Search · four archives
Search · four archives
14 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…
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…
Emmanuelle Lerat
Transposable elements (TEs) are recognized for their great impact on the functioning and evolution of their host genomes. They are associated to various deleterious effects, which has led to the evolution of regulatory epigenetic mechanisms to control their activity. Despite these negative effects, TEs are also…
Natalia Savytska, Peter Heutink, Vikas Bansal
The transcriptional activity of Transposable Elements (TEs) has been involved in numerous pathological processes, including neurodegenerative diseases such as amyotrophic lateral sclerosis and frontotemporal lobar degeneration. The TE expression analysis from short-read sequencing technologies is, however, challenging…
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…
Michel Choudalakis, Pavel Bashtrykov, Albert Jeltsch
Background Repeat elements (REs) play important roles for cell function in health and disease. However, RE enrichment analysis in short-read high-throughput sequencing (HTS) data, such as ChIP-seq, is a challenging task. Results Here, we present RepEnTools, a software package for genome-wide RE enrichment analysis of…
Zhezheng Song, Tasfia Zahin, Xiang Li, Mingfu Shao
A tandem repeat is a sequence of nucleotides that occurs as multiple contiguous and near-identical copies positioned next to each other. These repeats play critical roles in genetic diversity, gene regulation, and are strongly linked to various neurological and developmental disorders. While several methods exist for…
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…
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…
Matias Rodriguez, Wojciech Makałowski
Transposable elements (TEs) are major genomic components in most eukaryotic genomes and play an important role in genome evolution. However, despite their relevance the identification of TEs is not an easy task and a number of tools were developed to tackle this problem. To better understand how they perform, we tested…
Boyan Xu, Alois Cerbu, Christopher J. Tralie, Daven Lim + 2 more
'Ksenia Krasileva' 'Ozlem Keskin'] Protein domain annotation is typically done by predictive models such as HMMs trained on sequence motifs. However, sequence-based annotation methods are prone to error, particularly in calling domain boundaries and motifs within them. These methods are limited by a lack of structural…
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…
Tanner Stokes, Haoning Howard Cen, Philipp Kapranov, Iain J Gallagher + 7 more
'Iain J Gallagher' 'Andrew A. Pitsillides' 'Claude‐Henry Volmar' 'William E Kraus' 'James D. Johnson' 'Stuart M. Phillips' 'Claes Wahlestedt' 'James A. Timmons'] Title: Abstract Sequencing the human genome empowers translational medicine, facilitating transcriptome-wide molecular diagnosis, pathway biology, and drug…