Integrating high-throughput and computational data elucidates bacterial networks

Markus W CovertBernhard O Palsson


The flood of high-throughput biological data has led to the expectation that computational (or in silico) models can be used to direct biological discovery, enabling biologists to reconcile heterogeneous data types, find inconsistencies and systematically generate hypotheses. Such a process is fundamentally iterative, where each iteration involves making model predictions, obtaining experimental data, reconciling the predicted outcomes with experimental ones, and using discrepancies to update the in silico model. Here we have reconstructed, on the basis of information derived from literature and databases, the first integrated genome-scale computational model of a transcriptional regulatory and metabolic network. The model accounts for 1,010 genes in Escherichia coli, including 104 regulatory genes whose products together with other stimuli regulate the expression of 479 of the 906 genes in the reconstructed metabolic network. This model is able not only to predict the outcomes of high-throughput growth phenotyping and gene expression experiments, but also to indicate knowledge gaps and identify previously unknown components and interactions in the regulatory and metabolic networks. We find that a systems biology approach that ...Continue Reading


Sep 5, 1997·Science·F R BlattnerY Shao
May 11, 2000·Proceedings of the National Academy of Sciences of the United States of America·J S Edwards, B O Palsson
Jun 1, 2000·Proceedings of the National Academy of Sciences of the United States of America·K A Datsenko, B L Wanner
Oct 18, 2000·Nature·H JeongA L Barabási
Nov 4, 2000·Nature Biotechnology·B Palsson
Nov 10, 2001·Annual Review of Genomics and Human Genetics·T IdekerL Hood
Nov 16, 2001·Journal of Theoretical Biology·M W CovertB Palsson
Mar 2, 2002·Science·Hiroaki Kitano
Apr 23, 2002·Nature Genetics·Shai S Shen-OrrUri Alon
May 15, 2002·The Journal of Biological Chemistry·Markus W Covert, Bernhard Ø Palsson
Jul 4, 2002·Molecular & Cellular Proteomics : MCP·Timothy J GriffinRuedi Aebersold
Nov 5, 2002·Proceedings of the National Academy of Sciences of the United States of America·Daniel SegrèGeorge M Church
Jan 10, 2003·Nucleic Acids Research·Jeremy D GlasnerNicole T Perna
Apr 3, 2003·Nature Reviews. Genetics·Barry R Bochner
Apr 8, 2003·Trends in Biotechnology·Nathan D PriceBernhard O Palsson
Apr 18, 2003·Journal of Bacteriology·Jennifer L Reed, Bernhard Ø Palsson
May 20, 2003·The Journal of Biological Chemistry·Kirsty SalmonRobert P Gunsalus
Sep 4, 2003·Genome Biology·Jennifer L ReedBernhard O Palsson
Sep 26, 2003·Omics : a Journal of Integrative Biology·Jochen FörsterJens Nielsen
Oct 14, 2003·Nature Biotechnology·Ziv Bar-JosephDavid K Gifford
Oct 16, 2003·Genome Research·Markus J HerrgårdBernhard Ø Palsson
Nov 5, 2003·Genome Research·Rosa María Gutiérrez-RíosJulio Collado-Vides

❮ Previous
Next ❯


Apr 2, 2008·Journal of Molecular Evolution·Tong ZhouClaus O Wilke
Feb 7, 2007·Chromosome Research : an International Journal on the Molecular, Supramolecular and Evolutionary Aspects of Chromosome Biology·Christophe Lavelle, Alex Sigal
Aug 26, 2010·Molecular Biotechnology·Chen-Hsiang Yeang
Apr 16, 2005·Current Opinion in Biotechnology·Eddy J SmidBas Teusink
Jun 18, 2005·Current Opinion in Biotechnology·Irina Borodina, Jens Nielsen
Jun 1, 2005·Trends in Biotechnology·Sang Yup LeeTae Yong Kim
Apr 9, 2005·Trends in Microbiology·Klaas J Hellingwerf
Apr 6, 2005·Trends in Pharmacological Sciences·Sean EkinsTatiana Nikolskaya
Sep 24, 2008·Sheng wu gong cheng xue bao = Chinese journal of biotechnology·Ping AoXiaomei Zhu
Aug 20, 2008·Nature Biotechnology·Tomer ShlomiEytan Ruppin
Jan 8, 2013·Nature Biotechnology·Mark P BrynildsenJames J Collins
Oct 8, 2004·Nature Biotechnology·Bernhard Palsson
Oct 8, 2004·Nature Biotechnology·Eugene C ButcherEric J Kunkel
Mar 15, 2005·Nature Biotechnology·Diego di BernardoJames J Collins
Jun 10, 2008·Nature Biotechnology·Adam M Feist, Bernhard Ø Palsson
Jul 20, 2007·Nature Chemical Biology·Tudor I OpreaMark D Rintoul
May 31, 2011·Nature Genetics·Balázs SzappanosBalázs Papp
Nov 5, 2013·Nature Methods·Jayodita C SanghviMarkus W Covert
Nov 14, 2006·Nature Methods·Michael D LynchRyan T Gill
Jan 9, 2010·Nature Protocols·Ines Thiele, Bernhard Ø Palsson
Sep 3, 2011·Nature Protocols·Jan SchellenbergerBernhard Ø Palsson
Feb 24, 2006·Nature Reviews. Molecular Cell Biology·Andrew R Joyce, Bernhard Ø Palsson
Sep 18, 2008·Nature Reviews. Molecular Cell Biology·Guy Karlebach, Ron Shamir
Nov 20, 2004·Nature Reviews. Microbiology·Jeffrey Green, Mark S Paget
Oct 21, 2004·Nature Reviews. Microbiology·Nathan D PriceBernhard Ø Palsson
Sep 22, 2005·Nature Reviews. Microbiology·Thijs J G EttemaJohn van der Oost
Jan 1, 2009·Nature Reviews. Microbiology·Adam M FeistBernhard Ø Palsson
Mar 1, 2012·Nature Reviews. Microbiology·Nathan E LewisBernhard O Palsson
Jun 30, 2009·Molecular BioSystems·Javier CarreraAlfonso Jaramillo
Apr 7, 2009·Proceedings of the National Academy of Sciences of the United States of America·Joel F MoxleyGregory Stephanopoulos
Aug 4, 2010·Proceedings of the National Academy of Sciences of the United States of America·Jong Myoung ParkSang Yup Lee
Sep 30, 2010·Proceedings of the National Academy of Sciences of the United States of America·Sriram Chandrasekaran, Nathan D Price
Feb 9, 2011·Proceedings of the National Academy of Sciences of the United States of America·Sean P CorneliusAdilson E Motter
Aug 29, 2012·Proceedings of the National Academy of Sciences of the United States of America·Javier CarreraAlfonso Jaramillo
May 10, 2011·The Journal of Biological Chemistry·M Kenyon ApplebeeBernhard Ø Palsson
Oct 23, 2008·The Journal of Biological Chemistry·Jeffrey D Kearns, Alexander Hoffmann
Apr 7, 2006·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Irit Gat-ViksRon Shamir
Jan 31, 2009·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Robert Castelo, Alberto Roverato

❮ Previous
Next ❯

Related Concepts

Trending Feeds


Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.


Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.


Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.

Related Papers

Proceedings of the National Academy of Sciences of the United States of America
Christian L BarrettBernhard O Palsson
The Journal of Biological Chemistry
Markus W Covert, Bernhard O Palsson
Proceedings of the National Academy of Sciences of the United States of America
Jennifer L ReedBernhard O Palsson
© 2021 Meta ULC. All rights reserved