Development and application of a phylogenomic toolkit: resolving the evolutionary history of Madagascar's lemurs.

abstract：:Primordial dwarfism (PD) is a disease in which severely impaired fetal growth persists throughout postnatal development and results in stunted adult size. The condition is highly heterogeneous clinically, but the use of certain phenotypic aspects such as head circumference and facial appearance has proven helpful in d...

journal_title：Genome research

authors： Shaheen R,Faqeih E,Ansari S,Abdel-Salam G,Al-Hassnan ZN,Al-Shidi T,Alomar R,Sogaty S,Alkuraya FS

更新日期：2014-02-01 00:00:00

abstract：:Short tandem repeats (STRs) have a wide range of applications, including medical genetics, forensics, and genetic genealogy. High-throughput sequencing (HTS) has the potential to profile hundreds of thousands of STR loci. However, mainstream bioinformatics pipelines are inadequate for the task. These pipelines treat S...

journal_title：Genome research

authors： Gymrek M,Golan D,Rosset S,Erlich Y

更新日期：2012-06-01 00:00:00

abstract：:Contamination by present-day human and microbial DNA is one of the major hindrances for large-scale genomic studies using ancient biological material. We describe a new molecular method, U selection, which exploits one of the most distinctive features of ancient DNA--the presence of deoxyuracils--for selective enrichm...

journal_title：Genome research

authors： Gansauge MT,Meyer M

更新日期：2014-09-01 00:00:00

abstract：:X-linked Mental Retardation (XLMR) occurs in 1 in 600 males and is highly genetically heterogeneous. We used a novel human X chromosome cDNA microarray (XCA) to survey the expression profile of X-linked genes in lymphoblasts of XLMR males. Genes with altered expression verified by Northern blot and/or quantitative PCR...

journal_title：Genome research

authors： Zhang L,Jie C,Obie C,Abidi F,Schwartz CE,Stevenson RE,Valle D,Wang T

更新日期：2007-05-01 00:00:00

abstract：:The repressive capacity of cytosine DNA methylation is mediated by recruitment of silencing complexes by methyl-CpG binding domain (MBD) proteins. Despite MBD proteins being associated with silencing, we discovered that a family of arthropod Copia retrotransposons have incorporated a host-derived MBD. We functionally ...

journal_title：Genome research

authors： de Mendoza A,Pflueger J,Lister R

更新日期：2019-08-01 00:00:00

abstract：:We developed a microarray platform for PCR amplification-independent expression profiling of minute samples. A novel scanning system combined with specialized biochips enables detection down to individual fluorescent oligonucleotide molecules specifically hybridized to their complementary sequence over the entire bioc...

journal_title：Genome research

authors： Hesse J,Jacak J,Kasper M,Regl G,Eichberger T,Winklmayr M,Aberger F,Sonnleitner M,Schlapak R,Howorka S,Muresan L,Frischauf AM,Schütz GJ

更新日期：2006-08-01 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：:Most new genes arise by duplication of existing gene structures, after which relaxed selection on the new copy frequently leads to mutational inactivation of the duplicate; only rarely will a new gene with modified function emerge. Here we describe a unique mechanism of gene creation, whereby new combinations of funct...

journal_title：Genome research

authors： Babushok DV,Ohshima K,Ostertag EM,Chen X,Wang Y,Mandal PK,Okada N,Abrams CS,Kazazian HH Jr

更新日期：2007-08-01 00:00:00

abstract：:X inactivation equalizes the dosage of gene expression between the sexes, but some genes escape silencing and are thus expressed from both alleles in females. To survey X inactivation and escape in mouse, we performed RNA sequencing in Mus musculus x Mus spretus cells with complete skewing of X inactivation, relying o...

journal_title：Genome research

authors： Yang F,Babak T,Shendure J,Disteche CM

更新日期：2010-05-01 00:00:00

abstract：:Extracellular cues play critical roles in the establishment of the epigenome during development and may also contribute to epigenetic perturbations found in disease states. The direct role of the local tissue environment on the post-development human epigenome, however, remains unclear due to limitations in studies of...

