4.7 Article

Integration of omics data to generate and analyse COVID-19 specific genome-scale metabolic models

Related references

Note: Only part of the references are listed.
Article Biochemical Research Methods

Optimization of metabolomic data processing using NOREVA

Jianbo Fu et al.

Summary: A peak table is a typical output of metabolomic experiments, and its processing is crucial in metabolomics research. The NOREVA protocol, a newly developed software tool, evaluates and optimizes data processing through various workflows, making data processing more efficient.

NATURE PROTOCOLS (2022)

Article Biology

Reconstruction of tissue-specific genome-scale metabolic models for human cancer stem cells

Tania Barata et al.

Summary: CSCs contribute to the aggressiveness, metastasis, resistance to chemo/radio-therapy, and recurrence of cancer through metabolic reprogramming. Computational Genome-Scale Metabolic Models (GSMMs) help predict metabolic phenotypes, identify potential therapeutic targets, and discover known transcription factors, miRNAs, and antimetabolites that could be repurposed for cancer treatment.

COMPUTERS IN BIOLOGY AND MEDICINE (2022)

Article Infectious Diseases

Key summary of German national treatment guidance for hospitalized COVID-19 patients Key pharmacologic recommendations from a national German living guideline using an Evidence to Decision Framework (last updated 17.05.2021)

Jakob J. Malin et al.

Summary: This executive summary of a national living guideline provides rapid evidence-based recommendations on drug interventions for hospitalized patients with COVID-19, using systematic assessment and decision processes. 11 key recommendations for COVID-19 drug therapy are included in the guideline, with strong recommendations for corticosteroids and prophylactic anticoagulation as standard of care. The guidelines will be updated as new evidence emerges.

INFECTION (2022)

Article Biochemistry & Molecular Biology

Identification of Required Host Factors for SARS-CoV-2 Infection in Human Cells

Zharko Daniloski et al.

Summary: Researchers conducted a genome-scale CRISPR screen to identify host factors crucial for SARS-CoV-2 infection, highlighting genes related to ATPase proton pump, Retromer, and Commander complexes. Validating these gene targets through multiple methods, they found shared transcriptional changes in cholesterol biosynthesis when top-ranked genes were lost. Loss of RAB7A was shown to reduce viral entry by sequestering the ACE2 receptor inside cells, underscoring its importance early in the viral infection process.
Review Nutrition & Dietetics

Lipid profile as an indicator of COVID-19 severity: A systematic review and meta-analysis

Roshan Kumar Mahat et al.

Summary: This study conducted a systematic review and meta-analysis of 19 studies to evaluate the association of lipid profile with severity and mortality in COVID-19 patients. The findings suggest that levels of total cholesterol, HDL-C, and LDL-C are significantly decreased in severe cases, and HDL-C and LDL-C are lower in non-survivors compared to survivors. The lipid profile may be used for assessing the severity and prognosis of COVID-19.

CLINICAL NUTRITION ESPEN (2021)

Article Pharmacology & Pharmacy

Identification of Niemann-Pick C1 protein as a potential novel SARS-CoV-2 intracellular target

Isabel Garcia-Dorival et al.

Summary: The study found a novel interaction between the SARSCoV-2 nucleoprotein (N) and the cholesterol transporter NPC1, and identified compounds that can reduce viral infection, highlighting the importance of NPC1 for SARS-CoV-2 infection and suggesting a potential new therapeutic target against COVID-19.

ANTIVIRAL RESEARCH (2021)

Article Nutrition & Dietetics

Vitamin A in resistance to and recovery from infection: relevance to SARS-CoV2

C. B. Stephensen et al.

Summary: SARS-CoV2 infects respiratory epithelial cells via ACE2 receptor, causing viral pneumonia and multi-organ dysfunction in COVID-19. Nutritional deficiencies worsen disease severity, with vitamin A supplementation potentially improving immunity and respiratory function, while counteracting negative effects of the virus and some treatments.

BRITISH JOURNAL OF NUTRITION (2021)

Article Biochemistry & Molecular Biology

Genetic Screens Identify Host Factors for SARS-CoV-2 and Common Cold Coronaviruses

Ruofan Wang et al.

