Publications
Publications
94 peer-reviewed papers, from PubMed plus conference papers and chapters. See Google Scholar for preprints and citation counts.
2025
- Domain Knowledge Inclusive Monotonic Neural Network Guides Patient-Specific Induction of General Anesthesia DosingA A Pract 2025;19(8):e02034DOIPubMedAI in pathology and medicine
- Superior transplant recipient outcome prediction and pathology assessment using rapid deep learning applied to procurement kidney biopsiesSci Rep 2025;16(1):1921DOIPubMedFree full textAI in pathology and medicine
2024
- Development of a deep learning algorithm for Paneth cell density quantification for inflammatory bowel diseaseEBioMedicine 2024;110:105440DOIPubMedFree full textAI in pathology and medicine
- GAiN: An integrative tool utilizing generative adversarial neural networks for augmented gene expression analysisPatterns (N Y) 2024;5(2):100910DOIPubMedFree full textGenomics and bioinformatics
- Role of Artificial Intelligence in Kidney Pathology: Promises and PitfallsKidney360 2024;5(7):1044-1046DOIPubMedFree full textAI in pathology and medicine
- Understanding and mitigating the impact of race with adversarial autoencodersCommun Med (Lond) 2024;4(1):210DOIPubMedFree full textAI in pathology and medicine
2023
- Disentangling Socioeconomic Status and Race in Infant Brain, Birth Weight, and Gestational Age at Birth: A Neural Network AnalysisBiol Psychiatry Glob Open Sci 2023;4(1):135-144DOIPubMedFree full textAI in pathology and medicine
- Editorial: Advancements in computational studies of drug toxicityFront Pharmacol 2023;14:1230409DOIPubMedFree full textDrug metabolism and toxicity
- Message Passing Neural Networks Improve Prediction of Metabolite AuthenticityJ Chem Inf Model 2023;63(6):1675-1694DOIPubMedFree full textDrug metabolism and toxicity
- The gut microbiota of people with asthma influences lung inflammation in gnotobiotic miceiScience 2023;26(2):105991DOIPubMedFree full textGenomics and bioinformatics
2022
- A Deep Learning Approach for the Estimation of Glomerular Filtration RateIEEE Trans Nanobioscience 2022;21(4):560-569DOIPubMedAI in pathology and medicine
- Discovery of Novel Reductive Elimination Pathway for 10-HydroxywarfarinFront Pharmacol 2022;12:805133DOIPubMedFree full textDrug metabolism and toxicity
- The potential of artificial intelligence-based applications in kidney pathologyCurr Opin Nephrol Hypertens 2022;31(3):251-257DOIPubMedFree full textAI in pathology and medicine
2021
- 'Black Box' to 'Conversational' Machine Learning: Ondansetron Reduces Risk of Hospital-Acquired Venous ThromboembolismIEEE J Biomed Health Inform 2021;25(6):2204-2214DOIPubMedAI in pathology and medicine
- Bioactivation of Isoxazole-Containing Bromodomain and Extra-Terminal Domain (BET) InhibitorsMetabolites 2021;11(6)DOIPubMedFree full textDrug metabolism and toxicity
- Cal-Net: Jointly Learning Classification and Calibration On Imbalanced Binary Classification TasksIJCNN 2021:1-8DOIAI in pathology and medicine
- Deep Learning Coordinate-Free Quantum ChemistryJ Phys Chem A 2021;125(40):8978-8986DOIPubMedFree full textDeep learning of molecular structure
- Deep learning the structural determinants of protein biochemical properties by comparing structural ensembles with DiffNetsNat Commun 2021;12(1):3023DOIPubMedFree full textDeep learning of molecular structure
- Development and Validation of a Deep Learning Model to Quantify Glomerulosclerosis in Kidney Biopsy SpecimensJAMA Netw Open 2021;4(1):e2030939DOIPubMedFree full textAI in pathology and medicine
- Impacts of diphenylamine NSAID halogenation on bioactivation risksToxicology 2021;458:152832DOIPubMedFree full textDrug metabolism and toxicity
- Machine learning liver-injuring drug interactions with non-steroidal anti-inflammatory drugs (NSAIDs) from a retrospective electronic health record (EHR) cohortPLoS Comput Biol 2021;17(7):e1009053DOIPubMedFree full textDrug metabolism and toxicity
