S. Joshua Swamidass
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American medical researcher
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Biology Philosophy
Why Is S. Joshua Swamidass Influential?
(Suggest an Edit or Addition)According to Wikipedia, S. Joshua Swamidass is an American computational biologist, physician, academic, and author. He is an associate professor of Laboratory and Genomic Medicine, and a Faculty Lead of Translational Bioinformatics in the Institute for Informatics at Washington University in St. Louis.
S. Joshua Swamidass's Published Works
Number of citations in a given year to any of this author's works
Total number of citations to an author for the works they published in a given year. This highlights publication of the most important work(s) by the author
Published Works
- Opportunities and obstacles for deep learning in biology and medicine (2017) (1310)
- Graph kernels for chemical informatics (2005) (456)
- A survey of current trends in computational drug repositioning (2016) (383)
- Open Source Drug Discovery with the Malaria Box Compound Collection for Neglected Diseases and Beyond (2016) (324)
- Kernels for small molecules and the prediction of mutagenicity, toxicity and anti-cancer activity (2005) (198)
- ChemDB: a public database of small molecules and related chemoinformatics resources (2005) (171)
- XenoSite: Accurately Predicting CYP-Mediated Sites of Metabolism with Neural Networks (2013) (151)
- Modeling Epoxidation of Drug-like Molecules with a Deep Machine Learning Network (2015) (118)
- ChemDB update - full-text search and virtual chemical space (2007) (111)
- Structure-based inhibitor design of AccD5, an essential acyl-CoA carboxylase carboxyltransferase domain of Mycobacterium tuberculosis. (2006) (106)
- A CROC stronger than ROC: measuring, visualizing and optimizing early retrieval (2010) (102)
- Deep Learning Global Glomerulosclerosis in Transplant Kidney Frozen Sections (2018) (99)
- Bounds and Algorithms for Fast Exact Searches of Chemical Fingerprints in Linear and Sublinear Time (2007) (91)
- Mining small-molecule screens to repurpose drugs (2011) (81)
- Mathematical Correction for Fingerprint Similarity Measures to Improve Chemical Retrieval (2007) (76)
- Modeling Reactivity to Biological Macromolecules with a Deep Multitask Network (2016) (69)
- Site of reactivity models predict molecular reactivity of diverse chemicals with glutathione. (2015) (64)
- Discovery of Power-Laws in Chemical Space (2008) (64)
- One- to Four-Dimensional Kernels for Virtual Screening and the Prediction of Physical, Chemical, and Biological Properties (2007) (56)
- Influence Relevance Voting: An Accurate And Interpretable Virtual High Throughput Screening Method (2009) (53)
- XenoSite server: a web-available site of metabolism prediction tool (2015) (52)
- RS-WebPredictor: a server for predicting CYP-mediated sites of metabolism on drug-like molecules (2013) (52)
- Lossless Compression of Chemical Fingerprints Using Integer Entropy Codes Improves Storage and Retrieval (2007) (49)
- Standard operating procedure for somatic variant refinement of sequencing data with paired tumor and normal samples (2018) (48)
- A deep learning approach to automate refinement of somatic variant calling from cancer sequencing data (2018) (48)
- Deep Learning to Predict the Formation of Quinone Species in Drug Metabolism. (2017) (47)
- Functional census of mutation sequence spaces: the example of p53 cancer rescue mutants (2006) (46)
- Unsupervised detection of cancer driver mutations with parsimony-guided learning (2016) (45)
- A simple model predicts UGT-mediated metabolism (2016) (45)
- Statistically identifying tumor suppressors and oncogenes from pan-cancer genome-sequencing data (2015) (43)
- Accounting for proximal variants improves neoantigen prediction (2018) (36)
- Accounting for noise when clustering biological data (2012) (29)
- BEESEM: estimation of binding energy models using HT‐SELEX data (2017) (28)
- Machine learning liver-injuring drug interactions with non-steroidal anti-inflammatory drugs (NSAIDs) from a retrospective electronic health record (EHR) cohort (2021) (28)
- Bigger data, collaborative tools and the future of predictive drug discovery (2014) (25)
- Modeling Small-Molecule Reactivity Identifies Promiscuous Bioactive Compounds (2018) (25)
- Large scale study of multiple-molecule queries (2009) (25)
- Accurate and efficient target prediction using a potency-sensitive influence-relevance voter (2015) (24)
- Computational Approach to Structural Alerts: Furans, Phenols, Nitroaromatics, and Thiophenes. (2017) (24)
- ‘Black Box’ to ‘Conversational’ Machine Learning: Ondansetron Reduces Risk of Hospital-Acquired Venous Thromboembolism (2020) (24)
