Computational comparison of human genomic sequence assemblies for a region of chromosome 4.

abstract：:The prion protein (PrP), first identified in scrapie-infected rodents, is encoded by a single exon of a single-copy chromosomal gene. In addition to the protein-coding exon, PrP genes in mammals contain one or two 5'-noncoding exons. To learn more about the genomic organization of regions surrounding the PrP exons, we...

journal_title：Genome research

authors： Lee IY,Westaway D,Smit AF,Wang K,Seto J,Chen L,Acharya C,Ankener M,Baskin D,Cooper C,Yao H,Prusiner SB,Hood LE

更新日期：1998-10-01 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：:Large copy number variants (CNVs) have been recently found as structural polymorphisms of the human genome of still unknown biological significance. CNVs are significantly enriched in regions with segmental duplications or low-copy repeats (LCRs). Williams-Beuren syndrome (WBS) is a neurodevelopmental disorder caused ...

journal_title：Genome research

authors： Cuscó I,Corominas R,Bayés M,Flores R,Rivera-Brugués N,Campuzano V,Pérez-Jurado LA

更新日期：2008-05-01 00:00:00

abstract：:We previously described the whole-genome assembly program Arachne, presenting assemblies of simulated data for small to mid-sized genomes. Here we describe algorithmic adaptations to the program, allowing for assembly of mammalian-size genomes, and also improving the assembly of smaller genomes. Three principal change...

journal_title：Genome research

authors： Jaffe DB,Butler J,Gnerre S,Mauceli E,Lindblad-Toh K,Mesirov JP,Zody MC,Lander ES

更新日期：2003-01-01 00:00:00

abstract：:We used a combination of cDNA selection, exon amplification, and computational prediction from genomic sequence to isolate transcribed sequences from genomic DNA surrounding the familial Mediterranean fever (FMF) locus. Eighty-seven kb of genomic DNA around D16S3370, a marker showing a high degree of linkage disequili...

journal_title：Genome research

authors： Centola M,Chen X,Sood R,Deng Z,Aksentijevich I,Blake T,Ricke DO,Chen X,Wood G,Zaks N,Richards N,Krizman D,Mansfield E,Apostolou S,Liu J,Shafran N,Vedula A,Hamon M,Cercek A,Kahan T,Gumucio D,Callen DF,Richards

更新日期：1998-11-01 00:00:00

abstract：:GeneID is a program to predict genes in anonymous genomic sequences designed with a hierarchical structure. In the first step, splice sites, and start and stop codons are predicted and scored along the sequence using position weight matrices (PWMs). In the second step, exons are built from the sites. Exons are scored ...

journal_title：Genome research

authors： Parra G,Blanco E,Guigó R

更新日期：2000-04-01 00:00:00

abstract：:DNA methylation is found in many eukaryotes, but its function is still controversial. We have studied the methylation of plant and animal genomes using a PCR-based technique amenable for high throughput. Repetitive elements are methylated in both organisms, but whereas most mammalian exons are methylated, plant exons ...

journal_title：Genome research

authors： Rabinowicz PD,Palmer LE,May BP,Hemann MT,Lowe SW,McCombie WR,Martienssen RA

更新日期：2003-12-01 00:00:00

abstract：:We generated high-resolution maps of histone H3 lysine 9/14 acetylation (H3ac), histone H4 lysine 5/8/12/16 acetylation (H4ac), and histone H3 at lysine 4 mono-, di-, and trimethylation (H3K4me1, H3K4me2, H3K4me3, respectively) across the ENCODE regions. Studying each modification in five human cell lines including th...

journal_title：Genome research

authors： Koch CM,Andrews RM,Flicek P,Dillon SC,Karaöz U,Clelland GK,Wilcox S,Beare DM,Fowler JC,Couttet P,James KD,Lefebvre GC,Bruce AW,Dovey OM,Ellis PD,Dhami P,Langford CF,Weng Z,Birney E,Carter NP,Vetrie D,Dunham I

更新日期：2007-06-01 00:00:00

abstract：:In cancer cells, aberrant DNA methylation is commonly associated with transcriptional alterations, including silencing of tumor suppressor genes. However, multiple epigenetic mechanisms, including polycomb repressive marks, contribute to gene deregulation in cancer. To dissect the relative contribution of DNA methylat...

journal_title：Genome research

authors： Court F,Le Boiteux E,Fogli A,Müller-Barthélémy M,Vaurs-Barrière C,Chautard E,Pereira B,Biau J,Kemeny JL,Khalil T,Karayan-Tapon L,Verrelle P,Arnaud P

