FAN-C: a feature-rich framework for the analysis and visualisation of chromosome conformation capture data.

abstract：BACKGROUND:There are significant limitations in existing methods for the genome-wide identification of genes whose expression patterns affect traits. RESULTS:The transcriptomes of five tissues from 27 genetically diverse maize inbred lines were deeply sequenced to identify genes exhibiting high and low levels of expre...

journal_title：Genome biology

authors： Lin HY,Liu Q,Li X,Yang J,Liu S,Huang Y,Scanlon MJ,Nettleton D,Schnable PS

更新日期：2017-10-17 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：BACKGROUND:The recent reports of two circular RNAs (circRNAs) with strong potential to act as microRNA (miRNA) sponges suggest that circRNAs might play important roles in regulating gene expression. However, the global properties of circRNAs are not well understood. RESULTS:We developed a computational pipeline to ide...

journal_title：Genome biology

authors： Guo JU,Agarwal V,Guo H,Bartel DP

更新日期：2014-07-29 00:00:00

abstract：:In most eukaryotes, histones, which are the major structural components of chromatin, are expressed as a family of sequence variants encoded by multiple genes. Because different histone variants can contribute to a distinct or unique nucleosomal architecture, this heterogeneity can be exploited to regulate a wide rang...

journal_title：Genome biology

authors： Brown DT

更新日期：2001-01-01 00:00:00

abstract：:The spectrum of mutations discovered in cancer genomes can be explained by the activity of a few elementary mutational processes. We present a novel probabilistic method, EMu, to infer the mutational signatures of these processes from a collection of sequenced tumors. EMu naturally incorporates the tumor-specific oppo...

journal_title：Genome biology

authors： Fischer A,Illingworth CJ,Campbell PJ,Mustonen V

更新日期：2013-04-29 00:00:00

abstract：BACKGROUND:Despite decades of research, the molecular mechanisms responsible for the evolution of morphological diversity remain poorly understood. While current models assume that species-specific morphologies are governed by differential use of conserved genetic regulatory circuits, it is debated whether non-conserve...

journal_title：Genome biology

authors： Milde S,Hemmrich G,Anton-Erxleben F,Khalturin K,Wittlieb J,Bosch TC

更新日期：2009-01-01 00:00:00

abstract：:Despite major progress in dissecting the molecular pathways that control DNA methylation patterns in plants, little is known about the mechanisms that shape plant methylomes over evolutionary time. Drawing on recent intra- and interspecific epigenomic studies, we show that methylome evolution over long timescales is l...

journal_title：Genome biology

authors： Vidalis A,Živković D,Wardenaar R,Roquis D,Tellier A,Johannes F

更新日期：2016-12-20 00:00:00

abstract：:Many essential transcription factors have conserved roles in regulating biological programs, yet their genomic occupancy can diverge significantly. A new study demonstrates that such variations are primarily due to cis-regulatory sequences, rather than differences between the regulators or nuclear environments. ...

journal_title：Genome biology

authors： Zinzen RP,Furlong EE

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: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：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: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：:Transposase-Accessible Chromatin followed by sequencing (ATAC-seq) is a simple protocol for detection of open chromatin. Computational footprinting, the search for regions with depletion of cleavage events due to transcription factor binding, is poorly understood for ATAC-seq. We propose the first footprinting method ...

journal_title：Genome biology

authors： Li Z,Schulz MH,Look T,Begemann M,Zenke M,Costa IG

更新日期：2019-02-26 00:00:00

abstract：:Purification of proteins cross-linked to mRNAs has identified 800 mRNA-binding proteins and their characteristics. ...

journal_title：Genome biology

authors： Sibley CR,Attig J,Ule J

更新日期：2012-07-17 00:00:00

abstract：:Genomic regions with altered gene expression are a characteristic feature of cancer cells. We present a novel method for identifying such regions in gene expression maps. This method is based on total variation minimization, a classical signal restoration technique. In systematic evaluations, we show that our method c...

journal_title：Genome biology

authors： Nilsson B,Johansson M,Heyden A,Nelander S,Fioretos T

更新日期：2008-01-21 00:00:00

abstract：:Many differential gene expression analyses are conducted with an inadequate number of biological replicates. We describe an easy and effective RNA-seq approach using molecular barcoding to enable profiling of a large number of replicates simultaneously. This approach significantly improves the performance of different...

