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

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：:A report on the Cold Spring Harbor Asia conference on Genome Assisted Biology of Crops and Model Plant Systems Meeting, held in Suzhou, China, April 21-25, 2014. ...

journal_title：Genome biology

authors： Lee I

更新日期：2014-05-23 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：: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:The direct examination of large, unbiased samples of young gene duplicates in their early stages of evolution is crucial to understanding the origin, divergence and preservation of new genes. Furthermore, comparative analysis of multiple genomes is necessary to determine whether patterns of gene duplication ...

journal_title：Genome biology

authors： Katju V,Farslow JC,Bergthorsson U

更新日期：2009-01-01 00:00:00

abstract：:Droplet-based microfluidic devices have become widely used to perform single-cell RNA sequencing (scRNA-seq). However, ambient RNA present in the cell suspension can be aberrantly counted along with a cell's native mRNA and result in cross-contamination of transcripts between different cell populations. DecontX is a n...

journal_title：Genome biology

authors： Yang S,Corbett SE,Koga Y,Wang Z,Johnson WE,Yajima M,Campbell JD

更新日期：2020-03-05 00:00:00

abstract：BACKGROUND:X chromosome inactivation is a spectacular example of epigenetic silencing. In order to deduce how this complex system evolved, we examined X inactivation in a model marsupial, the tammar wallaby (Macropus eugenii). In marsupials, X inactivation is known to be paternal, incomplete and tissue-specific, and oc...

journal_title：Genome biology

authors： Al Nadaf S,Waters PD,Koina E,Deakin JE,Jordan KS,Graves JA

更新日期：2010-01-01 00:00:00

abstract：:ProSplicer is a database of putative alternative splicing information derived from the alignment of proteins, mRNA sequences and expressed sequence tags (ESTs) against human genomic DNA sequences. Proteins, mRNA and ESTs provide valuable evidence that can reveal splice variants of genes. The alternative splicing infor...

journal_title：Genome biology

authors： Huang HD,Horng JT,Lee CC,Liu BJ

更新日期：2003-01-01 00:00:00

abstract：:MiRNAs play important roles in many diseases including cancers. However computational prediction of miRNA target genes is challenging and the accuracies of existing methods remain poor. We report mirMark, a new machine learning-based method of miRNA target prediction at the site and UTR levels. This method uses experi...

journal_title：Genome biology

authors： Menor M,Ching T,Zhu X,Garmire D,Garmire LX

更新日期：2014-01-01 00:00:00

abstract：:An intriguing recent study examines the role of miR-1202, a glutamate receptor regulating microRNA, in regulating major depressive disorder. ...

journal_title：Genome biology

authors： Rucker JJ,McGuffin P

更新日期：2014-07-26 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：: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：:Ever since DNA microarrays were first applied to the quantitation of RNA levels, there has been considerable interest in generating a protein homolog that can be used to assay cellular protein expression. A recent paper describes the first microarray that can be used for such protein profiling. ...

journal_title：Genome biology

authors： Tomlinson IM,Holt LJ

更新日期：2001-01-01 00:00:00

abstract：:Map based cloning in Arabidopsis thaliana can be a difficult and time-consuming process, specifically if the phenotype is subtle and scoring labour intensive. Here, we have re-sequenced the 120-Mb genome of a novel Arabidopsis clock mutant early bird (ebi-1) in Wassilewskija (Ws-2). We demonstrate the utility of seque...

journal_title：Genome biology

authors： Ashelford K,Eriksson ME,Allen CM,D'Amore R,Johansson M,Gould P,Kay S,Millar AJ,Hall N,Hall A

更新日期：2011-01-01 00:00:00

abstract：BACKGROUND:Drug resistance remains a major public health challenge for malaria treatment and eradication. Individual loci associated with drug resistance to many antimalarials have been identified, but their epistasis with other resistance mechanisms has not yet been elucidated. RESULTS:We previously described two mut...

journal_title：Genome biology

authors： Herman JD,Rice DP,Ribacke U,Silterra J,Deik AA,Moss EL,Broadbent KM,Neafsey DE,Desai MM,Clish CB,Mazitschek R,Wirth DF

更新日期：2014-01-01 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

abstract：BACKGROUND:Neisseria meningitidis is an important human commensal and pathogen that causes several thousand deaths each year, mostly in young children. How the pathogen replicates and causes disease in the host is largely unknown, particularly the role of metabolism in colonization and disease. Completed genome sequenc...

journal_title：Genome biology

authors： Mendum TA,Newcombe J,Mannan AA,Kierzek AM,McFadden J

更新日期：2011-12-30 00:00:00

abstract：:Chromosome conformation capture data, particularly from high-throughput approaches such as Hi-C, are typically very complex to analyse. Existing analysis tools are often single-purpose, or limited in compatibility to a small number of data formats, frequently making Hi-C analyses tedious and time-consuming. Here, we p...