更新日期：2019-10-01 00:00:00

abstract：:Using both env and long terminal repeat (LTR) sequences, with maximal representation of genetic diversity within primate strains, we revise and expand the unique evolutionary history of human and simian T-cell leukemia/lymphotropic viruses (HTLV/STLV). Based on the robust application of three different phylogenetic al...

journal_title：Genome research

authors： Slattery JP,Franchini G,Gessain A

更新日期：1999-06-01 00:00:00

abstract：:MicroRNAs (miRNAs) are known to post-transcriptionally regulate target mRNAs through the 3'-UTR, which interacts mainly with the 5'-end of miRNA in animals. Here we identify many endogenous motifs within human 5'-UTRs specific to the 3'-ends of miRNAs. The 3'-end of conserved miRNAs in particular has significant inter...

journal_title：Genome research

authors： Lee I,Ajay SS,Yook JI,Kim HS,Hong SH,Kim NH,Dhanasekaran SM,Chinnaiyan AM,Athey BD

更新日期：2009-07-01 00:00:00

abstract：:Recent advances toward the characterization of Alzheimer's disease (AD) have permitted the identification of a dozen of genetic risk factors, although many more remain undiscovered. In parallel, works in the field of network biology have shown a strong link between protein connectivity and disease. In this manuscript,...

journal_title：Genome research

authors： Soler-López M,Zanzoni A,Lluís R,Stelzl U,Aloy P

更新日期：2011-03-01 00:00:00

abstract：:Chemical cues influence a range of behavioral responses in rodents. The involvement of protein odorants and odorant receptors in mediating reproductive behavior, foraging, and predator avoidance suggests that their genes may have been subject to adaptive evolution. We have estimated the consequences of selection on ro...

journal_title：Genome research

authors： Emes RD,Beatson SA,Ponting CP,Goodstadt L

更新日期：2004-04-01 00:00:00

abstract：:Through comparative studies of the model organism Arabidopsis thaliana and its close relative Brassica oleracea, we have identified conserved regions that represent potentially functional sequences overlooked by previous Arabidopsis genome annotation methods. A total of 454,274 whole genome shotgun sequences covering ...

journal_title：Genome research

authors： Ayele M,Haas BJ,Kumar N,Wu H,Xiao Y,Van Aken S,Utterback TR,Wortman JR,White OR,Town CD

更新日期：2005-04-01 00:00:00

abstract：:Duplication of the genome in mammalian cells occurs in a defined temporal order referred to as its replication-timing (RT) program. RT changes dynamically during development, regulated in units of 400-800 kb referred to as replication domains (RDs). Changes in RT are generally coordinated with transcriptional competen...

journal_title：Genome research

authors： Rivera-Mulia JC,Buckley Q,Sasaki T,Zimmerman J,Didier RA,Nazor K,Loring JF,Lian Z,Weissman S,Robins AJ,Schulz TC,Menendez L,Kulik MJ,Dalton S,Gabr H,Kahveci T,Gilbert DM

更新日期：2015-08-01 00:00:00

abstract：:CRISPR/Cas9-mediated targeted mutagenesis allows efficient generation of loss-of-function alleles in zebrafish. To date, this technology has been primarily used to generate genetic knockout animals. Nevertheless, the study of the function of certain loci might require tight spatiotemporal control of gene inactivation....

journal_title：Genome research

authors： Di Donato V,De Santis F,Auer TO,Testa N,Sánchez-Iranzo H,Mercader N,Concordet JP,Del Bene F

更新日期：2016-05-01 00:00:00

abstract：:Large numbers of expressed sequence tags (ESTs) continue to fill public and private databases with partial cDNA sequences. However, using this huge amount of ESTs to facilitate gene finding in genomic sequence imposes a challenge, especially to wet-lab scientists who often have limited computing resources. In an effor...

journal_title：Genome research

authors： Jiang J,Jacob HJ

更新日期：1998-03-01 00:00:00

abstract：:The Y centromere sequence of house mouse, Mus musculus, remains unknown despite our otherwise significant knowledge of the genome sequence of this important mammalian model organism. Here, we report the complete molecular characterization of the C57BL/6J chromosome Y centromere, which comprises a highly diverged minor...

journal_title：Genome research

authors： Pertile MD,Graham AN,Choo KH,Kalitsis P

更新日期：2009-12-01 00:00:00

abstract：:Despite recent progress in genome topology knowledge, the role of repeats, which make up the majority of mammalian genomes, remains elusive. Satellite repeats are highly abundant sequences that cluster around centromeres, attract pericentromeric heterochromatin, and aggregate into nuclear chromocenters. These nuclear ...

journal_title：Genome research

authors： Wijchers PJ,Geeven G,Eyres M,Bergsma AJ,Janssen M,Verstegen M,Zhu Y,Schell Y,Vermeulen C,de Wit E,de Laat W

