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Search · four archives
17 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…
Gustavo Sacomoto, Blerina Sinaimeri, Camille Marchet, Vincent Miele + 2 more
'Marie-France Sagot' 'Vincent Lacroix'] Abstract. The main challenge in de novo assembly of NGS data is certainly to deal with repeats that are longer than the reads. This is particularly true for RNAseq data, since coverage information cannot be used to flag repeated sequences, of which transposable elements are one…
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…
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…
Tamer Butto, Stefan Pastore, Max Müller, Kaushik Viswanathan Iyer + 6 more
Nanopore technology offers real-time sequencing opportunities, providing rapid access to sequenced data and allowing researchers to manage the sequencing process efficiently, resulting in cost-effective strategies. Here, we present focused case studies demonstrating the versatility of real-time transcriptomics analysis…
Darshan S Chandrashekar, Poulami Dey, Kshitish K Acharya
Background: Understanding the mechanism behind the transcriptional regulation of genes is still a challenge. Recent findings indicate that the genomic repeat elements (such as LINES, SINES and LTRs) could play an important role in the transcription control. Hence, it is important to further explore the role of genomic…
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…
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…
Jason D. Fernandes, Maximilian Haeussler, Armando Zamudio-Hurtado, W. James Kent + 2 more
Nearly half the human genome consists of repeat elements, and many of these sequences play important roles in biological functions. However repeat elements pose several unique challenges to current bioinformatic analyses and visualization tools, as short repeat sequences can map to multiple genomic loci resulting in…
Tin Nguyen, Zhiyu Zhao, Dongxiao Zhu
Transcriptome assembly from RNA-Seq reads is an active area of bioinformatics research. The ever-declining cost and the increasing depth of RNA-Seq have provided unprecedented opportunities to better identify expressed transcripts. However, the nonlinear transcript structures and the ultra-high throughput of RNA-Seq…
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…
Lu Zeng, R. Daniel Kortschak, Joy M. Raison, Terry Bertozzi + 1 more
Transposable Elements (TEs) are mobile DNA sequences that make up significant fractions of amniote genomes. However, they are difficult to detect and annotate ab initio because of their variable features, lengths and clade-specific variants. We have addressed this problem by refining and developing a Comprehensive ab…
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…
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…
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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…