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Lista de obras de Bernhard Palsson

A Consensus Genome-scale Reconstruction of Chinese Hamster Ovary Cell Metabolism.

artículo científico publicado en 2016

A Gapless, Unambiguous Genome Sequence of the Enterohemorrhagic Escherichia coli O157:H7 Strain EDL933.

artículo científico publicado en 2014

A Model for Designing Adaptive Laboratory Evolution Experiments

artículo científico publicado en 2017

A Multi-scale Computational Platform to Mechanistically Assess the Effect of Genetic Variation on Drug Responses in Human Erythrocyte Metabolism

artículo científico publicado en 2016

A Padawan Programmer's Guide to Developing Software Libraries

artículo científico publicado en 2017

A White-Box Machine Learning Approach for Revealing Antibiotic Mechanisms of Action

scientific article published on 09 May 2019

A biochemically-interpretable machine learning classifier for microbial GWAS

scientific article published on 22 May 2020

A c-type cytochrome and a transcriptional regulator responsible for enhanced extracellular electron transfer in Geobacter sulfurreducens revealed by adaptive evolution

article

A community effort towards a knowledge-base and mathematical model of the human pathogen Salmonella Typhimurium LT2

artículo científico publicado en 2011

A community-driven global reconstruction of human metabolism. ⬇️

artículo científico publicado en 2013

A comprehensive genome-scale reconstruction of Escherichia coli metabolism--2011. ⬇️

artículo científico publicado en 2011

A computational knowledge-base elucidates the response of Staphylococcus aureus to different media types

scientific article published on 09 January 2019

A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology

artículo científico publicado en 2008

A detailed genome-wide reconstruction of mouse metabolism based on human Recon 1.

artículo científico publicado en 2010

A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information

artículo científico publicado en 2007

A genome-scale metabolic reconstruction of Pseudomonas putida KT2440: iJN746 as a cell factory

artículo científico publicado en 2008

A genome-scale, constraint-based approach to systems biology of human metabolism

artículo científico publicado en 2007

A model-driven quantitative metabolomics analysis of aerobic and anaerobic metabolism in E. coli K-12 MG1655 that is biochemically and thermodynamically consistent

artículo científico publicado en 2013

A multi-tissue type genome-scale metabolic network for analysis of whole-body systems physiology ⬇️

artículo científico publicado el 31 de octubre de 2011

A protocol for generating a high-quality genome-scale metabolic reconstruction

artículo científico publicado en 2010

A road map for the development of community systems (CoSy) biology

artículo científico publicado en 2012

A streamlined ribosome profiling protocol for the characterization of microorganisms

artículo científico publicado en 2014

A systems approach to predict oncometabolites via context-specific genome-scale metabolic networks

artículo científico publicado en 2014

A unified resource for transcriptional regulation in Escherichia coli K-12 incorporating high-throughput-generated binding data into RegulonDB version 10.0

artículo científico publicado en 2018

A workflow for generating multi-strain genome-scale metabolic models of prokaryotes

artículo científico publicado en 2019

ALEdb 1.0: a database of mutations from adaptive laboratory evolution experimentation

article

Adaptation to the coupling of glycolysis to toxic methylglyoxal production in tpiA deletion strains of Escherichia coli requires synchronized and counterintuitive genetic changes

artículo científico publicado en 2018

Adaptations of Escherichia coli strains to oxidative stress are reflected in properties of their structural proteomes

scientific article published on 29 April 2020

Adaptive Evolution of Escherichia coli K-12 MG1655 during Growth on a Nonnative Carbon Source, -1,2-Propanediol

artículo científico publicado en 2010

Adaptive evolution of Escherichia coli K-12 MG1655 during growth on a Nonnative carbon source, L-1,2-propanediol

artículo científico publicado en 2010

Adaptive evolution reveals a tradeoff between growth rate and oxidative stress during naphthoquinone-based aerobic respiration

scientific article published on 25 November 2019

Adaptive laboratory evolution of Escherichia coli under acid stress

scientific article published on 18 October 2019

Adaptive laboratory evolution of a genome-reduced Escherichia coli

artículo científico publicado en 2019

Adaptive laboratory evolution resolves energy depletion to maintain high aromatic metabolite phenotypes in Escherichia coli strains lacking the Phosphotransferase System

artículo científico publicado en 2018

Advanced transcriptomic analysis reveals the role of efflux pumps and media composition in antibiotic responses of <i>Pseudomonas aeruginosa</i>

artículo científico publicado en 2022

Aerobic fermentation of D-glucose by an evolved cytochrome oxidase-deficient Escherichia coli strain

artículo científico publicado en 2008

An Organic Anion Transporter 1 (OAT1)-centered Metabolic Network

artículo científico publicado en 2016

An atlas of human metabolism

artículo científico publicado en 2020

An evaluation of Comparative Genome Sequencing (CGS) by comparing two previously-sequenced bacterial genomes

artículo científico publicado en 2007

An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR)

artículo científico publicado en 2003

An experimentally validated genome-scale metabolic reconstruction of Klebsiella pneumoniae MGH 78578, iYL1228.

artículo científico publicado en 2011

An experimentally-supported genome-scale metabolic network reconstruction for Yersinia pestis CO92.

artículo científico publicado en 2011

Analysis of metabolic capabilities using singular value decomposition of extreme pathway matrices

artículo científico publicado en 2003

Analysis of omics data with genome-scale models of metabolism

artículo científico publicado en 2012

Antibacterial mechanisms identified through structural systems pharmacology

artículo científico publicado en 2013

Antibiotic-Induced Changes to the Host Metabolic Environment Inhibit Drug Efficacy and Alter Immune Function.

artículo científico publicado en 2017

Applications of genome-scale metabolic reconstructions

artículo científico publicado en 2009

Automated in situ measurement of cell-specific antibody secretion and laser-mediated purification for rapid cloning of highly-secreting producers

artículo científico publicado en 2005

BOFdat: Generating biomass objective functions for genome-scale metabolic models from experimental data

artículo científico publicado en 2019

Basic and applied uses of genome‐scale metabolic network reconstructions of Escherichia coli ⬇️

artículo científico publicado el 1 de enero de 2013

BiGG Models 2020: multi-strain genome-scale models and expansion across the phylogenetic tree

artículo científico publicado en 2020

BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions

artículo científico publicado en 2010

Biochemical characterization of human gluconokinase and the proposed metabolic impact of gluconic acid as determined by constraint based metabolic network analysis

artículo científico publicado en 2014

Biomarkers are used to predict quantitative metabolite concentration profiles in human red blood cells.

