S Joshua Swamidass
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Opportunities and obstacles for deep learning in biology and medicine
T Ching, DS Himmelstein, BK Beaulieu-Jones, AA Kalinin, BT Do, ...
Journal of the royal society interface 15 (141), 20170387, 2018
Graph kernels for chemical informatics
L Ralaivola, SJ Swamidass, H Saigo, P Baldi
Neural networks 18 (8), 1093-1110, 2005
A survey of current trends in computational drug repositioning
J Li, S Zheng, B Chen, AJ Butte, SJ Swamidass, Z Lu
Briefings in bioinformatics 17 (1), 2-12, 2016
Open source drug discovery with the malaria box compound collection for neglected diseases and beyond
WC Van Voorhis, JH Adams, R Adelfio, V Ahyong, MH Akabas, P Alano, ...
PLoS pathogens 12 (7), e1005763, 2016
Kernels for small molecules and the prediction of mutagenicity, toxicity and anti-cancer activity
SJ Swamidass, J Chen, J Bruand, P Phung, L Ralaivola, P Baldi
Bioinformatics 21 (suppl_1), i359-i368, 2005
XenoSite: accurately predicting CYP-mediated sites of metabolism with neural networks
J Zaretzki, M Matlock, SJ Swamidass
Journal of chemical information and modeling 53 (12), 3373-3383, 2013
ChemDB: a public database of small molecules and related chemoinformatics resources
J Chen, SJ Swamidass, Y Dou, J Bruand, P Baldi
Bioinformatics 21 (22), 4133-4139, 2005
Modeling epoxidation of drug-like molecules with a deep machine learning network
TB Hughes, GP Miller, SJ Swamidass
ACS central science 1 (4), 168-180, 2015
ChemDB update—full-text search and virtual chemical space
JH Chen, E Linstead, SJ Swamidass, D Wang, P Baldi
Bioinformatics 23 (17), 2348-2351, 2007
Deep learning global glomerulosclerosis in transplant kidney frozen sections
JN Marsh, MK Matlock, S Kudose, TC Liu, TS Stappenbeck, JP Gaut, ...
IEEE transactions on medical imaging 37 (12), 2718-2728, 2018
Structure-based inhibitor design of AccD5, an essential acyl-CoA carboxylase carboxyltransferase domain of Mycobacterium tuberculosis
TW Lin, MM Melgar, D Kurth, SJ Swamidass, J Purdon, T Tseng, G Gago, ...
Proceedings of the National Academy of Sciences 103 (9), 3072-3077, 2006
A CROC stronger than ROC: measuring, visualizing and optimizing early retrieval
SJ Swamidass, CA Azencott, K Daily, P Baldi
Bioinformatics 26 (10), 1348-1356, 2010
Mining small-molecule screens to repurpose drugs
SJ Swamidass
Briefings in bioinformatics 12 (4), 327-335, 2011
Mathematical correction for fingerprint similarity measures to improve chemical retrieval
SJ Swamidass, P Baldi
Journal of chemical information and modeling 47 (3), 952-964, 2007
Bounds and algorithms for fast exact searches of chemical fingerprints in linear and sublinear time
SJ Swamidass, P Baldi
Journal of chemical information and modeling 47 (2), 302-317, 2007
Modeling reactivity to biological macromolecules with a deep multitask network
TB Hughes, NL Dang, GP Miller, SJ Swamidass
ACS central science 2 (8), 529-537, 2016
Site of reactivity models predict molecular reactivity of diverse chemicals with glutathione
TB Hughes, GP Miller, SJ Swamidass
Chemical research in toxicology 28 (4), 797-809, 2015
One-to four-dimensional kernels for virtual screening and the prediction of physical, chemical, and biological properties
CA Azencott, A Ksikes, SJ Swamidass, JH Chen, L Ralaivola, P Baldi
Journal of chemical information and modeling 47 (3), 965-974, 2007
XenoSite server: a web-available site of metabolism prediction tool
MK Matlock, TB Hughes, SJ Swamidass
Bioinformatics 31 (7), 1136-1137, 2015
Standard operating procedure for somatic variant refinement of sequencing data with paired tumor and normal samples
EK Barnell, P Ronning, KM Campbell, K Krysiak, BJ Ainscough, LM Sheta, ...
Genetics in Medicine 21 (4), 972-981, 2019
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