- Subcellular Localization and Ser-137 Phosphorylation Regulate Tumor-suppressive Activity of Profilin-1* (2015) (23)
- Learning a Local-Variable Model of Aromatic and Conjugated Systems (2018) (22)
- Inhibition of DNA Methyltransferases Blocks Mutant Huntingtin-Induced Neurotoxicity (2016) (22)
- Deep learning the structural determinants of protein biochemical properties by comparing structural ensembles with DiffNets (2021) (22)
- Deep learning quantification of percent steatosis in donor liver biopsy frozen sections (2020) (21)
- Development and Validation of a Deep Learning Model to Quantify Glomerulosclerosis in Kidney Biopsy Specimens (2021) (20)
- Scaffold network generator: a tool for mining molecular structures (2013) (20)
- An Economic Framework to Prioritize Confirmatory Tests after a High-Throughput Screen (2010) (18)
- Probabilistic Substructure Mining From Small‐Molecule Screens (2011) (18)
- Computationally Assessing the Bioactivation of Drugs by N-Dealkylation. (2018) (18)
- Extending P450 site-of-metabolism models with region-resolution data (2015) (17)
- The Overlooked Science of Genealogical Ancestry (2017) (14)
- Improved Prediction of CYP-Mediated Metabolism with Chemical Fingerprints (2015) (13)
- One- to Four-Dimensional Kernels for Virtual Screening and the Prediction of Physical, Chemical, and Biological Properties. (2007) (13)
- CYP2C19 and 3A4 Dominate Metabolic Clearance and Bioactivation of Terbinafine Based on Computational and Experimental Approaches. (2019) (13)
- The Metabolic Rainbow: Deep Learning Phase 1 Metabolism in Five Colors (2018) (12)
- Dual mechanisms suppress meloxicam bioactivation relative to sudoxicam. (2020) (11)
- Meloxicam methyl group determines enzyme specificity for thiazole bioactivation compared to sudoxicam. (2020) (11)
- Inhibition of DNA Methyltransferases Blocks Mutant Huntingtin-Induced Neurotoxicity. (2016) (11)
- Combined Analysis of Phenotypic and Target-Based Screening in Assay Networks (2014) (11)
- Lamisil (terbinafine) toxicity: Determining pathways to bioactivation through computational and experimental approaches (2018) (10)
- Comprehensive Kinetic and Modeling Analyses Revealed CYP2C9 and 3A4 Determine Terbinafine Metabolic Clearance and Bioactivation. (2019) (10)
- Deep learning long-range information in undirected graphs with wave networks (2018) (10)
- Enhancing the rate of scaffold discovery with diversity-oriented prioritization (2011) (9)
- Precision Medicine in Pancreatic Disease—Knowledge Gaps and Research Opportunities (2019) (9)
- Sharing Chemical Relationships Does Not Reveal Structures (2014) (8)
- Metabolic Forest: Predicting the Diverse Structures of Drug Metabolites (2020) (8)
- XenoNet: Inference and Likelihood of Intermediate Metabolite Formation (2020) (8)
- Automatically Detecting Workflows in PubChem (2012) (7)
- Securely Measuring the Overlap between Private Datasets with Cryptosets (2015) (7)
- Utility-Aware Screening with Clique-Oriented Prioritization (2012) (7)
- Significance of Multiple Bioactivation Pathways for Meclofenamate as Revealed through Modeling and Reaction Kinetics (2020) (7)
- Session Introduction (2005) (6)
- Site-Level Bioactivity of Small-Molecules from Deep-Learned Representations of Quantum Chemistry. (2020) (5)
- Managing missing measurements in small-molecule screens (2013) (5)
- Bridging the Gap Between Neural Network and Kernel Methods: Applications to Drug Discovery (2011) (4)
- Fair-Net: A Network Architecture For Reducing Performance Disparity Between Identifiable Sub-Populations (2021) (4)
- COMPUTATIONAL APPROACHES TO DRUG REPURPOSING AND PHARMACOLOG- SESSION INTRODUCTION (2013) (4)
- Standard operating procedure for somatic variant refinement of tumor sequencing data (2018) (4)
- Cal-Net: Jointly Learning Classification and Calibration On Imbalanced Binary Classification Tasks (2021) (3)
- Modeling the Bioactivation and Subsequent Reactivity of Drugs. (2021) (3)
- A Time-Embedding Network Models the Ontogeny of 23 Hepatic Drug Metabolizing Enzymes. (2019) (3)
- DiffNets: Self-supervised deep learning to identify the mechanistic basis for biochemical differences between protein variants (2020) (2)
- The Influence Relevance Voter : An Accurate And Interpretable Virtual High Throughput Screening Method (2009) (2)
- Using economic optimization to design high-throughput screens. (2013) (2)
- A Deep Learning Approach for the Estimation of Glomerular Filtration Rate (2022) (2)
- Bounds and Algorithms for Fast Exact Searches of Chemical Fingerprints in Linear and Sublinear Time. (2007) (2)
- Impacts of diphenylamine NSAID halogenation on bioactivation risks. (2021) (2)
- In Defense of Tim Keller (2017) (2)
