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ArticlesPeer ReviewedFull Text
Optimal dimensionality selection for independent component analysis of transcriptomic data
Author / Creator:McConn, John Luke ; Lamoureux, Cameron R ; Poudel, Saugat ; Palsson, Bernhard O ; Sastry, Anand V
Publisher:England: BioMed Central Ltd
Journal title:BMC bioinformatics, 2021-12, Vol.22 (1), p.584-584, Article 584
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RiboRid: A low cost, advanced, and ultra-efficient method to remove ribosomal RNA for bacterial transcriptomics
Author / Creator:Choe, Donghui ; Szubin, Richard ; Poudel, Saugat ; Sastry, Anand ; Song, Yoseb ; Lee, Yongjae ; Cho, Suhyung ; Palsson, Bernhard ; Cho, Byung-Kwan
Publisher:United States: Public Library of Science
Journal title:PLoS genetics, 2021-09, Vol.17 (9), p.e1009821-e1009821
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Independent component analysis recovers consistent regulatory signals from disparate datasets
Author / Creator:Sastry, Anand V ; Hu, Alyssa ; Heckmann, David ; Poudel, Saugat ; Kavvas, Erol ; Palsson, Bernhard O
Publisher:United States: Public Library of Science
Journal title:PLoS computational biology, 2021-02, Vol.17 (2), p.e1008647-e1008647
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A computational knowledge-base elucidates the response of Staphylococcus aureus to different media types
Author / Creator:Seif, Yara ; Monk, Jonathan M ; Mih, Nathan ; Tsunemoto, Hannah ; Poudel, Saugat ; Zuniga, Cristal ; Broddrick, Jared ; Zengler, Karsten ; Palsson, Bernhard O
Publisher:United States: Public Library of Science
Journal title:PLoS computational biology, 2019-01, Vol.15 (1), p.e1006644-e1006644
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Machine Learning of All Mycobacterium tuberculosis H37Rv RNA-seq Data Reveals a Structured Interplay between Metabolism, Stress Response, and Infection
Author / Creator:Yoo, Reo ; Rychel, Kevin ; Poudel, Saugat ; Al-Bulushi, Tahani ; Yuan, Yuan ; Chauhan, Siddharth ; Lamoureux, Cameron ; Palsson, Bernhard O ; Sastry, Anand
Publisher:United States: American Society for Microbiology
Journal title:mSphere, 2022-04, Vol.7 (2), p.e0003322-e0003322
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Coordination of CcpA and CodY Regulators in Staphylococcus aureus USA300 Strains
Author / Creator:Poudel, Saugat ; Hefner, Ying ; Szubin, Richard ; Sastry, Anand ; Gao, Ye ; Nizet, Victor ; Palsson, Bernhard O
Publisher:United States: American Society for Microbiology
Journal title:mSystems, 2022-12, Vol.7 (6), p.e0048022
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iModulonMiner and PyModulon: Software for unsupervised mining of gene expression compendia
Author / Creator:Sastry, Anand V ; Yuan, Yuan ; Poudel, Saugat ; Rychel, Kevin ; Yoo, Reo ; Lamoureux, Cameron R ; Li, Gaoyuan ; Burrows, Joshua T ; Chauhan, Siddharth ; Haiman, Zachary B ; Al Bulushi, Tahani ; Seif, Yara ; Palsson, Bernhard O ; Zielinski, Daniel C
Publisher:United States: Public Library of Science
Journal title:PLoS computational biology, 2024-10, Vol.20 (10), p.e1012546
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Pan-Genome Analysis of Transcriptional Regulation in Six Salmonella enterica Serovar Typhimurium Strains Reveals Their Different Regulatory Structures
Author / Creator:Yuan, Yuan ; Seif, Yara ; Rychel, Kevin ; Yoo, Reo ; Chauhan, Siddharth ; Poudel, Saugat ; Al-Bulushi, Tahani ; Palsson, Bernhard O ; Sastry, Anand V
Publisher:United States: American Society for Microbiology
Journal title:mSystems, 2022-12, Vol.7 (6), p.e0046722-e0046722
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Elucidating the CodY regulon in Staphylococcus aureus USA300 substrains TCH1516 and LAC
Author / Creator:Gao, Ye ; Poudel, Saugat ; Seif, Yara ; Shen, Zeyang ; Palsson, Bernhard O
Publisher:United States: American Society for Microbiology
Journal title:mSystems, 2023-06, Vol.8 (4), p.e0027923-e0027923
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Experimental Evolution Reveals Unifying Systems-Level Adaptations but Diversity in Driving Genotypes
Author / Creator:Kavvas, Erol S ; Long, Christopher P ; Sastry, Anand ; Poudel, Saugat ; Antoniewicz, Maciek R ; Ding, Yang ; Mohamed, Elsayed T ; Szubin, Richard ; Monk, Jonathan M ; Feist, Adam M ; Palsson, Bernhard O
Publisher:United States: American Society for Microbiology
Journal title:mSystems, 2022-12, Vol.7 (6), p.e0016522
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Independent component analysis reveals 49 independently modulated gene sets within the global transcriptional regulatory architecture of multidrug-resistant Acinetobacter baumannii
Author / Creator:Menon, Nitasha D ; Poudel, Saugat ; Sastry, Anand V ; Rychel, Kevin ; Szubin, Richard ; Dillon, Nicholas ; Tsunemoto, Hannah ; Hirose, Yujiro ; Nair, Bipin G ; Kumar, Geetha B ; Palsson, Bernhard O ; Nizet, Victor
Publisher:United States: American Society for Microbiology
