| Proteome allocation is linked to transcriptional regulation through a modularized transcriptome |
Patel A, McGrosso D, Hefner Y, Campeau A, Sastry AV, Maurya S, Rychel K, Gonzalez DJ, Palsson BO.
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2024 |
| Revealing systematic changes in the transcriptome during the transition from exponential growth to stationary phase. |
Lim HG, Gao Y, Rychel K, Lamoureux C, Lou XA, Palsson BO.
|
2024 |
| Independent component analysis reveals 49 independently modulated gene sets within the global transcriptional regulatory architecture of multidrug-resistant Acinetobacter baumannii. |
Menon ND, Poudel S, Sastry AV, Rychel K, Szubin R, Dillon N, Tsunemoto H, Hirose Y, Nair BG, Kumar GB, Palsson BO, Nizet V.
|
2024 |
| 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 |
| Pangenome analysis reveals the genetic basis for taxonomic classification of the Lactobacillaceae family |
Akanksha Rajput, Siddharth M. Chauhan, Omkar S. Mohite, Jason C. Hyun, Omid Ardalani, Leonie J. Jahn, Morten OA. Sommer, Bernhard O. Palsson
|
2023 |
| Adaptive Evolution of a Minimal Organism with a Synthetic Genome |
Sandberg, T.E., Wise, K.S., Dalldorf, C., Szubin, R., Feist, A.M., Glass, J.I., Palsson, B.O.
|
2023 |
| Comprehensive whole genome sequencing with hybrid assembly of multi-drug resistant Candida albicans isolate causing cerebral abscess |
Kumaraswamy M, Coady A, Szubin R, Martin TCS, Palsson B, Nizet V, Monk JM |
2023 |
| Reconstruction of the last bacterial common ancestor from 183 pangenomes reveals a versatile ancient core genome |
Hyun, J.C., Palsson, B.O.
|
2023 |
| Model-driven experimental design workflow expands understanding of regulatory role of Nac in Escherichia coli |
Park JY, Lee SM, Ebrahim A, Scott-Nevros ZK, Kim J, Yang L, Sastry A, Seo SW, Palsson BO, Kim D |
2023 |
| Machine learning uncovers the Pseudomonas syringae transcriptome in microbial communities and during infection |
Bajpe H, Rychel K, Lamoureux CR, Sastry AV, Palsson BO
|
2023 |
| Deep-learning optimized DEOCSU suite provides an iterable pipeline for accurate ChIP-exo peak calling |
Bang I, Lee SM, Park S, Park JY, Nong LK, Gao Y, Palsson BO, Kim D |
2023 |
| Recent advances in non-model bacterial chassis construction |
Hwang S, Joung C, Kim W, Palsson B, Cho B-K
|
2023 |
| Laboratory evolution reveals general and specific tolerance mechanisms for commodity chemicals |
Lennen RM, Lim HG, Jensen K, Mohammed ET, Phaneuf PV, Noh MH, Malla S, Börner RA, Chekina K, Özdemir E, Bonde I, Koza A, Maury J, Pedersen LE, Schöning LY, Sonnenschein N, Palsson BO, Nielsen AT, Sommer MOA, Herrgård MJ, Feist AM |
2023 |
| A multi-scale expression and regulation knowledge base for Escherichia coli |
Lamoureux CR, Decker KT, Sastry AV, Rychel K, Gao Y, McConn JL, Zielinski DC, Palsson BO
|
2023 |
| Revealing oxidative pentose metabolism in new Pseudomonas putida isolates |
Park, M. R., Gauttam, R., Fong, B., Chen, Y., Lim, H. G., Feist, A. M., Mukhopadhyay, A., Petzold, C. J., Simmons, B. A., & Singer, S. W. |
2023 |
| Laboratory evolution, transcriptomics, and modeling reveal mechanisms of paraquat tolerance |
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, Palsson BO.
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2023 |
| 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.
|
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.
|
2023 |
| The Escherichia coli Fur pan-regulon has few conserved but many unique regulatory targets |
|
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
|
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.
|
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 |