CICERO: a versatile method for detecting complex and diverse driver fusions using cancer RNA sequencing data.

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：:CRISPR-Cas9 gene editing has transformed our ability to rapidly interrogate the functional impact of somatic mutations in human cancers. Droplet-based technology enables the analysis of Cas9-introduced gene edits in thousands of single cells. Using this technology, we analyze Ba/F3 cells engineered to express single o...

journal_title：Genome biology

authors： Ten Hacken E,Clement K,Li S,Hernández-Sánchez M,Redd R,Wang S,Ruff D,Gruber M,Baranowski K,Jacob J,Flynn J,Jones KW,Neuberg D,Livak KJ,Pinello L,Wu CJ

更新日期：2020-10-20 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:Comparisons between C3 and C4 grasses often utilize C3 species from the subfamilies Ehrhartoideae or Pooideae and C4 species from the subfamily Panicoideae, two clades that diverged over 50 million years ago. The divergence of the C3 panicoid grass Dichanthelium oligosanthes from the independent C4 lineages ...

journal_title：Genome biology

authors： Studer AJ,Schnable JC,Weissmann S,Kolbe AR,McKain MR,Shao Y,Cousins AB,Kellogg EA,Brutnell TP

更新日期：2016-10-28 00:00:00

abstract：:A new generation of DNA-sequencing platforms will become commercially available over the next few years. These instruments will enable re-sequencing of human genomes at a previously unimagined throughput and low cost. Here, I examine why the 1,000 dollar human genome is an important goal for research and clinical diag...

journal_title：Genome biology

authors： Mardis ER

更新日期：2006-01-01 00:00:00

abstract：BACKGROUND:Alternative pre-mRNA splicing is an important gene regulation mechanism for expanding proteomic diversity in higher eukaryotes. Each splicing regulator can potentially influence a large group of alternative exons. Meanwhile, each alternative exon is controlled by multiple splicing regulators. The rapid accum...

journal_title：Genome biology

authors： Chen L,Zheng S

更新日期：2009-01-01 00:00:00

abstract：BACKGROUND:Although genetic or epigenetic alterations have been shown to affect the three-dimensional organization of genomes, the utility of chromatin conformation in the classification of human disease has never been addressed. RESULTS:Here, we explore whether chromatin conformation can be used to classify human leu...

journal_title：Genome biology

authors： Rousseau M,Ferraiuolo MA,Crutchley JL,Wang XQ,Miura H,Blanchette M,Dostie J

更新日期：2014-04-30 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：:DNA arrays are valuable tools in molecular biology laboratories. Their rapid acceptance was aided by the release of plans for a pin-spotting microarrayer by researchers at Stanford. Inkjet microarraying is a flexible, complementary technique that allows the synthesis of arrays of any oligonucleotide sequences de novo....

journal_title：Genome biology

authors： Lausted C,Dahl T,Warren C,King K,Smith K,Johnson M,Saleem R,Aitchison J,Hood L,Lasky SR

更新日期：2004-01-01 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:Sequencing the genomes of the first few eukaryotes created the impression that gene number shows no correlation with organism complexity, often referred to as the G-value paradox. Several attempts have previously been made to resolve this paradox, citing multifunctionality of proteins, alternative splicing, ...

journal_title：Genome biology

authors： Schad E,Tompa P,Hegyi H

更新日期：2011-12-19 00:00:00

abstract：:Key components of the programmed cell death pathway are conserved between Caenorhabditis elegans, Drosophila melanogaster and humans. The search for additional homologs has been facilitated by the availability of the entire genomic sequence for each of these organisms. ...

journal_title：Genome biology

authors： Tittel JN,Steller H

更新日期：2000-01-01 00:00:00

abstract：BACKGROUND:DNA methylation and the Polycomb repression system are epigenetic mechanisms that play important roles in maintaining transcriptional repression. Recent evidence suggests that DNA methylation can attenuate the binding of Polycomb protein components to chromatin and thus plays a role in determining their geno...

journal_title：Genome biology

authors： Reddington JP,Perricone SM,Nestor CE,Reichmann J,Youngson NA,Suzuki M,Reinhardt D,Dunican DS,Prendergast JG,Mjoseng H,Ramsahoye BH,Whitelaw E,Greally JM,Adams IR,Bickmore WA,Meehan RR

更新日期：2013-03-25 00:00:00

abstract：BACKGROUND:Methylation of nucleotides, notably in the forms of 5-methylcytosine (5mC) in DNA and N6-methyladenosine (m6A) in mRNA, carries important information for gene regulation. 5mC has been elucidated to participate in the regulation of fruit ripening, whereas the function of m6A in this process and the interplay ...

journal_title：Genome biology

authors： Zhou L,Tian S,Qin G

更新日期：2019-08-06 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：:CRISPR guide RNA libraries have been iteratively improved to provide increasingly efficient reagents, although their large size is a barrier for many applications. We design an optimised minimal genome-wide human CRISPR-Cas9 library (MinLibCas9) by mining existing large-scale gene loss-of-function datasets, resulting ...

journal_title：Genome biology

authors： Gonçalves E,Thomas M,Behan FM,Picco G,Pacini C,Allen F,Vinceti A,Sharma M,Jackson DA,Price S,Beaver CM,Dovey O,Parry-Smith D,Iorio F,Parts L,Yusa K,Garnett MJ

