhu Ma, Michael Ku Yu, Fan Zheng, Edward W. Huang, Jiawei Han 0001, Jian Peng 0001, Trey Ideker. 601-613 [doi]
- The diversity and disparity in biomedical informatics (DDBI) workshopWilliam M. Southerland, S. Joshua Swamidass, Philip R. O. Payne, Laura K. Wiley, ClarLynda R. Williams-DeVane. 614-617 [doi]
- Integrating community-level data resources for precision medicine researchWilliam S. Bush, Dana C. Crawford, Farren Briggs, Darcy Freedman, Chantel Sloan. 618-622 [doi]
- Machine learning and deep analytics for biocomputing: Call for better explainabilityDragutin Petkovic, Lester Kobzik, Christopher RĂ©. 623-627 [doi]
- Methods for examining data quality in healthcare integrated data repositoriesVojtech Huser, Michael G. Kahn, Jeffrey S. Brown, Ramkiran Gouripeddi. 628-633 [doi]
- Erratum: Identifying mutation specific cancer pathways using a structurally resolved protein interaction networkBillur Engin, Matan Hofree, Hannah Carter. 634 [doi]