S. J. Swamidass, Ph.D. - Publications

2007 University of California, Irvine, Irvine, CA 

41 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2016 Kumar RD, Swamidass SJ, Bose R. Unsupervised detection of cancer driver mutations with parsimony-guided learning. Nature Genetics. PMID 27618449 DOI: 10.1038/Ng.3658  1
2016 Pan Y, Daito T, Sasaki Y, Chung YH, Xing X, Pondugula S, Swamidass SJ, Wang T, Kim AH, Yano H. Inhibition of DNA Methyltransferases Blocks Mutant Huntingtin-Induced Neurotoxicity. Scientific Reports. 6: 31022. PMID 27516062 DOI: 10.1038/Srep31022  1
2015 Lusci A, Browning M, Fooshee D, Swamidass J, Baldi P. Accurate and efficient target prediction using a potency-sensitive influence-relevance voter. Journal of Cheminformatics. 7: 63. PMID 26719774 DOI: 10.1186/S13321-015-0110-6  0.84
2015 Swamidass SJ. Education: Initiatives to bridge faith and science. Nature. 523: 531. PMID 26223616 DOI: 10.1038/523531b  1
2015 Kumar RD, Searleman AC, Swamidass SJ, Griffith OL, Bose R. Statistically Identifying Tumor Suppressors and Oncogenes from Pan-Cancer Genome Sequencing Data. Bioinformatics (Oxford, England). PMID 26209800 DOI: 10.1093/Bioinformatics/Btv430  1
2015 Zaretzki J, Boehm KM, Swamidass SJ. Improved Prediction of CYP-Mediated Metabolism with Chemical Fingerprints. Journal of Chemical Information and Modeling. 55: 972-82. PMID 25871613 DOI: 10.1021/ci5005652  1
2015 Li J, Zheng S, Chen B, Butte AJ, Swamidass SJ, Lu Z. A survey of current trends in computational drug repositioning. Briefings in Bioinformatics. PMID 25832646 DOI: 10.1093/Bib/Bbv020  1
2015 Swamidass SJ, Matlock M, Rozenblit L. Securely measuring the overlap between private datasets with cryptosets. Plos One. 10: e0117898. PMID 25714898 DOI: 10.1371/Journal.Pone.0117898  1
2015 Zaretzki JM, Browning MR, Hughes TB, Swamidass SJ. Extending P450 site-of-metabolism models with region-resolution data. Bioinformatics (Oxford, England). 31: 1966-73. PMID 25697821 DOI: 10.1093/bioinformatics/btv100  1
2015 Diamond MI, Cai S, Boudreau A, Carey CJ, Lyle N, Pappu RV, Swamidass SJ, Bissell M, Piwnica-Worms H, Shao J. Subcellular localization and Ser-137 phosphorylation regulate tumor-suppressive activity of profilin-1. The Journal of Biological Chemistry. 290: 9075-86. PMID 25681442 DOI: 10.1074/Jbc.M114.619874  1
2015 Matlock MK, Hughes TB, Swamidass SJ. XenoSite server: a web-available site of metabolism prediction tool. Bioinformatics (Oxford, England). 31: 1136-7. PMID 25411327 DOI: 10.1093/bioinformatics/btu761  1
2015 Hughes TB, Miller GP, Swamidass SJ. Site of reactivity models predict molecular reactivity of diverse chemicals with glutathione Chemical Research in Toxicology. 28: 797-809. DOI: 10.1021/acs.chemrestox.5b00017  1
2014 Ekins S, Clark AM, Swamidass SJ, Litterman N, Williams AJ. Bigger data, collaborative tools and the future of predictive drug discovery. Journal of Computer-Aided Molecular Design. 28: 997-1008. PMID 24943138 DOI: 10.1007/s10822-014-9762-y  1
2014 Swamidass SJ, Schillebeeckx CN, Matlock M, Hurle MR, Agarwal P. Combined Analysis of Phenotypic and Target-Based Screening in Assay Networks. Journal of Biomolecular Screening. 19: 782-790. PMID 24563424 DOI: 10.1177/1087057114523068  1
