Searching journal content for articles similar to Semple et al. 12 (3): 424.

Displaying results 1-10 of 2193

For checked items

view abstracts
download to citation manager

Select this article
Method: Chromosome engineering to correct a complex rearrangement on Chromosome 8 reveals the effects of 8p syndrome on gene expression and neural differentiation
- Sophia N. Lee,
- Erin C. Banda,
- Lu Qiao,
- Sarah L. Thompson,
- Karan Singh,
- Ryan A. Hagenson,
- Teresa Davoli,
- Stefan F. Pinter,
- and Jason M. Sheltzer
Genome Res. March 2026 36: 547-560; Published in Advance January 12, 2026, doi:10.1101/gr.280425.125
...the missegregation of a specific chromosome. (B) Copy numbers of CSMD1, MICU3, and CRISPLD1 (a gene located on the q arm of Chromosome 8), in trisomic proband clones that were transiently transfected with KaryoCreate plasmids. Mean ± SEM; data from representative trials are shown (n ≥ 3 total trials). Genomic DNA...
Select this article
Method: A scalable computational framework for predicting gene expression from candidate cis-regulatory elements
- Qinhu Zhang,
- Siguo Wang,
- Zhipeng Li,
- Wenzheng Bao,
- Wenjian Liu,
- and De-Shuang Huang
Genome Res. February 2026 36: 361-374; Published in Advance January 16, 2026, doi:10.1101/gr.281219.125
....In this study, we introduce a scalable computational framework for predicting gene expression (ScPGE) from discrete cCREs identified by the Encyclopedia of DNA Elements (ENCODE). ScPGE first assembles DNA sequences, TF binding scores, and epigenomic tracks from discrete cCREs into three 3D tensors, respectively...
OPEN ACCESS ARTICLE
Select this article
Research: Contiguous and complete assemblies of Blastocystis gut microbiome–associated protists reveal evolutionary diversification to host ecology
- Abigail L. Lind,
- Nathan A. McDonald,
- Elias R. Gerrick,
- Ami S. Bhatt,
- and Katherine S. Pollard
Genome Res. June 2025 35: 1377-1390; Published in Advance April 22, 2025, doi:10.1101/gr.279080.124
...the ST4 strain BT1, Hi-C data were generated using a Phase Genomics Proximo Hi-C 2.0 kit, and the Phase Genomics Proximo Hi-C scaffolding platform was used to create chromosome-scale scaffolds from the hybrid assembled . The Hi-C scaffolding resulted only in modest improvements to the original assembly...
OPEN ACCESS ARTICLE
Select this article
Research: Cell-type- and chromosome-specific chromatin landscapes and DNA replication programs of Drosophila testis tumor stem cell–like cells
- Jennifer A. Urban,
- Daniel Ringwalt,
- John M. Urban,
- Wingel Xue,
- Ryan Gleason,
- Keji Zhao,
- and Xin Chen
Genome Res. January 2026 36: 83-101; Published in Advance December 10, 2025, doi:10.1101/gr.280809.125
...chromosome. Below the line plots are the genomic windows in which replication timing significantly differed between the GSC-like and CySC-like cells, for which the color indicates the cell type with earlier replication. Pericentromeric regions on Chromosomes 2 and 3 are indicated by gray boxes. Arrowheads...
OPEN ACCESS ARTICLE
Select this article
Research: Pangenome analysis reveals families of ubiquitin-ligase adaptors as key genomic divergence drivers that lead to hybrid incompatibility
- Dongying Xie,
- Pohao Ye,
- Yiming Ma,
- and Zhongying Zhao
Genome Res. March 2026 36: 506-521; Published in Advance February 17, 2026, doi:10.1101/gr.280885.125
.... 2020; Jiao et al. 2025). These interactions often fuel hybrid genomic conflicts. Short-read sequencing technologies have struggled to resolve such complexities owing to inherent limitations in assembly. In contrast, the advent of long-read sequencing technologies, such as of Pacific Biosciences (Pac...
Select this article