更新日期：2021-01-21 00:00:00

abstract：BACKGROUND:The Asian tiger mosquito Aedes albopictus is globally expanding and has become the main vector for human arboviruses in Europe. With limited antiviral drugs and vaccines available, vector control is the primary approach to prevent mosquito-borne diseases. A reliable and accurate DNA sequence of the Ae. albop...

journal_title：Genome biology

authors： Palatini U,Masri RA,Cosme LV,Koren S,Thibaud-Nissen F,Biedler JK,Krsticevic F,Johnston JS,Halbach R,Crawford JE,Antoshechkin I,Failloux AB,Pischedda E,Marconcini M,Ghurye J,Rhie A,Sharma A,Karagodin DA,Jenrette J,Ga

更新日期：2020-08-26 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：:Levels of transcripts sharing microRNA response elements are co-regulated. These RNA-RNA interactions imply that combinations of microRNAs modulate cell-specific transcript networks. ...

journal_title：Genome biology

authors： Marques AC,Tan J,Ponting CP

更新日期：2011-11-21 00:00:00

abstract：:Cryptochromes are photoreceptors that regulate entrainment by light of the circadian clock in plants and animals. They also act as integral parts of the central circadian oscillator in animal brains and as receptors controlling photomorphogenesis in response to blue or ultraviolet (UV-A) light in plants. Cryptochromes...

journal_title：Genome biology

authors： Lin C,Todo T

更新日期：2005-01-01 00:00:00

abstract：BACKGROUND:In microarray data analysis, the comparison of gene-expression profiles with respect to different conditions and the selection of biologically interesting genes are crucial tasks. Multivariate statistical methods have been applied to analyze these large datasets. Less work has been published concerning the a...

journal_title：Genome biology

authors： Landgrebe J,Wurst W,Welzl G

更新日期：2002-01-01 00:00:00

abstract：:Protein kinases with a conserved catalytic domain make up one of the largest 'superfamilies' of eukaryotic proteins and play many key roles in biology and disease. Efforts to identify and classify all the members of the eukaryotic protein kinase superfamily have recently culminated in the mining of essentially complet...

journal_title：Genome biology

authors： Hanks SK

更新日期：2003-01-01 00:00:00

abstract：:We describe an ontology for cell types that covers the prokaryotic, fungal, animal and plant worlds. It includes over 680 cell types. These cell types are classified under several generic categories and are organized as a directed acyclic graph. The ontology is available in the formats adopted by the Open Biological O...

journal_title：Genome biology

authors： Bard J,Rhee SY,Ashburner M

更新日期：2005-01-01 00:00:00

abstract：BACKGROUND:Massively parallel pyrosequencing systems have increased the efficiency of DNA sequencing, although the published per-base accuracy of a Roche GS20 is only 96%. In genome projects, highly redundant consensus assemblies can compensate for sequencing errors. In contrast, studies of microbial diversity that cat...

journal_title：Genome biology

authors： Huse SM,Huber JA,Morrison HG,Sogin ML,Welch DM

更新日期：2007-01-01 00:00:00

abstract：BACKGROUND:Molecular characterization of tumors has been critical for identifying important genes in cancer biology and for improving tumor classification and diagnosis. Long non-coding RNAs, as a new, relatively unstudied class of transcripts, provide a rich opportunity to identify both functional drivers and cancer-t...

journal_title：Genome biology

authors： Brunner AL,Beck AH,Edris B,Sweeney RT,Zhu SX,Li R,Montgomery K,Varma S,Gilks T,Guo X,Foley JW,Witten DM,Giacomini CP,Flynn RA,Pollack JR,Tibshirani R,Chang HY,van de Rijn M,West RB

更新日期：2012-08-28 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：BACKGROUND:Retroviral elements are pervasively transcribed and dynamically regulated during development. While multiple histone- and DNA-modifying enzymes have broadly been associated with their global silencing, little is known about how the many diverse retroviral families are each selectively recognized. RESULTS:He...

journal_title：Genome biology

authors： Mak KS,Burdach J,Norton LJ,Pearson RC,Crossley M,Funnell AP

更新日期：2014-04-30 00:00:00

abstract：BACKGROUND:MicroRNAs (miRNAs) are oligoribonucleotides with an important role in regulation of gene expression at the level of translation. Despite imperfect target complementarity, they can also significantly reduce mRNA levels. The validity of miRNA target gene predictions is difficult to assess at the protein level....

journal_title：Genome biology

authors： Arora A,Simpson DA

更新日期：2008-01-01 00:00:00

abstract：BACKGROUND:Human tissue is increasingly being whole genome sequenced as we transition into an era of genomic medicine. With this arises the potential to detect sequences originating from microorganisms, including pathogens amid the plethora of human sequencing reads. In cancer research, the tumorigenic ability of patho...

journal_title：Genome biology

authors： Gihawi A,Rallapalli G,Hurst R,Cooper CS,Leggett RM,Brewer DS

更新日期：2019-10-22 00:00:00

abstract：BACKGROUND:Despite their regional economic importance and being increasingly reared globally, the origins and evolution of the llama and alpaca remain poorly understood. Here we report reference genomes for the llama, and for the guanaco and vicuña (their putative wild progenitors), compare these with the published alp...

journal_title：Genome biology

authors： Fan R,Gu Z,Guang X,Marín JC,Varas V,González BA,Wheeler JC,Hu Y,Li E,Sun X,Yang X,Zhang C,Gao W,He J,Munch K,Corbett-Detig R,Barbato M,Pan S,Zhan X,Bruford MW,Dong C

更新日期：2020-07-02 00:00:00