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Anand Sastry - Publications

Affiliations: 
2020 University of California, San Diego, La Jolla, CA 
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46 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2024 Menon ND, Poudel S, Sastry AV, Rychel K, Szubin R, Dillon N, Tsunemoto H, Hirose Y, Nair BG, Kumar GB, Palsson BO, Nizet V. Independent component analysis reveals 49 independently modulated gene sets within the global transcriptional regulatory architecture of multidrug-resistant . Msystems. e0060623. PMID 38189271 DOI: 10.1128/msystems.00606-23  0.466
2023 Miano A, Rychel K, Lezia A, Sastry A, Palsson B, Hasty J. High-resolution temporal profiling of E. coli transcriptional response. Nature Communications. 14: 7606. PMID 37993418 DOI: 10.1038/s41467-023-43173-7  0.472
2023 Lamoureux CR, Decker KT, Sastry AV, Rychel K, Gao Y, McConn JL, Zielinski DC, Palsson BO. A multi-scale expression and regulation knowledge base for Escherichia coli. Nucleic Acids Research. PMID 37713610 DOI: 10.1093/nar/gkad750  0.774
2023 Rychel K, Tan J, Patel A, Lamoureux C, Hefner Y, Szubin R, Johnsen J, Mohamed ETT, Phaneuf PV, Anand A, Olson CA, Park JH, Sastry AV, Yang L, Feist AM, et al. Laboratory evolution, transcriptomics, and modeling reveal mechanisms of paraquat tolerance. Cell Reports. 42: 113105. PMID 37713311 DOI: 10.1016/j.celrep.2023.113105  0.817
2023 Bajpe H, Rychel K, Lamoureux CR, Sastry AV, Palsson BO. Machine learning uncovers the transcriptome in microbial communities and during infection. Msystems. e0043723. PMID 37638727 DOI: 10.1128/msystems.00437-23  0.514
2023 Hirose Y, Poudel S, Sastry AV, Rychel K, Lamoureux CR, Szubin R, Zielinski DC, Lim HG, Menon ND, Bergsten H, Uchiyama S, Hanada T, Kawabata S, Palsson BO, Nizet V. Elucidation of independently modulated genes in reveals carbon sources that control its expression of hemolytic toxins. Msystems. e0024723. PMID 37278526 DOI: 10.1128/msystems.00247-23  0.705
2023 Patel A, McGrosso D, Hefner Y, Campeau A, Sastry AV, Maurya S, Rychel K, Gonzalez DJ, Palsson BO. Proteome allocation is linked to transcriptional regulation through a modularized transcriptome. Biorxiv : the Preprint Server For Biology. PMID 36865326 DOI: 10.1101/2023.02.20.529291  0.539
2023 Park JY, Lee SM, Ebrahim A, Scott-Nevros ZK, Kim J, Yang L, Sastry A, Seo SW, Palsson BO, Kim D. Model-driven experimental design workflow expands understanding of regulatory role of Nac in . Nar Genomics and Bioinformatics. 5: lqad006. PMID 36685725 DOI: 10.1093/nargab/lqad006  0.83
2022 Poudel S, Hefner Y, Szubin R, Sastry A, Gao Y, Nizet V, Palsson BO. Coordination of CcpA and CodY Regulators in Staphylococcus aureus USA300 Strains. Msystems. e0048022. PMID 36321827 DOI: 10.1128/msystems.00480-22  0.83
2022 Yuan Y, Seif Y, Rychel K, Yoo R, Chauhan S, Poudel S, Al-Bulushi T, Palsson BO, Sastry AV. Pan-Genome Analysis of Transcriptional Regulation in Six Salmonella enterica Serovar Typhimurium Strains Reveals Their Different Regulatory Structures. Msystems. e0046722. PMID 36317888 DOI: 10.1128/msystems.00467-22  0.821
2022 Kavvas ES, Long CP, Sastry A, Poudel S, Antoniewicz MR, Ding Y, Mohamed ET, Szubin R, Monk JM, Feist AM, Palsson BO. Experimental Evolution Reveals Unifying Systems-Level Adaptations but Diversity in Driving Genotypes. Msystems. e0016522. PMID 36226969 DOI: 10.1128/msystems.00165-22  0.814