Summary: The study identified common host factors for three coronaviruses and critical host pathways supporting infection by all of them, including phosphatidylinositol phosphate biosynthesis and cholesterol homeostasis. Inhibition of these pathways reduced replication of all three coronaviruses, while the lysosomal protein TMEM106B appeared unique to SARS-CoV-2 infection. These findings provide important insights for understanding the coronavirus life cycle and developing host-directed therapies.
Article Microbiology

Functional interrogation of a SARS-CoV-2 host protein interactome identifies unique and shared coronavirus host factors

H-Heinrich Hoffmann et al.

Summary: A study utilizing CRISPR-Cas9 technology targeted 332 members of the SARS-CoV-2 protein interactome, revealing new insights about coronaviruses and providing important references for future outbreaks.

CELL HOST & MICROBE (2021)

Article Cell Biology

S-acylation controls SARS-CoV-2 membrane lipid organization and enhances infectivity

Francisco S. Mesquita et al.

Summary: During SARS-CoV-2 infection, spike protein undergoes lipid modification which controls its biosynthesis and degradation, promoting viral budding. This lipidation leads to the formation of cholesterol and sphingolipid-rich lipid nanodomains in the early Golgi, enhancing virus fusion capacity.

DEVELOPMENTAL CELL (2021)

Review Biochemical Research Methods

Role of Multiomics Data to Understand Host-Pathogen Interactions in COVID-19 Pathogenesis

Shalini Aggarwal et al.

Summary: This article critically analyzes the pathobiology of SARS-CoV-2 in humans using high-throughput omics technologies, revealing changes in biological pathways associated with COVID-19 disease. Further meta-analysis indicates significant alterations in immune response, fatty acid, and amino acid metabolism in COVID-19 patients.

JOURNAL OF PROTEOME RESEARCH (2021)

Article Medicine, General & Internal

Survival Factors and Metabolic Pathogenesis in Elderly Patients (≥65) With COVID-19: A Multi-Center Study

Qi Mei et al.

Summary: This study found that survival of elderly COVID-19 patients is mainly influenced by factors such as elevated D-Dimer, high immune-related metabolic index, and increased neutrophil-to-lymphocyte ratio. Dysregulation of metabolic pathways and specific therapeutic interventions may contribute to the development of drugs and vaccines against COVID-19.

FRONTIERS IN MEDICINE (2021)

Article Biochemistry & Molecular Biology

Genome-scale metabolic modeling reveals SARS-CoV-2-induced metabolic changes and antiviral targets

Kuoyuan Cheng et al.

Summary: The study utilized genome-scale metabolic modeling to analyze host metabolism changes during SARS-CoV-2 infection, predicted anti-viral targets, validated these targets using drug and genetic screening data, and provided potential anti-SARS-CoV-2 targets supported by clinical data for future evaluation.

MOLECULAR SYSTEMS BIOLOGY (2021)

Review Infectious Diseases

Low vitamin D status is associated with coronavirus disease 2019 outcomes: a systematic review and meta-analysis

Nanyang Liu et al.

Summary: Low vitamin D status is associated with an increased risk of COVID-19, and COVID-19-positive individuals tend to have lower levels of vitamin D. However, there is significant publication bias in the existing studies.

INTERNATIONAL JOURNAL OF INFECTIOUS DISEASES (2021)

Review Nutrition & Dietetics

Association of Vitamin D Status with SARS-CoV-2 Infection or COVID-19 Severity: A Systematic Review and Meta-analysis

Asma Kazemi et al.

Summary: This systematic review suggests a significant association between 25(OH)D and SARS-CoV-2 infection, COVID-19 severity, and mortality, although there are inconsistencies in some findings. Evidence regarding ICU admission, inflammation, hospitalization, and pulmonary complications is currently inconsistent and insufficient.

ADVANCES IN NUTRITION (2021)

Review Public, Environmental & Occupational Health

The Impact of Vitamin D Level on COVID-19 Infection: Systematic Review and Meta-Analysis

Amare Teshome et al.

Summary: This review summarized the available evidence on the association between Vitamin D levels and the risk of COVID-19 infection, showing that individuals with Vitamin-D deficiency were at a higher risk of acquiring COVID-19 compared to those with sufficient levels.

FRONTIERS IN PUBLIC HEALTH (2021)

Article Endocrinology & Metabolism

The serum metabolome of COVID-19 patients is distinctive and predictive

Ding Shi et al.

