Molecular archeology of L1 insertions in the human genome.

abstract：BACKGROUND:Light and carbon are two essential signals influencing plant growth and development. Little is known about how carbon and light signaling pathways intersect or influence one another to affect gene expression. RESULTS:Microarrays are used to investigate carbon and light signaling interactions at a genome-wid...

journal_title：Genome biology

authors： Thum KE,Shin MJ,Palenchar PM,Kouranov A,Coruzzi GM

更新日期：2004-01-01 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：: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:Chromatin organizes DNA and regulates its transcriptional activity through epigenetic modifications. Heterochromatic regions of the genome are generally transcriptionally silent, while euchromatin is more prone to transcription. During DNA replication, both genetic information and chromatin modifications mus...

journal_title：Genome biology

authors： Bourguet P,López-González L,Gómez-Zambrano Á,Pélissier T,Hesketh A,Potok ME,Pouch-Pélissier MN,Perez M,Da Ines O,Latrasse D,White CI,Jacobsen SE,Benhamed M,Mathieu O

更新日期：2020-11-25 00:00:00

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 army of the men of death, in John Bunyan's memorable phrase, has a new recruit, and fear has a new face: a face wearing a surgical mask. ...

journal_title：Genome biology

authors： Petsko GA

更新日期：2003-01-01 00:00:00

abstract：:Identification of causal mutations in barley and wheat is hampered by their large genomes and suppressed recombination. To overcome these obstacles, we have developed MutChromSeq, a complexity reduction approach based on flow sorting and sequencing of mutant chromosomes, to identify induced mutations by comparison to ...

journal_title：Genome biology

authors： Sánchez-Martín J,Steuernagel B,Ghosh S,Herren G,Hurni S,Adamski N,Vrána J,Kubaláková M,Krattinger SG,Wicker T,Doležel J,Keller B,Wulff BB

更新日期：2016-10-31 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：: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：:From worms to humans, recognizing and modifying a specific chromosome is essential for dosage compensation, the mechanism by which equal X-linked gene expression in males and females is achieved. Recent molecular genetic and biochemical studies have provided new insights into how regulatory factors in Drosophila are r...

journal_title：Genome biology

authors： Amrein H

更新日期：2000-01-01 00:00:00

abstract：BACKGROUND:Hemiascomycetous yeasts have intron-poor genomes with very few cases of alternative splicing. Most of the reported examples result from intron retention in Saccharomyces cerevisiae and some have been shown to be functionally significant. Here we used transcriptome-wide approaches to evaluate the mechanisms u...

journal_title：Genome biology

authors： Mekouar M,Blanc-Lenfle I,Ozanne C,Da Silva C,Cruaud C,Wincker P,Gaillardin C,Neuvéglise C

更新日期：2010-01-01 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：:Giving access to sequence and annotation data for genome assemblies is important because, while facilitating research, it places both assembly and annotation quality under scrutiny, resulting in improvements to both. Therefore we announce Avianbase, a resource for bird genomics, which provides access to data released ...

journal_title：Genome biology

authors： Eöry L,Gilbert MT,Li C,Li B,Archibald A,Aken BL,Zhang G,Jarvis E,Flicek P,Burt DW

更新日期：2015-01-29 00:00:00

abstract：:Toxin/antitoxin (TA) systems, viewed as essential regulators of growth arrest and programmed cell death, are widespread among prokaryotes, but remain sparsely annotated. We present RASTA-Bacteria, an automated method allowing quick and reliable identification of TA loci in sequenced prokaryotic genomes, whether they a...

journal_title：Genome biology

authors： Sevin EW,Barloy-Hubler F

更新日期：2007-01-01 00:00:00

abstract：BACKGROUND:The identification of signatures of natural selection has long been used as an approach to understanding the unique features of any given species. Genes within segmental duplications are overlooked in most studies of selection due to the limitations of draft nonhuman genome assemblies and to the methodologic...

journal_title：Genome biology

authors： Lorente-Galdos B,Bleyhl J,Santpere G,Vives L,Ramírez O,Hernandez J,Anglada R,Cooper GM,Navarro A,Eichler EE,Marques-Bonet T

更新日期：2013-01-29 00:00:00

abstract：BACKGROUND:Aberrant activation of the Hedgehog pathway drives tumorigenesis of many cancers, including glioblastoma. However, the sensitization mechanism of the G protein-coupled-like receptor smoothened (SMO), a key component of Hedgehog signaling, remains largely unknown. RESULTS:In this study, we describe a novel p...

journal_title：Genome biology

authors： Wu X,Xiao S,Zhang M,Yang L,Zhong J,Li B,Li F,Xia X,Li X,Zhou H,Liu D,Huang N,Yang X,Xiao F,Zhang N

