RuNAway Disease: A two cycle model for transmissible spongiform encephalopathies (TSEs) wherein

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：:Recent experiments show that properly controlled recombination between homologous DNA molecules is essential for the maintenance of genome stability and for the prevention of tumorigenesis. ...

journal_title：Genome biology

authors： Modesti M,Kanaar R

更新日期：2001-01-01 00:00:00

abstract：BACKGROUND:DNA methylation is a key epigenetic mechanism for driving and stabilizing cell-fate decisions. Local deposition and removal of DNA methylation are tightly coupled with transcription factor binding, although the relationship varies with the specific differentiation process. Conversion of monocytes to osteocla...

journal_title：Genome biology

authors： de la Rica L,Rodríguez-Ubreva J,García M,Islam AB,Urquiza JM,Hernando H,Christensen J,Helin K,Gómez-Vaquero C,Ballestar E

更新日期：2013-01-01 00:00:00

abstract：:Pooled CRISPR screens allow researchers to interrogate genetic causes of complex phenotypes at the genome-wide scale and promise higher specificity and sensitivity compared to competing technologies. Unfortunately, two problems exist, particularly for CRISPRi/a screens: variability in guide efficiency and large rare o...

journal_title：Genome biology

authors： Daley TP,Lin Z,Lin X,Liu Y,Wong WH,Qi LS

更新日期：2018-10-08 00:00:00

abstract：:A report of the fifth annual Personal Genomes and Medical Genomics meeting, held at Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA, November 14-17, 2012. ...

journal_title：Genome biology

authors： Highnam G,Mittelman D

更新日期：2012-12-19 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：:The N 6-methyladenosine (m6A) modification of mRNA has a crucial function in regulating pluripotency in murine stem cells: it facilitates resolution of naïve pluripotency towards differentiation. ...

journal_title：Genome biology

authors： Zhao BS,He C

更新日期：2015-02-22 00:00:00

abstract：BACKGROUND:Evolutionary centromere repositioning and human analphoid neocentromeres occurring in clinical cases are, very likely, two stages of the same phenomenon whose properties still remain substantially obscure. Chromosome 13 is the chromosome with the highest number of neocentromeres. We reconstructed the mammali...

journal_title：Genome biology

authors： Cardone MF,Alonso A,Pazienza M,Ventura M,Montemurro G,Carbone L,de Jong PJ,Stanyon R,D'Addabbo P,Archidiacono N,She X,Eichler EE,Warburton PE,Rocchi M

更新日期：2006-01-01 00:00:00

abstract：BACKGROUND:Maps depicting binary interactions between proteins can be powerful starting points for understanding biological systems. A proven technology for generating such maps is high-throughput yeast two-hybrid screening. In the most extensive screen to date, a Gal4-based two-hybrid system was used recently to detec...

journal_title：Genome biology

authors： Stanyon CA,Liu G,Mangiola BA,Patel N,Giot L,Kuang B,Zhang H,Zhong J,Finley RL Jr

更新日期：2004-01-01 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：:Your Gene structure Annotation Tool for Eukaryotes (yrGATE) provides an Annotation Tool and Community Utilities for worldwide web-based community genome and gene annotation. Annotators can evaluate gene structure evidence derived from multiple sources to create gene structure annotations. Administrators regulate the a...

journal_title：Genome biology

authors： Wilkerson MD,Schlueter SD,Brendel V

更新日期：2006-01-01 00:00:00

abstract：:Extracting biological information from microarray data requires appropriate statistical methods. The simplest statistical method for detecting differential expression is the t test, which can be used to compare two conditions when there is replication of samples. With more than two conditions, analysis of variance (AN...

journal_title：Genome biology

authors： Cui X,Churchill GA

更新日期：2003-01-01 00:00:00

abstract：:Large-scale biology among plant species, as well as comparative genomics of circadian clock architecture and clock-regulated output processes, have greatly advanced our understanding of the endogenous timing system in plants. ...

journal_title：Genome biology

authors： Staiger D,Shin J,Johansson M,Davis SJ

更新日期：2013-06-24 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:Two distinct classes of regulators have been implicated in regulating neuronal gene expression and mediating neuronal identity: transcription factors such as REST/NRSF (RE1 silencing transcription factor) and CREB (cAMP response element-binding protein), and microRNAs (miRNAs). How these two classes of regul...

journal_title：Genome biology

authors： Wu J,Xie X

更新日期：2006-01-01 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:Despite their regional economic importance and being increasingly reared globally, the origins and evolution of the llama and alpaca remain poorly understood. Here we report reference genomes for the llama, and for the guanaco and vicuña (their putative wild progenitors), compare these with the published alp...

journal_title：Genome biology

authors： Fan R,Gu Z,Guang X,Marín JC,Varas V,González BA,Wheeler JC,Hu Y,Li E,Sun X,Yang X,Zhang C,Gao W,He J,Munch K,Corbett-Detig R,Barbato M,Pan S,Zhan X,Bruford MW,Dong C

更新日期：2020-07-02 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 cell-cycle checkpoint kinase Chk1 is essential in mammalian cells due to its roles in controlling processes such as DNA replication, mitosis and DNA-damage responses. Despite its paramount importance, how Chk1 controls these functions remains unclear, mainly because very few Chk1 substrates have hitherto...

