An improved method for detecting and delineating genomic regions with altered gene expression in cancer.

abstract：BACKGROUND:The assessment and characterization of the gut microbiome has become a focus of research in the area of human autoimmune diseases. Ankylosing spondylitis is an inflammatory autoimmune disease and evidence showed that ankylosing spondylitis may be a microbiome-driven disease. RESULTS:To investigate the relat...

journal_title：Genome biology

authors： Wen C,Zheng Z,Shao T,Liu L,Xie Z,Le Chatelier E,He Z,Zhong W,Fan Y,Zhang L,Li H,Wu C,Hu C,Xu Q,Zhou J,Cai S,Wang D,Huang Y,Breban M,Qin N,Ehrlich SD

更新日期：2017-07-27 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:Diet is a major contributor to metabolic disease risk, but there is controversy as to whether increased incidences of diseases such as non-alcoholic fatty liver disease arise from consumption of saturated fats or free sugars. Here, we investigate whether a sub-set of triacylglycerols (TAGs) were associated w...

journal_title：Genome biology

authors： Sanders FWB,Acharjee A,Walker C,Marney L,Roberts LD,Imamura F,Jenkins B,Case J,Ray S,Virtue S,Vidal-Puig A,Kuh D,Hardy R,Allison M,Forouhi N,Murray AJ,Wareham N,Vacca M,Koulman A,Griffin JL

更新日期：2018-06-20 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:Pre-mRNA splicing is an essential step in gene expression that occurs co-transcriptionally in the cell nucleus, involving a large number of RNA binding protein splicing factors, in addition to core spliceosome components. Several of these proteins are required for the recognition of intronic sequence element...

journal_title：Genome biology

authors： Gama-Carvalho M,Barbosa-Morais NL,Brodsky AS,Silver PA,Carmo-Fonseca M

更新日期：2006-01-01 00:00:00

abstract：BACKGROUND:Despite the biological and economic significance of scleractinian reef-building corals, the lack of large molecular datasets for a representative range of species limits understanding of many aspects of their biology. Within the Scleractinia, based on molecular evidence, it is generally recognised that there...

journal_title：Genome biology

authors： Ying H,Cooke I,Sprungala S,Wang W,Hayward DC,Tang Y,Huttley G,Ball EE,Forêt S,Miller DJ

更新日期：2018-11-02 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：BACKGROUND:The C2H2 zinc finger (C2H2-ZF) is the most numerous protein domain in many metazoans, but is not as frequent or diverse in other eukaryotes. The biochemical and evolutionary mechanisms that underlie the diversity of this DNA-binding domain exclusively in metazoans are, however, mostly unknown. RESULTS:Here,...

journal_title：Genome biology

authors： Najafabadi HS,Garton M,Weirauch MT,Mnaimneh S,Yang A,Kim PM,Hughes TR

更新日期：2017-09-06 00:00:00

abstract：BACKGROUND:There is tremendous potential for genome sequencing to improve clinical diagnosis and care once it becomes routinely accessible, but this will require formalizing research methods into clinical best practices in the areas of sequence data generation, analysis, interpretation and reporting. The CLARITY Challe...

journal_title：Genome biology

authors： Brownstein CA,Beggs AH,Homer N,Merriman B,Yu TW,Flannery KC,DeChene ET,Towne MC,Savage SK,Price EN,Holm IA,Luquette LJ,Lyon E,Majzoub J,Neupert P,McCallie D Jr,Szolovits P,Willard HF,Mendelsohn NJ,Temme R,Finkel R

更新日期：2014-03-25 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：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：:Two recent studies demonstrate the power of integrating tumor genotype information with epigenetic and proteomic studies to discover potential therapeutic targets in breast cancer. ...

journal_title：Genome biology

authors： Sandoval GJ,Hahn WC

更新日期：2017-05-22 00:00:00

abstract：BACKGROUND:The discovery of cytosine hydroxymethylation (5hmC) as a mechanism that potentially controls DNA methylation changes typical of neoplasia prompted us to investigate its behaviour in colon cancer. 5hmC is globally reduced in proliferating cells such as colon tumours and the gut crypt progenitors, from which t...

journal_title：Genome biology

authors： Uribe-Lewis S,Stark R,Carroll T,Dunning MJ,Bachman M,Ito Y,Stojic L,Halim S,Vowler SL,Lynch AG,Delatte B,de Bony EJ,Colin L,Defrance M,Krueger F,Silva AL,Ten Hoopen R,Ibrahim AE,Fuks F,Murrell A

更新日期：2015-04-01 00:00:00

abstract：BACKGROUND:Cell lineage-specific DNA methylation patterns distinguish normal human leukocyte subsets and can be used to detect and quantify these subsets in peripheral blood. We have developed an approach that uses DNA methylation to simultaneously quantify multiple leukocyte subsets, enabling investigation of immune m...

journal_title：Genome biology

authors： Accomando WP,Wiencke JK,Houseman EA,Nelson HH,Kelsey KT

更新日期：2014-03-05 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：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：: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：: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 mobilization of transposable elements (TEs) is suppressed by host genome defense mechanisms. Recent studies showed that the cis-regulatory region of Arabidopsis thaliana COPIA78/ONSEN retrotransposons contains heat-responsive elements (HREs), which cause their activation during heat stress. However, it r...

journal_title：Genome biology

authors： Pietzenuk B,Markus C,Gaubert H,Bagwan N,Merotto A,Bucher E,Pecinka A

更新日期：2016-10-11 00:00:00

abstract：BACKGROUND:Hemispheric asymmetry in neuronal processes is a fundamental feature of the human brain and drives symptom lateralization in Parkinson's disease (PD), but its molecular determinants are unknown. Here, we identify divergent epigenetic patterns involved in hemispheric asymmetry by profiling DNA methylation in ...

journal_title：Genome biology

authors： Li P,Ensink E,Lang S,Marshall L,Schilthuis M,Lamp J,Vega I,Labrie V

更新日期：2020-03-09 00:00:00

abstract：BACKGROUND:Pseudomonas aeruginosa is a ubiquitous environmental bacterium and an important opportunistic human pathogen. Generally, the acquisition of genes in the form of pathogenicity islands distinguishes pathogenic isolates from nonpathogens. We therefore sequenced a highly virulent strain of P. aeruginosa, PA14, a...

journal_title：Genome biology

authors： Lee DG,Urbach JM,Wu G,Liberati NT,Feinbaum RL,Miyata S,Diggins LT,He J,Saucier M,Déziel E,Friedman L,Li L,Grills G,Montgomery K,Kucherlapati R,Rahme LG,Ausubel FM

更新日期：2006-01-01 00:00:00

abstract：:A recent study in Genome Biology has characterized the evolution of candidate hominoid-specific liver enhancers by using massively parallel reporter assays (MPRAs). ...

journal_title：Genome biology

authors： Kwon SB,Ernst J

更新日期：2018-08-14 00:00:00

abstract：:The first genome sequence of the extinct European wild aurochs reveals the genetic foundation of native British and Irish landraces of cattle.See related Research article: www.dx.doi.org/10.1186/s13059-015-0790-2. ...

journal_title：Genome biology

authors： Orlando L

更新日期：2015-10-26 00:00:00

abstract：BACKGROUND:Drug resistance remains a major public health challenge for malaria treatment and eradication. Individual loci associated with drug resistance to many antimalarials have been identified, but their epistasis with other resistance mechanisms has not yet been elucidated. RESULTS:We previously described two mut...

journal_title：Genome biology

authors： Herman JD,Rice DP,Ribacke U,Silterra J,Deik AA,Moss EL,Broadbent KM,Neafsey DE,Desai MM,Clish CB,Mazitschek R,Wirth DF

更新日期：2014-01-01 00:00:00

abstract：BACKGROUND:Understanding the embryonic stem cell (ESC) fate decision between self-renewal and proper differentiation is important for developmental biology and regenerative medicine. Attention has focused on mechanisms involving histone modifications, alternative pre-messenger RNA splicing, and cell-cycle progression. ...

journal_title：Genome biology

authors： Xu Y,Zhao W,Olson SD,Prabhakara KS,Zhou X

更新日期：2018-09-14 00:00:00

abstract：:The genetic and molecular analysis of circadian timekeeping mechanisms has accelerated as a result of the increasing volume of genomic markers and nucleotide sequence information. Completion of whole genome sequences and the use of differential gene expression technology will hasten the discovery of the clock output p...

journal_title：Genome biology

authors： Hardin PE

更新日期：2000-01-01 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：: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 duplication followed by divergence is one of the main sources of metabolic versatility. The patchwork and stepwise models of metabolic evolution help us to understand these processes, but their assumptions are relatively simplistic. We used a network-based approach to determine the influence of metaboli...

journal_title：Genome biology

authors： Díaz-Mejía JJ,Pérez-Rueda E,Segovia L

更新日期：2007-01-01 00:00:00

abstract：BACKGROUND:ADAR proteins are among the most extensively studied RNA binding proteins. They bind to their target and deaminate specific adenosines to inosines. ADAR activity is essential, and the editing of a subset of their targets is critical for viability. Recently, a huge number of novel ADAR targets were detected b...

journal_title：Genome biology

authors： Pinto Y,Cohen HY,Levanon EY

更新日期：2014-01-07 00:00:00