artículo científico publicado en 2017

Bringing Genomes to Life: The Use of Genome-Scale In Silico Models

Building the power house: recent advances in mitochondrial studies through proteomics and systems biology

artículo científico publicado en 2006

COBRAme: A computational framework for genome-scale models of metabolism and gene expression

artículo científico publicado en 2018

COBRApy: COnstraints-Based Reconstruction and Analysis for Python

artículo científico publicado en 2013

Can the protein occupancy landscape show the topologically isolated chromosomal domains in the E. coli genome?: An exciting prospect

artículo científico publicado en 2009

Candidate metabolic network states in human mitochondria. Impact of diabetes, ischemia, and diet.

artículo científico publicado en 2004

Candidate states of Helicobacter pylori's genome-scale metabolic network upon application of "loop law" thermodynamic constraints.

artículo científico publicado en 2006

Capsule deletion via a λ-Red knockout system perturbs biofilm formation and fimbriae expression in Klebsiella pneumoniae MGH 78578.

artículo científico publicado en 2014

Cellular responses to reactive oxygen species are predicted from molecular mechanisms

scientific article published on 03 July 2019

ChIP-exo interrogation of Crp, DNA, and RNAP holoenzyme interactions.

artículo científico publicado en 2018

Characterization and efficacy of PKH26 as a probe to study the replication history of the human hematopoietic KG1a progenitor cell line

artículo científico publicado en 2002

Characterization and modelling of interspecies electron transfer mechanisms and microbial community dynamics of a syntrophic association

artículo científico publicado en 2013

Characterization of CA-MRSA TCH1516 exposed to nafcillin in bacteriological and physiological media

artículo científico publicado en 2019

Characterizing Strain Variation in Engineered E. coli Using a Multi-Omics-Based Workflow.

artículo científico publicado en 2016

Characterizing posttranslational modifications in prokaryotic metabolism using a multiscale workflow

artículo científico publicado en 2018

Characterizing the interplay between multiple levels of organization within bacterial sigma factor regulatory networks

artículo científico publicado en 2013

Characterizing the metabolic phenotype: A phenotype phase plane analysis ⬇️

artículo científico publicado el 5 de enero de 2002

Citrate metabolism in red blood cells stored in additive solution-3.

artículo científico publicado en 2016

Comparative Analysis of Regulatory Elements between Escherichia coli and Klebsiella pneumoniae by Genome-Wide Transcription Start Site Profiling ⬇️

artículo científico publicado el 9 de agosto de 2012

Comparative Genome-Scale Metabolic Modeling of Metallo-Beta-Lactamase-Producing Multidrug-Resistant Klebsiella pneumoniae Clinical Isolates

scientific article published on 24 May 2019

Comparative genome sequencing of Escherichia coli allows observation of bacterial evolution on a laboratory timescale

artículo científico publicado en 2006

Comparative genome-scale modelling of Staphylococcus aureus strains identifies strain-specific metabolic capabilities linked to pathogenicity

artículo científico publicado en 2016

Comparison of metal-bound and unbound structures of aminopeptidase B proteins from Escherichia coli and Yersinia pestis

scientific article published on 19 April 2020

Comparison of network-based pathway analysis methods

artículo científico publicado en 2004

Comprehensive metabolomic study of platelets reveals the expression of discrete metabolic phenotypes during storage.

artículo científico publicado en 2014

Computing the functional proteome: recent progress and future prospects for genome-scale models

artículo científico publicado en 2015

Connecting extracellular metabolomic measurements to intracellular flux states in yeast

artículo científico publicado en 2009

Constraining the metabolic genotype-phenotype relationship using a phylogeny of in silico methods

artículo científico publicado en 2012

Constraint-based analysis of metabolic capacity of Salmonella typhimurium during host-pathogen interaction

artículo científico publicado en 2009

Constraint-based models predict metabolic and associated cellular functions.

artículo científico

Constraints-based models: regulation of gene expression reduces the steady-state solution space

artículo científico publicado en 2003

Context-specific metabolic networks are consistent with experiments

artículo científico publicado en 2008

Correction: Identification of Potential Pathway Mediation Targets in Toll-like Receptor Signaling

Coupling S-adenosylmethionine-dependent methylation to growth: Design and uses

artículo científico publicado en 2019

Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0.

scientific article published on 01 March 2019

Cross-compartment metabolic coupling enables flexible photoprotective mechanisms in the diatom Phaeodactylum tricornutum

scientific article published on 14 February 2019

Crystal structure of a hyperactive Escherichia coli glycerol kinase mutant Gly230 --> Asp obtained using microfluidic crystallization devices

artículo científico publicado en 2007

Cumulative Number of Cell Divisions as a Meaningful Timescale for Adaptive Laboratory Evolution of Escherichia coli ⬇️

artículo científico publicado el 18 de octubre de 2011

Dataset on economic analysis of mass production of algae in LED-based photobioreactors

De Novo assembly of the complete genome of an enhanced electricity-producing variant of Geobacter sulfurreducens using only short reads

artículo científico publicado en 2010

Deciphering Fur transcriptional regulatory network highlights its complex role beyond iron metabolism in Escherichia coli.

artículo científico publicado en 2014

Deciphering the regulatory codes in bacterial genomes ⬇️

artículo científico publicado el 15 de agosto de 2011

Deciphering the transcriptional regulatory logic of amino acid metabolism ⬇️

artículo científico publicado el 13 de noviembre de 2011

Decoding genome-wide GadEWX-transcriptional regulatory networks reveals multifaceted cellular responses to acid stress in Escherichia coli.

artículo científico publicado en 2015

Decoding the jargon of bottom-up metabolic systems biology

artículo científico publicado en 2015

Decomposing complex reaction networks using random sampling, principal component analysis and basis rotation

artículo científico publicado en 2009

DeepTFactor: A deep learning-based tool for the prediction of transcription factors

artículo científico publicado en 2021

Deletion of genes encoding cytochrome oxidases and quinol monooxygenase blocks the aerobic-anaerobic shift in Escherichia coli K-12 MG1655.

artículo científico publicado en 2010

Description and Interpretation of Adaptive Evolution of Escherichia coli K-12 MG1655 by Using a Genome-Scale In Silico Metabolic Model ⬇️

artículo científico publicado el 1 de noviembre de 2003

Description and analysis of metabolic connectivity and dynamics in the human red blood cell

artículo científico publicado en 2002

Detailing the optimality of photosynthesis in cyanobacteria through systems biology analysis

artículo científico publicado en 2012

Determination of redundancy and systems properties of the metabolic network of Helicobacter pylori using genome-scale extreme pathway analysis.

