Current status and applications of genome-scale metabolic models.


:Genome-scale metabolic models (GEMs) computationally describe gene-protein-reaction associations for entire metabolic genes in an organism, and can be simulated to predict metabolic fluxes for various systems-level metabolic studies. Since the first GEM for Haemophilus influenzae was reported in 1999, advances have been made to develop and simulate GEMs for an increasing number of organisms across bacteria, archaea, and eukarya. Here, we review current reconstructed GEMs and discuss their applications, including strain development for chemicals and materials production, drug targeting in pathogens, prediction of enzyme functions, pan-reactome analysis, modeling interactions among multiple cells or organisms, and understanding human diseases.


Genome Biol


Genome biology


Gu C,Kim GB,Kim WJ,Kim HU,Lee SY




Has Abstract


2019-06-13 00:00:00














  • Transcriptional profiling of long non-coding RNAs and novel transcribed regions across a diverse panel of archived human cancers.

    abstract:BACKGROUND:Molecular characterization of tumors has been critical for identifying important genes in cancer biology and for improving tumor classification and diagnosis. Long non-coding RNAs, as a new, relatively unstudied class of transcripts, provide a rich opportunity to identify both functional drivers and cancer-t...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Brunner AL,Beck AH,Edris B,Sweeney RT,Zhu SX,Li R,Montgomery K,Varma S,Gilks T,Guo X,Foley JW,Witten DM,Giacomini CP,Flynn RA,Pollack JR,Tibshirani R,Chang HY,van de Rijn M,West RB

    更新日期:2012-08-28 00:00:00

  • ELXR: a resource for rapid exon-directed sequence analysis.

    abstract::ELXR (Exon Locator and Extractor for Resequencing) streamlines the process of determining exon/intron boundaries and designing PCR and sequencing primers for high-throughput resequencing of exons. We have pre-computed ELXR primer sets for all exons identified from the human, mouse, and rat mRNA reference sequence (Ref...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Schageman JJ,Horton CJ,Niu S,Garner HR,Pertsemlidis A

    更新日期:2004-01-01 00:00:00

  • Comprehensive assessment of computational algorithms in predicting cancer driver mutations.

    abstract:BACKGROUND:The initiation and subsequent evolution of cancer are largely driven by a relatively small number of somatic mutations with critical functional impacts, so-called driver mutations. Identifying driver mutations in a patient's tumor cells is a central task in the era of precision cancer medicine. Over the deca...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Chen H,Li J,Wang Y,Ng PK,Tsang YH,Shaw KR,Mills GB,Liang H

    更新日期:2020-02-20 00:00:00

  • Interrogation of global mutagenesis data with a genome scale model of Neisseria meningitidis to assess gene fitness in vitro and in sera.

    abstract:BACKGROUND:Neisseria meningitidis is an important human commensal and pathogen that causes several thousand deaths each year, mostly in young children. How the pathogen replicates and causes disease in the host is largely unknown, particularly the role of metabolism in colonization and disease. Completed genome sequenc...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Mendum TA,Newcombe J,Mannan AA,Kierzek AM,McFadden J

    更新日期:2011-12-30 00:00:00

  • quantro: a data-driven approach to guide the choice of an appropriate normalization method.

    abstract::Normalization is an essential step in the analysis of high-throughput data. Multi-sample global normalization methods, such as quantile normalization, have been successfully used to remove technical variation. However, these methods rely on the assumption that observed global changes across samples are due to unwanted...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Hicks SC,Irizarry RA

    更新日期:2015-06-04 00:00:00

  • A fuzzy gene expression-based computational approach improves breast cancer prognostication.

    abstract::Early gene expression studies classified breast tumors into at least three clinically relevant subtypes. Although most current gene signatures are prognostic for estrogen receptor (ER) positive/human epidermal growth factor receptor 2 (HER2) negative breast cancers, few are informative for ER negative/HER2 negative an...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Haibe-Kains B,Desmedt C,Rothé F,Piccart M,Sotiriou C,Bontempi G

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  • Wheat functional genomics and engineering crop improvement.

