abstract：:The mammalian cell nucleus contains numerous discrete suborganelles named nuclear bodies. While recruitment of specific genomic regions into these large ribonucleoprotein (RNP) complexes critically contributes to higher-order functional chromatin organization, such regions remain ill-defined. We have developed the hig...

journal_title：Genome research

authors： Baudement MO,Cournac A,Court F,Seveno M,Parrinello H,Reynes C,Sabatier R,Bouschet T,Yi Z,Sallis S,Tancelin M,Rebouissou C,Cathala G,Lesne A,Mozziconacci J,Journot L,Forné T

更新日期：2018-11-01 00:00:00

abstract：:Despite the importance of duplicate genes for evolutionary adaptation, accurate gene annotation is often incomplete, incorrect, or lacking in regions of segmental duplication. We developed an approach combining long-read sequencing and hybridization capture to yield full-length transcript information and confidently d...

journal_title：Genome research

authors： Dougherty ML,Underwood JG,Nelson BJ,Tseng E,Munson KM,Penn O,Nowakowski TJ,Pollen AA,Eichler EE

更新日期：2018-10-01 00:00:00

abstract：:The capacity of the honey bee to produce three phenotypically distinct organisms (two female castes; queens and sterile workers, and haploid male drones) from one genotype represents one of the most remarkable examples of developmental plasticity in any phylum. The queen-worker morphological and reproductive divide is...

journal_title：Genome research

authors： Wojciechowski M,Lowe R,Maleszka J,Conn D,Maleszka R,Hurd PJ

更新日期：2018-10-01 00:00:00

abstract：:Metabolic homeostasis is sustained by complex biological networks that respond to nutrient availability. Genetic and environmental factors may disrupt this equilibrium, leading to metabolic disorders, including obesity and type 2 diabetes. To identify the genetic factors controlling metabolism, we performed quantitati...

journal_title：Genome research

authors： Gao AW,Sterken MG,Uit de Bos J,van Creij J,Kamble R,Snoek BL,Kammenga JE,Houtkooper RH

更新日期：2018-09-01 00:00:00

abstract：:Genomics data introduce a substantial computational burden as well as data privacy and ownership issues. Data sets generated by high-throughput sequencing platforms require immense amounts of computational resources to align to reference genomes and to call and annotate genomic variants. This problem is even more pron...

journal_title：Genome research

authors： Ozercan HI,Ileri AM,Ayday E,Alkan C

更新日期：2018-09-01 00:00:00

abstract：:Interactions mediated by cell surface receptors initiate important instructive signaling cues but can be difficult to detect in biochemical assays because they are often highly transient and membrane-embedded receptors are difficult to solubilize in their native conformation. Here, we address these biochemical challen...

journal_title：Genome research

authors： Sharma S,Bartholdson SJ,Couch ACM,Yusa K,Wright GJ

更新日期：2018-09-01 00:00:00

abstract：:Current methods struggle to reconstruct and visualize the genomic relationships of large numbers of bacterial genomes. GrapeTree facilitates the analyses of large numbers of allelic profiles by a static "GrapeTree Layout" algorithm that supports interactive visualizations of large trees within a web browser window. Gr...

journal_title：Genome research

authors： Zhou Z,Alikhan NF,Sergeant MJ,Luhmann N,Vaz C,Francisco AP,Carriço JA,Achtman M

更新日期：2018-09-01 00:00:00

abstract：:Long interspersed nuclear element-1 (LINE-1 or L1) retrotransposons are normally suppressed in somatic tissues mainly due to DNA methylation and antiviral defense. However, the mechanism to suppress L1s may be disrupted in cancers, thus allowing L1s to act as insertional mutagens and cause genomic rearrangement and in...

journal_title：Genome research

authors： Jung H,Choi JK,Lee EA

更新日期：2018-08-01 00:00:00

abstract：:Recent studies have analyzed large-scale data sets of gene expression to identify genes associated with interindividual variation in phenotypes ranging from cancer subtypes to drug sensitivity, promising new avenues of research in personalized medicine. However, gene expression data alone is limited in its ability to ...

