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ORCIDBernhard O. Palsson
Bernhard Ø. Palsson
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- affiliation: University of California, San Diego, USA
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Journal Articles
- 2024
[j85]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)- [j84]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) - [j83]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:
iModulonMiner and PyModulon: Software for unsupervised mining of gene expression compendia. PLoS Comput. Biol. 20(10): 1012546 (2024) - 2023
- [j82]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) - 2022
- [j81]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): 566 (2022) - [j80]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): 1077-1090 (2022) - [j79]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) - 2021
- [j78]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): 584 (2021) - [j77]Amir Akbari, Bernhard O. Palsson:
Scalable computation of intracellular metabolite concentrations. Comput. Chem. Eng. 145: 107164 (2021) - [j76]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): D112-D120 (2021) - [j75]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) - [j74]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) - [j73]Anand V. Sastry, Alyssa Hu, David Heckmann, Saugat Poudel, Erol S. Kavvas, Bernhard O. Palsson:
Independent component analysis recovers consistent regulatory signals from disparate datasets. PLoS Comput. Biol. 17(2) (2021) - [j72]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) - 2020
- [j71]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): 162 (2020) - [j70]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): D402-D406 (2020) - [j69]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) - 2019
- [j68]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): 2:1-2:15 (2019) - [j67]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): D1164-D1171 (2019) - [j66]Yara Seif, Jonathan M. Monk, Nathan Mih, Hannah Tsunemoto, Saugat Poudel, Cristal Zuñiga, 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) - [j65]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) - [j64]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) - [j63]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) - [j62]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) - 2018
- [j61]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): 2155-2157 (2018) - [j60]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): 25:1-25:15 (2018) - [j59]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): 31:1-31:9 (2018) - [j58]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): 66:1-66:10 (2018) - [j57]Elliot Rowe, Bernhard O. Palsson, Zachary A. King:
Escher-FBA: a web application for interactive flux balance analysis. BMC Syst. Biol. 12(1): 84:1-84:7 (2018) - [j56]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): 143:1-143:20 (2018) - [j55]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) - [j54]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) - [j53]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) - 2017
- [j52]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): 2487-2495 (2017) - [j51]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) - 2016
- [j50]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: 391 (2016) - [j49]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: 26 (2016) - [j48]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: 40 (2016) - [j47]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): 515-522 (2016) - [j46]James T. Yurkovich, Bernhard O. Palsson:
Solving Puzzles With Missing Pieces: The Power of Systems Biology [Point of View]. Proc. IEEE 104(1): 2-7 (2016) - [j45]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) - [j44]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) - 2015
- [j43]Nicolas Rodriguez, Alex Thomas, Leandro H. Watanabe, Ibrahim Y. Vazirabad, Victor Kofia, Harold F. Gómez, Florian Mittag, Jakob Matthes, Jan Rudolph, Finja Wrzodek, Eugen Netz, Alexander Diamantikos, Johannes Eichner, Roland Keller, Clemens Wrzodek, Sebastian Fröhlich, Nathan E. Lewis, Chris J. Myers, Nicolas Le Novère, Bernhard Ø. Palsson, Michael Hucka, Andreas Dräger:
JSBML 1.0: providing a smorgasbord of options to encode systems biology models. Bioinform. 31(20): 3383-3386 (2015) - [j42]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: 68 (2015) - [j41]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) - 2014
- [j40]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: 110 (2014) - [j39]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) - 2013
- [j38]Brian J. Schmidt, Ali Ebrahim, Thomas O. Metz, Joshua N. Adkins, Bernhard Ø. Palsson, Daniel R. Hyduke:
GIM3E: condition-specific models of cellular metabolism developed from metabolomics and expression data. Bioinform. 29(22): 2900-2908 (2013) - [j37]Ali Ebrahim, Joshua A. Lerman, Bernhard Ø. Palsson, Daniel R. Hyduke:
COBRApy: COnstraints-Based Reconstruction and Analysis for Python. BMC Syst. Biol. 7: 74 (2013) - [j36]Sirus Palsson, Timothy P. Hickling, Erica L. Bradshaw-Pierce, Michael Zager, Karin Jooss, Peter O'Brien, Mary E. Spilker, Bernhard Ø. Palsson, Paolo Vicini:
The development of a fully-integrated immune response model (FIRM) simulator of the immune response through integration of multiple subset models. BMC Syst. Biol. 7: 95 (2013) - [j35]Roger L. Chang, Lei Xie, Philip E. Bourne, Bernhard O. Palsson:
Antibacterial mechanisms identified through structural systems pharmacology. BMC Syst. Biol. 7: 102 (2013) - 2012
- [j34]Jan Schellenberger, Daniel C. Zielinski, Wing Choi, Sunthosh Madireddi, Vasiliy Portnoy, David A. Scott, Jennifer L. Reed, Andrei Osterman, Bernhard Ø. Palsson:
Predicting outcomes of steady-state 13C isotope tracing experiments using Monte Carlo sampling. BMC Syst. Biol. 6: 9 (2012) - [j33]Jeffrey D. Orth, Bernhard Ø. Palsson:
Gap-filling analysis of the iJO1366 Escherichia coli metabolic network reconstruction for discovery of metabolic functions. BMC Syst. Biol. 6: 30 (2012) - 2011
- [j32]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: 8 (2011) - [j31]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: 110 (2011) - [j30]Ottar Rolfsson, Bernhard Ø. Palsson, Ines Thiele:
The human metabolic reconstruction Recon 1 directs hypotheses of novel human metabolic functions. BMC Syst. Biol. 5: 155 (2011) - [j29]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: 163 (2011) - [j28]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: 180 (2011) - 2010
- [j27]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: 213 (2010) - [j26]Martin I. Sigurdsson, Neema Jamshidi, Eiríkur Steingrímsson, Ines Thiele, Bernhard Ø. Palsson:
A detailed genome-wide reconstruction of mouse metabolism based on human Recon 1. BMC Syst. Biol. 4: 140 (2010) - [j25]Roger L. Chang, Li Xie, Lei Xie, Philip E. Bourne, Bernhard Ø. Palsson:
Drug Off-Target Effects Predicted Using Structural Analysis in the Context of a Metabolic Network Model. PLoS Comput. Biol. 6(9) (2010) - 2009
- [j24]Christian L. Barrett, Markus J. Herrgård, Bernhard Ø. Palsson:
Decomposing complex reaction networks using random sampling, principal component analysis and basis rotation. BMC Syst. Biol. 3: 30 (2009) - [j23]Monica L. Mo, Bernhard Ø. Palsson, Markus J. Herrgård:
Connecting extracellular metabolomic measurements to intracellular flux states in yeast. BMC Syst. Biol. 3: 37 (2009) - [j22]Anu Raghunathan, Jennifer L. Reed, Sook-Il Shin, Bernhard Ø. Palsson, Simon Daefler:
Constraint-based analysis of metabolic capacity of Salmonella typhimurium during host-pathogen interaction. BMC Syst. Biol. 3: 38 (2009) - [j21]Neema Jamshidi, Bernhard O. Palsson:
Using in silico models to simulate dual perturbation experiments: procedure development and interpretation of outcomes. BMC Syst. Biol. 3: 44 (2009) - [j20]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) - [j19]Ines Thiele, Neema Jamshidi, Ronan M. T. Fleming, Bernhard O. Palsson:
Genome-Scale Reconstruction of Escherichia coli's Transcriptional and Translational Machinery: A Knowledge Base, Its Mathematical Formulation, and Its Functional Characterization. PLoS Comput. Biol. 5(3) (2009) - [j18]Erwin P. Gianchandani, Andrew R. Joyce, Bernhard O. Palsson, Jason A. Papin:
Functional States of the Genome-Scale Escherichia Coli Transcriptional Regulatory System. PLoS Comput. Biol. 5(6) (2009) - 2008
- [j17]Scott A. Becker, Bernhard O. Palsson:
Three factors underlying incorrect in silico predictions of essential metabolic genes. BMC Syst. Biol. 2: 14 (2008) - [j16]Juan Nogales, Bernhard Ø. Palsson, Ines Thiele:
A genome-scale metabolic reconstruction of Pseudomonas putida KT2440: iJN746 as a cell factory. BMC Syst. Biol. 2: 79 (2008) - [j15]Scott A. Becker, Bernhard O. Palsson:
Context-Specific Metabolic Networks Are Consistent with Experiments. PLoS Comput. Biol. 4(5) (2008) - [j14]Neema Jamshidi, Bernhard Ø. Palsson:
Top-Down Analysis of Temporal Hierarchy in Biochemical Reaction Networks. PLoS Comput. Biol. 4(9) (2008) - 2007
- [j13]Matthew Yeung, Ines Thiele, Bernhard O. Palsson:
Estimation of the number of extreme pathways for metabolic networks. BMC Bioinform. 8 (2007) - [j12]Neema Jamshidi, Bernhard Ø. Palsson:
Investigating the metabolic capabilities of Mycobacterium tuberculosis H37Rv using the in silico strain iNJ661 and proposing alternative drug targets. BMC Syst. Biol. 1: 26 (2007) - [j11]Osbaldo Resendis-Antonio, Jennifer L. Reed, Sergio Encarnación, Julio Collado-Vides, Bernhard Ø. Palsson:
Metabolic Reconstruction and Modeling of Nitrogen Fixation in Rhizobium etli. PLoS Comput. Biol. 3(10) (2007) - 2006
- [j10]Scott A. Becker, Nathan D. Price, Bernhard O. Palsson:
Metabolite coupling in genome-scale metabolic networks. BMC Bioinform. 7: 111 (2006) - [j9]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: 132 (2006) - [j8]Timothy E. Allen, Nathan D. Price, Andrew R. Joyce, Bernhard Ø. Palsson:
Long-Range Periodic Patterns in Microbial Genomes Indicate Significant Multi-Scale Chromosomal Organization. PLoS Comput. Biol. 2(1) (2006) - [j7]Christian L. Barrett, Bernhard O. Palsson:
Iterative Reconstruction of Transcriptional Regulatory Networks: An Algorithmic Approach. PLoS Comput. Biol. 2(5) (2006) - [j6]Markus J. Herrgård, Stephen S. Fong, Bernhard Ø. Palsson:
Identification of Genome-Scale Metabolic Network Models Using Experimentally Measured Flux Profiles. PLoS Comput. Biol. 2(7) (2006) - [j5]Erwin P. Gianchandani, Jason A. Papin, Nathan D. Price, Andrew R. Joyce, Bernhard Ø. Palsson:
Matrix Formalism to Describe Functional States of Transcriptional Regulatory Systems. PLoS Comput. Biol. 2(8) (2006) - 2005
- [j4]Steven L. Bell, Bernhard O. Palsson:
expa: a program for calculating extreme pathways in biochemical reaction networks. Bioinform. 21(8): 1739-1740 (2005) - [j3]Steven L. Bell, Bernhard O. Palsson:
Phenotype phase plane analysis using interior point methods. Comput. Chem. Eng. 29(3): 481-486 (2005) - 2001
- [j2]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): 286-287 (2001) - 2000
- [j1]Jeremy S. Edwards, Bernhard O. Palsson:
Metabolic flux balance analysis and the in silico analysis of Escherichia coli K-12 gene deletions. BMC Bioinform. 1: 1 (2000)
Conference and Workshop Papers
- 2019
- [c2]Laurence Yang, Michael A. Saunders, Jean-Christophe Lachance, Bernhard O. Palsson, José Bento:
Estimating Cellular Goals from High-Dimensional Biological Data. KDD 2019: 2202-2211 - 2017
- [c1]James T. Yurkovich, Laurence Yang, Bernhard O. Palsson:
Utilizing biomarkers to forecast quantitative metabolite concentration profiles in human red blood cells. CCTA 2017: 961-966
Reference Works
- 2009
- [r1]Nathan E. Lewis, Neema Jamshidi, Ines Thiele, Bernhard O. Palsson:
Metabolic Systems Biology. Encyclopedia of Complexity and Systems Science 2009: 5535-5552
Informal and Other Publications
- 2018
- [i1]Laurence Yang, José Bento, Jean-Christophe Lachance, Bernhard O. Palsson:
Genome-scale estimation of cellular objectives. CoRR abs/1807.04245 (2018)
Coauthor Index
Jonathan Monk
aka: Jonathan M. Monk
aka: Jonathan M. Monk
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