Method: A spectral component approach leveraging identity-by-descent graphs to address recent population structure in genomic analysis
- Ruhollah Shemirani,
- Gillian M. Belbin,
- Sinead Cullina,
- Christa Caggiano,
- Christopher R. Gignoux,
- Noah Zaitlen,
- and Eimear E. Kenny
Genome Res. March 2026 36: 534-546; Published in Advance December 23, 2025, doi:10.1101/gr.280659.125
...samples. Dots in either panel represent samples colored based on the deme of origin.The simulated data set included 50,000 diploid samples. Only the Chromosome 1 was simulated for computational tractability. We calculated PCs of common and rare variants. We then downsampled the data set to retain only...
OPEN ACCESS ARTICLE
Select this article
Research: Adaptation of centromeres to breakage through local genomic and epigenomic remodeling in wheat
- Jingwei Zhou,
- Yuhong Huang,
- Huan Ma,
- Yiqian Chen,
- Chuanye Chen,
- Fangpu Han,
- and Handong Su
Genome Res. November 2025 35: 2461-2471; Published in Advance September 30, 2025, doi:10.1101/gr.280913.125
...for safeguarding genomic stability. Due to their intricate and fragile nature, centromeres are susceptible to chromosomal rearrangements. However, the mechanisms preserving their functional integrity and supporting nuclear homeostasis following breakages remain enigmatic. In this study, we use wheat ditelosomic...
Select this article
Method: De novo antibody identification in human blood from full-length single B cell transcriptomics and matching haplotype-resolved germline assemblies
- John Beaulaurier,
- Lynn Ly,
- J. Andrew Duty,
- Carly Tyer,
- Christian Stevens,
- Chuan-Tien Hung,
- Akash Sookdeo,
- Alex W. Drong,
- Shreyas Kowdle,
- Axel Guzman-Solis,
- Domenico Tortorella,
- Daniel J. Turner,
- Sissel Juul,
- Scott Hickey,
- and Benhur Lee
Genome Res. April 2025 35: 929-941; Published in Advance March 21, 2025, doi:10.1101/gr.279392.124
...the IG kappa (IGK) locus on Chromosome 2 or the IG lambda (IGL) locus on Chromosome 22. The IG loci have complex genomic organization, high sequence diversity and undergo extensive rearrangement in B cells during antigen-mediated activation and maturation. Consequently, assembly of these loci benefits...
OPEN ACCESS ARTICLE
Select this article
Method: Full-resolution HLA and KIR gene annotations for human genome assemblies
- Ying Zhou,
- Li Song,
- and Heng Li
Genome Res. November 2024 34: 1931-1941; Published in Advance June 5, 2024, doi:10.1101/gr.278985.124
...a nontrivial task. Here, we describe Immuannot, a new computation tool to annotate the gene structures of HLA and KIR genes and to type the allele of each gene. Applying Immuannot to 56 regional and 212 whole- assemblies from previous studies, we annotate 9931 HLA and KIR genes and found that almost half...
Select this article
Method: Genetic complexity of killer-cell immunoglobulin-like receptor genes in human pangenome assemblies
- Tsung-Kai Hung,
- Wan-Chi Liu,
- Sheng-Kai Lai,
- Hui-Wen Chuang,
- Yi-Che Lee,
- Hong-Ye Lin,
- Chia-Lang Hsu,
- Chien-Yu Chen,
- Ya-Chien Yang,
- Jacob Shujui Hsu,
- and Pei-Lung Chen
Genome Res. August 2024 34: 1211-1223; Published in Advance September 9, 2024, doi:10.1101/gr.278358.123
...47 high-quality, haplotype-resolved assemblies (HPRC Year-1 release) (Wang et al. 2022; Liao et al. 2023), using Hifiasm (Cheng et al. 2021) and family trio samples from The 1000 Genomes Project (1KGP) (The 1000 Genomes Project Consortium 2015). The assembly of HG002, one of the 47 s...
OPEN ACCESS ARTICLE

For checked items

view abstracts
download to citation manager

Searching journal content for articles similar to Semple et al. 12 (3): 424.

Search Results

Modify Results

This search

Preprint Server

Current Issue

In This Issue

Citation format:
Results / page:
Results order: