Graphically-enabled integration of bioinformatics tools allowing parallel execution. - Kei-Hoi Cheung; Perry L. Miller; A. H. Sherman; Stephen B. Weston; Eric Stratmann; Martin H. Schultz; Michael Snyder 001; Anuj Kumar (AMIA, 2000)

TRIPLES: a database of gene function in Saccharomyces cerevisiae. - Anuj Kumar; Kei-Hoi Cheung; Petra Ross-MacDonald; Paulo S. R. Coelho; Perry L. Miller; Michael Snyder 001 (Nucleic Acids Res., 2000)

A metadata framework for interoperating heterogeneous genome data using XML. - Kei-Hoi Cheung; Aniruddha M. Deshpande; Nick P. Tosches; S. Nath; A. Agrawal; Perry L. Miller; Anuj Kumar; Michael Snyder 001 (AMIA, 2001)

An XML Application For Genomic Data Interoperation. - Kei-Hoi Cheung; Yang Liu 023; Anuj Kumar; Michael Snyder 001; Mark Gerstein; Perry L. Miller (BIBE, 2001)

YMD: a microarray database for large-scale gene expression analysis. - Kei-Hoi Cheung; Kevin P. White; Janet Hager; Mark Gerstein; Valerie Reinke; Kenneth Nelson; Peter Masiar; Ranjana Srivastava; Yuli Li; Ju Li; Hongyu Zhao 003; Jinming Li; et al. (AMIA, 2002)

A dynamic approach to mapping coordinates between microplates and microarrays. - Kei-Hoi Cheung; Janet Hager; Kenneth Nelson; Kevin P. White; Yuli Li; Michael Snyder 001; Kenneth R. Williams; Perry L. Miller (J. Biomed. Informatics, 2002)

The TRIPLES database: a community resource for yeast molecular biology. - Anuj Kumar; Kei-Hoi Cheung; Nick P. Tosches; Peter Masiar; Yang Liu 023; Perry L. Miller; Michael Snyder 001 (Nucleic Acids Res., 2002)

ExpressYourself: a modular platform for processing and visualizing microarray data - Nicholas M. Luscombe; Thomas E. Royce; Paul Bertone; Nathaniel Echols; Christine E. Horak; Joseph T. Chang; Michael Snyder 001; Mark Gerstein (Nucleic Acids Res., 2003)

Fast Optimal Genome Tiling with Applications to Microarray Design and Homology Search. - Piotr Berman; Paul Bertone; Bhaskar DasGupta; Mark Gerstein; Ming-Yang Kao; Michael Snyder 001 (J. Comput. Biol., 2004)

Analysis of Genomic Tiling Microarrays for Transcript Mapping and the Identification of Transcription Factor Binding Sites. - Joel S. Rozowsky; Paul Bertone; Thomas E. Royce; Sherman Weissman; Michael Snyder 001; Mark Gerstein (BSB, 2005)

Design Issues in Implementing a Portable Sample Tracking and Analysis Research Support (STARS) System for PCR Based Microarray Research. - Frederick G. Sayward; Jin Yang; Kenneth Nelson; Ghia Euskirchen; Alexander E. Urban; Paul Bertone; John Rinn; Sherman Weissman; Mark Gerstein; Michael Snyder 001; Perry L. Miller (CISS, 2006)

A supervised hidden markov model framework for efficiently segmenting tiling array data in transcriptional and chIP-chip experiments: systematically incorporating validated biological knowledge. - Jiang Du 003; Joel S. Rozowsky; Jan O. Korbel; Zhengdong D. Zhang; Thomas E. Royce; Martin H. Schultz; Michael Snyder 001; Mark Gerstein (Bioinform., 2006)

Modeling ChIP Sequencing In Silico with Applications. - Zhengdong D. Zhang; Joel S. Rozowsky; Michael Snyder 001; Joseph T. Chang; Mark Gerstein (PLoS Comput. Biol., 2008)

