Works by Shukla, Maulik

Results: 26

RNA-Rocket: an RNA-Seq analysis resource for infectious disease research.

Published in:

2015

By:

Warren, Andrew S.;
Aurrecoechea, Cristina;
Brunk, Brian;
Desai, Prerak;
Emrich, Scott;
Giraldo-Calderón, Gloria I.;
Harb, Omar;
Hix, Deborah;
Lawson, Daniel;
Machi, Dustin;
Chunhong Mao;
McClelland, Michael;
Nordberg, Eric;
Shukla, Maulik;
Vosshall, Leslie B.;
Wattam, Alice R.;
Will, Rebecca;
Hyun Seung Yoo;
Sobral, Bruno

Publication type:

Product Review

Curation, integration and visualization of bacterial virulence factors in PATRIC.

Published in:

Bioinformatics, 2015, v. 31, n. 2, p. 252, doi. 10.1093/bioinformatics/btu631

By:

Mao, Chunhong;
Abraham, David;
Wattam, Alice R.;
Wilson, Meredith J.C.;
Shukla, Maulik;
Yoo, Hyun Seung;
Sobral, Bruno W.

Publication type:

Article

Integration and visualization of host–pathogen data related to infectious diseases.

Published in:

Bioinformatics, 2011, v. 27, n. 16, p. 2279, doi. 10.1093/bioinformatics/btr391

By:

Driscoll, Timothy;
Gabbard, Joseph L.;
Mao, Chunhong;
Dalay, Oral;
Shukla, Maulik;
Freifeld, Clark C.;
Hoen, Anne Gatewood;
Brownstein, John S.;
Sobral, Bruno W.

Publication type:

Article

Enhanced Co-Expression Extrapolation (COXEN) Gene Selection Method for Building Anti-Cancer Drug Response Prediction Models.

Published in:

Genes, 2020, v. 11, n. 9, p. 1070, doi. 10.3390/genes11091070

By:

Zhu, Yitan;
Brettin, Thomas;
Evrard, Yvonne A.;
Xia, Fangfang;
Partin, Alexander;
Shukla, Maulik;
Yoo, Hyunseung;
Doroshow, James H.;
Stevens, Rick L.

Publication type:

Article

Predicting antimicrobial resistance using conserved genes.

Published in:

PLoS Computational Biology, 2020, v. 16, n. 10, p. 1, doi. 10.1371/journal.pcbi.1008319

By:

Nguyen, Marcus;
Olson, Robert;
Shukla, Maulik;
VanOeffelen, Margo;
Davis, James J.

Publication type:

Article

637. Whole-Genome Sequencing (WGS) of Isolates from Resolving (RB) and Persistent (PB) Methicillin-Resistant Staphylococcus aureus Bacteremia.

Published in:

Open Forum Infectious Diseases, 2019, v. 6, p. S295, doi. 10.1093/ofid/ofz360.705

By:

Sharma-Kuinkel, Batu K;
Medie, Felix;
Ruffin, Felicia;
Wattam, Rebecca;
Shukla, Maulik;
Davis, James;
Yeaman, Michael;
Fowler, Vance G

Publication type:

Article

Publisher Correction: Converting tabular data into images for deep learning with convolutional neural networks.

Published in:

2021

By:

Zhu, Yitan;
Brettin, Thomas;
Xia, Fangfang;
Partin, Alexander;
Shukla, Maulik;
Yoo, Hyunseung;
Evrard, Yvonne A.;
Doroshow, James H.;
Stevens, Rick L.

Publication type:

Correction Notice

Rickettsia Phylogenomics: Unwinding the Intricacies of Obligate Intracellular Life.

Published in:

PLoS ONE, 2008, v. 3, n. 4, p. 1, doi. 10.1371/journal.pone.0002018

By:

Gillespie, Joseph J.;
Williams, Kelly;
Shukla, Maulik;
Snyder, Eric E.;
Nordberg, Eric K.;
Ceraul, Shane M.;
Dharmanolla, Chitti;
Rainey, Daphne;
Soneja, Jeetendra;
Shallom, Joshua M.;
Dongre^Vishnubhat, Nataraj;
Wattam, Rebecca;
Purkayastha, Anjan;
Czar, Michael;
Crasta, Oswald;
Setubal, Joao C.;
Azad, Abdu F.;
Sobral, Bruno S.

Publication type:

Article

Antimicrobial Resistance Prediction in PATRIC and RAST.

Published in:

Scientific Reports, 2016, p. 27930, doi. 10.1038/srep27930

By:

Davis, James J.;
Boisvert, Sébastien;
Brettin, Thomas;
Kenyon, Ronald W.;
Mao, Chunhong;
Olson, Robert;
Overbeek, Ross;
Santerre, John;
Shukla, Maulik;
Wattam, Alice R.;
Will, Rebecca;
Xia, Fangfang;
Stevens, Rick

Publication type:

Article

RASTtk: A modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes.

