The telosome/shelterin complex and its functions.

abstract：:Many existing pipelines for scRNA-seq data apply pre-processing steps such as normalization or imputation to account for excessive zeros or "drop-outs." Here, we extensively analyze diverse UMI data sets to show that clustering should be the foremost step of the workflow. We observe that most drop-outs disappear once ...

journal_title：Genome biology

authors： Kim TH,Zhou X,Chen M

更新日期：2020-08-06 00:00:00

abstract：BACKGROUND:Subcellular messenger RNA localization is important in most eukaryotic cells, even in unicellular organisms like yeast for which this process has been underestimated. Microarrays are rarely used to study subcellular mRNA localization at whole-genome level, but can be adapted to that purpose. This work focuse...

journal_title：Genome biology

authors： Sylvestre J,Vialette S,Corral Debrinski M,Jacq C

更新日期：2003-01-01 00:00:00

abstract：:Field pathogenomics adds highly informative data to surveillance surveys by enabling rapid evaluation of pathogen variability, population structure and host genotype. ...

journal_title：Genome biology

authors： Derevnina L,Michelmore RW

更新日期：2015-03-02 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：:Studies of human genetic disorders have traditionally followed a reductionist paradigm. Traits are defined as Mendelian or complex based on family pedigree and population data, whereas alleles are deemed rare, common, benign, or deleterious based on their population frequencies. The availability of exome and genome da...

journal_title：Genome biology

authors： Katsanis N

更新日期：2016-11-17 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：:Exome sequencing is poised to yield substantial insights into human genetic variation and evolutionary history, but there are significant challenges to overcome before this becomes a reality. ...

journal_title：Genome biology

authors： Tennessen JA,O'Connor TD,Bamshad MJ,Akey JM

更新日期：2011-09-14 00:00:00

abstract：BACKGROUND:Trypanosoma brucei is the causative agent of human sleeping sickness and animal trypanosomiasis in sub-Saharan Africa, and it has been subdivided into three subspecies: Trypanosoma brucei gambiense and Trypanosoma brucei rhodesiense, which cause sleeping sickness in humans, and the nonhuman infective Trypano...

journal_title：Genome biology

authors： Cooper A,Tait A,Sweeney L,Tweedie A,Morrison L,Turner CM,MacLeod A

更新日期：2008-01-01 00:00:00

abstract：BACKGROUND:Foodborne outbreaks of Salmonella remain a pressing public health concern. We recently detected a large outbreak of Salmonella enterica serovar Enteritidis phage type 14b affecting more than 30 patients in our hospital. This outbreak was linked to community, national and European-wide cases. Hospital patient...

journal_title：Genome biology

authors： Quick J,Ashton P,Calus S,Chatt C,Gossain S,Hawker J,Nair S,Neal K,Nye K,Peters T,De Pinna E,Robinson E,Struthers K,Webber M,Catto A,Dallman TJ,Hawkey P,Loman NJ

更新日期：2015-05-30 00:00:00

abstract：:Genetic mapping and determination of the organization of the wheat genome are changing the wheat-breeding process. New initiatives to analyze the expressed portion of the wheat genome and structural analysis of the genomes of Arabidopsis and rice are increasing our knowledge of the genes that are linked to key agronom...

journal_title：Genome biology

authors： Francki M,Appels R

更新日期：2002-01-01 00:00:00

abstract：BACKGROUND:Transposable elements (TEs) are major components of large plant genomes and main drivers of genome evolution. The most recent assembly of hexaploid bread wheat recovered the highly repetitive TE space in an almost complete chromosomal context and enabled a detailed view into the dynamics of TEs in the A, B, ...

journal_title：Genome biology

authors： Wicker T,Gundlach H,Spannagl M,Uauy C,Borrill P,Ramírez-González RH,De Oliveira R,International Wheat Genome Sequencing Consortium.,Mayer KFX,Paux E,Choulet F

更新日期：2018-08-17 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:Gynecologic malignancy is one of the leading causes of mortality in female adults worldwide. Comprehensive genomic analysis has revealed a list of molecular aberrations that are essential to tumorigenesis, progression, and metastasis of gynecologic tumors. However, targeting such alterations has frequently l...

journal_title：Genome biology

authors： Sa JK,Hwang JR,Cho YJ,Ryu JY,Choi JJ,Jeong SY,Kim J,Kim MS,Paik ES,Lee YY,Choi CH,Kim TJ,Kim BG,Bae DS,Lee Y,Her NG,Shin YJ,Cho HJ,Kim JY,Seo YJ,Koo H,Oh JW,Lee T,Kim HS,Song SY,Bae JS,Park WY,Han HD

更新日期：2019-11-26 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：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：:Reliable orthology prediction is central to comparative genomics. Although orthology is defined by phylogenetic criteria, most automated prediction methods are based on pairwise sequence comparisons. Recently, automated phylogeny-based orthology prediction has emerged as a feasible alternative for genome-wide studies....