Integrating Sequencing Technologies in Personal Genomics: Optimal Low Cost Reconstruction of Structural Variants. - Jiang Du 003; Robert D. Bjornson; Zhengdong D. Zhang; Yong Kong; Michael Snyder 001; Mark B. Gerstein (PLoS Comput. Biol., 2009)

MOTIPS: Automated Motif Analysis for Predicting Targets of Modular Protein Domains. - Hugo Y. K. Lam; Philip M. Kim; Janine Mok; Raffi Tonikian; Sachdev S. Sidhu; Benjamin E. Turk; Michael Snyder 001; Mark B. Gerstein (BMC Bioinform., 2010)

RSEQtools: a modular framework to analyze RNA-Seq data using compact, anonymized data summaries. - Lukas Habegger; Andrea Sboner; Tara A. Gianoulis; Joel S. Rozowsky; Ashish Agarwal; Michael Snyder 001; Mark Gerstein (Bioinform., 2011)

Construction and Analysis of an Integrated Regulatory Network Derived from High-Throughput Sequencing Data. - Chao Cheng; Koon-Kiu Yan; Woochang Hwang; Jiang Qian; Nitin Bhardwaj; Joel S. Rozowsky; Zhi John Lu; Wei Niu; Pedro Alves; Masaomi Kato; Michael Snyder 001; Mark Gerstein (PLoS Comput. Biol., 2011)

Measuring the Evolutionary Rewiring of Biological Networks. - Chong Shou; Nitin Bhardwaj; Hugo Y. K. Lam; Koon-Kiu Yan; Philip M. Kim; Michael Snyder 001; Mark B. Gerstein (PLoS Comput. Biol., 2011)

Interpretome: A Freely Available, Modular, and Secure Personal Genome Interpretation Engine. - Konrad J. Karczewski; Robert P. Tirrell; Pablo Cordero; Nicholas P. Tatonetti; Joel T. Dudley; Keyan Salari; Michael Snyder 001; Russ B. Altman; Stuart K. Kim (Pacific Symposium on Biocomputing, 2012)

VAT: a computational framework to functionally annotate variants in personal genomes within a cloud-computing environment. - Lukas Habegger; Suganthi Balasubramanian; David Z. Chen; Ekta Khurana; Andrea Sboner; Arif Ozgun Harmanci; Joel S. Rozowsky; Declan Clarke; Michael Snyder 001; Mark Gerstein (Bioinform., 2012)

Copy Number Variation detection from 1000 Genomes project exon capture sequencing data. - Jiantao Wu; Krzysztof R. Grzeda; Chip Stewart; Fabian Grubert; Alexander E. Urban; Michael P. Snyder; Gabor T. Marth (BMC Bioinform., 2012)

Toward More Transparent and Reproducible Omics Studies Through a Common Metadata Checklist and Data Publications. - Eugene Kolker; Vural Özdemir; Lennart Martens; William Hancock; Gordon A. Anderson; Nathaniel Anderson; Sukru Aynacioglu; Ancha V. Baranova; Shawn R. Campagna; Rui Chen; John Choiniere; Stephen P. Dearth; et al. (Big Data, 2013)

Metadata Checklist for the Integrated Personal Omics Study: Proteomics and Metabolomics Experiments. - Michael Snyder 001; George Mias; Larissa Stanberry; Eugene Kolker (Big Data, 2013)

Personal genomes, quantitative dynamic omics and personalized medicine. - George Mias; Michael Snyder 001 (Quant. Biol., 2013)

Clustering reveals ubiquitous heterogeneity and asymmetry of genomic signals at functional elements. - Anshul Kundaje; Sofia Kyriazopoulou-Panagiotopoulou; Max W. Libbrecht; Cheryl L. Smith; Debasish Raha; Elliott E. Winters; Steven M. Johnson; Michael P. Snyder; Serafim Batzoglou; Arend Sidow (Adv. Math. Commun., 2013)

PATH-SCAN: A Reporting Tool for Identifying Clinically Actionable Variants. - Roxana Daneshjou; Zachary Zappala; Kimberly R. Kukurba; Sean M. Boyle; Kelly E. Ormond; Teri E. Klein; Michael Snyder 001; Carlos D. Bustamante; Russ B. Altman; Stephen B. Montgomery (Pacific Symposium on Biocomputing, 2014)