Published in:

Scientific Reports, 2015, p. 8365, doi. 10.1038/srep08365

By:

Brettin, Thomas;
Davis, James J.;
Disz, Terry;
Edwards, Robert A.;
Gerdes, Svetlana;
Olsen, Gary J.;
Olson, Robert;
Overbeek, Ross;
Parrello, Bruce;
Pusch, Gordon D.;
Shukla, Maulik;
Thomason, James A.;
Stevens, Rick;
Vonstein, Veronika;
Wattam, Alice R.;
Xia, Fangfang

Publication type:

Article

Data imbalance in drug response prediction: multi-objective optimization approach in deep learning setting.

Published in:

Briefings in Bioinformatics, 2025, v. 26, n. 2, p. 1, doi. 10.1093/bib/bbaf134

By:

Narykov, Oleksandr;
Zhu, Yitan;
Brettin, Thomas;
Evrard, Yvonne A;
Partin, Alexander;
Xia, Fangfang;
Shukla, Maulik;
Vasanthakumari, Priyanka;
Doroshow, James H;
Stevens, Rick L

Publication type:

Article

cross-study analysis of drug response prediction in cancer cell lines.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 1, p. 1, doi. 10.1093/bib/bbab356

By:

Xia, Fangfang;
Allen, Jonathan;
Balaprakash, Prasanna;
Brettin, Thomas;
Garcia-Cardona, Cristina;
Clyde, Austin;
Cohn, Judith;
Doroshow, James;
Duan, Xiaotian;
Dubinkina, Veronika;
Evrard, Yvonne;
Fan, Ya Ju;
Gans, Jason;
He, Stewart;
Lu, Pinyi;
Maslov, Sergei;
Partin, Alexander;
Shukla, Maulik;
Stahlberg, Eric;
Wozniak, Justin M

Publication type:

Article

genomic data resource for predicting antimicrobial resistance from laboratory-derived antimicrobial susceptibility phenotypes.

Published in:

Briefings in Bioinformatics, 2021, v. 22, n. 6, p. 1, doi. 10.1093/bib/bbab313

By:

VanOeffelen, Margo;
Nguyen, Marcus;
Aytan-Aktug, Derya;
Brettin, Thomas;
Dietrich, Emily M;
Kenyon, Ronald W;
Machi, Dustin;
Mao, Chunhong;
Olson, Robert;
Pusch, Gordon D;
Shukla, Maulik;
Stevens, Rick;
Vonstein, Veronika;
Warren, Andrew S;
Wattam, Alice R;
Yoo, Hyunseung;
Davis, James J

Publication type:

Article

Converting tabular data into images for deep learning with convolutional neural networks.

Published in:

Scientific Reports, 2021, v. 11, n. 1, p. 1, doi. 10.1038/s41598-021-90923-y

By:

Zhu, Yitan;
Brettin, Thomas;
Xia, Fangfang;
Partin, Alexander;
Shukla, Maulik;
Yoo, Hyunseung;
Evrard, Yvonne A.;
Doroshow, James H.;
Stevens, Rick L.

Publication type:

Article

Ensemble transfer learning for the prediction of anti-cancer drug response.

Published in:

Scientific Reports, 2020, v. 10, n. 1, p. 1, doi. 10.1038/s41598-020-74921-0

By:

Zhu, Yitan;
Brettin, Thomas;
Evrard, Yvonne A.;
Partin, Alexander;
Xia, Fangfang;
Shukla, Maulik;
Yoo, Hyunseung;
Doroshow, James H.;
Stevens, Rick L.

Publication type:

Article

PATtyFams: Protein Families for the Microbial Genomes in the PATRIC Database.

Published in:

Frontiers in Microbiology, 2016, p. 1, doi. 10.3389/fmicb.2016.00118

By:

Davis, James J.;
Shukla, Maulik;
Hyunseung Yoo;
Olson, Robert;
Gerdes, Svetlana;
Pusch, Gordon D.;
Vonstein, Veronika;
Olsen, Gary J.;
Wattam, Alice R.

Publication type:

Article

A Comprehensive Investigation of Active Learning Strategies for Conducting Anti-Cancer Drug Screening.

Published in:

Cancers, 2024, v. 16, n. 3, p. 530, doi. 10.3390/cancers16030530

By:

Vasanthakumari, Priyanka;
Zhu, Yitan;
Brettin, Thomas;
Partin, Alexander;
Shukla, Maulik;
Xia, Fangfang;
Narykov, Oleksandr;
Weil, Michael Ryan;
Stevens, Rick L.

Publication type:

Article

Integration of Computational Docking into Anti-Cancer Drug Response Prediction Models.

