14 papers · ranked by Valyu relevance
Dimitrios Vitsios, Ryan S. Dhindsa, Lawrence Middleton, Ayal B. Gussow + 1 more
'Ayal B. Gussow' 'Slavé Petrovski'] Elucidating functionality in non-coding regions is a key challenge in human genomics. It has been shown that intolerance to variation of coding and proximal non-coding sequence is a strong predictor of human disease relevance. Here, we integrate intolerance to variation, functional…
Slavé Petrovski, Ayal B. Gussow, Quanli Wang, Matt Halvorsen + 5 more
'Yujun Han' 'William H. Weir' 'Andrew S. Allen' 'David B. Goldstein' 'Chris Cotsapas'] Noncoding sequence contains pathogenic mutations. Yet, compared with mutations in protein-coding sequence, pathogenic regulatory mutations are notoriously difficult to recognize. Most fundamentally, we are not yet adept at…
Tristan J. Hayeck, Nicholas Stong, Evan Baugh, Ryan Dhindsa + 6 more
Genomic regions subject to purifying selection are of greater importance to the health and survival of an organism than regions not under such selection and therefore more likely to carry disease causing mutations in humans. Methods for identifying such regions can roughly be divided into those using cross species…
Beibei Wang, Siyuan Song, Song Cheng, Yihang Lin + 3 more
The rapid expansion of whole-genome sequencing (WGS) has highlighted the important contribution of noncoding variants to human disease, yet their pathogenic mechanisms remain difficult to resolve. Traditional statistical and experimental approaches often struggle to capture complex regulatory interactions or establish…
William M Brandler, Antaki Danny, Madhusudan Gujral, Morgan L Kleiber + 30 more
The genetic architecture of autism spectrum disorder (ASD) is known to consist of contributions from gene-disrupting de novo mutations and common variants of modest effect. We hypothesize that the unexplained heritability of ASD also includes rare inherited variants with intermediate effects. We investigated the…
Jordan S Kesner, Ziheng Chen, Alexis A Aparicio, Xuebing Wu
Translation is pervasive outside of canonical coding regions, occurring in lncRNAs, UTRs, and introns. While the resulting polypeptides are often non-functional, translation in noncoding regions is nonetheless necessary for the birth of new coding regions. The mechanisms underlying the surveillance of translation in…
Efthalia Moustakli, Nektaria Zagorianakou, Stylianos Makrydimas, Andreas Miltiadous + 3 more
Analysis of coding areas has long been used to study monogenic illnesses, but despite the extensive use of whole-exome sequencing (WES), up to half of suspected cases remain genetically unexplained. Variants outside coding areas can alter splicing, transcript stability, or gene regulation, compromising normal gene…
Dan Graur
Noncoding RNA (ncRNA) and long noncoding RNA (lncRNA) are scientifically invalid terms because they define molecular entities according to properties they do not possess and functions they do not perform. Here, I suggest retiring these two terms. Instead, I suggest using an evolutionary classification of genomic…
James A. Shapiro
This is a commentary on the article by Eviatar Nevo and Kexin Li entitled “Sympatric Speciation in Mole Rats and Wild Barley and Their Genome Repeatome Evolution: A Commentary”, published recently in Advanced Genetics.
Anyou Wang, Rong Hai
*Correspondence: A Wang anyou.wang@alumni.ucr.edu Abstract: Cancer is one of the leading causes of human death. Many efforts have made to understand its mechanism and have further identified many proteins and DNA sequence variations as suspected targets for therapy. However, drugs targeting these targets have low…
Zilin Li, Xihao Li, Hufeng Zhou, Sheila M. Gaynor + 57 more
Large-scale whole-genome sequencing studies have enabled analysis of noncoding rare variants’ (RVs) associations with complex human traits. Variant set analysis is a powerful approach to study RV association, and a key component of it is constructing RV sets for analysis. However, existing methods have limited ability…
Luis A. Martínez-Vaquero
This article may be downloaded for personal use only. Any other use requires prior permission of the author and AIP Publishing. This article appeared in L. A. Martinez-Vaquero, "Inequality leads to the evolution of intolerance in reputation-based populations", Chaos 33 (3), 033119 (2023) (doi.org/10.1063/5.0135376) and…
Anyou Wang, Rong Hai, Paul J. F. Rider, Qianchuan He
Results: Our system can accurately detect cancer vs healthy object with 96.3% of AUC of ROC (Area Under Curve of a Receiver Operating Characteristic curve). Intriguinely, with no more than 6 biomarkers, our approach can easily discriminate any individual cancer type vs normal with 99% to 100% AUC. Furthermore, a…
Chris Papadopoulos, Hugo Arbes, Nicolas Chevrollier, Sandra Blanchet + 7 more
Pervasive translation is a widespread phenomenon that plays an important role in de novo gene birth; however, its underlying mechanisms remain unclear. Based on multiple Ribosome Profiling (Ribo-Seq) datasets, we investigated the RiboSeq landscape of coding and noncoding regions of yeast. Therefore, we developed a…