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2020 – today
- 2022
[i2]Chase Cockrell, Scott Christley, Gary An:
Facilitating automated conversion of scientific knowledge into scientific simulation models with the Machine Assisted Generation, Calibration, and Comparison (MAGCC) Framework. CoRR abs/2204.10382 (2022)- 2021
- [j19]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:
The immuneML ecosystem for machine learning analysis of adaptive immune receptor repertoires. Nat. Mach. Intell. 3(11): 936-944 (2021) - [i1]Jared Ostmeyer, Scott Christley, Lindsay G. Cowell:
Dynamic Kernel Matching for Non-conforming Data: A Case Study of T-cell Receptor Datasets. CoRR abs/2103.10472 (2021) - 2020
- [j18]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:
The ADC API: A Web API for the Programmatic Query of the AIRR Data Commons. Frontiers Big Data 3: 22 (2020)
2010 – 2019
- 2017
- [j17]Jared Ostmeyer, Scott Christley, William Rounds, Inimary T. Toby, Benjamin M. Greenberg, Nancy Monson, Lindsay G. Cowell:
Statistical classifiers for diagnosing disease from immune repertoires: a case study using multiple sclerosis. BMC Bioinform. 18(1): 401:1-401:10 (2017) - [j16]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:
VDJPipe: a pipelined tool for pre-processing immune repertoire sequencing data. BMC Bioinform. 18(1): 448:1-448:5 (2017) - 2016
- [j15]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:
VDJML: a file format with tools for capturing the results of inferring immune receptor rearrangements. BMC Bioinform. 17(S-13): 333 (2016) - 2015
- [j14]Scott Christley, Chase Cockrell, Gary An:
Computational Studies of the Intestinal Host-Microbiota Interactome. Comput. 3(1): 2-28 (2015) - 2014
- [j13]Zhenzhen Zheng, Scott Christley, William T. Chiu, Ira L. Blitz, Xiaohui Xie, Ken W. Y. Cho, Qing Nie:
Inference of the Xenopus tropicalis embryonic regulatory network and spatial gene expression patterns. BMC Syst. Biol. 8: 3 (2014) - [j12]Chase Cockrell, Scott Christley, Gary An:
Investigation of Inflammation and Tissue Patterning in the Gut Using a Spatially Explicit General-Purpose Model of Enteric Tissue (SEGMEnT). PLoS Comput. Biol. 10(3) (2014) - 2013
- [c4]Chase Cockrell, Scott Christley, Gary An, Eugene Chang, Marc Ward:
Examining the dynamics of epithelial metaplasia and pouchitis in an ileal pouch with a spatially-explicit computational multi-scale gut model (MSGM). SpringSim (ADS) 2013: 4 - 2012
- [j11]Scott Christley, Gary An:
A proposal for augmenting biological model construction with a semi-intelligent computational modeling assistant. Comput. Math. Organ. Theory 18(4): 380-403 (2012) - 2011
- [j10]Ryan C. Kennedy, Maria F. Unger, Scott Christley, Frank H. Collins, Gregory R. Madey:
An automated homology-based approach for identifying transposable elements. BMC Bioinform. 12: 130 (2011) - [c3]Scott Christley, Gary An:
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) 2011: 37-44 - 2010
- [j9]Kenny Daily, Paul Rigor, Scott Christley, Xiaohui Xie, Pierre Baldi:
Data structures and compression algorithms for high-throughput sequencing technologies. BMC Bioinform. 11: 514 (2010) - [j8]Yuanfeng Wang, Scott Christley, Eric Mjolsness, Xiaohui Xie:
Parameter inference for discretely observed stochastic kinetic models using stochastic gradient descent. BMC Syst. Biol. 4: 99 (2010) - [j7]Scott Christley, Briana Lee, Xing Dai, Qing Nie:
Integrative multicellular biological modeling: a case study of 3D epidermal development using GPU algorithms. BMC Syst. Biol. 4: 107 (2010)
2000 – 2009
- 2009
- [j6]Scott Christley, Yiming Lu, Chen Li, Xiaohui Xie:
Human genomes as email attachments. Bioinform. 25(2): 274-275 (2009) - [j5]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:
VectorBase: a data resource for invertebrate vector genomics. Nucleic Acids Res. 37(Database-Issue): 583-587 (2009) - 2008
- [j4]Scott Christley, Neil F. Lobo, Gregory R. Madey:
Multiple organism algorithm for finding ultraconserved elements. BMC Bioinform. 9 (2008) - 2007
- [j3]Scott Christley, Xuelian Zhu, Stuart A. Newman, Mark S. Alber:
Multiscale Agent-based Simulation for Chondrogenic Pattern Formation in Vitro. Cybern. Syst. 38(7): 707-727 (2007) - [j2]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:
VectorBase: a home for invertebrate vectors of human pathogens. Nucleic Acids Res. 35(Database-Issue): 503-505 (2007) - [j1]Scott Christley, Mark S. Alber, Stuart A. Newman:
Patterns of Mesenchymal Condensation in a Multiscale, Discrete Stochastic Model. PLoS Comput. Biol. 3(4) (2007) - [c2]Scott Christley, Gregory R. Madey:
Analysis of Activity in the Open Source Software Development Community. HICSS 2007: 166 - 2005
- [c1]Jin Xu, Yongqin Gao, Scott Christley, Gregory R. Madey:
A Topological Analysis of the Open Souce Software Development Community. HICSS 2005
Coauthor Index
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