Journal title:mSystems, 2024-02, Vol.9 (2), p.e0060623
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Elucidation of independently modulated genes in Streptococcus pyogenes reveals carbon sources that control its expression of hemolytic toxins
Author / Creator:Hirose, Yujiro ; Poudel, Saugat ; Sastry, Anand V ; Rychel, Kevin ; Lamoureux, Cameron R ; Szubin, Richard ; Zielinski, Daniel C ; Lim, Hyun Gyu ; Menon, Nitasha D ; Bergsten, Helena ; Uchiyama, Satoshi ; Hanada, Tomoki ; Kawabata, Shigetada ; Palsson, Bernhard O ; Nizet, Victor
Publisher:United States: American Society for Microbiology
Journal title:mSystems, 2023-06, Vol.8 (3), p.e0024723-e0024723
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Pangenome Analytics Reveal Two-Component Systems as Conserved Targets in ESKAPEE Pathogens
Author / Creator:Rajput, Akanksha ; Seif, Yara ; Choudhary, Kumari Sonal ; Dalldorf, Christopher ; Poudel, Saugat ; Monk, Jonathan M ; Palsson, Bernhard O
Publisher:United States: American Society for Microbiology
Journal title:mSystems, 2021-01, Vol.6 (1)
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A genome-scale metabolic model of a globally disseminated hyperinvasive M1 strain of Streptococcus pyogenes
Author / Creator:Hirose, Yujiro ; Zielinski, Daniel C ; Poudel, Saugat ; Rychel, Kevin ; Baker, Jonathon L ; Toya, Yoshihiro ; Yamaguchi, Masaya ; Heinken, Almut ; Thiele, Ines ; Kawabata, Shigetada ; Palsson, Bernhard O ; Nizet, Victor
Publisher:United States: American Society for Microbiology
Journal title:mSystems, 2024-09, Vol.9 (9), p.e0073624
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Machine Learning of Bacterial Transcriptomes Reveals Responses Underlying Differential Antibiotic Susceptibility
Author / Creator:Sastry, Anand V ; Dillon, Nicholas ; Anand, Amitesh ; Poudel, Saugat ; Hefner, Ying ; Xu, Sibei ; Szubin, Richard ; Feist, Adam M ; Nizet, Victor ; Palsson, Bernhard
Publisher:United States: American Society for Microbiology
Journal title:mSphere, 2021-08, Vol.6 (4), p.e0044321
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Characterization of CA-MRSA TCH1516 exposed to nafcillin in bacteriological and physiological media
Author / Creator:Poudel, Saugat ; Tsunemoto, Hannah ; Meehan, Michael ; Szubin, Richard ; Olson, Connor A. ; Lamsa, Anne ; Seif, Yara ; Dillon, Nicholas ; Vrbanac, Alison ; Sugie, Joseph ; Dahesh, Samira ; Monk, Jonathan M. ; Dorrestein, Pieter C. ; Pogliano, Joseph ; Knight, Rob ; Nizet, Victor ; Palsson, Bernhard O. ; Feist, Adam M.
Publisher:London: Nature Publishing Group UK
Journal title:Scientific data, 2019-04, Vol.6 (1), p.43-43, Article 43
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Revealing 29 sets of independently modulated genes in Staphylococcus aureus, their regulators, and role in key physiological response
Author / Creator:Poudel, Saugat ; Tsunemoto, Hannah ; Seif, Yara ; Sastry, Anand V. ; Szubin, Richard ; Xu, Sibei ; Machado, Henrique ; Olson, Connor A. ; Anand, Amitesh ; Pogliano, Joe ; Nizet, Victor ; Palsson, Bernhard O.
Publisher:Washington: National Academy of Sciences
Journal title:Proceedings of the National Academy of Sciences - PNAS, 2020-07, Vol.117 (29), p.17228-17239
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Adaptive evolution reveals a tradeoff between growth rate and oxidative stress during naphthoquinone-based aerobic respiration
Author / Creator:Anand, Amitesh ; Chen, Ke ; Yang, Laurence ; Sastry, Anand V. ; Olson, Connor A. ; Poudel, Saugat ; Seif, Yara ; Hefner, Ying ; Phaneuf, Patrick V. ; Xu, Sibei ; Szubin, Richard ; Feist, Adam M. ; Palsson, Bernhard O.
Publisher:United States: National Academy of Sciences
Journal title:Proceedings of the National Academy of Sciences - PNAS, 2019-12, Vol.116 (50), p.25287-25292
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Updated and standardized genome-scale reconstruction of Mycobacterium tuberculosis H37Rv, iEK1011, simulates flux states indicative of physiological conditions
Author / Creator:Kavvas, Erol S ; Seif, Yara ; Yurkovich, James T ; Norsigian, Charles ; Poudel, Saugat ; Greenwald, William W ; Ghatak, Sankha ; Palsson, Bernhard O ; Monk, Jonathan M
Publisher:England: BioMed Central Ltd
Journal title:BMC systems biology, 2018-03, Vol.12 (1), p.25-25, Article 25
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Profiling the effect of nafcillin on HA-MRSA D712 using bacteriological and physiological media
Author / Creator:Rajput, Akanksha ; Poudel, Saugat ; Tsunemoto, Hannah ; Meehan, Michael ; Szubin, Richard ; Olson, Connor A. ; Lamsa, Anne ; Seif, Yara ; Dillon, Nicholas ; Vrbanac, Alison ; Sugie, Joseph ; Dahesh, Samira ; Monk, Jonathan M. ; Dorrestein, Pieter C. ; Knight, Rob ; Nizet, Victor ; Palsson, Bernhard O. ; Feist, Adam M. ; Pogliano, Joe
Publisher:London: Nature Publishing Group UK
Journal title:Scientific data, 2019-12, Vol.6 (1), p.322-6, Article 322
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Showing 1 to 20 of 28 results

