A-to-I RNA editing promotes developmental stage-specific gene and lncRNA expression.

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：:A rigorous analysis of the Merck-sponsored EST data with respect to known gene sequences increases the utility of the data set and helps refine methods for building a gene index. A highly curated human transcript data base was used as a reference data set of known genes. A detailed analysis of EST sequences derived fr...

journal_title：Genome research

authors： Aaronson JS,Eckman B,Blevins RA,Borkowski JA,Myerson J,Imran S,Elliston KO

更新日期：1996-09-01 00:00:00

abstract：:The Atlantic herring is a model species for exploring the genetic basis for ecological adaptation, due to its huge population size and extremely low genetic differentiation at selectively neutral loci. However, such studies have so far been hampered because of a highly fragmented genome assembly. Here, we deliver a ch...

journal_title：Genome research

authors： Pettersson ME,Rochus CM,Han F,Chen J,Hill J,Wallerman O,Fan G,Hong X,Xu Q,Zhang H,Liu S,Liu X,Haggerty L,Hunt T,Martin FJ,Flicek P,Bunikis I,Folkvord A,Andersson L

更新日期：2019-11-01 00:00:00

abstract：:A benchmark problem is described for the reconstruction and analysis of biochemical networks given sampled experimental data. The growth of the organisms is described in a bioreactor in which one substrate is fed into the reactor with a given feed rate and feed concentration. Measurements for some intracellular compon...

journal_title：Genome research

authors： Kremling A,Fischer S,Gadkar K,Doyle FJ,Sauter T,Bullinger E,Allgöwer F,Gilles ED

更新日期：2004-09-01 00:00:00

abstract：:The vomeronasal system of mice is thought to be specialized in the detection of pheromones. Two multigene families have been identified that encode proteins with seven putative transmembrane domains and that are expressed selectively in subsets of neurons of the vomeronasal organ. The products of these vomeronasal rec...

journal_title：Genome research

authors： Del Punta K,Rothman A,Rodriguez I,Mombaerts P

更新日期：2000-12-01 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：:Mammalian genomes contain many highly conserved nongenic sequences (CNGs) whose functional significance is poorly understood. Sets of CNGs have previously been identified by selecting the most conserved elements from a chromosome or genome, but in these highly selected samples, conservation may be unrelated to purifyi...

journal_title：Genome research

authors： Keightley PD,Kryukov GV,Sunyaev S,Halligan DL,Gaffney DJ

更新日期：2005-10-01 00:00:00

abstract：:The Mammalian Gene Collection (MGC) consortium (http://mgc.nci.nih.gov) seeks to establish publicly available collections of full-ORF cDNAs for several organisms of significance to biomedical research, including human. To date over 15,200 human cDNA clones containing full-length open reading frames (ORFs) have been id...

journal_title：Genome research

authors： Baross A,Butterfield YS,Coughlin SM,Zeng T,Griffith M,Griffith OL,Petrescu AS,Smailus DE,Khattra J,McDonald HL,McKay SJ,Moksa M,Holt RA,Marra MA

更新日期：2004-10-01 00:00:00

abstract：:We herein study genetic recombination in three cattle populations from France, New Zealand, and the Netherlands. We identify 2,395,177 crossover (CO) events in 94,516 male gametes, and 579,996 CO events in 25,332 female gametes. The average number of COs was found to be larger in males (23.3) than in females (21.4). T...

journal_title：Genome research

authors： Kadri NK,Harland C,Faux P,Cambisano N,Karim L,Coppieters W,Fritz S,Mullaart E,Baurain D,Boichard D,Spelman R,Charlier C,Georges M,Druet T

更新日期：2016-10-01 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：:Large-scale sequencing of human and model organism genomes will have a profound impact on our ability to use sequence data base searching to predict the biochemical functions of sequences of interest. Despite the great value of more sequences in the data bases, a huge increase in data base size will also have adverse ...

