Phylogeographic variation in recombination rates within a global clone of methicillin-resistant Staphylococcus aureus.

abstract：:A recent study in Genome Biology has characterized the evolution of candidate hominoid-specific liver enhancers by using massively parallel reporter assays (MPRAs). ...

journal_title：Genome biology

authors： Kwon SB,Ernst J

更新日期：2018-08-14 00:00:00

abstract：BACKGROUND:Protein synthesis is tightly regulated and alterations to translation are characteristic of many cancers.Translation regulation is largely exerted at initiation through the eukaryotic translation initiation factor 4 F (eIF4F). eIF4F is pivotal for oncogenic signaling as it integrates mitogenic signals to amp...

journal_title：Genome biology

authors： Rubio CA,Weisburd B,Holderfield M,Arias C,Fang E,DeRisi JL,Fanidi A

更新日期：2014-01-01 00:00:00

abstract：BACKGROUND:Comparisons between C3 and C4 grasses often utilize C3 species from the subfamilies Ehrhartoideae or Pooideae and C4 species from the subfamily Panicoideae, two clades that diverged over 50 million years ago. The divergence of the C3 panicoid grass Dichanthelium oligosanthes from the independent C4 lineages ...

journal_title：Genome biology

authors： Studer AJ,Schnable JC,Weissmann S,Kolbe AR,McKain MR,Shao Y,Cousins AB,Kellogg EA,Brutnell TP

更新日期：2016-10-28 00:00:00

abstract：:We describe here our experience in annotating the Drosophila melanogaster genome sequence, in the course of which we developed several new open-source software tools and a database schema to support large-scale genome annotation. We have developed these into an integrated and reusable software system for whole-genome ...

journal_title：Genome biology

authors： Mungall CJ,Misra S,Berman BP,Carlson J,Frise E,Harris N,Marshall B,Shu S,Kaminker JS,Prochnik SE,Smith CD,Smith E,Tupy JL,Wiel C,Rubin GM,Lewis SE

更新日期：2002-01-01 00:00:00

abstract：:The definition of cell identity is a central problem in biology. While single-cell RNA-seq provides a wealth of information regarding cell states, better methods are needed to map their identity, especially during developmental transitions. Here, we use repositories of cell type-specific transcriptomes to quantify ide...

journal_title：Genome biology

authors： Efroni I,Ip PL,Nawy T,Mello A,Birnbaum KD

更新日期：2015-01-22 00:00:00

abstract：BACKGROUND:Heterochromatin protein 1 (HP1) family proteins have a well-characterized role in heterochromatin packaging and gene regulation. Their function in organismal development, however, is less well understood. Here we used genome-wide expression profiling to assess novel functions of the Caenorhabditis elegans HP...

journal_title：Genome biology

authors： Meister P,Schott S,Bedet C,Xiao Y,Rohner S,Bodennec S,Hudry B,Molin L,Solari F,Gasser SM,Palladino F

更新日期：2011-12-20 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：:The mechanistic details of most disease-causing mutations remain poorly explored within the context of regulatory networks. We present a high-resolution three-dimensional integrated regulatory network (iRegNet3D) in the form of a web tool, where we resolve the interfaces of all known transcription factor (TF)-TF, TF-D...

journal_title：Genome biology

authors： Liang S,Tippens ND,Zhou Y,Mort M,Stenson PD,Cooper DN,Yu H

更新日期：2017-01-18 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：: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：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：:mtcPTM is an online repository of human and mouse phosphosites in which data are hierarchically organized to preserve biologically relevant experimental information, thus allowing straightforward comparisons of phosphorylation patterns found under different conditions. The database also contains the largest available ...

journal_title：Genome biology

authors： Jiménez JL,Hegemann B,Hutchins JR,Peters JM,Durbin R

更新日期：2007-01-01 00:00:00

abstract：:A recent study reveals a surprisingly high degree of change in the occupancy patterns of two transcription factors in the livers of five vertebrates. ...

journal_title：Genome biology

authors： Weirauch MT,Hughes TR

更新日期：2010-01-01 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:To understand the heterogeneous behaviors of individual cancer cells, it is essential to investigate gene expression levels as well as their divergence between different individual cells. Recent advances in next-generation sequencing-related technologies have enabled us to conduct a single-cell RNA-Seq analy...

journal_title：Genome biology

authors： Suzuki A,Matsushima K,Makinoshima H,Sugano S,Kohno T,Tsuchihara K,Suzuki Y

更新日期：2015-04-03 00:00:00

abstract：:Cytoscape is one of the most successful network biology analysis and visualization tools, but because of its interactive nature, its role in creating reproducible, scalable, and novel workflows has been limited. We describe Cytoscape Automation (CA), which marries Cytoscape to highly productive workflow systems, for e...

journal_title：Genome biology

authors： Otasek D,Morris JH,Bouças J,Pico AR,Demchak B

更新日期：2019-09-02 00:00:00

abstract：:A new generation of DNA-sequencing platforms will become commercially available over the next few years. These instruments will enable re-sequencing of human genomes at a previously unimagined throughput and low cost. Here, I examine why the 1,000 dollar human genome is an important goal for research and clinical diag...

