Bernhard O Palsson (Bernhard Palsson, B O Palsson, Bernhard Ø Palsson, Jaehyung Kim)

ORCID

Publication Activity (10 Years)

Years Active: 2017-2024
Publications (10 Years): 166

Top Venues

mSystems

Nature communications

Proceedings of the National Academy of Sciences of the United States of America

PLoS computational biology

This page only lists publications with an associated author ORCID identifier.

Publications

Amir Akbari, Zachary B Haiman, Bernhard O Palsson
A data-driven approach for timescale decomposition of biochemical reaction networks. mSystems 9 (2) (2024)
Nitasha D Menon, Saugat Poudel, Anand V Sastry, Kevin Rychel, Richard Szubin, Nicholas Dillon, Hannah Tsunemoto, Yujiro Hirose, Bipin G Nair, Geetha B Kumar, Bernhard O Palsson, Victor Nizet
Independent component analysis reveals 49 independently modulated gene sets within the global transcriptional regulatory architecture of multidrug-resistant Acinetobacter baumannii . mSystems (2024)
O Ardalani, Patrick V Phaneuf, Omkar S Mohite, L K Nielsen, Bernhard O Palsson
Pangenome reconstruction of Lactobacillaceae metabolism predicts species-specific metabolic traits. mSystems 9 (7) (2024)
Matin Nuhamunada, Omkar S Mohite, Patrick V Phaneuf, Bernhard O Palsson, Tilmann Weber
BGCFlow: systematic pangenome workflow for the analysis of biosynthetic gene clusters across large genomic datasets. Nucleic acids research 52 (10) (2024)
Andrew J Borchert, Alissa C Bleem, Hyun Gyu Lim, Kevin Rychel, Keven D Dooley, Zoe A Kellermyer, Tracy L Hodges, Bernhard O Palsson, Gregg T Beckham
Machine learning analysis of RB-TnSeq fitness data predicts functional gene modules in Pseudomonas putida KT2440. mSystems 9 (3) (2024)
Arjun Patel, Dominic McGrosso, Ying Hefner, Anaamika Campeau, Anand V Sastry, Svetlana Maurya, Kevin Rychel, David J Gonzalez, Bernhard O Palsson
Proteome allocation is linked to transcriptional regulation through a modularized transcriptome. Nature communications 15 (1) (2024)
Nitasha D Menon, Saugat Poudel, Anand V Sastry, Kevin Rychel, Richard Szubin, Nicholas Dillon, Hannah Tsunemoto, Yujiro Hirose, Bipin G Nair, Geetha B Kumar, Bernhard O Palsson, Victor Nizet
Independent component analysis reveals 49 independently modulated gene sets within the global transcriptional regulatory architecture of multidrug-resistant Acinetobacter baumannii . mSystems (2024)
Irina A Rodionova, Hyun Gyu Lim, Ye Gao, Dmitry A Rodionov, Ying Hutchison, Richard Szubin, Christopher Dalldorf, Jonathan Monk, Bernhard O Palsson
CyuR is a dual regulator for L-cysteine dependent antimicrobial resistance in Escherichia coli. Communications biology 7 (1) (2024)
Arjun Patel, Dominic McGrosso, Ying Hefner, Anaamika Campeau, Anand V Sastry, Svetlana Maurya, Kevin Rychel, David J Gonzalez, Bernhard O Palsson
Proteome allocation is linked to transcriptional regulation through a modularized transcriptome. Nature communications 15 (1) (2024)
Travis Nemkov, Daniel Stephenson, Eric J Earley, Gregory R Keele, Ariel Hay, Alicia Key, Zachary Haiman, Christopher Erickson, Monika Dzieciatkowska, Julie A Reisz, Amy Moore, Mars Stone, Xutao Deng, Steven Kleinman, Steven L Spitalnik, Eldad A Hod, Krystalyn E Hudson, Kirk C Hansen, Bernhard O Palsson, Gary A Churchill, Nareg Roubinian, Philip J Norris, Michael P Busch, James C Zimring, Grier P Page, Angelo D'Alessandro
Biological and Genetic Determinants of Glycolysis: Phosphofructokinase Isoforms Boost Energy Status of Stored Red Blood Cells and Transfusion Outcomes. bioRxiv : the preprint server for biology (2024)