journal_title：Genome biology

authors： Blasius M,Forment JV,Thakkar N,Wagner SA,Choudhary C,Jackson SP

更新日期：2011-08-18 00:00:00

abstract：BACKGROUND:Genome-wide DNA methylation (DNAm) profiling has allowed for the development of molecular predictors for a multitude of traits and diseases. Such predictors may be more accurate than the self-reported phenotypes and could have clinical applications. RESULTS:Here, penalized regression models are used to deve...

journal_title：Genome biology

authors： McCartney DL,Hillary RF,Stevenson AJ,Ritchie SJ,Walker RM,Zhang Q,Morris SW,Bermingham ML,Campbell A,Murray AD,Whalley HC,Gale CR,Porteous DJ,Haley CS,McRae AF,Wray NR,Visscher PM,McIntosh AM,Evans KL,Deary IJ,Mar

更新日期：2018-09-27 00:00:00

abstract：:Chromatin is not a uniform macromolecular entity; it contains different domains characterized by complex signatures of DNA and histone modifications. Such domains are organized both at a linear scale along the genome and spatially within the nucleus. We discuss recent discoveries regarding mechanisms that establish bo...

journal_title：Genome biology

authors： Vergara Z,Gutierrez C

更新日期：2017-05-23 00:00:00

abstract：BACKGROUND:The cinereous vulture, Aegypius monachus, is the largest bird of prey and plays a key role in the ecosystem by removing carcasses, thus preventing the spread of diseases. Its feeding habits force it to cope with constant exposure to pathogens, making this species an interesting target for discovering functio...

journal_title：Genome biology

authors： Chung O,Jin S,Cho YS,Lim J,Kim H,Jho S,Kim HM,Jun J,Lee H,Chon A,Ko J,Edwards J,Weber JA,Han K,O'Brien SJ,Manica A,Bhak J,Paek WK

更新日期：2015-10-21 00:00:00

abstract：BACKGROUND:In eukaryotic cells, oxidative phosphorylation (OXPHOS) uses the products of both nuclear and mitochondrial genes to generate cellular ATP. Interspecies comparative analysis of these genes, which appear to be under strong functional constraints, may shed light on the evolutionary mechanisms that act on a set...

journal_title：Genome biology

authors： Tripoli G,D'Elia D,Barsanti P,Caggese C

更新日期：2005-01-01 00:00:00

abstract：:A recent, genome-wide study shows that the transcriptional program underlying leaf senescence is active and complex, reflecting the activation of more than 2,000 genes in Arabidopsis, with gene products involved in a broad spectrum of regulatory, biochemical and cellular events. ...

journal_title：Genome biology

authors： Gepstein S

更新日期：2004-01-01 00:00:00

abstract：BACKGROUND:Polyploidy is ubiquitous in eukaryotic plant and fungal lineages, and it leads to the co-existence of several copies of similar or related genomes in one nucleus. In plants, polyploidy is considered a major factor in successful domestication. However, polyploidy challenges chromosome folding architecture in ...

journal_title：Genome biology

authors： Concia L,Veluchamy A,Ramirez-Prado JS,Martin-Ramirez A,Huang Y,Perez M,Domenichini S,Rodriguez Granados NY,Kim S,Blein T,Duncan S,Pichot C,Manza-Mianza D,Juery C,Paux E,Moore G,Hirt H,Bergounioux C,Crespi M,Mahfouz

更新日期：2020-04-29 00:00:00

abstract：:Absolute tumor DNA copy numbers can currently be achieved only on a single gene basis by using fluorescence in situ hybridization (FISH). We present GeneCount, a method for genome-wide calculation of absolute copy numbers from clinical array comparative genomic hybridization data. The tumor cell fraction is reliably e...

journal_title：Genome biology

authors： Lyng H,Lando M,Brøvig RS,Svendsrud DH,Johansen M,Galteland E,Brustugun OT,Meza-Zepeda LA,Myklebost O,Kristensen GB,Hovig E,Stokke T

更新日期：2008-01-01 00:00:00

abstract：:Somatic evolution of malignant cells produces tumors composed of multiple clonal populations, distinguished in part by rearrangements and copy number changes affecting chromosomal segments. Whole genome sequencing mixes the signals of sampled populations, diluting the signals of clone-specific aberrations, and complic...

journal_title：Genome biology

authors： McPherson AW,Roth A,Ha G,Chauve C,Steif A,de Souza CPE,Eirew P,Bouchard-Côté A,Aparicio S,Sahinalp SC,Shah SP

更新日期：2017-07-27 00:00:00

abstract：BACKGROUND:The genomic binding of CTCF is highly conserved across mammals, but the mechanisms that underlie its stability are poorly understood. One transcription factor known to functionally interact with CTCF in the context of X-chromosome inactivation is the ubiquitously expressed YY1. Because combinatorial transcri...

journal_title：Genome biology

authors： Schwalie PC,Ward MC,Cain CE,Faure AJ,Gilad Y,Odom DT,Flicek P

更新日期：2013-12-31 00:00:00

abstract：:Abhay Sharma brings two arguments in favor of transgenerational epigenetic inheritance (TGEI) in mammals when criticizing our work. He uses probability calculations and finds that the probability of obtaining the number of common changes in the in utero-exposed prospermatogonia and the same cells in the next generatio...

journal_title：Genome biology

authors： Szabó PE

更新日期：2016-05-16 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