journal_title：Genome research

authors： Hanson C,Cairns J,Wang L,Sinha S

更新日期：2018-08-01 00:00:00

abstract：:The allele fraction (AF) distribution, occurrence rate, and evolutionary contribution of postzygotic single-nucleotide mosaicisms (pSNMs) remain largely unknown. In this study, we developed a mathematical model to describe the accumulation and AF drift of pSNMs during the development of multicellular organisms. By app...

journal_title：Genome research

authors： Ye AY,Dou Y,Yang X,Wang S,Huang AY,Wei L

更新日期：2018-07-01 00:00:00

abstract：:The representation and discovery of transcription factor (TF) sequence binding specificities is critical for understanding gene regulatory networks and interpreting the impact of disease-associated noncoding genetic variants. We present a novel TF binding motif representation, the k-mer set memory (KSM), which consist...

journal_title：Genome research

authors： Guo Y,Tian K,Zeng H,Guo X,Gifford DK

更新日期：2018-06-01 00:00:00

abstract：:High-throughput sequencing is a revolutionary technology for the analysis of metagenomic samples. However, querying large volumes of reads against comprehensive DNA/RNA databases in a sensitive manner can be compute-intensive. Here, we present taxMaps, a highly efficient, sensitive, and fully scalable taxonomic classi...

journal_title：Genome research

authors： Corvelo A,Clarke WE,Robine N,Zody MC

更新日期：2018-05-01 00:00:00

abstract：:Microbial eukaryotes are integral components of natural microbial communities, and their inclusion is critical for many ecosystem studies, yet the majority of published metagenome analyses ignore eukaryotes. In order to include eukaryotes in environmental studies, we propose a method to recover eukaryotic genomes from...

journal_title：Genome research

authors： West PT,Probst AJ,Grigoriev IV,Thomas BC,Banfield JF

更新日期：2018-04-01 00:00:00

abstract：:Mammalian X and Y Chromosomes evolved from an ordinary autosomal pair. Genetic decay of the Y led to X Chromosome inactivation (XCI) in females, but some Y-linked genes were retained during the course of sex chromosome evolution, and many X-linked genes did not become subject to XCI. We reconstructed gene-by-gene dosa...

journal_title：Genome research

authors： Naqvi S,Bellott DW,Lin KS,Page DC

更新日期：2018-04-01 00:00:00

abstract：:Here, we report that CRISPR guide RNAs (gRNAs) with a 5'-triphosphate group (5'-ppp gRNAs) produced via in vitro transcription trigger RNA-sensing innate immune responses in human and murine cells, leading to cytotoxicity. 5'-ppp gRNAs in the cytosol are recognized by DDX58, which in turn activates type I interferon r...

journal_title：Genome research

authors： Kim S,Koo T,Jee HG,Cho HY,Lee G,Lim DG,Shin HS,Kim JS

更新日期：2018-02-22 00:00:00

abstract：:The very small fraction of putative binding sites (BSs) that are occupied by transcription factors (TFs) in vivo can be highly variable across different cell types. This observation has been partly attributed to changes in chromatin accessibility and histone modification (HM) patterns surrounding BSs. Previous studies...

journal_title：Genome research

authors： Xin B,Rohs R

更新日期：2018-01-11 00:00:00

abstract：:Sex chromosomes differentiated from different ancestral autosomes in various vertebrate lineages. Here, we trace the functional evolution of the XY Chromosomes of the green anole lizard (Anolis carolinensis), on the basis of extensive high-throughput genome, transcriptome and histone modification sequencing data and r...

journal_title：Genome research

authors： Marin R,Cortez D,Lamanna F,Pradeepa MM,Leushkin E,Julien P,Liechti A,Halbert J,Brüning T,Mössinger K,Trefzer T,Conrad C,Kerver HN,Wade J,Tschopp P,Kaessmann H

