|Recon3D enables a three-dimensional view of gene variation in human metabolism|
E Brunk, S Sahoo, DC Zielinski, A Altunkaya, A Dräger, N Mih, F Gatto, ...
Nature biotechnology 36 (3), 272, 2018
|i ML1515, a knowledgebase that computes Escherichia coli traits|
JM Monk, CJ Lloyd, E Brunk, N Mih, A Sastry, Z King, R Takeuchi, ...
Nature biotechnology 35 (10), 904-908, 2017
|Multi-omic data integration enables discovery of hidden biological regularities|
A Ebrahim, E Brunk, J Tan, EJ O'brien, D Kim, R Szubin, JA Lerman, ...
Nature communications 7 (1), 1-9, 2016
|Global transcriptional regulatory network for Escherichia coli robustly connects gene expression to transcription factor activities|
X Fang, A Sastry, N Mih, D Kim, J Tan, JT Yurkovich, CJ Lloyd, Y Gao, ...
Proceedings of the National Academy of Sciences 114 (38), 10286-10291, 2017
|The y-ome defines the 35% of Escherichia coli genes that lack experimental evidence of function|
S Ghatak, ZA King, A Sastry, BO Palsson
Nucleic acids research 47 (5), 2446-2454, 2019
|The Escherichia coli transcriptome mostly consists of independently regulated modules|
AV Sastry, Y Gao, R Szubin, Y Hefner, S Xu, D Kim, KS Choudhary, ...
Nature communications 10 (1), 1-14, 2019
|Systematic discovery of uncharacterized transcription factors in Escherichia coli K-12 MG1655|
Y Gao, JT Yurkovich, SW Seo, I Kabimoldayev, A Dräger, K Chen, ...
Nucleic acids research 46 (20), 10682-10696, 2018
|BOFdat: Generating biomass objective functions for genome-scale metabolic models from experimental data|
JC Lachance, CJ Lloyd, JM Monk, L Yang, AV Sastry, Y Seif, BO Palsson, ...
PLoS computational biology 15 (4), e1006971, 2019
|Cellular responses to reactive oxygen species are predicted from molecular mechanisms|
L Yang, N Mih, A Anand, JH Park, J Tan, JT Yurkovich, JM Monk, CJ Lloyd, ...
Proceedings of the National Academy of Sciences 116 (28), 14368-14373, 2019
|Adaptive evolution reveals a tradeoff between growth rate and oxidative stress during naphthoquinone-based aerobic respiration|
A Anand, K Chen, L Yang, AV Sastry, CA Olson, S Poudel, Y Seif, ...
Proceedings of the National Academy of Sciences 116 (50), 25287-25292, 2019
|Escherichia coli B2 strains prevalent in inflammatory bowel disease patients have distinct metabolic capabilities that enable colonization of intestinal mucosa|
X Fang, JM Monk, N Mih, B Du, AV Sastry, E Kavvas, Y Seif, L Smarr, ...
BMC systems biology 12 (1), 1-10, 2018
|ssbio: a Python framework for structural systems biology|
N Mih, E Brunk, K Chen, E Catoiu, A Sastry, E Kavvas, JM Monk, Z Zhang, ...
Bioinformatics 34 (12), 2155-2157, 2018
|OxyR is a convergent target for mutations acquired during adaptation to oxidative stress-prone metabolic states|
A Anand, K Chen, E Catoiu, AV Sastry, CA Olson, TE Sandberg, Y Seif, ...
Molecular biology and evolution 37 (3), 660-667, 2020
|Revealing 29 sets of independently modulated genes in Staphylococcus aureus, their regulators, and role in key physiological response|
S Poudel, H Tsunemoto, Y Seif, AV Sastry, R Szubin, S Xu, H Machado, ...
Proceedings of the National Academy of Sciences 117 (29), 17228-17239, 2020
|Adaptive laboratory evolution of Escherichia coli under acid stress|
B Du, CA Olson, AV Sastry, X Fang, PV Phaneuf, K Chen, M Wu, R Szubin, ...
Microbiology 166 (2), 141-148, 2020
|Machine learning in computational biology to accelerate high-throughput protein expression|
A Sastry, J Monk, H Tegel, M Uhlen, BO Palsson, J Rockberg, E Brunk
Bioinformatics 33 (16), 2487-2495, 2017
|Pseudogene repair driven by selection pressure applied in experimental evolution|
A Anand, CA Olson, L Yang, AV Sastry, E Catoiu, KS Choudhary, ...
Nature microbiology 4 (3), 386-389, 2019
|Machine learning uncovers independently regulated modules in the Bacillus subtilis transcriptome|
K Rychel, AV Sastry, BO Palsson
Nature communications 11 (1), 1-10, 2020
|Independent component analysis of E. coli's transcriptome reveals the cellular processes that respond to heterologous gene expression|
J Tan, AV Sastry, KS Fremming, SP Bjørn, A Hoffmeyer, S Seo, ...
Metabolic Engineering 61, 360-368, 2020
|Independent component analysis recovers consistent regulatory signals from disparate datasets|
AV Sastry, A Hu, D Heckmann, S Poudel, E Kavvas, BO Palsson
PLoS computational biology 17 (2), e1008647, 2021