更新日期：2015-07-01 00:00:00

abstract：:The Drosophila Enhancer of split complex [E(spl)-C] is a remarkable complex of genes many of which are effectors or modulators of Notch signaling. The complex contains different classes of genes including four bearded genes and seven basic helix-loop-helix (bHLH) genes. We examined the evolution of this unusual comple...

journal_title：Genome research

authors： Duncan EJ,Dearden PK

更新日期：2010-07-01 00:00:00

abstract：:Double anal fin (Da) is a medaka with an autosomal semidominant mutation that causes mirror image duplication of the ventral region concentrating on the caudal region. The chromosomal location of the Da gene and its sequence have remained unknown. We constructed a medaka linkage map as a first step to approach positio...

journal_title：Genome research

authors： Ohtsuka M,Makino S,Yoda K,Wada H,Naruse K,Mitani H,Shima A,Ozato K,Kimura M,Inoko H

更新日期：1999-12-01 00:00:00

abstract：:Fish-mammal genomic comparisons have proved powerful in identifying conserved noncoding elements likely to be cis-regulatory in nature, and the majority of those tested in vivo have been shown to act as tissue-specific enhancers associated with genes involved in transcriptional regulation of development. Although most...

journal_title：Genome research

authors： McEwen GK,Woolfe A,Goode D,Vavouri T,Callaway H,Elgar G

更新日期：2006-04-01 00:00:00

abstract：:In Drosophila melanogaster, there is an excess of genes duplicated by retroposition from the X chromosome to the autosomes. Most of those retrogenes that originated on the X chromosome have testis expression pattern. These observations could be explained by natural selection favoring genes that avoided spermatogenesis...

journal_title：Genome research

authors： Vibranovski MD,Zhang Y,Long M

更新日期：2009-05-01 00:00:00

abstract：:RNA-seq by poly(A) selection is currently the most common protocol for whole transcriptome sequencing as it provides a broad, detailed, and accurate view of the RNA landscape. Unfortunately, the utility of poly(A) libraries is greatly limited when the input RNA is degraded, which is the norm for research tissues and c...

journal_title：Genome research

authors： Cieslik M,Chugh R,Wu YM,Wu M,Brennan C,Lonigro R,Su F,Wang R,Siddiqui J,Mehra R,Cao X,Lucas D,Chinnaiyan AM,Robinson D

更新日期：2015-09-01 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：:Transposable elements (TEs) proliferate within the genome of their host, which responds by silencing them epigenetically. Much is known about the mechanisms of silencing in plants, particularly the role of siRNAs in guiding DNA methylation. In contrast, little is known about siRNA targeting patterns along the length o...

journal_title：Genome research

authors： Bousios A,Diez CM,Takuno S,Bystry V,Darzentas N,Gaut BS

更新日期：2016-02-01 00:00:00

abstract：:Single-cell sequencing (SCS) is a powerful new tool for investigating evolution and diversity in cancer and understanding the role of rare cells in tumor progression. These methods have begun to unravel key questions in cancer biology that have been difficult to address with bulk tumor measurements. Over the past five...

journal_title：Genome research

authors： Navin NE

更新日期：2015-10-01 00:00:00

abstract：:The epistatically interacting modifier loci (Apmt1 and Apmt2) accelerate the polyoma Middle-T (PyVT)-induced mammary tumor. To identify potential candidate genes loci, a combined bioinformatics and genomics strategy was used. On the basis of the assumption that the loci were functioning in the same or intersecting pat...

journal_title：Genome research

authors： Cozma D,Lukes L,Rouse J,Qiu TH,Liu ET,Hunter KW

更新日期：2002-06-01 00:00:00

abstract：:Gene duplication and alternative splicing are important sources of proteomic diversity. Despite research indicating that gene duplication and alternative splicing are negatively correlated, the evolutionary relationship between the two remains unclear. One manner in which alternative splicing and gene duplication may ...

journal_title：Genome research

authors： Lambert MJ,Cochran WO,Wilde BM,Olsen KG,Cooper CD

更新日期：2015-05-01 00:00:00

abstract：:It is critical to avoid delays in detecting strain manipulations, such as the addition/deletion of a gene or modification of genes for increased virulence or antibiotic resistance, using genome analysis during an epidemic outbreak or a bioterrorist attack. Our objective was to evaluate the efficiency of genome analysi...

journal_title：Genome research

authors： La Scola B,Elkarkouri K,Li W,Wahab T,Fournous G,Rolain JM,Biswas S,Drancourt M,Robert C,Audic S,Löfdahl S,Raoult D

更新日期：2008-05-01 00:00:00