Sushi.R: flexible, quantitative and integrative genomic visualizations for publication-quality multi-panel figures. - Douglas H. Phanstiel; Alan P. Boyle; Carlos L. Araya; Michael P. Snyder (Bioinform., 2014)

Comparative analysis of regulatory information and circuits across distant species Open. - Alan P. Boyle; Carlos L. Araya; Cathleen Brdlik; Philip Cayting; Chao Cheng; Yong Cheng; Kathryn Gardner; LaDeana W. Hillier; Judith Janette; Lixia Jiang; Dionna Kasper; Trupti Kawli; et al. (Nat., 2014)

Topologically associating domains are stable units of replication-timing regulation Open. - Benjamin D. Pope; Tyrone Ryba; Vishnu Dileep; Feng Yue; Wei-Sheng Wu; Olgert Denas; Daniel L. Vera; Yanli Wang; R. Scott Hansen; Theresa K. Canfield; Robert E. Thurman; Yong Cheng; et al. (Nat., 2014)

Mango: a bias-correcting ChIA-PET analysis pipeline. - Douglas H. Phanstiel; Alan P. Boyle; Nastaran Heidari; Michael P. Snyder (Bioinform., 2015)

Invited Talks at the AAAI Symposium on Well-Being Computing. - Rafael A. Calvo; Nick Haber; Catalin Voss; Michael Nova; Dennis Salins; Michael Snyder 001; Dennis P. Wall (AAAI Spring Symposia, 2016)

Genome assembly from synthetic long read clouds. - Volodymyr Kuleshov; Michael P. Snyder; Serafim Batzoglou (Bioinform., 2016)

Systematic evaluation of the impact of ChIP-seq read designs on genome coverage, peak identification, and allele-specific binding detection. - Qi Zhang; Xin Zeng; Samuel G. Younkin; Trupti Kawli; Michael P. Snyder; Sündüz Keles (BMC Bioinform., 2016)

Predicting Non-Small Cell Lung Cancer Diagnosis and Prognosis by Fully Automated Microscopic Pathology Image Features. - Kun-Hsing Yu; Ce Zhang 001; Gerald J. Berry; Russ B. Altman; Christopher Ré; Daniel L. Rubin; Michael Snyder 001 (AMIA, 2017)

Consumer Wearable Devices for Health Surveillance and Disease Monitoring. - Jessilyn Dunn; Xiao Li; Denis Salins; Michael Snyder 001 (CRI, 2017)

Harnessing Big Data for Precision Medicine: Infrastructures and Applications. - Kun-Hsing Yu; Steven N. Hart; Rachel L. Goldfeder; Qiangfeng Cliff Zhang; Stephen C. J. Parker; Michael Snyder 001 (PSB, 2017)

GATTACA: Lightweight Metagenomic Binning Using Kmer Counting. - Victoria Popic; Volodymyr Kuleshov; Michael P. Snyder; Serafim Batzoglou (RECOMB, 2017)

Cloud-based interactive analytics for terabytes of genomic variants data. - Cuiping Pan; Gregory McInnes; Nicole Deflaux; Michael Snyder 001; Jonathan Bingham; Somalee Datta; Philip S. Tsao (Bioinform., 2017)

Unraveling the Molecular Basis of Lung Adenocarcinoma Dedifferentiation and Prognosis by Integrating Omics and Histopathology. - Kun-Hsing Yu; Gerald J. Berry; Daniel L. Rubin; Christopher Ré; Russ B. Altman; Michael Snyder 001 (AMIA, 2018)

Omics AnalySIs System for PRecision Oncology (OASISPRO): a web-based omics analysis tool for clinical phenotype prediction. - Kun-Hsing Yu; Michael R. Fitzpatrick; Luke Pappas; Warren Chan; Jessica Kung; Michael Snyder 001 (Bioinform., 2018)

