当前位置： SCI文献检索 > GENOME BIOLOGY期刊下所有文献 > Current status and applications of genome-scale metabolic models.

Current status and applications of genome-scale metabolic models.

Abstract：

: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.

journal_name

Genome Biol

journal_title

Genome biology

authors

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

doi

10.1186/s13059-019-1730-3

subject

Has Abstract

pub_date

2019-06-13 00:00:00

pages

121

issue

1

eissn

1474-7596

issn

1474-760X

pii

10.1186/s13059-019-1730-3

journal_volume

20

pub_type

杂志文章,评审

相关文献

GENOME BIOLOGY文献大全
  • Molecular archeology of L1 insertions in the human genome.

    abstract：BACKGROUND:As the rough draft of the human genome sequence nears a finished product and other genome-sequencing projects accumulate sequence data exponentially, bioinformatics is emerging as an important tool for studies of transposon biology. In particular, L1 elements exhibit a variety of sequence structures after in...

    journal_title：Genome biology

    pub_type： 杂志文章

    doi：10.1186/gb-2002-3-10-research0052

    authors： Szak ST,Pickeral OK,Makalowski W,Boguski MS,Landsman D,Boeke JD

    更新日期：2002-09-19 00:00:00

  • Mapping-by-sequencing accelerates forward genetics in barley.

    abstract：:Mapping-by-sequencing has emerged as a powerful technique for genetic mapping in several plant and animal species. As this resequencing-based method requires a reference genome, its application to complex plant genomes with incomplete and fragmented sequence resources remains challenging. We perform exome sequencing o...

    journal_title：Genome biology

    pub_type： 杂志文章

    doi：10.1186/gb-2014-15-6-r78

    authors： Mascher M,Jost M,Kuon JE,Himmelbach A,Aßfalg A,Beier S,Scholz U,Graner A,Stein N

    更新日期：2014-06-10 00:00:00

  • The bovine lactation genome: insights into the evolution of mammalian milk.

    abstract：BACKGROUND:The newly assembled Bos taurus genome sequence enables the linkage of bovine milk and lactation data with other mammalian genomes. RESULTS:Using publicly available milk proteome data and mammary expressed sequence tags, 197 milk protein genes and over 6,000 mammary genes were identified in the bovine genome...

    journal_title：Genome biology

    pub_type： 杂志文章

    doi：10.1186/gb-2009-10-4-r43

    authors： Lemay DG,Lynn DJ,Martin WF,Neville MC,Casey TM,Rincon G,Kriventseva EV,Barris WC,Hinrichs AS,Molenaar AJ,Pollard KS,Maqbool NJ,Singh K,Murney R,Zdobnov EM,Tellam RL,Medrano JF,German JB,Rijnkels M

    更新日期：2009-01-01 00:00:00

  • iRegNet3D: three-dimensional integrated regulatory network for the genomic analysis of coding and non-coding disease mutations.

    abstract：:The mechanistic details of most disease-causing mutations remain poorly explored within the context of regulatory networks. We present a high-resolution three-dimensional integrated regulatory network (iRegNet3D) in the form of a web tool, where we resolve the interfaces of all known transcription factor (TF)-TF, TF-D...

    journal_title：Genome biology

    pub_type： 杂志文章

    doi：10.1186/s13059-016-1138-2

    authors： Liang S,Tippens ND,Zhou Y,Mort M,Stenson PD,Cooper DN,Yu H

    更新日期：2017-01-18 00:00:00

  • Decreasing miRNA sequencing bias using a single adapter and circularization approach.

    abstract：:The ability to accurately quantify all the microRNAs (miRNAs) in a sample is important for understanding miRNA biology and for development of new biomarkers and therapeutic targets. We develop a new method for preparing miRNA sequencing libraries, RealSeq®-AC, that involves ligating the miRNAs with a single adapter an...

    journal_title：Genome biology

    pub_type： 杂志文章

    doi：10.1186/s13059-018-1488-z

    authors： Barberán-Soler S,Vo JM,Hogans RE,Dallas A,Johnston BH,Kazakov SA

    更新日期：2018-09-03 00:00:00

  • RNA methylomes reveal the m6A-mediated regulation of DNA demethylase gene SlDML2 in tomato fruit ripening.

    abstract：BACKGROUND:Methylation of nucleotides, notably in the forms of 5-methylcytosine (5mC) in DNA and N6-methyladenosine (m6A) in mRNA, carries important information for gene regulation. 5mC has been elucidated to participate in the regulation of fruit ripening, whereas the function of m6A in this process and the interplay ...

    journal_title：Genome biology

    pub_type： 杂志文章

    doi：10.1186/s13059-019-1771-7

    authors： Zhou L,Tian S,Qin G

    更新日期：2019-08-06 00:00:00

  • Exploiting microarrays to reveal differential gene expression in the nervous system.

