Scott Christley

26 papers Journal 22Unranked 4
YearRankTypeTitle / Venue / Authors
2025 J jnl
Iterative refinement and goal articulation to optimize large language models for clinical information extraction.
npj Digit. Medicine
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, Payal Kapur
2022 J jnl
Facilitating automated conversion of scientific knowledge into scientific simulation models with the Machine Assisted Generation, Calibration, and Comparison (MAGCC) Framework.
CoRR
Chase Cockrell, Scott Christley, Gary An
2021 J jnl
Dynamic Kernel Matching for Non-conforming Data: A Case Study of T-cell Receptor Datasets.
CoRR
Jared Ostmeyer, Scott Christley, Lindsay G. Cowell
2021 J jnl
The immuneML ecosystem for machine learning analysis of adaptive immune receptor repertoires.
Nat. Mach. Intell.
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, Gabriel Balaban, Todd M. Brusko, Maria Chernigovskaya, Scott Christley, Lindsay G. Cowell, Robert Frank, Ivar Grytten, Sveinung Gundersen, Ingrid Hobæk Haff, Eivind Hovig, Ping-Han Hsieh, Günter Klambauer, Marieke L. Kuijjer, Christin Lund-Andersen, Antonio Martini, Thomas Minotto, Johan Pensar, Knut D. Rand, Enrico Riccardi, Philippe A. Robert, Artur Rocha, Andrei Slabodkin, Igor Snapkov, Ludvig Magne Sollid, Dmytro Titov, Cédric R. Weber, Michael Widrich, Gur Yaari, Victor Greiff, Geir Kjetil Sandve
2020 J jnl
The ADC API: A Web API for the Programmatic Query of the AIRR Data Commons.
Frontiers Big Data
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, Sarah Taylor, Jason A. Vander Heiden, Bojan Zimonja, Corey T. Watson, Brian Corrie, Lindsay G. Cowell
2017 J jnl
Statistical classifiers for diagnosing disease from immune repertoires: a case study using multiple sclerosis.
BMC Bioinform.
Jared Ostmeyer, Scott Christley, William Rounds, Inimary T. Toby, Benjamin M. Greenberg, Nancy Monson, Lindsay G. Cowell
2017 J jnl
VDJPipe: a pipelined tool for pre-processing immune repertoire sequencing data.
BMC Bioinform.
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
2016 J jnl
VDJML: a file format with tools for capturing the results of inferring immune receptor rearrangements.
BMC Bioinform.
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, Aaron M. Rosenfeld, William Rounds, Florian Rubelt, Walter Scarborough, Jamie K. Scott, Mohamed Uduman, Jason A. Vander Heiden, Richard H. Scheuermann, Nancy Monson, Steven H. Kleinstein, Lindsay G. Cowell
2015 J jnl
Computational Studies of the Intestinal Host-Microbiota Interactome.
Comput.
Scott Christley, Chase Cockrell, Gary An
2014 J jnl
Inference of the Xenopus tropicalis embryonic regulatory network and spatial gene expression patterns.
BMC Syst. Biol.
Zhenzhen Zheng, Scott Christley, William T. Chiu, Ira L. Blitz, Xiaohui Xie, Ken W. Y. Cho, Qing Nie
2014 J jnl
Investigation of Inflammation and Tissue Patterning in the Gut Using a Spatially Explicit General-Purpose Model of Enteric Tissue (SEGMEnT).
PLoS Comput. Biol.
Chase Cockrell, Scott Christley, Gary An
2013 — conf
Examining the dynamics of epithelial metaplasia and pouchitis in an ileal pouch with a spatially-explicit computational multi-scale gut model (MSGM).
SpringSim (ADS)
Chase Cockrell, Scott Christley, Gary An, Eugene Chang, Marc Ward
2012 J jnl
A proposal for augmenting biological model construction with a semi-intelligent computational modeling assistant.
Comput. Math. Organ. Theory
Scott Christley, Gary An
2011 — conf
A proposed method for dynamic knowledge representation via agent-directed composition from biomedical and simulation ontologies: an example using gut mucus layer dynamics.
SpringSim (ADS)
Scott Christley, Gary An
2011 J jnl
An automated homology-based approach for identifying transposable elements.
BMC Bioinform.
Ryan C. Kennedy, Maria F. Unger, Scott Christley, Frank H. Collins, Gregory R. Madey
2010 J jnl
Data structures and compression algorithms for high-throughput sequencing technologies.
BMC Bioinform.
Kenny Daily, Paul Rigor, Scott Christley, Xiaohui Xie, Pierre Baldi
2010 J jnl
Integrative multicellular biological modeling: a case study of 3D epidermal development using GPU algorithms.
BMC Syst. Biol.
Scott Christley, Briana Lee, Xing Dai, Qing Nie
2010 J jnl
Parameter inference for discretely observed stochastic kinetic models using stochastic gradient descent.
BMC Syst. Biol.
Yuanfeng Wang, Scott Christley, Eric Mjolsness, Xiaohui Xie
2009 J jnl
Human genomes as email attachments.
Bioinform.
Scott Christley, Yiming Lu, Chen Li, Xiaohui Xie
2009 J jnl
VectorBase: a data resource for invertebrate vector genomics.
Nucleic Acids Res.
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, Nathan Konopinski, Neil F. Lobo, Robert M. MacCallum, Gregory R. Madey, Karine Megy, Jason Meyer, Seth Redmond, David W. Severson, Eric O. Stinson, Pantelis Topalis, Ewan Birney, William M. Gelbart, Fotis C. Kafatos, Christos Louis, Frank H. Collins
2008 J jnl
Multiple organism algorithm for finding ultraconserved elements.
BMC Bioinform.
Scott Christley, Neil F. Lobo, Gregory R. Madey
2007 — conf
Analysis of Activity in the Open Source Software Development Community.
HICSS
Scott Christley, Gregory R. Madey
2007 J jnl
Multiscale Agent-based Simulation for Chondrogenic Pattern Formation
Cybern. Syst.
Scott Christley, Xuelian Zhu, Stuart A. Newman, Mark S. Alber
2007 J jnl
Patterns of Mesenchymal Condensation in a Multiscale, Discrete Stochastic Model.
PLoS Comput. Biol.
Scott Christley, Mark S. Alber, Stuart A. Newman
2007 J jnl
VectorBase: a home for invertebrate vectors of human pathogens.
Nucleic Acids Res.
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, Catherine A. Hill, Ryan C. Kennedy, Neil F. Lobo, Robert M. MacCallum, Gregory R. Madey, Karine Megy, Seth Redmond, Susan Russo, David W. Severson, Eric O. Stinson, Pantelis Topalis, Evgeni M. Zdobnov, Ewan Birney, William M. Gelbart, Fotis C. Kafatos, Christos Louis, Frank H. Collins
2005 — conf
A Topological Analysis of the Open Souce Software Development Community.
HICSS
Jin Xu, Yongqin Gao, Scott Christley, Gregory R. Madey