    abstract::Genetic mapping and determination of the organization of the wheat genome are changing the wheat-breeding process. New initiatives to analyze the expressed portion of the wheat genome and structural analysis of the genomes of Arabidopsis and rice are increasing our knowledge of the genes that are linked to key agronom...

    journal_title:Genome biology

    pub_type: 杂志文章,评审


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    更新日期:2002-01-01 00:00:00

  • SCALE: modeling allele-specific gene expression by single-cell RNA sequencing.

    abstract::Allele-specific expression is traditionally studied by bulk RNA sequencing, which measures average expression across cells. Single-cell RNA sequencing allows the comparison of expression distribution between the two alleles of a diploid organism and the characterization of allele-specific bursting. Here, we propose SC...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Jiang Y,Zhang NR,Li M

    更新日期:2017-04-26 00:00:00

  • Multi-tissue coexpression networks reveal unexpected subnetworks associated with disease.

    abstract:BACKGROUND:Obesity is a particularly complex disease that at least partially involves genetic and environmental perturbations to gene-networks connecting the hypothalamus and several metabolic tissues, resulting in an energy imbalance at the systems level. RESULTS:To provide an inter-tissue view of obesity with respec...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Dobrin R,Zhu J,Molony C,Argman C,Parrish ML,Carlson S,Allan MF,Pomp D,Schadt EE

    更新日期:2009-01-01 00:00:00

  • A compendium of Caenorhabditis elegans regulatory transcription factors: a resource for mapping transcription regulatory networks.

    abstract:BACKGROUND:Transcription regulatory networks are composed of interactions between transcription factors and their target genes. Whereas unicellular networks have been studied extensively, metazoan transcription regulatory networks remain largely unexplored. Caenorhabditis elegans provides a powerful model to study such...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Reece-Hoyes JS,Deplancke B,Shingles J,Grove CA,Hope IA,Walhout AJ

    更新日期:2005-01-01 00:00:00

  • Sirtuins: Sir2-related NAD-dependent protein deacetylases.

    abstract::Silent information regulator 2 (Sir2) proteins, or sirtuins, are protein deacetylases dependent on nicotine adenine dinucleotide (NAD) and are found in organisms ranging from bacteria to humans. In eukaryotes, sirtuins regulate transcriptional repression, recombination, the cell-division cycle, microtubule organizatio...

    journal_title:Genome biology

    pub_type: 杂志文章,评审


    authors: North BJ,Verdin E

    更新日期:2004-01-01 00:00:00

  • The R-spondin protein family.

    abstract::The four vertebrate R-spondin proteins are secreted agonists of the canonical Wnt/β-catenin signaling pathway. These proteins are approximately 35 kDa, and are characterized by two amino-terminal furin-like repeats, which are necessary and sufficient for Wnt signal potentiation, and a thrombospondin domain situated mo...

    journal_title:Genome biology

    pub_type: 杂志文章,评审


    authors: de Lau WB,Snel B,Clevers HC

    更新日期:2012-01-01 00:00:00

  • Genetic subtraction profiling identifies genes essential for Arabidopsis reproduction and reveals interaction between the female gametophyte and the maternal sporophyte.

    abstract:BACKGROUND:The embryo sac contains the haploid maternal cell types necessary for double fertilization and subsequent seed development in plants. Large-scale identification of genes expressed in the embryo sac remains cumbersome because of its inherent microscopic and inaccessible nature. We used genetic subtraction and...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Johnston AJ,Meier P,Gheyselinck J,Wuest SE,Federer M,Schlagenhauf E,Becker JD,Grossniklaus U

    更新日期:2007-01-01 00:00:00

  • External signals shape the epigenome.

    abstract::A new study shows how a single cytokine, interleukin-4, regulates hematopoietic lineage choice by activating the JAK3-STAT6 pathway, which causes dendritic-cell-specific DNA demethylation. ...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Lennartsson A

    更新日期:2016-02-01 00:00:00

  • A simple strategy for heritable chromosomal deletions in zebrafish via the combinatorial action of targeting nucleases.

