4.5 Article

Quantitative prediction of conditional vulnerabilities in regulatory and metabolic networks using PRIME

相关参考文献

注意:仅列出部分参考文献,下载原文获取全部文献信息。
Article Cell Biology

Intricate Genetic Programs Controlling Dormancy in Mycobacterium tuberculosis

Eliza J. R. Peterson et al.

CELL REPORTS (2020)

Article Biochemistry & Molecular Biology

Path-seq identifies an essential mycolate remodeling program for mycobacterial host adaptation

Eliza J. R. Peterson et al.

MOLECULAR SYSTEMS BIOLOGY (2019)

Article Biochemical Research Methods

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

Laurent Heirendt et al.

NATURE PROTOCOLS (2019)

Article Immunology

Modeling the Metabolic State of Mycobacterium tuberculosis Upon Infection

Rienk A. Rienksma et al.

FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY (2018)

Article Biochemical Research Methods

Combining inferred regulatory and reconstructed metabolic networks enhances phenotype prediction in yeast

Zhuo Wang et al.

PLoS Computational Biology (2017)

Article Biochemistry & Molecular Biology

COLOMBOS v3.0: leveraging gene expression compendia for cross- species analyses

Marco Moretto et al.

NUCLEIC ACIDS RESEARCH (2016)

Article Biochemistry & Molecular Biology

An experimentally supported model of the Bacillus subtilis global transcriptional regulatory network

Mario L. Arrieta-Ortiz et al.

MOLECULAR SYSTEMS BIOLOGY (2015)

Article Multidisciplinary Sciences

The DNA-binding network of Mycobacterium tuberculosis

Kyle J. Minch et al.

NATURE COMMUNICATIONS (2015)

Article Biochemical Research Methods

Integrated Modeling of Gene Regulatory and Metabolic Networks in Mycobacterium tuberculosis

Shuyi Ma et al.

PLOS COMPUTATIONAL BIOLOGY (2015)

Article Biochemistry & Molecular Biology

A system-level model for the microbial regulatory genome

Aaron N. Brooks et al.

MOLECULAR SYSTEMS BIOLOGY (2014)

Article Biochemistry & Molecular Biology

A high-resolution network model for global gene regulation in Mycobacterium tuberculosis

Eliza J. R. Peterson et al.

NUCLEIC ACIDS RESEARCH (2014)

Article Microbiology

Reduced Drug Uptake in Phenotypically Resistant Nutrient-Starved Nonreplicating Mycobacterium tuberculosis

Jansy Sarathy et al.

ANTIMICROBIAL AGENTS AND CHEMOTHERAPY (2013)

Article Biochemical Research Methods

Bayesian analysis of gene essentiality based on sequencing of transposon insertion libraries

Michael A. DeJesus et al.

BIOINFORMATICS (2013)

Article Biochemical Research Methods

Robust data-driven incorporation of prior knowledge into the inference of dynamic regulatory networks

Alex Greenfield et al.

BIOINFORMATICS (2013)

Article Biochemistry & Molecular Biology

Intracellular Mycobacterium tuberculosis Exploits Host-derived Fatty Acids to Limit Metabolic Stress

Wonsik Lee et al.

JOURNAL OF BIOLOGICAL CHEMISTRY (2013)

Article Multidisciplinary Sciences

The Mycobacterium tuberculosis regulatory network and hypoxia

James E. Galagan et al.

NATURE (2013)

Article Biochemical Research Methods

Fast gapped-read alignment with Bowtie 2

Ben Langmead et al.

NATURE METHODS (2012)

Article Medicine, Research & Experimental

NSR-seq transcriptional profiling enables identification of a gene signature of Plasmodium falciparum parasites infecting children

Marissa Vignali et al.

JOURNAL OF CLINICAL INVESTIGATION (2011)

Article Biotechnology & Applied Microbiology

EMILiO: A fast algorithm for genome-scale strain design

Laurence Yang et al.

METABOLIC ENGINEERING (2011)

Article Infectious Diseases

Time-kill kinetics of anti-tuberculosis drugs, and emergence of resistance, in relation to metabolic activity of Mycobacterium tuberculosis

Jurriaan E. M. de Steenwinkel et al.

JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY (2010)

Article Biotechnology & Applied Microbiology

What is flux balance analysis?

Jeffrey D. Orth et al.

NATURE BIOTECHNOLOGY (2010)

Article Multidisciplinary Sciences

Probabilistic integrative modeling of genome-scale metabolic and regulatory networks in Escherichia coli and Mycobacterium tuberculosis

Sriram Chandrasekaran et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2010)

Article Multidisciplinary Sciences

The protonmotive force is required for maintaining ATP homeostasis and viability of hypoxic, nonreplicating Mycobacterium tuberculosis

Srinivasa P. S. Rao et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2008)

Article Multidisciplinary Sciences

Mycobacterial persistance requires the utilization of host cholesterol

Amit K. Pandey et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2008)

Article Biochemical Research Methods

Context-specific metabolic networks are consistent with experiments

Scott A. Becker et al.

PLOS COMPUTATIONAL BIOLOGY (2008)

Article Biotechnology & Applied Microbiology

The Inferelator: an algorithm for learning parsimonious regulatory networks from systems-biology data sets de novo

Richard Bonneau et al.

GENOME BIOLOGY (2006)

Article Biotechnology & Applied Microbiology

OptKnock: A bilevel programming framework for identifying gene knockout strategies for microbial strain optimization

AP Burgard et al.

BIOTECHNOLOGY AND BIOENGINEERING (2003)

Article Biology

Regulation of gene expression in flux balance models of metabolism

MW Covert et al.

JOURNAL OF THEORETICAL BIOLOGY (2001)