Introgression maintains the genetic integrity of the mating-type determining chromosome of the fungus Neurospora tetrasperma.

abstract：:In this communication, we describe the use of specialized transposons (Tn5 derivatives) to create deletions in the Escherichia coli K-12 chromosome. These transposons are essentially rearranged composite transposons that have been assembled to promote the use of the internal transposon ends, resulting in intramolecula...

journal_title：Genome research

authors： Goryshin IY,Naumann TA,Apodaca J,Reznikoff WS

更新日期：2003-04-01 00:00:00

abstract：:Large-scale genetic studies are highly dependent on efficient and scalable multiplex SNP assays. In this study, we report the development of Molecular Inversion Probe technology with four-color, single array detection, applied to large-scale genotyping of up to 12,000 SNPs per reaction. While generating 38,429 SNP ass...

journal_title：Genome research

authors： Hardenbol P,Yu F,Belmont J,Mackenzie J,Bruckner C,Brundage T,Boudreau A,Chow S,Eberle J,Erbilgin A,Falkowski M,Fitzgerald R,Ghose S,Iartchouk O,Jain M,Karlin-Neumann G,Lu X,Miao X,Moore B,Moorhead M,Namsaraev E,

更新日期：2005-02-01 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：:Genomic comparisons provide evidence for ancient genome-wide duplications in a diverse array of animals and plants. We developed a birth-death model to identify evidence for genome duplication in EST data, and applied a mixture model to estimate the age distribution of paralogous pairs identified in EST sets for speci...

journal_title：Genome research

authors： Cui L,Wall PK,Leebens-Mack JH,Lindsay BG,Soltis DE,Doyle JJ,Soltis PS,Carlson JE,Arumuganathan K,Barakat A,Albert VA,Ma H,dePamphilis CW

更新日期：2006-06-01 00:00:00

abstract：:A total of 202 genes were cytogenetically mapped to goat chromosomes, multiplying by five the total number of regional gene localizations in domestic ruminants (255). This map encompasses 249 and 173 common anchor loci regularly spaced along human and murine chromosomes, respectively, which makes it possible to perfor...

journal_title：Genome research

authors： Schibler L,Vaiman D,Oustry A,Giraud-Delville C,Cribiu EP

更新日期：1998-09-01 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：: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：:There are numerous examples from the genomes of viruses, mitochondria, and chromosomes that adjacent genes can overlap, sharing at least one nucleotide. Overlaps have been hypothesized to be involved in genome size minimization and as a regulatory mechanism of gene expression. Here we show that overlapping genes are a...

journal_title：Genome research

authors： Johnson ZI,Chisholm SW

更新日期：2004-11-01 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：: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：: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：:C2H2 zinc finger proteins represent the largest and most enigmatic class of human transcription factors. Their C2H2-ZF arrays are highly variable, indicating that most will have unique DNA binding motifs. However, most of the binding motifs have not been directly determined. In addition, little is known about whether ...

journal_title：Genome research

authors： Schmitges FW,Radovani E,Najafabadi HS,Barazandeh M,Campitelli LF,Yin Y,Jolma A,Zhong G,Guo H,Kanagalingam T,Dai WF,Taipale J,Emili A,Greenblatt JF,Hughes TR

更新日期：2016-12-01 00:00:00

abstract：:Rhesus macaque is an Old World monkey that shared a common ancestor with human ∼25 Myr ago and is an important animal model for human disease studies. A deep understanding of its genetics is therefore required for both biomedical and evolutionary studies. Among structural variants, inversions represent a driving force...

journal_title：Genome research

authors： Maggiolini FAM,Sanders AD,Shew CJ,Sulovari A,Mao Y,Puig M,Catacchio CR,Dellino M,Palmisano D,Mercuri L,Bitonto M,Porubský D,Cáceres M,Eichler EE,Ventura M,Dennis MY,Korbel JO,Antonacci F

更新日期：2020-11-01 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：:We have determined the complete sequence of 951,695 bp from the class I region of H2, the mouse major histocompatibility complex (Mhc) from strain 129/Sv (haplotype bc). The sequence contains 26 genes. The sequence spans from the last 50 kb of the H2-T region, including 2 class I genes and 3 class I pseudogenes, and i...

journal_title：Genome research

authors： Takada T,Kumánovics A,Amadou C,Yoshino M,Jones EP,Athanasiou M,Evans GA,Fischer Lindahl K

更新日期：2003-04-01 00:00:00

abstract：:Long sequencing reads generated by single-molecule sequencing technology offer the possibility of dramatically improving the contiguity of genome assemblies. The biggest challenge today is that long reads have relatively high error rates, currently around 15%. The high error rates make it difficult to use this data al...

