Detecting Functional Modules from Protein Interaction Networks. - Feng Luo 001; Richard H. Scheuermann (IMSCCS (1), 2006)

Components of the antigen processing and presentation pathway revealed by gene expression microarray analysis following B cell antigen receptor (BCR) stimulation. - Jamie A. Lee; Robert S. Sinkovits; Dennis Mock; Eva L. Rab; Jennifer Cai; Peng Yang; Brian Saunders; Robert C. Hsueh; Sangdun Choi; Shankar Subramaniam; Richard H. Scheuermann (BMC Bioinform., 2006)

A distribution free summarization method for Affymetrix GeneChip® arrays. - Zhongxue Chen; Monnie McGee; Qingzhong Liu; Richard H. Scheuermann (Bioinform., 2007)

Ontology development for biological systems: immunology. - Alexander D. Diehl; Jamie A. Lee; Richard H. Scheuermann; Judith A. Blake (Bioinform., 2007)

Modular organization of protein interaction networks. - Feng Luo 001; Yunfeng Yang; Chin-Fu Chen; Roger L. Chang; Jizhong Zhou; Richard H. Scheuermann (Bioinform., 2007)

Exploring Core/Periphery Structures in Protein Interaction Networks Provides Structure-Property Relation Insights. - Thomas Grindinger; Feng Luo 001; Xiu-Feng Wan; Richard H. Scheuermann (BIBM, 2008)

BioHealthBase: informatics support in the elucidation of influenza virus host-pathogen interactions and virulence. - R. Burke Squires; Catherine Macken; Adolfo Garcia-Sastre; Shubhada Godbole; Jyothi Noronha; Victoria Hunt; Roger L. Chang; Christopher N. Larsen; Edward B. Klem; Kevin Biersack; Richard H. Scheuermann (Nucleic Acids Res., 2008)

Development and Evaluation of a Study Design Typology for Human Research. - Simona Carini; Brad Pollock; Harold P. Lehmann; Suzanne Bakken; Edward M. Barbour; Davera Gabriel; Herbert K. Hagler; Caryn R. Harper; Shamim Mollah; Meredith Nahm; Hien H. Nguyen; Richard H. Scheuermann; et al. (AMIA, 2009)

Core and periphery structures in protein interaction networks. - Feng Luo 001; Bo Li 036; Xiu-Feng Wan; Richard H. Scheuermann (BMC Bioinform., 2009)

An improved ontological representation of dendritic cells as a paradigm for all cell types. - Anna Maria Masci; Cecilia N. Arighi; Alexander D. Diehl; Anne E. Lieberman; Chris Mungall; Richard H. Scheuermann; Barry Smith 001; Lindsay G. Cowell (BMC Bioinform., 2009)

FuGEFlow: data model and markup language for flow cytometry. - Yu Qian; Olga Tchuvatkina; Josef Spidlen; Peter Wilkinson; Maura Gasparetto; Andrew R. Jones; Frank J. Manion; Richard H. Scheuermann; Rafick-Pierre Sekaly; Ryan Remy Brinkman (BMC Bioinform., 2009)

Sequence Feature Variant Type (SFVT) Analysis of the HLA Genetic Association in Juvenile Idiopathic Arthritis. - Glenys Thomson; Nishanth Marthandan; Jill A. Hollenbach; Steven J. Mack; Henry A. Erlich; Richard M. Single; Matthew J. Waller; Steven G. E. Marsh; Paula A. Guidry; David R. Karp; Richard H. Scheuermann; Susan D. Thompson; et al. (Pacific Symposium on Biocomputing, 2010)

GO-Bayes: Gene Ontology-based overrepresentation analysis using a Bayesian approach. - Song Zhang 001; Jing Cao; Y. Megan Kong; Richard H. Scheuermann (Bioinform., 2010)

Deterministic graph-theoretic algorithm for detecting modules in biological interaction networks. - Roger L. Chang; Feng Luo 001; Stuart Johnson; Richard H. Scheuermann (Int. J. Bioinform. Res. Appl., 2010)

Identifying Differentially Expressed Genes based on probe level data for GeneChip arrays. - Zhongxue Chen; Monnie McGee; Qingzhong Liu; Y. Megan Kong; Xudong Huang; Jack Y. Yang; Richard H. Scheuermann (Int. J. Comput. Biol. Drug Des., 2010)

