A computational investigation of kinetoplastid trans-splicing.

abstract：BACKGROUND:Reconstruction of ancestral karyotypes is critical for our understanding of genome evolution, allowing for the identification of the gross changes that shaped extant genomes. The identification of such changes and their time of occurrence can shed light on the biology of each species, clade and their evoluti...

journal_title：Genome biology

authors： Damas J,Kim J,Farré M,Griffin DK,Larkin DM

更新日期：2018-10-05 00:00:00

abstract：:The first highly specific knockouts of a microRNA, miR155, in mice result in multiple defects in adaptive immunity, and also show the feasibility of investigating at least some microRNAs by gene knockout. ...

journal_title：Genome biology

authors： Moffett HF,Novina CD

更新日期：2007-01-01 00:00:00

abstract：BACKGROUND:Bread wheat is one of the most important and broadly studied crops. However, due to the complexity of its genome and incomplete genome collection of wild populations, the bread wheat genome landscape and domestication history remain elusive. RESULTS:By investigating the whole-genome resequencing data of 93 ...

journal_title：Genome biology

authors： Cheng H,Liu J,Wen J,Nie X,Xu L,Chen N,Li Z,Wang Q,Zheng Z,Li M,Cui L,Liu Z,Bian J,Wang Z,Xu S,Yang Q,Appels R,Han D,Song W,Sun Q,Jiang Y

更新日期：2019-07-12 00:00:00

abstract：BACKGROUND:Pseudogenes reveal ancestral gene functions. Some obligate intracellular bacteria, such as Mycobacterium leprae and Rickettsia spp., carry substantial fractions of pseudogenes. Until recently, horizontal gene transfers were considered to be rare events in obligate host-associated bacteria. RESULTS:We presen...

journal_title：Genome biology

authors： Fuxelius HH,Darby AC,Cho NH,Andersson SG

更新日期：2008-01-01 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：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:During the maternal-to-zygotic transition (MZT) vast changes in the embryonic transcriptome are produced by a combination of two processes: elimination of maternally provided mRNAs and synthesis of new transcripts from the zygotic genome. Previous genome-wide analyses of the MZT have been restricted to whole...

journal_title：Genome biology

authors： Siddiqui NU,Li X,Luo H,Karaiskakis A,Hou H,Kislinger T,Westwood JT,Morris Q,Lipshitz HD

更新日期：2012-02-20 00:00:00

abstract：:Improving the quality and coverage of the protein interactome is of tantamount importance for biomedical research, particularly given the various sources of uncertainty in high-throughput techniques. We introduce a structure-based framework, Coev2Net, for computing a single confidence score that addresses both false-p...

journal_title：Genome biology

authors： Hosur R,Peng J,Vinayagam A,Stelzl U,Xu J,Perrimon N,Bienkowska J,Berger B

更新日期：2012-08-31 00:00:00

abstract：BACKGROUND:The time of locus replication during S-phase is tightly regulated and correlates with chromatin state. Embryonic stem (ES) cells have an unusual chromatin profile where many developmental regulator genes that are not yet expressed are marked by both active and repressive histone modifications. This poised or...

journal_title：Genome biology

authors： Jørgensen HF,Azuara V,Amoils S,Spivakov M,Terry A,Nesterova T,Cobb BS,Ramsahoye B,Merkenschlager M,Fisher AG

更新日期：2007-01-01 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：: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：:A report on the 23rd Fungal Genetics Conference, Pacific Grove, USA, 15-20 March 2005. ...

journal_title：Genome biology

authors： Dean R,Mitchell T,Donofrio N,Jeong JS,Powell A

更新日期：2005-01-01 00:00:00

abstract：:Gene regulatory networks (GRNs) are rapidly being delineated, but their quality and biological meaning are often questioned. Here, I argue that biological meaning is challenging to define and discuss reasons why GRN validation should be interpreted cautiously. ...

journal_title：Genome biology

authors： Walhout AJ

更新日期：2011-01-01 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: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:Epigenetic mechanisms such as chromatin accessibility impact transcription factor binding to DNA and transcriptional specificity. The androgen receptor (AR), a master regulator of the male phenotype and prostate cancer pathogenesis, acts primarily through ligand-activated transcription of target genes. Altho...

journal_title：Genome biology

authors： Tewari AK,Yardimci GG,Shibata Y,Sheffield NC,Song L,Taylor BS,Georgiev SG,Coetzee GA,Ohler U,Furey TS,Crawford GE,Febbo PG

更新日期：2012-10-03 00:00:00

abstract：BACKGROUND:The nature of the protein molecular clock, the protein-specific rate of amino acid substitutions, is among the central questions of molecular evolution. Protein expression level is the dominant determinant of the clock rate in a number of organisms. It has been suggested that highly expressed proteins evolve...

