Chemical genomics in yeast.

abstract：:A report of the 6th Georgia Tech-Oak Ridge National Lab International Conference on Bioinformatics 'In silico Biology: Gene Discovery and Systems Genomics', Atlanta, USA, 15-17 November, 2007. ...

journal_title：Genome biology

authors： Weng Z,Guigó R

更新日期：2008-01-01 00:00:00

abstract：:Rhomboid proteases are the largest family of enzymes that hydrolyze peptide bonds within the cell membrane. Although discovered to be serine proteases only a decade ago, rhomboid proteases are already considered to be the best understood intramembrane proteases. The presence of rhomboid proteins in all domains of life...

journal_title：Genome biology

authors： Urban S,Dickey SW

更新日期：2011-10-27 00:00:00

abstract：:The four vertebrate R-spondin proteins are secreted agonists of the canonical Wnt/β-catenin signaling pathway. These proteins are approximately 35 kDa, and are characterized by two amino-terminal furin-like repeats, which are necessary and sufficient for Wnt signal potentiation, and a thrombospondin domain situated mo...

journal_title：Genome biology

authors： de Lau WB,Snel B,Clevers HC

更新日期：2012-01-01 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：: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：BACKGROUND:As the rough draft of the human genome sequence nears a finished product and other genome-sequencing projects accumulate sequence data exponentially, bioinformatics is emerging as an important tool for studies of transposon biology. In particular, L1 elements exhibit a variety of sequence structures after in...

journal_title：Genome biology

authors： Szak ST,Pickeral OK,Makalowski W,Boguski MS,Landsman D,Boeke JD

更新日期：2002-09-19 00:00:00

abstract：:Genome editing holds remarkable promise to transform human medicine as new therapies that can directly address the genetic causes of disease. However, concerns remain about possible undesired biological consequences of genome editors, particularly the introduction of unintended 'off-target' mutations. Here, we discuss...

journal_title：Genome biology

authors： Cheng Y,Tsai SQ

更新日期：2018-12-22 00:00:00

abstract：BACKGROUND:Seed germination involves progression from complete metabolic dormancy to a highly active, growing seedling. Many factors regulate germination and these interact extensively, forming a complex network of inputs that control the seed-to-seedling transition. Our understanding of the direct regulation of gene e...

journal_title：Genome biology

authors： Narsai R,Gouil Q,Secco D,Srivastava A,Karpievitch YV,Liew LC,Lister R,Lewsey MG,Whelan J

更新日期：2017-09-15 00:00:00

abstract：BACKGROUND:Early single-cell RNA-seq (scRNA-seq) studies suggested that it was unusual to see more than one isoform being produced from a gene in a single cell, even when multiple isoforms were detected in matched bulk RNA-seq samples. However, these studies generally did not consider the impact of dropouts or isoform ...

journal_title：Genome biology

authors： Westoby J,Artemov P,Hemberg M,Ferguson-Smith A

更新日期：2020-03-23 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：:How viruses evolve within hosts can dictate infection outcomes; however, reconstructing this process is challenging. We evaluate our multiplexed amplicon approach, PrimalSeq, to demonstrate how virus concentration, sequencing coverage, primer mismatches, and replicates influence the accuracy of measuring intrahost vir...

journal_title：Genome biology

authors： Grubaugh ND,Gangavarapu K,Quick J,Matteson NL,De Jesus JG,Main BJ,Tan AL,Paul LM,Brackney DE,Grewal S,Gurfield N,Van Rompay KKA,Isern S,Michael SF,Coffey LL,Loman NJ,Andersen KG

更新日期：2019-01-08 00:00:00

abstract：:The discovery of several new structured non-coding RNAs in bacterial and archaeal genomes and metagenomes raises burning questions about their biological and biochemical functions. ...

journal_title：Genome biology

authors： Westhof E

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：:From worms to humans, recognizing and modifying a specific chromosome is essential for dosage compensation, the mechanism by which equal X-linked gene expression in males and females is achieved. Recent molecular genetic and biochemical studies have provided new insights into how regulatory factors in Drosophila are r...

journal_title：Genome biology

authors： Amrein H

更新日期：2000-01-01 00:00:00

abstract：BACKGROUND:Next-generation sequencing (NGS) is a powerful tool for understanding both patterns of descent over time and space (phylogeography) and the molecular processes underpinning genome divergence in pathogenic bacteria. Here, we describe a synthesis between these perspectives by employing a recently developed Bay...

journal_title：Genome biology

authors： Castillo-Ramírez S,Corander J,Marttinen P,Aldeljawi M,Hanage WP,Westh H,Boye K,Gulay Z,Bentley SD,Parkhill J,Holden MT,Feil EJ

