Comparative and functional genomics reveals genetic diversity and determinants of host specificity among reference strains and a large collection of Chinese isolates of the phytopathogen Xanthomonas campestris pv. campestris.

abstract：:Mapping-by-sequencing has emerged as a powerful technique for genetic mapping in several plant and animal species. As this resequencing-based method requires a reference genome, its application to complex plant genomes with incomplete and fragmented sequence resources remains challenging. We perform exome sequencing o...

journal_title：Genome biology

authors： Mascher M,Jost M,Kuon JE,Himmelbach A,Aßfalg A,Beier S,Scholz U,Graner A,Stein N

更新日期：2014-06-10 00:00:00

abstract：BACKGROUND:Recent phylogenetic analyses have identified Amborella trichopoda, an understory tree species endemic to the forests of New Caledonia, as sister to a clade including all other known flowering plant species. The Amborella genome is a unique reference for understanding the evolution of angiosperm genomes becau...

journal_title：Genome biology

authors： Zuccolo A,Bowers JE,Estill JC,Xiong Z,Luo M,Sebastian A,Goicoechea JL,Collura K,Yu Y,Jiao Y,Duarte J,Tang H,Ayyampalayam S,Rounsley S,Kudrna D,Paterson AH,Pires JC,Chanderbali A,Soltis DE,Chamala S,Barbazuk B,So

更新日期：2011-01-01 00:00:00

abstract：BACKGROUND:Simple sequence repeats (SSRs) in DNA have been traditionally thought of as functionally unimportant and have been studied mainly as genetic markers. A recent handful of studies have shown, however, that SSRs in different positions of a gene can play important roles in determining protein function, genetic d...

journal_title：Genome biology

authors： Lawson MJ,Zhang L

更新日期：2006-01-01 00:00:00

abstract：BACKGROUND:Gene dosage change is a mild perturbation that is a valuable tool for pathway reconstruction in Drosophila. While it is often assumed that reducing gene dose by half leads to two-fold less expression, there is partial autosomal dosage compensation in Drosophila, which may be mediated by feedback or buffering...

journal_title：Genome biology

authors： Malone JH,Cho DY,Mattiuzzo NR,Artieri CG,Jiang L,Dale RK,Smith HE,McDaniel J,Munro S,Salit M,Andrews J,Przytycka TM,Oliver B

更新日期：2012-04-24 00:00:00

abstract：BACKGROUND:Microarray technology is increasingly being applied in biological and medical research to address a wide range of problems, such as the classification of tumors. An important statistical problem associated with tumor classification is the identification of new tumor classes using gene-expression profiles. Tw...

journal_title：Genome biology

authors： Dudoit S,Fridlyand J

更新日期：2002-06-25 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：:Your Gene structure Annotation Tool for Eukaryotes (yrGATE) provides an Annotation Tool and Community Utilities for worldwide web-based community genome and gene annotation. Annotators can evaluate gene structure evidence derived from multiple sources to create gene structure annotations. Administrators regulate the a...

journal_title：Genome biology

authors： Wilkerson MD,Schlueter SD,Brendel V

更新日期：2006-01-01 00:00:00

abstract：BACKGROUND:Complete genomic sequences of closely related organisms, such as the chlamydiae, afford the opportunity to assess significant strain differences against a background of many shared characteristics. The chlamydiae are ubiquitous intracellular parasites that are important pathogens of humans and other organism...

journal_title：Genome biology

authors： Xie G,Bonner CA,Jensen RA

更新日期：2002-08-29 00:00:00

abstract：BACKGROUND:Parasitism is a highly successful mode of life and one that requires suites of gene adaptations to permit survival within a potentially hostile host. Among such adaptations is the secretion of proteins capable of modifying or manipulating the host environment. Nippostrongylus brasiliensis is a well-studied m...

journal_title：Genome biology

authors： Harcus YM,Parkinson J,Fernández C,Daub J,Selkirk ME,Blaxter ML,Maizels RM

更新日期：2004-01-01 00:00:00

abstract：:Short hairpin RNAs can provide stable gene silencing via RNA interference. Recent studies have shown toxicity in vivo that appears to be related to saturation of the endogenous microRNA pathway. Will these findings limit the therapeutic use of such hairpins? ...

journal_title：Genome biology

authors： Snøve O Jr,Rossi JJ

更新日期：2006-01-01 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：BACKGROUND:Protein synthesis is tightly regulated and alterations to translation are characteristic of many cancers.Translation regulation is largely exerted at initiation through the eukaryotic translation initiation factor 4 F (eIF4F). eIF4F is pivotal for oncogenic signaling as it integrates mitogenic signals to amp...

journal_title：Genome biology

authors： Rubio CA,Weisburd B,Holderfield M,Arias C,Fang E,DeRisi JL,Fanidi A

更新日期：2014-01-01 00:00:00

abstract：:The use of DNA sequences to estimate the timing of evolutionary events is increasingly popular, although it is fraught with practical difficulties. But the exponential growth of relevant information and improved methods of analysis are providing increasingly reliable sequence-derived dates, and it may become possible ...

journal_title：Genome biology

authors： Wray GA

更新日期：2002-01-01 00:00:00

abstract：:Cytoscape is one of the most successful network biology analysis and visualization tools, but because of its interactive nature, its role in creating reproducible, scalable, and novel workflows has been limited. We describe Cytoscape Automation (CA), which marries Cytoscape to highly productive workflow systems, for e...

