Maulik Shukla
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The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST)
R Overbeek, R Olson, GD Pusch, GJ Olsen, JJ Davis, T Disz, RA Edwards, ...
Nucleic acids research 42 (D1), D206-D214, 2014
The PATRIC Bioinformatics Resource Center: expanding data and analysis capabilities
JJ Davis, AR Wattam, RK Aziz, T Brettin, R Butler, RM Butler, P Chlenski, ...
Nucleic acids research 48 (D1), D606-D612, 2020
RASTtk: a modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes
T Brettin, JJ Davis, T Disz, RA Edwards, S Gerdes, GJ Olsen, R Olson, ...
Scientific reports 5 (1), 1-6, 2015
KBase: the United States department of energy systems biology knowledgebase
AP Arkin, RW Cottingham, CS Henry, NL Harris, RL Stevens, S Maslov, ...
Nature biotechnology 36 (7), 566-569, 2018
Rickettsia phylogenomics: unwinding the intricacies of obligate intracellular life
JJ Gillespie, K Williams, M Shukla, EE Snyder, EK Nordberg, SM Ceraul, ...
PloS one 3 (4), e2018, 2008
Photosynthetic acclimation is reflected in specific patterns of gene expression in drought-stressed loblolly pine
JI Watkinson, AA Sioson, C Vasquez-Robinet, M Shukla, D Kumar, M Ellis, ...
Plant Physiology 133 (4), 1702-1716, 2003
Antimicrobial resistance prediction in PATRIC and RAST
JJ Davis, S Boisvert, T Brettin, RW Kenyon, C Mao, R Olson, R Overbeek, ...
Scientific reports 6 (1), 1-12, 2016
A Rickettsia genome overrun by mobile genetic elements provides insight into the acquisition of genes characteristic of an obligate intracellular lifestyle
JJ Gillespie, V Joardar, KP Williams, T Driscoll, JB Hostetler, E Nordberg, ...
Journal of bacteriology 194 (2), 376-394, 2012
Atomic level computational identification of ligand migration pathways between solvent and binding site in myoglobin
JZ Ruscio, D Kumar, M Shukla, MG Prisant, TM Murali, AV Onufriev
Proceedings of the National Academy of Sciences 105 (27), 9204-9209, 2008
Analysis of Ten Brucella Genomes Reveals Evidence for Horizontal Gene Transfer Despite a Preferred Intracellular Lifestyle
AR Wattam, KP Williams, EE Snyder, NF Almeida Jr, M Shukla, ...
Journal of bacteriology 191 (11), 3569-3579, 2009
Developing an in silico minimum inhibitory concentration panel test for Klebsiella pneumoniae
M Nguyen, T Brettin, S Long, JM Musser, RJ Olsen, R Olson, M Shukla, ...
Scientific reports 8 (1), 1-11, 2018
Molecular architecture of early dissemination and massive second wave of the SARS-CoV-2 virus in a major metropolitan area
SW Long, RJ Olsen, PA Christensen, DW Bernard, JJ Davis, M Shukla, ...
MBio 11 (6), e02707-20, 2020
Comparative phylogenomics and evolution of the Brucellae reveal a path to virulence
AR Wattam, JT Foster, SP Mane, SM Beckstrom-Sternberg, ...
Journal of bacteriology 196 (5), 920-930, 2014
PATtyFams: protein families for the microbial genomes in the PATRIC database
JJ Davis, S Gerdes, GJ Olsen, R Olson, GD Pusch, M Shukla, V Vonstein, ...
Frontiers in microbiology 7, 118, 2016
Predicting tumor cell line response to drug pairs with deep learning
F Xia, M Shukla, T Brettin, C Garcia-Cardona, J Cohn, JE Allen, S Maslov, ...
BMC bioinformatics 19 (18), 71-79, 2018
Host-Interactive Genes in Amerindian Helicobacter pylori Diverge from Their Old World Homologs and Mediate Inflammatory Responses
SP Mane, MG Dominguez-Bello, MJ Blaser, BW Sobral, R Hontecillas, ...
Journal of bacteriology 192 (12), 3078-3092, 2010
Assembly, annotation, and comparative genomics in PATRIC, the all bacterial bioinformatics resource center
AR Wattam, T Brettin, JJ Davis, S Gerdes, R Kenyon, D Machi, C Mao, ...
Comparative Genomics, 79-101, 2018
PATRIC as a unique resource for studying antimicrobial resistance
DA Antonopoulos, R Assaf, RK Aziz, T Brettin, C Bun, N Conrad, JJ Davis, ...
Briefings in bioinformatics 20 (4), 1094-1102, 2019
The DOE systems biology knowledgebase (KBase)
AP Arkin, RL Stevens, RW Cottingham, S Maslov, CS Henry, P Dehal, ...
BioRxiv, 096354, 2016
An Evaluation of Information Visualization in Attention-Limited Environments.
JP Somervell, DS McCrickard, C North, M Shukla
VisSym, 211-216, 2002
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Articles 1–20