Overcoming the ontology enrichment bottleneck with Quick Term Templates. - Philippe Rocca-Serra; Alan Ruttenberg; Martin J. O'Connor; Patricia L. Whetzel; Daniel Schober; Jay Greenbaum; Mélanie Courtot; Ryan Remy Brinkman; Susanna-Assunta Sansone; Richard H. Scheuermann; Bjoern Peters (Appl. Ontology, 2011)

Hematopoietic cell types: Prototype for a revised cell ontology. - Alexander D. Diehl; Alison Deckhut Augustine; Judith A. Blake; Lindsay G. Cowell; Elizabeth S. Gold; Timothy A. Gondré-Lewis; Anna Maria Masci; Terrence F. Meehan; Penelope A. Morel; Anastasia Nijnik; Bjoern Peters; Bali Pulendran; et al. (J. Biomed. Informatics, 2011)

Toward an ontology-based framework for clinical research databases. - Y. Megan Kong; Carl Dahlke; Qun Xiang; Yu Qian; David R. Karp; Richard H. Scheuermann (J. Biomed. Informatics, 2011)

Ontologies for clinical and translational research: Introduction. - Barry Smith 001; Richard H. Scheuermann (J. Biomed. Informatics, 2011)

A Machine Learning Approach for Identifying Anatomical Locations of Actionable Findings in Radiology Reports. - Kirk Roberts; Bryan Rink; Sanda M. Harabagiu; Richard H. Scheuermann; Seth M. Toomay; Travis Browning; Teresa Bosler; Ronald M. Peshock (AMIA, 2012)

ViPR: an open bioinformatics database and analysis resource for virology research. - Brett E. Pickett; Eva L. Sadat; Yun Zhang 021; Jyothi Noronha; R. Burke Squires; Victoria Hunt; Mengya Liu; Sanjeev Kumar; Sam Zaremba; Zhiping Gu; Liwei Zhou; Christopher N. Larsen; et al. (Nucleic Acids Res., 2012)

GenePattern Flow Cytometry Suite. - Josef Spidlen; Aaron Barsky; Karin Breuer; Peter Carr 004; Marc-Danie Nazaire; Barbara A. Hill; Yu Qian; Ted Liefeld; Michael Reich; Jill P. Mesirov; Peter Wilkinson; Richard H. Scheuermann; et al. (Source Code Biol. Medicine, 2013)

FlowGate: towards extensible and scalable web-based flow cytometry data analysis. - Yu Qian; Hyunsoo Kim; Shweta Purawat; Jianwu Wang 001; Rick Stanton; Alexandra Lee; Weijia Xu; Ilkay Altintas; Robert S. Sinkovits; Richard H. Scheuermann (XSEDE, 2015)

flowCL: ontology-based cell population labelling in flow cytometry. - Mélanie Courtot; Justin Meskas; Alexander D. Diehl; Radina Droumeva; Raphael Gottardo; Adrin Jalali; Mohammad Jafar Taghiyar; Holden T. Maecker; J. Philip McCoy; Alan Ruttenberg; Richard H. Scheuermann; Ryan Remy Brinkman (Bioinform., 2015)

VDJML: a file format with tools for capturing the results of inferring immune receptor rearrangements. - Inimary T. Toby; Mikhail K. Levin; Edward Salinas; Scott Christley; Sanchita Bhattacharya; Felix Breden; Adam Buntzman; Brian Corrie; John M. Fonner; Namita T. Gupta; Uri Hershberg; Nishanth Marthandan; et al. (BMC Bioinform., 2016)

Production of a Preliminary Quality Control Pipeline for Single Nuclei RNA-Seq and Its Application in the Analysis of Cell Type Diversity of Post-Mortem Human Brain Neocortex. - Brian D. Aevermann; Jamison M. McCorrison; Pratap Venepally; Rebecca D. Hodge; Trygve E. Bakken; Jeremy A. Miller; Mark Novotny; Danny N. Tran; Francisco Diez-Fuertes; Lena Christiansen; Fan Zhang; Frank Steemers; et al. (PSB, 2017)