- Meloxicam methyl group determines enzyme specificity for thiazole bioactivation compared to sudoxicamToxicol Lett 2021;338:10-20DOIPubMedFree full textDrug metabolism and toxicity
- Modeling the Bioactivation and Subsequent Reactivity of DrugsChem Res Toxicol 2021;34(2):584-600DOIPubMedFree full textDrug metabolism and toxicity
- Significance of Multiple Bioactivation Pathways for Meclofenamate as Revealed through Modeling and Reaction KineticsDrug Metab Dispos 2021;49(2):133-141DOIPubMedFree full textDrug metabolism and toxicity
2020
- Deep learning quantification of percent steatosis in donor liver biopsy frozen sectionsEBioMedicine 2020;60:103029DOIPubMedFree full textAI in pathology and medicine
- Dual mechanisms suppress meloxicam bioactivation relative to sudoxicamToxicology 2020;440:152478DOIPubMedFree full textDrug metabolism and toxicity
- Metabolic Forest: Predicting the Diverse Structures of Drug MetabolitesJ Chem Inf Model 2020;60(10):4702-4716DOIPubMedFree full textDrug metabolism and toxicity
- Site-Level Bioactivity of Small-Molecules from Deep-Learned Representations of Quantum ChemistryJ Phys Chem A 2020;124(44):9194-9202DOIPubMedFree full textDeep learning of molecular structure
- The Metabolic Rainbow: Deep Learning Phase I Metabolism in Five ColorsJ Chem Inf Model 2020;60(3):1146-1164DOIPubMedFree full textDrug metabolism and toxicity
- XenoNet: Inference and Likelihood of Intermediate Metabolite FormationJ Chem Inf Model 2020;60(7):3431-3449DOIPubMedFree full textDrug metabolism and toxicity
2019
- A Time-Embedding Network Models the Ontogeny of 23 Hepatic Drug Metabolizing EnzymesChem Res Toxicol 2019;32(8):1707-1721DOIPubMedFree full textDrug metabolism and toxicity
- Accounting for proximal variants improves neoantigen predictionNat Genet 2019;51(1):175-179DOIPubMedFree full textGenomics and bioinformatics
- Comprehensive kinetic and modeling analyses revealed CYP2C9 and 3A4 determine terbinafine metabolic clearance and bioactivationBiochem Pharmacol 2019;170:113661DOIPubMedFree full textDrug metabolism and toxicity
- CYP2C19 and 3A4 Dominate Metabolic Clearance and Bioactivation of Terbinafine Based on Computational and Experimental ApproachesChem Res Toxicol 2019;32(6):1151-1164DOIPubMedFree full textDrug metabolism and toxicity
- Deep learning long-range information in undirected graphs with wave networksIJCNN 2019:1-8DOIDeep learning of molecular structure
- Precision Medicine in Pancreatic Disease-Knowledge Gaps and Research Opportunities: Summary of a National Institute of Diabetes and Digestive and Kidney Diseases WorkshopPancreas 2019;48(10):1250-1258DOIPubMedFree full textGenomics and bioinformatics
- Standard operating procedure for somatic variant refinement of sequencing data with paired tumor and normal samplesGenet Med 2019;21(4):972-981DOIPubMedFree full textGenomics and bioinformatics
2018
- A deep learning approach to automate refinement of somatic variant calling from cancer sequencing dataNat Genet 2018;50(12):1735-1743DOIPubMedFree full textGenomics and bioinformatics
- Computationally Assessing the Bioactivation of Drugs by N-DealkylationChem Res Toxicol 2018;31(2):68-80DOIPubMedFree full textDrug metabolism and toxicity
- Deep Learning Global Glomerulosclerosis in Transplant Kidney Frozen SectionsIEEE Trans Med Imaging 2018;37(12):2718-2728DOIPubMedFree full textAI in pathology and medicine
- Lamisil (terbinafine) toxicity: Determining pathways to bioactivation through computational and experimental approachesBiochem Pharmacol 2018;156:10-21DOIPubMedFree full textDrug metabolism and toxicity
- Learning a Local-Variable Model of Aromatic and Conjugated SystemsACS Cent Sci 2018;4(1):52-62DOIPubMedFree full textDeep learning of molecular structure
- Modeling Small-Molecule Reactivity Identifies Promiscuous Bioactive CompoundsJ Chem Inf Model 2018;58(8):1483-1500DOIPubMedFree full textDrug metabolism and toxicity
