Dynamic systems.

Abstract:

:A report of the Wellcome Trust Functional Genomics and Systems Biology Conference, Hinxton, UK, 29 November to 1 December 2011.

journal_name

Genome Biol

journal_title

Genome biology

authors

Bakal C

doi

10.1186/gb-2012-13-1-312

subject

Has Abstract

pub_date

2012-01-30 00:00:00

pages

312

issue

1

eissn

1474-7596

issn

1474-760X

pii

gb-2012-13-1-312

journal_volume

13

pub_type

  • Modular organization in the reductive evolution of protein-protein interaction networks.

    abstract:BACKGROUND:The variation in the sizes of the genomes of distinct life forms remains somewhat puzzling. The organization of proteins into domains and the different mechanisms that regulate gene expression are two factors that potentially increase the capacity of genomes to create more complex systems. High-throughput pr...

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    authors: Tamames J,Moya A,Valencia A

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  • Chromatin Central: towards the comparative proteome by accurate mapping of the yeast proteomic environment.

    abstract:BACKGROUND:Understanding the design logic of living systems requires the understanding and comparison of proteomes. Proteomes define the commonalities between organisms more precisely than genomic sequences. Because uncertainties remain regarding the accuracy of proteomic data, several issues need to be resolved before...

    journal_title:Genome biology

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    doi:10.1186/gb-2008-9-11-r167

    authors: Shevchenko A,Roguev A,Schaft D,Buchanan L,Habermann B,Sakalar C,Thomas H,Krogan NJ,Shevchenko A,Stewart AF

    更新日期:2008-01-01 00:00:00

  • Going beyond genetics to discover cancer targets.

    abstract::Two recent studies demonstrate the power of integrating tumor genotype information with epigenetic and proteomic studies to discover potential therapeutic targets in breast cancer. ...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/s13059-017-1238-7

    authors: Sandoval GJ,Hahn WC

    更新日期:2017-05-22 00:00:00

  • Impact of transposable elements on genome structure and evolution in bread wheat.

    abstract:BACKGROUND:Transposable elements (TEs) are major components of large plant genomes and main drivers of genome evolution. The most recent assembly of hexaploid bread wheat recovered the highly repetitive TE space in an almost complete chromosomal context and enabled a detailed view into the dynamics of TEs in the A, B, ...

    journal_title:Genome biology

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    doi:10.1186/s13059-018-1479-0

    authors: Wicker T,Gundlach H,Spannagl M,Uauy C,Borrill P,Ramírez-González RH,De Oliveira R,International Wheat Genome Sequencing Consortium.,Mayer KFX,Paux E,Choulet F

    更新日期:2018-08-17 00:00:00

  • Multiclass classification of microarray data with repeated measurements: application to cancer.

    abstract::Prediction of the diagnostic category of a tissue sample from its gene-expression profile and selection of relevant genes for class prediction have important applications in cancer research. We have developed the uncorrelated shrunken centroid (USC) and error-weighted, uncorrelated shrunken centroid (EWUSC) algorithms...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/gb-2003-4-12-r83

    authors: Yeung KY,Bumgarner RE

    更新日期:2003-01-01 00:00:00

  • Evolution enters the genomic era.

    abstract::A report on the 18th Congress of the European Society for Evolutionary Biology (ESEB), Aarhus, Denmark, 20-25 August, 2001. ...

    journal_title:Genome biology

    pub_type:

    doi:10.1186/gb-2001-2-11-reports4026

    authors: Liberles DA

    更新日期:2001-01-01 00:00:00

  • All Your Base: a fast and accurate probabilistic approach to base calling.

    abstract::The accuracy of base calls produced by Illumina sequencers is adversely affected by several processes, with laser cross-talk and cluster phasing being prominent. We introduce an explicit statistical model of the sequencing process that generalizes current models of phasing and cross-talk and forms the basis of a base ...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/gb-2012-13-2-r13

    authors: Massingham T,Goldman N

    更新日期:2012-02-29 00:00:00

  • Visualization of pseudogenes in intracellular bacteria reveals the different tracks to gene destruction.

    abstract:BACKGROUND:Pseudogenes reveal ancestral gene functions. Some obligate intracellular bacteria, such as Mycobacterium leprae and Rickettsia spp., carry substantial fractions of pseudogenes. Until recently, horizontal gene transfers were considered to be rare events in obligate host-associated bacteria. RESULTS:We presen...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/gb-2008-9-2-r42

    authors: Fuxelius HH,Darby AC,Cho NH,Andersson SG

    更新日期:2008-01-01 00:00:00

  • Age and sun exposure-related widespread genomic blocks of hypomethylation in nonmalignant skin.

    abstract:BACKGROUND:Aging and sun exposure are the leading causes of skin cancer. It has been shown that epigenetic changes, such as DNA methylation, are well established mechanisms for cancer, and also have emerging roles in aging and common disease. Here, we directly ask whether DNA methylation is altered following skin aging...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/s13059-015-0644-y

    authors: Vandiver AR,Irizarry RA,Hansen KD,Garza LA,Runarsson A,Li X,Chien AL,Wang TS,Leung SG,Kang S,Feinberg AP

