xCell: digitally portraying the tissue cellular heterogeneity landscape.

abstract：:Advances in sequencing technology have led to a sharp decrease in the cost of 'data generation'. But is this sufficient to ensure cost-effective and efficient 'knowledge generation'? ...

journal_title：Genome biology

authors： Sboner A,Mu XJ,Greenbaum D,Auerbach RK,Gerstein MB

更新日期：2011-08-25 00:00:00

abstract：:The Network of Cancer Genes (NCG) is a manually curated repository of 2372 genes whose somatic modifications have known or predicted cancer driver roles. These genes were collected from 275 publications, including two sources of known cancer genes and 273 cancer sequencing screens of more than 100 cancer types from 34...

journal_title：Genome biology

authors： Repana D,Nulsen J,Dressler L,Bortolomeazzi M,Venkata SK,Tourna A,Yakovleva A,Palmieri T,Ciccarelli FD

更新日期：2019-01-03 00:00:00

abstract：:According to a recent article published in Genome Biology, Duggan and coworkers sequenced and partially assembled five genomes of smallpox vaccines from the nineteenth century. No information regarding the ends of genomes was presented, and they are important to understand the evolutionary relationship of the differen...

journal_title：Genome biology

authors： Brinkmann A,Souza ARV,Esparza J,Nitsche A,Damaso CR

更新日期：2020-12-04 00:00:00

abstract：BACKGROUND:Some years ago we established an N-ethyl-N-nitrosourea screen for modifiers of transgene variegation in the mouse and a preliminary description of the first six mutant lines, named MommeD1-D6, has been published. We have reported the underlying genes in three cases: MommeD1 is a mutation in SMC hinge domain ...

journal_title：Genome biology

authors： Ashe A,Morgan DK,Whitelaw NC,Bruxner TJ,Vickaryous NK,Cox LL,Butterfield NC,Wicking C,Blewitt ME,Wilkins SJ,Anderson GJ,Cox TC,Whitelaw E

更新日期：2008-01-01 00:00:00

abstract：:A report of the Keystone Symposia joint meetings on DNA Methylation and Epigenomics held in Keystone, Colorado, USA, 29 March to 3 April, 2015. ...

journal_title：Genome biology

authors： Chatterjee A,Eccles MR

更新日期：2015-05-21 00:00:00

abstract：:DNA transposons are efficient tools in transgenesis and have therefore become popular in the analysis of the regulatory genome in vertebrates via enhancer trap screens. Here, I discuss recent progress in this field of research, with a focus on the application of one of these transposons, namely the medaka fish derived...

journal_title：Genome biology

authors： Korzh V

更新日期：2007-01-01 00:00:00

abstract：BACKGROUND:It has been hypothesized that rapid divergence in centromere sequences accompanies rapid karyotypic change during speciation. However, the reuse of breakpoints coincident with centromeres in the evolution of divergent karyotypes poses a potential paradox. In distantly related species where the same centromer...

journal_title：Genome biology

authors： Bulazel KV,Ferreri GC,Eldridge MD,O'Neill RJ

更新日期：2007-01-01 00:00:00

abstract：:Improving the quality and coverage of the protein interactome is of tantamount importance for biomedical research, particularly given the various sources of uncertainty in high-throughput techniques. We introduce a structure-based framework, Coev2Net, for computing a single confidence score that addresses both false-p...

journal_title：Genome biology

authors： Hosur R,Peng J,Vinayagam A,Stelzl U,Xu J,Perrimon N,Bienkowska J,Berger B

更新日期：2012-08-31 00:00:00

abstract：BACKGROUND:RNA editing encompasses a post-transcriptional process in which the genomically templated sequence is enzymatically altered and introduces a modified base into the edited transcript. Mammalian C-to-U RNA editing represents a distinct subtype of base modification, whose prototype is intestinal apolipoprotein ...

journal_title：Genome biology

authors： Blanc V,Park E,Schaefer S,Miller M,Lin Y,Kennedy S,Billing AM,Ben Hamidane H,Graumann J,Mortazavi A,Nadeau JH,Davidson NO

更新日期：2014-06-19 00:00:00

abstract：:We present a new method, Fine-Mapping of Adaptive Variation (FineMAV), which combines population differentiation, derived allele frequency, and molecular functionality to prioritize positively selected candidate variants for functional follow-up. We calibrate and test FineMAV using eight experimentally validated "gold...

journal_title：Genome biology

authors： Szpak M,Mezzavilla M,Ayub Q,Chen Y,Xue Y,Tyler-Smith C

更新日期：2018-01-17 00:00:00

abstract：BACKGROUND:Candida glabrata is a pathogenic yeast of increasing medical concern. It has been regarded as asexual since it was first described in 1917, yet phylogenetic analyses have revealed that it is more closely related to sexual yeasts than other Candida species. We show here that the C. glabrata genome contains ma...

journal_title：Genome biology

authors： Wong S,Fares MA,Zimmermann W,Butler G,Wolfe KH

更新日期：2003-01-01 00:00:00

abstract：:A report on the Cold Spring Harbor Laboratory meeting on the Evolution of Developmental Diversity, Cold Spring Harbor, NY, USA, 17-21 April 2002. ...

journal_title：Genome biology

authors： King N

更新日期：2002-07-15 00:00:00

abstract：BACKGROUND:Despite decades of research, the agent responsible for transmitting spongiform encephalopathies (TSEs) has not been identified. The Prion hypothesis, which dominates the field, supposes that modified host PrP protein, termed PrPSc, acts as the transmissible agent. This model fits the observation that TSE dis...

journal_title：Genome biology

authors： Gibson TJ

更新日期：2001-01-01 00:00:00

abstract：BACKGROUND:Protein domains are protein regions that are shared among different proteins and are frequently functionally and structurally independent from the rest of the protein. Novel domain combinations have a major role in evolutionary innovation. However, the relative contributions of the different molecular mechan...

journal_title：Genome biology

authors： Buljan M,Frankish A,Bateman A

更新日期：2010-01-01 00:00:00

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

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

abstract：:Gene-expression profiling has yielded important information about simple systems, but complex tissues have not yet been widely profiled. Four recent studies of mammalian skeletal muscles have added to the catalogs of their gene expression differences, but have yet to lead to better understanding of the molecular proce...

journal_title：Genome biology

authors： Hampson R,Hughes SM

更新日期：2001-01-01 00:00:00

abstract：:A report of the fifth annual Personal Genomes and Medical Genomics meeting, held at Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA, November 14-17, 2012. ...

journal_title：Genome biology

authors： Highnam G,Mittelman D

更新日期：2012-12-19 00:00:00

abstract：BACKGROUND:Whole genome sequencing of marine cyanobacteria has revealed an unprecedented degree of genomic variation and streamlining. With a size of 1.66 megabase-pairs, Prochlorococcus sp. MED4 has the most compact of these genomes and it is enigmatic how the few identified regulatory proteins efficiently sustain the...

journal_title：Genome biology

authors： Axmann IM,Kensche P,Vogel J,Kohl S,Herzel H,Hess WR

更新日期：2005-01-01 00:00:00

abstract：BACKGROUND:Heterochromatin protein 1 (HP1) family proteins have a well-characterized role in heterochromatin packaging and gene regulation. Their function in organismal development, however, is less well understood. Here we used genome-wide expression profiling to assess novel functions of the Caenorhabditis elegans HP...

journal_title：Genome biology

authors： Meister P,Schott S,Bedet C,Xiao Y,Rohner S,Bodennec S,Hudry B,Molin L,Solari F,Gasser SM,Palladino F

更新日期：2011-12-20 00:00:00

abstract：:A report on the Genome-Based Pathogen Biology meeting, Hinxton, UK, 7-10 July 2002. ...

