A Topological Analysis of the Open Souce Software Development Community. - Jin Xu; Yongqin Gao; Scott Christley; Gregory R. Madey (HICSS, 2005)

Analysis of Activity in the Open Source Software Development Community. - Scott Christley; Gregory R. Madey (HICSS, 2007)

Multiscale Agent-based Simulation for Chondrogenic Pattern Formation in Vitro. - Scott Christley; Xuelian Zhu; Stuart A. Newman; Mark S. Alber (Cybern. Syst., 2007)

VectorBase: a home for invertebrate vectors of human pathogens. - Daniel Lawson; Peter Arensburger; Peter Atkinson; Nora J. Besansky; Robert V. Bruggner; Ryan Butler; Kathryn S. Campbell; George K. Christophides; Scott Christley; Emmanuel Dialynas; David B. Emmert; Martin Hammond; et al. (Nucleic Acids Res., 2007)

Patterns of Mesenchymal Condensation in a Multiscale, Discrete Stochastic Model. - Scott Christley; Mark S. Alber; Stuart A. Newman (PLoS Comput. Biol., 2007)

Multiple organism algorithm for finding ultraconserved elements. - Scott Christley; Neil F. Lobo; Gregory R. Madey (BMC Bioinform., 2008)

Human genomes as email attachments. - Scott Christley; Yiming Lu; Chen Li 001; Xiaohui Xie (Bioinform., 2009)

VectorBase: a data resource for invertebrate vector genomics. - Daniel Lawson; Peter Arensburger; Peter Atkinson; Nora J. Besansky; Robert V. Bruggner; Ryan Butler; Kathryn S. Campbell; George K. Christophides; Scott Christley; Emmanuel Dialynas; Martin Hammond; Catherine A. Hill; et al. (Nucleic Acids Res., 2009)

Data structures and compression algorithms for high-throughput sequencing technologies. - Kenny Daily; Paul Rigor; Scott Christley; Xiaohui Xie; Pierre Baldi (BMC Bioinform., 2010)

Integrative multicellular biological modeling: a case study of 3D epidermal development using GPU algorithms. - Scott Christley; Briana Lee; Xing Dai; Qing Nie (BMC Syst. Biol., 2010)

Parameter inference for discretely observed stochastic kinetic models using stochastic gradient descent. - Yuanfeng Wang; Scott Christley; Eric Mjolsness; Xiaohui Xie (BMC Syst. Biol., 2010)

A proposed method for dynamic knowledge representation via agent-directed composition from biomedical and simulation ontologies: an example using gut mucus layer dynamics. - Scott Christley; Gary An (SpringSim (ADS), 2011)

An automated homology-based approach for identifying transposable elements. - Ryan C. Kennedy; Maria F. Unger; Scott Christley; Frank H. Collins; Gregory R. Madey (BMC Bioinform., 2011)

A proposal for augmenting biological model construction with a semi-intelligent computational modeling assistant. - Scott Christley; Gary An (Comput. Math. Organ. Theory, 2012)

Examining the dynamics of epithelial metaplasia and pouchitis in an ileal pouch with a spatially-explicit computational multi-scale gut model (MSGM). - Chase Cockrell; Scott Christley; Gary An; Eugene Chang; Marc Ward (SpringSim (ADS), 2013)

Inference of the Xenopus tropicalis embryonic regulatory network and spatial gene expression patterns. - Zhenzhen Zheng; Scott Christley; William T. Chiu; Ira L. Blitz; Xiaohui Xie; Ken W. Y. Cho; Qing Nie (BMC Syst. Biol., 2014)

Investigation of Inflammation and Tissue Patterning in the Gut Using a Spatially Explicit General-Purpose Model of Enteric Tissue (SEGMEnT). - Chase Cockrell; Scott Christley; Gary An (PLoS Comput. Biol., 2014)

Computational Studies of the Intestinal Host-Microbiota Interactome. - Scott Christley; Chase Cockrell; Gary An (Comput., 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)

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)

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)

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)

Facilitating automated conversion of scientific knowledge into scientific simulation models with the Machine Assisted Generation, Calibration, and Comparison (MAGCC) Framework. - Chase Cockrell; Scott Christley; Gary An (CoRR, 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)