journal_title：Genome research

authors： Smith RF

更新日期：1996-08-01 00:00:00

abstract：:The rate of transcription elongation plays an important role in the timing of expression of full-length transcripts as well as in the regulation of alternative splicing. In this study, we coupled Bru-seq technology with 5,6-dichlorobenzimidazole 1-β-D-ribofuranoside (DRB) to estimate the elongation rates of over 2000 ...

journal_title：Genome research

authors： Veloso A,Kirkconnell KS,Magnuson B,Biewen B,Paulsen MT,Wilson TE,Ljungman M

更新日期：2014-06-01 00:00:00

abstract：:Developments in microarray and high-throughput sequencing (HTS) technologies have resulted in a rapid expansion of research into epigenomic changes that occur in normal development and in the progression of disease, such as cancer. Not surprisingly, copy number variation (CNV) has a direct effect on HTS read densities...

journal_title：Genome research

authors： Robinson MD,Strbenac D,Stirzaker C,Statham AL,Song J,Speed TP,Clark SJ

更新日期：2012-12-01 00:00:00

abstract：:Gene expression can be regulated at multiple levels, but it is not known if and how there is broad coordination between regulation at the transcriptional and post-transcriptional levels. Transcription factors and chromatin regulate gene expression transcriptionally, whereas microRNAs (miRNAs) are small regulatory RNAs...

journal_title：Genome research

authors： Shivram H,Le SV,Iyer VR

更新日期：2019-02-01 00:00:00

abstract：:In the search for common genetic variants that contribute to prevalent human diseases, patterns of linkage disequilibrium (LD) among linked markers should be considered when selecting SNPs. Genotyping efficiency can be increased by choosing tagging SNPs (tagSNPs) in LD with other SNPs. However, it remains to be seen w...

journal_title：Genome research

authors： González-Neira A,Ke X,Lao O,Calafell F,Navarro A,Comas D,Cann H,Bumpstead S,Ghori J,Hunt S,Deloukas P,Dunham I,Cardon LR,Bertranpetit J

更新日期：2006-03-01 00:00:00

abstract：:Short insertions and deletions (indels) are the second most abundant form of human genetic variation, but our understanding of their origins and functional effects lags behind that of other types of variants. Using population-scale sequencing, we have identified a high-quality set of 1.6 million indels from 179 indivi...

journal_title：Genome research

authors： Montgomery SB,Goode DL,Kvikstad E,Albers CA,Zhang ZD,Mu XJ,Ananda G,Howie B,Karczewski KJ,Smith KS,Anaya V,Richardson R,Davis J,1000 Genomes Project Consortium.,MacArthur DG,Sidow A,Duret L,Gerstein M,Makova KD,Marc

更新日期：2013-05-01 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：:Population genetics has evolved from a theory-driven field with little empirical data into a data-driven discipline in which genome-scale data sets test the limits of available models and computational analysis methods. In humans and a few model organisms, analyses of whole-genome sequence polymorphism data are curren...

journal_title：Genome research

authors： Pool JE,Hellmann I,Jensen JD,Nielsen R

更新日期：2010-03-01 00:00:00

abstract：:We describe a new method, Tag-seq, which employs ultra high-throughput sequencing of 21 base pair cDNA tags for sensitive and cost-effective gene expression profiling. We compared Tag-seq data to LongSAGE data and observed improved representation of several classes of rare transcripts, including transcription factors,...

journal_title：Genome research

authors： Morrissy AS,Morin RD,Delaney A,Zeng T,McDonald H,Jones S,Zhao Y,Hirst M,Marra MA

更新日期：2009-10-01 00:00:00

abstract：:The densities of transposable elements (TEs) in the human genome display substantial variation both within individual chromosomes and among chromosome types (autosomes and the two sex chromosomes). Finding an explanation for this variability has been challenging, especially in light of genome landscapes unique to the ...

journal_title：Genome research

authors： Kvikstad EM,Makova KD

更新日期：2010-05-01 00:00:00

abstract：:Tissue development and function are exquisitely dependent on proper regulation of gene expression, but it remains controversial whether the genomic signals controlling this process are subject to strong selective constraint. While some studies show that highly constrained noncoding regions act to enhance transcription...