Christopher Dalldorf, Kevin Rychel, Richard Szubin, Ying Hefner, Arjun Patel, Daniel C Zielinski, Bernhard O Palsson
The hallmarks of a tradeoff in transcriptomes that balances stress and growth functions. mSystems 9 (7) (2024)
Christopher Dalldorf, Kevin Rychel, Richard Szubin, Ying Hefner, Arjun Patel, Daniel C Zielinski, Bernhard O Palsson
The hallmarks of a tradeoff in transcriptomes that balances stress and growth functions. mSystems 9 (7) (2024)
Jiao Zhao, Ke Chen, Bernhard O Palsson, Laurence Yang
StressME: Unified computing framework of Escherichia coli metabolism, gene expression, and stress responses. PLoS computational biology 20 (2) (2024)
Arjun Patel, Dominic McGrosso, Ying Hefner, Anaamika Campeau, Anand V Sastry, Svetlana Maurya, Kevin Rychel, David J Gonzalez, Bernhard O Palsson
Proteome allocation is linked to transcriptional regulation through a modularized transcriptome. Nature communications 15 (1) (2024)
Nitasha D Menon, Saugat Poudel, Anand V Sastry, Kevin Rychel, Richard Szubin, Nicholas Dillon, Hannah Tsunemoto, Yujiro Hirose, Bipin G Nair, Geetha B Kumar, Bernhard O Palsson, Victor Nizet
Independent component analysis reveals 49 independently modulated gene sets within the global transcriptional regulatory architecture of multidrug-resistant Acinetobacter baumannii . mSystems 9 (2) (2024)
Jonathan Josephs-Spaulding, Akanksha Rajput, Ying Hefner, Richard Szubin, Archana Balasubramanian, Gaoyuan Li, Daniel C Zielinski, Leonie Jahn, Morten Sommer, Patrick V Phaneuf, Bernhard O Palsson
Reconstructing the transcriptional regulatory network of probiotic L. reuteri is enabled by transcriptomics and machine learning. mSystems 9 (3) (2024)
Yujiro Hirose, Daniel C Zielinski, Saugat Poudel, Kevin Rychel, Jonathon L Baker, Yoshihiro Toya, Masaya Yamaguchi, Almut Heinken, Ines Thiele, Shigetada Kawabata, Bernhard O Palsson, Victor Nizet
A genome-scale metabolic model of a globally disseminated hyperinvasive M1 strain of Streptococcus pyogenes . mSystems (2024)
Matin Nuhamunada, Omkar S Mohite, Patrick V Phaneuf, Bernhard O Palsson, Tilmann Weber
BGCFlow: systematic pangenome workflow for the analysis of biosynthetic gene clusters across large genomic datasets. Nucleic acids research 52 (10) (2024)
Cameron R Lamoureux, Patrick V Phaneuf, Bernhard O Palsson, Daniel C Zielinski
Escherichia coli non-coding regulatory regions are highly conserved. NAR genomics and bioinformatics 6 (2) (2024)
Andrew J Borchert, Alissa C Bleem, Hyun Gyu Lim, Kevin Rychel, Keven D Dooley, Zoe A Kellermyer, Tracy L Hodges, Bernhard O Palsson, Gregg T Beckham
Machine learning analysis of RB-TnSeq fitness data predicts functional gene modules in Pseudomonas putida KT2440. mSystems 9 (3) (2024)
Amir Akbari, Zachary B Haiman, Bernhard O Palsson
A data-driven approach for timescale decomposition of biochemical reaction networks. mSystems 9 (2) (2024)
Travis Nemkov, Daniel Stephenson, Eric J Earley, Gregory R Keele, Ariel Hay, Alicia Key, Zachary Haiman, Christopher Erickson, Monika Dzieciatkowska, Julie A Reisz, Amy Moore, Mars Stone, Xutao Deng, Steven Kleinman, Steven L Spitalnik, Eldad A Hod, Krystalyn E Hudson, Kirk C Hansen, Bernhard O Palsson, Gary A Churchill, Nareg Roubinian, Philip J Norris, Michael P Busch, James C Zimring, Grier P Page, Angelo D'Alessandro
Biological and Genetic Determinants of Glycolysis: Phosphofructokinase Isoforms Boost Energy Status of Stored Red Blood Cells and Transfusion Outcomes. bioRxiv : the preprint server for biology (2024)