artículo científico publicado en 2002

Determining the control circuitry of redox metabolism at the genome-scale

artículo científico publicado en 2014

Development of network-based pathway definitions: the need to analyze real metabolic networks

article

Directed Metabolic Pathway Evolution Enables Functional Pterin-Dependent Aromatic-Amino-Acid Hydroxylation in Escherichia coli

artículo científico publicado en 2020

Dissecting the genetic and metabolic mechanisms of adaptation to the knockout of a major metabolic enzyme in Escherichia coli

artículo científico publicado en 2017

Do genome-scale models need exact solvers or clearer standards?

artículo científico publicado en 2015

Drug Off-Target Effects Predicted Using Structural Analysis in the Context of a Metabolic Network Model ⬇️

artículo científico publicado el 23 de septiembre de 2010

DynamicME: dynamic simulation and refinement of integrated models of metabolism and protein expression

Effect of trisodium citrate treatment on hybridoma cell viability

Effects of abiotic stressors on lutein production in the green microalga Dunaliella salina.

artículo científico publicado en 2014

Elimination of thermodynamically infeasible loops in steady-state metabolic models

artículo científico publicado en 2011

Elucidating dynamic metabolic physiology through network integration of quantitative time-course metabolomics.

artículo científico publicado en 2017

Elucidating the Regulatory Elements for Transcription Termination and Posttranscriptional Processing in the Streptomyces clavuligerus Genome

Engineering synergy in biotechnology

artículo científico

Enhancement of carotenoid biosynthesis in the green microalga Dunaliella salina with light-emitting diodes and adaptive laboratory evolution.

artículo científico publicado en 2012

Enzyme promiscuity shapes adaptation to novel growth substrates

scientific article published on 08 April 2019

Enzyme promiscuity shapes evolutionary innovation and optimization

article

Escher-FBA: a web application for interactive flux balance analysis

scholarly article by Elliot Rowe published in September 2018

Escher: A Web Application for Building, Sharing, and Embedding Data-Rich Visualizations of Biological Pathways

artículo científico publicado en 2015

Escherichia coli K-12 undergoes adaptive evolution to achieve in silico predicted optimal growth

artículo científico publicado en 2002

Estimating Metabolic Equilibrium Constants: Progress and Future Challenges

artículo científico publicado en 2018

Evaluation of rate law approximations in bottom-up kinetic models of metabolism

artículo científico publicado en 2016

Evolution and regulation of nitrogen flux through compartmentalized metabolic networks in a marine diatom

artículo científico publicado en 2019

Evolution of E. coli on [U-13C]Glucose Reveals a Negligible Isotopic Influence on Metabolism and Physiology

artículo científico publicado en 2016

Evolution of gene knockout strains of E. coli reveal regulatory architectures governed by metabolism

scientific article published in Nature Communications

Expa: a program for calculating extreme pathways in biochemical reaction networks

artículo científico publicado en 2004

Expanded metabolic reconstruction of Helicobacter pylori (iIT341 GSM/GPR): an in silico genome-scale characterization of single- and double-deletion mutants

artículo científico publicado en 2005

Expanding the uses of genome-scale models with protein structures

scientific article published on 01 November 2019

Experimental and computational assessment of conditionally essential genes in Escherichia coli

artículo científico publicado en 2006

Experimentally Validated Reconstruction and Analysis of a Genome-Scale Metabolic Model of an Anaerobic Neocallimastigomycota Fungus

scientific article published on 15 February 2021

Exploiting adaptive laboratory evolution of Streptomyces clavuligerus for antibiotic discovery and overproduction ⬇️

artículo científico publicado en 2012

Extreme pathway analysis of human red blood cell metabolism

artículo científico publicado en 2002

Extreme pathway lengths and reaction participation in genome-scale metabolic networks

artículo científico publicado en 2002

Extreme pathways and Kirchhoff's second law.

artículo científico publicado en 2002

Fast growth phenotype of E. coli K-12 from adaptive laboratory evolution does not require intracellular flux rewiring

artículo científico publicado en 2017

Flagellar biosynthesis in silico: building quantitative models of regulatory networks

artículo científico publicado en 2004

Flux-concentration duality in dynamic nonequilibrium biological networks

artículo científico publicado en 2009

Formulating genome-scale kinetic models in the post-genome era.

artículo científico publicado en 2008

Functional and metabolic effects of adaptive glycerol kinase (GLPK) mutants in Escherichia coli

artículo científico publicado en 2011

Functional characterization of alternate optimal solutions of Escherichia coli's transcriptional and translational machinery

artículo científico publicado en 2010

Functional interrogation of Plasmodium genus metabolism identifies species- and stage-specific differences in nutrient essentiality and drug targeting

artículo científico publicado en 2018

Functional pathways for metabolic network-based data analysis: the MetPath algorithm

Functional states of the genome-scale Escherichia coli transcriptional regulatory system

artículo científico publicado en 2009

GIM3E: condition-specific models of cellular metabolism developed from metabolomics and expression data

artículo científico publicado en 2013

Gapless, Unambiguous Genome Sequence for Escherichia coli C, a Workhorse of Industrial Biology

scientific article published on 04 October 2018

Gastrointestinal Surgery for Inflammatory Bowel Disease Persistently Lowers Microbiome and Metabolome Diversity

artículo científico publicado en 2020

Gene expression profiling and the use of genome-scale in silico models of Escherichia coli for analysis: providing context for content

artículo científico publicado en 2009

Generation of an atlas for commodity chemical production in Escherichia coli and a novel pathway prediction algorithm, GEM-Path

artículo científico publicado en 2014

Genetic Basis of Growth Adaptation of Escherichia coli after Deletion of pgi, a Major Metabolic Gene ⬇️

artículo científico publicado el 4 de noviembre de 2010

Genetic Determinants Enabling Medium-Dependent Adaptation to Nafcillin in Methicillin-Resistant Staphylococcus aureus

scientific article published on 31 March 2020

Genetics. Predicting microbial growth

artículo científico publicado en 2014

Genome Sequence Comparison of Staphylococcus aureus TX0117 and a Beta-Lactamase-Cured Derivative Shows Increased Cationic Peptide Resistance Accompanying Mutations in relA and mnaA

artículo científico publicado en 2020

Genome-Scale Analysis of the Uses of the Escherichia coli Genome: Model-Driven Analysis of Heterogeneous Data Sets ⬇️

artículo científico publicado el 1 de noviembre de 2003

Genome-Scale Model Reveals Metabolic Basis of Biomass Partitioning in a Model Diatom

artículo científico publicado en 2016

Genome-Scale Network Modeling

Genome-Scale Reconstruction, Modeling, and Simulation of E. coli℉s Metabolic Network

scholarly article published 2009

Genome-scale analysis of Methicillin-resistant Staphylococcus aureus USA300 reveals a tradeoff between pathogenesis and drug resistance.

