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... The main goal and promise of comparative genomics has been to create a comprehensive catalog of genomic information and function across the phenomenal diversity of living systems. A recent study has demonstrated the evolutionary insights possible by generating high-quality whole-genome assemblies from multiple species of a clade. ...
... Growing popularity and diversity of genomic data demand portable and versatile genome browsers. Here, we present an open source programming library called GIVE that facilitates the creation of personalized genome browsers without requiring a system administrator. By inserting HTML tags, one can add to a personal webpage interactive visualization of multiple types of genomics data, including genome ...
... Mammalian genomes are folded in a hierarchy of compartments, topologically associating domains (TADs), subTADs, and looping interactions. Currently, there is a great need to evaluate the link between chromatin topology and genome function across many biological conditions and genetic perturbations. Hi-C can generate genome-wide maps of looping interactions but is intractable for high-throughput co ...
... This SnapShot provides a list of the tumor types characterized by The Cancer Genome Atlas (TCGA) program. Key findings shown are the most relevant discoveries described in each marker paper for the tumor type. ...
... Due to some error captions for Fig. 1 and Fig. 2 have somehow been switched and needs to be read as: Fig. 1: Genome organization of Taro bacilliform CH virus (TaBCHV) Hawaii Srain. ...
mitochondrial genome, etc ; Bayesian theory; Taeniidae; genes; mitochondria; nucleotide sequences; phylogeny; Show all 7 Subjects
Abstract:
... The taxonomic concept for the family Paruterinidae is controversial, especially concerning the position of the genus Cladotaenia, since the latter genus has been placed sometimes in other families, i.e. in the Taeniidae or in the distinct family Cladotaeniidae; finding a solution based on morphological data is difficult and molecular data on paruterinids and related groups are scarce. In this stud ...
genome, etc ; gene editing; gene therapy; genomics; loci; nucleases; screening; Show all 7 Subjects
Abstract:
... Programmable artificial nucleases have transitioned over the past decade from ZFNs and TALENs to CRISPR/Cas systems, which have been ubiquitously used with great success to modify genomes. The efficiencies of knockout and knockin vary widely among distinct cell types and genomic loci and depend on the nuclease delivery and cleavage efficiencies. Moreover, genetically modified cells are almost phen ...
... BACKGROUND: The majority of eukaryotic genomes are unfinished due to the algorithmic challenges of assembling them. A variety of assembly and scaffolding tools are available, but it is not always obvious which tool or parameters to use for a specific genome size and complexity. It is, therefore, common practice to produce multiple assemblies using different assemblers and parameters, then select t ...
genome; genome assembly, etc ; genomics; high-throughput nucleotide sequencing; industry; loci; Show all 6 Subjects
Abstract:
... Assembly of reference-quality genomes from next-generation sequencing data is a key challenge in genomics. Recently, we and others have shown that Hi-C data can be used to address several outstanding challenges in the field of genome assembly. This principle has since been developed in academia and industry, and has been used in the assembly of several major genomes. In this paper, we explore the ...
mitochondrial genome; nuclear genome, etc ; bacteria; genes; information processing; mitochondria; Show all 6 Subjects
Abstract:
... Mutualistic bacteria and mitochondria have small genomes that harbor host-essential genes. A major question is why a distinct bacterial or mitochondrial genome is needed to encode these functions. The dual location of genes demand two sets of information processing systems, coordination of gene expression and elaborate transport systems. A simpler solution would be to harbor all genes in a single ...
... A recent study in Genome Biology has characterized the evolution of candidate hominoid-specific liver enhancers by using massively parallel reporter assays (MPRAs). ...
... Phylogenomics has ushered in an age of discordance. Analyses often reveal abundant discordances among phylogenies of different parts of genomes, as well as incongruences between species trees obtained using different methods or data partitions. Researchers are often left trying to make sense of such incongruences. Interpretive ways of measuring and visualizing discordance are needed, both among al ...
... The repair of chromosomal double‐strand breaks (DSBs) by homologous recombination is essential to maintain genome integrity. The key step in DSB repair is the RecA/Rad51‐mediated process to match sequences at the broken end to homologous donor sequences that can be used as a template to repair the lesion. Here, in reviewing research about DSB repair, I consider the many factors that appear to play ...
genome, etc ; databases; helminths; nucleotide sequences; Show all 4 Subjects
Abstract:
... Advancements in genome sequencing have led to the rapid accumulation of uncharacterized ‘hypothetical proteins’ in the public databases. Here we provide a community perspective and some best-practice approaches for the accurate functional annotation of uncharacterized genomic sequences. ...
... Unfortunately in page 116, second paragraph, the sentence that starts with “Other exceptions include…” was incorrectly published. The complete correct sentence is given below. ...
genome, etc ; diagnostic techniques; genetically modified organisms; haploidy; loop-mediated isothermal amplification; probability; screening; Show all 7 Subjects
Abstract:
... Loop-mediated isothermal amplification (LAMP) has been widely used in many fields of molecular diagnostics, including detection of genetically modified organisms (GMOs). Herein, we report a collaborative ring trial validation of three established visual LAMP assays targeting three common GM elements, namely CaMV35S promoter, FMV35S promoter and NOS terminator, respectively. The high specificity of ...
genome, etc ; Danio rerio; angiogenesis; biomedical research; gene editing; giant cells; models; neoplasms; sprouting; therapeutics; Show all 10 Subjects
Abstract:
... Angiogenesis is a distinct process which follows sprouting angiogenesis (SA) and intussusceptive angiogenesis (IA) forming the basis for various physiological and pathological scenarios. Angiogenesis is a double edged sword exerting both desirable and discernible effects owing to the referred microenvironment. Therapeutic interventions to promote angiogenesis in regenerative medicine is essential ...
mitochondrial genome, etc ; Macrosteles quadrilineatus; codons; data collection; insects; monophyly; transfer RNA; Show all 7 Subjects
Abstract:
... Comparative studies of leafhopper mitochondrial genomes suggest that genome rearrangements are very rare in these insects but that nucleotide sequences are informative of phylogenetic relationships at various levels of divergence. A recent study reported that tRNA cluster trnW-trnC-trnY is rearranged to trnC-trnW-trnY in the Aster Leafhopper, Macrosteles quadrilineatus, an economically important N ...
mitochondrial genome, etc ; Aphididae; Cervaphis quercus; Greenidea; genes; insects; phylogeny; statistical analysis; Show all 8 Subjects
Abstract:
... The complete mitochondrial genome of Greenidea psidii was sequenced and compared with the genomes of other aphid species. The G. psidii mitogenome is 16,202 bp long with an A + T content of 85.4%, comprising 37 genes arranged in the same order as the inferred insect ancestral arrangement, a control region and a special repeat region between trnE and trnF. G. psidii is the first representative poss ...