journal_title：Genome biology

authors： Simpson AJ

更新日期：2002-08-27 00:00:00

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

authors： Jiang Y,Zhang NR,Li M

更新日期：2017-04-26 00:00:00

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

authors： Xia X,Kung AL

更新日期：2009-01-01 00:00:00

abstract：BACKGROUND:One way in which the accuracy of gene structure prediction in vertebrate DNA sequences can be improved is by analyzing alignments with multiple related species, since functional regions of genes tend to be more conserved. RESULTS:We describe DOGFISH, a vertebrate gene finder consisting of a cleanly separate...

journal_title：Genome biology

authors： Carter D,Durbin R

更新日期：2006-01-01 00:00:00

abstract：BACKGROUND:CRISPR-Cas systems have been broadly embraced as effective tools for genome engineering applications, with most studies to date utilizing the Streptococcus pyogenes Cas9. Here we characterize and manipulate the smaller, 1053 amino acid nuclease Staphylococcus aureus Cas9. RESULTS:We find that the S. aureus ...

journal_title：Genome biology

authors： Friedland AE,Baral R,Singhal P,Loveluck K,Shen S,Sanchez M,Marco E,Gotta GM,Maeder ML,Kennedy EM,Kornepati AV,Sousa A,Collins MA,Jayaram H,Cullen BR,Bumcrot D

更新日期：2015-11-24 00:00:00

abstract：BACKGROUND:The development of complex organisms is believed to involve progressive restrictions in cellular fate. Understanding the scope and features of chromatin dynamics during embryogenesis, and identifying regulatory elements important for directing developmental processes remain key goals of developmental biology...

journal_title：Genome biology

authors： Thomas S,Li XY,Sabo PJ,Sandstrom R,Thurman RE,Canfield TK,Giste E,Fisher W,Hammonds A,Celniker SE,Biggin MD,Stamatoyannopoulos JA

更新日期：2011-01-01 00:00:00

abstract：BACKGROUND:Adult T cell acute lymphoblastic leukemia (T-ALL) is a rare disease that affects less than 10 individuals in one million. It has been less studied than its cognate pediatric malignancy, which is more prevalent. A higher percentage of the adult patients relapse, compared to children. It is thus essential to s...

journal_title：Genome biology

authors： Sentís I,Gonzalez S,Genescà E,García-Hernández V,Muiños F,Gonzalez C,López-Arribillaga E,Gonzalez J,Fernandez-Ibarrondo L,Mularoni L,Espinosa L,Bellosillo B,Ribera JM,Bigas A,Gonzalez-Perez A,Lopez-Bigas N

更新日期：2020-11-23 00:00:00

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

authors： Vitkup D,Kharchenko P,Wagner A

更新日期：2006-01-01 00:00:00

abstract：BACKGROUND:The C2H2 zinc finger (C2H2-ZF) is the most numerous protein domain in many metazoans, but is not as frequent or diverse in other eukaryotes. The biochemical and evolutionary mechanisms that underlie the diversity of this DNA-binding domain exclusively in metazoans are, however, mostly unknown. RESULTS:Here,...

journal_title：Genome biology

authors： Najafabadi HS,Garton M,Weirauch MT,Mnaimneh S,Yang A,Kim PM,Hughes TR

更新日期：2017-09-06 00:00:00

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

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

更新日期：2007-01-01 00:00:00

abstract：:Stochastic changes in DNA methylation (i.e., spontaneous epimutations) contribute to methylome diversity in plants. Here, we describe AlphaBeta, a computational method for estimating the precise rate of such stochastic events using pedigree-based DNA methylation data as input. We demonstrate how AlphaBeta can be emplo...

journal_title：Genome biology

authors： Shahryary Y,Symeonidi A,Hazarika RR,Denkena J,Mubeen T,Hofmeister B,van Gurp T,Colomé-Tatché M,Verhoeven KJF,Tuskan G,Schmitz RJ,Johannes F

更新日期：2020-10-06 00:00:00