Summary: The serum metabolome of COVID-19 patients is distinctive and can be used for investigating pathogenesis, determining a diagnosis, predicting severe cases, and improving treatment. Specific metabolites were found to distinguish COVID-19 patients from healthy controls and predict disease progression, with some being recovered after discharge.

METABOLISM-CLINICAL AND EXPERIMENTAL (2021)

Article Biochemical Research Methods

Genome Scale-Differential Flux Analysis reveals deregulation of lung cell metabolism on SARS-CoV-2 infection

Piyush Nanda et al.

Summary: Researchers developed a metabolic model of host human cells infected with SARS-CoV-2, predicting rapid virus growth rates. Flux analysis identified lipid metabolism as severely affected during infection, with key enzymes directly interacting with viral proteins. The study demonstrates the importance of metabolic flux analysis in understanding disease biology and potential therapeutic interventions.

PLOS COMPUTATIONAL BIOLOGY (2021)

Article Biology

SARS-CoV-2 requires cholesterol for viral entry and pathological syncytia formation

David W. Sanders et al.

Summary: Enveloped viruses induce multinucleated cells through membrane fusion mechanisms, which facilitate replication and immune evasion. A study on SARS-CoV-2 spike protein and ACE2 receptor interaction revealed the importance of biophysical aspects of the membrane, particularly cholesterol-rich regions, in spike-mediated fusion. This finding may provide molecular basis for positive outcomes in COVID-19 patients taking statins and suggest new therapeutic strategies targeting the membranes of fusogenic viruses.

ELIFE (2021)

Article Physiology

Alteration in the Lipid Profile and the Desaturases Activity in Patients With Severe Pneumonia by SARS-CoV-2

Israel Perez-Torres et al.

Summary: The lipid metabolism of host cells is hijacked by SARS-CoV-2, causing changes in fatty acid profiles and desaturase activity, leading to alterations in total fatty acids, phospholipids, and non-esterified fatty acids. These changes may facilitate virus replication while also triggering the host cell's defense mechanisms to repair damage caused by the virus to cell membranes.

FRONTIERS IN PHYSIOLOGY (2021)

Article Endocrinology & Metabolism

Vitamin D and lumisterol novel metabolites can inhibit SARS-CoV-2 replication machinery enzymes

Shariq Qayyum et al.

Summary: The study found that metabolites of vitamin D and lumisterol can inhibit key enzymes in the SARS-CoV-2 replication machinery, suggesting a novel potential for antiviral drug research.

AMERICAN JOURNAL OF PHYSIOLOGY-ENDOCRINOLOGY AND METABOLISM (2021)

Article Biochemistry & Molecular Biology

Antiviral strategies targeting host factors and mechanisms obliging plus ssRNA viral pathogens

Supreeti Mahajan et al.

Summary: Researchers suggest that targeting host factors instead of viral enzymes is an alternative antiviral strategy that increases the threshold of antiviral resistance and provides broad-spectrum antiviral action against different viruses.

BIOORGANIC & MEDICINAL CHEMISTRY (2021)

Review Cardiac & Cardiovascular Systems

A systematic review and meta-analysis of effect of vitamin D levels on the incidence of COVID-19

Luiza Szarpak et al.

Summary: This meta-analysis found that low serum vitamin D levels are significantly associated with the risk of COVID-19 infection, especially in the deficiency risk groups where supplementation of vitamin D is indicated.

CARDIOLOGY JOURNAL (2021)

Article Biochemistry & Molecular Biology

Genome-scale metabolic modelling of SARS-CoV-2 in cancer cells reveals an increased shift to glycolytic energy production

Elisabeth Yaneske et al.

Summary: The study examined the interaction between COVID-19 and cancer, revealing metabolic alterations triggered by SARS-CoV-2 infection, as well as the impact on cellular biology and energy production pathways.

FEBS LETTERS (2021)

Review Biochemistry & Molecular Biology

The Molecular Basis of COVID-19 Pathogenesis, Conventional and Nanomedicine Therapy

Shirin Kouhpayeh et al.

Summary: This article mainly discusses the pathophysiological mechanisms of the novel coronavirus, including the activation of the RAS signaling pathway, oxidative stress, and cell death. Potential therapeutic targets and drugs for inhibiting viral activity and reducing oxidative stress are also explored in depth.

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2021)

Review Biochemistry & Molecular Biology

Therapeutic and prognostic role of vitamin D for COVID-19 infection: A systematic review and meta-analysis of 43 observational studies

Fausto Petrelli et al.

