Single-cell profiling of lncRNAs in the developing human brain.

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: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：:Identifying the biochemical basis of microbial phenotypes is a main objective of comparative genomics. Here we present a novel method using multivariate machine learning techniques for comparing automatically derived metabolic reconstructions of sequenced genomes on a large scale. Applying our method to 266 genomes di...

journal_title：Genome biology

authors： Kastenmüller G,Schenk ME,Gasteiger J,Mewes HW

更新日期：2009-01-01 00:00:00

abstract：:A report on the 2004 meeting on Molecular Genetics of Bacteria and Bacteriophages, Cold Spring Harbor, USA, 25-29 August 2004. ...

journal_title：Genome biology

authors： Lawrence JG

更新日期：2004-01-01 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：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: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：:The spatial organization of chromatin in the nucleus has been implicated in regulating gene expression. Maps of high-frequency interactions between different segments of chromatin have revealed topologically associating domains (TADs), within which most of the regulatory interactions are thought to occur. TADs are not...

journal_title：Genome biology

authors： An L,Yang T,Yang J,Nuebler J,Xiang G,Hardison RC,Li Q,Zhang Y

更新日期：2019-12-18 00:00:00

abstract：:Not so fast. The Iqbal et. al. study and the associated Whitelaw commentary highlight the appropriately high standards of study design and interpretation needed to obtain good evidence for or against epigenetic inheritance. Please see related article: www.dx.doi.org/10.1186/s13059-015-0714-1. ...

journal_title：Genome biology

authors： Nadeau JH

更新日期：2015-07-11 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：:Numerous methods have been developed to analyse RNA sequencing (RNA-seq) data, but most rely on the availability of a reference genome, making them unsuitable for non-model organisms. Here we present superTranscripts, a substitute for a reference genome, where each gene with multiple transcripts is represented by a si...

journal_title：Genome biology

authors： Davidson NM,Hawkins ADK,Oshlack A

更新日期：2017-08-04 00:00:00

abstract：BACKGROUND:Many genome-wide collections of candidate cis-regulatory elements (cCREs) have been defined using genomic and epigenomic data, but it remains a major challenge to connect these elements to their target genes. RESULTS:To facilitate the development of computational methods for predicting target genes, we deve...

journal_title：Genome biology

authors： Moore JE,Pratt HE,Purcaro MJ,Weng Z

更新日期：2020-01-22 00:00:00

abstract：BACKGROUND:Alcoholism presents widespread social and human health problems. Alcohol sensitivity, the development of tolerance to alcohol and susceptibility to addiction vary in the population. Genetic factors that predispose to alcoholism remain largely unknown due to extensive genetic and environmental variation in hu...

journal_title：Genome biology

authors： Morozova TV,Anholt RR,Mackay TF

更新日期：2006-01-01 00:00:00

abstract：BACKGROUND:Bacillus subtilis is an organism of interest because of its extensive industrial applications, its similarity to pathogenic organisms, and its role as the model organism for Gram-positive, sporulating bacteria. In this work, we introduce a new genome-scale metabolic model of B. subtilis 168 called iBsu1103. ...

journal_title：Genome biology

authors： Henry CS,Zinner JF,Cohoon MP,Stevens RL

更新日期：2009-01-01 00:00:00

abstract：BACKGROUND:In eukaryotic organisms, gene expression is regulated at multiple levels during the processes of transcription and translation. The absence of a tight regulatory network for transcription in the human malaria parasite suggests that gene expression may largely be controlled at post-transcriptional and transla...

journal_title：Genome biology

authors： Bunnik EM,Chung DW,Hamilton M,Ponts N,Saraf A,Prudhomme J,Florens L,Le Roch KG

更新日期：2013-11-22 00:00:00

abstract：:A report of the Keystone Symposium 'DNA Replication and Recombination' held in Keystone, USA, 27 February to 4 March 2011. ...

journal_title：Genome biology

authors： Johansson E,Speck C,Chabes A

更新日期：2011-01-01 00:00:00

abstract：BACKGROUND:The newly assembled Bos taurus genome sequence enables the linkage of bovine milk and lactation data with other mammalian genomes. RESULTS:Using publicly available milk proteome data and mammary expressed sequence tags, 197 milk protein genes and over 6,000 mammary genes were identified in the bovine genome...

journal_title：Genome biology

authors： Lemay DG,Lynn DJ,Martin WF,Neville MC,Casey TM,Rincon G,Kriventseva EV,Barris WC,Hinrichs AS,Molenaar AJ,Pollard KS,Maqbool NJ,Singh K,Murney R,Zdobnov EM,Tellam RL,Medrano JF,German JB,Rijnkels M