    abstract::Precise and effective genome-editing tools are essential for functional genomics and gene therapy. Targeting nucleases have been successfully used to edit genomes. However, whole-locus or element-specific deletions abolishing transcript expression have not previously been reported. Here, we show heritable targeting of...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Lim S,Wang Y,Yu X,Huang Y,Featherstone MS,Sampath K

    更新日期:2013-07-01 00:00:00

  • Escape from X inactivation in mice and humans.

    abstract::A subset of X-linked genes escapes silencing by X inactivation and is expressed from both X chromosomes in mammalian females. Species-specific differences in the identity of these genes have recently been discovered, suggesting a role in the evolution of sex differences. Chromatin analyses have aimed to discover how g...

    journal_title:Genome biology

    pub_type: 杂志文章,评审


    authors: Berletch JB,Yang F,Disteche CM

    更新日期:2010-01-01 00:00:00

  • Functional analysis of transcription factor binding sites in human promoters.

    abstract:BACKGROUND:The binding of transcription factors to specific locations in the genome is integral to the orchestration of transcriptional regulation in cells. To characterize transcription factor binding site function on a large scale, we predicted and mutagenized 455 binding sites in human promoters. We carried out func...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Whitfield TW,Wang J,Collins PJ,Partridge EC,Aldred SF,Trinklein ND,Myers RM,Weng Z

    更新日期:2012-09-26 00:00:00

  • Influence of metabolic network structure and function on enzyme evolution.

    abstract:BACKGROUND:Most studies of molecular evolution are focused on individual genes and proteins. However, understanding the design principles and evolutionary properties of molecular networks requires a system-wide perspective. In the present work we connect molecular evolution on the gene level with system properties of a...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Vitkup D,Kharchenko P,Wagner A

    更新日期:2006-01-01 00:00:00

  • Genotyping structural variants in pangenome graphs using the vg toolkit.

    abstract::Structural variants (SVs) remain challenging to represent and study relative to point mutations despite their demonstrated importance. We show that variation graphs, as implemented in the vg toolkit, provide an effective means for leveraging SV catalogs for short-read SV genotyping experiments. We benchmark vg against...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Hickey G,Heller D,Monlong J,Sibbesen JA,Sirén J,Eizenga J,Dawson ET,Garrison E,Novak AM,Paten B

    更新日期:2020-02-12 00:00:00

  • Capture Hi-C identifies a novel causal gene, IL20RA, in the pan-autoimmune genetic susceptibility region 6q23.

    abstract:BACKGROUND:The identification of causal genes from genome-wide association studies (GWAS) is the next important step for the translation of genetic findings into biologically meaningful mechanisms of disease and potential therapeutic targets. Using novel chromatin interaction detection techniques and allele specific as...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: McGovern A,Schoenfelder S,Martin P,Massey J,Duffus K,Plant D,Yarwood A,Pratt AG,Anderson AE,Isaacs JD,Diboll J,Thalayasingam N,Ospelt C,Barton A,Worthington J,Fraser P,Eyre S,Orozco G

    更新日期:2016-11-01 00:00:00

  • Epigenetic engineering and the art of epigenetic manipulation.

    abstract::A report on the Epigenetic Engineering Meeting hosted by the Barts Institute of Cancer, held in London, UK, May 7, 2014. ...

    journal_title:Genome biology



    authors: Magnani L

    更新日期:2014-01-01 00:00:00

  • An amplicon-based sequencing framework for accurately measuring intrahost virus diversity using PrimalSeq and iVar.

    abstract::How viruses evolve within hosts can dictate infection outcomes; however, reconstructing this process is challenging. We evaluate our multiplexed amplicon approach, PrimalSeq, to demonstrate how virus concentration, sequencing coverage, primer mismatches, and replicates influence the accuracy of measuring intrahost vir...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Grubaugh ND,Gangavarapu K,Quick J,Matteson NL,De Jesus JG,Main BJ,Tan AL,Paul LM,Brackney DE,Grewal S,Gurfield N,Van Rompay KKA,Isern S,Michael SF,Coffey LL,Loman NJ,Andersen KG

    更新日期:2019-01-08 00:00:00

  • Comparative genomics of gene-family size in closely related bacteria.