journal_title：Genome biology

authors： Otasek D,Morris JH,Bouças J,Pico AR,Demchak B

更新日期：2019-09-02 00:00:00

abstract：:Normalization is critical for removing systematic variation from microarray data. For two-color microarray platforms, intensity-dependent lowess normalization is commonly used to correct relative gene expression values for biases. Here we outline a normalization method for use when the assumptions of lowess normalizat...

journal_title：Genome biology

authors： Oshlack A,Emslie D,Corcoran LM,Smyth GK

更新日期：2007-01-01 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:Immunolabeling of metaphase chromosome spreads can map components of the human epigenome at the single cell level. Previously, there has been no systematic attempt to explore the potential of this approach for epigenomic mapping and thereby to complement approaches based on chromatin immunoprecipitation (ChI...

journal_title：Genome biology

authors： Terrenoire E,McRonald F,Halsall JA,Page P,Illingworth RS,Taylor AM,Davison V,O'Neill LP,Turner BM

更新日期：2010-01-01 00:00:00

abstract：:Single-cell RNA-seq in samples from the human neocortex demonstrate that long noncoding RNAs (lncRNAs) are abundantly expressed in specific individual brain cells, despite being hard to detect in bulk samples. This result suggests that the lncRNAs might have important functions in specific cell types in the brain. ...

journal_title：Genome biology

authors： Ma Q,Chang HY

更新日期：2016-04-14 00:00:00

abstract：:ELXR (Exon Locator and Extractor for Resequencing) streamlines the process of determining exon/intron boundaries and designing PCR and sequencing primers for high-throughput resequencing of exons. We have pre-computed ELXR primer sets for all exons identified from the human, mouse, and rat mRNA reference sequence (Ref...

journal_title：Genome biology

authors： Schageman JJ,Horton CJ,Niu S,Garner HR,Pertsemlidis A

更新日期：2004-01-01 00:00:00

abstract：:We describe a tool, THoR, that automatically creates and curates multiple sequence alignments representing protein domains. This exploits both PSI-BLAST and HMMER algorithms and provides an accurate and comprehensive alignment for any domain family. The entire process is designed for use via a web-browser, with simple...

journal_title：Genome biology

authors： Dickens NJ,Ponting CP

更新日期：2003-01-01 00:00:00

abstract：BACKGROUND:Understanding the design logic of living systems requires the understanding and comparison of proteomes. Proteomes define the commonalities between organisms more precisely than genomic sequences. Because uncertainties remain regarding the accuracy of proteomic data, several issues need to be resolved before...

journal_title：Genome biology

authors： Shevchenko A,Roguev A,Schaft D,Buchanan L,Habermann B,Sakalar C,Thomas H,Krogan NJ,Shevchenko A,Stewart AF

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: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：BACKGROUND:In eukaryotic cells, oxidative phosphorylation (OXPHOS) uses the products of both nuclear and mitochondrial genes to generate cellular ATP. Interspecies comparative analysis of these genes, which appear to be under strong functional constraints, may shed light on the evolutionary mechanisms that act on a set...

journal_title：Genome biology

authors： Tripoli G,D'Elia D,Barsanti P,Caggese C

更新日期：2005-01-01 00:00:00

abstract：BACKGROUND:Host-associated microbiomes, the microorganisms occurring inside and on host surfaces, influence evolutionary, immunological, and ecological processes. Interactions between host and microbiome affect metabolism and contribute to host adaptation to changing environments. Meta-analyses of host-associated bacte...

journal_title：Genome biology

authors： Woodhams DC,Bletz MC,Becker CG,Bender HA,Buitrago-Rosas D,Diebboll H,Huynh R,Kearns PJ,Kueneman J,Kurosawa E,LaBumbard BC,Lyons C,McNally K,Schliep K,Shankar N,Tokash-Peters AG,Vences M,Whetstone R

更新日期：2020-02-03 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：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：:To discover driver fusions beyond canonical exon-to-exon chimeric transcripts, we develop CICERO, a local assembly-based algorithm that integrates RNA-seq read support with extensive annotation for candidate ranking. CICERO outperforms commonly used methods, achieving a 95% detection rate for 184 independently validat...

journal_title：Genome biology

authors： Tian L,Li Y,Edmonson MN,Zhou X,Newman S,McLeod C,Thrasher A,Liu Y,Tang B,Rusch MC,Easton J,Ma J,Davis E,Trull A,Michael JR,Szlachta K,Mullighan C,Baker SJ,Downing JR,Ellison DW,Zhang J

更新日期：2020-05-28 00:00:00

abstract：BACKGROUND:Gene expression signatures indicative of tumor proliferative capacity and tumor-immune cell interactions have emerged as principal biology-driven predictors of breast cancer outcomes. How these signatures relate to one another in biological and prognostic contexts remains to be clarified. RESULTS:To investi...

journal_title：Genome biology

authors： Nagalla S,Chou JW,Willingham MC,Ruiz J,Vaughn JP,Dubey P,Lash TL,Hamilton-Dutoit SJ,Bergh J,Sotiriou C,Black MA,Miller LD

更新日期：2013-04-29 00:00:00

abstract：BACKGROUND:Gene loss, inversions, translocations, and other chromosomal rearrangements vary among species, resulting in different rates of structural genome evolution. Major chromosomal rearrangements are rare in most eukaryotes, giving large regions with the same genes in the same order and orientation across species....

journal_title：Genome biology

authors： Hane JK,Rouxel T,Howlett BJ,Kema GH,Goodwin SB,Oliver RP

更新日期：2011-01-01 00:00:00