Fast Metagenomic Binning via Hashing and Bayesian Clustering. - Victoria Popic; Volodymyr Kuleshov; Michael P. Snyder; Serafim Batzoglou (J. Comput. Biol., 2018)

Classifying Non-Small Cell Lung Cancer Histopathology Types and Transcriptomic Subtypes using Convolutional Neural Networks. - Kun-Hsing Yu; Feiran Wang; Gerald J. Berry; Christopher Ré; Russ B. Altman; Michael Snyder 001; Isaac S. Kohane (AMIA, 2019)

Multiomics modeling of the immunome, transcriptome, microbiome, proteome and metabolome adaptations during human pregnancy. - Mohammad Sajjad Ghaemi; Daniel B. DiGiulio; Kévin Contrepois; Benjamin J. Callahan; Thuy T. M. Ngo; Brittany Lee-McMullen; Benoit Lehallier; Anna Robaczewska; David Mcilwain; Yael Rosenberg-Hasson; Ronald J. Wong; Cecele Quaintance; et al. (Bioinform., 2019)

The human body at cellular resolution: the NIH Human Biomolecular Atlas Program. - Michael P. Snyder; Shin Lin; Amanda Posgai; Mark Atkinson; Aviv Regev; Jennifer Rood; Orit Rozenblatt-Rosen; Leslie Gaffney; Anna Hupalowska; Rahul Satija; Nils Gehlenborg; Jay Shendure; et al. (Nat., 2019)

Active Learning Pipeline for Brain Mapping in a High Performance Computing Environment. - Adam Michaleas; Lars Gjesteby; Michael P. Snyder; David Chavez; Meagan Ash; Matthew A. Melton; Damon G. Lamb; Sara N. Burke; Kevin J. Otto; Lee Kamentsky; Webster Guan; Kwanghun Chung; et al. (HPEC, 2020)

Classifying non-small cell lung cancer types and transcriptomic subtypes using convolutional neural networks. - Kun-Hsing Yu; Feiran Wang; Gerald J. Berry; Christopher Ré; Russ B. Altman; Michael Snyder 001; Isaac S. Kohane (J. Am. Medical Informatics Assoc., 2020)

Learning Personal Food Preferences via Food Logs Embedding. - Ahmed A. Metwally; Ariel K. Leong; Aman Desai; Anvith Nagarjuna; Dalia Perelman; Michael Snyder 001 (BIBM, 2021)

Predictive Signatures for Lung Adenocarcinoma Prognostic Trajectory by Multiomics Data Integration and Ensemble Learning. - Hayan Lee; Gilbert Feng; Ed Esplin; Michael P. Snyder (ISMCO, 2021)

Heart Rate and CGM Feature Representation Diabetes Detection From Heart Rate: Learning Joint Features of Heart Rate and Continuous Glucose Monitors Yields Better Representations. - Hootan Rashtian; Solmaz Shariat Torbaghan; Salar Rahili; Michael P. Snyder; Nima Aghaeepour (IEEE Access, 2021)

Hummingbird: efficient performance prediction for executing genomic applications in the cloud. - Amir Bahmani; Ziye Xing; Vandhana Krishnan; Utsab Ray; Frank Mueller 001; Amir Alavi; Philip S. Tsao; Michael P. Snyder; Cuiping Pan (Bioinform., 2021)

RobNorm: model-based robust normalization method for labeled quantitative mass spectrometry proteomics data. - Meng Wang 007; Lihua Jiang; Ruiqi Jian; Joanne Y. Chan; Qing Liu; Michael Snyder 001; Hua Tang (Bioinform., 2021)

AdaTiSS: a novel data-Adaptive robust method for identifying Tissue Specificity Scores. - Meng Wang 007; Lihua Jiang; Michael P. Snyder (Bioinform., 2021)

Benchmarking workflows to assess performance and suitability of germline variant calling pipelines in clinical diagnostic assays. - Vandhana Krishnan; Sowmithri Utiramerur; Zena Ng; Somalee Datta; Michael Snyder 001; Euan A. Ashley (BMC Bioinform., 2021)