更新日期：2021-01-14 00:00:00

abstract：BACKGROUND:Acute myeloid leukemia (AML) comprises a group of diseases characterized by the abnormal development of malignant myeloid cells. Recent studies have demonstrated an important role for aberrant transcriptional regulation in AML pathophysiology. Although several transcription factors (TFs) involved in myeloid ...

journal_title：Genome biology

authors： Chang LW,Payton JE,Yuan W,Ley TJ,Nagarajan R,Stormo GD

更新日期：2008-01-01 00:00:00

abstract：BACKGROUND:Protein domains display a range of structural diversity, with numerous additions and deletions of secondary structural elements between related domains. We have observed a small number of cases of surprising large-scale deletions of core elements of structural domains. We propose a new concept called domain ...

journal_title：Genome biology

authors： Prakash A,Bateman A

更新日期：2015-04-30 00:00:00

abstract：BACKGROUND:Four hypervariable minisatellite loci were scored on a panel of 116 individuals of various geographical origins representing a large part of the diversity present in house mouse subspecies. Internal structures of alleles were determined by minisatellite variant repeat mapping PCR to produce maps of interming...

journal_title：Genome biology

authors： Bonhomme F,Rivals E,Orth A,Grant GR,Jeffreys AJ,Bois PR

更新日期：2007-01-01 00:00:00

abstract：BACKGROUND:Rice blast disease is caused by the filamentous Ascomycetous fungus Magnaporthe oryzae and results in significant annual rice yield losses worldwide. Infection by this and many other fungal plant pathogens requires the development of a specialized infection cell called an appressorium. The molecular processe...

journal_title：Genome biology

authors： Oh Y,Donofrio N,Pan H,Coughlan S,Brown DE,Meng S,Mitchell T,Dean RA

更新日期：2008-01-01 00:00:00

abstract：:A report on the Cold Spring Harbor Laboratory/Wellcome Trust conference on Network Biology, Hinxton, UK, 27-31 August 2008. ...

journal_title：Genome biology

authors： Ahnert SE,Teichmann SA

更新日期：2008-10-27 00:00:00

abstract：:Stochastic changes in DNA methylation (i.e., spontaneous epimutations) contribute to methylome diversity in plants. Here, we describe AlphaBeta, a computational method for estimating the precise rate of such stochastic events using pedigree-based DNA methylation data as input. We demonstrate how AlphaBeta can be emplo...

journal_title：Genome biology

authors： Shahryary Y,Symeonidi A,Hazarika RR,Denkena J,Mubeen T,Hofmeister B,van Gurp T,Colomé-Tatché M,Verhoeven KJF,Tuskan G,Schmitz RJ,Johannes F

更新日期：2020-10-06 00:00:00

abstract：:Genetic studies have identified more than 150 autoimmune loci, and next-generation sequencing will identify more. Is it time to make human the model organism for autoimmune research? ...

journal_title：Genome biology

authors： Plenge R

更新日期：2010-01-01 00:00:00

abstract：BACKGROUND:Symbiotic bacteria known as rhizobia interact with the roots of legumes and induce the formation of nitrogen-fixing nodules. In rhizobia, essential genes for symbiosis are compartmentalized either in symbiotic plasmids or in chromosomal symbiotic islands. To understand the structure and evolution of the symb...

journal_title：Genome biology

authors： González V,Bustos P,Ramírez-Romero MA,Medrano-Soto A,Salgado H,Hernández-González I,Hernández-Celis JC,Quintero V,Moreno-Hagelsieb G,Girard L,Rodríguez O,Flores M,Cevallos MA,Collado-Vides J,Romero D,Dávila G

更新日期：2003-01-01 00:00:00

abstract：:Following publication of the original article [1], the authors reported the following errors. ...

journal_title：Genome biology

authors： Lee H,McManus CJ,Cho DY,Eaton M,Renda F,Somma MP,Cherbas L,May G,Powell S,Zhang D,Zhan L,Resch A,Andrews J,Celniker SE,Cherbas P,Przytycka TM,Gatti M,Oliver B,Graveley B,MacAlpine D

更新日期：2019-03-11 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: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：:A report of the Second International Conference/Workshop on the Genomic Impact of Eukaryotic Transposable Elements, Pacific Grove, USA, 6-10 February 2009. ...

journal_title：Genome biology

authors： Ivics Z

更新日期：2009-01-01 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:Structural variants (SVs) are known to play important roles in a variety of cancers, but their origins and functional consequences are still poorly understood. Many SVs are thought to emerge from errors in the repair processes following DNA double strand breaks (DSBs). RESULTS:We used experimentally quantif...

journal_title：Genome biology

authors： Ballinger TJ,Bouwman BAM,Mirzazadeh R,Garnerone S,Crosetto N,Semple CA

更新日期：2019-02-08 00:00:00