journal_title：Genome biology

authors： Mardis ER

更新日期：2006-01-01 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:RNA sequencing has opened new avenues for the study of transcriptome composition. Significant evidence has accumulated showing that the human transcriptome contains in excess of a hundred thousand different transcripts. However, it is still not clear to what extent this diversity prevails when considering th...

journal_title：Genome biology

authors： Gonzàlez-Porta M,Frankish A,Rung J,Harrow J,Brazma A

更新日期：2013-07-01 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：BACKGROUND:DNA methylation and the Polycomb repression system are epigenetic mechanisms that play important roles in maintaining transcriptional repression. Recent evidence suggests that DNA methylation can attenuate the binding of Polycomb protein components to chromatin and thus plays a role in determining their geno...

journal_title：Genome biology

authors： Reddington JP,Perricone SM,Nestor CE,Reichmann J,Youngson NA,Suzuki M,Reinhardt D,Dunican DS,Prendergast JG,Mjoseng H,Ramsahoye BH,Whitelaw E,Greally JM,Adams IR,Bickmore WA,Meehan RR

更新日期：2013-03-25 00:00:00

abstract：:Droplet-based single-cell RNA sequencing protocols have dramatically increased the throughput of single-cell transcriptomics studies. A key computational challenge when processing these data is to distinguish libraries for real cells from empty droplets. Here, we describe a new statistical method for calling cells fro...

journal_title：Genome biology

authors： Lun ATL,Riesenfeld S,Andrews T,Dao TP,Gomes T,participants in the 1st Human Cell Atlas Jamboree.,Marioni JC

更新日期：2019-03-22 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：BACKGROUND:Recent advancements in next-generation sequencing have rapidly improved our ability to study genomic material at an unprecedented scale. Despite substantial improvements in sequencing technologies, errors present in the data still risk confounding downstream analysis and limiting the applicability of sequenc...

journal_title：Genome biology

authors： Mitchell K,Brito JJ,Mandric I,Wu Q,Knyazev S,Chang S,Martin LS,Karlsberg A,Gerasimov E,Littman R,Hill BL,Wu NC,Yang HT,Hsieh K,Chen L,Littman E,Shabani T,Enik G,Yao D,Sun R,Schroeder J,Eskin E,Zelikovsky A,S

更新日期：2020-03-17 00:00:00

abstract：BACKGROUND:The annual fish Nothobranchius furzeri is the vertebrate with the shortest known life span in captivity. Fish of the GRZ strain live only three to four months under optimal laboratory conditions, show explosive growth, early sexual maturation and age-dependent physiological and behavioral decline, and expres...

journal_title：Genome biology

authors： Reichwald K,Lauber C,Nanda I,Kirschner J,Hartmann N,Schories S,Gausmann U,Taudien S,Schilhabel MB,Szafranski K,Glöckner G,Schmid M,Cellerino A,Schartl M,Englert C,Platzer M

更新日期：2009-02-11 00:00:00

abstract：BACKGROUND:X chromosome inactivation is a spectacular example of epigenetic silencing. In order to deduce how this complex system evolved, we examined X inactivation in a model marsupial, the tammar wallaby (Macropus eugenii). In marsupials, X inactivation is known to be paternal, incomplete and tissue-specific, and oc...

journal_title：Genome biology

authors： Al Nadaf S,Waters PD,Koina E,Deakin JE,Jordan KS,Graves JA

更新日期：2010-01-01 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：:The ability to accurately quantify all the microRNAs (miRNAs) in a sample is important for understanding miRNA biology and for development of new biomarkers and therapeutic targets. We develop a new method for preparing miRNA sequencing libraries, RealSeq®-AC, that involves ligating the miRNAs with a single adapter an...

journal_title：Genome biology

authors： Barberán-Soler S,Vo JM,Hogans RE,Dallas A,Johnston BH,Kazakov SA

更新日期：2018-09-03 00:00:00

abstract：BACKGROUND:Bacillus subtilis is an organism of interest because of its extensive industrial applications, its similarity to pathogenic organisms, and its role as the model organism for Gram-positive, sporulating bacteria. In this work, we introduce a new genome-scale metabolic model of B. subtilis 168 called iBsu1103. ...

journal_title：Genome biology

authors： Henry CS,Zinner JF,Cohoon MP,Stevens RL

更新日期：2009-01-01 00:00:00

abstract：BACKGROUND:Dictyostelium discoideum is a eukaryote with a simple lifestyle and a relatively small genome whose sequence has been fully determined. It is widely used for studies on cell signaling, movement and multicellular development. Ras guanine-nucleotide exchange factors (RasGEFs) are the proteins that activate Ras...

journal_title：Genome biology

authors： Wilkins A,Szafranski K,Fraser DJ,Bakthavatsalam D,Müller R,Fisher PR,Glöckner G,Eichinger L,Noegel AA,Insall RH

更新日期：2005-01-01 00:00:00