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ORCID23rd PSB 2018: The Big Island of Hawaii, Hawaii, USA
- Russ B. Altman, A. Keith Dunker, Lawrence Hunter, Marylyn D. Ritchie, Teri E. Klein:
Biocomputing 2018: Proceedings of the Pacific Symposium, The Big Island of Hawaii, Hawaii, USA, January 3-7, 2018. 2018
Applications of Genetics, Genomics and Bioinformatics in Drug Discovery
- Richard Bourgon, Frederick E. Dewey, Zhengyan Kan, Shuyu D. Li:
Session Introduction. 1-7 - Xintong Chen, Sander M. Houten, Kimaada Allette, Robert P. Sebra, Gustavo Stolovitzky, Bojan Losic:
Characterization of drug-induced splicing complexity in prostate cancer cell line using long read technology. 8-19 - Peyton Greenside, Maureen Hillenmeyer, Anshul Kundaje:
Prediction of protein-ligand interactions from paired protein sequence motifs and ligand substructures. 20-31 - 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 A. Sontag, Joel Dudley:
Cell-specific prediction and application of drug-induced gene expression . 32-43 - Yunan Luo, Sheng Wang, Jinfeng Xiao, Jian Peng:
Large-scale integration of heterogeneous pharmacogenomic data for identifying drug mechanism of action. 44-55 - Emily K. Mallory, Ambika Acharya, Stefano E. Rensi, Peter J Turnbaugh, Roselie A. Bright, Russ B. Altman:
Chemical reaction vector embeddings: towards predicting drug metabolism in the human gut microbiome. 56-67 - Milo R. Smith, Benjamin S. Glicksberg, Li Li, Rong Chen, Hirofumi Morishita, Joel T. Dudley:
Loss-of-function of neuroplasticity-related genes confers risk for human neurodevelopmental disorders. 68-79 - Gregory P. Way, Casey S. Greene:
Extracting a biologically relevant latent space from cancer transcriptomes with variational autoencoders. 80-91 - Jielin Xu, Kelly Regan-Fendt, Siyuan Deng, William E. Carson III, Philip R. O. Payne, Fuhai Li:
Diffusion mapping of drug targets on disease signaling network elements reveals drug combination strategies. 92-103
Challenges of Pattern Recognition in Biomedical Data
- Shefali Setia Verma, Anurag Verma, Anna Okula Basile, Marta Byrska-Bishop, Christian Darabos:
Session Introduction. 104-110 - Monica Agrawal, Marinka Zitnik, Jure Leskovec:
Large-scale analysis of disease pathways in the human interactome. 111-122 - Brett K. Beaulieu-Jones, Patryk Orzechowski, Jason H. Moore:
Mapping patient trajectories using longitudinal extraction and deep learning in the MIMIC-III Critical Care Database. 123-132 - Tiffany J. Callahan, William A. Baumgartner Jr., Michael Bada, Adrianne L. Stefanski, Ignacio Tripodi, Elizabeth K. White, Lawrence E. Hunter:
OWL-NETS: Transforming OWL representations for improved network inference. 133-144 - Benjamin S. Glicksberg, Riccardo Miotto, Kipp W. Johnson, Khader Shameer, Li Li, Rong Chen, Joel T. Dudley:
Automated disease cohort selection using word embeddings from Electronic Health Records. 145-156 - Lia X. Harrington, Gregory P. Way, Jennifer A. Doherty, Casey S. Greene:
Functional network community detection can disaggregate and filter multiple underlying pathways in enrichment analyses. 157-167 - Hyun-Hwan Jeong, Hari Krishna Yalamanchili, Caiwei Guo, Joshua M. Shulman, Zhandong Liu:
An ultra-fast and scalable quantification pipeline for transposable elements from next generation sequencing data. 168-179 - Kipp W. Johnson, Benjamin S. Glicksberg, Rachel Hodos, Khader Shameer, Joel T. Dudley:
Causal inference on electronic health records to assess blood pressure treatment targets: An application of the parametric g formula. 180-191 - Randal S. Olson, William G. La Cava, Zairah Mustahsan, Akshay Varik, Jason H. Moore:
Data-driven advice for applying machine learning to bioinformatics problems. 192-203 - Dragutin Petkovic, Russ B. Altman, Mike Wong, Arthur Vigil:
Improving the explainability of Random Forest classifier - user centered approach. 204-215 - Katherine Shoemaker, Brian P. Hobbs, Karthik Bharath, Chaan S. Ng, Veerabhadran Baladandayuthapani:
Tree-based methods for characterizing tumor density heterogeneity. 216-227 - Yogasudha Veturi, Marylyn D. Ritchie:
How powerful are summary-based methods for identifying expression-trait associations under different genetic architectures?. 228-239
Democratizing Health Data for Translational Research
- Philip R. O. Payne, Nigam H. Shah, Jessica D. Tenenbaum, Lara M. Mangravite:
Session introduction. 240-246 - Subha Madhavan, Deborah Ritter, Christine Micheel, Shruti Rao, Angshumoy Roy, Dmitriy Sonkin, Matthew McCoy, Malachi Griffith, Obi L. Griffith, Peter B. McGarvey, Shashikant Kulkarni:
ClinGen Cancer Somatic Working Group - Standardizing and democratizing access to cancer molecular diagnostic data to drive translational research. 247-258 - Jason H. Moore, Maksim Shestov, Peter Schmitt, Randal S. Olson:
A heuristic method for simulating open-data of arbitrary complexity that can be used to compare and evaluate machine learning methods. 259-267 - Vivekanand Sharma, Indra Neil Sarkar:
Identifying natural health product and dietary supplement information within adverse event reporting systems. 268-279 - Jessica D. Tenenbaum, Colette Blach:
Best practices and lessons learned from reuse of 4 patient-derived metabolomics datasets in Alzheimer's disease. 280-291 - John Darrell Van Horn, Lily Fierro, Jeana Kamdar, Jonathan Gordon, Crystal Stewart, Avnish Bhattrai, Sumiko Abe, Xiaoxiao Lei, Caroline O'Driscoll, Aakanchha Sinha, Priyambada Jain, Gully Burns, Kristina Lerman, José Luis Ambite:
Democratizing data science through data science training. 292-303
Imaging Genomics
- Heng Huang, Li Shen, Paul M. Thompson, Kun Huang, Junzhou Huang, Lin Yang:
Session introduction. 304-306 - Bhim 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:
Heritability estimates on resting state fMRI data using the ENIGMA analysis pipeline. 307-318 - Benjamin Chidester, Minh N. Do, Jian Ma:
Discriminative bag-of-cells for imaging-genomics. 319-330 - Lichy Han, Maulik R. Kamdar:
MRI to MGMT: Predicting methylation status in glioblastoma patients using convolutional recurrent neural networks. 331-342 - Chenglong Huang, Albert Zhang, Guanghua Xiao:
Deep integrative analysis for survival prediction. 343-352 - Zhouyuan Huo, Dinggang Shen, Heng Huang:
Genotype-Phenotype association study via new multi-task learning model. 353-364 - Jason E. Miller, Manu K. Shivakumar, Shannon L. Risacher, Andrew J. Saykin, SeungGeun Lee, Kwangsik Nho, Dokyoon Kim:
Codon bias among synonymous rare variants is associated with Alzheimer's disease imaging biomarker. 365-376 - Arunima Srivastava, Chaitanya Kulkarni, Parag Mallick, Kun Huang, Raghu Machiraju:
Building trans-omics evidence: using imaging and 'omics' to characterize cancer profiles. 377-388
Precision Medicine: From Diplotypes to Disparities Towards Improved Health and Therapies
- Dana C. Crawford, Alexander A. Morgan, Joshua C. Denny, Bruce J. Aronow, Steven E. Brenner:
Session Introduction. 389-399 - Joanne Berghout, Qike Li, Nima Pouladi, Jianrong Li, Yves A. Lussier:
Single subject transcriptome analysis to identify functionally signed gene set or pathway activity. 400-411 - Chih-Lin Chi, Lu He, Kourosh Ravvaz, John Weissert, Peter J. Tonellato:
Using simulation and optimization approach to improve outcome through warfarin precision treatment. 412-423 - Alexandra E. Fish, Dana C. Crawford, John A. Capra, William S. Bush:
Local ancestry transitions modify snp-trait associations. 424-435 - Anika Gupta, Min Woo Sun, Kelley M. Paskov, Nate Tyler Stockham, Jae-Yoon Jung, Dennis P. Wall:
Coalitional game theory as a promising approach to identify candidate autism genes. 436-447 - Binglan Li, Shefali S. Verma, Yogasudha Veturi, Anurag Verma, Yuki Bradford, David W. Haas, Marylyn D. Ritchie:
Evaluation of PrediXcan for prioritizing GWAS associations and predicting gene expression. 448-459 - Alena Orlenko, Jason H. Moore, Patryk Orzechowski, Randal S. Olson, Junmei Cairns, Pedro J. Caraballo, Richard M. Weinshilboum, Liewei Wang, Matthew K. Breitenstein:
Considerations for automated machine learning in clinical metabolic profiling: Altered homocysteine plasma concentration associated with metformin exposure. 460-471 - Sarah Poole, Nigam Shah:
Addressing vital sign alarm fatigue using personalized alarm thresholds. 472-483 - Samir Rachid Zaim, Qike Li, A. Grant Schissler, Yves A. Lussier:
Emergence of pathway-level composite biomarkers from converging gene set signals of heterogeneous transcriptomic responses. 484-495 - Jason Westra, Nicholas Hartman, Bethany Lake, Gregory Shearer, Nathan L. Tintle:
Analyzing metabolomics data for association with genotypes using two-component Gaussian mixture distributions. 496-506
Reading Between the Genes: Computational Models to Discover Function from Noncoding DNA
- Yves A. Lussier, Joanne Berghout, Francesca Vitali, Kenneth S. Ramos, Maricel G. Kann, Jason H. Moore:
Session Introduction. 507-511 - Travers Ching, Lana X. Garmire:
Pan-cancer analysis of expressed somatic nucleotide variants in long intergenic non-coding RNA. 512-523 - Jiali Han, Jianrong Li, Ikbel Achour, Lorenzo L. Pesce, Ian T. Foster, Haiquan Li, Yves A. Lussier:
Convergent downstream candidate mechanisms of independent intergenic polymorphisms between co-classified diseases implicate epistasis among noncoding elements. 524-535 - Travis S. Johnson, Sihong Li, Jonathan R. Kho, Kun Huang, Yan Zhang:
Network analysis of pseudogene-gene relationships: from pseudogene evolution to their functional potentials. 536-547 - Elisabetta Manduchi, Alessandra Chesi, Molly A. Hall, Struan F. A. Grant, Jason H. Moore:
Leveraging putative enhancer-promoter interactions to investigate two-way epistasis in Type 2 Diabetes GWAS. 548-558
Advances in Text Mining and Visualization for Precision Medicine
- Graciela Gonzalez-Hernandez, Abeed Sarker, Karen O'Connor, Casey S. Greene, Hongfang Liu:
Session Introduction. 559-565 - Mayla Boguslav, K. Bretonnel Cohen, William A. Baumgartner Jr., Lawrence E. Hunter:
Improving precision in concept normalization. 566-577 - Edward W. Huang, Sheng Wang, ChengXiang Zhai:
VisAGE: Integrating external knowledge into electronic medical record visualization. 578-589 - Paul Previde, Brook Thomas, Mike Wong, Emily K. Mallory, Dragutin Petkovic, Russ B. Altman, Anagha Kulkarni:
GeneDive: A gene interaction search and visualization tool to facilitate precision medicine. 590-601 - Sheng Wang, Jianzhu Ma, Michael Ku Yu, Fan Zheng, Edward W. Huang, Jiawei Han, Jian Peng, Trey Ideker:
Annotating gene sets by mining large literature collections with protein networks. 601-613
Workshops
- William M. Southerland, S. Joshua Swamidass, Philip R. O. Payne, Laura K. Wiley, ClarLynda R. Williams-DeVane:
The diversity and disparity in biomedical informatics (DDBI) workshop. 614-617 - William S. Bush, Dana C. Crawford, Farren Briggs, Darcy Freedman, Chantel Sloan:
Integrating community-level data resources for precision medicine research. 618-622 - Dragutin Petkovic, Lester Kobzik, Christopher Ré:
Machine learning and deep analytics for biocomputing: Call for better explainability. 623-627 - Vojtech Huser, Michael G. Kahn, Jeffrey S. Brown, Ramkiran Gouripeddi:
Methods for examining data quality in healthcare integrated data repositories. 628-633
Erratum
- Billur Engin, Matan Hofree, Hannah Carter:
Erratum: Identifying mutation specific cancer pathways using a structurally resolved protein interaction network. 634
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