2014 Matlock M, Swamidass SJ. Sharing chemical relationships does not reveal structures. Journal of Chemical Information and Modeling. 54: 37-48. PMID 24289228 DOI: 10.1021/ci400399a  1
2014 Swamidass SJ, Lu ZY, Agarwal P, Bull AJ. Computational approaches to drug repurposing and pharmacology 19th Pacific Symposium On Biocomputing, Psb 2014. 110-113.  1
2013 Zaretzki J, Matlock M, Swamidass SJ. XenoSite: accurately predicting CYP-mediated sites of metabolism with neural networks. Journal of Chemical Information and Modeling. 53: 3373-83. PMID 24224933 DOI: 10.1021/ci400518g  1
2013 Matlock MK, Zaretzki JM, Swamidass SJ. Scaffold network generator: a tool for mining molecular structures. Bioinformatics (Oxford, England). 29: 2655-6. PMID 23918250 DOI: 10.1093/bioinformatics/btt448  1
2013 Browning MR, Calhoun BT, Swamidass SJ. Managing missing measurements in small-molecule screens. Journal of Computer-Aided Molecular Design. 27: 469-78. PMID 23585219 DOI: 10.1007/s10822-013-9642-x  1
2013 Swamidass SJ. Using economic optimization to design high-throughput screens. Future Medicinal Chemistry. 5: 9-11. PMID 23256806 DOI: 10.4155/fmc.12.186  1
2013 Sloutsky R, Jimenez N, Swamidass SJ, Naegle KM. Accounting for noise when clustering biological data. Briefings in Bioinformatics. 14: 423-36. PMID 23063929 DOI: 10.1093/bib/bbs057  1
2012 Calhoun BT, Browning MR, Chen BR, Bittker JA, Swamidass SJ. Automatically detecting workflows in PubChem. Journal of Biomolecular Screening. 17: 1071-9. PMID 22693105 DOI: 10.1177/1087057112449054  1
2012 Swamidass SJ, Calhoun BT, Bittker JA, Bodycombe NE, Clemons PA. Utility-aware screening with clique-oriented prioritization. Journal of Chemical Information and Modeling. 52: 29-37. PMID 22117901 DOI: 10.1021/Ci2003285  1
2011 Swamidass SJ, Calhoun BT, Bittker JA, Bodycombe NE, Clemons PA. Enhancing the rate of scaffold discovery with diversity-oriented prioritization. Bioinformatics (Oxford, England). 27: 2271-8. PMID 21685049 DOI: 10.1093/Bioinformatics/Btr369  1
2011 Baldi P, Azencott C, Swamidass SJ. Bridging the gap between neural network and kernel methods: Applications to drug discovery Frontiers in Artificial Intelligence and Applications. 226: 3-13. DOI: 10.3233/978-1-60750-692-8-3  1
2011 Ranu S, Calhoun BT, Singh AK, Swamidass SJ. Probabilistic substructure mining from small-molecule screens Molecular Informatics. 30: 809-815. DOI: 10.1002/minf.201100058  1
2010 Swamidass SJ, Bittker JA, Bodycombe NE, Ryder SP, Clemons PA. An economic framework to prioritize confirmatory tests after a high-throughput screen. Journal of Biomolecular Screening. 15: 680-6. PMID 20547534 DOI: 10.1177/1087057110372803  1
2010 Swamidass SJ, Azencott CA, Daily K, Baldi P. A CROC stronger than ROC: measuring, visualizing and optimizing early retrieval. Bioinformatics (Oxford, England). 26: 1348-56. PMID 20378557 DOI: 10.1093/Bioinformatics/Btq140  1
2009 Nasr RJ, Swamidass SJ, Baldi PF. Large scale study of multiple-molecule queries. Journal of Cheminformatics. 1: 7. PMID 20298525 DOI: 10.1186/1758-2946-1-7  1
