S Joshua Swamidass

Summary

Affiliation: Washington University School of Medicine
Country: USA

Publications

  1. pmc An economic framework to prioritize confirmatory tests after a high-throughput screen
    S Joshua Swamidass
    Division of Laboratory and Genomic Medicine, Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO 63110, USA
    J Biomol Screen 15:680-6. 2010
  2. pmc Utility-aware screening with clique-oriented prioritization
    S Joshua Swamidass
    Division of Laboratory and Genomic Medicine, Department of Pathology and Immunology, Washington University School of Medicine, St Louis, Missouri, USA
    J Chem Inf Model 52:29-37. 2012
  3. doi request reprint Mining small-molecule screens to repurpose drugs
    S Joshua Swamidass
    Division of Laboratory and Genomic Medicine, Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
    Brief Bioinform 12:327-35. 2011
  4. doi request reprint Managing missing measurements in small-molecule screens
    Michael R Browning
    Division of Laboratory and Genomic Medicine, Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
    J Comput Aided Mol Des 27:469-78. 2013
  5. doi request reprint Automatically detecting workflows in PubChem
    Bradley T Calhoun
    Washington University School of Medicine, 660 S Euclid, St Louis, MO 63108, USA
    J Biomol Screen 17:1071-9. 2012
  6. doi request reprint Accounting for noise when clustering biological data
    Roman Sloutsky
    Division of Biology and Biomedical Sciences, Washington University in St Louis, One Brookings Drive, Brauer 2004, St Louis, MO 63130, USA
    Brief Bioinform 14:423-36. 2013
  7. doi request reprint Scaffold network generator: a tool for mining molecular structures
    Matt K Matlock
    Department of Pathology and Immunology, Washington University School of Medicine, Campus Box 1097, Whitaker Hall, St Louis, MO 63130, USA
    Bioinformatics 29:2655-6. 2013
  8. pmc Enhancing the rate of scaffold discovery with diversity-oriented prioritization
    S Joshua Swamidass
    Division of Laboratory and Genomic Medicine, Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
    Bioinformatics 27:2271-8. 2011
  9. doi request reprint Securely Measuring the Overlap between Private Datasets with Cryptosets
    S Joshua Swamidass
    Department of Pathology, Washington University School of Medicine, St Louis, MO, USA
    PLoS ONE 10:e0117898. 2015
  10. doi request reprint Sharing chemical relationships does not reveal structures
    Matthew Matlock
    Washington University School of Medicine, Department of Pathology and Immunology, St Louis, Missouri 63110, United States
    J Chem Inf Model 54:37-48. 2014

Collaborators

  • Paul A Clemons
  • Tao Wei Huang
  • Kristen M Naegle
  • Jed Zaretzki
  • Matthew Matlock
  • Michael R Browning
  • Bradley T Calhoun
  • Roman Sloutsky
  • Matt K Matlock
  • Jed M Zaretzki
  • Patrik Rydberg
  • Curt M Breneman
  • Nicolas Jimenez
  • Charles Bergeron
  • Brian R Chen
  • Joshua A Bittker

