The first five years of single-cell cancer genomics and beyond.

abstract：:The genome size of Pseudoalteromonas haloplanktis, a ubiquitous and easily cultured marine bacterium, was measured as a step toward estimating the genome complexity of marine bacterioplankton. To determine total genome size, we digested P. haloplanktis DNA with the restriction endonucleases Notl and Sfil, separated th...

journal_title：Genome research

authors： Lanoil BD,Ciuffetti LM,Giovannoni SJ

更新日期：1996-12-01 00:00:00

abstract：:Genome-wide association studies (GWAS) have consistently implicated noncoding variation within the TCF7L2 locus with type 2 diabetes (T2D) risk. While this locus represents the strongest genetic determinant for T2D risk in humans, it remains unclear how these noncoding variants affect disease etiology. To test the hyp...

journal_title：Genome research

authors： Savic D,Ye H,Aneas I,Park SY,Bell GI,Nobrega MA

更新日期：2011-09-01 00:00:00

abstract：:As the Human Genome Project moves into its sequencing phase, a serious problem has arisen. The same problem has been increasingly vexing in the closing phase of the Caenorhabditis elegans project. The difficulty lies in sequencing efficiently through certain regions in which the templates (DNA substrates for the seque...

journal_title：Genome research

authors： McMurray AA,Sulston JE,Quail MA

更新日期：1998-05-01 00:00:00

abstract：:The human genome is estimated to contain 23,000 to 33,000 retropseudogenes. To study the properties of genes giving rise to these retroelements, we compared the structure and expression of genes with or without known retropseudogenes. Four main features have emerged from the analysis of 181 genes associated to retrops...

journal_title：Genome research

authors： Gonçalves I,Duret L,Mouchiroud D

更新日期：2000-05-01 00:00:00

abstract：:Mycoplasma mycoides subsp. mycoidesSC (MmymySC)is the etiological agent of contagious bovine pleuropneumonia (CBPP), a highly contagious respiratory disease in cattle. The genome of Mmymy SC type strain PG1(T) has been sequenced to map all the genes and to facilitate further studies regarding the cell function of the ...

journal_title：Genome research

authors： Westberg J,Persson A,Holmberg A,Goesmann A,Lundeberg J,Johansson KE,Pettersson B,Uhlén M

更新日期：2004-02-01 00:00:00

abstract：:Long and short interspersed elements (LINEs and SINEs) are retroelements that make up almost half of the human genome. L1 and Alu represent the most prolific human LINE and SINE families, respectively. Only a few Alu elements are able to retropose, and the factors determining their retroposition capacity are poorly un...

journal_title：Genome research

authors： Roy-Engel AM,Salem AH,Oyeniran OO,Deininger L,Hedges DJ,Kilroy GE,Batzer MA,Deininger PL

更新日期：2002-09-01 00:00:00

abstract：:The exponential growth of pathogen nucleic acid sequences available in public domain databases has invited their direct use in pathogen detection, identification, and surveillance strategies. DNA microarray technology has offered the potential for the direct DNA sequence analysis of a broad spectrum of pathogens of in...

journal_title：Genome research

authors： Lin B,Wang Z,Vora GJ,Thornton JA,Schnur JM,Thach DC,Blaney KM,Ligler AG,Malanoski AP,Santiago J,Walter EA,Agan BK,Metzgar D,Seto D,Daum LT,Kruzelock R,Rowley RK,Hanson EH,Tibbetts C,Stenger DA

更新日期：2006-04-01 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：:Although it is well understood that selection shapes the polymorphism pattern in Drosophila, signatures of classic selective sweeps are scarce. Here, we focus on Drosophila mauritiana, an island endemic, which is closely related to Drosophila melanogaster. Based on a new, annotated genome sequence, we characterized th...

journal_title：Genome research

authors： Nolte V,Pandey RV,Kofler R,Schlötterer C

更新日期：2013-01-01 00:00:00

abstract：:The main objectives of the study reported here were to construct a molecular map of wild emmer wheat, Triticum dicoccoides, to characterize the marker-related anatomy of the genome, and to evaluate segregation and recombination patterns upon crossing T. dicoccoides with its domesticated descendant Triticum durum (cult...

journal_title：Genome research

authors： Peng J,Korol AB,Fahima T,Röder MS,Ronin YI,Li YC,Nevo E

更新日期：2000-10-01 00:00:00

abstract：:Many CpG islands have tissue-dependent and differentially methylated regions (T-DMRs) in normal cells and tissues. To elucidate how DNA methyltransferases (Dnmts) participate in methylation of the genomic components, we investigated the genome-wide DNA methylation pattern of the T-DMRs with Dnmt1-, Dnmt3a-, and/or Dnm...

journal_title：Genome research

authors： Hattori N,Abe T,Hattori N,Suzuki M,Matsuyama T,Yoshida S,Li E,Shiota K

更新日期：2004-09-01 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：:The draft Fugu rubripes genome was released in 2002, at which time relatively few cDNAs were available to aid in the annotation of genes. The data presented here describe the sequencing and analysis of 24,398 expressed sequence tags (ESTs) generated from 15 different adult and juvenile Fugu tissues, 74% of which match...

journal_title：Genome research

authors： Clark MS,Edwards YJ,Peterson D,Clifton SW,Thompson AJ,Sasaki M,Suzuki Y,Kikuchi K,Watabe S,Kawakami K,Sugano S,Elgar G,Johnson SL

更新日期：2003-12-01 00:00:00

abstract：:Targeted genotyping of transcriptome-scale genetic markers is highly attractive for genetic, ecological, and evolutionary studies, but achieving this goal in a cost-effective manner remains a major challenge, especially for laboratories working on nonmodel organisms. Here, we develop a high-throughput, sequencing-base...

journal_title：Genome research

authors： Lv J,Jiao W,Guo H,Liu P,Wang R,Zhang L,Zeng Q,Hu X,Bao Z,Wang S

更新日期：2018-12-01 00:00:00

abstract：:Large-scale gene expression studies and genomic sequencing projects are providing vast amounts of information that can be used to identify or predict cellular regulatory processes. Genes can be clustered on the basis of the similarity of their expression profiles or function and these clusters are likely to contain ge...

journal_title：Genome research

authors： Jakt LM,Cao L,Cheah KS,Smith DK

更新日期：2001-01-01 00:00:00

abstract：:In-gel competitive reassociation (IGCR) is a method of differential subtraction to enrich polymorphic DNA restriction fragments between two DNA samples without probes or specific sequence information. Here, we show that by combining IGCR and expressed sequence tags (EST) array hybridization, polymorphic DNA fragments ...

journal_title：Genome research

authors： Gotoh K,Oishi M

更新日期：2003-03-01 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：: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：:Aberrant DNA methylation (DNAm) was first linked to cancer over 25 yr ago. Since then, many studies have associated hypermethylation of tumor suppressor genes and hypomethylation of oncogenes to the tumorigenic process. However, most of these studies have been limited to the analysis of promoters and CpG islands (CGIs...

journal_title：Genome research

authors： Feber A,Wilson GA,Zhang L,Presneau N,Idowu B,Down TA,Rakyan VK,Noon LA,Lloyd AC,Stupka E,Schiza V,Teschendorff AE,Schroth GP,Flanagan A,Beck S

更新日期：2011-04-01 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：:Alternative splicing (AS) creates multiple mRNA transcripts from a single gene. While AS is known to contribute to gene regulation and proteome diversity in animals, the study of its importance in plants is in its early stages. However, recently available plant genome and transcript sequence data sets are enabling a g...

journal_title：Genome research

authors： Barbazuk WB,Fu Y,McGinnis KM

更新日期：2008-09-01 00:00:00

abstract：:Orthologous genes that maintain a single-copy status in a broad range of species may indicate a selection against gene duplication. If this is the case, then duplicates of such genes that do survive may have escaped the dosage control by rapid and sizable changes in their function. To test this hypothesis and to devel...

journal_title：Genome research

authors： Ciccarelli FD,von Mering C,Suyama M,Harrington ED,Izaurralde E,Bork P

更新日期：2005-03-01 00:00:00

abstract：:Bidirectional promoters have received considerable attention because of their ability to regulate two downstream genes (divergent genes). They are also highly abundant, directing the transcription of approximately 11% of genes in the human genome. We categorized the presence of DNA sequence motifs, binding of transcri...

journal_title：Genome research

authors： Lin JM,Collins PJ,Trinklein ND,Fu Y,Xi H,Myers RM,Weng Z

更新日期：2007-06-01 00:00:00

abstract：:High-throughput sequencing of cDNA (RNA-seq) is a widely deployed transcriptome profiling and annotation technique, but questions about the performance of different protocols and platforms remain. We used a newly developed pool of 96 synthetic RNAs with various lengths, and GC content covering a 2(20) concentration ra...

journal_title：Genome research

authors： Jiang L,Schlesinger F,Davis CA,Zhang Y,Li R,Salit M,Gingeras TR,Oliver B

更新日期：2011-09-01 00:00:00

abstract：:Chromosomal aberrations have been thought to be random events. However, recent findings introduce a new paradigm in which certain DNA segments have the potential to adopt unusual conformations that lead to genomic instability and nonrandom chromosomal rearrangement. One of the best-studied examples is the palindromic ...

journal_title：Genome research

authors： Inagaki H,Ohye T,Kogo H,Kato T,Bolor H,Taniguchi M,Shaikh TH,Emanuel BS,Kurahashi H

更新日期：2009-02-01 00:00:00

abstract：:Chicken B cells create their immunoglobulin repertoire within the Bursa of Fabricius by gene conversion. The high homologous recombination activity is shared by the bursal B-cell-derived DT40 cell line, which integrates transfected DNA constructs at high rates into its endogenous loci. Targeted integration in DT40 is ...

journal_title：Genome research

authors： Abdrakhmanov I,Lodygin D,Geroth P,Arakawa H,Law A,Plachy J,Korn B,Buerstedde JM

更新日期：2000-12-01 00:00:00

abstract：:Fragile sites are gaps and breaks in metaphase chromosomes generated by specific culture conditions. Fragile site FRA3B is the most unstable site and is directly involved in the breakpoints of deletion and translocation in a wide spectrum of cancers. To learn about the general characteristics of common fragile sites, ...

journal_title：Genome research

authors： Mulvihill DJ,Wang YH

更新日期：2004-07-01 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：: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

abstract：:The study of genetic variability within natural populations of pathogens may provide insight into their evolution and pathogenesis. We used a Mycobacterium tuberculosis high-density oligonucleotide microarray to detect small-scale genomic deletions among 19 clinically and epidemiologically well-characterized isolates ...

journal_title：Genome research

authors： Kato-Maeda M,Rhee JT,Gingeras TR,Salamon H,Drenkow J,Smittipat N,Small PM

更新日期：2001-04-01 00:00:00