更新日期：2017-12-01 00:00:00

abstract：:The centromere is the structural unit responsible for the faithful segregation of chromosomes. Although regulation of centromeric function by epigenetic factors has been well-studied, the contributions of the underlying DNA sequences have been much less well defined, and existing methodologies for studying centromere ...

journal_title：Genome research

authors： Contreras-Galindo R,Fischer S,Saha AK,Lundy JD,Cervantes PW,Mourad M,Wang C,Qian B,Dai M,Meng F,Chinnaiyan A,Omenn GS,Kaplan MH,Markovitz DM

更新日期：2017-12-01 00:00:00

abstract：:Intra-tumor heterogeneity poses substantial challenges for cancer treatment. A tumor's composition can be deduced by reconstructing its mutational history. Central to current approaches is the infinite sites assumption that every genomic position can only mutate once over the lifetime of a tumor. The validity of this ...

journal_title：Genome research

authors： Kuipers J,Jahn K,Raphael BJ,Beerenwinkel N

更新日期：2017-11-01 00:00:00

abstract：:The impact of inherited genetic variation on gene expression in humans is well-established. The majority of known expression quantitative trait loci (eQTLs) impact expression of local genes (cis-eQTLs). More research is needed to identify effects of genetic variation on distant genes (trans-eQTLs) and understand their...

journal_title：Genome research

authors： Yang F,Wang J,GTEx Consortium.,Pierce BL,Chen LS

更新日期：2017-11-01 00:00:00

abstract：:Hi-C is a powerful technology for studying genome-wide chromatin interactions. However, current methods for assessing Hi-C data reproducibility can produce misleading results because they ignore spatial features in Hi-C data, such as domain structure and distance dependence. We present HiCRep, a framework for assessin...

journal_title：Genome research

authors： Yang T,Zhang F,Yardımcı GG,Song F,Hardison RC,Noble WS,Yue F,Li Q

更新日期：2017-11-01 00:00:00

abstract：:Cellular senescence is a mechanism that virtually irreversibly suppresses the proliferative capacity of cells in response to various stress signals. This includes the expression of activated oncogenes, which causes Oncogene-Induced Senescence (OIS). A body of evidence points to the involvement in OIS of chromatin reor...

journal_title：Genome research

authors： Lenain C,de Graaf CA,Pagie L,Visser NL,de Haas M,de Vries SS,Peric-Hupkes D,van Steensel B,Peeper DS

更新日期：2017-10-01 00:00:00

abstract：:To understand disease mechanisms, a large-scale analysis of human-yeast genetic interactions was performed. Of 1305 human disease genes assayed, 20 genes exhibited strong toxicity in yeast. Human-yeast genetic interactions were identified by en masse transformation of the human disease genes into a pool of 4653 homozy...

journal_title：Genome research

authors： Jo M,Chung AY,Yachie N,Seo M,Jeon H,Nam Y,Seo Y,Kim E,Zhong Q,Vidal M,Park HC,Roth FP,Suk K

更新日期：2017-09-01 00:00:00

abstract：:Natural selection that affected modern humans early in their evolution has likely shaped some of the traits that set present-day humans apart from their closest extinct and living relatives. The ability to detect ancient natural selection in the human genome could provide insights into the molecular basis for these hu...

journal_title：Genome research

authors： Peyrégne S,Boyle MJ,Dannemann M,Prüfer K

更新日期：2017-09-01 00:00:00

abstract：:Intra-tumoral genetic heterogeneity has been characterized across cancers by genome sequencing of bulk tumors, including chronic lymphocytic leukemia (CLL). In order to more accurately identify subclones, define phylogenetic relationships, and probe genotype-phenotype relationships, we developed methods for targeted m...

