Changes in the organization of the genome during the mammalian cell cycle.

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：BACKGROUND:Neuropsychiatric disorders are common forms of disability in humans. Despite recent progress in deciphering the genetics of these disorders, their phenotypic complexity continues to be a major challenge. Mendelian neuropsychiatric disorders are rare but their study has the potential to unravel novel mechanis...

journal_title：Genome biology

authors： Shamseldin HE,Masuho I,Alenizi A,Alyamani S,Patil DN,Ibrahim N,Martemyanov KA,Alkuraya FS

更新日期：2016-09-27 00:00:00

abstract：BACKGROUND:Nuclear factor I-A (NFI-A), a phylogenetically conserved transcription/replication protein, plays a crucial role in mouse brain development. Previous studies have shown that disruption of the Nfia gene in mice leads to perinatal lethality, corpus callosum agenesis, and hydrocephalus. RESULTS:To identify pot...

journal_title：Genome biology

authors： Wong YW,Schulze C,Streichert T,Gronostajski RM,Schachner M,Tilling T

更新日期：2007-01-01 00:00:00

abstract：BACKGROUND:Over the past years a variety of host restriction genes have been identified in human and mammals that modulate retrovirus infectivity, replication, assembly, and/or cross-species transmission. Among these host-encoded restriction factors, the APOBEC3 (A3; apolipoprotein B mRNA-editing catalytic polypeptide ...

journal_title：Genome biology

authors： Münk C,Beck T,Zielonka J,Hotz-Wagenblatt A,Chareza S,Battenberg M,Thielebein J,Cichutek K,Bravo IG,O'Brien SJ,Löchelt M,Yuhki N

更新日期：2008-01-01 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：UNLABELLED:Ancient DNA is typically highly degraded with appreciable cytosine deamination, and contamination with present-day DNA often complicates the identification of endogenous molecules. Together, these factors impede accurate assembly of the endogenous ancient mitochondrial genome. We present schmutzi, an iterati...

journal_title：Genome biology

authors： Renaud G,Slon V,Duggan AT,Kelso J

更新日期：2015-10-12 00:00:00

abstract：:We develop PIRCh-seq, a method which enables a comprehensive survey of chromatin-associated RNAs in a histone modification-specific manner. We identify hundreds of chromatin-associated RNAs in several cell types with substantially less contamination by nascent transcripts. Non-coding RNAs are found enriched on chromat...

journal_title：Genome biology

authors： Fang J,Ma Q,Chu C,Huang B,Li L,Cai P,Batista PJ,Tolentino KEM,Xu J,Li R,Du P,Qu K,Chang HY

更新日期：2019-12-20 00:00:00

abstract：BACKGROUND:Protein domains are commonly used to assess the functional roles and evolutionary relationships of proteins and protein families. Here, we use the Pfam protein family database to examine a set of candidate partial domains. Pfam protein domains are often thought of as evolutionarily indivisible, structurally ...

journal_title：Genome biology

authors： Triant DA,Pearson WR

更新日期：2015-05-15 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：:According to a recent article published in Genome Biology, Duggan and coworkers sequenced and partially assembled five genomes of smallpox vaccines from the nineteenth century. No information regarding the ends of genomes was presented, and they are important to understand the evolutionary relationship of the differen...

journal_title：Genome biology

authors： Brinkmann A,Souza ARV,Esparza J,Nitsche A,Damaso CR

更新日期：2020-12-04 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: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：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：:We polled the Editorial Board of Genome Biology to ask where they see genomics going in the next few years. Here are some of their responses. ...

journal_title：Genome biology

authors： Cheifet B

更新日期：2019-01-22 00:00:00

abstract：:A report of the Wellcome Trust Functional Genomics and Systems Biology Conference, Hinxton, UK, 29 November to 1 December 2011. ...

journal_title：Genome biology

authors： Bakal C

更新日期：2012-01-30 00:00:00

abstract：:A report on the Cold Spring Harbor Asia conference on Genome Assisted Biology of Crops and Model Plant Systems Meeting, held in Suzhou, China, April 21-25, 2014. ...

journal_title：Genome biology

authors： Lee I

更新日期：2014-05-23 00:00:00

abstract：:Ever since DNA microarrays were first applied to the quantitation of RNA levels, there has been considerable interest in generating a protein homolog that can be used to assay cellular protein expression. A recent paper describes the first microarray that can be used for such protein profiling. ...

journal_title：Genome biology

authors： Tomlinson IM,Holt LJ

更新日期：2001-01-01 00:00:00

abstract：:Piwi-interacting RNAs (piRNAs) originate from genomic regions dubbed piRNA clusters. How cluster transcripts are selected for processing into piRNAs is not understood. We discuss evidence for the involvement of chromatin structure and maternally inherited piRNAs in determining their fate. ...

