Redistribution of H3K27me3 upon DNA hypomethylation results in de-repression of Polycomb target genes.

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

authors： Szabó PE

更新日期：2016-05-16 00:00:00

abstract：:Single-cell transcriptomics requires a method that is sensitive, accurate, and reproducible. Here, we present CEL-Seq2, a modified version of our CEL-Seq method, with threefold higher sensitivity, lower costs, and less hands-on time. We implemented CEL-Seq2 on Fluidigm's C1 system, providing its first single-cell, on-...

journal_title：Genome biology

authors： Hashimshony T,Senderovich N,Avital G,Klochendler A,de Leeuw Y,Anavy L,Gennert D,Li S,Livak KJ,Rozenblatt-Rosen O,Dor Y,Regev A,Yanai I

更新日期：2016-04-28 00:00:00

abstract：BACKGROUND:Obligate pathogenic bacteria lose more genes relative to facultative pathogens, which, in turn, lose more genes than free-living bacteria. It was suggested that the increased gene loss in obligate pathogens may be due to a reduction in the effectiveness of purifying selection. Less attention has been given t...

journal_title：Genome biology

authors： Hershberg R,Tang H,Petrov DA

更新日期：2007-01-01 00:00:00

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

authors： Gabaldón T

更新日期：2008-10-30 00:00:00

abstract：BACKGROUND:The role played by microRNAs (miRs) as common regulators in physiologic processes such as development and various disease states was recently highlighted. Retinitis pigmentosa (RP) linked to RHO (which encodes rhodopsin) is the most frequent form of inherited retinal degeneration that leads to blindness, for...

journal_title：Genome biology

authors： Loscher CJ,Hokamp K,Kenna PF,Ivens AC,Humphries P,Palfi A,Farrar GJ

更新日期：2007-01-01 00:00:00

abstract：:The recent completion of the DNA sequence of human chromosome 21 has provided the first look at the 225 genes that are candidates for involvement in Down syndrome (trisomy 21). A broad functional classification of these genes, their expression data and evolutionary conservation, and comparison with the gene content of...

journal_title：Genome biology

authors： Gardiner K,Davisson M

更新日期：2000-01-01 00:00:00

abstract：BACKGROUND:Transcription factors (TFs) play a central role in regulating gene expression by interacting with cis-regulatory DNA elements associated with their target genes. Recent surveys have examined the DNA binding specificities of most Saccharomyces cerevisiae TFs, but a comprehensive evaluation of their data has b...

journal_title：Genome biology

authors： Gordân R,Murphy KF,McCord RP,Zhu C,Vedenko A,Bulyk ML

更新日期：2011-12-21 00:00:00

abstract：BACKGROUND:Maps depicting binary interactions between proteins can be powerful starting points for understanding biological systems. A proven technology for generating such maps is high-throughput yeast two-hybrid screening. In the most extensive screen to date, a Gal4-based two-hybrid system was used recently to detec...

journal_title：Genome biology

authors： Stanyon CA,Liu G,Mangiola BA,Patel N,Giot L,Kuang B,Zhang H,Zhong J,Finley RL Jr

更新日期：2004-01-01 00:00:00

abstract：:The genome-wide investigation of DNA methylation levels has been limited to reference transposable element positions. The methylation analysis of non-reference and mobile transposable elements has only recently been performed, but required both genome resequencing and MethylC-seq datasets. We have created epiTEome, a ...

journal_title：Genome biology

authors： Daron J,Slotkin RK

更新日期：2017-05-12 00:00:00

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

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

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

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

abstract：:Piwi-interacting RNAs (piRNAs) originate from genomic regions dubbed piRNA clusters. How cluster transcripts are selected for processing into piRNAs is not understood. We discuss evidence for the involvement of chromatin structure and maternally inherited piRNAs in determining their fate. ...

journal_title：Genome biology

authors： Le Thomas A,Tóth KF,Aravin AA

更新日期：2014-01-27 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：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

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

abstract：BACKGROUND:Long noncoding RNAs (lncRNAs) form an abundant class of transcripts, but the function of the majority of them remains elusive. While it has been shown that some lncRNAs are bound by ribosomes, it has also been convincingly demonstrated that these transcripts do not code for proteins. To obtain a comprehensiv...

journal_title：Genome biology

authors： van Heesch S,van Iterson M,Jacobi J,Boymans S,Essers PB,de Bruijn E,Hao W,MacInnes AW,Cuppen E,Simonis M

