Evidence for widespread subfunctionalization of splice forms in vertebrate genomes.

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：:A new algorithm, WABA, was developed for doing large-scale alignments between genomic DNA of different species. WABA was used to align 8 million bases of Caenorhabditis briggsae genomic DNA against the entire 97-million-base Caenorhabditis elegans genome. The alignment, including C. briggsae homologs of 154 geneticall...

journal_title：Genome research

authors： Kent WJ,Zahler AM

更新日期：2000-08-01 00:00:00

abstract：:Dictyostelium discoideum (DD), an extensively studied model organism for cell and developmental biology, belongs to the most derived group 4 of social amoebas, a clade of altruistic multicellular organisms. To understand genome evolution over long time periods and the genetic basis of social evolution, we sequenced th...

journal_title：Genome research

authors： Heidel AJ,Lawal HM,Felder M,Schilde C,Helps NR,Tunggal B,Rivero F,John U,Schleicher M,Eichinger L,Platzer M,Noegel AA,Schaap P,Glöckner G

更新日期：2011-11-01 00:00:00

abstract：:Double minutes (dmin) and homogeneously staining regions (hsr) are the cytogenetic hallmarks of genomic amplification in cancer. Different mechanisms have been proposed to explain their genesis. Recently, our group showed that the MYC-containing dmin in leukemia cases arise by excision and amplification (episome model...

journal_title：Genome research

authors： Storlazzi CT,Lonoce A,Guastadisegni MC,Trombetta D,D'Addabbo P,Daniele G,L'Abbate A,Macchia G,Surace C,Kok K,Ullmann R,Purgato S,Palumbo O,Carella M,Ambros PF,Rocchi M

更新日期：2010-09-01 00:00:00

abstract：:Microsatellites are abundant in vertebrate genomes, but their sequence representation and length distributions vary greatly within each family of repeats (e.g., tetranucleotides). Biophysical studies of 82 synthetic single-stranded oligonucleotides comprising all tetra- and trinucleotide repeats revealed an inverse co...

journal_title：Genome research

authors： Bacolla A,Larson JE,Collins JR,Li J,Milosavljevic A,Stenson PD,Cooper DN,Wells RD

更新日期：2008-10-01 00:00:00

abstract：:The most widely appreciated role of DNA is to encode protein, yet the exact portion of the human genome that is translated remains to be ascertained. We previously developed PhyloCSF, a widely used tool to identify evolutionary signatures of protein-coding regions using multispecies genome alignments. Here, we present...

journal_title：Genome research

authors： Mudge JM,Jungreis I,Hunt T,Gonzalez JM,Wright JC,Kay M,Davidson C,Fitzgerald S,Seal R,Tweedie S,He L,Waterhouse RM,Li Y,Bruford E,Choudhary JS,Frankish A,Kellis M

更新日期：2019-12-01 00:00:00

abstract：:Translocations are a common class of chromosomal aberrations and can cause disease by physically disrupting genes or altering their regulatory environment. Some translocations, apparently balanced at the microscopic level, include deletions, duplications, insertions, or inversions at the molecular level. Traditionally...

journal_title：Genome research

authors： Sobreira NL,Gnanakkan V,Walsh M,Marosy B,Wohler E,Thomas G,Hoover-Fong JE,Hamosh A,Wheelan SJ,Valle D

更新日期：2011-10-01 00:00:00

abstract：:Current generation DNA sequencing instruments are moving closer to seamlessly sequencing genomes of entire populations as a routine part of scientific investigation. However, while significant inroads have been made identifying small nucleotide variation and structural variations in DNA that impact phenotypes of inter...

journal_title：Genome research

authors： Schadt EE,Banerjee O,Fang G,Feng Z,Wong WH,Zhang X,Kislyuk A,Clark TA,Luong K,Keren-Paz A,Chess A,Kumar V,Chen-Plotkin A,Sondheimer N,Korlach J,Kasarskis A

更新日期：2013-01-01 00:00:00

abstract：:Single-nucleotide polymorphisms (SNPs) are the most frequently found DNA sequence variations in the human genome. It has been argued that a dense set of SNP markers can be used to identify genetic factors associated with complex disease traits. Because all high-throughput genotyping methods require precise sequence kn...

journal_title：Genome research

authors： Taillon-Miller P,Piernot EE,Kwok PY

更新日期：1999-05-01 00:00:00

abstract：:Mutational analysis of large genes with complex genomic structures plays an important role in medical genetics. Technical limitations associated with current mutation screening protocols have placed increased emphasis on the development of new technologies to simplify these procedures. High-density arrays of >90,000-o...

journal_title：Genome research

authors： Hacia JG,Sun B,Hunt N,Edgemon K,Mosbrook D,Robbins C,Fodor SP,Tagle DA,Collins FS

更新日期：1998-12-01 00:00:00

abstract：:Regulatory sequences in higher genomes can map large distances from gene coding regions, and cannot yet be identified by simple inspection of primary DNA sequence information. Here we describe an efficient method of surveying large genomic regions for gene regulatory information, and subdividing complex sets of distan...

journal_title：Genome research

authors： Mortlock DP,Guenther C,Kingsley DM

更新日期：2003-09-01 00:00:00

abstract：:In mammals, genome-wide chromatin maps and immunofluorescence studies show that broad domains of repressive histone modifications are present on pericentromeric and telomeric repeats and on the inactive X chromosome. However, only a few autosomal loci such as silent Hox gene clusters have been shown to lie in broad do...

journal_title：Genome research

authors： Pauler FM,Sloane MA,Huang R,Regha K,Koerner MV,Tamir I,Sommer A,Aszodi A,Jenuwein T,Barlow DP

更新日期：2009-02-01 00:00:00

abstract：:Previous approaches to mutation detection in mRNA from the neurofibromatosis 1 (NF1) locus have required the PCR amplification of five or more overlapping cDNA segments to screen the entire 8.5-kb open reading frame (ORF). Systematically, these assays do not detect deletions that span the region of overlap (usually 1-...

journal_title：Genome research

authors： Martinez JM,Breidenbach HH,Cawthon R

更新日期：1996-01-01 00:00:00

abstract：:The need to translate genes to function has positioned the rat as an invaluable animal model for genomic research. The significant increase in genomic resources in recent years has had an immediate functional application in the rat. Many of the resources for translational research are already in place and are ready to...

journal_title：Genome research

authors： Lazar J,Moreno C,Jacob HJ,Kwitek AE

更新日期：2005-12-01 00:00:00

abstract：:Detecting rare sequence variants in genomic DNA is central to the analysis of de novo mutation and recombination events and the detection of rare pathological mutations in mixed cell populations. Current PCR techniques suffer from noise that limits detection to variants present at a frequency of at least 10(-4)-10(-5)...

journal_title：Genome research

authors： Jeffreys AJ,May CA

更新日期：2003-10-01 00:00:00

abstract：:MicroRNAs (miRNAs) are major post-transcriptional regulators of gene expression, yet their origins and functional evolution in mammals remain little understood due to the lack of appropriate comparative data. Using RNA sequencing, we have generated extensive and comparable miRNA data for five organs in six species tha...

journal_title：Genome research

authors： Meunier J,Lemoine F,Soumillon M,Liechti A,Weier M,Guschanski K,Hu H,Khaitovich P,Kaessmann H

更新日期：2013-01-01 00:00:00

abstract：:Transposable elements (TEs) are an integral part of the host transcriptome. TE-containing noncoding RNAs (ncRNAs) show considerable tissue specificity and play important roles during development, including stem cell maintenance and cell differentiation. Recent advances in single-cell RNA-seq (scRNA-seq) revolutionized...

journal_title：Genome research

authors： Shao W,Wang T

更新日期：2021-01-01 00:00:00

abstract：:We report the construction of a dense linkage map of the rat genome integrating 767 simple sequence length polymorphism markers, combined over three crosses with high rates of polymorphism. F2 populations from WKY x S (n = 159), BN x S (n = 91), and BN x GK (n = 139) were selected and genotyped for combinations of mic...