    abstract：:Microarrays have been used in a wide variety of experimental systems, but realizing their full potential is contingent on sophisticated and rigorous experimental design and data analysis. This article highlights what is needed to get the most out of microarrays in terms of accurately and effectively revealing differen...

    journal_title：Genome biology

    pub_type： 杂志文章

    doi：10.1186/gb-2003-4-2-105

    authors： Griffin RS,Mills CD,Costigan M,Woolf CJ

    更新日期：2003-01-01 00:00:00

  • Membrane transporters and protein traffic networks differentially affecting metal tolerance: a genomic phenotyping study in yeast.

    abstract：BACKGROUND:The cellular mechanisms that underlie metal toxicity and detoxification are rather variegated and incompletely understood. Genomic phenotyping was used to assess the roles played by all nonessential Saccharomyces cerevisiae proteins in modulating cell viability after exposure to cadmium, nickel, and other me...

    journal_title：Genome biology

    pub_type： 杂志文章

    doi：10.1186/gb-2008-9-4-r67

    authors： Ruotolo R,Marchini G,Ottonello S

    更新日期：2008-04-07 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

    pub_type：

    doi：10.1186/gb4179

    authors： Magnani L

    更新日期：2014-01-01 00:00:00

  • Hemispheric asymmetry in the human brain and in Parkinson's disease is linked to divergent epigenetic patterns in neurons.

    abstract：BACKGROUND:Hemispheric asymmetry in neuronal processes is a fundamental feature of the human brain and drives symptom lateralization in Parkinson's disease (PD), but its molecular determinants are unknown. Here, we identify divergent epigenetic patterns involved in hemispheric asymmetry by profiling DNA methylation in ...

    journal_title：Genome biology

    pub_type： 杂志文章

    doi：10.1186/s13059-020-01960-1

    authors： Li P,Ensink E,Lang S,Marshall L,Schilthuis M,Lamp J,Vega I,Labrie V

    更新日期：2020-03-09 00:00:00

  • The WUS homeobox-containing (WOX) protein family.

    abstract：:The WOX genes form a plant-specific subclade of the eukaryotic homeobox transcription factor superfamily, which is characterized by the presence of a conserved DNA-binding homeodomain. The analysis of WOX gene expression and function shows that WOX family members fulfill specialized functions in key developmental proc...

    journal_title：Genome biology

    pub_type： 杂志文章,评审

    doi：10.1186/gb-2009-10-12-248

    authors： van der Graaff E,Laux T,Rensing SA

    更新日期：2009-01-01 00:00:00

  • Rapid draft sequencing and real-time nanopore sequencing in a hospital outbreak of Salmonella.

    abstract：BACKGROUND:Foodborne outbreaks of Salmonella remain a pressing public health concern. We recently detected a large outbreak of Salmonella enterica serovar Enteritidis phage type 14b affecting more than 30 patients in our hospital. This outbreak was linked to community, national and European-wide cases. Hospital patient...

    journal_title：Genome biology

    pub_type： 杂志文章

    doi：10.1186/s13059-015-0677-2

    authors： Quick J,Ashton P,Calus S,Chatt C,Gossain S,Hawker J,Nair S,Neal K,Nye K,Peters T,De Pinna E,Robinson E,Struthers K,Webber M,Catto A,Dallman TJ,Hawkey P,Loman NJ

    更新日期：2015-05-30 00:00:00

  • Phylogeographic variation in recombination rates within a global clone of methicillin-resistant Staphylococcus aureus.

    abstract：BACKGROUND:Next-generation sequencing (NGS) is a powerful tool for understanding both patterns of descent over time and space (phylogeography) and the molecular processes underpinning genome divergence in pathogenic bacteria. Here, we describe a synthesis between these perspectives by employing a recently developed Bay...

    journal_title：Genome biology

    pub_type： 杂志文章

    doi：10.1186/gb-2012-13-12-r126

    authors： Castillo-Ramírez S,Corander J,Marttinen P,Aldeljawi M,Hanage WP,Westh H,Boye K,Gulay Z,Bentley SD,Parkhill J,Holden MT,Feil EJ

    更新日期：2012-12-27 00:00:00

  • Investigating enhancer evolution with massively parallel reporter assays.

    abstract：:A recent study in Genome Biology has characterized the evolution of candidate hominoid-specific liver enhancers by using massively parallel reporter assays (MPRAs). ...

    journal_title：Genome biology

    pub_type： 杂志文章

    doi：10.1186/s13059-018-1502-5

    authors： Kwon SB,Ernst J

    更新日期：2018-08-14 00:00:00

  • Genomic parasites and genome evolution.

    abstract：:A report of the Second International Conference/Workshop on the Genomic Impact of Eukaryotic Transposable Elements, Pacific Grove, USA, 6-10 February 2009. ...

    journal_title：Genome biology

    pub_type：

    doi：10.1186/gb-2009-10-4-306

    authors： Ivics Z

    更新日期：2009-01-01 00:00:00

  • A basis for a visual language for describing, archiving and analyzing functional models of complex biological systems.

    abstract：BACKGROUND:We propose that a computerized, internet-based graphical description language for systems biology will be essential for describing, archiving and analyzing complex problems of biological function in health and disease. RESULTS:We outline here a conceptual basis for designing such a language and describe Bio...

    journal_title：Genome biology

    pub_type： 杂志文章

    doi：10.1186/gb-2001-2-4-research0012

    authors： Cook DL,Farley JF,Tapscott SJ

    更新日期：2001-01-01 00:00:00

  • Inhibition of RNA polymerase II allows controlled mobilisation of retrotransposons for plant breeding.

    abstract：BACKGROUND:Retrotransposons play a central role in plant evolution and could be a powerful endogenous source of genetic and epigenetic variability for crop breeding. To ensure genome integrity several silencing mechanisms have evolved to repress retrotransposon mobility. Even though retrotransposons fully depend on tra...

    journal_title：Genome biology

    pub_type： 杂志文章

    doi：10.1186/s13059-017-1265-4

    authors： Thieme M,Lanciano S,Balzergue S,Daccord N,Mirouze M,Bucher E

    更新日期：2017-07-07 00:00:00

  • Normalization of boutique two-color microarrays with a high proportion of differentially expressed probes.

    abstract：:Normalization is critical for removing systematic variation from microarray data. For two-color microarray platforms, intensity-dependent lowess normalization is commonly used to correct relative gene expression values for biases. Here we outline a normalization method for use when the assumptions of lowess normalizat...

    journal_title：Genome biology

    pub_type： 杂志文章

    doi：10.1186/gb-2007-8-1-r2

    authors： Oshlack A,Emslie D,Corcoran LM,Smyth GK

    更新日期：2007-01-01 00:00:00

  • VlincRNAs controlled by retroviral elements are a hallmark of pluripotency and cancer.

    abstract：BACKGROUND:The function of the non-coding portion of the human genome remains one of the most important questions of our time. Its vast complexity is exemplified by the recent identification of an unusual and notable component of the transcriptome - very long intergenic non-coding RNAs, termed vlincRNAs. RESULTS:Here ...

    journal_title：Genome biology

    pub_type： 杂志文章

    doi：10.1186/gb-2013-14-7-r73

    authors： St Laurent G,Shtokalo D,Dong B,Tackett MR,Fan X,Lazorthes S,Nicolas E,Sang N,Triche TJ,McCaffrey TA,Xiao W,Kapranov P

    更新日期：2013-07-22 00:00:00

  • Conserved rules govern genetic interaction degree across species.

    abstract：BACKGROUND:Synthetic genetic interactions have recently been mapped on a genome scale in the budding yeast Saccharomyces cerevisiae, providing a functional view of the central processes of eukaryotic life. Currently, comprehensive genetic interaction networks have not been determined for other species, and we therefore...

    journal_title：Genome biology

    pub_type： 杂志文章

    doi：10.1186/gb-2012-13-7-r57

    authors： Koch EN,Costanzo M,Bellay J,Deshpande R,Chatfield-Reed K,Chua G,D'Urso G,Andrews BJ,Boone C,Myers CL

    更新日期：2012-07-02 00:00:00

  • Protein-protein interactions of the hyperthermophilic archaeon Pyrococcus horikoshii OT3.

    abstract：BACKGROUND:Although 2,061 proteins of Pyrococcus horikoshii OT3, a hyperthermophilic archaeon, have been predicted from the recently completed genome sequence, the majority of proteins show no similarity to those from other organisms and are thus hypothetical proteins of unknown function. Because most proteins operate ...

    journal_title：Genome biology

    pub_type： 杂志文章

    doi：10.1186/gb-2005-6-12-r98

    authors： Usui K,Katayama S,Kanamori-Katayama M,Ogawa C,Kai C,Okada M,Kawai J,Arakawa T,Carninci P,Itoh M,Takio K,Miyano M,Kidoaki S,Matsuda T,Hayashizaki Y,Suzuki H

    更新日期：2005-01-01 00:00:00

  • Reduced intrinsic DNA curvature leads to increased mutation rate.

    abstract：BACKGROUND:Mutation rates vary across the genome. Many trans factors that influence mutation rates have been identified, as have specific sequence motifs at the 1-7-bp scale, but cis elements remain poorly characterized. The lack of understanding regarding why different sequences have different mutation rates hampers o...