更新日期：2014-01-07 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:Rates of recombination can vary among genomic regions in eukaryotes, and this is believed to have major effects on their genome organization in terms of base composition, DNA repeat density, intron size, evolutionary rates and gene order. In highly self-fertilizing species such as Arabidopsis thaliana, howev...

journal_title：Genome biology

authors： Marais G,Charlesworth B,Wright SI

更新日期：2004-01-01 00:00:00

abstract：:A report on the 11th Cold Spring Harbor Laboratory/Wellcome Trust conference on Genome Informatics, Cold Spring Harbor Laboratories, New York, USA, November 2-5, 2011. ...

journal_title：Genome biology

authors： Chambers EV,Kindt AS,Semple CA

更新日期：2011-12-28 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:There are significant limitations in existing methods for the genome-wide identification of genes whose expression patterns affect traits. RESULTS:The transcriptomes of five tissues from 27 genetically diverse maize inbred lines were deeply sequenced to identify genes exhibiting high and low levels of expre...

journal_title：Genome biology

authors： Lin HY,Liu Q,Li X,Yang J,Liu S,Huang Y,Scanlon MJ,Nettleton D,Schnable PS

更新日期：2017-10-17 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：:The majority of disease resistance genes in plants encode nucleotide-binding site leucine-rich repeat (NBS-LRR) proteins. This large family is encoded by hundreds of diverse genes per genome and can be subdivided into the functionally distinct TIR-domain-containing (TNL) and CC-domain-containing (CNL) subfamilies. The...

journal_title：Genome biology

authors： McHale L,Tan X,Koehl P,Michelmore RW

更新日期：2006-01-01 00:00:00

abstract：:The honey bee Apis mellifera displays the most complex behavior of any insect. This, and its utility to humans, makes it a fascinating object of study for biologists. Such studies are now further enabled by the release of the honey-bee genome sequence. ...

journal_title：Genome biology

authors： Ashburner M,Kyriacou CP

更新日期：2006-01-01 00:00:00

abstract：BACKGROUND:Growth rate is central to the development of cells in all organisms. However, little is known about the impact of changing growth rates. We used continuous cultures to control growth rate and studied the transcriptional program of the model eukaryote Saccharomyces cerevisiae, with generation times varying be...

journal_title：Genome biology

authors： Regenberg B,Grotkjaer T,Winther O,Fausbøll A,Akesson M,Bro C,Hansen LK,Brunak S,Nielsen J

更新日期：2006-01-01 00:00:00

abstract：:Cytoscape is one of the most successful network biology analysis and visualization tools, but because of its interactive nature, its role in creating reproducible, scalable, and novel workflows has been limited. We describe Cytoscape Automation (CA), which marries Cytoscape to highly productive workflow systems, for e...

journal_title：Genome biology

authors： Otasek D,Morris JH,Bouças J,Pico AR,Demchak B

更新日期：2019-09-02 00:00:00

abstract：:A variety of base editors have been developed to achieve C-to-T editing in different genomic contexts. Here, we compare a panel of five base editors on their C-to-T editing efficiencies and product purity at commonly editable sites, including some human pathogenic C-to-T mutations. We further profile the accessibiliti...

journal_title：Genome biology

authors： Wang Y,Gao R,Wu J,Xiong YC,Wei J,Zhang S,Yang B,Chen J,Yang L

更新日期：2019-10-23 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：: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：:The iCLIP and eCLIP techniques facilitate the detection of protein-RNA interaction sites at high resolution, based on diagnostic events at crosslink sites. However, previous methods do not explicitly model the specifics of iCLIP and eCLIP truncation patterns and possible biases. We developed PureCLIP ( https://github....

journal_title：Genome biology

authors： Krakau S,Richard H,Marsico A

更新日期：2017-12-28 00:00:00

abstract：BACKGROUND:Bread wheat is an allohexaploid species with a 16-Gb genome that has large intergenic regions, which presents a big challenge for pinpointing regulatory elements and further revealing the transcriptional regulatory mechanisms. Chromatin profiling to characterize the combinatorial patterns of chromatin signat...

journal_title：Genome biology

authors： Li Z,Wang M,Lin K,Xie Y,Guo J,Ye L,Zhuang Y,Teng W,Ran X,Tong Y,Xue Y,Zhang W,Zhang Y

更新日期：2019-07-15 00:00:00