2022 Rajput A, Tsunemoto H, Sastry AV, Szubin R, Rychel K, Chauhan SM, Pogliano J, Palsson BO. Advanced transcriptomic analysis reveals the role of efflux pumps and media composition in antibiotic responses of Pseudomonas aeruginosa. Nucleic Acids Research. 50: 9675-9688. PMID 36095122 DOI: 10.1093/nar/gkac743  0.471
2022 Radi MS, SalcedoSora JE, Kim SH, Sudarsan S, Sastry AV, Kell DB, Herrgård MJ, Feist AM. Membrane transporter identification and modulation via adaptive laboratory evolution. Metabolic Engineering. PMID 35598887 DOI: 10.1016/j.ymben.2022.05.004  0.714
2022 Lim HG, Rychel K, Sastry AV, Bentley GJ, Mueller J, Schindel HS, Larsen PE, Laible PD, Guss AM, Niu W, Johnson CW, Beckham GT, Feist AM, Palsson BO. Machine-learning from Pseudomonas putida KT2440 transcriptomes reveals its transcriptional regulatory network. Metabolic Engineering. PMID 35489688 DOI: 10.1016/j.ymben.2022.04.004  0.836
2022 Xavier JB, Monk JM, Poudel S, Norsigian CJ, Sastry AV, Liao C, Bento J, Suchard MA, Arrieta-Ortiz ML, Peterson EJR, Baliga NS, Stoeger T, Ruffin F, Richardson RAK, Gao CA, et al. Mathematical models to study the biology of pathogens and the infectious diseases they cause. Iscience. 25: 104079. PMID 35359802 DOI: 10.1016/j.isci.2022.104079  0.772
2022 Rajput A, Tsunemoto H, Sastry AV, Szubin R, Rychel K, Sugie J, Pogliano J, Palsson BO. Machine learning from Pseudomonas aeruginosa transcriptomes identifies independently modulated sets of genes associated with known transcriptional regulators. Nucleic Acids Research. PMID 35357493 DOI: 10.1093/nar/gkac187  0.549
2022 Yoo R, Rychel K, Poudel S, Al-Bulushi T, Yuan Y, Chauhan S, Lamoureux C, Palsson BO, Sastry A. Machine Learning of All Mycobacterium tuberculosis H37Rv RNA-seq Data Reveals a Structured Interplay between Metabolism, Stress Response, and Infection. Msphere. e0003322. PMID 35306876 DOI: 10.1128/msphere.00033-22  0.813
2021 McConn JL, Lamoureux CR, Poudel S, Palsson BO, Sastry AV. Optimal dimensionality selection for independent component analysis of transcriptomic data. Bmc Bioinformatics. 22: 584. PMID 34879815 DOI: 10.1186/s12859-021-04497-7  0.786
2021 Chauhan SM, Poudel S, Rychel K, Lamoureux C, Yoo R, Al Bulushi T, Yuan Y, Palsson BO, Sastry AV. Machine Learning Uncovers a Data-Driven Transcriptional Regulatory Network for the Crenarchaeal Thermoacidophile . Frontiers in Microbiology. 12: 753521. PMID 34777307 DOI: 10.3389/fmicb.2021.753521  0.817
2021 Choe D, Szubin R, Poudel S, Sastry A, Song Y, Lee Y, Cho S, Palsson B, Cho BK. RiboRid: A low cost, advanced, and ultra-efficient method to remove ribosomal RNA for bacterial transcriptomics. Plos Genetics. 17: e1009821. PMID 34570751 DOI: 10.1371/journal.pgen.1009821  0.76
2021 Sastry AV, Dillon N, Anand A, Poudel S, Hefner Y, Xu S, Szubin R, Feist AM, Nizet V, Palsson B. Machine Learning of Bacterial Transcriptomes Reveals Responses Underlying Differential Antibiotic Susceptibility. Msphere. 6: e0044321. PMID 34431696 DOI: 10.1128/mSphere.00443-21  0.799
2021 Rodionova IA, Gao Y, Sastry A, Hefner Y, Lim HG, Rodionov DA, Saier MH, Palsson BO. Identification of a transcription factor, PunR, that regulates the purine and purine nucleoside transporter punC in E. coli. Communications Biology. 4: 991. PMID 34413462 DOI: 10.1038/s42003-021-02516-0  0.813
2021 Anand A, Olson CA, Sastry AV, Patel A, Szubin R, Yang L, Feist AM, Palsson BO. Restoration of fitness lost due to dysregulation of the pyruvate dehydrogenase complex is triggered by ribosomal binding site modifications. Cell Reports. 35: 108961. PMID 33826886 DOI: 10.1016/j.celrep.2021.108961  0.811
