Consensus clustering and functional interpretation of gene-expression data.

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：:Repeated DNA elements and region-specific protein modifications combine within chromosomes to form a transcriptionally silent chromatin structure called heterochromatin. Recent work in the fission yeast Schizosaccharomyces pombe reveals that RNA is also an integral component of silent heterochromatin, providing a new ...

journal_title：Genome biology

authors： Bailis JM,Forsburg SL

更新日期：2002-01-01 00:00:00

abstract：BACKGROUND:The recent availability of genome sequences has provided unparalleled insights into the broad-scale patterns of transposable element (TE) sequences in eukaryotic genomes. Nevertheless, the difficulties that TEs pose for genome assembly and annotation have prevented detailed, quantitative inferences about the...

journal_title：Genome biology

authors： Bergman CM,Quesneville H,Anxolabéhère D,Ashburner M

更新日期：2006-01-01 00:00:00

abstract：:A new approach to rapid, genome-wide identification and ranking of horizontal transfer candidate proteins is presented. The method is quantitative, reproducible, and computationally undemanding. It can be combined with genomic signature and/or phylogenetic tree-building procedures to improve accuracy and efficiency. T...

journal_title：Genome biology

authors： Podell S,Gaasterland T

更新日期：2007-01-01 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：: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：:Each human has approximately 50 to 280 frameshifting indels, yet their implications are unknown. We created SIFT Indel, a prediction method for frameshifting indels that has 84% accuracy. The percentage of human frameshifting indels predicted to be gene-damaging is negatively correlated with allele frequency. We also ...

journal_title：Genome biology

authors： Hu J,Ng PC

更新日期：2012-02-09 00:00:00

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：:Many existing pipelines for scRNA-seq data apply pre-processing steps such as normalization or imputation to account for excessive zeros or "drop-outs." Here, we extensively analyze diverse UMI data sets to show that clustering should be the foremost step of the workflow. We observe that most drop-outs disappear once ...

journal_title：Genome biology

authors： Kim TH,Zhou X,Chen M

更新日期：2020-08-06 00:00:00

abstract：BACKGROUND:The binding of transcription factors to specific locations in the genome is integral to the orchestration of transcriptional regulation in cells. To characterize transcription factor binding site function on a large scale, we predicted and mutagenized 455 binding sites in human promoters. We carried out func...

journal_title：Genome biology

authors： Whitfield TW,Wang J,Collins PJ,Partridge EC,Aldred SF,Trinklein ND,Myers RM,Weng Z

更新日期：2012-09-26 00:00:00

abstract：BACKGROUND:Mutations in genes encoding ribosomal proteins (RPs) have been shown to cause an array of cellular and developmental defects in a variety of organisms. In Drosophila melanogaster, disruption of RP genes can result in the 'Minute' syndrome of dominant, haploinsufficient phenotypes, which include prolonged dev...

journal_title：Genome biology

authors： Marygold SJ,Roote J,Reuter G,Lambertsson A,Ashburner M,Millburn GH,Harrison PM,Yu Z,Kenmochi N,Kaufman TC,Leevers SJ,Cook KR

更新日期：2007-01-01 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:The development of complex organisms is believed to involve progressive restrictions in cellular fate. Understanding the scope and features of chromatin dynamics during embryogenesis, and identifying regulatory elements important for directing developmental processes remain key goals of developmental biology...

journal_title：Genome biology

authors： Thomas S,Li XY,Sabo PJ,Sandstrom R,Thurman RE,Canfield TK,Giste E,Fisher W,Hammonds A,Celniker SE,Biggin MD,Stamatoyannopoulos JA

更新日期：2011-01-01 00:00:00

abstract：BACKGROUND:Protein domains display a range of structural diversity, with numerous additions and deletions of secondary structural elements between related domains. We have observed a small number of cases of surprising large-scale deletions of core elements of structural domains. We propose a new concept called domain ...

journal_title：Genome biology

authors： Prakash A,Bateman A

更新日期：2015-04-30 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：:The majority of people in the developed world spend more than 90% of their lives indoors. Here, we examine our understanding of the bacteria that co-inhabit our artificial world and how they might influence human health. ...

journal_title：Genome biology

authors： Kelley ST,Gilbert JA

更新日期：2013-02-28 00:00:00

abstract：:The nuclear genome sequence of Amborella trichopoda, the sister species to all other extant angiosperms, will be an exceptional resource for plant genomics. ...

