Author details

Full Name

Maulik Shukla

Affiliation

University of Chicago

ORCID

Career Start Year

2003

Papers

H Index

Expertise

CM4AI Collaborator

PMID	Paper Title	Journal Title	Published Year
36350631	Introducing the Bacterial and Viral Bioinformatics Resource Center (BV-BRC): a resource combining PATRIC, IRDÂ and ViPR.	Nucleic Acids Res	2023
37054986	US National Institutes of Health Prioritization of SARS-CoV-2 Variants.	Emerg Infect Dis	2023
36960342	Data augmentation and multimodal learning for predicting drug response in patient-derived xenografts from gene expressions and histology images.	Front Med (Lausanne)	2023
34524425	A cross-study analysis of drug response prediction in cancer cell lines.	Brief Bioinform	2022
36507076	TULIP: An RNA-seq-based Primary Tumor Type Prediction Tool Using Convolutional Neural Networks.	Cancer Inform	2022
36451881	GenSLMs: Genome-scale language models reveal SARS-CoV-2 evolutionary dynamics.	bioRxiv	2022
36353215	Early detection of emerging SARS-CoV-2 variants of interest for experimental evaluation.	Front Bioinform	2022
34001007	Learning curves for drug response prediction in cancer cell lines.	BMC Bioinformatics	2021
34878296	Analysis of the ARTIC Version 3 and Version 4 SARS-CoV-2 Primers and Their Impact on the Detection of the G142D Amino Acid Substitution in the Spike Protein.	Microbiol Spectr	2021
34379107	A genomic data resource for predicting antimicrobial resistance from laboratory-derived antimicrobial susceptibility phenotypes.	Brief Bioinform	2021
34211076	Publisher Correction: Converting tabular data into images for deep learning with convolutional neural networks.	Sci Rep	2021
34059739	Converting tabular data into images for deep learning with convolutional neural networks.	Sci Rep	2021
32503990	A synthesis of bacterial and archaeal phenotypic trait data.	Sci Data	2020
31667520	The PATRIC Bioinformatics Resource Center: expanding data and analysis capabilities.	Nucleic Acids Res	2020
33024977	Molecular Architecture of Early Dissemination and Massive Second Wave of the SARS-CoV-2 Virus in a Major Metropolitan Area.	medRxiv	2020
33075053	Predicting antimicrobial resistance using conserved genes.	PLoS Comput Biol	2020
33127862	Molecular Architecture of Early Dissemination and Massive Second Wave of the SARS-CoV-2 Virus in a Major Metropolitan Area.	mBio	2020
33093487	Ensemble transfer learning for the prediction of anti-cancer drug response.	Sci Rep	2020
32933072	Enhanced Co-Expression Extrapolation (COXEN) Gene Selection Method for Building Anti-Cancer Drug Response Prediction Models.	Genes (Basel)	2020
28968762	PATRIC as a unique resource for studying antimicrobial resistance.	Brief Bioinform	2019
32914016	Genomic Analysis of Metastatic Solid Tumors in Veterans: Findings From the VHA National Precision Oncology Program.	JCO Precis Oncol	2019
29323230	Developing an in silico minimum inhibitory concentration panel test for Klebsiella pneumoniae.	Sci Rep	2018
29979655	KBase: The United States Department of Energy Systems Biology Knowledgebase.	Nat Biotechnol	2018
30577754	Predicting tumor cell line response to drug pairs with deep learning.	BMC Bioinformatics	2018