- Opportunities and obstacles for deep learning in biology and medicineJ R Soc Interface 2018;15(141)DOIPubMedFree full textAI in pathology and medicine
- The diversity and disparity in biomedical informatics (DDBI) workshopPac Symp Biocomput 2018;23:614-617PubMedFree full textAI in pathology and medicine
2017
- BEESEM: estimation of binding energy models using HT-SELEX dataBioinformatics 2017;33(15):2288-2295DOIPubMedFree full textGenomics and bioinformatics
- Computational Approach to Structural Alerts: Furans, Phenols, Nitroaromatics, and ThiophenesChem Res Toxicol 2017;30(4):1046-1059DOIPubMedFree full textDrug metabolism and toxicity
- Deep Learning to Predict the Formation of Quinone Species in Drug MetabolismChem Res Toxicol 2017;30(2):642-656DOIPubMedFree full textDrug metabolism and toxicity
2016
- A simple model predicts UGT-mediated metabolismBioinformatics 2016;32(20):3183-3189DOIPubMedFree full textDrug metabolism and toxicity
- A survey of current trends in computational drug repositioningBrief Bioinform 2016;17(1):2-12DOIPubMedFree full textScreening and drug repurposing
- Inhibition of DNA Methyltransferases Blocks Mutant Huntingtin-Induced NeurotoxicitySci Rep 2016;6:31022DOIPubMedFree full textGenomics and bioinformatics
- Modeling Reactivity to Biological Macromolecules with a Deep Multitask NetworkACS Cent Sci 2016;2(8):529-37DOIPubMedFree full textDrug metabolism and toxicity
- Open Source Drug Discovery with the Malaria Box Compound Collection for Neglected Diseases and BeyondPLoS Pathog 2016;12(7):e1005763DOIPubMedFree full textScreening and drug repurposing
- Unsupervised detection of cancer driver mutations with parsimony-guided learningNat Genet 2016;48(10):1288-94DOIPubMedFree full textGenomics and bioinformatics
2015
- Accurate and efficient target prediction using a potency-sensitive influence-relevance voterJ Cheminform 2015;7:63DOIPubMedFree full textChemical informatics
- Extending P450 site-of-metabolism models with region-resolution dataBioinformatics 2015;31(12):1966-73DOIPubMedDrug metabolism and toxicity
- Improved Prediction of CYP-Mediated Metabolism with Chemical FingerprintsJ Chem Inf Model 2015;55(5):972-82DOIPubMedDrug metabolism and toxicity
- Modeling Epoxidation of Drug-like Molecules with a Deep Machine Learning NetworkACS Cent Sci 2015;1(4):168-80DOIPubMedFree full textDrug metabolism and toxicity
- Securely measuring the overlap between private datasets with cryptosetsPLoS One 2015;10(2):e0117898DOIPubMedFree full textChemical informatics
- Site of reactivity models predict molecular reactivity of diverse chemicals with glutathioneChem Res Toxicol 2015;28(4):797-809DOIPubMedFree full textDrug metabolism and toxicity
- Statistically identifying tumor suppressors and oncogenes from pan-cancer genome-sequencing dataBioinformatics 2015;31(22):3561-8DOIPubMedFree full textGenomics and bioinformatics
- Subcellular localization and Ser-137 phosphorylation regulate tumor-suppressive activity of profilin-1J Biol Chem 2015;290(14):9075-86DOIPubMedFree full textGenomics and bioinformatics
- XenoSite server: a web-available site of metabolism prediction toolBioinformatics 2015;31(7):1136-7DOIPubMedDrug metabolism and toxicity
2014
- Bigger data, collaborative tools and the future of predictive drug discoveryJ Comput Aided Mol Des 2014;28(10):997-1008DOIPubMedFree full textChemical informatics
- Combined Analysis of Phenotypic and Target-Based Screening in Assay NetworksJ Biomol Screen 2014;19(5):782-90DOIPubMedScreening and drug repurposing
- Sharing chemical relationships does not reveal structuresJ Chem Inf Model 2014;54(1):37-48DOIPubMedChemical informatics
2013
- Accounting for noise when clustering biological dataBrief Bioinform 2013;14(4):423-36DOIPubMedGenomics and bioinformatics
- Drug repositioning from the combined evaluation of phenotypic and target-based screeningAMIA Jt Summits Transl Sci Proc 2013;2013:161PubMedScreening and drug repurposing