journal_title：Genome research

authors： Wang L,Fan J,Francis JM,Georghiou G,Hergert S,Li S,Gambe R,Zhou CW,Yang C,Xiao S,Cin PD,Bowden M,Kotliar D,Shukla SA,Brown JR,Neuberg D,Alessi DR,Zhang CZ,Kharchenko PV,Livak KJ,Wu CJ

更新日期：2017-08-01 00:00:00

abstract：:Structured elements of RNA molecules are essential in, e.g., RNA stabilization, localization, and protein interaction, and their conservation across species suggests a common functional role. We computationally screened vertebrate genomes for conserved RNA structures (CRSs), leveraging structure-based, rather than seq...

journal_title：Genome research

authors： Seemann SE,Mirza AH,Hansen C,Bang-Berthelsen CH,Garde C,Christensen-Dalsgaard M,Torarinsson E,Yao Z,Workman CT,Pociot F,Nielsen H,Tommerup N,Ruzzo WL,Gorodkin J

更新日期：2017-08-01 00:00:00

abstract：:Long noncoding RNAs (lncRNAs) play a conserved role in regulating gene expression, chromatin dynamics, and cell differentiation. They serve as a platform for RNA interference (RNAi)-mediated heterochromatin formation or DNA methylation in many eukaryotic organisms. We found in Schizosaccharomyces pombe that heterochro...

journal_title：Genome research

authors： Brönner C,Salvi L,Zocco M,Ugolini I,Halic M

更新日期：2017-07-01 00:00:00

abstract：:The nuclear space is not a homogeneous biochemical environment. Many studies have demonstrated that the transcriptional activity of a gene is linked to its positioning within the nuclear space. Following the discovery of lamin-associated domains (LADs), which are transcriptionally repressed chromatin regions, the nonr...

journal_title：Genome research

authors： Bi X,Cheng YJ,Hu B,Ma X,Wu R,Wang JW,Liu C

更新日期：2017-07-01 00:00:00

abstract：:CTCF is an architectural protein with a critical role in connecting higher-order chromatin folding in pluripotent stem cells. Recent reports have suggested that CTCF binding is more dynamic during development than previously appreciated. Here, we set out to understand the extent to which shifts in genome-wide CTCF occ...

journal_title：Genome research

authors： Beagan JA,Duong MT,Titus KR,Zhou L,Cao Z,Ma J,Lachanski CV,Gillis DR,Phillips-Cremins JE

更新日期：2017-07-01 00:00:00

abstract：:Epigenetic mechanisms are believed to play key roles in the establishment of cell-specific transcription programs. Accordingly, the modified bases 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) have been observed in DNA of genomic regulatory regions such as enhancers, and oxidation of 5mC into 5hmC by Ten-e...

journal_title：Genome research

authors： Mahé EA,Madigou T,Sérandour AA,Bizot M,Avner S,Chalmel F,Palierne G,Métivier R,Salbert G

更新日期：2017-06-01 00:00:00

abstract：:Transcriptomic genome-wide analyses demonstrate massive variation of alternative splicing in many physiological and pathological situations. One major challenge is now to establish the biological contribution of alternative splicing variation in physiological- or pathological-associated cellular phenotypes. Toward thi...

journal_title：Genome research

authors： Tranchevent LC,Aubé F,Dulaurier L,Benoit-Pilven C,Rey A,Poret A,Chautard E,Mortada H,Desmet FO,Chakrama FZ,Moreno-Garcia MA,Goillot E,Janczarski S,Mortreux F,Bourgeois CF,Auboeuf D

更新日期：2017-06-01 00:00:00

abstract：:While metagenomics has emerged as a technology of choice for analyzing bacterial populations, the assembly of metagenomic data remains challenging, thus stifling biological discoveries. Moreover, recent studies revealed that complex bacterial populations may be composed from dozens of related strains, thus further amp...