Edward Alexander Catoiu, Nathan Mih, Maxwell Lu, Bernhard O Palsson
Establishing comprehensive quaternary structural proteomes from genome sequence. bioRxiv : the preprint server for biology (2024)
Matin Nuhamunada, Omkar S Mohite, Patrick V Phaneuf, Bernhard O Palsson, Tilmann Weber
BGCFlow: systematic pangenome workflow for the analysis of biosynthetic gene clusters across large genomic datasets. Nucleic acids research (2024)
Arjun Patel, Dominic McGrosso, Ying Hefner, Anaamika Campeau, Anand V Sastry, Svetlana Maurya, Kevin Rychel, David J Gonzalez, Bernhard O Palsson
Proteome allocation is linked to transcriptional regulation through a modularized transcriptome. Nature communications 15 (1) (2024)
Amir Akbari, Zachary B Haiman, Bernhard O Palsson
A data-driven approach for timescale decomposition of biochemical reaction networks. mSystems 9 (2) (2024)
Amir Akbari, Zachary B Haiman, Bernhard O Palsson
A data-driven approach for timescale decomposition of biochemical reaction networks. mSystems (2024)
Cameron R Lamoureux, Patrick V Phaneuf, Bernhard O Palsson, Daniel C Zielinski
Escherichia coli non-coding regulatory regions are highly conserved. NAR genomics and bioinformatics 6 (2) (2024)
Jonathan Josephs-Spaulding, Akanksha Rajput, Ying Hefner, Richard Szubin, Archana Balasubramanian, Gaoyuan Li, Daniel C Zielinski, Leonie Jahn, Morten Sommer, Patrick V Phaneuf, Bernhard O Palsson
Reconstructing the transcriptional regulatory network of probiotic L. reuteri is enabled by transcriptomics and machine learning. mSystems (2024)
Tue Sparholt Jørgensen, Omkar S Mohite, Eva B Sterndorff, Maria Alvarez-Arevalo, Kai Blin, Thomas J Booth, Pep Charusanti, David Faurdal, Troels Ø Hansen, Matin Nuhamunada, Anna-Sophie Mourched, Bernhard O Palsson, Tilmann Weber
A treasure trove of 1034 actinomycete genomes. Nucleic acids research (2024)
O Ardalani, Patrick V Phaneuf, Omkar S Mohite, L K Nielsen, Bernhard O Palsson
Pangenome reconstruction of Lactobacillaceae metabolism predicts species-specific metabolic traits. mSystems (2024)
Nitasha D Menon, Saugat Poudel, Anand V Sastry, Kevin Rychel, Richard Szubin, Nicholas Dillon, Hannah Tsunemoto, Yujiro Hirose, Bipin G Nair, Geetha B Kumar, Bernhard O Palsson, Victor Nizet
Independent component analysis reveals 49 independently modulated gene sets within the global transcriptional regulatory architecture of multidrug-resistant Acinetobacter baumannii . mSystems 9 (2) (2024)
Nitasha D Menon, Saugat Poudel, Anand V Sastry, Kevin Rychel, Richard Szubin, Nicholas Dillon, Hannah Tsunemoto, Yujiro Hirose, Bipin G Nair, Geetha B Kumar, Bernhard O Palsson, Victor Nizet
Independent component analysis reveals 49 independently modulated gene sets within the global transcriptional regulatory architecture of multidrug-resistant Acinetobacter baumannii . mSystems 9 (2) (2024)
Christopher Dalldorf, Kevin Rychel, Richard Szubin, Ying Hefner, Arjun Patel, Daniel C Zielinski, Bernhard O Palsson
The hallmarks of a tradeoff in transcriptomes that balances stress and growth functions. mSystems 9 (7) (2024)
Jonathan Josephs-Spaulding, Akanksha Rajput, Ying Hefner, Richard Szubin, Archana Balasubramanian, Gaoyuan Li, Daniel C Zielinski, Leonie Jahn, Morten Sommer, Patrick V Phaneuf, Bernhard O Palsson
Reconstructing the transcriptional regulatory network of probiotic L. reuteri is enabled by transcriptomics and machine learning. mSystems 9 (3) (2024)
