Altered retinal microRNA expression profile in a mouse model of retinitis pigmentosa.

abstract：BACKGROUND:DNA replication plays an important role in mutagenesis, yet little is known about how it interacts with other mutagenic processes. Here, we use somatic mutation signatures-each representing a mutagenic process-derived from 3056 patients spanning 19 cancer types to quantify the strand asymmetry of mutational ...

journal_title：Genome biology

authors： Tomkova M,Tomek J,Kriaucionis S,Schuster-Böckler B

更新日期：2018-09-10 00:00:00

abstract：:Genomic and proteomic studies have identified hundreds of proteins from mitochondria. A recent study has added a functional twist to these systematic approaches and identified novel mitochondrial modifiers and regulators. ...

journal_title：Genome biology

authors： Dimmer KS,Rapaport D

更新日期：2008-01-01 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:The influence of genetic variation on complex diseases is potentially mediated through a range of highly dynamic epigenetic processes exhibiting temporal variation during development and later life. Here we present a catalogue of the genetic influences on DNA methylation (methylation quantitative trait loci ...

journal_title：Genome biology

authors： Gaunt TR,Shihab HA,Hemani G,Min JL,Woodward G,Lyttleton O,Zheng J,Duggirala A,McArdle WL,Ho K,Ring SM,Evans DM,Davey Smith G,Relton CL

更新日期：2016-03-31 00:00:00

abstract：BACKGROUND:DNA methylation is a key epigenetic mechanism for driving and stabilizing cell-fate decisions. Local deposition and removal of DNA methylation are tightly coupled with transcription factor binding, although the relationship varies with the specific differentiation process. Conversion of monocytes to osteocla...

journal_title：Genome biology

authors： de la Rica L,Rodríguez-Ubreva J,García M,Islam AB,Urquiza JM,Hernando H,Christensen J,Helin K,Gómez-Vaquero C,Ballestar E

更新日期：2013-01-01 00:00:00

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

authors： Cook DL,Farley JF,Tapscott SJ

更新日期：2001-01-01 00:00:00

abstract：:A recent study explores the genome content of uncultured unicellular marine eukaryotes and provides insights about interactions between uncultured eukaryotes and other biological entities. ...

journal_title：Genome biology

authors： Worden AZ,Dupont C,Allen AE

更新日期：2011-06-27 00:00:00

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

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

abstract：:Vascular endothelia comprise a diverse population of cells that specialize in response to genetic programs and environmental cues to take on distinct roles in different vessels, tissues, and organs, and in response to pathophysiological stresses. Characterization of endothelial-cell diversity will facilitate the devel...

journal_title：Genome biology

authors： Conway EM,Carmeliet P

更新日期：2004-01-01 00:00:00

abstract：:We describe a bioinformatic tool, Tumor Aberration Prediction Suite (TAPS), for the identification of allele-specific copy numbers in tumor samples using data from Affymetrix SNP arrays. It includes detailed visualization of genomic segment characteristics and iterative pattern recognition for copy number identificati...

journal_title：Genome biology

authors： Rasmussen M,Sundström M,Göransson Kultima H,Botling J,Micke P,Birgisson H,Glimelius B,Isaksson A

更新日期：2011-10-24 00:00:00

abstract：BACKGROUND:Reliable information extraction applications have been a long sought goal of the biomedical text mining community, a goal that if reached would provide valuable tools to benchside biologists in their increasingly difficult task of assimilating the knowledge contained in the biomedical literature. We present ...

journal_title：Genome biology

authors： Baumgartner WA Jr,Lu Z,Johnson HL,Caporaso JG,Paquette J,Lindemann A,White EK,Medvedeva O,Cohen KB,Hunter L

更新日期：2008-01-01 00:00:00

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

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

更新日期：2005-01-01 00:00:00

abstract：:Compared to RNA-sequencing transcript differential analysis, gene-level differential expression analysis is more robust and experimentally actionable. However, the use of gene counts for statistical analysis can mask transcript-level dynamics. We demonstrate that 'analysis first, aggregation second,' where the p value...

journal_title：Genome biology

authors： Yi L,Pimentel H,Bray NL,Pachter L

更新日期：2018-04-12 00:00:00

abstract：:In a recent study, Petrovski and Goldstein reported that (non-Finnish) Europeans have significantly fewer nonsynonymous singletons in Online Mendelian Inheritance in Man (OMIM) disease genes compared with Africans, Latinos, South Asians, East Asians, and other unassigned non-Europeans. We use simulations of Exome Aggr...

journal_title：Genome biology

authors： Kessler MD,O'Connor TD

更新日期：2017-02-27 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

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

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

abstract：UNLABELLED:Ancient DNA is typically highly degraded with appreciable cytosine deamination, and contamination with present-day DNA often complicates the identification of endogenous molecules. Together, these factors impede accurate assembly of the endogenous ancient mitochondrial genome. We present schmutzi, an iterati...