journal_title：Genome biology

authors： Gabaldón T

更新日期：2008-10-30 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：:A report of the Keystone Symposia joint meetings on DNA Methylation and Epigenomics held in Keystone, Colorado, USA, 29 March to 3 April, 2015. ...

journal_title：Genome biology

authors： Chatterjee A,Eccles MR

更新日期：2015-05-21 00:00:00

abstract：BACKGROUND:Targeted deep sequencing is increasingly used to detect low-allelic fraction variants; it is therefore essential that errors that constitute baseline noise and impose a practical limit on detection are characterized. In the present study, we systematically evaluate the extent to which errors are incurred dur...

journal_title：Genome biology

authors： Park G,Park JK,Shin SH,Jeon HJ,Kim NKD,Kim YJ,Shin HT,Lee E,Lee KH,Son DS,Park WY,Park D

更新日期：2017-07-21 00:00:00

abstract：:A new study shows how a single cytokine, interleukin-4, regulates hematopoietic lineage choice by activating the JAK3-STAT6 pathway, which causes dendritic-cell-specific DNA demethylation. ...

journal_title：Genome biology

authors： Lennartsson A

更新日期：2016-02-01 00:00:00

abstract：:How viruses evolve within hosts can dictate infection outcomes; however, reconstructing this process is challenging. We evaluate our multiplexed amplicon approach, PrimalSeq, to demonstrate how virus concentration, sequencing coverage, primer mismatches, and replicates influence the accuracy of measuring intrahost vir...

journal_title：Genome biology

authors： Grubaugh ND,Gangavarapu K,Quick J,Matteson NL,De Jesus JG,Main BJ,Tan AL,Paul LM,Brackney DE,Grewal S,Gurfield N,Van Rompay KKA,Isern S,Michael SF,Coffey LL,Loman NJ,Andersen KG

更新日期：2019-01-08 00:00:00

abstract：:Tissues are complex milieus consisting of numerous cell types. Several recent methods have attempted to enumerate cell subsets from transcriptomes. However, the available methods have used limited sources for training and give only a partial portrayal of the full cellular landscape. Here we present xCell, a novel gene...

journal_title：Genome biology

authors： Aran D,Hu Z,Butte AJ

更新日期：2017-11-15 00:00:00

abstract：BACKGROUND:One challenge facing biologists is to tease out useful information from massive data sets for further analysis. A pathway-based analysis may shed light by projecting candidate genes onto protein functional relationship networks. We are building such a pathway-based analysis system. RESULTS:We have construct...

journal_title：Genome biology

authors： Wu G,Feng X,Stein L

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：:A recent study has used serial analysis of gene expression to compare mouse forelimb and hindlimb gene-expression profiles. The method successfully identified known regulators of limb identity and has generated a candidate set of differentially expressed genes that may regulate limb identity. ...

journal_title：Genome biology

authors： Logan M

更新日期：2002-01-01 00:00:00

abstract：BACKGROUND:Francisella tularensis subspecies tularensis and holarctica are pathogenic to humans, whereas the two other subspecies, novicida and mediasiatica, rarely cause disease. To uncover the factors that allow subspecies tularensis and holarctica to be pathogenic to humans, we compared their genome sequences with t...

journal_title：Genome biology

authors： Rohmer L,Fong C,Abmayr S,Wasnick M,Larson Freeman TJ,Radey M,Guina T,Svensson K,Hayden HS,Jacobs M,Gallagher LA,Manoil C,Ernst RK,Drees B,Buckley D,Haugen E,Bovee D,Zhou Y,Chang J,Levy R,Lim R,Gillett W,Guenth

更新日期：2007-01-01 00:00:00

abstract：:The subcellular localization of the entire proteome of an organism, the yeast Saccharomyces cerevisiae, has been revealed for the first time. Comparison with less comprehensive studies of mammalian cells provides insights into the localization of the mammalian proteome. ...

journal_title：Genome biology

authors： Simpson JC,Pepperkok R

更新日期：2003-01-01 00:00:00

abstract：BACKGROUND:MicroRNAs (miRNAs) are oligoribonucleotides with an important role in regulation of gene expression at the level of translation. Despite imperfect target complementarity, they can also significantly reduce mRNA levels. The validity of miRNA target gene predictions is difficult to assess at the protein level....

journal_title：Genome biology

authors： Arora A,Simpson DA

更新日期：2008-01-01 00:00:00

abstract：BACKGROUND:Genome structures are dynamic and non-randomly organized in the nucleus of higher eukaryotes. To maximize the accuracy and coverage of three-dimensional genome structural models, it is important to integrate all available sources of experimental information about a genome's organization. It remains a major c...

journal_title：Genome biology

authors： Li Q,Tjong H,Li X,Gong K,Zhou XJ,Chiolo I,Alber F

更新日期：2017-07-31 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