    更新日期:2015-04-16 00:00:00

  • Retrozymes are a unique family of non-autonomous retrotransposons with hammerhead ribozymes that propagate in plants through circular RNAs.

    abstract:BACKGROUND:Catalytic RNAs, or ribozymes, are regarded as fossils of a prebiotic RNA world that have remained in the genomes of modern organisms. The simplest ribozymes are the small self-cleaving RNAs, like the hammerhead ribozyme, which have been historically considered biological oddities restricted to some RNA patho...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/s13059-016-1002-4

    authors: Cervera A,Urbina D,de la Peña M

    更新日期:2016-06-23 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

  • A comparison of automatic cell identification methods for single-cell RNA sequencing data.

    abstract:BACKGROUND:Single-cell transcriptomics is rapidly advancing our understanding of the cellular composition of complex tissues and organisms. A major limitation in most analysis pipelines is the reliance on manual annotations to determine cell identities, which are time-consuming and irreproducible. The exponential growt...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/s13059-019-1795-z

    authors: Abdelaal T,Michielsen L,Cats D,Hoogduin D,Mei H,Reinders MJT,Mahfouz A

    更新日期:2019-09-09 00:00:00

  • Whole-genome screening indicates a possible burst of formation of processed pseudogenes and Alu repeats by particular L1 subfamilies in ancestral primates.

    abstract:BACKGROUND:Abundant pseudogenes are a feature of mammalian genomes. Processed pseudogenes (PPs) are reverse transcribed from mRNAs. Recent molecular biological studies show that mammalian long interspersed element 1 (L1)-encoded proteins may have been involved in PP reverse transcription. Here, we present the first com...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/gb-2003-4-11-r74

    authors: Ohshima K,Hattori M,Yada T,Gojobori T,Sakaki Y,Okada N

    更新日期:2003-01-01 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

  • 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

  • DeconstructSigs: delineating mutational processes in single tumors distinguishes DNA repair deficiencies and patterns of carcinoma evolution.

    abstract:BACKGROUND:Analysis of somatic mutations provides insight into the mutational processes that have shaped the cancer genome, but such analysis currently requires large cohorts. We develop deconstructSigs, which allows the identification of mutational signatures within a single tumor sample. RESULTS:Application of decon...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/s13059-016-0893-4

    authors: Rosenthal R,McGranahan N,Herrero J,Taylor BS,Swanton C

    更新日期:2016-02-22 00:00:00

  • Detection and analysis of alternative splicing in Yarrowia lipolytica reveal structural constraints facilitating nonsense-mediated decay of intron-retaining transcripts.

    abstract:BACKGROUND:Hemiascomycetous yeasts have intron-poor genomes with very few cases of alternative splicing. Most of the reported examples result from intron retention in Saccharomyces cerevisiae and some have been shown to be functionally significant. Here we used transcriptome-wide approaches to evaluate the mechanisms u...

    journal_title:Genome biology

    pub_type: 杂志文章

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    authors: Mekouar M,Blanc-Lenfle I,Ozanne C,Da Silva C,Cruaud C,Wincker P,Gaillardin C,Neuvéglise C

    更新日期:2010-01-01 00:00:00

  • Gene editing of the multi-copy H2A.B gene and its importance for fertility.

    abstract:BACKGROUND:Altering the biochemical makeup of chromatin by the incorporation of histone variants during development represents a key mechanism in regulating gene expression. The histone variant H2A.B, H2A.B.3 in mice, appeared late in evolution and is most highly expressed in the testis. In the mouse, it is encoded by ...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/s13059-019-1633-3

    authors: Anuar ND,Kurscheid S,Field M,Zhang L,Rebar E,Gregory P,Buchou T,Bowles J,Koopman P,Tremethick DJ,Soboleva TA

    更新日期:2019-01-31 00:00:00

  • High-resolution genomic analysis: the tumor-immune interface comes into focus.

    abstract::A genomic analysis of heterogeneous colorectal tumor samples has uncovered interactions between immunophenotype and various aspects of tumor biology, with implications for informing the choice of immunotherapies for specific patients and guiding the design of personalized neoantigen-based vaccines. ...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/s13059-015-0631-3

    authors: Havel JJ,Chan TA

    更新日期:2015-03-31 00:00:00

  • Zinc finger nuclease-based double-strand breaks attenuate malaria parasites and reveal rare microhomology-mediated end joining.

    abstract:BACKGROUND:Genome editing of malaria parasites is key to the generation of live attenuated parasites used in experimental vaccination approaches. DNA repair in Plasmodium generally occurs only through homologous recombination. This has been used to generate transgenic parasites that lack one to three genes, leading to ...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/s13059-015-0811-1

    authors: Singer M,Marshall J,Heiss K,Mair GR,Grimm D,Mueller AK,Frischknecht F

    更新日期:2015-11-17 00:00:00

  • Molecular mechanisms of spindle function.