journal_title：Genome biology

authors： Plata G,Gottesman ME,Vitkup D

更新日期：2010-01-01 00:00:00

abstract：SUMMARY:The large transforming growth factor-beta (TGFbeta) superfamily of secreted proteins regulate the growth, development and differentiation of cells in diverse organisms, including nematode worms, flies, mice and humans. Signals are initiated upon binding of TGFbeta superfamily members to cell-surface serine/thre...

journal_title：Genome biology

authors： Attisano L,Lee-Hoeflich ST

更新日期：2001-01-01 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:The lifelong accumulation of somatic mutations underlies age-related phenotypes and cancer. Mutagenic forces are thought to shape the genome of aging cells in a tissue-specific way. Whole genome analyses of somatic mutation patterns, based on both types and genomic distribution of variants, can shed light on...

journal_title：Genome biology

authors： Franco I,Helgadottir HT,Moggio A,Larsson M,Vrtačnik P,Johansson A,Norgren N,Lundin P,Mas-Ponte D,Nordström J,Lundgren T,Stenvinkel P,Wennberg L,Supek F,Eriksson M

更新日期：2019-12-18 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：:Transposable elements (TEs) are notable drivers of genetic innovation. Over evolutionary time, TE insertions can supply new promoter, enhancer, and insulator elements to protein-coding genes and establish novel, species-specific gene regulatory networks. Conversely, ongoing TE-driven insertional mutagenesis, nonhomolo...

journal_title：Genome biology

authors： Gerdes P,Richardson SR,Mager DL,Faulkner GJ

更新日期：2016-05-09 00:00:00

abstract：BACKGROUND:The genetic provenance of domesticated plants and the routes along which they were disseminated in prehistory have been a long-standing source of debate. Much of this debate has focused on identifying centers of origins for individual crops. However, many important crops show clear genetic signatures of mult...

journal_title：Genome biology

authors： Poets AM,Fang Z,Clegg MT,Morrell PL

更新日期：2015-08-21 00:00:00

abstract：:Compared to RNA-sequencing transcript differential analysis, gene-level differential expression analysis is more robust and experimentally actionable. However, the use of gene counts for statistical analysis can mask transcript-level dynamics. We demonstrate that 'analysis first, aggregation second,' where the p value...

journal_title：Genome biology

authors： Yi L,Pimentel H,Bray NL,Pachter L

更新日期：2018-04-12 00:00:00

abstract：BACKGROUND:Mitogen-activated protein kinases (MAPKs) are key regulators of immune responses in animals and plants. In Arabidopsis, perception of microbe-associated molecular patterns (MAMPs) activates the MAPKs MPK3, MPK4 and MPK6. Increasing information depicts the molecular events activated by MAMPs in plants, but th...

journal_title：Genome biology

authors： Frei dit Frey N,Garcia AV,Bigeard J,Zaag R,Bueso E,Garmier M,Pateyron S,de Tauzia-Moreau ML,Brunaud V,Balzergue S,Colcombet J,Aubourg S,Martin-Magniette ML,Hirt H

更新日期：2014-06-30 00:00:00

abstract：:We demonstrate that loss-of-function yeast phenotypes are predictable by guilt-by-association in functional gene networks. Testing 1,102 loss-of-function phenotypes from genome-wide assays of yeast reveals predictability of diverse phenotypes, spanning cellular morphology, growth, metabolism, and quantitative cell sha...

journal_title：Genome biology

authors： McGary KL,Lee I,Marcotte EM

更新日期：2007-01-01 00:00:00

abstract：:Transcription factor binding sites compete for a limited pool of bioavailable transcription factor molecules to fine tune gene expression. ...

journal_title：Genome biology

authors： Karreth FA,Tay Y,Pandolfi PP

更新日期：2014-04-28 00:00:00

abstract：BACKGROUND:Adult T cell acute lymphoblastic leukemia (T-ALL) is a rare disease that affects less than 10 individuals in one million. It has been less studied than its cognate pediatric malignancy, which is more prevalent. A higher percentage of the adult patients relapse, compared to children. It is thus essential to s...

journal_title：Genome biology

authors： Sentís I,Gonzalez S,Genescà E,García-Hernández V,Muiños F,Gonzalez C,López-Arribillaga E,Gonzalez J,Fernandez-Ibarrondo L,Mularoni L,Espinosa L,Bellosillo B,Ribera JM,Bigas A,Gonzalez-Perez A,Lopez-Bigas N

更新日期：2020-11-23 00:00:00

abstract：BACKGROUND:Synthetic genetic interactions have recently been mapped on a genome scale in the budding yeast Saccharomyces cerevisiae, providing a functional view of the central processes of eukaryotic life. Currently, comprehensive genetic interaction networks have not been determined for other species, and we therefore...

journal_title：Genome biology

authors： Koch EN,Costanzo M,Bellay J,Deshpande R,Chatfield-Reed K,Chua G,D'Urso G,Andrews BJ,Boone C,Myers CL

更新日期：2012-07-02 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