2021 Sastry AV, Hu A, Heckmann D, Poudel S, Kavvas E, Palsson BO. Independent component analysis recovers consistent regulatory signals from disparate datasets. Plos Computational Biology. 17: e1008647. PMID 33529205 DOI: 10.1371/journal.pcbi.1008647  0.816
2020 Rychel K, Sastry AV, Palsson BO. Machine learning uncovers independently regulated modules in the Bacillus subtilis transcriptome. Nature Communications. 11: 6338. PMID 33311500 DOI: 10.1038/s41467-020-20153-9  0.523
2020 Choudhary KS, Kleinmanns JA, Decker K, Sastry AV, Gao Y, Szubin R, Seif Y, Palsson BO. Elucidation of Regulatory Modes for Five Two-Component Systems in Escherichia coli Reveals Novel Relationships. Msystems. 5. PMID 33172971 DOI: 10.1128/mSystems.00980-20  0.819
2020 Rychel K, Decker K, Sastry AV, Phaneuf PV, Poudel S, Palsson BO. iModulonDB: a knowledgebase of microbial transcriptional regulation derived from machine learning. Nucleic Acids Research. PMID 33045728 DOI: 10.1093/nar/gkaa810  0.821
2020 Lamoureux CR, Choudhary KS, King ZA, Sandberg TE, Gao Y, Sastry AV, Phaneuf PV, Choe D, Cho BK, Palsson BO. The Bitome: digitized genomic features reveal fundamental genome organization. Nucleic Acids Research. PMID 32976587 DOI: 10.1093/nar/gkaa774  0.79
2020 Tan J, Sastry AV, Fremming KS, Bjørn SP, Hoffmeyer A, Seo S, Voldborg BG, Palsson BO. Independent component analysis of E. coli's transcriptome reveals the cellular processes that respond to heterologous gene expression. Metabolic Engineering. PMID 32710928 DOI: 10.1016/J.Ymben.2020.07.002  0.801
2020 Poudel S, Tsunemoto H, Seif Y, Sastry AV, Szubin R, Xu S, Machado H, Olson CA, Anand A, Pogliano J, Nizet V, Palsson BO. Revealing 29 sets of independently modulated genes in , their regulators, and role in key physiological response. Proceedings of the National Academy of Sciences of the United States of America. PMID 32616573 DOI: 10.1073/Pnas.2008413117  0.806
2019 Sastry AV, Gao Y, Szubin R, Hefner Y, Xu S, Kim D, Choudhary KS, Yang L, King ZA, Palsson BO. The Escherichia coli transcriptome mostly consists of independently regulated modules. Nature Communications. 10: 5536. PMID 31797920 DOI: 10.1038/S41467-019-13483-W  0.778
2019 Anand A, Chen K, Yang L, Sastry AV, Olson CA, Poudel S, Seif Y, Hefner Y, Phaneuf PV, Xu S, Szubin R, Feist AM, Palsson BO. Adaptive evolution reveals a tradeoff between growth rate and oxidative stress during naphthoquinone-based aerobic respiration. Proceedings of the National Academy of Sciences of the United States of America. PMID 31767748 DOI: 10.1073/Pnas.1909987116  0.785
2019 Anand A, Chen K, Catoiu E, Sastry AV, Olson CA, Sandberg TE, Seif Y, Xu S, Szubin R, Yang L, Feist AM, Palsson BO. OxyR is a convergent target for mutations acquired during adaptation to oxidative stress-prone metabolic states. Molecular Biology and Evolution. PMID 31651953 DOI: 10.1093/Molbev/Msz251  0.814
2019 Du B, Olson CA, Sastry AV, Fang X, Phaneuf PV, Chen K, Wu M, Szubin R, Xu S, Gao Y, Hefner Y, Feist AM, Palsson BO. Adaptive laboratory evolution of under acid stress. Microbiology (Reading, England). PMID 31625833 DOI: 10.1099/Mic.0.000867  0.795