- Managing missing measurements in small-molecule screensJ Comput Aided Mol Des 2013;27(5):469-78DOIPubMedScreening and drug repurposing
- RS-WebPredictor: a server for predicting CYP-mediated sites of metabolism on drug-like moleculesBioinformatics 2013;29(4):497-8DOIPubMedFree full textDrug metabolism and toxicity
- Scaffold network generator: a tool for mining molecular structuresBioinformatics 2013;29(20):2655-6DOIPubMedScreening and drug repurposing
- Using economic optimization to design high-throughput screensFuture Med Chem 2013;5(1):9-11DOIPubMedScreening and drug repurposing
- XenoSite: accurately predicting CYP-mediated sites of metabolism with neural networksJ Chem Inf Model 2013;53(12):3373-83DOIPubMedDrug metabolism and toxicity
2012
- Automatically detecting workflows in PubChemJ Biomol Screen 2012;17(8):1071-9DOIPubMedScreening and drug repurposing
- Utility-aware screening with clique-oriented prioritizationJ Chem Inf Model 2012;52(1):29-37DOIPubMedFree full textScreening and drug repurposing
2011
- Enhancing the rate of scaffold discovery with diversity-oriented prioritizationBioinformatics 2011;27(16):2271-8DOIPubMedFree full textScreening and drug repurposing
- Mining small-molecule screens to repurpose drugsBrief Bioinform 2011;12(4):327-35DOIPubMedScreening and drug repurposing
- Probabilistic Substructure Mining From Small-Molecule ScreensMol Inform 2011;30(9):809-15DOIPubMedChemical informatics
2010
- A CROC stronger than ROC: measuring, visualizing and optimizing early retrievalBioinformatics 2010;26(10):1348-56DOIPubMedFree full textChemical informatics
- An economic framework to prioritize confirmatory tests after a high-throughput screenJ Biomol Screen 2010;15(6):680-6DOIPubMedFree full textScreening and drug repurposing
2009
- Influence relevance voting: an accurate and interpretable virtual high throughput screening methodJ Chem Inf Model 2009;49(4):756-66DOIPubMedFree full textChemical informatics
- Large scale study of multiple-molecule queriesJ Cheminform 2009;1(1):7DOIPubMedFree full textChemical informatics
2008
- Discovery of power-laws in chemical spaceJ Chem Inf Model 2008;48(6):1138-51DOIPubMedChemical informatics
2007
- Bounds and algorithms for fast exact searches of chemical fingerprints in linear and sublinear timeJ Chem Inf Model 2007;47(2):302-17DOIPubMedFree full textChemical informatics
- ChemDB update--full-text search and virtual chemical spaceBioinformatics 2007;23(17):2348-51DOIPubMedChemical informatics
- Lossless compression of chemical fingerprints using integer entropy codes improves storage and retrievalJ Chem Inf Model 2007;47(6):2098-109DOIPubMedFree full textChemical informatics
- Mathematical correction for fingerprint similarity measures to improve chemical retrievalJ Chem Inf Model 2007;47(3):952-64DOIPubMedChemical informatics
- One- to four-dimensional kernels for virtual screening and the prediction of physical, chemical, and biological propertiesJ Chem Inf Model 2007;47(3):965-74DOIPubMedChemical informatics
2006
- Functional census of mutation sequence spaces: the example of p53 cancer rescue mutantsIEEE/ACM Trans Comput Biol Bioinform 2006;3(2):114-25DOIPubMedFree full textGenomics and bioinformatics
- Statistical Distribution of Chemical FingerprintsLect Notes Comput Sci 2006:11-18DOIChemical informatics
- Structure-based inhibitor design of AccD5, an essential acyl-CoA carboxylase carboxyltransferase domain of Mycobacterium tuberculosisProc Natl Acad Sci U S A 2006;103(9):3072-7DOIPubMedFree full textScreening and drug repurposing
2005
- ChemDB: a public database of small molecules and related chemoinformatics resourcesBioinformatics 2005;21(22):4133-9DOIPubMedChemical informatics
- Graph kernels for chemical informaticsNeural Netw 2005;18(8):1093-110DOIPubMedChemical informatics
- Kernels for small molecules and the prediction of mutagenicity, toxicity and anti-cancer activityBioinformatics 2005;21 Suppl 1:i359-68DOIPubMedChemical informatics
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