Detail Information

Publications12

  1. pmc An economic framework to prioritize confirmatory tests after a high-throughput screen
    S Joshua Swamidass
    Division of Laboratory and Genomic Medicine, Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO 63110, USA
    J Biomol Screen 15:680-6. 2010
    ..Validated with retrospective simulations and prospective experiments, this strategy identified 157 additional actives that had been erroneously labeled inactive in at least one real-world screening experiment...
  2. pmc Utility-aware screening with clique-oriented prioritization
    S Joshua Swamidass
    Division of Laboratory and Genomic Medicine, Department of Pathology and Immunology, Washington University School of Medicine, St Louis, Missouri, USA
    J Chem Inf Model 52:29-37. 2012
    ..The utility-aware algorithm used to implement COP is general enough to implement several other important models of screener preferences...
  3. doi request reprint Mining small-molecule screens to repurpose drugs
    S Joshua Swamidass
    Division of Laboratory and Genomic Medicine, Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
    Brief Bioinform 12:327-35. 2011
    ..Despite these methods' limitations, it is hopeful that they will accelerate the discovery of new uses for known drugs, but this hope has not yet been realized...
  4. doi request reprint Managing missing measurements in small-molecule screens
    Michael R Browning
    Division of Laboratory and Genomic Medicine, Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
    J Comput Aided Mol Des 27:469-78. 2013
    ..In particular, this method can rapidly and economically identify novel active molecules, each of which could have novel function in either binding or selectivity in addition to representing new intellectual property...
  5. doi request reprint Automatically detecting workflows in PubChem
    Bradley T Calhoun
    Washington University School of Medicine, 660 S Euclid, St Louis, MO 63108, USA
    J Biomol Screen 17:1071-9. 2012
    ..A Python implementation of the algorithm is available online, and a searchable database of all PubChem workflows is available at http://swami.wustl.edu/flow...
  6. doi request reprint Accounting for noise when clustering biological data
    Roman Sloutsky
    Division of Biology and Biomedical Sciences, Washington University in St Louis, One Brookings Drive, Brauer 2004, St Louis, MO 63130, USA
    Brief Bioinform 14:423-36. 2013
    ..These methods span a range of assumptions about the statistical properties of the noise and can therefore be applied to virtually any biological data source. ..
  7. doi request reprint Scaffold network generator: a tool for mining molecular structures
    Matt K Matlock
    Department of Pathology and Immunology, Washington University School of Medicine, Campus Box 1097, Whitaker Hall, St Louis, MO 63130, USA
    Bioinformatics 29:2655-6. 2013
    ..Substantially improving on existing software, SNG is robust enough to work on millions of molecules at a time with a simple command-line interface...
  8. pmc Enhancing the rate of scaffold discovery with diversity-oriented prioritization
    S Joshua Swamidass
    Division of Laboratory and Genomic Medicine, Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
    Bioinformatics 27:2271-8. 2011
    ..The number of active scaffolds better reflects the success of the screen than the number of active molecules. Many existing algorithms for deciding which hits should be sent for confirmatory testing neglect this concern...
  9. doi request reprint Securely Measuring the Overlap between Private Datasets with Cryptosets
    S Joshua Swamidass
    Department of Pathology, Washington University School of Medicine, St Louis, MO, USA
    PLoS ONE 10:e0117898. 2015
    ..We empirically and theoretically assess both the accuracy of these estimates and the security of the approach, demonstrating that cryptosets are informative, with a stable accuracy, and secure. ..
  10. doi request reprint Sharing chemical relationships does not reveal structures
    Matthew Matlock
    Washington University School of Medicine, Department of Pathology and Immunology, St Louis, Missouri 63110, United States
    J Chem Inf Model 54:37-48. 2014
    ..This approach makes it possible to share data across institutions, and may securely enable collaborative analysis that can yield insight into both specific projects and screening technology as a whole. ..
  11. doi request reprint XenoSite: accurately predicting CYP-mediated sites of metabolism with neural networks
    Jed Zaretzki
    Department of Pathology and Immunology, Washington University School of Medicine, St Louis, Missouri 63130, United States
    J Chem Inf Model 53:3373-83. 2013
    ..Moreover, XenoSite output is interpretable as a probability, which reflects both the confidence of the model that a particular atom is metabolized and the statistical likelihood that its prediction for that atom is correct...
  12. pmc RS-WebPredictor: a server for predicting CYP-mediated sites of metabolism on drug-like molecules
    Jed Zaretzki
    Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO 63130, USA
    Bioinformatics 29:497-8. 2013
    ..Server execution time is fast, taking on average 2s to encode a submitted molecule and 1s to apply a given model, allowing for high-throughput use in lead optimization projects...