Travis Nemkov, Daniel Stephenson, Eric J Earley, Gregory R Keele, Ariel Hay, Alicia Key, Zachary Haiman, Christopher Erickson, Monika Dzieciatkowska, Julie A Reisz, Amy Moore, Mars Stone, Xutao Deng, Steven Kleinman, Steven L Spitalnik, Eldad A Hod, Krystalyn E Hudson, Kirk C Hansen, Bernhard O Palsson, Gary A Churchill, Nareg Roubinian, Philip J Norris, Michael P Busch, James C Zimring, Grier P Page, Angelo D'Alessandro
Biological and Genetic Determinants of Glycolysis: Phosphofructokinase Isoforms Boost Energy Status of Stored Red Blood Cells and Transfusion Outcomes. bioRxiv : the preprint server for biology (2024)
Christopher Dalldorf, Kevin Rychel, Richard Szubin, Ying Hefner, Arjun Patel, Daniel C Zielinski, Bernhard O Palsson
The hallmarks of a tradeoff in transcriptomes that balances stress and growth functions. mSystems (2024)
Shankar Subramaniam, Metin Akay, Mark A Anastasio, Vasudev Bailey, David A Boas, Ashutosh Chilkoti, Jennifer R Cochran, Vicki L Colvin, Tejal A Desai, James S Duncan, Frederick H Epstein, Stephanie I Fraley, Cecilia Maria Giachelli, Kathryn Jane Grande-Allen, Jordan J Green, Xiang-Dong Edward Guo, Isaac B Hilton, Jay D Humphrey, Chris R Johnson, George Em Karniadakis, Michael R King, Robert F Kirsch, Sanjay Kumar, Cato T Laurencin, Song Li, Richard L Lieber, Nigel H Lovell, Prashant Mali, Stephanie A Pasquesi, David F Meaney, Brenda M Ogle, Bernhard O Palsson, Nicholas A Peppas, Eric J Perreault, Richard D Rabbitt, Lori A Setton, Lonnie D Shea, Sanjeev G Shroff, Kirk Shung, Andreas Savas Tolias, Marjolein C H van der Meulen, Shyni Varghese, Gordana Vunjak-Novakovic, John A White, Raimond L Winslow, Jianyi Jay Zhang, Kun Zhang, Charles Zukoski
Grand Challenges at the Interface of Engineering and Medicine. IEEE open journal of engineering in medicine and biology 5 (2024)
Jiao Zhao, Ke Chen, Bernhard O Palsson, Laurence Yang
StressME: Unified computing framework of Escherichia coli metabolism, gene expression, and stress responses. PLoS computational biology 20 (2) (2024)
Amir Akbari, Bernhard O Palsson
Multi-scale reactor designs extend the physical limits of CO 2 fixation. bioRxiv : the preprint server for biology (2024)
O Ardalani, Patrick V Phaneuf, Omkar S Mohite, L K Nielsen, Bernhard O Palsson
Pangenome reconstruction of Lactobacillaceae metabolism predicts species-specific metabolic traits. mSystems 9 (7) (2024)
Tue Sparholt Jørgensen, Omkar S Mohite, Eva B Sterndorff, Maria Alvarez-Arevalo, Kai Blin, Thomas J Booth, Pep Charusanti, David Faurdal, Troels Ø Hansen, Matin Nuhamunada, Anna-Sophie Mourched, Bernhard O Palsson, Tilmann Weber
A treasure trove of 1034 actinomycete genomes. Nucleic acids research 52 (13) (2024)
Nitasha D Menon, Saugat Poudel, Anand V Sastry, Kevin Rychel, Richard Szubin, Nicholas Dillon, Hannah Tsunemoto, Yujiro Hirose, Bipin G Nair, Geetha B Kumar, Bernhard O Palsson, Victor Nizet
Independent component analysis reveals 49 independently modulated gene sets within the global transcriptional regulatory architecture of multidrug-resistant Acinetobacter baumannii . mSystems 9 (2) (2024)
Arjun Patel, Dominic McGrosso, Ying Hefner, Anaamika Campeau, Anand V Sastry, Svetlana Maurya, Kevin Rychel, David J Gonzalez, Bernhard O Palsson
Proteome allocation is linked to transcriptional regulation through a modularized transcriptome. Nature communications 15 (1) (2024)
Jiao Zhao, Ke Chen, Bernhard O Palsson, Laurence Yang
StressME: Unified computing framework of Escherichia coli metabolism, gene expression, and stress responses. PLoS computational biology 20 (2) (2024)
