Joshua Swamidass, S.: search on Z-Library

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1

XenoSite: Accurately Predicting CYP-Mediated Sites of Metabolism with Neural Networks

Zaretzki, Jed, Matlock, Matthew, Swamidass, S. Joshua

Journal:

Journal of Chemical Information and Modeling

Year:

2013

Language:

english

File:

PDF, 1.93 MB

english, 2013

2

Discovery of Power-Laws in Chemical Space

Benz, Ryan W., Swamidass, S. Joshua, Baldi, Pierre

Journal:

Journal of Chemical Information and Modeling

Year:

2008

Language:

english

File:

PDF, 1.62 MB

english, 2008

3

XenoNet: Inference and Likelihood of Intermediate Metabolite Formation

Flynn, Noah, Dang, Na Le, Ward, Michael, Swamidass, S. Joshua

Journal:

Journal of Chemical Information and Modeling

Year:

2020

File:

PDF, 1.33 MB

2020

4

Erratum: Erratum: Inhibition of DNA Methyltransferases Blocks Mutant Huntingtin-Induced Neurotoxicity

Pan, Yanchun, Daito, Takuji, Sasaki, Yo, Chung, Yong Hee, Xing, Xiaoyun, Pondugula, Santhi, Swamidass, S. Joshua, Wang, Ting, Kim, Albert H., Yano, Hiroko

Journal:

Scientific Reports

Year:

2016

Language:

english

File:

PDF, 120 KB

english, 2016

5

Modeling Reactivity to Biological Macromolecules with a Deep Multitask Network

Hughes, Tyler B., Dang, Na Le, Miller, Grover P., Swamidass, S. Joshua

Journal:

ACS Central Science

Year:

2016

Language:

english

File:

PDF, 1.86 MB

english, 2016

6

BEESEM: estimation of binding energy models using HT-SELEX data

Ruan, Shuxiang, Swamidass, S. Joshua, Stormo, Gary D.

Journal:

Year:

2017

Language:

english

File:

PDF, 316 KB

english, 2017

7

Learning a Local-Variable Model of Aromatic and Conjugated Systems

Matlock, Matthew K., Dang, Na Le, Swamidass, S. Joshua

Journal:

ACS Central Science

Year:

2018

Language:

english

File:

PDF, 3.68 MB

english, 2018

8

Comprehensive Kinetic and Modeling Analyses Revealed CYP2C9 and 3A4 Determine Terbinafine Metabolic Clearance and Bioactivation

Barnette, Dustyn A., Davis, Mary A., Flynn, Noah, Pidugu, Anirudh S., Joshua Swamidass, S., Miller, Grover P.

Journal:

Biochemical Pharmacology

Year:

2019

File:

PDF, 2.37 MB

2019

9

Accurate and efficient target prediction using a potency-sensitive influence-relevance voter

Lusci, Alessandro, Fooshee, David, Browning, Michael, Swamidass, Joshua, Baldi, Pierre

Journal:

Journal of Cheminformatics

Year:

2015

Language:

english

File:

PDF, 1.19 MB

english, 2015

10

[WORLD SCIENTIFIC Proceedings of the Pacific Symposium - Kohala Coast, Hawaii, USA (3 – 7 January 2018)] Biocomputing 2018 - The diversity and disparity in biomedical informatics (DDBI) workshop

Southerland, William M., Swamidass, S. Joshua, Payne, Philip R. O., Wiley, Laura, Williams-DeVane, ClarLynda

Language:

english

File:

PDF, 591 KB

english

11

The end of evolution?

Lents, Nathan H., Swamidass, S. Joshua, Lenski, Richard E.