    abstract::The key molecules involved in regulating the assembly and function of the mitotic spindle are shared by evolutionarily divergent species. Studies in different model systems are leading to convergent conclusions about the central role of microtubule nucleation and dynamics and of kinesin-related motor proteins in spind...

    journal_title:Genome biology

    pub_type: 杂志文章,评审

    doi:10.1186/gb-2000-1-1-reviews101

    authors: Walczak CE

    更新日期:2000-01-01 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

    doi:10.1186/gb-2009-10-5-r55

    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

  • Assembling allopolyploid genomes: no longer formidable.

    abstract::A combined approach of whole genome shotgun sequencing and ultra-high density linkage mapping using skim sequencing of a segregating population is effective for assembling allopolyploid genomes. ...

    journal_title:Genome biology

    pub_type: 信件

    doi:10.1186/s13059-015-0585-5

    authors: Ming R,Man Wai C

    更新日期:2015-01-31 00:00:00

  • Large-scale assignment of orthology: back to phylogenetics?

    abstract::Reliable orthology prediction is central to comparative genomics. Although orthology is defined by phylogenetic criteria, most automated prediction methods are based on pairwise sequence comparisons. Recently, automated phylogeny-based orthology prediction has emerged as a feasible alternative for genome-wide studies....

    journal_title:Genome biology

    pub_type: 杂志文章,评审

    doi:10.1186/gb-2008-9-10-235

    authors: Gabaldón T

    更新日期:2008-10-30 00:00:00

  • Exome-chip meta-analysis identifies novel loci associated with cardiac conduction, including ADAMTS6.

    abstract:BACKGROUND:Genome-wide association studies conducted on QRS duration, an electrocardiographic measurement associated with heart failure and sudden cardiac death, have led to novel biological insights into cardiac function. However, the variants identified fall predominantly in non-coding regions and their underlying me...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/s13059-018-1457-6

    authors: Prins BP,Mead TJ,Brody JA,Sveinbjornsson G,Ntalla I,Bihlmeyer NA,van den Berg M,Bork-Jensen J,Cappellani S,Van Duijvenboden S,Klena NT,Gabriel GC,Liu X,Gulec C,Grarup N,Haessler J,Hall LM,Iorio A,Isaacs A,Li-Gao R,

    更新日期:2018-07-17 00:00:00

  • Characterization of taxonomically restricted genes in a phylum-restricted cell type.

    abstract:BACKGROUND:Despite decades of research, the molecular mechanisms responsible for the evolution of morphological diversity remain poorly understood. While current models assume that species-specific morphologies are governed by differential use of conserved genetic regulatory circuits, it is debated whether non-conserve...

    journal_title:Genome biology

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    authors: Milde S,Hemmrich G,Anton-Erxleben F,Khalturin K,Wittlieb J,Bosch TC

    更新日期:2009-01-01 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. ...

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    doi:10.1186/gb-2011-12-12-135

    authors: Good BM,Su AI

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  • 5-hydroxymethylcytosine marks promoters in colon that resist DNA hypermethylation in cancer.

    abstract:BACKGROUND:The discovery of cytosine hydroxymethylation (5hmC) as a mechanism that potentially controls DNA methylation changes typical of neoplasia prompted us to investigate its behaviour in colon cancer. 5hmC is globally reduced in proliferating cells such as colon tumours and the gut crypt progenitors, from which t...

    journal_title:Genome biology

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    doi:10.1186/s13059-015-0605-5

    authors: Uribe-Lewis S,Stark R,Carroll T,Dunning MJ,Bachman M,Ito Y,Stojic L,Halim S,Vowler SL,Lynch AG,Delatte B,de Bony EJ,Colin L,Defrance M,Krueger F,Silva AL,Ten Hoopen R,Ibrahim AE,Fuks F,Murrell A

    更新日期:2015-04-01 00:00:00

  • Transcript copy number estimation using a mouse whole-genome oligonucleotide microarray.

    abstract::The ability to quantitatively measure the expression of all genes in a given tissue or cell with a single assay is an exciting promise of gene-expression profiling technology. An in situ-synthesized 60-mer oligonucleotide microarray designed to detect transcripts from all mouse genes was validated, as well as a set of...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/gb-2005-6-7-r61

    authors: Carter MG,Sharov AA,VanBuren V,Dudekula DB,Carmack CE,Nelson C,Ko MS

    更新日期:2005-01-01 00:00:00

  • Using the canary genome to decipher the evolution of hormone-sensitive gene regulation in seasonal singing birds.

    abstract:BACKGROUND:While the song of all songbirds is controlled by the same neural circuit, the hormone dependence of singing behavior varies greatly between species. For this reason, songbirds are ideal organisms to study ultimate and proximate mechanisms of hormone-dependent behavior and neuronal plasticity. RESULTS:We pre...

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