Andrew J Borchert, Alissa C Bleem, Hyun Gyu Lim, Kevin Rychel, Keven D Dooley, Zoe A Kellermyer, Tracy L Hodges, Bernhard O Palsson, Gregg T Beckham
Machine learning analysis of RB-TnSeq fitness data predicts functional gene modules in Pseudomonas putida KT2440. mSystems 9 (3) (2024)
Antoine Champie, Jean-Christophe Lachance, Anand Sastry, Dominick Matteau, Colton J Lloyd, Frédéric Grenier, Cameron R Lamoureux, Simon Jeanneau, Adam M Feist, Pierre-Étienne Jacques, Bernhard O Palsson, Sébastien Rodrigue
Diagnosis and mitigation of the systemic impact of genome reduction in Escherichia coli DGF-298. mBio (2024)
Donghui Choe, Connor A Olson, Richard Szubin, Hannah Yang, Jaemin Sung, Adam M Feist, Bernhard O Palsson
Advancing the scale of synthetic biology via cross-species transfer of cellular functions enabled by iModulon engraftment. Nature communications 15 (1) (2024)
Christopher Dalldorf, Kevin Rychel, Richard Szubin, Ying Hefner, Arjun Patel, Daniel C Zielinski, Bernhard O Palsson
The hallmarks of a tradeoff in transcriptomes that balances stress and growth functions. mSystems (2024)
Travis Nemkov, Daniel Stephenson, Eric J Earley, Gregory R Keele, Ariel Hay, Alicia Key, Zachary Haiman, Christopher Erickson, Monika Dzieciatkowska, Julie A Reisz, Amy Moore, Mars Stone, Xutao Deng, Steven Kleinman, Steven L Spitalnik, Eldad A Hod, Krystalyn E Hudson, Kirk C Hansen, Bernhard O Palsson, Gary A Churchill, Nareg Roubinian, Philip J Norris, Michael P Busch, James C Zimring, Grier P Page, Angelo D'Alessandro
Biological and Genetic Determinants of Glycolysis: Phosphofructokinase Isoforms Boost Energy Status of Stored Red Blood Cells and Transfusion Outcomes. bioRxiv : the preprint server for biology (2024)
Christopher Dalldorf, Kevin Rychel, Richard Szubin, Ying Hefner, Arjun Patel, Daniel C Zielinski, Bernhard O Palsson
The hallmarks of a tradeoff in transcriptomes that balances stress and growth functions. mSystems (2024)
Amir Akbari, Zachary B Haiman, Bernhard O Palsson
A data-driven approach for timescale decomposition of biochemical reaction networks. mSystems 9 (2) (2024)
Jiao Zhao, Ke Chen, Bernhard O Palsson, Laurence Yang
StressME: Unified computing framework of Escherichia coli metabolism, gene expression, and stress responses. PLoS computational biology 20 (2) (2024)
Adil Mardinglu, Bernhard O Palsson
Genome-scale models in human metabologenomics. Nature reviews. Genetics (2024)
Jongoh Shin, Daniel C Zielinski, Bernhard O Palsson
Modulating bacterial function utilizing A knowledge base of transcriptional regulatory modules. Nucleic acids research (2024)
Donghui Choe, Connor A Olson, Richard Szubin, Hannah Yang, Jaemin Sung, Adam M Feist, Bernhard O Palsson
Advancing the scale of synthetic biology via cross-species transfer of cellular functions enabled by iModulon engraftment. Nature communications 15 (1) (2024)
Amir Akbari, Zachary B Haiman, Bernhard O Palsson
A data-driven approach for timescale decomposition of biochemical reaction networks. mSystems (2024)
Jiao Zhao, Ke Chen, Bernhard O Palsson, Laurence Yang
StressME: Unified computing framework of Escherichia coli metabolism, gene expression, and stress responses. PLoS computational biology 20 (2) (2024)
O Ardalani, Patrick V Phaneuf, Omkar S Mohite, L K Nielsen, Bernhard O Palsson
Pangenome reconstruction of Lactobacillaceae metabolism predicts species-specific metabolic traits. mSystems 9 (7) (2024)