Journal:

Year:

2019

File:

PDF, 492 KB

2019

12

Unsupervised detection of cancer driver mutations with parsimony-guided learning

Kumar, Runjun D, Swamidass, S Joshua, Bose, Ron

Journal:

Nature Genetics

Year:

2016

Language:

english

File:

PDF, 7.76 MB

english, 2016

13

Computational Approach to Structural Alerts: Furans, Phenols, Nitroaromatics, and Thiophenes

Dang, Na Le, Hughes, Tyler B., Miller, Grover P., Swamidass, S. Joshua

Journal:

Chemical Research in Toxicology

Year:

2017

Language:

english

File:

PDF, 3.75 MB

english, 2017

14

Computationally Assessing the Bioactivation of Drugs by N-Dealkylation

Dang, Na Le, Hughes, Tyler B., Miller, Grover Paul, Swamidass, S. Joshua

Journal:

Chemical Research in Toxicology

Year:

2018

Language:

english

File:

PDF, 1.05 MB

english, 2018

15

Mathematical Correction for Fingerprint Similarity Measures to Improve Chemical Retrieval

Swamidass, S. Joshua, Baldi, Pierre

Journal:

Journal of Chemical Information and Modeling

Year:

2007

Language:

english

File:

PDF, 298 KB

english, 2007

16

[IEEE 2019 International Joint Conference on Neural Networks (IJCNN) - Budapest, Hungary (2019.7.14-2019.7.19)] 2019 International Joint Conference on Neural Networks (IJCNN) - Deep learning long-range information in undirected graphs with wave networks

Matlock, Matthew K., Datta, Arghya, Dang, Na Le, Jiang, Kevin, Swamidass, S. Joshua

Year:

2019

File:

PDF, 1.40 MB

2019

17

Extending P450 site-of-metabolism models with region-resolution data

Zaretzki, Jed M., Browning, Michael R., Hughes, Tyler B., Swamidass, S. Joshua

Journal:

Year:

2015

Language:

english

File:

PDF, 690 KB

english, 2015

18

CYP2C19 and 3A4 dominate metabolic clearance and bioactivation of terbinafine based on computational and experimental approaches

Davis, Mary Alexandra, Barnette, Dustyn A, FLynn, Noah R, Pidugu, Anirudh S, Swamidass, S. Joshua, Boysen, Gunnar, Miller, Grover Paul

Journal:

Chemical Research in Toxicology

Year:

2019

Language:

english

File:

PDF, 2.01 MB

english, 2019

19

Sharing Chemical Relationships Does Not Reveal Structures

Matlock, Matthew, Swamidass, S. Joshua

Journal:

Journal of Chemical Information and Modeling

Year:

2014

Language:

english

File:

PDF, 1.50 MB

english, 2014

20

Statistically Identifying Tumor Suppressors and Oncogenes from Pan-Cancer Genome Sequencing Data

Kumar, Runjun D., Searleman, Adam C., Swamidass, S. Joshua, Griffith, Obi L., Bose, Ron

Journal:

Year:

2015

Language:

english

File:

PDF, 513 KB

english, 2015

21

Accounting for proximal variants improves neoantigen prediction

Hundal, Jasreet, Kiwala, Susanna, Feng, Yang-Yang, Liu, Connor J., Govindan, Ramaswamy, Chapman, William C., Uppaluri, Ravindra, Swamidass, S. Joshua, Griffith, Obi L., Mardis, Elaine R., Griffith, Ma

Journal:

Nature Genetics

Year:

2018

Language:

english

File:

PDF, 1.81 MB

english, 2018

22

"Black Box" to "Conversational" Machine Learning: Ondansetron Reduces Risk of Hospital-Acquired Venous Thromboembolism

Datta, Arghya, Matlock, Matthew K., Dang, Na Le, Moulin, Thiago, Woeltje, Keith F., Yanik, Elizabeth L., Swamidass, Sanjay Joshua

Journal:

IEEE Journal of Biomedical and Health Informatics

Year:

2020

File:

PDF, 431 KB

2020

23

Using economic optimization to design high-throughput screens

Swamidass, S Joshua

Journal:

Future Medicinal Chemistry

Year:

2013

File:

PDF, 735 KB

2013

24

Education: Initiatives to bridge faith and science

Swamidass, S. Joshua

Journal:

Year:

2015

Language:

english

File:

PDF, 323 KB

english, 2015

25

A Time-Embedding Network Models the Ontogeny of 23 Hepatic Drug Metabolizing Enzymes

Matlock, Matthew Kelly, Tambe, Abhik, Elliott-Higgins, Jack, Hines, Ronald N, Miller, Grover Paul, Swamidass, S. Joshua

Journal:

Chemical Research in Toxicology

Year:

2019

Language:

english

File:

PDF, 2.86 MB

english, 2019

26

One- to Four-Dimensional Kernels for Virtual Screening and the Prediction of Physical, Chemical, and Biological Properties