更新日期：2009-01-01 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:Mitogen-activated protein kinases (MAPKs) are key regulators of immune responses in animals and plants. In Arabidopsis, perception of microbe-associated molecular patterns (MAMPs) activates the MAPKs MPK3, MPK4 and MPK6. Increasing information depicts the molecular events activated by MAMPs in plants, but th...

journal_title：Genome biology

authors： Frei dit Frey N,Garcia AV,Bigeard J,Zaag R,Bueso E,Garmier M,Pateyron S,de Tauzia-Moreau ML,Brunaud V,Balzergue S,Colcombet J,Aubourg S,Martin-Magniette ML,Hirt H

更新日期：2014-06-30 00:00:00

abstract：BACKGROUND:Estrogens and their receptors are important in human development, physiology and disease. In this study, we utilized an integrated genome-wide molecular and computational approach to characterize the interaction between the activated estrogen receptor (ER) and the regulatory elements of candidate target gene...

journal_title：Genome biology

authors： Lin CY,Ström A,Vega VB,Kong SL,Yeo AL,Thomsen JS,Chan WC,Doray B,Bangarusamy DK,Ramasamy A,Vergara LA,Tang S,Chong A,Bajic VB,Miller LD,Gustafsson JA,Liu ET

更新日期：2004-01-01 00:00:00

abstract：:We demonstrate that loss-of-function yeast phenotypes are predictable by guilt-by-association in functional gene networks. Testing 1,102 loss-of-function phenotypes from genome-wide assays of yeast reveals predictability of diverse phenotypes, spanning cellular morphology, growth, metabolism, and quantitative cell sha...

journal_title：Genome biology

authors： McGary KL,Lee I,Marcotte EM

更新日期：2007-01-01 00:00:00

abstract：:A report on the 64th annual American Society of Human Genetics meeting held in San Diego, USA, 18-22 October, 2014. ...

journal_title：Genome biology

authors： Reppell M,Koch E,Peter BM,Novembre J

更新日期：2014-12-17 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：:Recent experiments show that properly controlled recombination between homologous DNA molecules is essential for the maintenance of genome stability and for the prevention of tumorigenesis. ...

journal_title：Genome biology

authors： Modesti M,Kanaar R

更新日期：2001-01-01 00:00:00

abstract：BACKGROUND:The distributed genome hypothesis (DGH) posits that chronic bacterial pathogens utilize polyclonal infection and reassortment of genic characters to ensure persistence in the face of adaptive host defenses. Studies based on random sequencing of multiple strain libraries suggested that free-living bacterial s...

journal_title：Genome biology

authors： Hogg JS,Hu FZ,Janto B,Boissy R,Hayes J,Keefe R,Post JC,Ehrlich GD

更新日期：2007-01-01 00:00:00

abstract：BACKGROUND:Osteogenesis is a highly regulated developmental process and continues during the turnover and repair of mature bone. Runx2, the master regulator of osteoblastogenesis, directs a transcriptional program essential for bone formation through genetic and epigenetic mechanisms. While individual Runx2 gene target...

journal_title：Genome biology

authors： Wu H,Whitfield TW,Gordon JA,Dobson JR,Tai PW,van Wijnen AJ,Stein JL,Stein GS,Lian JB

更新日期：2014-03-21 00:00:00

abstract：:The army of the men of death, in John Bunyan's memorable phrase, has a new recruit, and fear has a new face: a face wearing a surgical mask. ...

journal_title：Genome biology

authors： Petsko GA

更新日期：2003-01-01 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:The genomic binding of CTCF is highly conserved across mammals, but the mechanisms that underlie its stability are poorly understood. One transcription factor known to functionally interact with CTCF in the context of X-chromosome inactivation is the ubiquitously expressed YY1. Because combinatorial transcri...

journal_title：Genome biology

authors： Schwalie PC,Ward MC,Cain CE,Faure AJ,Gilad Y,Odom DT,Flicek P

更新日期：2013-12-31 00:00:00

abstract：:Genetic mapping and determination of the organization of the wheat genome are changing the wheat-breeding process. New initiatives to analyze the expressed portion of the wheat genome and structural analysis of the genomes of Arabidopsis and rice are increasing our knowledge of the genes that are linked to key agronom...

journal_title：Genome biology

authors： Francki M,Appels R

更新日期：2002-01-01 00:00:00