journal_title：Genome research

authors： Bihoreau MT,Gauguier D,Kato N,Hyne G,Lindpaintner K,Rapp JP,James MR,Lathrop GM

更新日期：1997-05-01 00:00:00

abstract：:Remnants of more than 3 million transposable elements, primarily retroelements, comprise nearly half of the human genome and have generated much speculation concerning their evolutionary significance. We have exploited the draft human genome sequence to examine the distributions of retroelements on a genome-wide scale...

journal_title：Genome research

authors： Medstrand P,van de Lagemaat LN,Mager DL

更新日期：2002-10-01 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：:Metagenomic projects generate short, overlapping fragments of DNA sequence, each deriving from a different individual. We report a new method for inferring the scaled mutation rate, theta = 2Neu, and the scaled exponential growth rate, R = Ner, from the site-frequency spectrum of these data while accounting for sequen...

journal_title：Genome research

authors： Johnson PL,Slatkin M

更新日期：2006-10-01 00:00:00

abstract：:Genome-scale metabolic models promise important insights into cell function. However, the definition of pathways and functional network modules within these models, and in the biochemical literature in general, is often based on intuitive reasoning. Although mathematical methods have been proposed to identify modules,...

journal_title：Genome research

authors： Bundy JG,Papp B,Harmston R,Browne RA,Clayson EM,Burton N,Reece RJ,Oliver SG,Brindle KM

更新日期：2007-04-01 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：:We have developed a computer program that aligns spliced sequences to genomic sequences, using local alignment algorithms and heuristics to put together a global spliced alignment. Spidey can produce reliable alignments quickly, even when confronted with noise from alternative splicing, polymorphisms, sequencing error...

journal_title：Genome research

authors： Wheelan SJ,Church DM,Ostell JM

更新日期：2001-11-01 00:00:00

abstract：:Retrotransposons commonly encode a reverse transcriptase (RT), but other functional domains are variable. The acquisition of new domains is the dominant evolutionary force that brings structural variety to retrotransposons. Non-long-terminal-repeat (non-LTR) retrotransposons are classified into two groups by their str...

journal_title：Genome research

authors： Kojima KK,Fujiwara H

更新日期：2005-08-01 00:00:00

abstract：:Whole-genome sequencing using massively parallel sequencing technologies enables accurate detection of somatic rearrangements in cancer. Pinpointing large numbers of rearrangement breakpoints to base-pair resolution allows analysis of rearrangement microhomology and genomic location for every sample. Here we analyze 9...

journal_title：Genome research

authors： Drier Y,Lawrence MS,Carter SL,Stewart C,Gabriel SB,Lander ES,Meyerson M,Beroukhim R,Getz G

更新日期：2013-02-01 00:00:00

abstract：:Meiotic recombination, including crossovers (COs) and gene conversions (GCs), impacts natural variation and is an important evolutionary force. COs increase genetic diversity by redistributing existing variation, whereas GCs can alter allelic frequency. Here, we sequenced Arabidopsis Landsberg erecta (Ler) and two set...

journal_title：Genome research

authors： Lu P,Han X,Qi J,Yang J,Wijeratne AJ,Li T,Ma H

更新日期：2012-03-01 00:00:00

abstract：:Aberrations of protein-coding genes are a focus of cancer genomics; however, the impact of oncogenes on expression of the ~50% of transcripts without protein-coding potential, including long noncoding RNAs (lncRNAs), has been largely uncharacterized. Activating mutations in the BRAF oncogene are present in >70% of mel...

journal_title：Genome research

authors： Flockhart RJ,Webster DE,Qu K,Mascarenhas N,Kovalski J,Kretz M,Khavari PA

更新日期：2012-06-01 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：:In plants there are several classes of 21-24-nt short RNAs that regulate gene expression. The most conserved class is the microRNAs (miRNAs), although some miRNAs are found only in specific species. We used high-throughput pyrosequencing to identify conserved and nonconserved miRNAs and other short RNAs in tomato frui...

journal_title：Genome research

authors： Moxon S,Jing R,Szittya G,Schwach F,Rusholme Pilcher RL,Moulton V,Dalmay T

更新日期：2008-10-01 00:00:00