Published in:

Cancers, 2024, v. 16, n. 1, p. 50, doi. 10.3390/cancers16010050

By:

Narykov, Oleksandr;
Zhu, Yitan;
Brettin, Thomas;
Evrard, Yvonne A.;
Partin, Alexander;
Shukla, Maulik;
Xia, Fangfang;
Clyde, Austin;
Vasanthakumari, Priyanka;
Doroshow, James H.;
Stevens, Rick L.

Publication type:

Article

TULIP: An RNA-seq-based Primary Tumor Type Prediction Tool Using Convolutional Neural Networks.

Published in:

Cancer Informatics, 2022, p. 1, doi. 10.1177/11769351221139491

By:

Jones, Sara;
Beyers, Matthew;
Shukla, Maulik;
Xia, Fangfang;
Brettin, Thomas;
Stevens, Rick;
Weil, M Ryan;
Ranganathan Ganakammal, Satishkumar

Publication type:

Article

TULIP: An RNA-seq-based Primary Tumor Type Prediction Tool Using Convolutional Neural Networks.

Published in:

Cancer Informatics, 2022, v. 21, p. 1, doi. 10.1177/11769351221139491

By:

Jones, Sara;
Beyers, Matthew;
Shukla, Maulik;
Fangfang Xia;
Brettin, Thomas;
Stevens, Rick;
Weil, M. Ryan;
Ganakammal, Satishkumar Ranganathan

Publication type:

Article

Enabling comparative modeling of closely related genomes: example genus Brucella.

Published in:

2015

By:

Faria, José;
Edirisinghe, Janaka;
Davis, James;
Disz, Terrence;
Hausmann, Anna;
Henry, Christopher;
Olson, Robert;
Overbeek, Ross;
Pusch, Gordon;
Shukla, Maulik;
Vonstein, Veronika;
Wattam, Alice

Publication type:

Report

Predicting tumor cell line response to drug pairs with deep learning.

Published in:

BMC Bioinformatics, 2018, v. 19, n. 18, p. 71, doi. 10.1186/s12859-018-2509-3

By:

Xia, Fangfang;
Shukla, Maulik;
Brettin, Thomas;
Garcia-Cardona, Cristina;
Cohn, Judith;
Allen, Jonathan E.;
Maslov, Sergei;
Holbeck, Susan L.;
Doroshow, James H.;
Evrard, Yvonne A.;
Stahlberg, Eric A.;
Stevens, Rick L.

Publication type:

Article

PATRIC, the bacterial bioinformatics database and analysis resource.

Published in:

Nucleic Acids Research, 2014, v. 42, n. D1, p. D581, doi. 10.1093/nar/gkt1099

By:

Wattam, Alice R.;
Abraham, David;
Dalay, Oral;
Disz, Terry L.;
Driscoll, Timothy;
Gabbard, Joseph L.;
Gillespie, Joseph J.;
Gough, Roger;
Hix, Deborah;
Kenyon, Ronald;
Machi, Dustin;
Mao, Chunhong;
Nordberg, Eric K.;
Olson, Robert;
Overbeek, Ross;
Pusch, Gordon D.;
Shukla, Maulik;
Schulman, Julie;
Stevens, Rick L.;
Sullivan, Daniel E.

Publication type:

Article

The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST).

Published in:

Nucleic Acids Research, 2014, v. 42, n. D1, p. D206, doi. 10.1093/nar/gkt1226

By:

Overbeek, Ross;
Olson, Robert;
Pusch, Gordon D.;
Olsen, Gary J.;
Davis, James J.;
Disz, Terry;
Edwards, Robert A.;
Gerdes, Svetlana;
Parrello, Bruce;
Shukla, Maulik;
Vonstein, Veronika;
Wattam, Alice R.;
Xia, Fangfang;
Stevens, Rick

Publication type:

Article

Data Integration for Dynamic and Sustainable Systems Biology Resources: Challenges and Lessons Learned.

Published in:

Chemistry & Biodiversity, 2010, v. 7, n. 5, p. 1124, doi. 10.1002/cbdv.200900317

By:

Sullivan, Daniel E.;
Gabbard, Joseph L.;
Shukla, Maulik;
Sobral, Bruno

Publication type:

Article

Learning curves for drug response prediction in cancer cell lines.

Published in:

BMC Bioinformatics, 2021, v. 22, p. 1, doi. 10.1186/s12859-021-04163-y

By:

Partin, Alexander;
Brettin, Thomas;
Evrard, Yvonne A.;
Zhu, Yitan;
Yoo, Hyunseung;
Xia, Fangfang;
Jiang, Songhao;
Clyde, Austin;
Shukla, Maulik;
Fonstein, Michael;
Doroshow, James H.;
Stevens, Rick L.

Publication type:

Article