Donghui Choe, Connor A Olson, Richard Szubin, Hannah Yang, Jaemin Sung, Adam M Feist, Bernhard O Palsson
Advancing the scale of synthetic biology via cross-species transfer of cellular functions enabled by iModulon engraftment. Nature communications 15 (1) (2024)
Yuan Yuan, Tahani Al Bulushi, Anand V Sastry, Cigdem Sancar, Richard Szubin, Susan S Golden, Bernhard O Palsson
Machine learning reveals the transcriptional regulatory network and circadian dynamics of Synechococcus elongatus PCC 7942. Proceedings of the National Academy of Sciences of the United States of America 121 (38) (2024)
Jonathan Josephs-Spaulding, Akanksha Rajput, Ying Hefner, Richard Szubin, Archana Balasubramanian, Gaoyuan Li, Daniel C Zielinski, Leonie Jahn, Morten Sommer, Patrick V Phaneuf, Bernhard O Palsson
Reconstructing the transcriptional regulatory network of probiotic L. reuteri is enabled by transcriptomics and machine learning. mSystems 9 (3) (2024)
Andrew J Borchert, Alissa C Bleem, Hyun Gyu Lim, Kevin Rychel, Keven D Dooley, Zoe A Kellermyer, Tracy L Hodges, Bernhard O Palsson, Gregg T Beckham
Machine learning analysis of RB-TnSeq fitness data predicts functional gene modules in Pseudomonas putida KT2440. mSystems (2024)
Tue Sparholt Jørgensen, Omkar S Mohite, Eva B Sterndorff, Maria Alvarez-Arevalo, Kai Blin, Thomas J Booth, Pep Charusanti, David Faurdal, Troels Ø Hansen, Matin Nuhamunada, Anna-Sophie Mourched, Bernhard O Palsson, Tilmann Weber
A treasure trove of 1034 actinomycete genomes. Nucleic acids research 52 (13) (2024)
Amir Akbari, Zachary B Haiman, Bernhard O Palsson
A data-driven approach for timescale decomposition of biochemical reaction networks. mSystems (2024)
Amir Akbari, Bernhard O Palsson
Metabolic homeostasis and growth in abiotic cells. Proceedings of the National Academy of Sciences of the United States of America 120 (19) (2023)
Christopher Dalldorf, Kevin Rychel, Richard Szubin, Ying Hefner, Arjun Patel, Daniel Zielinski, Bernhard O Palsson
The hallmarks of a tradeoff in transcriptomes that balances stress and growth functions. Research square (2023)
Irina A Rodionova, Hyun Gyu Lim, Dmitry A Rodionov, Ying Hutchison, Christopher Dalldorf, Ye Gao, Jonathan Monk, Bernhard O Palsson
CyuR is a Dual Regulator for L-Cysteine Dependent Antimicrobial Resistance in Escherichia coli . bioRxiv : the preprint server for biology (2023)
Christopher Dalldorf, Kevin Rychel, Richard Szubin, Ying Hefner, Arjun Patel, Daniel Zielinski, Bernhard O Palsson
The hallmarks of a tradeoff in transcriptomes that balances stress and growth functions. Research square (2023)
Edward Alexander Catoiu, Patrick V Phaneuf, Jonathan M Monk, Bernhard O Palsson
Whole-genome sequences from wild-type and laboratory-evolved strains define the alleleome and establish its hallmarks. Proceedings of the National Academy of Sciences of the United States of America 120 (15) (2023)
Jason C Hyun, Jonathan M Monk, Richard Szubin, Ying Hefner, Bernhard O Palsson
Global pathogenomic analysis identifies known and candidate genetic antimicrobial resistance determinants in twelve species. Nature communications 14 (1) (2023)
Amir Akbari, Bernhard O Palsson
Metabolic homeostasis and growth in abiotic cells. Proceedings of the National Academy of Sciences of the United States of America 120 (19) (2023)
Erhard Bremer, Alexandra Calteau, Antoine Danchin, Fleur A E Roland, John D Helmann, Claudine Médigue, Bernhard O Palsson, Agnieszka Sekowska, David Vallenet, Abril Zuniga, Cristal Zuñiga
A model industrial workhorse: Bacillus subtilis strain 168 and its genome after a quarter of a century. Microbial biotechnology (2023)
Nathan Mih, Maxwell Lu, Bernhard O Palsson, Edward Alexander Catoiu
Establishing comprehensive quaternary structural proteomes from genome sequence. Research square (2023)
Amir Akbari, Bernhard O Palsson
Metabolic homeostasis and growth in abiotic cells. Proceedings of the National Academy of Sciences of the United States of America 120 (19) (2023)
Amir Akbari, Bernhard O Palsson
Metabolic homeostasis and growth in abiotic cells. Proceedings of the National Academy of Sciences of the United States of America 120 (19) (2023)
Christopher Dalldorf, Kevin Rychel, Richard Szubin, Ying Hefner, Arjun Patel, Daniel Zielinski, Bernhard O Palsson
The hallmarks of a tradeoff in transcriptomes that balances stress and growth functions. Research square (2023)
Ye Gao, Ina Bang, Yara Seif, Donghyuk Kim, Bernhard O Palsson
The Escherichia coli Fur pan-regulon has few conserved but many unique regulatory targets. Nucleic acids research (2023)
Cameron R Lamoureux, Katherine T Decker, Anand V Sastry, Kevin Rychel, Ye Gao, John Luke McConn, Daniel C Zielinski, Bernhard O Palsson
A multi-scale expression and regulation knowledge base for Escherichia coli. Nucleic acids research (2023)
Sourav Chowdhury, Daniel C Zielinski, Christopher Dalldorf, Joao V Rodrigues, Bernhard O Palsson, Eugene I Shakhnovich
Empowering drug off-target discovery with metabolic and structural analysis. Nature communications 14 (1) (2023)
Joon Young Park, Sang-Mok Lee, Ali Ebrahim, Zoe K Scott-Nevros, Bernhard O Palsson, Laurence Yang, Anand V Sastry, Sang Woo Seo, Bernhard O Palsson, Donghyuk Kim
Model-driven experimental design workflow expands understanding of regulatory role of Nac in Escherichia coli . NAR genomics and bioinformatics 5 (1) (2023)
Joon Young Park, Sang-Mok Lee, Ali Ebrahim, Zoe K Scott-Nevros, Bernhard O Palsson, Laurence Yang, Anand V Sastry, Sang Woo Seo, Bernhard O Palsson, Donghyuk Kim
Model-driven experimental design workflow expands understanding of regulatory role of Nac in Escherichia coli . NAR genomics and bioinformatics 5 (1) (2023)
Joon Young Park, Sang-Mok Lee, Ali Ebrahim, Zoe K Scott-Nevros, Bernhard O Palsson, Laurence Yang, Anand V Sastry, Sang Woo Seo, Bernhard O Palsson, Donghyuk Kim
Model-driven experimental design workflow expands understanding of regulatory role of Nac in Escherichia coli . NAR genomics and bioinformatics 5 (1) (2023)
Amir Akbari, Bernhard O Palsson
Metabolic homeostasis and growth in abiotic cells. Proceedings of the National Academy of Sciences of the United States of America 120 (19) (2023)
Jason C Hyun, Bernhard O Palsson
Reconstruction of the last bacterial common ancestor from 183 pangenomes reveals a versatile ancient core genome. Genome biology 24 (1) (2023)
Gi Bae Kim, Ji Yeon Kim, Jong An Lee, Charles J Norsigian, Bernhard O Palsson, Sang Yup Lee
Functional annotation of enzyme-encoding genes using deep learning with transformer layers. Nature communications 14 (1) (2023)
Christopher Dalldorf, Kevin Rychel, Richard Szubin, Ying Hefner, Arjun Patel, Daniel Zielinski, Bernhard O Palsson
The hallmarks of a tradeoff in transcriptomes that balances stress and growth functions. Research square (2023)
Amir Akbari, Bernhard O Palsson
Metabolic homeostasis and growth in abiotic cells. Proceedings of the National Academy of Sciences of the United States of America 120 (19) (2023)
Amir Akbari, Bernhard O Palsson
