cis-Regulatory Element Prediction in Mammalian Genomes. - Asim S. Siddiqui; Gordon Robertson; Misha Bilenky; Tamara Astakhova; Obi L. Griffith; Maik Hassel; Keven Lin; Stephen B. Montgomery; Mehrdad Oveisi; Erin Pleasance; Neil Robertson 004; Monica C. Sleumer; et al. (CSB Workshops, 2005)

Discovering significant OPSM subspace clusters in massive gene expression data. - Byron J. Gao; Obi L. Griffith; Martin Ester; Steven J. M. Jones (KDD, 2006)

ORegAnno: an open access database and curation system for literature-derived promoters, transcription factor binding sites and regulatory variation. - Stephen B. Montgomery; Obi L. Griffith; Monica C. Sleumer; Casey M. Bergman; Misha Bilenky; Erin Pleasance; Y. Prychyna; X. Zhang; Steven J. M. Jones (Bioinform., 2006)

cisRED: a database system for genome-scale computational discovery of regulatory elements. - Gordon Robertson; Misha Bilenky; Keven Lin; An He; W. Yuen; M. Dagpinar; Richard Varhol; Kevin Teague; Obi L. Griffith; X. Zhang; Y. Pan; Maik Hassel; et al. (Nucleic Acids Res., 2006)

A Survey of Genomic Properties for the Detection of Regulatory Polymorphisms. - Stephen B. Montgomery; Obi L. Griffith; Johanna M. Schuetz; Angela Brooks-Wilson; Steven J. M. Jones (PLoS Comput. Biol., 2007)

ORegAnno: an open-access community-driven resource for regulatory annotation. - Obi L. Griffith; Stephen B. Montgomery; Bridget Bernier; Bryan Chu; Katayoon Kasaian; Stein Aerts; Shaun Mahony; Monica C. Sleumer; Mikhail Bilenky; Maximilian Haeussler; Malachi Griffith; Steven M. Gallo; et al. (Nucleic Acids Res., 2008)

KiWi: A Scalable Subspace Clustering Algorithm for Gene Expression Analysis - Obi L. Griffith; Byron J. Gao; Mikhail Bilenky; Yuliya Prichyna; Martin Ester; Steven J. M. Jones (CoRR, 2009)

Genomic analysis of a rare human tumor. - Steven J. M. Jones; Janessa Laskin; Yvonne Y. Li; Obi L. Griffith; Jianghong An; Mikhail Bilenky; Yaron S. N. Butterfield; Timothee Cezard; Eric Chuah; Richard Corbett; Anthony P. Fejes; Malachi Griffith; et al. (BMC Bioinform., 2010)

On the Deep Order-Preserving Submatrix Problem: A Best Effort Approach. - Byron J. Gao; Obi L. Griffith; Martin Ester; Hui Xiong 001; Qiang Zhao; Steven J. M. Jones (IEEE Trans. Knowl. Data Eng., 2012)

SciClone: Inferring Clonal Architecture and Tracking the Spatial and Temporal Patterns of Tumor Evolution. - Christopher A. Miller 002; Brian S. White; Nathan D. Dees; Malachi Griffith; John S. Welch; Obi L. Griffith; Ravi Vij; Michael H. Tomasson; Timothy A. Graubert; Matthew J. Walter; Matthew J. Ellis; William S. Schierding; et al. (PLoS Comput. Biol., 2014)

Statistically identifying tumor suppressors and oncogenes from pan-cancer genome-sequencing data. - Runjun D. Kumar; Adam C. Searleman; S. Joshua Swamidass; Obi L. Griffith; Ron Bose (Bioinform., 2015)

Genome Modeling System: A Knowledge Management Platform for Genomics. - Malachi Griffith; Obi L. Griffith; Scott M. Smith; Avinash Ramu; Matthew B. Callaway; Anthony M. Brummett; Michael J. Kiwala; Adam C. Coffman; Allison A. Regier; Benjamin J. Oberkfell; Gabriel E. Sanderson; Thomas P. Mooney; et al. (PLoS Comput. Biol., 2015)

Informatics for RNA Sequencing: A Web Resource for Analysis on the Cloud. - Malachi Griffith; Jason R. Walker; Nicholas C. Spies; Benjamin J. Ainscough; Obi L. Griffith (PLoS Comput. Biol., 2015)

GenVisR: Genomic Visualizations in R. - Zachary L. Skidmore; Alex H. Wagner; Robert Lesurf; Katie M. Campbell; Jason Kunisaki; Obi L. Griffith; Malachi Griffith (Bioinform., 2016)

ORegAnno 3.0: a community-driven resource for curated regulatory annotation. - Robert Lesurf; Kelsy C. Cotto; Grace Wang; Malachi Griffith; Katayoon Kasaian; Steven J. M. Jones; Stephen B. Montgomery; Obi L. Griffith (Nucleic Acids Res., 2016)

DGIdb 2.0: mining clinically relevant drug-gene interactions. - Alex H. Wagner; Adam C. Coffman; Benjamin J. Ainscough; Nicholas C. Spies; Zachary L. Skidmore; Katie M. Campbell; Kilannin Krysiak; Deng Pan; Joshua F. McMichael; James M. Eldred; Jason R. Walker; Richard K. Wilson; et al. (Nucleic Acids Res., 2016)

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 B. McGarvey; Shashikant Kulkarni (PSB, 2018)

Integration of the Drug-Gene Interaction Database (DGIdb 4.0) with open crowdsource efforts. - Sharon L. Freshour; Susanna Kiwala; Kelsy C. Cotto; Adam C. Coffman; Joshua F. McMichael; Jonathan J. Song; Malachi Griffith; Obi L. Griffith; Alex H. Wagner (Nucleic Acids Res., 2021)

Bam-readcount - rapid generation of basepair-resolution sequence metrics. - Ajay Khanna; David E. Larson; Srivatsan Sridhar; Matthew Mosior; Travis E. Abbott; Susanna Kiwala; Timothy J. Ley; Eric J. Duncavage; Matthew J. Walter; Jason R. Walker; Obi L. Griffith; Malachi Griffith; et al. (J. Open Source Softw., 2022)

CIViCdb 2022: evolution of an open-access cancer variant interpretation knowledgebase. - Kilannin Krysiak; Arpad M. Danos; Jason Saliba; Joshua F. McMichael; Adam C. Coffman; Susanna Kiwala; Erica K. Barnell; Lana Sheta; Cameron J. Grisdale; Lynzey Kujan; Shahil Pema; Jake Lever; et al. (Nucleic Acids Res., 2023)

GAiN: An integrative tool utilizing generative adversarial neural networks for augmented gene expression analysis. - Michael R. Waters; Matthew Inkman; Kay Jayachandran; Roman M. Kowalchuk; Clifford Robinson; Julie K. Schwarz; S. Joshua Swamidass; Obi L. Griffith; Jeffrey J. Szymanski; Jin Zhang 038 (Patterns, 2024)

CeRTS: certainty retrieval token search in large language model clinical information extraction. - Lars E. Schimmelpfennig; Kriti Bhattarai; Inez Y. Oh; Jake Lever; Obi L. Griffith; Malachi Griffith; Albert M. Lai; Zachary B. Abrams (J. Biomed. Informatics, 2025)