Summary: Vitamin D plays a protective role by modulating the immune system and systemic inflammatory response, reducing the risk and severity of COVID-19 infection. Patients with deficient vitamin D levels are more likely to be infected with COVID-19, and are more likely to experience severe symptoms and death.

JOURNAL OF STEROID BIOCHEMISTRY AND MOLECULAR BIOLOGY (2021)

Review Endocrinology & Metabolism

The link between COVID-19 and VItamin D (VIVID): A systematic review and meta-analysis

Aya Bassatne et al.

Summary: There are studies on the impact of vitamin D levels and supplementation on health outcomes related to COVID-19, but the current evidence is not sufficient to determine specific correlations.

METABOLISM-CLINICAL AND EXPERIMENTAL (2021)

Article Virology

All-Trans Retinoic Acid Exhibits Antiviral Effect against SARS-CoV-2 by Inhibiting 3CLpro Activity

Takeshi Morita et al.

Summary: The global pandemic of COVID-19 caused by SARS-CoV-2 continues to spread, and the major protease 3CLpro of SARS-CoV-2 is an important target for antiviral drug development. ATRA has been identified as an inhibitor of 3CLpro and has shown antiviral effects against SARS-CoV-2 and its variants of concern.

VIRUSES-BASEL (2021)

Article Nutrition & Dietetics

Vitamin A Plasma Levels in COVID-19 Patients: A Prospective Multicenter Study and Hypothesis

Phil-Robin Tepasse et al.

Summary: This study found that in COVID-19 patients, plasma levels of vitamin A decrease during acute inflammation, and significantly reduced plasma levels of vitamin A are associated with ARDS and mortality.

NUTRIENTS (2021)

Article Microbiology

Discovery of re-purposed drugs that slow SARS-CoV-2 replication in human cells

Adam Pickard et al.

Summary: The study evaluated a range of human cell types for their ability to support SARS-CoV-2 replication and screened 1971 FDA-approved drugs. Hepatocytes, kidney glomerulus, and proximal tubule cells were particularly effective in supporting virus replication in-line with reported proteinuria and liver damage in COVID-19 patients. The study identified 35 drugs that reduced viral replication in Vero cells and human hepatocytes, with certain drugs like amodiaquine, atovaquone, and vitamin D3 showing promise in slowing SARS-CoV-2 replication in human cells.

PLOS PATHOGENS (2021)

Article Genetics & Heredity

Genome-Scale Metabolic Model of Infection with SARS-CoV-2 Mutants Confirms Guanylate Kinase as Robust Potential Antiviral Target

Alina Renz et al.

Summary: The ongoing COVID-19 pandemic poses a threat to humankind, with no antiviral treatment available for patients and mutation variants of SARS-CoV-2 impacting vaccine efficacy. Research has refined a metabolic model of host-virus interaction, identifying potential antiviral targets and highlighting the need for further study and development of antiviral therapies.

GENES (2021)

Article Biochemistry & Molecular Biology

Low Levels of Few Micronutrients May Impact COVID-19 Disease Progression: An Observational Study on the First Wave

Teresa-Maria Tomasa-Irriguible et al.

Summary: The study found that high percentages of COVID-19 patients had low levels of zinc, vitamin A, B-6, C, and D, while fewer had low levels of vitamin E. Low levels of vitamin A and zinc were associated with ICU admission, while older patients had higher mortality rates. Randomized clinical trials are needed to further investigate the role of micronutrient supplementation in COVID-19 treatment.

METABOLITES (2021)

Review Public, Environmental & Occupational Health

Cholesterol and Triglyceride Concentrations, COVID-19 Severity, and Mortality: A Systematic Review and Meta-Analysis With Meta-Regression

Angelo Zinellu et al.

Summary: A systematic review and meta-analysis found significantly lower lipid levels in hospitalized COVID-19 patients with severe disease or non-survivor status, which could be important for risk stratification and monitoring in this group. The study indicates potential associations between lipid profile alterations and disease severity and mortality in COVID-19 patients.

FRONTIERS IN PUBLIC HEALTH (2021)

Article Endocrinology & Metabolism

Pharmacological inhibition of fatty acid synthesis blocks SARS-CoV-2 replication

Junjun Chu et al.