Metabolic homeostasis and growth in abiotic cells. Proceedings of the National Academy of Sciences of the United States of America 120 (19) (2023)
Yuan Yuan, Yara Seif, Kevin Rychel, Reo Yoo, Siddharth Chauhan, Saugat Poudel, Tahani Al-Bulushi, Bernhard O Palsson, Anand V Sastry
Pan-Genome Analysis of Transcriptional Regulation in Six Salmonella enterica Serovar Typhimurium Strains Reveals Their Different Regulatory Structures. mSystems (2022)
Anaëlle Fait, Yara Seif, Kasper Mikkelsen, Saugat Poudel, Jerry M Wells, Bernhard O Palsson, Hanne Ingmer
Adaptive laboratory evolution and independent component analysis disentangle complex vancomycin adaptation trajectories. Proceedings of the National Academy of Sciences of the United States of America 119 (30) (2022)
Donghui Choe, Uigi Kim, Soonkyu Hwang, Sang Woo Seo, Donghyuk Kim, Suhyung Cho, Bernhard O Palsson, Byung Kwan Cho
Revealing Causes for False-Positive and False-Negative Calling of Gene Essentiality in Escherichia coli Using Transposon Insertion Sequencing. mSystems 8 (1) (2022)
Bernhard O Palsson, Bernhard O Palsson
Is the kinetome conserved? Molecular systems biology 18 (2) (2022)
Amitesh Anand, Arjun Patel, Ke Chen, Connor A Olson, Patrick V Phaneuf, Cameron Lamoureux, Ying Hefner, Richard Szubin, Adam M Feist, Bernhard O Palsson
Laboratory evolution of synthetic electron transport system variants reveals a larger metabolic respiratory system and its plasticity. Nature communications 13 (1) (2022)
Elliot L Weiss, Mingxu Fang, Arnaud Taton, Richard Szubin, Bernhard O Palsson, B Greg Mitchell, Susan S Golden
An unexpected role for leucyl aminopeptidase in UV tolerance revealed by a genome-wide fitness assessment in a model cyanobacterium. Proceedings of the National Academy of Sciences of the United States of America 119 (45) (2022)
Donghui Choe, Uigi Kim, Soonkyu Hwang, Sang Woo Seo, Donghyuk Kim, Suhyung Cho, Bernhard O Palsson, Byung Kwan Cho
Revealing Causes for False-Positive and False-Negative Calling of Gene Essentiality in Escherichia coli Using Transposon Insertion Sequencing. mSystems (2022)
Erol S Kavvas, Christopher P Long, Anand Sastry, Saugat Poudel, Maciek R Antoniewicz, Yang Ding, Elsayed T Mohamed, Richard Szubin, Jonathan M Monk, Adam M Feist, Bernhard O Palsson
Experimental Evolution Reveals Unifying Systems-Level Adaptations but Diversity in Driving Genotypes. mSystems (2022)
Donghui Choe, Uigi Kim, Soonkyu Hwang, Sang Woo Seo, Donghyuk Kim, Suhyung Cho, Bernhard O Palsson, Byung Kwan Cho
Revealing Causes for False-Positive and False-Negative Calling of Gene Essentiality in Escherichia coli Using Transposon Insertion Sequencing. mSystems 8 (1) (2022)
Donghui Choe, Uigi Kim, Soonkyu Hwang, Sang Woo Seo, Donghyuk Kim, Suhyung Cho, Bernhard O Palsson, Byung Kwan Cho
Revealing Causes for False-Positive and False-Negative Calling of Gene Essentiality in Escherichia coli Using Transposon Insertion Sequencing. mSystems 8 (1) (2022)
Akanksha Rajput, Hannah Tsunemoto, Anand V Sastry, Richard Szubin, Kevin Rychel, Siddharth M Chauhan, Joe Pogliano, Bernhard O Palsson
Advanced transcriptomic analysis reveals the role of efflux pumps and media composition in antibiotic responses of Pseudomonas aeruginosa. Nucleic acids research 50 (17) (2022)

Bernhard O Palsson.css-eqlu8i{font-size:small;padding-left:4px;} (Bernhard Palsson, B O Palsson, Bernhard Ø Palsson, Jaehyung Kim)

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Bernhard O Palsson (Bernhard Palsson, B O Palsson, Bernhard Ø Palsson, Jaehyung Kim)