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Optimal dimensionality selection for independent component analysis of transcriptomic data

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RiboRid: A low cost, advanced, and ultra-efficient method to remove ribosomal RNA for bacterial transcriptomics

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Independent component analysis recovers consistent regulatory signals from disparate datasets

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A computational knowledge-base elucidates the response of Staphylococcus aureus to different media types

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Machine Learning of All Mycobacterium tuberculosis H37Rv RNA-seq Data Reveals a Structured Interplay between Metabolism, Stress Response, and Infection

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Coordination of CcpA and CodY Regulators in Staphylococcus aureus USA300 Strains

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iModulonMiner and PyModulon: Software for unsupervised mining of gene expression compendia

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Pan-Genome Analysis of Transcriptional Regulation in Six Salmonella enterica Serovar Typhimurium Strains Reveals Their Different Regulatory Structures

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Elucidating the CodY regulon in Staphylococcus aureus USA300 substrains TCH1516 and LAC

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Experimental Evolution Reveals Unifying Systems-Level Adaptations but Diversity in Driving Genotypes

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Independent component analysis reveals 49 independently modulated gene sets within the global transcriptional regulatory architecture of multidrug-resistant Acinetobacter baumannii

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Elucidation of independently modulated genes in Streptococcus pyogenes reveals carbon sources that control its expression of hemolytic toxins

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Pangenome Analytics Reveal Two-Component Systems as Conserved Targets in ESKAPEE Pathogens

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A genome-scale metabolic model of a globally disseminated hyperinvasive M1 strain of Streptococcus pyogenes

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Machine Learning of Bacterial Transcriptomes Reveals Responses Underlying Differential Antibiotic Susceptibility

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Characterization of CA-MRSA TCH1516 exposed to nafcillin in bacteriological and physiological media

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Revealing 29 sets of independently modulated genes in Staphylococcus aureus, their regulators, and role in key physiological response

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Adaptive evolution reveals a tradeoff between growth rate and oxidative stress during naphthoquinone-based aerobic respiration

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Updated and standardized genome-scale reconstruction of Mycobacterium tuberculosis H37Rv, iEK1011, simulates flux states indicative of physiological conditions

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Profiling the effect of nafcillin on HA-MRSA D712 using bacteriological and physiological media

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