Beyond Low Earth Orbit: Biomonitoring, Artificial Intelligence, and Precision Space Health. - Ryan T. Scott; Erik L. Antonsen; Lauren M. Sanders; Jaden J. A. Hastings; Seung-Min Park; Graham Mackintosh; Robert J. Reynolds; Adrienne L. Hoarfrost; Aenor Sawyer; Casey S. Greene; Benjamin S. Glicksberg; Corey A. Theriot; et al. (CoRR, 2021)

Beyond Low Earth Orbit: Biological Research, Artificial Intelligence, and Self-Driving Labs. - Lauren M. Sanders; Jason H. Yang; Ryan T. Scott; Amina Ann Qutub; Héctor García Martín; Daniel C. Berrios; Jaden J. A. Hastings; Jon Rask; Graham Mackintosh; Adrienne L. Hoarfrost; Stuart J. Chalk; John Kalantari; et al. (CoRR, 2021)

iNetModels 2.0: an interactive visualization and database of multi-omics data. - Muhammad Arif 007; Cheng Zhang 002; Xiangyu Li; Cem Güngör; Bugra Çakmak; Metin Arslantürk; Abdellah Tebani; Berkay Özcan; Oguzhan Subas; Wenyu Zhou; Brian Piening; Hasan Turkez; et al. (Nucleic Acids Res., 2021)

Swarm: A federated cloud framework for large-scale variant analysis. - Amir Bahmani; Kyle Ferriter; Vandhana Krishnan; Arash Alavi 003; Amir Alavi; Philip S. Tsao; Michael P. Snyder; Cuiping Pan (PLoS Comput. Biol., 2021)

Axon Tracing and Centerline Detection using Topologically-Aware 3D U-Nets. - Dylan Pollack; Lars A. Gjesteby; Michael Snyder 001; David Chavez; Lee Kamentsky; Kwanghun Chung; Laura J. Brattain (EMBC, 2022)

Deep learning-based pseudo-mass spectrometry imaging analysis for precision medicine. - Xiaotao Shen; Wei Shao 008; Chuchu Wang; Liang Liang; Songjie Chen; Sai Zhang; Mirabela Rusu; Michael P. Snyder (Briefings Bioinform., 2022)

Robust identification of temporal biomarkers in longitudinal omics studies. - Ahmed A. Metwally; Tom Zhang; Si Wu; Ryan Kellogg; Wenyu Zhou; Kévin Contrepois; Hua Tang; Michael Snyder 001 (Bioinform., 2022)

metID: an R package for automatable compound annotation for LC-MS-based data. - Xiaotao Shen; Si Wu; Liang Liang; Songjie Chen; Kévin Contrepois; Zheng-Jiang Zhu; Michael P. Snyder (Bioinform., 2022)

massDatabase: utilities for the operation of the public compound and pathway database. - Xiaotao Shen; Chuchu Wang; Michael P. Snyder (Bioinform., 2022)

A method for intelligent allocation of diagnostic testing by leveraging data from commercial wearable devices: a case study on COVID-19. - Md Mobashir Hasan Shandhi; Peter J. Cho; Ali R. Roghanizad; Karnika Singh; Will Ke Wang; Oana M. Enache; Amanda Stern; Rami Sbahi; Bilge Tatar; Sean Fiscus; Qi Xuan Khoo; Yvonne Kuo; et al. (npj Digit. Medicine, 2022)

Early prediction and longitudinal modeling of preeclampsia from multiomics. - Ivana Maric; Kévin Contrepois; Mira N. Moufarrej; Ina A. Stelzer; Dorien Feyaerts; Xiaoyuan Han; Andy Tang; Natalie Stanley; Ronald J. Wong; Gavin M. Traber; Mathew Ellenberger; Alan L. Chang; et al. (Patterns, 2022)

CliniDigest: A Case Study in Large Language Model Based Large-Scale Summarization of Clinical Trial Descriptions. - Renee D. White; Tristan Peng; Pann Sripitak; Alexander Rosenberg Johansen; Michael Snyder 001 (GoodIT, 2023)