29277864	Assembly, Annotation, and Comparative Genomics in PATRIC, the All Bacterial Bioinformatics Resource Center.	Methods Mol Biol	2018
27899627	Improvements to PATRIC, the all-bacterial Bioinformatics Database and Analysis Resource Center.	Nucleic Acids Res	2017
26903996	PATtyFams: Protein Families for the Microbial Genomes in the PATRIC Database.	Front Microbiol	2016
27297683	Antimicrobial Resistance Prediction in PATRIC and RAST.	Sci Rep	2016
25273106	Curation, integration and visualization of bacterial virulence factors in PATRIC.	Bioinformatics	2015
28324362	Enabling comparative modeling of closely related genomes: example genus Brucella.	3 Biotech	2015
25666585	RASTtk: a modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes.	Sci Rep	2015
25573919	RNA-Rocket: an RNA-Seq analysis resource for infectious disease research.	Bioinformatics	2015
24225323	PATRIC, the bacterial bioinformatics database and analysis resource.	Nucleic Acids Res	2014
25172288	Comparative genomic analysis at the PATRIC, a bioinformatic resource center.	Methods Mol Biol	2014
24336939	Comparative phylogenomics and evolution of the Brucellae reveal a path to virulence.	J Bacteriol	2014
24293654	The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST).	Nucleic Acids Res	2014
23332401	Database resources for the tuberculosis community.	Tuberculosis (Edinb)	2013
23287603	Functional assignment of Mycobacterium tuberculosis proteome revealed by genome-scale fold-recognition.	Tuberculosis (Edinb)	2013
22056929	A Rickettsia genome overrun by mobile genetic elements provides insight into the acquisition of genes characteristic of an obligate intracellular lifestyle.	J Bacteriol	2012
22930339	Comparative genomics of early-diverging Brucella strains reveals a novel lipopolysaccharide biosynthesis pathway.	mBio	2012
23131829	Comparative genomics of early-diverging Brucella strains reveals a novel lipopolysaccharide biosynthesis pathway.	mBio	2012
21712250	Integration and visualization of host-pathogen data related to infectious diseases.	Bioinformatics	2011
21896772	PATRIC: the comprehensive bacterial bioinformatics resource with a focus on human pathogenic species.	Infect Immun	2011
20400544	Host-interactive genes in Amerindian Helicobacter pylori diverge from their Old World homologs and mediate inflammatory responses.	J Bacteriol	2010
20491070	Data integration for dynamic and sustainable systems biology resources: challenges and lessons learned.	Chem Biodivers	2010
19346311	Analysis of ten Brucella genomes reveals evidence for horizontal gene transfer despite a preferred intracellular lifestyle.	J Bacteriol	2009
18599444	Atomic level computational identification of ligand migration pathways between solvent and binding site in myoglobin.	Proc Natl Acad Sci U S A	2008
19194535	Rickettsia phylogenomics: unwinding the intricacies of obligate intracellular life.	PLoS One	2008
17142235	PATRIC: the VBI PathoSystems Resource Integration Center.	Nucleic Acids Res	2007
14681533	Photosynthetic acclimation is reflected in specific patterns of gene expression in drought-stressed loblolly pine.	Plant Physiol	2003

