Searching journal content for articles similar to Ye et al. 36 (2): 421.

Displaying results 1-10 of 5889

For checked items

view abstracts
download to citation manager

Select this article
Research: Variation in the fitness impact of translationally optimal codons among animals
- Florian Bénitière,
- Tristan Lefébure,
- and Laurent Duret
Genome Res. March 2025 35: 446-458; Published in Advance February 10, 2025, doi:10.1101/gr.279837.124
...to the gene expression level. First, the higher the expression level of a given gene, the stronger the impact of its translation speed on the pool of free ribosomes. Second, for a given mistranslation rate, the cost of erroneous protein production (in terms of waste of resources and of direct toxic effect...
Select this article
Method: Read-level genotyping of short tandem repeats using long reads and single-nucleotide variation with STRkit
- David R. Lougheed,
- Tomi Pastinen,
- and Guillaume Bourque
Genome Res. March 2026 36: 578-588; Published in Advance January 15, 2026, doi:10.1101/gr.280766.125
...Institute, Kansas City, Missouri 64108, USA; 4Victor Phillip Dahdaleh Institute of Genomic Medicine at McGill University, Montréal, Québec H3A 0G1, Canada Corresponding authors: david.lougheed@mail.mcgill.ca, guil.bourque@mcgill.caAbstractVariation in short tandem repeats (STRs) is implicated in Mendelian...
Select this article
Method: BINDER achieves accurate identification of hierarchical TADs by comprehensively characterizing consensus TAD boundaries
- Yangyang Liu,
- Bingqiang Liu,
- and Juntao Liu
Genome Res. May 2025 35: 1194-1208; Published in Advance March 17, 2025, doi:10.1101/gr.279647.124
...variations among TUGs, TNGs, and TDGs from ST to GR, suggesting a potential impact of THCs on gene transcriptional activity (Fig. 6B,C).View larger version: In this window In a new window Figure 6. THC unveils genomic dynamics during cellular differentiation. (A) Distribution of THCs of 1013 eligible genes...
Select this article
Method: Autoencoders for genomic variation analysis
- Margarita Geleta,
- Daniel Mas Montserrat,
- Xavier Giro-i-Nieto,
- and Alexander G. Ioannidis
Genome Res. February 2026 36: 348-360; Published in Advance January 20, 2026, doi:10.1101/gr.280086.124
...are needed in order to properly capture the genetic composition of populations. Here, we explore deep learning techniques, namely, variational autoencoders (VAEs), to process genomic data from a population perspective. We show the power of VAEs for a variety of tasks relating to the interpretation...
OPEN ACCESS ARTICLE
Select this article
Research: T2T-CHM13 improves read mapping and detection of clinically relevant genetic variation in the Swedish population
- Daniel Schmitz,
- Adam Ameur,
- and Åsa Johansson
Genome Res. November 2025 35: 2377-2388; Published in Advance September 16, 2025, doi:10.1101/gr.279320.124
...moderate and low impact, respectively, and the remaining 6.4% were rated high impact (Fig. 4B). Our results thus suggest that improved gene coverage facilitates detection of functionally relevant variation.We identified 17,446 LoF variants using T2T-CHM13, an increase from GRCh37 and GRCh38 (Table 1...
OPEN ACCESS ARTICLE
Select this article
Research: Landscape of microRNA and target expression variation and covariation in single mouse embryonic stem cells
- Marcel Tarbier,
- Sebastian D. Mackowiak,
- Vaishnovi Sekar,
- Franziska Bonath,
- Etka Yapar,
- Bastian Fromm,
- Omid R. Faridani,
- Inna Biryukova,
- and Marc R. Friedländer
Genome Res. February 2026 36: 291-302; Published in Advance January 12, 2026, doi:10.1101/gr.279914.124