journal_title：Genome research

authors： Cheng Y,King DC,Dore LC,Zhang X,Zhou Y,Zhang Y,Dorman C,Abebe D,Kumar SA,Chiaromonte F,Miller W,Green RD,Weiss MJ,Hardison RC

更新日期：2008-12-01 00:00:00

abstract：:In diploid mammalian genomes, parental alleles can exhibit different methylation patterns (allele-specific DNA methylation, ASM), which have been documented in a small number of cases except for the imprinted regions and X chromosomes in females. We carried out a chromosome-wide survey of ASM across 16 human pluripote...

journal_title：Genome research

authors： Shoemaker R,Deng J,Wang W,Zhang K

更新日期：2010-07-01 00:00:00

abstract：:A subset of colorectal cancers was postulated to have the CpG island methylator phenotype (CIMP), a higher propensity for CpG island DNA methylation. The validity of CIMP, its molecular basis, and its prognostic value remain highly controversial. Using MBD-isolated genome sequencing, we mapped and compared genome-wide...

journal_title：Genome research

authors： Xu Y,Hu B,Choi AJ,Gopalan B,Lee BH,Kalady MF,Church JM,Ting AH

更新日期：2012-02-01 00:00:00

abstract：:We have developed a novel quantitative method for rapidly assessing the CpG methylation density of a DNA region in mammalian cells. After bisulfite modification of genomic DNA, the region of interest is PCR amplified with primers containing two dam sites (GATC). The purified PCR products are then incubated with 14C-la...

journal_title：Genome research

authors： Galm O,Rountree MR,Bachman KE,Jair KW,Baylin SB,Herman JG

更新日期：2002-01-01 00:00:00

abstract：:Evolutionary constraints on gene regulatory elements are poorly understood: Little is known about how the strength of transcription factor binding correlates with DNA sequence conservation, and whether transcription factor binding sites can evolve rapidly while retaining their function. Here we use the model of the NF...

journal_title：Genome research

authors： Copley RR,Totrov M,Linnell J,Field S,Ragoussis J,Udalova IA

更新日期：2007-09-01 00:00:00

abstract：:Diversity in the antigen-binding receptors of the immune system has long been a primary interest of biologists. Recently it has been suggested that polymorphism in regulatory (noncoding) gene segments is of substantial importance as well. Here, we survey the level of variation in MHC class II gene promoters in man and...

journal_title：Genome research

authors： Cowell LG,Kepler TB,Janitz M,Lauster R,Mitchison NA

更新日期：1998-02-01 00:00:00

abstract：:Gene amplification occurs in most solid tumors and is associated with poor prognosis. Amplification of 20q13.2 is common to several tumor types including breast cancer. The 1 Mb of sequence spanning the 20q13.2 breast cancer amplicon is one of the most exhaustively studied segments of the human genome. These studies h...

journal_title：Genome research

authors： Collins C,Volik S,Kowbel D,Ginzinger D,Ylstra B,Cloutier T,Hawkins T,Predki P,Martin C,Wernick M,Kuo WL,Alberts A,Gray JW

更新日期：2001-06-01 00:00:00

abstract：:Variation in the composition of the human oral microbiome in health and disease has been observed. We have characterized inter- and intra-individual variation of microbial communities of 107 individuals in one of the largest cohorts to date (264 saliva samples), using culture-independent 16S rRNA pyrosequencing. We ex...

journal_title：Genome research

authors： Stahringer SS,Clemente JC,Corley RP,Hewitt J,Knights D,Walters WA,Knight R,Krauter KS

更新日期：2012-11-01 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：:A large number of cis-regulatory motifs involved in transcriptional control have been identified, but the regulatory context and biological processes in which many of them function are unknown. Here, we computationally identify the sets of human core promoters targeted by motifs, and systematically characterize their ...

journal_title：Genome research

authors： Sinha S,Adler AS,Field Y,Chang HY,Segal E

更新日期：2008-03-01 00:00:00