Self-Supervised Learning to Improve Topology-Optimized Axon Segmentation and Centerline Detection. - Nina I. Shamsi; Lars A. Gjesteby; David Chavez; Michael Snyder 001; Brian S. Eastwood; Matthew G. Fay; Nathan J. O'Connor; Jack R. Glaser; Charles R. Gerfen; Laura J. Brattain (ISBI, 2023)

Semi-supervised Cooperative Learning for Multiomics Data Fusion. - Daisy Yi Ding; Xiaotao Shen; Michael Snyder 001; Robert Tibshirani (ML4MHD, 2023)

Digital health application integrating wearable data and behavioral patterns improves metabolic health. - Ashkan Dehghani Zahedani; Arvind Veluvali; Tracey McLaughlin; Nima Aghaeepour; Amir Hosseinian; Saransh Agarwal; Jingyi Ruan; Shital Tripathi; Mark Woodward; Noosheen Hashemi; Michael Snyder 001 (npj Digit. Medicine, 2023)

Biological research and self-driving labs in deep space supported by artificial intelligence. - Lauren M. Sanders; Ryan T. Scott; Jason H. Yang; Amina Ann Qutub; Héctor García Martín; Daniel C. Berrios; Jaden J. A. Hastings; Jon Rask; Graham Mackintosh; Adrienne L. Hoarfrost; Stuart J. Chalk; John Kalantari; et al. (Nat. Mac. Intell., 2023)

Biomonitoring and precision health in deep space supported by artificial intelligence. - Ryan T. Scott; Lauren M. Sanders; Erik L. Antonsen; Jaden J. A. Hastings; Seung-Min Park; Graham Mackintosh; Robert J. Reynolds; Adrienne L. Hoarfrost; Aenor Sawyer; Casey S. Greene; Benjamin S. Glicksberg; Corey A. Theriot; et al. (Nat. Mac. Intell., 2023)

PRS-Net: Interpretable Polygenic Risk Scores via Geometric Learning. - Han Li 018; Jianyang Zeng 001; Michael P. Snyder; Sai Zhang (RECOMB, 2024)

Longitudinal urine metabolic profiling and gestational age prediction in human pregnancy. - Xiaotao Shen; Songjie Chen; Liang Liang; Monika Avina; Hanyah Zackriah; Laura Jelliffe-Pawlowski; Larry Rand; Michael P. Snyder (Briefings Bioinform., 2024)

Correction: Digital health application integrating wearable data and behavioral patterns improves metabolic health. - Ashkan Dehghani Zahedani; Tracey McLaughlin; Arvind Veluvali; Nima Aghaeepour; Amir Hosseinian; Saransh Agarwal; Jingyi Ruan; Shital Tripathi; Mark Woodward; Noosheen Hashemi; Michael Snyder 001 (npj Digit. Medicine, 2024)

High-resolution lifestyle profiling and metabolic subphenotypes of type 2 diabetes. - Heyjun Park; Ahmed A. Metwally; Alireza Delfarah; Yue Wu; Dalia Perelman; Caleb Mayer; Curtis McGinity; Majid Rodgar; Alessandra Celli; Tracey McLaughlin; Emmanuel Mignot; Michael Snyder 001 (npj Digit. Medicine, 2025)

Impact of digital health interventions on glycemic control and weight management. - Arvind Veluvali; Ashkan Dehghani Zahedani; Amir Hosseinian; Nima Aghaeepour; Tracey McLaughlin; Mark Woodward; Alex Ditullio; Noosheen Hashemi; Michael P. Snyder (npj Digit. Medicine, 2025)

A statistical framework for multi-trait rare variant analysis in large-scale whole-genome sequencing studies. - Xihao Li; Han Chen; Margaret Sunitha Selvaraj; Eric Van Buren; Hufeng Zhou; Yuxuan Wang 008; Ryan Sun; Zachary R. McCaw; Zhi Yu; Min-Zhi Jiang; Daniel DiCorpo; Sheila M. Gaynor; et al. (Nat. Comput. Sci., 2025)