Summary: Cellular lipid synthesis is crucial for SARS-CoV-2 replication. Inhibitors of fatty acid synthase, such as the approved anti-obesity drug orlistat, show potential for preventing and treating COVID-19 by inhibiting viral replication.

NATURE METABOLISM (2021)

Review Medicine, General & Internal

Influence of 25-hydroxy-cholecalciferol levels on SARS-CoV-2 infection and COVID-19 severity: A systematic review and meta-analysis

Andrea Crafa et al.

Summary: This study found significant associations between serum 25(OH)D levels and SARS-CoV-2 infection, severe COVID-19, and patient mortality. Patients with vitamin D deficiency are more likely to develop severe COVID-19.

ECLINICALMEDICINE (2021)

Letter Biochemistry & Molecular Biology

Palmitoylation of SARS-CoV-2 S protein is essential for viral infectivity

Zhuanchang Wu et al.

SIGNAL TRANSDUCTION AND TARGETED THERAPY (2021)

Review Biochemical Research Methods

Computational strategies to combat COVID-19: useful tools to accelerate SARS-CoV-2 and coronavirus research

Franziska Hufsky et al.

Summary: This review explores bioinformatics workflows and tools for the detection, analysis, tracking, evaluation, research, detection of drug targets, and development of therapeutic strategies related to SARS-CoV-2, providing valuable insights for the ongoing COVID-19 pandemic.

BRIEFINGS IN BIOINFORMATICS (2021)

Article Health Care Sciences & Services

Machine learning-based prediction of COVID-19 diagnosis based on symptoms

Yazeed Zoabi et al.

Summary: Using a machine learning approach and simple features, COVID-19 test results can be accurately predicted to assist medical staff in patient triaging, particularly in situations with limited healthcare resources.

NPJ DIGITAL MEDICINE (2021)

Article Biochemical Research Methods

ANPELA: analysis and performance assessment of the label-free quantification workflow for metaproteomic studies

Jing Tang et al.

BRIEFINGS IN BIOINFORMATICS (2020)

Review Infectious Diseases

Coronavirus 2019-nCoV: A brief perspective from the front line

Qingmei Han et al.

JOURNAL OF INFECTION (2020)

Article Biochemistry & Molecular Biology

Imbalanced Host Response to SARS-CoV-2 Drives Development of COVID-19

Daniel Blanco-Melo et al.

Article Biochemistry & Molecular Biology

Proteomic and Metabolomic Characterization of COVID-19 Patient Sera

Bo Shen et al.

Article Biochemistry & Molecular Biology

An atlas of human metabolism

Jonathan L. Robinson et al.

SCIENCE SIGNALING (2020)

Article Biochemistry & Molecular Biology

NOREVA: enhanced normalization and evaluation of time-course and multi-class metabolomic data

Qingxia Yang et al.

NUCLEIC ACIDS RESEARCH (2020)

Article Biochemical Research Methods

FBA reveals guanylate kinase as a potential target for antiviral therapies against SARS-CoV-2

Alina Renz et al.

BIOINFORMATICS (2020)

Article Multidisciplinary Sciences

Cholesterol 25-hydroxylase suppresses SARS-CoV-2 replication by blocking membrane fusion

Ruochen Zeng et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2020)

Article Endocrinology & Metabolism

HDL-scavenger receptor B type 1 facilitates SARS-CoV-2 entry

Congwen Wei et al.

NATURE METABOLISM (2020)

Review Endocrinology & Metabolism

A metabolic handbook for the COVID-19 pandemic

Janelle S. Ayres

NATURE METABOLISM (2020)

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 Biochemical Research Methods

Increasing consensus of context-specific metabolic models by integrating data-inferred cell functions

Anne Richelle et al.

PLOS COMPUTATIONAL BIOLOGY (2019)

Review Immunology

Hijacking the Supplies: Metabolism as a Novel Facet of Virus-Host Interaction

Katharine A. Mayer et al.

FRONTIERS IN IMMUNOLOGY (2019)

Article Biochemical Research Methods

Jaccard/Tanimoto similarity test and estimation methods for biological presence-absence data

Neo Christopher Chung et al.

BMC BIOINFORMATICS (2019)

Article Multidisciplinary Sciences

SREBP-dependent lipidomic reprogramming as a broad-spectrum antiviral target

Shuofeng Yuan et al.

NATURE COMMUNICATIONS (2019)

Review Biotechnology & Applied Microbiology

Current status and applications of genome-scale metabolic models

Changdai Gu et al.