更新日期：2012-12-27 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：:The WOX genes form a plant-specific subclade of the eukaryotic homeobox transcription factor superfamily, which is characterized by the presence of a conserved DNA-binding homeodomain. The analysis of WOX gene expression and function shows that WOX family members fulfill specialized functions in key developmental proc...

journal_title：Genome biology

authors： van der Graaff E,Laux T,Rensing SA

更新日期：2009-01-01 00:00:00

abstract：BACKGROUND:Type II DNA topoisomerases (TOP2) regulate DNA topology by generating transient double stranded breaks during replication and transcription. Topoisomerase II beta (TOP2B) facilitates rapid gene expression and functions at the later stages of development and differentiation. To gain new insight into the genom...

journal_title：Genome biology

authors： Uusküla-Reimand L,Hou H,Samavarchi-Tehrani P,Rudan MV,Liang M,Medina-Rivera A,Mohammed H,Schmidt D,Schwalie P,Young EJ,Reimand J,Hadjur S,Gingras AC,Wilson MD

更新日期：2016-08-31 00:00:00

abstract：BACKGROUND:We describe the distribution of indels in the 44 Encyclopedia of DNA Elements (ENCODE) regions (about 1% of the human genome) and evaluate the potential contributions of small insertion and deletion polymorphisms (indels) to human genetic variation. We relate indels to known genomic annotation features and m...

journal_title：Genome biology

authors： Clark TG,Andrew T,Cooper GM,Margulies EH,Mullikin JC,Balding DJ

更新日期：2007-01-01 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：:Prokaryotic cyanobacteria express robust circadian (daily) rhythms under the control of a central clock. Recent studies shed light on the mechanisms governing circadian rhythms in cyanobacteria and highlight key differences between prokaryotic and eukaryotic clocks. ...

journal_title：Genome biology

authors： Johnson CH

更新日期：2004-01-01 00:00:00

abstract：:The protein folding game Foldit shows that games are an effective way to recruit, engage and organize ordinary citizens to help solve difficult scientific problems. ...

journal_title：Genome biology

authors： Good BM,Su AI

更新日期：2011-12-28 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

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：BACKGROUND:Plant-microbe interactions feature complex signal interplay between pathogens and their hosts. Phytophthora species comprise a destructive group of fungus-like plant pathogens, collectively affecting a wide range of plants important to agriculture and natural ecosystems. Despite the availability of genome se...

journal_title：Genome biology

authors： Jupe J,Stam R,Howden AJ,Morris JA,Zhang R,Hedley PE,Huitema E

更新日期：2013-06-25 00:00:00

abstract：BACKGROUND:Many different methods exist to adjust for variability in cell-type mixture proportions when analyzing DNA methylation studies. Here we present the result of an extensive simulation study, built on cell-separated DNA methylation profiles from Illumina Infinium 450K methylation data, to compare the performanc...

journal_title：Genome biology

authors： McGregor K,Bernatsky S,Colmegna I,Hudson M,Pastinen T,Labbe A,Greenwood CM

更新日期：2016-05-03 00:00:00

abstract：BACKGROUND:Two distinct classes of regulators have been implicated in regulating neuronal gene expression and mediating neuronal identity: transcription factors such as REST/NRSF (RE1 silencing transcription factor) and CREB (cAMP response element-binding protein), and microRNAs (miRNAs). How these two classes of regul...

journal_title：Genome biology

authors： Wu J,Xie X

更新日期：2006-01-01 00:00:00

abstract：:DNA shuffling has proven to be a powerful technique for the directed evolution of proteins. A mix of theoretical and applied research has now provided insights into how recombination can be guided to more efficiently generate proteins and even organisms with altered functions. ...

journal_title：Genome biology

authors： Bacher JM,Reiss BD,Ellington AD

更新日期：2002-07-31 00:00:00

abstract：:Tissues are complex milieus consisting of numerous cell types. Several recent methods have attempted to enumerate cell subsets from transcriptomes. However, the available methods have used limited sources for training and give only a partial portrayal of the full cellular landscape. Here we present xCell, a novel gene...

journal_title：Genome biology

authors： Aran D,Hu Z,Butte AJ

更新日期：2017-11-15 00:00:00

abstract：:Microarray analysis using clustering algorithms can suffer from lack of inter-method consistency in assigning related gene-expression profiles to clusters. Obtaining a consensus set of clusters from a number of clustering methods should improve confidence in gene-expression analysis. Here we introduce consensus cluste...

journal_title：Genome biology

authors： Swift S,Tucker A,Vinciotti V,Martin N,Orengo C,Liu X,Kellam P

更新日期：2004-01-01 00:00:00