Search · four archives
Search · four archives
16 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…
Ying Chen, Andre Sim, Yuk Kei Wan, Keith Yeo + 4 more
Most approaches to transcript quantification rely on fixed reference annotations. However, the transcriptome is dynamic, and depending on the context, such static annotations contain inactive isoforms for some genes while they are incomplete for others. To address this, we have developed Bambu, a method that performs…
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…
B. Poggiali, L. Putzeys, J. D. Andersen, A. Vidaki
The human genome is dominated by repetitive DNA, whose genetic and epigenetic variation plays a key role in gene regulation, genome stability, and disease. Recent advances in long-read sequencing now enable large-scale, haplotype-resolved, and DNA methylation-informative analysis of the human genome, including on…
Ludwig Mann, Kristin Balasch, Nicola Schmidt, Tony Heitkam
Despite the many cheap and fast ways to generate genomic data, good and exact genome assembly is still a problem, with especially the repeats being vastly underrepresented and often misassembled. As short reads in low coverage are already sufficient to represent the repeat landscape of any given genome, many read…
Yoshiki Tanaka, Rei Kajitani, Takehiko Itoh
Repeat sequences in the genome can be classified into interspersed and tandem repeats, both of which are important for understanding genome evolution and important traits such as disease. They are also noteworthy as regions of high frequency of genome rearrangement in somatic cells and high inter-individual diversity.…
Atsushi Takeda, Daisuke Nonaka, Yuta Imazu, Tsukasa Fukunaga + 1 more
Interspersed repeats occupy a large part of many eukaryotic genomes, and thus their accurate annotation is essential for various genome analyses. Database-free de novo repeat detection approaches are powerful for annotating genomes that lack well-curated repeat databases. However, existing tools do not yet have…
Tao Zou, Yuhao Mao, Junchen Ye, Bowen Du
Dynamic graph learning equips the edges with time attributes and allows multiple links between two nodes, which is a crucial technology for understanding evolving data scenarios like traffic prediction and recommendation systems. Existing works obtain the evolving patterns mainly depending on the most recent neighbor…
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…
Matthew Disney, Amirhossein Taghavi, Jared Baisden, Jessica Childs-Disney + 1 more
RNA G4C2 and C4G2 repeat expansions in the chromosome 9 open reading frame 72 gene (C9orf72) are the most common cause of genetically defined amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), referred to as c9ALS/FTD. The gene is bidirectionally transcribed, producing G4C2 repeats, r(G4C2)exp, in…
Rui Zhu, Xiaopu Zhou, Haixu Tang, Stephen W. Scherer + 1 more
Trained on massive cross-species DNA corpora, DNA Large language Models (LLMs) learned the fundamental "grammar" and evolutionary patterns of genomic sequences. This makes them powerful priors for DNA sequence modeling, particularly across long distances. Yet, two major constraints hinder their use: the quadratic…
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…
Dian Meng, Bao-Cai Xing, Xinlei Huang, Yanran Liu + 4 more
Test-Time Training layers Authors: ['Dian Meng' 'Bao-Cai Xing' 'Xinlei Huang' 'Yanran Liu' 'Yijun Zhou' 'Yujie Xiao' 'Zitong Yu' 'Xubin Zheng'] Single-cell multi-omics (scMulti-omics) refers to the paired multimodal data, such as Cellular Indexing of Transcriptomes and Epitopes by Sequencing (CITE-seq), where the…
Authors not listed
The WRN helicase has recently emerged as a promising therapeutic target for microsatellite instability (MSI)-high cancers. Here, we report LXW-P1, a potent WRN degrader derived from marine bromotyrosine alkaloids. Its molecular target was identified using an AI-guided, pathway-informed perturbation transcriptomics…
Pelin Icer Baykal, Paweł P. Łabaj, Florian Markowetz, Lynn M. Schriml + 3 more
'Lynn M. Schriml' 'Daniel J. Stekhoven' 'Serghei Mangul' 'Niko Beerenwinkel'] In biomedical research, validation of a new scientific discovery is tied to the reproducibility of its experimental results. However, in genomics, the definition and implementation of reproducibility still remain imprecise. Here, we argue…