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Scott Christley
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Journal Articles
- 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) - 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) - 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) - 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) - 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) - 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)
Conference and Workshop Papers
- 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 - 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 - 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
Informal and Other Publications
- 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
- [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)
Coauthor Index
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