Machine learning uncovers independently regulated modules in the Bacillus subtilis transcriptome.

by Rychel, Kevin, Sastry, Anand V, Palsson, Bernhard O
Published 2020

Recon3D enables a three-dimensional view of gene variation in human metabolism.

by Brunk, Elizabeth, Sahoo, Swagatika, Zielinski, Daniel C, Altunkaya, Ali, Dräger, Andreas, Mih, Nathan, Gatto, Francesco, Nilsson, Avlant, Preciat Gonzalez, German Andres, Aurich, Maike Kathrin, Prlić, Andreas, Sastry, Anand, Danielsdottir, Anna D, Heinken, Almut, Noronha, Alberto, Rose, Peter W, Burley, Stephen K, Fleming, Ronan MT, Nielsen, Jens, Thiele, Ines, Palsson, Bernhard O
Published 2018

The Escherichia coli transcriptome mostly consists of independently regulated modules.

by Sastry, Anand V, Gao, Ye, Szubin, Richard, Hefner, Ying, Xu, Sibei, Kim, Donghyuk, Choudhary, Kumari Sonal, Yang, Laurence, King, Zachary A, Palsson, Bernhard O
Published 2019

Multi-omic data integration enables discovery of hidden biological regularities.

by Ebrahim, Ali, Brunk, Elizabeth, Tan, Justin, O'Brien, Edward J, Kim, Donghyuk, Szubin, Richard, Lerman, Joshua A, Lechner, Anna, Sastry, Anand, Bordbar, Aarash, Feist, Adam M, Palsson, Bernhard O
Published 2016

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

by Choe, Donghui, Szubin, Richard, Poudel, Saugat, Sastry, Anand, Song, Yoseb, Lee, Yongjae, Cho, Suhyung, Palsson, Bernhard, Cho, Byung-Kwan
Published 2021

iModulonDB: a knowledgebase of microbial transcriptional regulation derived from machine learning.

by Rychel, Kevin, Decker, Katherine, Sastry, Anand V, Phaneuf, Patrick V, Poudel, Saugat, Palsson, Bernhard O
Published 2021

Identification of a transcription factor, PunR, that regulates the purine and purine nucleoside transporter punC in E. coli.

by Rodionova, Irina A, Gao, Ye, Sastry, Anand, Hefner, Ying, Lim, Hyun Gyu, Rodionov, Dmitry A, Saier, Milton H, Palsson, Bernhard O
Published 2021

Systematic discovery of uncharacterized transcription factors in Escherichia coli K-12 MG1655.

by Gao, Ye, Yurkovich, James T, Seo, Sang Woo, Kabimoldayev, Ilyas, Dräger, Andreas, Chen, Ke, Sastry, Anand V, Fang, Xin, Mih, Nathan, Yang, Laurence, Eichner, Johannes, Cho, Byung-Kwan, Kim, Donghyuk, Palsson, Bernhard O
Published 2018

Machine learning from Pseudomonas aeruginosa transcriptomes identifies independently modulated sets of genes associated with known transcriptional regulators.

by Rajput, Akanksha, Tsunemoto, Hannah, Sastry, Anand V, Szubin, Richard, Rychel, Kevin, Sugie, Joseph, Pogliano, Joe, Palsson, Bernhard O
Published 2022

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

by 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
Published 2020

BOFdat: Generating biomass objective functions for genome-scale metabolic models from experimental data.

by Lachance, Jean-Christophe, Lloyd, Colton J, Monk, Jonathan M, Yang, Laurence, Sastry, Anand V, Seif, Yara, Palsson, Bernhard O, Rodrigue, Sébastien, Feist, Adam M, King, Zachary A, Jacques, Pierre-Étienne
Published 2019

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

by 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
Published 2019

Decomposing the symphony of Escherichia coli gene expression

by Sastry, Anand Varun
Published 2020

Escherichia coli B2 strains prevalent in inflammatory bowel disease patients have distinct metabolic capabilities that enable colonization of intestinal mucosa.

by Fang, Xin, Monk, Jonathan M, Mih, Nathan, Du, Bin, Sastry, Anand V, Kavvas, Erol, Seif, Yara, Smarr, Larry, Palsson, Bernhard O
Published 2018

Machine Learning of Bacterial Transcriptomes Reveals Responses Underlying Differential Antibiotic Susceptibility.

by Sastry, Anand V, Dillon, Nicholas, Anand, Amitesh, Poudel, Saugat, Hefner, Ying, Xu, Sibei, Szubin, Richard, Feist, Adam M, Nizet, Victor, Palsson, Bernhard
Published 2021

Elucidation of Regulatory Modes for Five Two-Component Systems in Escherichia coli Reveals Novel Relationships.

by Choudhary, Kumari Sonal, Kleinmanns, Julia A, Decker, Katherine, Sastry, Anand V, Gao, Ye, Szubin, Richard, Seif, Yara, Palsson, Bernhard O
Published 2020