    abstract:BACKGROUND:The wealth of genomic data in bacteria is helping microbiologists understand the factors involved in gene innovation. Among these, the expansion and reduction of gene families appears to have a fundamental role in this, but the factors influencing gene family size are unclear. RESULTS:The relative content o...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Pushker R,Mira A,Rodríguez-Valera F

    更新日期:2004-01-01 00:00:00

  • A human functional protein interaction network and its application to cancer data analysis.

    abstract:BACKGROUND:One challenge facing biologists is to tease out useful information from massive data sets for further analysis. A pathway-based analysis may shed light by projecting candidate genes onto protein functional relationship networks. We are building such a pathway-based analysis system. RESULTS:We have construct...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Wu G,Feng X,Stein L

    更新日期:2010-01-01 00:00:00

  • Mining physical protein-protein interactions from the literature.

    abstract:BACKGROUND:Deciphering physical protein-protein interactions is fundamental to elucidating both the functions of proteins and biological processes. The development of high-throughput experimental technologies such as the yeast two-hybrid screening has produced an explosion in data relating to interactions. Since manual...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Huang M,Ding S,Wang H,Zhu X

    更新日期:2008-01-01 00:00:00

  • RASTA-Bacteria: a web-based tool for identifying toxin-antitoxin loci in prokaryotes.

    abstract::Toxin/antitoxin (TA) systems, viewed as essential regulators of growth arrest and programmed cell death, are widespread among prokaryotes, but remain sparsely annotated. We present RASTA-Bacteria, an automated method allowing quick and reliable identification of TA loci in sequenced prokaryotic genomes, whether they a...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Sevin EW,Barloy-Hubler F

    更新日期:2007-01-01 00:00:00

  • Preferential binding of HIF-1 to transcriptionally active loci determines cell-type specific response to hypoxia.

    abstract:BACKGROUND:Hypoxia-inducible factor 1 (HIF-1) plays a key role in cellular adaptation to hypoxia. To better understand the determinants of HIF-1 binding and transactivation, we used ChIP-chip and gene expression profiling to define the relationship between the epigenetic landscape, sites of HIF-1 binding, and genes tra...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Xia X,Kung AL

    更新日期:2009-01-01 00:00:00

  • Discovery and functional prioritization of Parkinson's disease candidate genes from large-scale whole exome sequencing.

    abstract:BACKGROUND:Whole-exome sequencing (WES) has been successful in identifying genes that cause familial Parkinson's disease (PD). However, until now this approach has not been deployed to study large cohorts of unrelated participants. To discover rare PD susceptibility variants, we performed WES in 1148 unrelated cases an...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Jansen IE,Ye H,Heetveld S,Lechler MC,Michels H,Seinstra RI,Lubbe SJ,Drouet V,Lesage S,Majounie E,Gibbs JR,Nalls MA,Ryten M,Botia JA,Vandrovcova J,Simon-Sanchez J,Castillo-Lizardo M,Rizzu P,Blauwendraat C,Chouhan AK

    更新日期:2017-01-30 00:00:00

  • bin3C: exploiting Hi-C sequencing data to accurately resolve metagenome-assembled genomes.

    abstract::Most microbes cannot be easily cultured, and metagenomics provides a means to study them. Current techniques aim to resolve individual genomes from metagenomes, so-called metagenome-assembled genomes (MAGs). Leading approaches depend upon time series or transect studies, the efficacy of which is a function of communit...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: DeMaere MZ,Darling AE

    更新日期:2019-02-26 00:00:00

  • Roles of piRNAs in transposon and pseudogene regulation of germline mRNAs and lncRNAs.

    abstract::PIWI proteins, a subfamily of PAZ/PIWI Domain family RNA-binding proteins, are best known for their function in silencing transposons and germline development by partnering with small noncoding RNAs called PIWI-interacting RNAs (piRNAs). However, recent studies have revealed multifaceted roles of the PIWI-piRNA pathwa...

    journal_title:Genome biology

    pub_type: 杂志文章,评审


    authors: Wang C,Lin H

    更新日期:2021-01-08 00:00:00