journal_title：Genome research

authors： Lay FD,Triche TJ Jr,Tsai YC,Su SF,Martin SE,Daneshmand S,Skinner EC,Liang G,Chihara Y,Jones PA

更新日期：2014-04-01 00:00:00

abstract：:Designing effective and accurate tools for identifying the functional and structural elements in a genome remains at the frontier of genome annotation owing to incompleteness and inaccuracy of the data, limitations in the computational models, and shifting paradigms in genomics, such as alternative splicing. We presen...

journal_title：Genome research

authors： Florea L,Di Francesco V,Miller J,Turner R,Yao A,Harris M,Walenz B,Mobarry C,Merkulov GV,Charlab R,Dew I,Deng Z,Istrail S,Li P,Sutton G

更新日期：2005-01-01 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：:Somatic L1 retrotransposition events have been shown to occur in epithelial cancers. Here, we attempted to determine how early somatic L1 insertions occurred during the development of gastrointestinal (GI) cancers. Using L1-targeted resequencing (L1-seq), we studied different stages of four colorectal cancers arising ...

journal_title：Genome research

authors： Ewing AD,Gacita A,Wood LD,Ma F,Xing D,Kim MS,Manda SS,Abril G,Pereira G,Makohon-Moore A,Looijenga LH,Gillis AJ,Hruban RH,Anders RA,Romans KE,Pandey A,Iacobuzio-Donahue CA,Vogelstein B,Kinzler KW,Kazazian HH Jr,Sol

更新日期：2015-10-01 00:00:00

abstract：:Chromosomal rearrangements and copy number variants (CNVs) play key roles in genome evolution and genetic disease; however, the molecular mechanisms underlying these types of structural genomic variation are not fully understood. The availability of complete genome sequences for two bird species, the chicken and the z...

journal_title：Genome research

authors： Völker M,Backström N,Skinner BM,Langley EJ,Bunzey SK,Ellegren H,Griffin DK

更新日期：2010-04-01 00:00:00

abstract：:The genetics of aging in the yeast Saccharomyces cerevisiae has involved the manipulation of individual genes in laboratory strains. We have instituted a quantitative genetic analysis of the yeast replicative lifespan by sampling the natural genetic variation in a wild yeast isolate. Haploid segregants from a cross be...

journal_title：Genome research

authors： Stumpferl SW,Brand SE,Jiang JC,Korona B,Tiwari A,Dai J,Seo JG,Jazwinski SM

更新日期：2012-10-01 00:00:00

abstract：:Maize (Zea mays L. ssp. mays), one of the most important agricultural crops in the world, originated by hybridization of two closely related progenitors. To investigate the fate of its genes after tetraploidization, we analyzed the sequence of five duplicated regions from different chromosomal locations. We also compa...

journal_title：Genome research

authors： Lai J,Ma J,Swigonová Z,Ramakrishna W,Linton E,Llaca V,Tanyolac B,Park YJ,Jeong OY,Bennetzen JL,Messing J

更新日期：2004-10-01 00:00:00

abstract：:Natural killer (NK) cells are innate lymphocytes important for early host defense against infectious pathogens and surveillance against malignant transformation. Resting murine NK cells regulate the translation of effector molecule mRNAs (e.g., granzyme B, GzmB) through unclear molecular mechanisms. MicroRNAs (miRNAs)...

journal_title：Genome research

authors： Fehniger TA,Wylie T,Germino E,Leong JW,Magrini VJ,Koul S,Keppel CR,Schneider SE,Koboldt DC,Sullivan RP,Heinz ME,Crosby SD,Nagarajan R,Ramsingh G,Link DC,Ley TJ,Mardis ER