    journal_title：Genome biology

    pub_type： 杂志文章

    doi：10.1186/s13059-018-1525-y

    authors： Duan C,Huan Q,Chen X,Wu S,Carey LB,He X,Qian W

    更新日期：2018-09-14 00:00:00

  • Wheat rusts never sleep but neither do sequencers: will pathogenomics transform the way plant diseases are managed?

    abstract：:Field pathogenomics adds highly informative data to surveillance surveys by enabling rapid evaluation of pathogen variability, population structure and host genotype. ...

    journal_title：Genome biology

    pub_type： 杂志文章

    doi：10.1186/s13059-015-0615-3

    authors： Derevnina L,Michelmore RW

    更新日期：2015-03-02 00:00:00

  • OnTAD: hierarchical domain structure reveals the divergence of activity among TADs and boundaries.

    abstract：:The spatial organization of chromatin in the nucleus has been implicated in regulating gene expression. Maps of high-frequency interactions between different segments of chromatin have revealed topologically associating domains (TADs), within which most of the regulatory interactions are thought to occur. TADs are not...

    journal_title：Genome biology

    pub_type： 杂志文章

    doi：10.1186/s13059-019-1893-y

    authors： An L,Yang T,Yang J,Nuebler J,Xiang G,Hardison RC,Li Q,Zhang Y

    更新日期：2019-12-18 00:00:00

  • Deep sequencing reveals cell-type-specific patterns of single-cell transcriptome variation.

    abstract：BACKGROUND:Differentiation of metazoan cells requires execution of different gene expression programs but recent single-cell transcriptome profiling has revealed considerable variation within cells of seeming identical phenotype. This brings into question the relationship between transcriptome states and cell phenotype...

    journal_title：Genome biology

    pub_type： 杂志文章

    doi：10.1186/s13059-015-0683-4

    authors： Dueck H,Khaladkar M,Kim TK,Spaethling JM,Francis C,Suresh S,Fisher SA,Seale P,Beck SG,Bartfai T,Kuhn B,Eberwine J,Kim J

    更新日期：2015-06-09 00:00:00

  • Response to "Variable directionality of gene expression changes across generations does not constitute negative evidence of epigenetic inheritance" Sharma, A. Environmental Epigenetics, 2015, 1-5.

    abstract：:Abhay Sharma brings two arguments in favor of transgenerational epigenetic inheritance (TGEI) in mammals when criticizing our work. He uses probability calculations and finds that the probability of obtaining the number of common changes in the in utero-exposed prospermatogonia and the same cells in the next generatio...

    journal_title：Genome biology

    pub_type： 评论,信件

    doi：10.1186/s13059-016-0978-0

    authors： Szabó PE

    更新日期：2016-05-16 00:00:00

  • Divergence in cis-regulatory networks: taking the 'species' out of cross-species analysis.

    abstract：:Many essential transcription factors have conserved roles in regulating biological programs, yet their genomic occupancy can diverge significantly. A new study demonstrates that such variations are primarily due to cis-regulatory sequences, rather than differences between the regulators or nuclear environments. ...

    journal_title：Genome biology

    pub_type： 杂志文章,评审

    doi：10.1186/gb-2008-9-11-240

    authors： Zinzen RP,Furlong EE

    更新日期：2008-01-01 00:00:00

  • Constitutive patterns of gene expression regulated by RNA-binding proteins.

    abstract：BACKGROUND:RNA-binding proteins regulate a number of cellular processes, including synthesis, folding, translocation, assembly and clearance of RNAs. Recent studies have reported that an unexpectedly large number of proteins are able to interact with RNA, but the partners of many RNA-binding proteins are still uncharac...

    journal_title：Genome biology

    pub_type： 杂志文章

    doi：10.1186/gb-2014-15-1-r13

    authors： Cirillo D,Marchese D,Agostini F,Livi CM,Botta-Orfila T,Tartaglia GG

    更新日期：2014-01-02 00:00:00

  • The rhomboid protease family: a decade of progress on function and mechanism.

    abstract：:Rhomboid proteases are the largest family of enzymes that hydrolyze peptide bonds within the cell membrane. Although discovered to be serine proteases only a decade ago, rhomboid proteases are already considered to be the best understood intramembrane proteases. The presence of rhomboid proteins in all domains of life...

    journal_title：Genome biology

    pub_type： 杂志文章,评审

    doi：10.1186/gb-2011-12-10-231

    authors： Urban S,Dickey SW

    更新日期：2011-10-27 00:00:00

  • Games with a scientific purpose.

    abstract：:The protein folding game Foldit shows that games are an effective way to recruit, engage and organize ordinary citizens to help solve difficult scientific problems. ...

    journal_title：Genome biology

    pub_type： 杂志文章

    doi：10.1186/gb-2011-12-12-135

    authors： Good BM,Su AI

    更新日期：2011-12-28 00:00:00