Search · four archives
Search · four archives
18 papers · ranked by Valyu relevance
Roman E. Reggiardo, Sreelakshmi Velandi Maroli, Vikas Peddu, Andrew E. Davidson + 6 more
'Andrew E. Davidson' 'Alexander Hill' 'Erin LaMontagne' 'Yassmin Al Aaraj' 'Miten Jain' 'Stephen Y. Chan' 'Daniel H. Kim'] Liquid biopsies provide a means for the profiling of cell-free RNAs secreted by cells throughout the body. Although well-annotated coding and non-coding transcripts in blood are readily detectable…
Ana Luiza Franco, Wenjia Gu, Petr Novák, Ilia J. Leitch + 2 more
'Lyderson F. Viccini' 'Andrew R. Leitch'] Title: Abstract Repetitive DNA contributes significantly to plant genome size, adaptation, and evolution. However, little is understood about the transcription of repeats. This is addressed here in the plant green foxtail millet (Setaria viridis). First, we used RepeatExplorer2…
Kathryn O'Neill, David Brocks, Molly Gale Hammell
Next-generation sequencing approaches have fundamentally changed the types of questions that can be asked about gene function and regulation. With the goal of approaching truly genome-wide quantifications of all the interaction partners and downstream effects of particular genes, these quantitative assays have allowed…
Gerardo Patiño-Guillén, Jovan Pešović, Marko Panić, Max Earle + 5 more
Short tandem repeat expansions underlie a class of neurological and neuromuscular diseases known as repeat expansion disorders, yet the precise characterisation of these repeats remains technically challenging. Conventional amplification-based methods fail to resolve repeat length accurately due to amplification bias…
Veena P Gnanakkan, Andrew E Jaffe, Lixin Dai, Jie Fu + 4 more
'Sarah J Wheelan' 'Hyam I Levitsky' 'Jef D Boeke' 'Kathleen H Burns'] Background Although transposable element (TE) derived DNA accounts for more than half of mammalian genomes and initiates a significant proportion of RNA transcripts, high throughput methods are rarely leveraged specifically to detect expression from…
Xiao Yang, Srinivas Aluru, Karin S Dorman
Background High-throughput short read sequencing is revolutionizing genomics and systems biology research by enabling cost-effective deep coverage sequencing of genomes and transcriptomes. Error detection and correction are crucial to many short read sequencing applications including de novo genome sequencing, genome…
Joanna Moreton, Abril Izquierdo, Richard D. Emes
De novo assembly of a complete transcriptome without the need for a guiding reference genome is attractive, particularly where the cost and complexity of generating a eukaryote genome is prohibitive. The transcriptome should not however be seen as just a quick and cheap alternative to building a complete genome.…
Michelle Almeida da Paz, Sarah Warger, Leila Taher
Background Standard ChIP-seq and RNA-seq processing pipelines typically disregard sequencing reads whose origin is ambiguous (“multimappers”). This usual practice has potentially important consequences for the functional interpretation of the data: genomic elements belonging to clusters composed of highly similar…
Hani Z. Girgis
Background With rapid advancements in technology, the sequences of thousands of species’ genomes are becoming available. Within the sequences are repeats that comprise significant portions of genomes. Successful annotations thus require accurate discovery of repeats. As species-specific elements, repeats in newly…
Chong Chu, Jingwen Pei, Yufeng Wu
Background Repeat elements are important components of most eukaryotic genomes. Most existing tools for repeat analysis rely either on high quality reference genomes or existing repeat libraries. Thus, it is still challenging to do repeat analysis for species with highly repetitive or complex genomes which often do not…
Wai Yee Wong, Oleg Simakov, John Hancock
Repetitive elements comprise a large proportion of many metazoan genomes. Three major classes exist: DNA elements (cut and paste propagation), retroelement (copy paste propagation) and simple repeats (not autonomous). The length of individual repeat elements can vary from a few base pairs (simple repeats) to a dozen…
Jason D. Fernandes, Armando Zamudio-Hurtado, Hiram Clawson, W. James Kent + 3 more
'W. James Kent' 'David Haussler' 'Sofie R. Salama' 'Maximilian Haeussler'] Background Nearly half the human genome consists of repeat elements, most of which are retrotransposons, and many of which play important biological roles. However repeat elements pose several unique challenges to current bioinformatic analyses…
Thomas D Otto, Leonardo HF Gomes, Marcelo Alves-Ferreira, Antonio B de Miranda + 1 more
'Antonio B de Miranda' 'Wim M Degrave'] Background Genome survey sequences (GSS) offer a preliminary global view of a genome since, unlike ESTs, they cover coding as well as non-coding DNA and include repetitive regions of the genome. A more precise estimation of the nature, quantity and variability of repetitive…
Xingyu Liao, Wufei Zhu, Juexiao Zhou, Haoyang Li + 3 more
Repetitive DNA sequences playing critical roles in driving evolution, inducing variation, and regulating gene expression. In this review, we summarized the definition, arrangement, and structural characteristics of repeats. Besides, we introduced diverse biological functions of repeats and reviewed existing methods for…
Krishnakumar Vaithianathan
Neurodegenerative disorders such as Alzheimer’s disease exhibit highly organized patterns of regional brain vulnerability, yet the biological mechanisms underlying this spatial selectivity remain incompletely understood. While previous imaging-transcriptomic studies have primarily focused on correlation-based analyses…
Lulu Shang, Xiang Zhou
Spatial transcriptomics are a collection of genomic technologies that have enabled transcriptomic profiling on tissues with spatial localization information. Analyzing spatial transcriptomic data is computationally challenging, as the data collected from various spatial transcriptomic technologies are often noisy and…
Yang Gui, Chao Li, Yan Xu
Spatial transcriptomics (ST) technologies have emerged as an effective tool to identify the spatial architecture of tissues, facilitating a comprehensive understanding of organ function and the tissue microenvironment. Spatial domain identification is the first and most critical step in ST data analysis, which requires…
Eric D. Sun, Rong Ma, Paloma Navarro Negredo, Anne Brunet + 1 more
'James Zou'] Whole-transcriptome spatial profiling of genes at single-cell resolution remains a challenge. To address this limitation, spatial gene expression prediction methods have been developed to infer the spatial expression of unmeasured transcripts, but the quality of these predictions can vary greatly. Here we…