Bernhard O. Palsson

Publication Activity (10 Years)

Years Active: 2000-2024
Publications (10 Years): 44

Top Topics

Systems Biology

Biochemical Networks

Gene Expression

Escherichia Coli

Top Venues

PLoS Comput. Biol.

BMC Syst. Biol.

Nucleic Acids Res.

Publications

Jiao Zhao, Ke Chen, Bernhard O. Palsson, Laurence Yang
StressME: Unified computing framework of Escherichia coli metabolism, gene expression, and stress responses. PLoS Comput. Biol. 20 (2) (2024)
Sizhe Qiu, Xinlong Wan, Yueshan Liang, Cameron R. Lamoureux, Amir Akbari, Bernhard O. Palsson, Daniel C. Zielinski
Inferred regulons are consistent with regulator binding sequences in E. coli. PLoS Comput. Biol. 20 (1) (2024)
Ina Bang, Sang-Mok Lee, Seojoung Park, Joon Young Park, Linh Khanh Nong, Ye Gao, Bernhard O. Palsson, Donghyuk Kim
Deep-learning optimized DEOCSU suite provides an iterable pipeline for accurate ChIP-exo peak calling. Briefings Bioinform. 24 (2) (2023)
Amir Akbari, Bernhard O. Palsson
Positively charged mineral surfaces promoted the accumulation of organic intermediates at the origin of metabolism. PLoS Comput. Biol. 18 (8) (2022)
Max van 't Hof, Omkar S. Mohite, Jonathan M. Monk, Tilmann Weber, Bernhard O. Palsson, Morten O. A. Sommer
High-quality genome-scale metabolic network reconstruction of probiotic bacterium Escherichia coli Nissle 1917. BMC Bioinform. 23 (1) (2022)
Katherine Decker, Ye Gao, Kevin Rychel, Tahani Al bulushi, Siddharth m Chauhan, Donghyuk Kim, Byung-Kwan Cho, Bernhard O. Palsson
proChIPdb: a chromatin immunoprecipitation database for prokaryotic organisms. Nucleic Acids Res. 50 (D1) (2022)
Zachary B. Haiman, Daniel C. Zielinski, Yuko Koike, James T. Yurkovich, Bernhard O. Palsson
MASSpy: Building, simulating, and visualizing dynamic biological models in Python using mass action kinetics. PLoS Comput. Biol. 17 (1) (2021)
Amir Akbari, Bernhard O. Palsson
Scalable computation of intracellular metabolite concentrations. Comput. Chem. Eng. 145 (2021)
Kevin Rychel, Katherine Decker, Anand V. Sastry, Patrick V. Phaneuf, Saugat Poudel, Bernhard O. Palsson
iModulonDB: a knowledgebase of microbial transcriptional regulation derived from machine learning. Nucleic Acids Res. 49 (Database-Issue) (2021)
Anand V. Sastry, Alyssa Hu, David Heckmann, Saugat Poudel, Erol Kavvas, Bernhard O. Palsson
Independent component analysis recovers consistent regulatory signals from disparate datasets. PLoS Comput. Biol. 17 (2) (2021)
Ke Chen, Amitesh Anand, Connor A. Olson, Troy E. Sandberg, Ye Gao, Nathan Mih, Bernhard O. Palsson
Bacterial fitness landscapes stratify based on proteome allocation associated with discrete aero-types. PLoS Comput. Biol. 17 (1) (2021)
Colton J. Lloyd, Jonathan Monk, Laurence Yang, Ali Ebrahim, Bernhard O. Palsson
Computation of condition-dependent proteome allocation reveals variability in the macro and micro nutrient requirements for growth. PLoS Comput. Biol. 17 (6) (2021)
John Luke McConn, Cameron R. Lamoureux, Saugat Poudel, Bernhard O. Palsson, Anand V. Sastry
Optimal dimensionality selection for independent component analysis of transcriptomic data. BMC Bioinform. 22 (1) (2021)
Nathan Mih, Jonathan M. Monk, Xin Fang, Edward Catoiu, David Heckmann, Laurence Yang, Bernhard O. Palsson
Adaptations of Escherichia coli strains to oxidative stress are reflected in properties of their structural proteomes. BMC Bioinform. 21 (1) (2020)
Jason C. Hyun, Erol S. Kavvas, Jonathan M. Monk, Bernhard O. Palsson
Machine learning with random subspace ensembles identifies antimicrobial resistance determinants from pan-genomes of three pathogens. PLoS Comput. Biol. 16 (3) (2020)
Charles J. Norsigian, Neha Pusarla, John Luke McConn, James T. Yurkovich, Andreas Dräger, Bernhard O. Palsson, Zachary A. King
BiGG Models 2020: multi-strain genome-scale models and expansion across the phylogenetic tree. Nucleic Acids Res. 48 (Database-Issue) (2020)
Yara Seif, Jonathan M. Monk, Nathan Mih, Hannah Tsunemoto, Saugat Poudel, Cristal Zuniga, Jared Broddrick, Karsten Zengler, Bernhard O. Palsson
A computational knowledge-base elucidates the response of Staphylococcus aureus to different media types. PLoS Comput. Biol. 15 (1) (2019)
Laurence Yang, Ali Ebrahim, Colton J. Lloyd, Michael A. Saunders, Bernhard O. Palsson
DynamicME: dynamic simulation and refinement of integrated models of metabolism and protein expression. BMC Syst. Biol. 13 (1) (2019)
Bin Du, Laurence Yang, Colton J. Lloyd, Xin Fang, Bernhard O. Palsson
Genome-scale model of metabolism and gene expression provides a multi-scale description of acid stress responses in Escherichia coli. PLoS Comput. Biol. 15 (12) (2019)
Patrick V. Phaneuf, Dennis Gosting, Bernhard O. Palsson, Adam M. Feist
ALEdb 1.0: a database of mutations from adaptive laboratory evolution experimentation. Nucleic Acids Res. 47 (Database-Issue) (2019)
Laurence Yang, Michael A. Saunders, Jean-Christophe Lachance, Bernhard O. Palsson, José Bento
Estimating Cellular Goals from High-Dimensional Biological Data. KDD (2019)
Jinyuan Yan, Henri Estanbouli, Chen Liao, Wook Kim, Jonathan M. Monk, Rayees Rahman, Mini Kamboj, Bernhard O. Palsson, Weigang Qiu, João B. Xavier
Systems-level analysis of NalD mutation, a recurrent driver of rapid drug resistance in acute Pseudomonas aeruginosa infection. PLoS Comput. Biol. 15 (12) (2019)
Jean-Christophe Lachance, Colton J. Lloyd, Jonathan M. Monk, Laurence Yang, Anand Sastry, Yara Seif, Bernhard O. Palsson, Sébastien Rodrigue, Adam M. Feist, Zachary A. King, Pierre-Étienne Jacques
BOFdat: Generating biomass objective functions for genome-scale metabolic models from experimental data. PLoS Comput. Biol. 15 (4) (2019)
Chuankai Cheng, Edward J. O'Brien, Douglas McCloskey, Jose Utrilla, Connor A. Olson, Ryan A. LaCroix, Troy E. Sandberg, Adam M. Feist, Bernhard O. Palsson, Zachary A. King
Laboratory evolution reveals a two-dimensional rate-yield tradeoff in microbial metabolism. PLoS Comput. Biol. 15 (6) (2019)
Erol S. Kavvas, Yara Seif, James T. Yurkovich, Charles J. Norsigian, Saugat Poudel, William W. Greenwald, Sankha Ghatak, Bernhard O. Palsson, Jonathan M. Monk
Updated and standardized genome-scale reconstruction of Mycobacterium tuberculosis H37Rv, iEK1011, simulates flux states indicative of physiological conditions. BMC Syst. Biol. 12 (1) (2018)
Alyaa M. Abdel-Haleem, Hooman Hefzi, Katsuhiko Mineta, Xin Gao, Takashi Gojobori, Bernhard O. Palsson, Nathan E. Lewis, Neema Jamshidi
Functional interrogation of Plasmodium genus metabolism identifies species- and stage-specific differences in nutrient essentiality and drug targeting. PLoS Comput. Biol. 14 (1) (2018)
Elliot Rowe, Bernhard O. Palsson, Zachary A. King
Escher-FBA: a web application for interactive flux balance analysis. BMC Syst. Biol. 12 (1) (2018)
James T. Yurkovich, Miguel A. Alcantar, Zachary B. Haiman, Bernhard O. Palsson
Network-level allosteric effects are elucidated by detailing how ligand-binding events modulate utilization of catalytic potentials. PLoS Comput. Biol. 14 (8) (2018)
James T. Yurkovich, Aarash Bordbar, Ólafur E. Sigurjónsson, Bernhard O. Palsson
Systems biology as an emerging paradigm in transfusion medicine. BMC Syst. Biol. 12 (1) (2018)
Colton J. Lloyd, Ali Ebrahim, Laurence Yang, Zachary A. King, Edward Catoiu, Edward J. O'Brien, Joanne K. Liu, Bernhard O. Palsson
COBRAme: A computational framework for genome-scale models of metabolism and gene expression. PLoS Comput. Biol. 14 (7) (2018)
Laurence Yang, José Bento, Jean-Christophe Lachance, Bernhard O. Palsson
Genome-scale estimation of cellular objectives. CoRR (2018)
Gabriela I. Guzmán, Connor A. Olson, Ying Hefner, Patrick V. Phaneuf, Edward Catoiu, Lais B. Crepaldi, Lucas Goldschmidt Micas, Bernhard O. Palsson, Adam M. Feist
Reframing gene essentiality in terms of adaptive flexibility. BMC Syst. Biol. 12 (1) (2018)
Nathan Mih, Elizabeth Brunk, Ke Chen, Edward Catoiu, Anand Sastry, Erol S. Kavvas, Jonathan M. Monk, Zhen Zhang, Bernhard O. Palsson
ssbio: a Python framework for structural systems biology. Bioinform. 34 (12) (2018)
Xin Fang, Jonathan M. Monk, Nathan Mih, Bin Du, Anand Sastry, Erol S. Kavvas, Yara Seif, Larry Smarr, Bernhard O. Palsson
Escherichia coli B2 strains prevalent in inflammatory bowel disease patients have distinct metabolic capabilities that enable colonization of intestinal mucosa. BMC Syst. Biol. 12 (1) (2018)
Anand Sastry, Jonathan Monk, Hanna Tegel, Mathias Uhlen, Bernhard O. Palsson, Johan Rockberg, Elizabeth Brunk
Machine learning in computational biology to accelerate high-throughput protein expression. Bioinform. 33 (16) (2017)
James T. Yurkovich, Laurence Yang, Bernhard O. Palsson
Utilizing biomarkers to forecast quantitative metabolite concentration profiles in human red blood cells. CCTA (2017)
James T. Yurkovich, Laurence Yang, Bernhard O. Palsson
Biomarkers are used to predict quantitative metabolite concentration profiles in human red blood cells. PLoS Comput. Biol. 13 (3) (2017)
Laurence Yang, Ding Ma, Ali Ebrahim, Colton J. Lloyd, Michael A. Saunders, Bernhard O. Palsson
solveME: fast and reliable solution of nonlinear ME models. BMC Bioinform. 17 (2016)
Bin Du, Daniel C. Zielinski, Erol S. Kavvas, Andreas Dräger, Justin Tan, Zhen Zhang, Kayla E. Ruggiero, Garri A. Arzumanyan, Bernhard O. Palsson
Evaluation of rate law approximations in bottom-up kinetic models of metabolism. BMC Syst. Biol. 10 (2016)
Zachary A. King, Justin Lu, Andreas Dräger, Philip Miller, Stephen Federowicz, Joshua A. Lerman, Ali Ebrahim, Bernhard O. Palsson, Nathan E. Lewis
BiGG Models: A platform for integrating, standardizing and sharing genome-scale models. Nucleic Acids Res. 44 (Database-Issue) (2016)
Edward J. O'Brien, Jose Utrilla, Bernhard O. Palsson
Quantification and Classification of E. coli Proteome Utilization and Unused Protein Costs across Environments. PLoS Comput. Biol. 12 (6) (2016)
Nathan Mih, Elizabeth Brunk, Aarash Bordbar, Bernhard O. Palsson
A Multi-scale Computational Platform to Mechanistically Assess the Effect of Genetic Variation on Drug Responses in Human Erythrocyte Metabolism. PLoS Comput. Biol. 12 (7) (2016)
James T. Yurkovich, Bernhard O. Palsson
Solving Puzzles With Missing Pieces: The Power of Systems Biology [Point of View]. Proc. IEEE 104 (1) (2016)
Elizabeth Brunk, Nathan Mih, Jonathan Monk, Zhen Zhang, Edward J. O'Brien, Spencer E. Bliven, Ke Chen, Roger L. Chang, Philip E. Bourne, Bernhard O. Palsson
Systems biology of the structural proteome. BMC Syst. Biol. 10 (2016)
Zachary A. King, Andreas Dräger, Ali Ebrahim, Nikolaus Sonnenschein, Nathan E. Lewis, Bernhard O. Palsson
Escher: A Web Application for Building, Sharing, and Embedding Data-Rich Visualizations of Biological Pathways. PLoS Comput. Biol. 11 (8) (2015)
Andreas Dräger, Daniel C. Zielinski, Roland Keller, Matthias Rall, Johannes Eichner, Bernhard O. Palsson, Andreas Zell
SBMLsqueezer 2: context-sensitive creation of kinetic equations in biochemical networks. BMC Syst. Biol. 9 (2015)
Hojung Nam, Miguel Campodonico, Aarash Bordbar, Daniel R. Hyduke, Sangwoo Kim, Daniel C. Zielinski, Bernhard O. Palsson
A Systems Approach to Predict Oncometabolites via Context-Specific Genome-Scale Metabolic Networks. PLoS Comput. Biol. 10 (9) (2014)
Joanne K. Liu, Edward J. O'Brien, Joshua A. Lerman, Karsten Zengler, Bernhard O. Palsson, Adam M. Feist
Reconstruction and modeling protein translocation and compartmentalization in Escherichia coli at the genome-scale. BMC Syst. Biol. 8 (2014)
Roger L. Chang, Lei Xie, Philip E. Bourne, Bernhard O. Palsson
Antibacterial mechanisms identified through structural systems pharmacology. BMC Syst. Biol. 7 (2013)
Pep Charusanti, Sadhana Chauhan, Kathleen McAteer, Joshua A. Lerman, Daniel R. Hyduke, Vladimir L. Motin, Charles Ansong, Joshua N. Adkins, Bernhard O. Palsson
An experimentally-supported genome-scale metabolic network reconstruction for Yersinia pestis CO92. BMC Syst. Biol. 5 (2011)
Aarash Bordbar, Neema Jamshidi, Bernhard O. Palsson
iAB-RBC-283: A proteomically derived knowledge-base of erythrocyte metabolism that can be used to simulate its physiological and patho-physiological states. BMC Syst. Biol. 5 (2011)
Ines Thiele, Daniel R. Hyduke, Benjamin Steeb, Guy Fankam, Douglas K. Allen, Susanna Bazzani, Pep Charusanti, Feng-Chi Chen, Ronan M. T. Fleming, Chao A. Hsiung, Sigrid C. J. De Keersmaecker, Yu-Chieh Liao, Kathleen Marchal, Monica L. Mo, Emre Özdemir, Anu Raghunathan, Jennifer L. Reed, Sook-Il Shin, Sara Sigurbjörnsdóttir, Jonas Steinmann, Suresh Sudarsan, Neil Swainston, Inge M. Thijs, Karsten Zengler, Bernhard O. Palsson, Joshua N. Adkins, Dirk Bumann
A community effort towards a knowledge-base and mathematical model of the human pathogen Salmonella Typhimurium LT2. BMC Syst. Biol. 5 (2011)
Aarash Bordbar, Adam M. Feist, Renata Usaite-Black, Joseph Woodcock, Bernhard O. Palsson, Iman Famili
A multi-tissue type genome-scale metabolic network for analysis of whole-body systems physiology. BMC Syst. Biol. 5 (2011)
Jan Schellenberger, Junyoung O. Park, Tom M. Conrad, Bernhard O. Palsson
BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions. BMC Bioinform. 11 (2010)
Ines Thiele, Neema Jamshidi, Ronan M. T. Fleming, Bernhard O. Palsson
's Transcriptional and Translational Machinery: A Knowledge Base, Its Mathematical Formulation, and Its Functional Characterization. PLoS Comput. Biol. 5 (3) (2009)
Erwin P. Gianchandani, Andrew R. Joyce, Bernhard O. Palsson, Jason A. Papin
Transcriptional Regulatory System. PLoS Comput. Biol. 5 (6) (2009)
Neema Jamshidi, Bernhard O. Palsson
Using in silico models to simulate dual perturbation experiments: procedure development and interpretation of outcomes. BMC Syst. Biol. 3 (2009)
Fan Li, Ines Thiele, Neema Jamshidi, Bernhard O. Palsson
Identification of Potential Pathway Mediation Targets in Toll-like Receptor Signaling. PLoS Comput. Biol. 5 (2) (2009)
Scott A. Becker, Bernhard O. Palsson
Context-Specific Metabolic Networks Are Consistent with Experiments. PLoS Comput. Biol. 4 (5) (2008)
Scott A. Becker, Bernhard O. Palsson
Three factors underlying incorrect in silico predictions of essential metabolic genes. BMC Syst. Biol. 2 (2008)
Matthew Yeung, Ines Thiele, Bernhard O. Palsson
Estimation of the number of extreme pathways for metabolic networks. BMC Bioinform. 8 (2007)
Christian L. Barrett, Nathan D. Price, Bernhard O. Palsson
Network-level analysis of metabolic regulation in the human red blood cell using random sampling and singular value decomposition. BMC Bioinform. 7 (2006)
Christian L. Barrett, Bernhard O. Palsson
Iterative Reconstruction of Transcriptional Regulatory Networks: An Algorithmic Approach. PLoS Comput. Biol. 2 (5) (2006)
Scott A. Becker, Nathan D. Price, Bernhard O. Palsson
Metabolite coupling in genome-scale metabolic networks. BMC Bioinform. 7 (2006)
Steven L. Bell, Bernhard O. Palsson
expa: a program for calculating extreme pathways in biochemical reaction networks. Bioinform. 21 (8) (2005)
Steven L. Bell, Bernhard O. Palsson
Phenotype phase plane analysis using interior point methods. Comput. Chem. Eng. 29 (3) (2005)
Neema Jamshidi, Jeremy S. Edwards, Tom Fahland, George M. Church, Bernhard O. Palsson
Dynamic simulation of the human red blood cell metabolic network. Bioinform. 17 (3) (2001)
Jeremy S. Edwards, Bernhard O. Palsson
K-12 gene deletions. BMC Bioinform. 1 (2000)