GENOME BIOLOGY (2019)

Article Mathematical & Computational Biology

Flux sampling is a powerful tool to study metabolism under changing environmental conditions

Helena A. Herrmann et al.

NPJ SYSTEMS BIOLOGY AND APPLICATIONS (2019)

Article Biochemical Research Methods

RAVEN 2.0: A versatile toolbox for metabolic network reconstruction and a case study on Streptomyces coelicolor

Hao Wang et al.

PLOS COMPUTATIONAL BIOLOGY (2018)

Article Biotechnology & Applied Microbiology

Genome scale metabolic modeling of cancer

Avlant Nilsson et al.

METABOLIC ENGINEERING (2017)

Article Biochemistry & Molecular Biology

NOREVA: normalization and evaluation of MS-based metabolomics data

Bo Li et al.

NUCLEIC ACIDS RESEARCH (2017)

Article Biochemistry & Molecular Biology

A Systematic Evaluation of Methods for Tailoring Genome-Scale Metabolic Models

Sjoerd Opdam et al.

CELL SYSTEMS (2017)

Article Biotechnology & Applied Microbiology

Near-optimal probabilistic RNA-seq quantification

Nicolas L. Bray et al.

NATURE BIOTECHNOLOGY (2016)

Review Physiology

Applicatons of Genome-Scale Metabolic Models in Biotechnology and Systems Medicine

Cheng Zhang et al.

FRONTIERS IN PHYSIOLOGY (2016)

Article Biochemistry & Molecular Biology

Metabolic Network Prediction of Drug Side Effects

Itay Shaked et al.

CELL SYSTEMS (2016)

Article Biotechnology & Applied Microbiology

Comparison and Analysis of Objective Functions in Flux Balance Analysis

Carlos Eduardo Garcia Sanchez et al.

BIOTECHNOLOGY PROGRESS (2014)

Article Biochemistry & Molecular Biology

Identification of anticancer drugs for hepatocellular carcinoma through personalized genome-scale metabolic modeling

Rasmus Agren et al.

MOLECULAR SYSTEMS BIOLOGY (2014)

Review Genetics & Heredity

Constraint-based models predict metabolic and associated cellular functions

Aarash Bordbar et al.

NATURE REVIEWS GENETICS (2014)

Article Biochemistry & Molecular Biology

The sequence read archive: explosive growth of sequencing data

Yuichi Kodama et al.

NUCLEIC ACIDS RESEARCH (2012)

Article Biochemical Research Methods

Reconstruction of Genome-Scale Active Metabolic Networks for 69 Human Cell Types and 16 Cancer Types Using INIT

Rasmus Agren et al.

PLOS COMPUTATIONAL BIOLOGY (2012)

Review Physiology

Integration of expression data in genome-scale metabolic network reconstructions

Anna S. Blazier et al.

FRONTIERS IN PHYSIOLOGY (2012)

Article Biochemistry & Molecular Biology

The Sequence Read Archive

Rasko Leinonen et al.

NUCLEIC ACIDS RESEARCH (2011)

Article Biochemical Research Methods

iMAT: an integrative metabolic analysis tool

Hadas Zur et al.

BIOINFORMATICS (2010)

Article Biochemical Research Methods

Computationally efficient flux variability analysis

Steinn Gudmundsson et al.

BMC BIOINFORMATICS (2010)

Article Biochemistry & Molecular Biology

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

Nathan E. Lewis et al.

MOLECULAR SYSTEMS BIOLOGY (2010)

Article Biotechnology & Applied Microbiology

What is flux balance analysis?

Jeffrey D. Orth et al.

NATURE BIOTECHNOLOGY (2010)

Article Biochemical Research Methods

Flux balance analysis of biological systems: applications and challenges

Karthik Raman et al.

BRIEFINGS IN BIOINFORMATICS (2009)

Editorial Material Biochemistry & Molecular Biology

Seeking Membranes: Positive-Strand RNA Virus Replication Complexes

Mark R. Denison

PLOS BIOLOGY (2008)

Article Biochemical Research Methods

Context-specific metabolic networks are consistent with experiments

Scott A. Becker et al.

PLOS COMPUTATIONAL BIOLOGY (2008)

Article Biochemical Research Methods

COPASI- A COmplex PAthway SImulator

Stefan Hoops et al.

BIOINFORMATICS (2006)