journal_title：Genome biology

authors： Renaud G,Slon V,Duggan AT,Kelso J

更新日期：2015-10-12 00:00:00

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

authors： Havel JJ,Chan TA

更新日期：2015-03-31 00:00:00

abstract：:In predicting hierarchical protein function annotations, such as terms in the Gene Ontology (GO), the simplest approach makes predictions for each term independently. However, this approach has the unfortunate consequence that the predictor may assign to a single protein a set of terms that are inconsistent with one a...

journal_title：Genome biology

authors： Obozinski G,Lanckriet G,Grant C,Jordan MI,Noble WS

更新日期：2008-01-01 00:00:00

abstract：:We describe a method for extracting Boolean implications (if-then relationships) in very large amounts of gene expression microarray data. A meta-analysis of data from thousands of microarrays for humans, mice, and fruit flies finds millions of implication relationships between genes that would be missed by other meth...

journal_title：Genome biology

authors： Sahoo D,Dill DL,Gentles AJ,Tibshirani R,Plevritis SK

更新日期：2008-10-30 00:00:00

abstract：:Many drugs have unknown, controversial or multiple mechanisms of action. Four recent 'chemical genomic' studies, using genome-scale collections of yeast gene deletions that were either arrayed or barcoded, have presented complementary approaches to identifying gene-drug and pathway-drug interactions. ...

journal_title：Genome biology

authors： Brenner C

更新日期：2004-01-01 00:00:00

abstract：BACKGROUND:DNA methylation and the Polycomb repression system are epigenetic mechanisms that play important roles in maintaining transcriptional repression. Recent evidence suggests that DNA methylation can attenuate the binding of Polycomb protein components to chromatin and thus plays a role in determining their geno...

journal_title：Genome biology

authors： Reddington JP,Perricone SM,Nestor CE,Reichmann J,Youngson NA,Suzuki M,Reinhardt D,Dunican DS,Prendergast JG,Mjoseng H,Ramsahoye BH,Whitelaw E,Greally JM,Adams IR,Bickmore WA,Meehan RR

更新日期：2013-03-25 00:00:00

abstract：:The EpiGRAPH web service http://epigraph.mpi-inf.mpg.de/ enables biologists to uncover hidden associations in vertebrate genome and epigenome datasets. Users can upload sets of genomic regions and EpiGRAPH will test multiple attributes (including DNA sequence, chromatin structure, epigenetic modifications and evolutio...

journal_title：Genome biology

authors： Bock C,Halachev K,Büch J,Lengauer T

更新日期：2009-02-10 00:00:00

abstract：BACKGROUND:Neuropsychiatric disorders are common forms of disability in humans. Despite recent progress in deciphering the genetics of these disorders, their phenotypic complexity continues to be a major challenge. Mendelian neuropsychiatric disorders are rare but their study has the potential to unravel novel mechanis...

journal_title：Genome biology

authors： Shamseldin HE,Masuho I,Alenizi A,Alyamani S,Patil DN,Ibrahim N,Martemyanov KA,Alkuraya FS

更新日期：2016-09-27 00:00:00

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

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

abstract：BACKGROUND:DNase-seq and ATAC-seq are broadly used methods to assay open chromatin regions genome-wide. The single nucleotide resolution of DNase-seq has been further exploited to infer transcription factor binding sites (TFBSs) in regulatory regions through footprinting. Recent studies have demonstrated the sequence b...

journal_title：Genome biology

authors： Karabacak Calviello A,Hirsekorn A,Wurmus R,Yusuf D,Ohler U

更新日期：2019-02-21 00:00:00

abstract：:A report of the recent EMBO Conference 'From Functional Genomics to Systems Biology' held at the EMBL Advanced Training Centre, Heidelberg, Germany, 13-16 November 2010. ...

journal_title：Genome biology

authors： Fordyce P,Ingolia N

更新日期：2011-01-01 00:00:00

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

authors： Derevnina L,Michelmore RW

更新日期：2015-03-02 00:00:00

abstract：BACKGROUND:Human pluripotent stem cells (hPSCs) provide powerful models for studying cellular differentiations and unlimited sources of cells for regenerative medicine. However, a comprehensive single-cell level differentiation roadmap for hPSCs has not been achieved. RESULTS:We use high throughput single-cell RNA-seq...

journal_title：Genome biology

authors： Han X,Chen H,Huang D,Chen H,Fei L,Cheng C,Huang H,Yuan GC,Guo G

更新日期：2018-04-05 00:00:00

abstract：BACKGROUND:The development of mass spectrometric (MS) techniques now allows the investigation of very complex protein mixtures ranging from subcellular structures to tissues. Body fluids are also popular targets of proteomic analysis because of their potential for biomarker discovery. Seminal plasma has not yet receive...

journal_title：Genome biology

authors： Pilch B,Mann M

更新日期：2006-01-01 00:00:00