更新日期：2010-11-01 00:00:00

abstract：:Size sexual dimorphism occurs in almost all mammals. In Portuguese Water Dogs, much of the difference in skeletal size between females and males is due to the interaction between a Quantitative Trait Locus (QTL) on the X-chromosome and a QTL linked to Insulin-like Growth Factor 1 (IGF-1) on the CFA 15 autosome. In fem...

journal_title：Genome research

authors： Chase K,Carrier DR,Adler FR,Ostrander EA,Lark KG

更新日期：2005-12-01 00:00:00

abstract：:Noncoding RNA (ncRNA) constitutes a significant portion of the mammalian transcriptome. Emerging evidence suggests that it regulates gene expression in cis or trans by modulating the chromatin structure. To uncover the functional role of ncRNA in chromatin organization, we deep sequenced chromatin-associated RNAs (CAR...

journal_title：Genome research

authors： Mondal T,Rasmussen M,Pandey GK,Isaksson A,Kanduri C

更新日期：2010-07-01 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：: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 report the genome-wide mapping of ORC1 binding sites in mammals, by chromatin immunoprecipitation and parallel sequencing (ChIP-seq). ORC1 binding sites in HeLa cells were validated as active DNA replication origins (ORIs) using Repli-seq, a method that allows identification of ORI-containing regions by parallel se...

journal_title：Genome research

authors： Dellino GI,Cittaro D,Piccioni R,Luzi L,Banfi S,Segalla S,Cesaroni M,Mendoza-Maldonado R,Giacca M,Pelicci PG

更新日期：2013-01-01 00:00:00

abstract：:CLONEPICKER is a software pipeline that integrates sequence data with BAC clone fingerprints to dynamically select a minimal overlapping clone set covering the whole genome. In the Rat Genome Sequencing Project (RGSP), a hybrid strategy of "clone by clone" and "whole genome shotgun" approaches was used to maximize the...

journal_title：Genome research

authors： Chen R,Sodergren E,Weinstock GM,Gibbs RA

更新日期：2004-04-01 00:00:00

abstract：:Human genomic data of many types are readily available, but the complexity and scale of human molecular biology make it difficult to integrate this body of data, understand it from a systems level, and apply it to the study of specific pathways or genetic disorders. An investigator could best explore a particular prot...

journal_title：Genome research

authors： Huttenhower C,Haley EM,Hibbs MA,Dumeaux V,Barrett DR,Coller HA,Troyanskaya OG

更新日期：2009-06-01 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：:Understanding the consequences of regulatory variation in the human genome remains a major challenge, with important implications for understanding gene regulation and interpreting the many disease-risk variants that fall outside of protein-coding regions. Here, we provide a direct window into the regulatory consequen...

journal_title：Genome research

authors： Battle A,Mostafavi S,Zhu X,Potash JB,Weissman MM,McCormick C,Haudenschild CD,Beckman KB,Shi J,Mei R,Urban AE,Montgomery SB,Levinson DF,Koller D

更新日期：2014-01-01 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：: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：:Although changes in chromatin are integral to transcriptional reprogramming during cellular differentiation, it is currently unclear how chromatin modifications are targeted to specific loci. To systematically identify transcription factors (TFs) that can direct chromatin changes during cell fate decisions, we model t...

journal_title：Genome research

authors： Arnold P,Schöler A,Pachkov M,Balwierz PJ,Jørgensen H,Stadler MB,van Nimwegen E,Schübeler D

更新日期：2013-01-01 00:00:00

abstract：:Although more than thirty mammalian genomes have been sequenced to draft quality, very few of these include the Y chromosome. This has limited our understanding of the evolutionary dynamics of gene persistence and loss, our ability to identify conserved regulatory elements, as well our knowledge of the extent to which...

journal_title：Genome research

authors： Li G,Davis BW,Raudsepp T,Pearks Wilkerson AJ,Mason VC,Ferguson-Smith M,O'Brien PC,Waters PD,Murphy WJ

更新日期：2013-09-01 00:00:00