SoDA: implementation of a 3D alignment algorithm for inference of antigen receptor recombinations. - Joseph M. Volpe; Lindsay G. Cowell; Thomas B. Kepler (Bioinform., 2006)

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)

Dispositions and the Infectious Disease Ontology. - Albert Goldfain; Barry Smith 001; Lindsay G. Cowell (FOIS, 2010)

owl_cpp, a C++ Library for Working with OWL Ontologies. - Mikhail K. Levin; Alan Ruttenberg; Anna Maria Masci; Lindsay G. Cowell (ICBO, 2011)

Connecting Ontologies for the Representation of Biological Pathways. - Anna Maria Masci; Mikhail K. Levin; Alan Ruttenberg; Lindsay G. Cowell (ICBO, 2011)

Bridging Multiple Ontologies: Representation of the Liver Immune Response. - Anna Maria Masci; Jeffrey Roach; Bernard de Bono; Pierre Grenon; Lindsay G. Cowell (ICBO, 2011)

Logical Development of the Cell Ontology. - Terrence F. Meehan; Anna Maria Masci; Amina Abdulla; Lindsay G. Cowell; Judith A. Blake; Christopher J. Mungall; Alexander D. Diehl (BMC Bioinform., 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)

Towards an ontological representation of resistance: The case of MRSA. - Albert Goldfain; Barry Smith 001; Lindsay G. Cowell (J. Biomed. Informatics, 2011)

Constructing a Lattice of Infectious Disease Ontologies from a Staphylococcus aureus Isolate Repository. - Albert Goldfain; Lindsay G. Cowell; Barry Smith 001 (ICBO, 2012)

Design and Evaluation of a Bacterial Clinical Infectious Diseases Ontology. - Claire L. Gordon; Stephanie Pouch; Lindsay G. Cowell; Mary Regina Boland; Heather L. Platt; Albert Goldfain; Chunhua Weng (AMIA, 2013)

Ontological Representation of CDC Active Bacterial Core Surveillance Case Reports. - Albert Goldfain; Barry Smith 001; Lindsay G. Cowell (ICBO, 2014)

owlcpp: a C++ library for working with OWL ontologies. - Mikhail K. Levin; Lindsay G. Cowell (J. Biomed. Semant., 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)

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)

Statistical classifiers for diagnosing disease from immune repertoires: a case study using multiple sclerosis. - Jared Ostmeyer; Scott Christley; William Rounds; Inimary T. Toby; Benjamin M. Greenberg; Nancy Monson; Lindsay G. Cowell (BMC Bioinform., 2017)

Machine learning on sequential data using a recurrent weighted average. - Jared Ostmeyer; Lindsay G. Cowell (Neurocomputing, 2019)

The ADC API: A Web API for the Programmatic Query of the AIRR Data Commons. - Scott Christley; Ademar Aguiar; George Blanck; Felix Breden; Syed Ahmad Chan Bukhari; Christian E. Busse; Jerome Jaglale; Srilakshmy L. Harikrishnan; Uri Laserson; Bjoern Peters; Artur Rocha; Chaim A. Schramm; et al. (Frontiers Big Data, 2020)

The Infectious Disease Ontology in the age of COVID-19. - Shane Babcock; John Beverley; Lindsay G. Cowell; Barry Smith 001 (J. Biomed. Semant., 2021)

Dynamic Kernel Matching for Non-conforming Data: A Case Study of T-cell Receptor Datasets. - Jared Ostmeyer; Scott Christley; Lindsay G. Cowell (CoRR, 2021)

The immuneML ecosystem for machine learning analysis of adaptive immune receptor repertoires. - Milena Pavlovic; Lonneke Scheffer; Keshav Motwani; Chakravarthi Kanduri; Radmila Kompova; Nikolay Vazov; Knut Waagan; Fabian L. M. Bernal; Alexandre Almeida Costa; Brian Corrie; Rahmad Akbar; Ghadi S. Al Hajj; et al. (Nat. Mach. Intell., 2021)

Coordinating Coronavirus Research: The Virus Infectious Disease Ontology. - John Beverley; Yongqun He; Barry Smith 001; Shane Babcock; Eric Merrell; Lindsay G. Cowell; Regina Hurley; Sebastian Deusing (ICBO, 2022)

Iterative refinement and goal articulation to optimize large language models for clinical information extraction. - David Hein; Alana Christie; Michael J. Holcomb; Bingqing Xie; Aj Jain; Joseph Vento; Dinesh Rakheja; Ameer Hamza Shakur; Scott Christley; Lindsay G. Cowell; James Brugarolas; Andrew R. Jamieson; et al. (npj Digit. Medicine, 2025)