2009 Swamidass SJ, Azencott CA, Lin TW, Gramajo H, Tsai SC, Baldi P. Influence relevance voting: an accurate and interpretable virtual high throughput screening method. Journal of Chemical Information and Modeling. 49: 756-66. PMID 19391629 DOI: 10.1021/Ci8004379  1
2008 Benz RW, Swamidass SJ, Baldi P. Discovery of power-laws in chemical space. Journal of Chemical Information and Modeling. 48: 1138-51. PMID 18522387 DOI: 10.1021/Ci700353M  1
2007 Baldi P, Benz RW, Hirschberg DS, Swamidass SJ. Lossless compression of chemical fingerprints using integer entropy codes improves storage and retrieval. Journal of Chemical Information and Modeling. 47: 2098-109. PMID 17967006 DOI: 10.1021/Ci700200N  1
2007 Chen JH, Linstead E, Swamidass SJ, Wang D, Baldi P. ChemDB update--full-text search and virtual chemical space. Bioinformatics (Oxford, England). 23: 2348-51. PMID 17599932 DOI: 10.1093/Bioinformatics/Btm341  1
2007 Swamidass SJ, Baldi P. Mathematical correction for fingerprint similarity measures to improve chemical retrieval. Journal of Chemical Information and Modeling. 47: 952-64. PMID 17444629 DOI: 10.1021/Ci600526A  1
2007 Azencott CA, Ksikes A, Swamidass SJ, Chen JH, Ralaivola L, Baldi P. One- to four-dimensional kernels for virtual screening and the prediction of physical, chemical, and biological properties. Journal of Chemical Information and Modeling. 47: 965-74. PMID 17338509 DOI: 10.1021/Ci600397P  1
2007 Swamidass SJ, Baldi P. Bounds and algorithms for fast exact searches of chemical fingerprints in linear and sublinear time. Journal of Chemical Information and Modeling. 47: 302-17. PMID 17326616 DOI: 10.1021/Ci600358F  1
2006 Danziger SA, Swamidass SJ, Zeng J, Dearth LR, Lu Q, Chen JH, Cheng J, Hoang VP, Saigo H, Luo R, Baldi P, Brachmann RK, Lathrop RH. Functional census of mutation sequence spaces: the example of p53 cancer rescue mutants. Ieee/Acm Transactions On Computational Biology and Bioinformatics / Ieee, Acm. 3: 114-25. PMID 17048398 DOI: 10.1109/Tcbb.2006.22  1
2006 Lin TW, Melgar MM, Kurth D, Swamidass SJ, Purdon J, Tseng T, Gago G, Baldi P, Gramajo H, Tsai SC. Structure-based inhibitor design of AccD5, an essential acyl-CoA carboxylase carboxyltransferase domain of Mycobacterium tuberculosis. Proceedings of the National Academy of Sciences of the United States of America. 103: 3072-7. PMID 16492739 DOI: 10.1073/Pnas.0510580103  1
2005 Chen J, Swamidass SJ, Dou Y, Bruand J, Baldi P. ChemDB: a public database of small molecules and related chemoinformatics resources. Bioinformatics (Oxford, England). 21: 4133-9. PMID 16174682 DOI: 10.1093/Bioinformatics/Bti683  1
2005 Ralaivola L, Swamidass SJ, Saigo H, Baldi P. Graph kernels for chemical informatics. Neural Networks : the Official Journal of the International Neural Network Society. 18: 1093-110. PMID 16157471 DOI: 10.1016/J.Neunet.2005.07.009  1
2005 Swamidass SJ, Chen J, Bruand J, Phung P, Ralaivola L, Baldi P. Kernels for small molecules and the prediction of mutagenicity, toxicity and anti-cancer activity. Bioinformatics (Oxford, England). 21: i359-68. PMID 15961479 DOI: 10.1093/Bioinformatics/Bti1055  1
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