2019 Yang L, Mih N, Anand A, Park JH, Tan J, Yurkovich JT, Monk JM, Lloyd CJ, Sandberg TE, Seo SW, Kim D, Sastry AV, Phaneuf P, Gao Y, Broddrick JT, et al. Cellular responses to reactive oxygen species are predicted from molecular mechanisms. Proceedings of the National Academy of Sciences of the United States of America. PMID 31270234 DOI: 10.1073/Pnas.1905039116  0.725
2019 Lachance JC, Lloyd CJ, Monk JM, Yang L, Sastry AV, Seif Y, Palsson BO, Rodrigue S, Feist AM, King ZA, Jacques PÉ. BOFdat: Generating biomass objective functions for genome-scale metabolic models from experimental data. Plos Computational Biology. 15: e1006971. PMID 31009451 DOI: 10.1371/Journal.Pcbi.1006971  0.798
2019 Ghatak S, King ZA, Sastry A, Palsson BO. The y-ome defines the 35% of Escherichia coli genes that lack experimental evidence of function. Nucleic Acids Research. PMID 30698741 DOI: 10.1093/Nar/Gkz030  0.481
2019 Anand A, Olson CA, Yang L, Sastry AV, Catoiu E, Choudhary KS, Phaneuf PV, Sandberg TE, Xu S, Hefner Y, Szubin R, Feist AM, Palsson BO. Pseudogene repair driven by selection pressure applied in experimental evolution. Nature Microbiology. PMID 30692668 DOI: 10.1038/S41564-018-0340-2  0.776
2018 Gao Y, Yurkovich JT, Seo SW, Kabimoldayev I, Dräger A, Chen K, Sastry AV, Fang X, Mih N, Yang L, Eichner J, Cho BK, Kim D, Palsson BO. Systematic discovery of uncharacterized transcription factors in Escherichia coli K-12 MG1655. Nucleic Acids Research. PMID 30137486 DOI: 10.1093/Nar/Gky752  0.806
2018 Fang X, Monk JM, Mih N, Du B, Sastry AV, Kavvas E, Seif Y, Smarr L, Palsson BO. Escherichia coli B2 strains prevalent in inflammatory bowel disease patients have distinct metabolic capabilities that enable colonization of intestinal mucosa. Bmc Systems Biology. 12: 66. PMID 29890970 DOI: 10.1186/S12918-018-0587-5  0.773
2018 Brunk E, Sahoo S, Zielinski DC, Altunkaya A, Dräger A, Mih N, Gatto F, Nilsson A, Preciat Gonzalez GA, Aurich MK, Prlić A, Sastry A, Danielsdottir AD, Heinken A, Noronha A, et al. Recon3D enables a three-dimensional view of gene variation in human metabolism. Nature Biotechnology. PMID 29457794 DOI: 10.1038/Nbt.4072  0.794
2018 Mih N, Brunk E, Chen K, Catoiu E, Sastry A, Kavvas E, Monk JM, Zhang Z, Palsson BO, Valencia A. ssbio: A Python Framework for Structural Systems Biology. Bioinformatics (Oxford, England). PMID 29444205 DOI: 10.1093/Bioinformatics/Bty077  0.775
2017 Monk JM, Lloyd CJ, Brunk E, Mih N, Sastry A, King Z, Takeuchi R, Nomura W, Zhang Z, Mori H, Feist AM, Palsson BO. iML1515, a knowledgebase that computes Escherichia coli traits. Nature Biotechnology. 35: 904-908. PMID 29020004 DOI: 10.1038/Nbt.3956  0.75
2017 Fang X, Sastry A, Mih N, Kim D, Tan J, Yurkovich JT, Lloyd CJ, Gao Y, Yang L, Palsson BO. Global transcriptional regulatory network for Escherichia coli robustly connects gene expression to transcription factor activities. Proceedings of the National Academy of Sciences of the United States of America. PMID 28874552 DOI: 10.1073/Pnas.1702581114  0.798
2017 Sastry A, Monk J, Tegel H, Uhlén M, Palsson BO, Rockberg J, Brunk E. Machine Learning in Computational Biology to Accelerate High-Throughput Protein Expression. Bioinformatics (Oxford, England). PMID 28398465 DOI: 10.1093/Bioinformatics/Btx207  0.789
2016 Ebrahim A, Brunk E, Tan J, O'Brien EJ, Kim D, Szubin R, Lerman JA, Lechner A, Sastry A, Bordbar A, Feist AM, Palsson BO. Multi-omic data integration enables discovery of hidden biological regularities. Nature Communications. 7: 13091. PMID 27782110 DOI: 10.1038/Ncomms13091  0.778
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