journal_title：Genome research

authors： Zimin AV,Puiu D,Luo MC,Zhu T,Koren S,Marçais G,Yorke JA,Dvořák J,Salzberg SL

更新日期：2017-05-01 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：: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：:Comparative genomics is a promising approach to the challenging problem of eukaryotic regulatory element identification, because functional noncoding sequences may be conserved across species from evolutionary constraints. We systematically analyzed known human and Saccharomyces cerevisiae regulatory elements and disc...

journal_title：Genome research

authors： Liu Y,Liu XS,Wei L,Altman RB,Batzoglou S

更新日期：2004-03-01 00:00:00

abstract：:The very small fraction of putative binding sites (BSs) that are occupied by transcription factors (TFs) in vivo can be highly variable across different cell types. This observation has been partly attributed to changes in chromatin accessibility and histone modification (HM) patterns surrounding BSs. Previous studies...

journal_title：Genome research

authors： Xin B,Rohs R

更新日期：2018-01-11 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：:The regulation of gene expression is mediated at the transcriptional level by enhancer regions that are bound by sequence-specific transcription factors (TFs). Recent studies have shown that the in vivo binding sites of single TFs differ between developmental or cellular contexts. How this context-specific binding is ...

journal_title：Genome research

authors： Yáñez-Cuna JO,Dinh HQ,Kvon EZ,Shlyueva D,Stark A

更新日期：2012-10-01 00:00:00

abstract：:Analyzing vertebrate genomes requires rapid mRNA/DNA and cross-species protein alignments. A new tool, BLAT, is more accurate and 500 times faster than popular existing tools for mRNA/DNA alignments and 50 times faster for protein alignments at sensitivity settings typically used when comparing vertebrate sequences. B...

journal_title：Genome research

authors： Kent WJ

更新日期：2002-04-01 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：: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

abstract：:Genomic imprinting is a developmentally important mechanism that involves both differential DNA methylation and allelic histone modifications. Through detailed comparative characterization, a large imprinted domain mapping to chromosome 7q21 in humans and proximal chromosome 6 in mice was redefined. This domain is org...

journal_title：Genome research

authors： Monk D,Wagschal A,Arnaud P,Müller PS,Parker-Katiraee L,Bourc'his D,Scherer SW,Feil R,Stanier P,Moore GE

更新日期：2008-08-01 00:00:00

abstract：:Initially thought to play a restricted role in calcium homeostasis, the pleiotropic actions of vitamin D in biology and their clinical significance are only now becoming apparent. However, the mode of action of vitamin D, through its cognate nuclear vitamin D receptor (VDR), and its contribution to diverse disorders, ...

journal_title：Genome research

authors： Ramagopalan SV,Heger A,Berlanga AJ,Maugeri NJ,Lincoln MR,Burrell A,Handunnetthi L,Handel AE,Disanto G,Orton SM,Watson CT,Morahan JM,Giovannoni G,Ponting CP,Ebers GC,Knight JC

更新日期：2010-10-01 00:00:00

abstract：:Infections by Shiga toxin-producing Escherichia coli O157:H7 (STEC O157) are the predominant cause of bloody diarrhea and hemolytic uremic syndrome in the United States. In silico comparison of the two complete STEC O157 genomes (Sakai and EDL933) revealed a strikingly high level of sequence identity in orthologous pr...

journal_title：Genome research

authors： Zhang W,Qi W,Albert TJ,Motiwala AS,Alland D,Hyytia-Trees EK,Ribot EM,Fields PI,Whittam TS,Swaminathan B

更新日期：2006-06-01 00:00:00

abstract：:Interindividual variability in response to chemicals and drugs is a common regulatory concern. It is assumed that xenobiotic-induced adverse reactions have a strong genetic basis, but many mechanism-based investigations have not been successful in identifying susceptible individuals. While recent advances in pharmacog...

journal_title：Genome research

authors： Harrill AH,Watkins PB,Su S,Ross PK,Harbourt DE,Stylianou IM,Boorman GA,Russo MW,Sackler RS,Harris SC,Smith PC,Tennant R,Bogue M,Paigen K,Harris C,Contractor T,Wiltshire T,Rusyn I,Threadgill DW

更新日期：2009-09-01 00:00:00

abstract：:The phenotypic variation of living organisms is shaped by genetics, environment, and their interaction. Understanding phenotypic plasticity under natural conditions is hindered by the apparently complex environment and the interacting genes and pathways. Herein, we report findings from the dissection of rice flowering...

journal_title：Genome research

authors： Guo T,Mu Q,Wang J,Vanous AE,Onogi A,Iwata H,Li X,Yu J

更新日期：2020-05-01 00:00:00