- Erratum: Inhibition of DNA Methyltransferases Blocks Mutant Huntingtin-Induced Neurotoxicity (2016) (1)
- Lamisil (terbinafine): determining bioactivation pathways using computational modeling and experimental approaches (2019) (1)
- The end of evolution? (2019) (1)
- The diversity and disparity in biomedical informatics (DDBI) workshop (2018) (1)
- The asthma gut microbiota influences lung inflammation in gnotobiotic mice (2022) (1)
- Education: Initiatives to bridge faith and science (2015) (1)
- A Genealogical Rapprochement on Adam? (2017) (1)
- Tumor Suppressor Heterogeneous Biomedical Database Integration Using a Hybrid Strategy (2005) (1)
- Bioactivation of Isoxazole-Containing Bromodomain and Extra-Terminal Domain (BET) Inhibitors (2021) (1)
- Statistical Distribution of Chemical Fingerprints (2005) (1)
- Deep Learning Coordinate-Free Quantum Chemistry. (2021) (1)
- BioLogos Deletes an Article (2021) (1)
- Three Stories on Adam (2018) (1)
- Standard operating procedure for somatic variant refinement of sequencing data with paired tumor and normal samples (2018) (1)
- How does the isolation of Tasmania impact recent universal ancestry? (2019) (0)
- The gut microbiota of people with asthma influences lung inflammation in gnotobiotic mice (2023) (0)
- The potential of artificial intelligence-based applications in kidney pathology (2022) (0)
- I Was Wrong on “Monophyletic” (2020) (0)
- DiffNets: deep learning the structural determinants of proteins biochemical properties by comparing different structural ensembles (2020) (0)
- Bring The Questions of Artificial Intelligence (2019) (0)
- Discovery of Novel Reductive Elimination Pathway for 10-Hydroxywarfarin (2022) (0)
- More Than Just Apes (2016) (0)
- DEPLOYMENT OF A DEEP LEARNING MODEL TO ASSIST PATHOLOGISTS WITH DONOR KIDNEY BIOPSY EVALUATION (2022) (0)
- Cancer and Evolution (2018) (0)
- The Misunderstood Science of Genetic Bottlenecks (2022) (0)
- The Garden Path To 1+1=3 (2020) (0)
- Message Passing Neural Networks Improve Prediction of Metabolite Authenticity (2023) (0)
- Reworking the Science of Adam (2018) (0)
- Diffnets for Deep Learning the Structural Determinants of Proteins Biochemical Properties by Comparing Different Structural Ensembles (2021) (0)
- Genome analysis Statistically identifying tumor suppressors and oncogenes from pan-cancer genome-sequencing data (2015) (0)
- Accounting for proximal variants improves neoantigen prediction (2018) (0)
- Modeling the Metabolism and Subsequent Reactivity of Drugs (2017) (0)
- Opportunities and obstacles for deep learning in biology and medicine: 2019 update (2019) (0)
- Modeling P450 SItes of Metabolism (LB596) (2014) (0)
- The Biological Meaning of Race (2020) (0)
- A Sign of Disparity: Racial/Ethnic Composition of Treatment Centers is an Independent Risk Factor in SPRINT Trial (2017) (0)
- Is evolutionary science in conflict with Adam and Eve? (2021) (0)
- Modeling Reactivity to Soft , Hard , and Biological Targets with a Deep Learning Network (2015) (0)
- Dr James Tour and the Great Pascal (2017) (0)
- 247 – Deep Learning Algorithm Accurately Predicts Percent Steatosis in Donor Liver Biopsy Frozen Sections (2019) (0)
- Opportunities and obstacles for deep learning in biology and medicine [update in progress] (2020) (0)
- Evolution and Functional Information (2017) (0)
- Why We Talk About Race (2021) (0)
- A deep learning approach to automate refinement of somatic variant calling from cancer sequencing data (2018) (0)
- Faculty Opinions recommendation of An inside-out origin for the eukaryotic cell. (2017) (0)
- May More Scientists Care About Adam and Eve (2021) (0)
- A New, Old, and Ancient Conversation Begins (2019) (0)
- Disentangling Socioeconomic Status and Race in Infant Outcomes: A Neural Network Analysis (2021) (0)
- Why I Went Public on Evolution (2020) (0)
- I Agree With Behe (2019) (0)
- Drug repositioning from the combined evaluation of phenotypic and target-based screening. (2013) (0)
- Brief Population Bottlenecks Are Beyond The Genetic Streetlight (2021) (0)
- P166 - The sudoxicam family: Identifying how thiazole structure determines bioactivation relevance (2020) (0)
- A Fair Hearing for Behe (2019) (0)
- A U-Turn on Adam and Eve (2021) (0)
- Initiatives to bridge faith and science: Education (2015) (0)
- Source Drug Discovery with the Malaria Box Compound Collection for Neglected Diseases and Beyond Citation (2016) (0)
- Very High Accuracy Prediction of UDP‐Glucuronosyltransferase Sites of Metabolism (2015) (0)
- 22. Standardization and systematization of somatic variant refinement using a standard operating procedure and deep learning (2019) (0)
- Is COVID-19 Created or Designed? (2020) (0)
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