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 | 1987 | 2018 |
Graph kernels for chemical informatics L Ralaivola, SJ Swamidass, H Saigo, P Baldi Neural networks 18 (8), 1093-1110, 2005 | 598 | 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 | 531 | 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 | 296 | 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 | 246 | 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 | 224 | 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 | 217 | 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 | 188 | 2015 |
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 | 148 | 2018 |
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 | 148 | 2007 |
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 | 134 | 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 | 132 | 2010 |
Mining small-molecule screens to repurpose drugs SJ Swamidass Briefings in bioinformatics 12 (4), 327-335, 2011 | 124 | 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 | 122 | 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 | 109 | 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 | 98 | 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 | 93 | 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 | 86 | 2007 |
XenoSite server: a web-available site of metabolism prediction tool MK Matlock, TB Hughes, SJ Swamidass Bioinformatics 31 (7), 1136-1137, 2015 | 83 | 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 | 79 | 2019 |