1 - 50 of 50

Alexandra J Lee

University of Pennsylvania

Career Start Year 2015

Number of shared co-authors 4

Allison L Creason

Oregon Health and Science University

Career Start Year 2010

Number of shared co-authors 0

Chien-Chi Lo

Los Alamos National Laboratory

Career Start Year 2009

Number of shared co-authors 4

Bin Hu

Los Alamos National Laboratory

Career Start Year 2008

Number of shared co-authors 5

Jan Baumbach

University of Hamburg

Career Start Year 2006

Number of shared co-authors 0

Christopher J Fields

University of Illinois Urbana-Champaign

Career Start Year 2005

Number of shared co-authors 1

Joshua Orvis

Institute for Genome Sciences, University of Maryland School of Medicine

Career Start Year 2004

Number of shared co-authors 6

Vera van Noort

Leiden University, Institute of Biology Leiden

Career Start Year 2003

Number of shared co-authors 0

Alice C McHardy

Computational Biology of Infection Research, Helmholtz Centre for Infection Research

Career Start Year 2003

Number of shared co-authors 12

Kyle Ellrott

Oregon Health & Science University

Career Start Year 2002

Number of shared co-authors 2

Samuel V Angiuoli

Personal Genome Diagnostics Inc.

Career Start Year 2001

Number of shared co-authors 6

Weizhong Li

J. Craig Venter Institute

Career Start Year 2000

Number of shared co-authors 4

Karsten Hokamp

Smurfit Institute of Genetics, Trinity College of Dublin

Career Start Year 1999

Number of shared co-authors 1

Nicola Mulder

University of Cape Town

Career Start Year 1999

Number of shared co-authors 4

James E Bray

University of Oxford

Career Start Year 1999

Number of shared co-authors 2

Jessica Vamathevan

European Bioinformatics Institute (EMBL-EBI)

Career Start Year 1999

Number of shared co-authors 1

Nicholas J Loman

University of Birmingham

Career Start Year 1998

Number of shared co-authors 0

Jonathan Crabtree

Institute for Genome Sciences, University of Maryland School of Medicine

Career Start Year 1998

Number of shared co-authors 6

David R Powell

Biomedicine Discovery Institute, Monash University

Career Start Year 1998

Number of shared co-authors 2

Ana Tereza Ribeiro de Vasconcelos

The National Laboratory for Scientific Computing (LNCC)

Career Start Year 1997

Number of shared co-authors 2

Arnab Pain

King Abdullah University of Science and Technology

Career Start Year 1997

Number of shared co-authors 4

Iddo Friedberg

Iowa State University

Career Start Year 1997

Number of shared co-authors 8

Fiona S L Brinkman

Simon Fraser University

Career Start Year 1995

Number of shared co-authors 1

Joseph L DeRisi

University of California San Francisco

Career Start Year 1994

Number of shared co-authors 4

Bonnie Berger

Massachusetts Institute of Technology

Career Start Year 1994

Number of shared co-authors 2

Jason E McDermott

Pacific Northwest National Laboratory

Career Start Year 1993

Number of shared co-authors 1

Granger Sutton

J. Craig Venter Institute

Career Start Year 1993

Number of shared co-authors 7

Steven L Salzberg

Center for Computational Biology, Johns Hopkins University

Career Start Year 1992

Number of shared co-authors 9

Owen White

Institute for Genome Sciences, University of Maryland School of Medicine

Career Start Year 1988

Number of shared co-authors 14

Richard Bonneau

Center for Computational Biology (CCB), Flatiron Institute, Simons Foundation

Career Start Year 1983

Number of shared co-authors 5

row(s) 1 - 30 of 30

Thomas Brettin

University of Chicago

Co-authored papers 22

Hyunseung Yoo

Translational Research Center, Inha University Hospital

Co-authored papers 22

Rick Stevens

Argonne National Laboratory

Co-authored papers 22

James J Davis

University of Chicago

Co-authored papers 19

Fangfang Xia

University of Chicago

Co-authored papers 18

Bruno W Sobral

Co-authored papers 17

Robert Olson

University of Chicago

Co-authored papers 16

Ronald W Kenyon

Co-authored papers 11

Yvonne A Evrard

Frederick National Laboratory for Cancer Research, Inc.

Co-authored papers 8

James H Doroshow

National Cancer Institute, National Institutes of Health

Co-authored papers 8

Gary J Olsen

University of Illinois

Co-authored papers 8

Bruce Parrello

University of Chicago

Co-authored papers 7

Neal Conrad

University of Chicago

Co-authored papers 6

Rebecca Will

Co-authored papers 6

Emily M Dietrich

University of Chicago

Co-authored papers 6

Jo??o C Setubal

Chemistry Institute, Universidade de Sao Paulo - USP

Co-authored papers 5

Dan Murphy-Olson

Argonne National Laboratory

Co-authored papers 4

Oswald Crasta

Co-authored papers 4

Richard H Scheuermann

J. Craig Venter Institute

Co-authored papers 3

Sergei Maslov

University of Illinois Urbana-Champaign

Co-authored papers 3

Christopher S Henry

Argonne National Laboratory

Co-authored papers 3

Christopher Bun

Argonne National Laboratory

Co-authored papers 3

Dan Sullivan

Co-authored papers 3

Tian Xue

Co-authored papers 2

Janaka N Edirisinghe

Computation Institute, University of Chicago

Co-authored papers 2

Anjan Purkayastha

Co-authored papers 2

Robert A Edwards

Co-authored papers 2

Christian M Zmasek

J. Craig Venter Institute

Co-authored papers 2

Chengdong Zhang

Co-authored papers 2

James Thomason

USDA-ARS Laboratory at Cold Spring Harbor Laboratory

Co-authored papers 2

1 - 30

Author Details

Column Actions

Recommended Authors

Collaborators