...). However, this average repression effect was small relative to the overall natural variation of expression between cells (Fig. 5A), suggesting that the natural variation of expression overshadows the impact of the miRNAs at the RNA level (see Discussion section). We next looked at median changes of Target...
OPEN ACCESS ARTICLE
Select this article
Research: Long-read sequencing reveals HBV integration patterns and oncogenic impact on early-onset hepatocellular carcinoma
- Yao Wang,
- Dong Yu,
- Yue Mei,
- ZhiDa Fu,
- Jian Lin,
- Di Wu,
- Yuan Yang,
- and Hongli Yan
Genome Res. November 2025 35: 2389-2405; Published in Advance September 16, 2025, doi:10.1101/gr.279889.124
...; however, its oncogenic mechanisms remain incompletely understood because of limitations in detection methods and sample availability. In this study, we employ Oxford Nanopore Technologies (ONT) whole- sequencing and full-length transcriptome sequencing to characterize HBV integration events at the genomic...
Select this article
Research: Genetic variation in recalcitrant repetitive regions of the Drosophila melanogaster genome
- Harsh G. Shukla,
- Mahul Chakraborty,
- and J.J. Emerson
Genome Res. September 2025 35: 2023-2040; Published in Advance July 16, 2025, doi:10.1101/gr.280728.125
...Genetic variation in recalcitrant repetitive regions of the Drosophila melanogaster Harsh G. Shukla1,2, Mahul Chakraborty3 and J.J. Emerson1,4 1Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, California 92697, USA; 2Graduate Program in Mathematical...
OPEN ACCESS ARTICLE
Select this article
Method: Characterizing tandem repeat complexities across long-read sequencing platforms with TREAT and otter
- Niccoló Tesi,
- Alex Salazar,
- Yaran Zhang,
- Sven van der Lee,
- Marc Hulsman,
- Lydian Knoop,
- Sanduni Wijesekera,
- Jana Krizova,
- Anne-Fleur Schneider,
- Maartje Pennings,
- Kristel Sleegers,
- Erik-Jan Kamsteeg,
- Marcel Reinders,
- and Henne Holstege
Genome Res. November 2024 34: 1942-1953; Published in Advance October 15, 2024, doi:10.1101/gr.279351.124
...These authors contributed equally to this work. Corresponding authors: n.tesi@amsterdamumc.nl, a.n.salazar@amsterdamumc.nl, h.holstege@amsterdamumc.nlAbstractTandem repeats (TRs) play important roles in genomic variation and disease risk in humans. Long-read sequencing allows for the accurate characterization...
OPEN ACCESS ARTICLE
Select this article
Resource: A harmonized public resource of deeply sequenced diverse human genomes
- Zan Koenig,
- Mary T. Yohannes,
- Lethukuthula L. Nkambule,
- Xuefang Zhao,
- Julia K. Goodrich,
- Heesu Ally Kim,
- Michael W. Wilson,
- Grace Tiao,
- Stephanie P. Hao,
- Nareh Sahakian,
- Katherine R. Chao,
- Mark A. Walker,
- Yunfei Lyu,
- gnomAD Project Consortium,
- Heidi L. Rehm,
- Benjamin M. Neale,
- Michael E. Talkowski,
- Mark J. Daly,
- Harrison Brand,
- Konrad J. Karczewski,
- Elizabeth G. Atkinson,
- and Alicia R. Martin
Genome Res. May 2024 34: 796-809; Published in Advance May 15, 2024, doi:10.1101/gr.278378.123
...-in-class, publicly released, harmonized, and jointly called resource of HGDP + 1kGP on GRCh38 that will facilitate analyses of diverse cohorts. This globally representative haplotype resource better captures the breadth of genetic variation across diverse geographical regions than does previous component studies...

For checked items

view abstracts
download to citation manager

Searching journal content for articles similar to Ye et al. 36 (2): 421.

Search Results

Modify Results

This search

Preprint Server

Current Issue

In This Issue

Citation format:
Results / page:
Results order: