Bernhard Ø. Palsson

20 papers Journal 20
YearRankTypeTitle / Venue / Authors
2026 J jnl
PREFER: An Ontology for the PREcision FERmentation Community.
CoRR
Txell Amigó, Shawn Zheng Kai Tan, Angel Luu Phanthanourak, Sebastian Schulz, Pasquale D. Colaianni, Dominik M. Maszczyk, Ester Milesi, Ivan Schlembach, Mykhaylo Semenov Petrov, Marta Reventós Montané, Lars Keld Nielsen, Jochen Förster, Bernhard Ø. Palsson, Suresh Sudarsan, Alberto Santos
2015 J jnl
JSBML 1.0: providing a smorgasbord of options to encode systems biology models.
Bioinform.
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
2013 J jnl
COBRApy: COnstraints-Based Reconstruction and Analysis for Python.
BMC Syst. Biol.
Ali Ebrahim, Joshua A. Lerman, Bernhard Ø. Palsson, Daniel R. Hyduke
2013 J jnl
GIM
Bioinform.
Brian J. Schmidt, Ali Ebrahim, Thomas O. Metz, Joshua N. Adkins, Bernhard Ø. Palsson, Daniel R. Hyduke
2013 J jnl
The development of a fully-integrated immune response model (FIRM) simulator of the immune response through integration of multiple subset models.
BMC Syst. Biol.
Sirus Palsson, Timothy P. Hickling, Erica L. Bradshaw-Pierce, Michael Zager, Karin Jooss, Peter O'Brien, Mary E. Spilker, Bernhard Ø. Palsson, Paolo Vicini
2012 J jnl
Gap-filling analysis of the iJO1366 Escherichia coli metabolic network reconstruction for discovery of metabolic functions.
BMC Syst. Biol.
Jeffrey D. Orth, Bernhard Ø. Palsson
2012 J jnl
Predicting outcomes of steady-state
BMC Syst. Biol.
Jan Schellenberger, Daniel C. Zielinski, Wing Choi, Sunthosh Madireddi, Vasiliy Portnoy, David A. Scott, Jennifer L. Reed, Andrei Osterman, Bernhard Ø. Palsson
2011 J jnl
The human metabolic reconstruction Recon 1 directs hypotheses of novel human metabolic functions.
BMC Syst. Biol.
Ottar Rolfsson, Bernhard Ø. Palsson, Ines Thiele
2010 J jnl
A detailed genome-wide reconstruction of mouse metabolism based on human Recon 1.
BMC Syst. Biol.
Martin I. Sigurdsson, Neema Jamshidi, Eiríkur Steingrímsson, Ines Thiele, Bernhard Ø. Palsson
2010 J jnl
Drug Off-Target Effects Predicted Using Structural Analysis in the Context of a Metabolic Network Model.
PLoS Comput. Biol.
Roger L. Chang, Li Xie, Lei Xie, Philip E. Bourne, Bernhard Ø. Palsson
2009 J jnl
Connecting extracellular metabolomic measurements to intracellular flux states in yeast.
BMC Syst. Biol.
Monica L. Mo, Bernhard Ø. Palsson, Markus J. Herrgård
2009 J jnl
Constraint-based analysis of metabolic capacity of Salmonella typhimurium during host-pathogen interaction.
BMC Syst. Biol.
Anu Raghunathan, Jennifer L. Reed, Sook-Il Shin, Bernhard Ø. Palsson, Simon Daefler
2009 J jnl
Decomposing complex reaction networks using random sampling, principal component analysis and basis rotation.
BMC Syst. Biol.
Christian L. Barrett, Markus J. Herrgård, Bernhard Ø. Palsson
2008 J jnl
A genome-scale metabolic reconstruction of Pseudomonas putida KT2440: iJN746 as a cell factory.
BMC Syst. Biol.
Juan Nogales, Bernhard Ø. Palsson, Ines Thiele
2008 J jnl
Top-Down Analysis of Temporal Hierarchy in Biochemical Reaction Networks.
PLoS Comput. Biol.
Neema Jamshidi, Bernhard Ø. Palsson
2007 J jnl
Investigating the metabolic capabilities of Mycobacterium tuberculosis H37Rv using the in silico strain iNJ661 and proposing alternative drug targets.
BMC Syst. Biol.
Neema Jamshidi, Bernhard Ø. Palsson
2007 J jnl
Metabolic Reconstruction and Modeling of Nitrogen Fixation in
PLoS Comput. Biol.
Osbaldo Resendis-Antonio, Jennifer L. Reed, Sergio Encarnación, Julio Collado-Vides, Bernhard Ø. Palsson
2006 J jnl
Identification of Genome-Scale Metabolic Network Models Using Experimentally Measured Flux Profiles.
PLoS Comput. Biol.
Markus J. Herrgård, Stephen S. Fong, Bernhard Ø. Palsson
2006 J jnl
Long-Range Periodic Patterns in Microbial Genomes Indicate Significant Multi-Scale Chromosomal Organization.
PLoS Comput. Biol.
Timothy E. Allen, Nathan D. Price, Andrew R. Joyce, Bernhard Ø. Palsson
2006 J jnl
Matrix Formalism to Describe Functional States of Transcriptional Regulatory Systems.
PLoS Comput. Biol.
Erwin P. Gianchandani, Jason A. Papin, Nathan D. Price, Andrew R. Joyce, Bernhard Ø. Palsson