Bernhard O. Palsson

71 papers A* 1Journal 68Unranked 1
YearRankTypeTitle / Venue / Authors
2025 J jnl
RBC-GEM: A genome-scale metabolic model for systems biology of the human red blood cell.
PLoS Comput. Biol.
Zachary B. Haiman, Alicia Key, Angelo D'alessandro, Bernhard O. Palsson
2024 J jnl
Inferred regulons are consistent with regulator binding sequences in E. coli.
PLoS Comput. Biol.
Sizhe Qiu, Xinlong Wan, Yueshan Liang, Cameron R. Lamoureux, Amir Akbari, Bernhard O. Palsson, Daniel C. Zielinski
2024 J jnl
StressME: Unified computing framework of Escherichia coli metabolism, gene expression, and stress responses.
PLoS Comput. Biol.
Jiao Zhao, Ke Chen, Bernhard O. Palsson, Laurence Yang
2024 J jnl
iModulonMiner and PyModulon: Software for unsupervised mining of gene expression compendia.
PLoS Comput. Biol.
Anand V. Sastry, Yuan Yuan, Saugat Poudel, Kevin Rychel, Reo Yoo, Cameron R. Lamoureux, Gaoyuan Li, Joshua T. Burrows, Siddharth Chauhan, Zachary B. Haiman, Tahani Al Bulushi, Yara Seif, Bernhard O. Palsson, Daniel C. Zielinski
2023 J jnl
Deep-learning optimized DEOCSU suite provides an iterable pipeline for accurate ChIP-exo peak calling.
Briefings Bioinform.
Ina Bang, Sang-Mok Lee, Seojoung Park, Joon Young Park, Linh Khanh Nong, Ye Gao, Bernhard O. Palsson, Donghyuk Kim
2022 J jnl
High-quality genome-scale metabolic network reconstruction of probiotic bacterium Escherichia coli Nissle 1917.
BMC Bioinform.
Max van 't Hof, Omkar S. Mohite, Jonathan M. Monk, Tilmann Weber, Bernhard O. Palsson, Morten O. A. Sommer
2022 J jnl
Positively charged mineral surfaces promoted the accumulation of organic intermediates at the origin of metabolism.
PLoS Comput. Biol.
Amir Akbari, Bernhard O. Palsson
2022 J jnl
proChIPdb: a chromatin immunoprecipitation database for prokaryotic organisms.
Nucleic Acids Res.
Katherine Decker, Ye Gao, Kevin Rychel, Tahani Al Bulushi, Siddharth M. Chauhan, Donghyuk Kim, Byung-Kwan Cho, Bernhard O. Palsson
2021 J jnl
Bacterial fitness landscapes stratify based on proteome allocation associated with discrete aero-types.
PLoS Comput. Biol.
Ke Chen, Amitesh Anand, Connor A. Olson, Troy E. Sandberg, Ye Gao, Nathan Mih, Bernhard O. Palsson
2021 J jnl
Computation of condition-dependent proteome allocation reveals variability in the macro and micro nutrient requirements for growth.
PLoS Comput. Biol.
Colton J. Lloyd, Jonathan Monk, Laurence Yang, Ali Ebrahim, Bernhard O. Palsson
2021 J jnl
Independent component analysis recovers consistent regulatory signals from disparate datasets.
PLoS Comput. Biol.
Anand V. Sastry, Alyssa Hu, David Heckmann, Saugat Poudel, Erol S. Kavvas, Bernhard O. Palsson
2021 J jnl
MASSpy: Building, simulating, and visualizing dynamic biological models in Python using mass action kinetics.
PLoS Comput. Biol.
Zachary B. Haiman, Daniel C. Zielinski, Yuko Koike, James T. Yurkovich, Bernhard O. Palsson
2021 J jnl
Optimal dimensionality selection for independent component analysis of transcriptomic data.
BMC Bioinform.
John Luke McConn, Cameron R. Lamoureux, Saugat Poudel, Bernhard O. Palsson, Anand V. Sastry
2021 J jnl
Scalable computation of intracellular metabolite concentrations.
Comput. Chem. Eng.
Amir Akbari, Bernhard O. Palsson
2021 J jnl
iModulonDB: a knowledgebase of microbial transcriptional regulation derived from machine learning.
Nucleic Acids Res.
Kevin Rychel, Katherine Decker, Anand V. Sastry, Patrick V. Phaneuf, Saugat Poudel, Bernhard O. Palsson
2020 J jnl
Adaptations of Escherichia coli strains to oxidative stress are reflected in properties of their structural proteomes.
BMC Bioinform.
Nathan Mih, Jonathan M. Monk, Xin Fang, Edward Catoiu, David Heckmann, Laurence Yang, Bernhard O. Palsson
2020 J jnl
BiGG Models 2020: multi-strain genome-scale models and expansion across the phylogenetic tree.
Nucleic Acids Res.
Charles J. Norsigian, Neha Pusarla, John Luke McConn, James T. Yurkovich, Andreas Dräger, Bernhard O. Palsson, Zachary A. King
2020 J jnl
Machine learning with random subspace ensembles identifies antimicrobial resistance determinants from pan-genomes of three pathogens.
PLoS Comput. Biol.
Jason C. Hyun, Erol S. Kavvas, Jonathan M. Monk, Bernhard O. Palsson
2019 J jnl
A computational knowledge-base elucidates the response of Staphylococcus aureus to different media types.
PLoS Comput. Biol.
Yara Seif, Jonathan M. Monk, Nathan Mih, Hannah Tsunemoto, Saugat Poudel, Cristal Zuñiga, Jared Broddrick, Karsten Zengler, Bernhard O. Palsson
2019 J jnl
ALEdb 1.0: a database of mutations from adaptive laboratory evolution experimentation.
Nucleic Acids Res.
Patrick V. Phaneuf, Dennis Gosting, Bernhard O. Palsson, Adam M. Feist
2019 J jnl
BOFdat: Generating biomass objective functions for genome-scale metabolic models from experimental data.
PLoS Comput. Biol.
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
2019 J jnl
DynamicME: dynamic simulation and refinement of integrated models of metabolism and protein expression.
BMC Syst. Biol.
Laurence Yang, Ali Ebrahim, Colton J. Lloyd, Michael A. Saunders, Bernhard O. Palsson
2019 A* conf
Estimating Cellular Goals from High-Dimensional Biological Data.
KDD
Laurence Yang, Michael A. Saunders, Jean-Christophe Lachance, Bernhard O. Palsson, José Bento
2019 J jnl
Genome-scale model of metabolism and gene expression provides a multi-scale description of acid stress responses in Escherichia coli.
PLoS Comput. Biol.
Bin Du, Laurence Yang, Colton J. Lloyd, Xin Fang, Bernhard O. Palsson
2019 J jnl
Laboratory evolution reveals a two-dimensional rate-yield tradeoff in microbial metabolism.
PLoS Comput. Biol.
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
2019 J jnl
Systems-level analysis of NalD mutation, a recurrent driver of rapid drug resistance in acute Pseudomonas aeruginosa infection.
PLoS Comput. Biol.
Jinyuan Yan, Henri Estanbouli, Chen Liao, Wook Kim, Jonathan M. Monk, Rayees Rahman, Mini Kamboj, Bernhard O. Palsson, Weigang Qiu, João B. Xavier
2018 J jnl
COBRAme: A computational framework for genome-scale models of metabolism and gene expression.
PLoS Comput. Biol.
Colton J. Lloyd, Ali Ebrahim, Laurence Yang, Zachary A. King, Edward Catoiu, Edward J. O'Brien, Joanne K. Liu, Bernhard O. Palsson
2018 J jnl
Escher-FBA: a web application for interactive flux balance analysis.
BMC Syst. Biol.
Elliot Rowe, Bernhard O. Palsson, Zachary A. King
2018 J jnl
Escherichia coli B2 strains prevalent in inflammatory bowel disease patients have distinct metabolic capabilities that enable colonization of intestinal mucosa.
BMC Syst. Biol.
Xin Fang, Jonathan M. Monk, Nathan Mih, Bin Du, Anand Sastry, Erol S. Kavvas, Yara Seif, Larry Smarr, Bernhard O. Palsson
2018 J jnl
Functional interrogation of Plasmodium genus metabolism identifies species- and stage-specific differences in nutrient essentiality and drug targeting.
PLoS Comput. Biol.
Alyaa M. Abdel-Haleem, Hooman Hefzi, Katsuhiko Mineta, Xin Gao, Takashi Gojobori, Bernhard O. Palsson, Nathan E. Lewis, Neema Jamshidi
2018 J jnl
Genome-scale estimation of cellular objectives.
CoRR
Laurence Yang, José Bento, Jean-Christophe Lachance, Bernhard O. Palsson
2018 J jnl
Network-level allosteric effects are elucidated by detailing how ligand-binding events modulate utilization of catalytic potentials.
PLoS Comput. Biol.
James T. Yurkovich, Miguel A. Alcantar, Zachary B. Haiman, Bernhard O. Palsson
2018 J jnl
Reframing gene essentiality in terms of adaptive flexibility.
BMC Syst. Biol.
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
2018 J jnl
Systems biology as an emerging paradigm in transfusion medicine.
BMC Syst. Biol.
James T. Yurkovich, Aarash Bordbar, Ólafur E. Sigurjónsson, Bernhard O. Palsson
2018 J jnl
Updated and standardized genome-scale reconstruction of Mycobacterium tuberculosis H37Rv, iEK1011, simulates flux states indicative of physiological conditions.
BMC Syst. Biol.
Erol S. Kavvas, Yara Seif, James T. Yurkovich, Charles J. Norsigian, Saugat Poudel, William W. Greenwald, Sankha Ghatak, Bernhard O. Palsson, Jonathan M. Monk
2018 J jnl
ssbio: a Python framework for structural systems biology.
Bioinform.
Nathan Mih, Elizabeth Brunk, Ke Chen, Edward Catoiu, Anand Sastry, Erol S. Kavvas, Jonathan M. Monk, Zhen Zhang, Bernhard O. Palsson
2017 J jnl
Biomarkers are used to predict quantitative metabolite concentration profiles in human red blood cells.
PLoS Comput. Biol.
James T. Yurkovich, Laurence Yang, Bernhard O. Palsson
2017 J jnl
Machine learning in computational biology to accelerate high-throughput protein expression.
Bioinform.
Anand Sastry, Jonathan Monk, Hanna Tegel, Mathias Uhlen, Bernhard O. Palsson, Johan Rockberg, Elizabeth Brunk
2017 — conf
Utilizing biomarkers to forecast quantitative metabolite concentration profiles in human red blood cells.
CCTA
James T. Yurkovich, Laurence Yang, Bernhard O. Palsson
2016 J jnl
A Multi-scale Computational Platform to Mechanistically Assess the Effect of Genetic Variation on Drug Responses in Human Erythrocyte Metabolism.
PLoS Comput. Biol.
Nathan Mih, Elizabeth Brunk, Aarash Bordbar, Bernhard O. Palsson
2016 J jnl
BiGG Models: A platform for integrating, standardizing and sharing genome-scale models.
Nucleic Acids Res.
Zachary A. King, Justin Lu, Andreas Dräger, Philip Miller, Stephen Federowicz, Joshua A. Lerman, Ali Ebrahim, Bernhard O. Palsson, Nathan E. Lewis
2016 J jnl
Evaluation of rate law approximations in bottom-up kinetic models of metabolism.
BMC Syst. Biol.
Bin Du, Daniel C. Zielinski, Erol S. Kavvas, Andreas Dräger, Justin Tan, Zhen Zhang, Kayla E. Ruggiero, Garri A. Arzumanyan, Bernhard O. Palsson
2016 J jnl
Quantification and Classification of E. coli Proteome Utilization and Unused Protein Costs across Environments.
PLoS Comput. Biol.
Edward J. O'Brien, Jose Utrilla, Bernhard O. Palsson
2016 J jnl
Solving Puzzles With Missing Pieces: The Power of Systems Biology [Point of View].
Proc. IEEE
James T. Yurkovich, Bernhard O. Palsson
2016 J jnl
Systems biology of the structural proteome.
BMC Syst. Biol.
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
2016 J jnl
solveME: fast and reliable solution of nonlinear ME models.
BMC Bioinform.
Laurence Yang, Ding Ma, Ali Ebrahim, Colton J. Lloyd, Michael A. Saunders, Bernhard O. Palsson
2015 J jnl
Escher: A Web Application for Building, Sharing, and Embedding Data-Rich Visualizations of Biological Pathways.
PLoS Comput. Biol.
Zachary A. King, Andreas Dräger, Ali Ebrahim, Nikolaus Sonnenschein, Nathan E. Lewis, Bernhard O. Palsson
2015 J jnl
SBMLsqueezer 2: context-sensitive creation of kinetic equations in biochemical networks.
BMC Syst. Biol.
Andreas Dräger, Daniel C. Zielinski, Roland Keller, Matthias Rall, Johannes Eichner, Bernhard O. Palsson, Andreas Zell
2014 J jnl
A Systems Approach to Predict Oncometabolites via Context-Specific Genome-Scale Metabolic Networks.
PLoS Comput. Biol.
Hojung Nam, Miguel Campodonico, Aarash Bordbar, Daniel R. Hyduke, Sangwoo Kim, Daniel C. Zielinski, Bernhard O. Palsson
2014 J jnl
Reconstruction and modeling protein translocation and compartmentalization in Escherichia coli at the genome-scale.
BMC Syst. Biol.
Joanne K. Liu, Edward J. O'Brien, Joshua A. Lerman, Karsten Zengler, Bernhard O. Palsson, Adam M. Feist
2013 J jnl
Antibacterial mechanisms identified through structural systems pharmacology.
BMC Syst. Biol.
Roger L. Chang, Lei Xie, Philip E. Bourne, Bernhard O. Palsson
2011 J jnl
A community effort towards a knowledge-base and mathematical model of the human pathogen Salmonella Typhimurium LT2.
BMC Syst. Biol.
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
2011 J jnl
A multi-tissue type genome-scale metabolic network for analysis of whole-body systems physiology.
BMC Syst. Biol.
Aarash Bordbar, Adam M. Feist, Renata Usaite-Black, Joseph Woodcock, Bernhard O. Palsson, Iman Famili
2011 J jnl
An experimentally-supported genome-scale metabolic network reconstruction for Yersinia pestis CO92.
BMC Syst. Biol.
Pep Charusanti, Sadhana Chauhan, Kathleen McAteer, Joshua A. Lerman, Daniel R. Hyduke, Vladimir L. Motin, Charles Ansong, Joshua N. Adkins, Bernhard O. Palsson
2011 J jnl
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.
Aarash Bordbar, Neema Jamshidi, Bernhard O. Palsson
2010 J jnl
BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions.
BMC Bioinform.
Jan Schellenberger, Junyoung O. Park, Tom M. Conrad, Bernhard O. Palsson
2009 J jnl
Functional States of the Genome-Scale
PLoS Comput. Biol.
Erwin P. Gianchandani, Andrew R. Joyce, Bernhard O. Palsson, Jason A. Papin
2009 J jnl
Genome-Scale Reconstruction of
PLoS Comput. Biol.
Ines Thiele, Neema Jamshidi, Ronan M. T. Fleming, Bernhard O. Palsson
2009 J jnl
Identification of Potential Pathway Mediation Targets in Toll-like Receptor Signaling.
PLoS Comput. Biol.
Fan Li, Ines Thiele, Neema Jamshidi, Bernhard O. Palsson
2009 — ch.
Metabolic Systems Biology.
Encyclopedia of Complexity and Systems Science
Nathan E. Lewis, Neema Jamshidi, Ines Thiele, Bernhard O. Palsson
2009 J jnl
Using in silico models to simulate dual perturbation experiments: procedure development and interpretation of outcomes.
BMC Syst. Biol.
Neema Jamshidi, Bernhard O. Palsson
2008 J jnl
Context-Specific Metabolic Networks Are Consistent with Experiments.
PLoS Comput. Biol.
Scott A. Becker, Bernhard O. Palsson
2008 J jnl
Three factors underlying incorrect in silico predictions of essential metabolic genes.
BMC Syst. Biol.
Scott A. Becker, Bernhard O. Palsson
2007 J jnl
Estimation of the number of extreme pathways for metabolic networks.
BMC Bioinform.
Matthew Yeung, Ines Thiele, Bernhard O. Palsson
2006 J jnl
Iterative Reconstruction of Transcriptional Regulatory Networks: An Algorithmic Approach.
PLoS Comput. Biol.
Christian L. Barrett, Bernhard O. Palsson
2006 J jnl
Metabolite coupling in genome-scale metabolic networks.
BMC Bioinform.
Scott A. Becker, Nathan D. Price, Bernhard O. Palsson
2006 J jnl
Network-level analysis of metabolic regulation in the human red blood cell using random sampling and singular value decomposition.
BMC Bioinform.
Christian L. Barrett, Nathan D. Price, Bernhard O. Palsson
2005 J jnl
Phenotype phase plane analysis using interior point methods.
Comput. Chem. Eng.
Steven L. Bell, Bernhard O. Palsson
2005 J jnl
expa: a program for calculating extreme pathways in biochemical reaction networks.
Bioinform.
Steven L. Bell, Bernhard O. Palsson
2001 J jnl
Dynamic simulation of the human red blood cell metabolic network.
Bioinform.
Neema Jamshidi, Jeremy S. Edwards, Tom Fahland, George M. Church, Bernhard O. Palsson
2000 J jnl
Metabolic flux balance analysis and the
BMC Bioinform.
Jeremy S. Edwards, Bernhard O. Palsson