Azencott, Chloé-Agathe, Ksikes, Alexandre, Swamidass, S. Joshua, Chen, Jonathan H., Ralaivola, Liva, Baldi, Pierre

Journal:

Journal of Chemical Information and Modeling

Year:

2007

Language:

english

File:

PDF, 140 KB

english, 2007

27

Site-Level Bioactivity of Small-Molecules from Deep-Learned Representations of Quantum Chemistry

Sarullo, Kathryn, Matlock, Matthew K., Swamidass, S. Joshua

Journal:

Journal of Physical Chemistry A

Year:

2020

File:

PDF, 1.58 MB

2020

28

Large scale study of multiple-molecule queries

Ramzi J Nasr, S Joshua Swamidass, Pierre F Baldi

Journal:

Journal of Cheminformatics

Year:

2009

Language:

english

File:

PDF, 758 KB

english, 2009

29

Subcellular Localization and Ser-137 Phosphorylation Regulate Tumor-suppressive Activity of Profilin-1

Diamond, Marc I., Cai, Shirong, Boudreau, Aaron, Carey, Clifton J., Lyle, Nicholas, Pappu, Rohit V., Swamidass, S. Joshua, Bissell, Mina, Piwnica-Worms, Helen, Shao, Jieya

Journal:

Journal of Biological Chemistry

Year:

2015

Language:

english

File:

PDF, 3.39 MB

english, 2015

30

Modeling Small-Molecule Reactivity Identifies Promiscuous Bioactive Compounds

Matlock, Matthew Kelly, Hughes, Tyler B., Dahlin, Jayme L., Swamidass, S. Joshua

Journal:

Journal of Chemical Information and Modeling

Year:

2018

Language:

english

File:

PDF, 4.85 MB

english, 2018

31

Bigger data, collaborative tools and the future of predictive drug discovery

Ekins, Sean, Clark, Alex M., Swamidass, S. Joshua, Litterman, Nadia, Williams, Antony J.

Journal:

Journal of Computer-Aided Molecular Design

Year:

2014

Language:

english

File:

PDF, 661 KB

english, 2014

32

The Metabolic Rainbow: Deep Learning Phase I Metabolism in Five Colors

Dang, Na Le, Matlock, Matthew Kelly, Hughes, Tyler B., Swamidass, S. Joshua

Journal:

Journal of Chemical Information and Modeling

Year:

2020

File:

PDF, 7.16 MB

2020

33

Improved Prediction of CYP-Mediated Metabolism with Chemical Fingerprints

Zaretzki, Jed, Boehm, Kevin M., Swamidass, S. Joshua

Journal:

Journal of Chemical Information and Modeling

Year:

2015

Language:

english

File:

PDF, 2.37 MB

english, 2015

34

Inhibition of DNA Methyltransferases Blocks Mutant Huntingtin-Induced Neurotoxicity

Pan, Yanchun, Daito, Takuji, Sasaki, Yo, Chung, Yong Hee, Xing, Xiaoyun, Pondugula, Santhi, Swamidass, S. Joshua, Wang, Ting, Kim, Albert H., Yano, Hiroko

Journal:

Scientific Reports

Year:

2016

Language:

english

File:

PDF, 2.09 MB

english, 2016

35

Securely Measuring the Overlap between Private Datasets with Cryptosets

Swamidass, S. Joshua, Matlock, Matthew, Rozenblit, Leon, Arthur, Jonathan

Journal:

Year:

2015

Language:

english

File:

PDF, 2.70 MB

english, 2015

36

Deep learning quantification of percent steatosis in donor liver biopsy frozen sections

Sun, Lulu, Marsh, Jon N., Matlock, Matthew K., Chen, Ling, Gaut, Joseph P., Brunt, Elizabeth M., Swamidass, S. Joshua, Liu, Ta-Chiang

Journal:

Year:

2020

File:

PDF, 2.37 MB

2020

37

Probabilistic Substructure Mining From Small-Molecule Screens

Sayan Ranu, Bradley T. Calhoun, Ambuj K. Singh, S. Joshua Swamidass

Journal:

Molecular Informatics

Year:

2011

Language:

english

File:

PDF, 297 KB

english, 2011

38

Site of Reactivity Models Predict Molecular Reactivity of Diverse Chemicals with Glutathione

Hughes, Tyler B., Miller, Grover P., Swamidass, S. Joshua

Journal:

Chemical Research in Toxicology

Year:

2015

Language:

english

File:

PDF, 584 KB

english, 2015

39

Influence Relevance Voting: An Accurate And Interpretable Virtual High Throughput Screening Method

Swamidass, S. Joshua, Azencott, Chloé-Agathe, Lin, Ting-Wan, Gramajo, Hugo, Tsai, Shiou-Chuan, Baldi, Pierre

Journal:

Journal of Chemical Information and Modeling

Year:

2009

Language:

english

File:

PDF, 983 KB

english, 2009

40

Modeling Epoxidation of Drug-like Molecules with a Deep Machine Learning Network

Hughes, Tyler B., Miller, Grover P., Swamidass, S. Joshua

Journal:

ACS Central Science

Year:

2015

Language:

english

File:

PDF, 3.08 MB

english, 2015

41

Utility-Aware Screening with Clique-Oriented Prioritization

Swamidass, S. Joshua, Calhoun, Bradley T., Bittker, Joshua A., Bodycombe, Nicole E., Clemons, Paul A.

Journal:

Journal of Chemical Information and Modeling

Year:

2012

Language:

english

File:

PDF, 1.62 MB

english, 2012

42

Bounds and Algorithms for Fast Exact Searches of Chemical Fingerprints in Linear and Sublinear Time

Swamidass, S. Joshua, Baldi, Pierre

Journal:

Journal of Chemical Information and Modeling

Year:

2007

Language:

english

File:

PDF, 407 KB

english, 2007

43

NIH Public Access

Swamidass, S Joshua, Baldi, Pierre

Year:

2008

Language:

english

File:

PDF, 1.97 MB

english, 2008

44

P166 - The sudoxicam family: Identifying how thiazole structure determines bioactivation relevance

Barnette, Dustyne, Davis, Mary A., Ward, Michael, Swamidass, S. Joshua, Miller, Grover P.

Journal:

Drug Metabolism and Pharmacokinetics

Year:

2020

File:

PDF, 43 KB

2020

45

Deep Learning to Predict the Formation of Quinone Species in Drug Metabolism

Hughes, Tyler B., Swamidass, S. Joshua

Journal:

Chemical Research in Toxicology

Year:

2017

Language:

english

File:

PDF, 5.60 MB

english, 2017

46

Deep Learning Global Glomerulosclerosis in Transplant Kidney Frozen Sections

Marsh, Jon N., Matlock, Matthew K., Kudose, Satoru, Liu, Ta-Chiang, Stappenbeck, Thaddeus S., Gaut, Joseph P., Swamidass, S. Joshua

Journal:

IEEE Transactions on Medical Imaging

Year:

2018

Language:

english

File:

PDF, 9.00 MB

english, 2018

47

The Metabolic Forest: Predicting the Diverse Structures of Drug Metabolites

Hughes, Tyler B., Dang, Na Le, Kumar, Ayush, Flynn, Noah, Swamidass, S. Joshua

Journal:

Journal of Chemical Information and Modeling

Year:

2020

File:

PDF, 3.18 MB

2020

48

Lamisil (terbinafine) Toxicity: Determining pathways to bioactivation through computational and experimental approaches

Barnette, Dustyn A., Davis, Mary A., Dang, Na L., Pidugu, Anirudh S., Hughes, Tyler, Joshua Swamidass, S., Boysen, Gunnar, Miller, Grover P.

Journal:

Biochemical Pharmacology

Year:

2018

Language:

english

File:

PDF, 1.55 MB

english, 2018

49

Lossless Compression of Chemical Fingerprints Using Integer Entropy Codes Improves Storage and Retrieval

Baldi, Pierre, Benz, Ryan W., Hirschberg, Daniel S., Swamidass, S. Joshua

Journal:

Journal of Chemical Information and Modeling

Year:

2007

Language:

english

File:

PDF, 258 KB

english, 2007

50

Using economic optimization to design high-throughput screens

Swamidass, S Joshua

Journal:

Future Medicinal Chemistry

Year:

2013

Language:

english

File:

PDF, 735 KB

english, 2013

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