journal_title：Genome biology

authors： Kruse K,Hug CB,Vaquerizas JM

更新日期：2020-12-17 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：:A large number of histone modifications has been implicated in the regulation of gene expression. Together, these modifications have the potential to form a complex combinatorial regulatory code. Genome-wide mapping approaches provide new opportunities to decipher this code, but they may suffer from systematic biases....

journal_title：Genome biology

authors： van Leeuwen F,van Steensel B

更新日期：2005-01-01 00:00:00

abstract：BACKGROUND:Although aberrant DNA methylation has been observed previously in acute lymphoblastic leukemia (ALL), the patterns of differential methylation have not been comprehensively determined in all subtypes of ALL on a genome-wide scale. The relationship between DNA methylation, cytogenetic background, drug resista...

journal_title：Genome biology

authors： Nordlund J,Bäcklin CL,Wahlberg P,Busche S,Berglund EC,Eloranta ML,Flaegstad T,Forestier E,Frost BM,Harila-Saari A,Heyman M,Jónsson OG,Larsson R,Palle J,Rönnblom L,Schmiegelow K,Sinnett D,Söderhäll S,Pastinen T,Gusta

更新日期：2013-09-24 00:00:00

abstract：:Genomic regions with altered gene expression are a characteristic feature of cancer cells. We present a novel method for identifying such regions in gene expression maps. This method is based on total variation minimization, a classical signal restoration technique. In systematic evaluations, we show that our method c...

journal_title：Genome biology

authors： Nilsson B,Johansson M,Heyden A,Nelander S,Fioretos T

更新日期：2008-01-21 00:00:00

abstract：:A report of the First Golden Helix Symposium 'Copy Number Variation (CNV) and Genomic Alterations in Health and Disease', Athens, Greece, 28-29 November 2008. ...

journal_title：Genome biology

authors： Le Caignec C,Redon R

更新日期：2009-01-01 00:00:00

abstract：BACKGROUND:Light and carbon are two essential signals influencing plant growth and development. Little is known about how carbon and light signaling pathways intersect or influence one another to affect gene expression. RESULTS:Microarrays are used to investigate carbon and light signaling interactions at a genome-wid...

journal_title：Genome biology

authors： Thum KE,Shin MJ,Palenchar PM,Kouranov A,Coruzzi GM

更新日期：2004-01-01 00:00:00

abstract：BACKGROUND:Population genetic theory predicts that rapid adaptation is largely driven by complex traits encoded by many loci of small effect. Because large-effect loci are quickly fixed in natural populations, they should not contribute much to rapid adaptation. RESULTS:To investigate the genetic architecture of therm...

journal_title：Genome biology

authors： Mallard F,Nolte V,Tobler R,Kapun M,Schlötterer C

更新日期：2018-08-20 00:00:00

abstract：BACKGROUND:The initiation and subsequent evolution of cancer are largely driven by a relatively small number of somatic mutations with critical functional impacts, so-called driver mutations. Identifying driver mutations in a patient's tumor cells is a central task in the era of precision cancer medicine. Over the deca...

journal_title：Genome biology

authors： Chen H,Li J,Wang Y,Ng PK,Tsang YH,Shaw KR,Mills GB,Liang H

更新日期：2020-02-20 00:00:00

abstract：:Normalization is an essential step in the analysis of high-throughput data. Multi-sample global normalization methods, such as quantile normalization, have been successfully used to remove technical variation. However, these methods rely on the assumption that observed global changes across samples are due to unwanted...

journal_title：Genome biology

authors： Hicks SC,Irizarry RA

更新日期：2015-06-04 00:00:00

abstract：BACKGROUND:Many eukaryotic genomes encode cis-natural antisense transcripts (cis-NATs). Sense and antisense transcripts may form double-stranded RNAs that are processed by the RNA interference machinery into small interfering RNAs (siRNAs). A few so-called nat-siRNAs have been reported in plants, mammals, Drosophila, a...

journal_title：Genome biology

authors： Zhang X,Xia J,Lii YE,Barrera-Figueroa BE,Zhou X,Gao S,Lu L,Niu D,Chen Z,Leung C,Wong T,Zhang H,Guo J,Li Y,Liu R,Liang W,Zhu JK,Zhang W,Jin H

更新日期：2012-01-01 00:00:00

abstract：BACKGROUND:The identification of causal genes from genome-wide association studies (GWAS) is the next important step for the translation of genetic findings into biologically meaningful mechanisms of disease and potential therapeutic targets. Using novel chromatin interaction detection techniques and allele specific as...

journal_title：Genome biology

authors： McGovern A,Schoenfelder S,Martin P,Massey J,Duffus K,Plant D,Yarwood A,Pratt AG,Anderson AE,Isaacs JD,Diboll J,Thalayasingam N,Ospelt C,Barton A,Worthington J,Fraser P,Eyre S,Orozco G

更新日期：2016-11-01 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