journal_title：Genome biology

authors： Li Y,Yang H,Zhang H,Liu Y,Shang H,Zhao H,Zhang T,Tu Q

更新日期：2020-03-23 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

abstract：:Recent work has identified the human NOD-like receptor NLRX1 as a negative regulator of intracellular signaling leading to type I interferon production. Here we discuss these findings and the questions and implications they raise regarding the function of NOD-like receptors in the antiviral response. ...

journal_title：Genome biology

authors： Pietras EM,Cheng G

更新日期：2008-04-25 00:00:00

abstract：BACKGROUND:Genome editing of malaria parasites is key to the generation of live attenuated parasites used in experimental vaccination approaches. DNA repair in Plasmodium generally occurs only through homologous recombination. This has been used to generate transgenic parasites that lack one to three genes, leading to ...

journal_title：Genome biology

authors： Singer M,Marshall J,Heiss K,Mair GR,Grimm D,Mueller AK,Frischknecht F

更新日期：2015-11-17 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：:Genome-scale metabolic models (GEMs) computationally describe gene-protein-reaction associations for entire metabolic genes in an organism, and can be simulated to predict metabolic fluxes for various systems-level metabolic studies. Since the first GEM for Haemophilus influenzae was reported in 1999, advances have be...

journal_title：Genome biology

authors： Gu C,Kim GB,Kim WJ,Kim HU,Lee SY

更新日期：2019-06-13 00:00:00

abstract：BACKGROUND:Many genome-wide collections of candidate cis-regulatory elements (cCREs) have been defined using genomic and epigenomic data, but it remains a major challenge to connect these elements to their target genes. RESULTS:To facilitate the development of computational methods for predicting target genes, we deve...

journal_title：Genome biology

authors： Moore JE,Pratt HE,Purcaro MJ,Weng Z

更新日期：2020-01-22 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：:Silent information regulator 2 (Sir2) proteins, or sirtuins, are protein deacetylases dependent on nicotine adenine dinucleotide (NAD) and are found in organisms ranging from bacteria to humans. In eukaryotes, sirtuins regulate transcriptional repression, recombination, the cell-division cycle, microtubule organizatio...

journal_title：Genome biology

authors： North BJ,Verdin E

更新日期：2004-01-01 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:Xanthomonas campestris pathovar campestris (Xcc) is the causal agent of black rot disease of crucifers worldwide. The molecular genetic diversity and host specificity of Xcc are poorly understood. RESULTS:We constructed a microarray based on the complete genome sequence of Xcc strain 8004 and investigated t...

journal_title：Genome biology

authors： He YQ,Zhang L,Jiang BL,Zhang ZC,Xu RQ,Tang DJ,Qin J,Jiang W,Zhang X,Liao J,Cao JR,Zhang SS,Wei ML,Liang XX,Lu GT,Feng JX,Chen B,Cheng J,Tang JL

更新日期：2007-01-01 00:00:00

abstract：:A report of the recent EMBO Conference 'From Functional Genomics to Systems Biology' held at the EMBL Advanced Training Centre, Heidelberg, Germany, 13-16 November 2010. ...

journal_title：Genome biology

authors： Fordyce P,Ingolia N

更新日期：2011-01-01 00:00:00

abstract：BACKGROUND:Diffuse large B-cell lymphoma (DLBCL) is an aggressive disease, with 30% to 40% of patients failing to be cured with available primary therapy. microRNAs (miRNAs) are RNA molecules that attenuate expression of their mRNA targets. To characterize the DLBCL miRNome, we sequenced miRNAs from 92 DLBCL and 15 ben...

journal_title：Genome biology

authors： Lim EL,Trinh DL,Scott DW,Chu A,Krzywinski M,Zhao Y,Robertson AG,Mungall AJ,Schein J,Boyle M,Mottok A,Ennishi D,Johnson NA,Steidl C,Connors JM,Morin RD,Gascoyne RD,Marra MA

更新日期：2015-01-29 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:Tumors comprise a complex microenvironment of interacting malignant and stromal cell types. Much of our understanding of the tumor microenvironment comes from in vitro studies isolating the interactions between malignant cells and a single stromal cell type, often along a single pathway. RESULT:To develop a...

journal_title：Genome biology

authors： Gentles AJ,Hui AB,Feng W,Azizi A,Nair RV,Bouchard G,Knowles DA,Yu A,Jeong Y,Bejnood A,Forgó E,Varma S,Xu Y,Kuong A,Nair VS,West R,van de Rijn M,Hoang CD,Diehn M,Plevritis SK

更新日期：2020-05-07 00:00:00