| A treasure trove of 1034 actinomycete genomes |
Jørgensen TS, Mohite OS, Sterndorff EB, Alvarez-Arevalo M, Blin K, Booth TJ, Charusanti P, Faurdal D, Hansen TØ, Nuhamunada M, Mourched AS, Palsson BØ, Weber T.
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2024 |
| Decomposition of the pangenome matrix reveals a structure in gene distribution in the Escherichia coli species |
Chauhan SM, Ardalani O, Hyun JC, Monk JM, Phaneuf PV, Palsson BO.
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2024 |
| A data-driven approach for timescale decomposition of biochemical reaction networks |
Akbari A, Haiman ZB, Palsson BO
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2024 |
| Pangenome reconstruction of Lactobacillaceae metabolism predicts species-specific metabolic traits |
Ardalani O, Phaneuf PV, Mohite OS, Nielsen LK, Palsson BO.
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2024 |
| Inferred regulons are consistent with regulator binding sequences in E. coli. |
Qiu S, Wan X, Liang Y, Lamoureux CR, Akbari A, Palsson BO, Zielinski DC.
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2024 |
| Phosphofructokinase isoforms boost energy status of stored red blood cells and transfusion outcomes. |
Nemkov T, Stephenson D, Earley EJ, Keele GR, Hay A, Key A, Haiman ZB, Erickson C, Dzieciatkowska M, Reisz JA, Moore A, Stone M, Deng X, Kleinman S, Spitalnik SL, Hod EA, Hudson KE, Hansen KC, Palsson BO, Churchill GA, Roubinian N, Norris PJ, Busch MP, Zimring JC, Page GP, D'Alessandro A.
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2024 |
| Machine learning analysis of RB-TnSeq fitness data predicts functional gene modules in Pseudomonas putida KT2440 |
Borchert AJ, Bleem AC, Lim HG, Rychel K, Dooley KD, Kellermyer ZA, Hodges TL, Palsson BO, Beckham GT
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2024 |
| Meta-analysis Driven Strain Design for Mitigating Oxidative Stresses Important in Biomanufacturing |
Phaneuf PV, Kim SH, Rychel K, Rode C, Beulig F, Palsson BO, Yang L
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2024 |
| Reconstructing the transcriptional regulatory network of probiotic L. reuteri is enabled by transcriptomics and machine learning |
Josephs-Spaulding J, Rajput A, Hefner Y, Szubin R, Balasubramanian A, Li G, Zielinski DC, Jahn L, Sommer M, Phaneuf P, Palsson BO.
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2024 |
| Modulating bacterial function utilizing A knowledge base of transcriptional regulatory modules |
Shin J, Zielinski DC, Palsson BO
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2024 |
| Unified computing framework of Escherichia coli metabolism, gene expression, and stress responses |
Zhao J, Chen K, Palsson BO, Yang L.
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2024 |
| Machine-Learning Analysis of Streptomyces coelicolor Transcriptomes Reveals a Transcription Regulatory Network Encompassing Biosynthetic Gene Clusters |
Lee Y, Choe D, Palsson BO, Cho BK.
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2024 |
| Advancing the scale of synthetic biology via cross-species transfer of cellular functions enabled by iModulon engraftment |
Choe D, Olson CA, Szubin R, Yang H, Sung J, Feist AM, Palsson BO
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2024 |
| Machine learning reveals the transcriptional regulatory network and circadian dynamics of Synechococcus elongatusPCC 7942 |
Yuan Y, Al Bulushi T, Sastry AV, Sancar C, Szubin R, Golden SS, Palsson BO.
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2024 |
| Reduction-to-synthesis: the dominant approach to genome-scale synthetic biology |
Kim K, Choe D, Cho S, Palsson B, Cho BK.
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2024 |
| Genome-scale models in human metabologenomics |
Mardinoglu A, Palsson BØ
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2024 |
| Serial adaptive laboratory evolution enhances mixed carbon metabolic capacity of Escherichia coli |
Kim K, Choe D, Kang M, Cho SH, Cho S, Jeong KJ, Palsson B, Cho BK
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2024 |
| CyuR is a dual regulator for L-cysteine dependent antimicrobial resistance in Escherichia coli |
Rodionova IA, Lim HG, Gao Y, Rodionov DA, Hutchison Y, Szubin R, Dalldorf C, Monk J, Palsson BO
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2024 |
| Grand Challenges at the Interface of Engineering and Medicine |
Subramaniam S, Akay M, Anastasio MA, Bailey V, Boas D, Bonato P, Chilkoti A, Cochran JR, Colvin V, Desai TA, Duncan JS, Epstein FH, Fraley S, Giachelli C, Grande-Allen KJ, Green J, Guo XE, Hilton IB, Humphrey JD, Johnson CR, Karniadakis G, King MR, Kirsch RF, Kumar S, Laurencin CT, Li S, Lieber RL, Lovell N, Mali P, Margulies SS, Meaney DF, Ogle B, Palsson B, A Peppas N, Perreault EJ, Rabbitt R, Setton LA, Shea LD, Shroff SG, Shung K, Tolias AS, van der Meulen MCH, Varghese S, Vunjak-Novakovic G, White JA, Winslow R, Zhang J, Zhang K, Zukoski C, Miller MI.
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2024 |
| A genome-scale metabolic model of a globally disseminated hyperinvasive M1 strain of Streptococcus pyogenes |
Hirose Y, Zielinski DC, Poudel S, Rychel K, Baker JL, Toya Y, Yamaguchi M, Heinken A, Thiele I, Kawabata S, Palsson BO, Nizet V.
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2024 |
| A model industrial workhorse: Bacillus subtilis strain 168 and its genome after a quarter of a century |
Bremer E, Calteau A, Danchin A, Harwood C, Helmann JD, Médigue C, Palsson BO, Sekowska A, Vallenet D, Zuniga A, Zuniga C |
2023 |
| Differential Expression Analysis Utilizing Condition-Specific Metabolic Pathways |
Mattei, G., Gan, Z., Ramazzotti, M., Palsson, B.O., Zielinski, D.C.
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2023 |
| Whole-genome sequences from wild-type and laboratory-evolved strains define the alleleome and establish its hallmarks |
Catoiu EA, Phaneuf P, Monk J, Palsson BO |
2023 |
| Modeling Red Blood Cell Metabolism in the Omics Era |
Key A, Haiman Z, Palsson BO, D’Alessandro A.
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2023 |
| The Escherichia coli Fur pan-regulon has few conserved but many unique regulatory targets |
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2023 |
| Functional annotation of enzyme-encoding genes using deep learning with transformer layers |
Kim GB, Kim JY, Lee JA, Norsigian CJ, Palsson BO, Lee SY
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2023 |
| Metabolic homeostasis and growth in abiotic cells |
Akbari A, Palsson BO |
2023 |
| High-resolution temporal profiling of E. coli transcriptional response |
Miano A, Rychel K, Lezia A, Sastry A, Palsson B, Hasty J.
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2023 |
| Systems biology of competency in Vibrio natriegens is revealed by applying novel data analytics to the transcriptome |
Shin J, Rychel K, Palsson BO. |
2023 |
| Global pathogenomic analysis identifies known and candidate genetic antimicrobial resistance determinants in twelve species |
Hyun JC, Monk JM, Szubin R, Hefner Y, Palsson BO
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2023 |