journal_title：Genome research

authors： Nurk S,Meleshko D,Korobeynikov A,Pevzner PA

更新日期：2017-05-01 00:00:00

abstract：:Long sequencing reads generated by single-molecule sequencing technology offer the possibility of dramatically improving the contiguity of genome assemblies. The biggest challenge today is that long reads have relatively high error rates, currently around 15%. The high error rates make it difficult to use this data al...

journal_title：Genome research

authors： Zimin AV,Puiu D,Luo MC,Zhu T,Koren S,Marçais G,Yorke JA,Dvořák J,Salzberg SL

更新日期：2017-05-01 00:00:00

abstract：:The most polymorphic part of the human genome, the MHC, encodes over 160 proteins of diverse function. Half of them, including the HLA class I and II genes, are directly involved in immune responses. Consequently, the MHC region strongly associates with numerous diseases and clinical therapies. Notoriously, the MHC re...

journal_title：Genome research

authors： Norman PJ,Norberg SJ,Guethlein LA,Nemat-Gorgani N,Royce T,Wroblewski EE,Dunn T,Mann T,Alicata C,Hollenbach JA,Chang W,Shults Won M,Gunderson KL,Abi-Rached L,Ronaghi M,Parham P

更新日期：2017-05-01 00:00:00

abstract：:Chronic bacterial infections of the lung are the leading cause of morbidity and mortality in cystic fibrosis patients. Tracking bacterial evolution during chronic infections can provide insights into how host selection pressures-including immune responses and therapeutic interventions-shape bacterial genomes. We carri...

journal_title：Genome research

authors： Lee AH,Flibotte S,Sinha S,Paiero A,Ehrlich RL,Balashov S,Ehrlich GD,Zlosnik JE,Mell JC,Nislow C

更新日期：2017-04-01 00:00:00

abstract：:DNA methylation at the promoter of a gene is presumed to render it silent, yet a sizable fraction of genes with methylated proximal promoters exhibit elevated expression. Here, we show, through extensive analysis of the methylome and transcriptome in 34 tissues, that in many such cases, transcription is initiated by a...

journal_title：Genome research

authors： Sarda S,Das A,Vinson C,Hannenhalli S

更新日期：2017-04-01 00:00:00

abstract：:Up-frameshift protein 1 (UPF1) is an ATP-dependent RNA helicase that has essential roles in RNA surveillance and in post-transcriptional gene regulation by promoting the degradation of mRNAs. Previous studies revealed that UPF1 is associated with the 3' untranslated region (UTR) of target mRNAs via as-yet-unknown sequ...

journal_title：Genome research

authors： Imamachi N,Salam KA,Suzuki Y,Akimitsu N

更新日期：2017-03-01 00:00:00

abstract：:Phenotypic differences within populations and between closely related species are often driven by variation and evolution of gene expression. However, most analyses have focused on the effects of genomic variation at cis-regulatory elements such as promoters and enhancers that control transcriptional activity, and lit...

journal_title：Genome research

authors： Ma L,Zhao B,Chen K,Thomas A,Tuteja JH,He X,He C,White KP

更新日期：2017-03-01 00:00:00

abstract：:A-to-I RNA editing is a conserved widespread phenomenon in which adenosine (A) is converted to inosine (I) by adenosine deaminases (ADARs) in double-stranded RNA regions, mainly noncoding. Mutations in ADAR enzymes in Caenorhabditis elegans cause defects in normal development but are not lethal as in human and mouse. ...

journal_title：Genome research

authors： Goldstein B,Agranat-Tamir L,Light D,Ben-Naim Zgayer O,Fishman A,Lamm AT

更新日期：2017-03-01 00:00:00

abstract：:Eukaryotic DNA replication initiates from multiple discrete sites in the genome, termed origins of replication (origins). Prior to S phase, multiple origins are poised to initiate replication by recruitment of the pre-replicative complex (pre-RC). For proper replication to occur, origin activation must be tightly regu...

journal_title：Genome research

authors： Rodriguez J,Lee L,Lynch B,Tsukiyama T

更新日期：2017-02-01 00:00:00