journal_title：Genome biology

authors： Soltis DE,Albert VA,Leebens-Mack J,Palmer JD,Wing RA,dePamphilis CW,Ma H,Carlson JE,Altman N,Kim S,Wall PK,Zuccolo A,Soltis PS

更新日期：2008-01-01 00:00:00

abstract：BACKGROUND:Single-cell transcriptomics is rapidly advancing our understanding of the cellular composition of complex tissues and organisms. A major limitation in most analysis pipelines is the reliance on manual annotations to determine cell identities, which are time-consuming and irreproducible. The exponential growt...

journal_title：Genome biology

authors： Abdelaal T,Michielsen L,Cats D,Hoogduin D,Mei H,Reinders MJT,Mahfouz A

更新日期：2019-09-09 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：:PIWI proteins, a subfamily of PAZ/PIWI Domain family RNA-binding proteins, are best known for their function in silencing transposons and germline development by partnering with small noncoding RNAs called PIWI-interacting RNAs (piRNAs). However, recent studies have revealed multifaceted roles of the PIWI-piRNA pathwa...

journal_title：Genome biology

authors： Wang C,Lin H

更新日期：2021-01-08 00:00:00

abstract：:The mechanistic details of most disease-causing mutations remain poorly explored within the context of regulatory networks. We present a high-resolution three-dimensional integrated regulatory network (iRegNet3D) in the form of a web tool, where we resolve the interfaces of all known transcription factor (TF)-TF, TF-D...

journal_title：Genome biology

authors： Liang S,Tippens ND,Zhou Y,Mort M,Stenson PD,Cooper DN,Yu H

更新日期：2017-01-18 00:00:00

abstract：BACKGROUND:Polydnaviruses, double-stranded DNA viruses with segmented genomes, have evolved as obligate endosymbionts of parasitoid wasps. Virus particles are replication deficient and produced by female wasps from proviral sequences integrated into the wasp genome. These particles are co-injected with eggs into caterp...

journal_title：Genome biology

authors： Desjardins CA,Gundersen-Rindal DE,Hostetler JB,Tallon LJ,Fadrosh DW,Fuester RW,Pedroni MJ,Haas BJ,Schatz MC,Jones KM,Crabtree J,Forberger H,Nene V

更新日期：2008-01-01 00:00:00

abstract：BACKGROUND:Mutation rates vary across the genome. Many trans factors that influence mutation rates have been identified, as have specific sequence motifs at the 1-7-bp scale, but cis elements remain poorly characterized. The lack of understanding regarding why different sequences have different mutation rates hampers o...

journal_title：Genome biology

authors： Duan C,Huan Q,Chen X,Wu S,Carey LB,He X,Qian W

更新日期：2018-09-14 00:00:00

abstract：BACKGROUND:The vast number of precise intercellular connections within vertebrate nervous systems is only partly explained by the comparatively few known extracellular guidance cues. Large families of neural orphan receptor proteins have been identified and are likely to contribute to these recognition processes but du...

journal_title：Genome biology

authors： Söllner C,Wright GJ

更新日期：2009-01-01 00:00:00

abstract：:Swine production has been an important part of our lives since the late Mesolithic or early Neolithic periods, and ranks number one in world meat production. Pig production also contributes to high-value-added medical markets in the form of pharmaceuticals, heart valves, and surgical materials. Genetic engineering, in...

journal_title：Genome biology

authors： Clark KJ,Carlson DF,Fahrenkrug SC

更新日期：2007-01-01 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：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：: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:Genome structures are dynamic and non-randomly organized in the nucleus of higher eukaryotes. To maximize the accuracy and coverage of three-dimensional genome structural models, it is important to integrate all available sources of experimental information about a genome's organization. It remains a major c...

journal_title：Genome biology

authors： Li Q,Tjong H,Li X,Gong K,Zhou XJ,Chiolo I,Alber F

更新日期：2017-07-31 00:00:00

abstract：:Genetic studies have identified more than 150 autoimmune loci, and next-generation sequencing will identify more. Is it time to make human the model organism for autoimmune research? ...

journal_title：Genome biology

authors： Plenge R

更新日期：2010-01-01 00:00:00