| 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), 272-281, 2018 | 717 | 2018 |
| iML1515, 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 | 550 | 2017 |
| 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), 5536, 2019 | 216 | 2019 |
| 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), 13091, 2016 | 178 | 2016 |
| 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 | 147 | 2019 |
| 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 | 115 | 2017 |
| 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 | 107 | 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 | 105 | 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 | 98 | 2019 |
| iModulonDB: a knowledgebase of microbial transcriptional regulation derived from machine learning K Rychel, K Decker, AV Sastry, PV Phaneuf, S Poudel, BO Palsson Nucleic acids research 49 (D1), D112-D120, 2021 | 94 | 2021 |
| 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 | 74 | 2020 |
| Adaptive evolution reveals a tradeoff between growth rate and oxidative stress during naphthoquinone-based aerobic respiration A Anand, KE Chen, L Yang, AV Sastry, CA Olson, S Poudel, Y Seif, ... Proceedings of the National Academy of Sciences 116 (50), 25287-25292, 2019 | 71 | 2019 |
| Machine learning uncovers independently regulated modules in the Bacillus subtilis transcriptome K Rychel, AV Sastry, BO Palsson Nature communications 11 (1), 6338, 2020 | 70 | 2020 |
| 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 | 65 | 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 | 52 | 2020 |
| 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, 1-10, 2018 | 52 | 2018 |
| Antibody optimization enabled by artificial intelligence predictions of binding affinity and naturalness S Bachas, G Rakocevic, D Spencer, AV Sastry, R Haile, JM Sutton, ... BioRxiv, 2022.08. 16.504181, 2022 | 50 | 2022 |
| 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 | 45 | 2020 |
| Machine-learning from Pseudomonas putida KT2440 transcriptomes reveals its transcriptional regulatory network HG Lim, K Rychel, AV Sastry, GJ Bentley, J Mueller, HS Schindel, ... Metabolic Engineering 72, 297-310, 2022 | 44 | 2022 |
| Optimal dimensionality selection for independent component analysis of transcriptomic data JL McConn, CR Lamoureux, S Poudel, BO Palsson, AV Sastry BMC bioinformatics 22, 1-13, 2021 | 43 | 2021 |