artículo científico publicado en 2018

Genome-scale determination of 5´ and 3´ boundaries of RNA transcripts in Streptomyces genomes

publication published on 15 December 2020

Genome-scale in silico models of E. coli have multiple equivalent phenotypic states: assessment of correlated reaction subsets that comprise network states.

artículo científico publicado en 2004

Genome-scale metabolic model of Helicobacter pylori 26695.

artículo científico publicado en 2002

Genome-scale metabolic modeling reveals key features of a minimal gene set

artículo científico publicado en 2021

Genome-scale metabolic models highlight stage-specific differences in essential metabolic pathways in Trypanosoma cruzi

artículo científico publicado en 2020

Genome-scale metabolic reconstructions of multiple Salmonella strains reveal serovar-specific metabolic traits

artículo científico publicado en 2018

Genome-scale microbial in silico models: the constraints-based approach.

artículo científico publicado en 2003

Genome-scale model of metabolism and gene expression provides a multi-scale description of acid stress responses in Escherichia coli

scientific article published on 06 December 2019

Genome-scale models of microbial cells: evaluating the consequences of constraints

artículo científico publicado en 2004

Genome-scale network analysis of imprinted human metabolic genes

artículo científico publicado en 2009

Genome-scale reconstruction and in silico analysis of the Clostridium acetobutylicum ATCC 824 metabolic network

artículo científico publicado en 2008

Genome-scale reconstruction of Escherichia coli's transcriptional and translational machinery: a knowledge base, its mathematical formulation, and its functional characterization

artículo científico publicado en 2009

Genome-scale reconstruction of metabolic network in Bacillus subtilis based on high-throughput phenotyping and gene essentiality data

artículo científico publicado en 2007

Genome-scale reconstruction of the Lrp regulatory network in Escherichia coli

scholarly article

Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network

artículo científico publicado en 2003

Genome-scale reconstruction of the metabolic network in Staphylococcus aureus N315: an initial draft to the two-dimensional annotation

artículo científico publicado en 2005

Genome-scale reconstruction of the sigma factor network in Escherichia coli: topology and functional states.

artículo científico publicado en 2014

Genome-scale reconstructions of the mammalian secretory pathway predict metabolic costs and limitations of protein secretion

Genome-scale reconstructions of the mammalian secretory pathway predict metabolic costs and limitations of protein secretion

scientific article published on 02 January 2020

Genome-wide Reconstruction of OxyR and SoxRS Transcriptional Regulatory Networks under Oxidative Stress in Escherichia coli K-12 MG1655.

artículo científico publicado en 2015

Genome-wide analysis of Fis binding in Escherichia coli indicates a causative role for A-/AT-tracts

artículo científico publicado en 2008

Genomewide identification of protein binding locations using chromatin immunoprecipitation coupled with microarray

artículo científico publicado en 2008

Genomic landscapes of Chinese hamster ovary cell lines as revealed by the Cricetulus griseus draft genome

artículo científico publicado en 2013

Global Rebalancing of Cellular Resources by Pleiotropic Point Mutations Illustrates a Multi-scale Mechanism of Adaptive Evolution

artículo científico publicado en 2016

Global reconstruction of the human metabolic network based on genomic and bibliomic data ⬇️

artículo científico publicado en 2007

Growth Adaptation of and Deletion Strains Diverges From a Similar Initial Perturbation of the Transcriptome

article published in 2018

H. influenzae Consortium: integrative study of H. influenzae-human interactions

artículo científico publicado en 2002

Hierarchical thinking in network biology: the unbiased modularization of biochemical networks.

artículo científico publicado en 2004

High-quality genome-scale metabolic modelling of Pseudomonas putida highlights its broad metabolic capabilities

scientific article published on 11 November 2019

High-throughput laser-mediated in situ cell purification with high purity and yield

artículo científico publicado en 2004

High-throughput mutation detection underlying adaptive evolution of Escherichia coli-K12.

artículo científico publicado en 2004

How to set up collaborations between academia and industrial biotech companies

artículo científico publicado en 2015

Identification of a transcription factor, PunR, that regulates the purine and purine nucleoside transporter punC in E. coli

artículo científico publicado en 2021

Identification of genome-scale metabolic network models using experimentally measured flux profiles

artículo científico publicado en 2006

Identification of growth-coupled production strains considering protein costs and kinetic variability

Identification of potential pathway mediation targets in Toll-like receptor signaling

artículo científico publicado en 2009

Identified metabolic signature for assessing red blood cell unit quality is associated with endothelial damage markers and clinical outcomes.

artículo científico publicado en 2016

Identifying constraints that govern cell behavior: a key to converting conceptual to computational models in biology?

artículo científico publicado en 2003

Immobilization of Escherichia coli RNA polymerase and location of binding sites by use of chromatin immunoprecipitation and microarrays

artículo científico publicado en 2005

Impact of individual mutations on increased fitness in adaptively evolved strains of Escherichia coli

artículo científico publicado en 2008

Impact of insertion sequences on convergent evolution of Shigella species

scientific article published on 09 July 2020

Improving collaboration by standardization efforts in systems biology.

artículo científico publicado en 2014

In Silico Metabolic Model and Protein Expression of Haemophilus influenzae Strain Rd KW20 in Rich Medium

artículo científico publicado en 2004

In silico analysis of SNPs and other high-throughput data

artículo científico publicado en 2007

In silico biology through "omics".

artículo científico publicado en 2002

In silico biotechnology. Era of reconstruction and interrogation

artículo científico publicado en 2004

In silico design and adaptive evolution of Escherichia coli for production of lactic acid.

artículo científico publicado en 2005

In silico method for modelling metabolism and gene product expression at genome scale

artículo científico publicado en 2012

In situ to in silico and back: elucidating the physiology and ecology of Geobacter spp. using genome-scale modelling

artículo científico publicado en 2010

Inactivation of a Mismatch-Repair System Diversifies Genotypic Landscape of Escherichia coli During Adaptive Laboratory Evolution

scientific article published on 16 August 2019

Inferring the metabolism of human orphan metabolites from their metabolic network context affirms human gluconokinase activity

artículo científico publicado en 2013

Initial proteome analysis of model microorganism Haemophilus influenzae strain Rd KW20.

artículo científico publicado en 2003

Insight into human alveolar macrophage and M. tuberculosis interactions via metabolic reconstructions

artículo científico publicado en 2010

Integrated analysis of metabolic phenotypes in Saccharomyces cerevisiae

artículo científico publicado en 2004

Integrated analysis of regulatory and metabolic networks reveals novel regulatory mechanisms in Saccharomyces cerevisiae

artículo científico publicado en 2006

Integrating high-throughput and computational data elucidates bacterial networks

artículo científico publicado en 2004

Intracellular metabolite profiling of platelets: Evaluation of extraction processes and chromatographic strategies

artículo científico publicado en 2012

Investigating the metabolic capabilities of Mycobacterium tuberculosis H37Rv using the in silico strain iNJ661 and proposing alternative drug targets

artículo científico publicado en 2007

Ion mobility derived collision cross sections to support metabolomics applications.

artículo científico publicado en 2014

Ion mobility-derived collision cross section as an additional measure for lipid fingerprinting and identification

artículo científico publicado en 2014

Iron competition triggers antibiotic biosynthesis in Streptomyces coelicolor during coculture with Myxococcus xanthus

artículo científico publicado en 2020

Isotopomer analysis of myocardial substrate metabolism: a systems biology approach

artículo científico publicado en 2006

Iterative reconstruction of transcriptional regulatory networks: an algorithmic approach

artículo científico publicado en 2006

JSBML 1.0: providing a smorgasbord of options to encode systems biology models

artículo científico publicado en 2015

Kinetic profiling of metabolic specialists demonstrates stability and consistency of in vivo enzyme turnover numbers

scientific article published on 01 September 2020

Laboratory Evolution to Alternating Substrate Environments Yields Distinct Phenotypic and Genetic Adaptive Strategies

artículo científico publicado en 2017

Laboratory evolution reveals a two-dimensional rate-yield tradeoff in microbial metabolism

scientific article published on 03 June 2019

Large-scale evaluation of in silico gene deletions in Saccharomyces cerevisiae

artículo científico publicado en 2003

Large-scale in silico modeling of metabolic interactions between cell types in the human brain

artículo científico publicado en 2010

Latent pathway activation and increased pathway capacity enable Escherichia coli adaptation to loss of key metabolic enzymes

artículo científico publicado en 2005

Linkage of Organic Anion Transporter-1 to Metabolic Pathways through Integrated “Omics”-driven Network and Functional Analysis ⬇️

artículo científico publicado el 12 de julio de 2011

List of Contributors

Literature mining supports a next-generation modeling approach to predict cellular byproduct secretion

artículo científico publicado en 2016

Long-range periodic patterns in microbial genomes indicate significant multi-scale chromosomal organization.

artículo científico publicado en 2006

MEMOTE for standardized genome-scale metabolic model testing

artículo científico publicado en 2020

MID Max: LC-MS/MS Method for Measuring the Precursor and Product Mass Isotopomer Distributions of Metabolic Intermediates and Cofactors for Metabolic Flux Analysis Applications

artículo científico publicado en 2015

MS/MS networking guided analysis of molecule and gene cluster families.

artículo científico publicado en 2013

Machine Learning of Bacterial Transcriptomes Reveals Responses Underlying Differential Antibiotic Susceptibility

Machine learning and structural analysis of Mycobacterium tuberculosis pan-genome identifies genetic signatures of antibiotic resistance

artículo científico publicado en 2018

Machine learning applied to enzyme turnover numbers reveals protein structural correlates and improves metabolic models

scholarly article by David Heckmann et al published 7 December 2018 in Nature Communications

Machine learning from Pseudomonas aeruginosa transcriptomes identifies independently modulated sets of genes associated with known transcriptional regulators

artículo científico publicado en 2022

Machine learning in computational biology to accelerate high-throughput protein expression.

artículo científico

Machine learning uncovers independently regulated modules in the Bacillus subtilis transcriptome

artículo científico publicado en 2020

Machine learning with random subspace ensembles identifies antimicrobial resistance determinants from pan-genomes of three pathogens

artículo científico publicado en 2020

Mannose and fructose metabolism in red blood cells during cold storage in SAGM.

artículo científico publicado en 2017

Mass action stoichiometric simulation models: incorporating kinetics and regulation into stoichiometric models

artículo científico publicado en 2010

Matrix formalism to describe functional states of transcriptional regulatory systems

artículo científico publicado en 2006

Maximizing biomass productivity and cell density of Chlorella vulgaris by using light-emitting diode-based photobioreactor

artículo científico publicado en 2012

Memote: A community-driven effort towards a standardized genome-scale metabolic model test suite

Metabolic Flux Balancing: Basic Concepts, Scientific and Practical Use

Metabolic Models of Protein Allocation Call for the Kinetome

artículo científico publicado en 2017

Metabolic Systems Analysis of Shock-Induced Endotheliopathy (SHINE) in Trauma: A New Research Paradigm

artículo científico publicado en 2019

Metabolic analysis of adaptive evolution for in silico-designed lactate-producing strains

artículo científico publicado en 2006

Metabolic and genetic basis for auxotrophies in Gram-negative species

artículo científico publicado en 2020

Metabolic characterization of Escherichia coli strains adapted to growth on lactate

artículo científico publicado en 2007

Metabolic fate of adenine in red blood cells during storage in SAGM solution.

artículo científico publicado en 2016

Metabolic gene-deletion strains of Escherichia coli evolve to computationally predicted growth phenotypes

artículo científico publicado en 2004

Metabolic modelling of microbes: the flux-balance approach

artículo científico publicado en 2002

Metabolic network reconstruction of Chlamydomonas offers insight into light-driven algal metabolism.

artículo científico publicado en 2011

Metabolic pathways in the post-genome era.

artículo científico publicado en 2003

Metabolic reconstruction and modeling of nitrogen fixation in Rhizobium etli

artículo científico publicado en 2007

Metabolic systems biology

artículo científico publicado en 2009

Metabolite coupling in genome-scale metabolic networks

artículo científico publicado en 2006

Metabolomic analysis of platelets during storage: a comparison between apheresis- and buffy coat-derived platelet concentrates.

artículo científico publicado en 2014

Metabolomics comparison of red cells stored in four additive solutions reveals differences in citrate anticoagulant permeability and metabolism

artículo científico publicado en 2017

Metagenomics-Based, Strain-Level Analysis of Escherichia coli From a Time-Series of Microbiome Samples From a Crohn's Disease Patient

artículo científico publicado en 2018

Microbial laboratory evolution in the era of genome-scale science

artículo científico publicado en 2011

Microbial regulatory and metabolic networks.

artículo científico publicado en 2007

Microbiology. Topping off a multiscale balancing act.

artículo científico publicado en 2010

Minimal cells, maximal knowledge

artículo científico publicado en 2019

Minimal metabolic pathway structure is consistent with associated biomolecular interactions

artículo científico publicado en 2014

Model-driven discovery of underground metabolic functions in Escherichia coli

artículo científico publicado en 2015

Model-driven evaluation of the production potential for growth-coupled products of Escherichia coli

artículo científico publicado en 2009

Model-driven multi-omic data analysis elucidates metabolic immunomodulators of macrophage activation

artículo científico publicado en 2012

Modeling Method for Increased Precision and Scope of Directly Measurable Fluxes at a Genome-Scale

artículo científico publicado en 2016

Modeling genome-wide enzyme evolution predicts strong epistasis underlying catalytic turnover rates

artículo científico publicado en 2018

Modeling methanogenesis with a genome-scale metabolic reconstruction of Methanosarcina barkeri

artículo científico publicado en 2006

Modeling the multi-scale mechanisms of macromolecular resource allocation.

artículo científico publicado en 2018

Monitoring metabolites consumption and secretion in cultured cells using ultra-performance liquid chromatography quadrupole-time of flight mass spectrometry (UPLC-Q-ToF-MS).

artículo científico publicado en 2011

Monte Carlo sampling can be used to determine the size and shape of the steady-state flux space

artículo científico publicado en 2004

Multi-omic data integration enables discovery of hidden biological regularities

artículo científico publicado en 2016

Multi-omics Quantification of Species Variation of Escherichia coli Links Molecular Features with Strain Phenotypes

artículo científico publicado en 2016

Multidimensional analytical approach based on UHPLC-UV-ion mobility-MS for the screening of natural pigments

artículo científico publicado en 2015

Multiple Optimal Phenotypes Overcome Redox and Glycolytic Intermediate Metabolite Imbalances in Escherichia coli pgi Knockout Evolutions

scientific article published on 17 September 2018

Multiple-omic data analysis of Klebsiella pneumoniae MGH 78578 reveals its transcriptional architecture and regulatory features

artículo científico publicado en 2012

Multiplex secretome engineering enhances recombinant protein production and purity

artículo científico publicado en 2020

Multiscale modeling of metabolism and macromolecular synthesis in E. coli and its application to the evolution of codon usage

artículo científico publicado en 2012

Multispecific Drug Transporter Slc22a8 (Oat3) Regulates Multiple Metabolic and Signaling Pathways ⬇️

artículo científico publicado el 6 de agosto de 2013

Murine Sca-1(+)/Lin(-) cells and human KG1a cells exhibit multiple pseudopod morphologies during migration

artículo científico publicado en 2002

Network context and selection in the evolution to enzyme specificity.

artículo científico publicado en 2012

Network reconstruction of platelet metabolism identifies metabolic signature for aspirin resistance

artículo científico publicado en 2014

Network-based analysis of metabolic regulation in the human red blood cell

artículo científico publicado en 2003

Network-based prediction of human tissue-specific metabolism

artículo científico publicado en 2008

Network-level allosteric effects are elucidated by detailing how ligand-binding events modulate utilization of catalytic potentials

artículo científico publicado en 2018

Network-level analysis of metabolic regulation in the human red blood cell using random sampling and singular value decomposition

artículo científico publicado en 2006

Next-generation genome-scale models for metabolic engineering.

artículo científico

Omic data from evolved E. coli are consistent with computed optimal growth from genome-scale models

artículo científico publicado en 2010

Optimizing genome-scale network reconstructions

artículo científico publicado en 2014

Optoinjection for efficient targeted delivery of a broad range of compounds and macromolecules into diverse cell types.

artículo científico publicado en 2006

OxyR Is a Convergent Target for Mutations Acquired during Adaptation to Oxidative Stress-Prone Metabolic States

scientific article published on 01 March 2020

PCR-based tandem epitope tagging system for Escherichia coli genome engineering

artículo científico publicado en 2006

Pan-Genome Analysis of Transcriptional Regulation in Six Salmonella enterica Serovar Typhimurium Strains Reveals Their Different Regulatory Structures

artículo científico publicado en 2022

Parallel adaptive evolution cultures of Escherichia coli lead to convergent growth phenotypes with different gene expression states

artículo científico publicado en 2005

Personalized Whole-Cell Kinetic Models of Metabolism for Discovery in Genomics and Pharmacodynamics

artículo científico publicado en 2015

Pharmacogenomic and clinical data link non-pharmacokinetic metabolic dysregulation to drug side effect pathogenesis

artículo científico publicado en 2015

Predicting gene essentiality using genome-scale in silico models

artículo científico publicado en 2008

Predicting outcomes of steady-state 13C isotope tracing experiments using Monte Carlo sampling ⬇️

artículo científico publicado el 30 de enero de 2012

Predicting the metabolic capabilities of Synechococcus elongatus PCC 7942 adapted to different light regimes

artículo científico publicado en 2018

Prediction of intracellular metabolic states from extracellular metabolomic data

artículo científico publicado en 2014

Primary transcriptome and translatome analysis determines transcriptional and translational regulatory elements encoded in the Streptomyces clavuligerus genome

artículo científico publicado en 2019

Principles of proteome allocation are revealed using proteomic data and genome-scale models

artículo científico publicado en 2016

Probing the basis for genotype-phenotype relationships

artículo científico publicado en 2009

Proceedings of the Food and Drug Administration's public workshop on new red blood cell product regulatory science 2016.

artículo científico publicado en 2017

Profiling the effect of nafcillin on HA-MRSA D712 using bacteriological and physiological media

scientific article published on 17 December 2019

Proteomic analysis of Chinese hamster ovary cells

artículo científico publicado en 2012

Pseudogene repair driven by selection pressure applied in experimental evolution

scientific article published on 28 January 2019

Publisher Correction: MEMOTE for standardized genome-scale metabolic model testing

artículo científico publicado en 2020

Quantification and Classification of E. coli Proteome Utilization and Unused Protein Costs across Environments

artículo científico publicado en 2016

Quantitative -omic data empowers bottom-up systems biology

artículo científico publicado en 2018

Quantitative feature extraction from the Chinese hamster ovary bioprocess bibliome using a novel meta-analysis workflow

artículo científico publicado en 2016

Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0

artículo científico publicado en 2011

Quantitative time-course metabolomics in human red blood cells reveal the temperature dependence of human metabolic networks

artículo científico publicado en 2017

RNA polymerase mutants found through adaptive evolution reprogram Escherichia coli for optimal growth in minimal media

artículo científico publicado en 2010

Recon3D enables a three-dimensional view of gene variation in human metabolism.

artículo científico publicado en 2018

Reconciling Gene Expression Data With Known Genome-Scale Regulatory Network Structures ⬇️

artículo científico publicado el 14 de octubre de 2003

Reconciling a Salmonella enterica metabolic model with experimental data confirms that overexpression of the glyoxylate shunt can rescue a lethal ppc deletion mutant

artículo científico publicado en 2013

Reconstructing metabolic flux vectors from extreme pathways: defining the alpha-spectrum

artículo científico publicado en 2003

Reconstructing organisms in silico: genome-scale models and their emerging applications

artículo científico publicado en 2020

Reconstruction and Use of Microbial Metabolic Networks: the Core Escherichia coli Metabolic Model as an Educational Guide

artículo científico publicado en 2010

Reconstruction and Validation of a Genome-Scale Metabolic Model of Streptococcus oralis (iCJ415), a Human Commensal and Opportunistic Pathogen

artículo científico publicado en 2020

Reconstruction and functional characterization of the human mitochondrial metabolic network based on proteomic and biochemical data

artículo científico publicado en 2004

Reconstruction and modeling protein translocation and compartmentalization in Escherichia coli at the genome-scale

artículo científico publicado en 2014

Reconstruction and validation of Saccharomyces cerevisiae iND750, a fully compartmentalized genome-scale metabolic model

artículo científico publicado en 2004

Reconstruction annotation jamborees: a community approach to systems biology

artículo científico publicado en 2010

Reconstruction of cellular signalling networks and analysis of their properties

artículo científico publicado en 2005

Reconstruction of microbial transcriptional regulatory networks

artículo científico publicado en 2004

Redefining fundamental concepts of transcription initiation in bacteria

artículo científico publicado en 2020

Reframing gene essentiality in terms of adaptive flexibility

article

Reliable and efficient solution of genome-scale models of Metabolism and macromolecular Expression

artículo científico publicado en 2017

Revealing 29 sets of independently modulated genes in Staphylococcus aureus, their regulators, and role in key physiological response

artículo científico publicado en 2020

Revealing genome-scale transcriptional regulatory landscape of OmpR highlights its expanded regulatory roles under osmotic stress in Escherichia coli K-12 MG1655

artículo científico publicado en 2017

Revealing key determinants of clonal variation in transgene expression in recombinant CHO cells using targeted genome editing

artículo científico publicado en 2018

RiboRid: A low cost, advanced, and ultra-efficient method to remove ribosomal RNA for bacterial transcriptomics

artículo científico publicado en 2021

SBML Level 3: an extensible format for the exchange and reuse of biological models

artículo científico publicado en 2020

SBMLsqueezer 2: context-sensitive creation of kinetic equations in biochemical networks

artículo científico publicado en 2015

STATR: A simple analysis pipeline of Ribo-Seq in bacteria

scientific article published on 28 January 2020

Saccharomyces cerevisiae phenotypes can be predicted by using constraint-based analysis of a genome-scale reconstructed metabolic network

artículo científico publicado en 2003

Salmonella modulates metabolism during growth under conditions that induce expression of virulence genes ⬇️

artículo científico publicado en 2013

Scalable method to determine mutations that occur during adaptive evolution of Escherichia coli

artículo científico publicado en 2003

Sensitive and accurate identification of protein-DNA binding events in ChIP-chip assays using higher order derivative analysis ⬇️

artículo científico publicado el 4 de noviembre de 2010

Sequence-based analysis of metabolic demands for protein synthesis in prokaryotes

artículo científico publicado en 2003

Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking

artículo científico publicado en 2016

Strain-Specific Metabolic Requirements Revealed by a Defined Minimal Medium for Systems Analyses of Staphylococcus aureus

scientific article published on 16 October 2019

Structural and operational complexity of the Geobacter sulfurreducens genome.

artículo científico publicado en 2010

Structural systems biology evaluation of metabolic thermotolerance in Escherichia coli

artículo científico publicado en 2013

Structure of galactarate dehydratase, a new fold in an enolase involved in bacterial fitness after antibiotic treatment

artículo científico publicado en 2019

Studying Salmonellae and Yersiniae host-pathogen interactions using integrated 'omics and modeling

artículo científico publicado en 2013

Sugar-stimulated CO2 sequestration by the green microalga Chlorella vulgaris

scientific article published on 09 November 2018

Synthetic Biology Tools for Novel Secondary Metabolite Discovery in Streptomyces

scientific article published on 01 May 2019

Synthetic cross-phyla gene replacement and evolutionary assimilation of major enzymes

artículo científico publicado en 2020

Systematic condition-dependent annotation of metabolic genes

artículo científico publicado en 2007

Systematic discovery of uncharacterized transcription factors in Escherichia coli K-12 MG1655

artículo científico publicado en 2018

Systematizing the generation of missing metabolic knowledge

artículo científico publicado en 2010

Systemic metabolic reactions are obtained by singular value decomposition of genome-scale stoichiometric matrices

artículo científico publicado en 2003

Systems Biology and Pangenome of Salmonella O-Antigens

artículo científico publicado en 2019

Systems analysis of energy metabolism elucidates the affected respiratory chain complex in Leigh's syndrome

artículo científico publicado en 2007

Systems analysis of metabolism in platelet concentrates during storage in platelet additive solution

artículo científico publicado en 2018

Systems approach to refining genome annotation

artículo científico publicado en 2006

Systems assessment of transcriptional regulation on central carbon metabolism by Cra and CRP.

artículo científico publicado en 2018

Systems biology analysis of drivers underlying hallmarks of cancer cell metabolism

artículo científico publicado en 2017

Systems biology analysis of the Clostridioides difficile core-genome contextualizes microenvironmental evolutionary pressures leading to genotypic and phenotypic divergence

artículo científico publicado en 2020

Systems biology and biotechnology of Streptomyces species for the production of secondary metabolites

artículo científico publicado en 2013

Systems biology as a foundation for genome-scale synthetic biology

artículo científico publicado en 2006

Systems biology definition of the core proteome of metabolism and expression is consistent with high-throughput data.

artículo científico publicado en 2015

Systems biology of SNPs

artículo científico publicado en 2006

Systems biology of stored blood cells: can it help to extend the expiration date?

artículo científico publicado en 2012

Systems biology of the human red blood cell

artículo científico publicado en 2006

Systems biology of the structural proteome

artículo científico publicado en 2016

Systems-level analysis of NalD mutation, a recurrent driver of rapid drug resistance in acute Pseudomonas aeruginosa infection

artículo científico publicado en 2019

Technologies and approaches to elucidate and model the virulence program of salmonella

artículo científico publicado en 2011

Temperature-Dependent Estimation of Gibbs Energies Using an Updated Group-Contribution Method

artículo científico publicado en 2018

The COMBREX project: design, methodology, and initial results

artículo científico publicado en 2013

The Escherichia coli transcriptome mostly consists of independently regulated modules

scientific article published on 04 December 2019

The JAK-STAT signaling network in the human B-cell: an extreme signaling pathway analysis

artículo científico publicado en 2004

The PurR regulon in Escherichia coli K-12 MG1655 ⬇️

artículo científico publicado el 13 de mayo de 2011

The Staphylococcus aureus Two-Component System AgrAC Displays Four Distinct Genomic Arrangements That Delineate Genomic Virulence Factor Signatures

The Staphylococcus aureus Two-Component System AgrAC Displays Four Distinct Genomic Arrangements That Delineate Genomic Virulence Factor Signatures.

artículo científico publicado en 2018

The Transcription Unit Architecture of Streptomyces lividans TK24

scientific article published on 06 September 2019

The aldehyde dehydrogenase, AldA, is essential for L-1,2-propanediol utilization in laboratory-evolved Escherichia coli.

artículo científico publicado en 2016

The architecture of ArgR-DNA complexes at the genome-scale in Escherichia coli

artículo científico publicado en 2015

The biomass objective function

artículo científico publicado en 2010

The challenges of integrating multi-omic data sets

artículo científico publicado en 2010

The convex basis of the left null space of the stoichiometric matrix leads to the definition of metabolically meaningful pools

artículo científico publicado en 2003

The development of a fully-integrated immune response model (FIRM) simulator of the immune response through integration of multiple subset models.

artículo científico publicado en 2013

The econometrics of evolution

artículo científico publicado en 2005

The emergence of adaptive laboratory evolution as an efficient tool for biological discovery and industrial biotechnology

artículo científico publicado en 2019

The evolution of molecular biology into systems biology

artículo científico publicado en 2004

The genomic sequence of the Chinese hamster ovary (CHO)-K1 cell line

artículo científico publicado en 2011

The global transcriptional regulatory network for metabolism in Escherichia coli exhibits few dominant functional states.

artículo científico publicado en 2005

The growing scope of applications of genome-scale metabolic reconstructions using Escherichia coli

artículo científico publicado en 2008

The human metabolic reconstruction Recon 1 directs hypotheses of novel human metabolic functions

artículo científico publicado en 2011

The model organism as a system: integrating 'omics' data sets

artículo científico publicado en 2006

The quantitative metabolome is shaped by abiotic constraints

artículo científico publicado en 2021

The transcription unit architecture of the Escherichia coli genome

artículo científico publicado en 2009

The y-ome defines the 35% of Escherichia coli genes that lack experimental evidence of function

article

Thermodynamic favorability and pathway yield as evolutionary tradeoffs in biosynthetic pathway choice

article published in the Proceedings of the National Academy of Sciences of the United States of America

Thermosensitivity of growth is determined by chaperone-mediated proteome reallocation

artículo científico publicado en 2017

Thirteen years of building constraint-based in silico models of Escherichia coli

artículo científico publicado en 2003

Thirty complete Streptomyces genome sequences for mining novel secondary metabolite biosynthetic gene clusters

artículo científico publicado en 2020

Three factors underlying incorrect in silico predictions of essential metabolic genes

artículo científico publicado en 2008

Three-dimensional structural view of the central metabolic network of Thermotoga maritima

artículo científico publicado en 2009

Top-down analysis of temporal hierarchy in biochemical reaction networks

artículo científico publicado en 2008

Topological analysis of mass-balanced signaling networks: a framework to obtain network properties including crosstalk

artículo científico publicado en 2004

Topological and kinetic determinants of the modal matrices of dynamic models of metabolism

artículo científico publicado en 2017

Toward whole cell modeling and simulation: comprehensive functional genomics through the constraint-based approach

artículo científico publicado en 2007

Towards genome-scale signalling network reconstructions

artículo científico publicado en 2010

Towards multidimensional genome annotation

artículo científico publicado en 2006

Transcriptional regulation in constraints-based metabolic models of Escherichia coli

artículo científico publicado en 2002

Transcriptional regulation of the fad regulon genes of Escherichia coli by ArcA.

artículo científico publicado en 2006

Transcriptome and translatome profiles of Streptomyces species in different growth phases

scientific article published on 08 May 2020

Two-dimensional annotation of genomes

artículo científico publicado en 2004

UPLC-UV-MS(E) analysis for quantification and identification of major carotenoid and chlorophyll species in algae.

artículo científico publicado en 2012

Understanding human metabolic physiology: a genome-to-systems approach

artículo científico publicado en 2008

Uniform sampling of steady-state flux spaces: means to design experiments and to interpret enzymopathies.

artículo científico publicado en 2004

Unraveling the functions of uncharacterized transcription factors in Escherichia coli using ChIP-exo

artículo científico publicado en 2021

Untangling the web of functional and physical interactions in yeast

artículo científico publicado en 2005

Updated and standardized genome-scale reconstruction of Mycobacterium tuberculosis H37Rv, iEK1011, simulates flux states indicative of physiological conditions

artículo científico publicado en 2018

Use of adaptive laboratory evolution to discover key mutations enabling rapid growth of Escherichia coli K-12 MG1655 on glucose minimal medium

artículo científico publicado en 2014

Use of randomized sampling for analysis of metabolic networks

artículo científico publicado en 2008

Using Genome-scale Models to Predict Biological Capabilities

artículo científico publicado en 2015

Using in silico models to simulate dual perturbation experiments: procedure development and interpretation of outcomes

artículo científico publicado en 2009

Using metabolic flux data to further constrain the metabolic solution space and predict internal flux patterns: the Escherichia coli spectrum

artículo científico publicado en 2004

What Makes a Bacterial Species Pathogenic?:Comparative Genomic Analysis of the Genus Leptospira

artículo científico publicado en 2016

What do cells actually want?

artículo científico publicado en 2016

What is flux balance analysis?

artículo científico publicado en 2010

Whole-Genome Sequencing of Invasion-Resistant Cells Identifies Laminin α2 as a Host Factor for Bacterial Invasion

artículo científico publicado en 2017

Whole-genome resequencing of Escherichia coli K-12 MG1655 undergoing short-term laboratory evolution in lactate minimal media reveals flexible selection of adaptive mutations

artículo científico publicado en 2009

iAB-RBC-283: A proteomically derived knowledge-base of erythrocyte metabolism that can be used to simulate its physiological and patho-physiological states ⬇️

artículo científico publicado el 12 de julio de 2011

iCN718, an Updated and Improved Genome-Scale Metabolic Network Reconstruction of Acinetobacter baumannii AYE.

artículo científico publicado en 2018

iML1515, a knowledgebase that computes Escherichia coli traits.

artículo científico publicado en 2017

k-Cone analysis: determining all candidate values for kinetic parameters on a network scale

artículo científico publicado en 2004

proChIPdb: a chromatin immunoprecipitation database for prokaryotic organisms

scientific article published on 16 October 2021

solveME: fast and reliable solution of nonlinear ME models

artículo científico publicado en 2016

ssbio: A Python Framework for Structural Systems Biology

artículo científico publicado en 2018

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