Cell type discovery and representation in the era of high-content single cell phenotyping. - Trygve E. Bakken; Lindsay G. Cowell; Brian D. Aevermann; Mark Novotny; Rebecca D. Hodge; Jeremy A. Miller; Alexandra Lee; Ivan Chang; Jamison M. McCorrison; Bali Pulendran; Yu Qian; Nicholas J. Schork; et al. (BMC Bioinform., 2017)

VDJPipe: a pipelined tool for pre-processing immune repertoire sequencing data. - Scott Christley; Mikhail K. Levin; Inimary T. Toby; John M. Fonner; Nancy Monson; William Rounds; Florian Rubelt; Walter Scarborough; Richard H. Scheuermann; Lindsay G. Cowell (BMC Bioinform., 2017)

Influenza Research Database: An integrated bioinformatics resource for influenza virus research. - Yun Zhang 021; Brian D. Aevermann; Tavis K. Anderson; David F. Burke; Gwenaelle Dauphin; Zhiping Gu; Sherry He; Sanjeev Kumar; Christopher N. Larsen; Alexandra J. Lee; Xiaomei Li; Catherine Macken; et al. (Nucleic Acids Res., 2017)

Bayesian Trees for Automated Cytometry Data Analysis. - Disi Ji; Eric T. Nalisnick; Yu Qian; Richard H. Scheuermann; Padhraic Smyth (MLHC, 2018)

Abstract: Explainable artificial intelligence and single cell genomics to understand the cellular complexity of human brain. - Richard H. Scheuermann (BIBM, 2021)

Standardization of assay representation in the Ontology for Biomedical Investigations. - Randi Vita; Jie Zheng 001; Rebecca C. Jackson; Damion M. Dooley; James A. Overton; Mark A. Miller; Daniel C. Berrios; Richard H. Scheuermann; Yongqun He; Hande Küçük-McGinty; Mathias Brochhausen; Aisyah Yu Lin; et al. (Database J. Biol. Databases Curation, 2021)

FR-Match: robust matching of cell type clusters from single cell RNA sequencing data using the Friedman-Rafsky non-parametric test. - Yun Zhang 021; Brian D. Aevermann; Trygve E. Bakken; Jeremy A. Miller; Rebecca D. Hodge; Ed S. Lein; Richard H. Scheuermann (Briefings Bioinform., 2021)

Early detection of emerging SARS-CoV-2 variants of interest for experimental evaluation. - Zachary S. Wallace; James J. Davis 002; Anna Maria Niewiadomska; Robert D. Olson; Maulik Shukla; Rick Stevens; Yun Zhang 021; Christian M. Zmasek; Richard H. Scheuermann (Frontiers Bioinform., 2022)

FastMix: a versatile data integration pipeline for cell type-specific biomarker inference. - Yun Zhang 021; Hao Sun; Aishwarya Mandava; Brian D. Aevermann; Tobias R. Kollmann; Richard H. Scheuermann; Xing Qiu; Yu Qian (Bioinform., 2022)

Introducing the Bacterial and Viral Bioinformatics Resource Center (BV-BRC): a resource combining PATRIC, IRD and ViPR. - Robert D. Olson; Rida Assaf; Thomas S. Brettin; Neal Conrad; Clark Cucinell; James J. Davis 002; Donald M. Dempsey; Allan Dickerman; Emily M. Dietrich; Ronald W. Kenyon; Mehmet Kuscuoglu; Elliot J. Lefkowitz; et al. (Nucleic Acids Res., 2023)

A cell-level discriminative neural network model for diagnosis of blood cancers. - Edgar E. Robles; Ye Jin; Padhraic Smyth; Richard H. Scheuermann; Jack D. Bui; Huan-You Wang; Jean Oak; Yu Qian (Bioinform., 2023)

The Cell Ontology in the age of single-cell omics. - Shawn Zheng Kai Tan; Aleix Puig-Barbe; Damien Goutte-Gattat; Caroline Eastwood; Brian D. Aevermann; Alida Avola; James P. Balhoff; Ismail Ugur Bayindir; Jasmine Belfiore; Anita R. Caron; David S. Fischer; Nancy George; et al. (CoRR, 2025)