journal_title：Genome biology

authors： Le Thomas A,Tóth KF,Aravin AA

更新日期：2014-01-27 00:00:00

abstract：:We used scaled factorial moments to search for intermittency in the log expression ratios (LERs) for thousands of genes spotted on cDNA microarrays (gene chips). Results indicate varying levels of intermittency in gene expression. The observation of intermittency in the data analyzed provides a complimentary handle on...

journal_title：Genome biology

authors： Peterson LE,Lau K

更新日期：2002-05-29 00:00:00

abstract：BACKGROUND:The human genome contains "dark" gene regions that cannot be adequately assembled or aligned using standard short-read sequencing technologies, preventing researchers from identifying mutations within these gene regions that may be relevant to human disease. Here, we identify regions with few mappable reads ...

journal_title：Genome biology

authors： Ebbert MTW,Jensen TD,Jansen-West K,Sens JP,Reddy JS,Ridge PG,Kauwe JSK,Belzil V,Pregent L,Carrasquillo MM,Keene D,Larson E,Crane P,Asmann YW,Ertekin-Taner N,Younkin SG,Ross OA,Rademakers R,Petrucelli L,Fryer JD

更新日期：2019-05-20 00:00:00

abstract：BACKGROUND:Polydnaviruses, double-stranded DNA viruses with segmented genomes, have evolved as obligate endosymbionts of parasitoid wasps. Virus particles are replication deficient and produced by female wasps from proviral sequences integrated into the wasp genome. These particles are co-injected with eggs into caterp...

journal_title：Genome biology

authors： Desjardins CA,Gundersen-Rindal DE,Hostetler JB,Tallon LJ,Fadrosh DW,Fuester RW,Pedroni MJ,Haas BJ,Schatz MC,Jones KM,Crabtree J,Forberger H,Nene V

更新日期：2008-01-01 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：:Gene-expression profiling has yielded important information about simple systems, but complex tissues have not yet been widely profiled. Four recent studies of mammalian skeletal muscles have added to the catalogs of their gene expression differences, but have yet to lead to better understanding of the molecular proce...

journal_title：Genome biology

authors： Hampson R,Hughes SM

更新日期：2001-01-01 00:00:00

abstract：:A report on the Epigenetic Engineering Meeting hosted by the Barts Institute of Cancer, held in London, UK, May 7, 2014. ...

journal_title：Genome biology

authors： Magnani L

更新日期：2014-01-01 00:00:00

abstract：BACKGROUND:mRNA processing is critical for gene expression. A challenge in regulating mRNA processing is how to recognize the actual mRNA processing sites, such as splice and polyadenylation sites, when the sequence content is insufficient for this purpose. Previous studies suggested that RNA structure affects mRNA pro...

journal_title：Genome biology

authors： Liu Z,Liu Q,Yang X,Zhang Y,Norris M,Chen X,Cheema J,Zhang H,Ding Y

更新日期：2021-01-04 00:00:00

abstract：BACKGROUND:Whole genome sequencing of marine cyanobacteria has revealed an unprecedented degree of genomic variation and streamlining. With a size of 1.66 megabase-pairs, Prochlorococcus sp. MED4 has the most compact of these genomes and it is enigmatic how the few identified regulatory proteins efficiently sustain the...

journal_title：Genome biology

authors： Axmann IM,Kensche P,Vogel J,Kohl S,Herzel H,Hess WR

更新日期：2005-01-01 00:00:00

abstract：BACKGROUND:Malaria is a one of the most important infectious diseases and is caused by parasitic protozoa of the genus Plasmodium. Previously, quantitative characterization of the P. falciparum transcriptome demonstrated that the strictly controlled progression of these parasites through their intra-erythrocytic develo...

journal_title：Genome biology

authors： Foth BJ,Zhang N,Mok S,Preiser PR,Bozdech Z

更新日期：2008-01-01 00:00:00

abstract：:The explosive growth in taxonomic metagenome profiling methods over the past years has created a need for systematic comparisons using relevant performance criteria. The Open-community Profiling Assessment tooL (OPAL) implements commonly used performance metrics, including those of the first challenge of the initiativ...

journal_title：Genome biology

authors： Meyer F,Bremges A,Belmann P,Janssen S,McHardy AC,Koslicki D

更新日期：2019-03-04 00:00:00

abstract：BACKGROUND:The direct examination of large, unbiased samples of young gene duplicates in their early stages of evolution is crucial to understanding the origin, divergence and preservation of new genes. Furthermore, comparative analysis of multiple genomes is necessary to determine whether patterns of gene duplication ...

journal_title：Genome biology

authors： Katju V,Farslow JC,Bergthorsson U

更新日期：2009-01-01 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