Searching journal content for articles similar to Bates et al. 36 (3): 433.

Displaying results 1-10 of 579

For checked items

view abstracts
download to citation manager

Select this article
Mini-Review: A Hitchhiker's Guide to long-read genomic analysis
- Medhat Mahmoud,
- Daniel P. Agustinho,
- and Fritz J. Sedlazeck
Genome Res. April 2025 35: 545-558; doi:10.1101/gr.279975.124
...-seq (including epigenetic modifications). We recommend that readers interested in more details about the two platforms read the review by Logsdon et al. (2020).Both PacBio and ONT excel in resolving repetitive elements and identifying complex genomic variants, including structural variants (SVs), which have...
Select this article
Research: Transcriptome-wide systematic search does not detect A-to-I RNA editing in cis-antisense RNA duplexes
- Zohar Rosenwasser,
- Roni Cohen-Fultheim,
- Ofir Shliefer,
- Erez Y. Levanon,
- and Eli Eisenberg
Genome Res. March 12, 2026 gr.280820.125; Published in Advance March 12, 2026, doi:10.1101/gr.280820.125
...), and similar results were reported for the mouse(Kiyosawa et al. 2003), Drosophila(Misra et al. 2002), Arabidopsis(Meyers et al. 2004; Wang et al. 2014), and rice s(Osato et al. 2003). In addition, many long intergenic non-coding RNAs (lincRNAs) have been identified as antisense transcripts, further...
- Abstract
- Full Text (PDF)
OPEN ACCESS ARTICLEACCEPTED MANUSCRIPT
Select this article
Method: Highly efficient and scarless genome editing via essential gene-coupled homology-directed repair
- Joo Hye Yeo,
- Hyongbum Henry Kim,
- Sang Ho Oh,
- and Jinu Lee
Genome Res. April 15, 2026 gr.281194.125; Published in Advance April 15, 2026, doi:10.1101/gr.281194.125
...disrupt endogenous gene regulation and 106 compromise genomic stability. Thus, selection cassettes are sometimes placed in 107 intronic regions to mitigate this limitation (Wang et al. 2022); however, these can 108 interfere with splicing and generate aberrant transcripts. Meanwhile, “safe harbor” loci...
- Abstract
- Full Text (PDF)
ACCEPTED MANUSCRIPT
Select this article
Research: Genome-wide nucleosome and transcription factor responses to genetic perturbations reveal chromatin-mediated mechanisms of transcriptional regulation
- Kevin Moyung,
- Yulong Li,
- Heather K. MacAlpine,
- Alexander J. Hartemink,
- and David M. MacAlpine
Genome Res. January 2026 36: 115-128; Published in Advance December 9, 2025, doi:10.1101/gr.279637.124
...factor-specific antibodies; the exact mechanisms of the interplay of all TFs and nucleosomes have yet to be explored with respect to transcription.To address these challenges, here we develop a systematic, genetic approach to simultaneously profile nucleosome and TF changes in response to single-gene...
Select this article
Method: Deep structural clustering reveals hidden systematic biases in RNA sequencing data
- Qiang Su,
- Yi Long,
- Deming Gou,
- Junmin Quan,
- Xiaoming Zhou,
- and Qizhou Lian
Genome Res. November 2025 35: 2563-2577; Published in Advance September 19, 2025, doi:10.1101/gr.280713.125
...analysis, providing comprehensive exploration of gene expression across diverse biological contexts. However, RNA-seq data are susceptible to various biases that can significantly compromise the accuracy and reliability of transcript quantification. This study investigates the influence of high...
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
...to improve the performance of identifying distal cCRE–gene interactions by incorporating chromatin loops into the ScPGE model.In fact, several key hyperparameters—such as DNA sequence length, nonredundant TF motifs, and cell-specific cCREs—have yet to be systematically explored. Based on the GM12878 and K562...
OPEN ACCESS ARTICLE
Select this article
Resource: Single-nucleus multiomic profiling of the aging mouse substantia nigra reveals conserved gene alterations linked to Parkinson's disease
- Kangli Wang,
- Weikun Xia,
- Yingli Gu,
- Songpeng Zu,
- Qian Yang,
- Maria Luisa Amaral,
- Yaozhi Wang,
- Allen Wang,
- Xiang-Dong Fu,
- William C. Mobley,
- and Bing Ren
Genome Res. April 2026 36: 849-864; Published in Advance March 4, 2026, doi:10.1101/gr.281113.125
...aging (Fig. 2D,E; Gulen et al. 2023). The cCRE–gene maps provide an opportunity to further explore the regulatory networks and identify putative enhancers and potential transcription factors involved in these pathways. We identified 80 putative enhancers related to these genes, and motif enrichment...
OPEN ACCESS ARTICLE
Select this article
Method: Recovering gene regulatory networks in single-cell multi-omics data with PRISM-GRN
- Wenhao Zhang,
- Lan Cao,
- Xiaoxuan Gu,
- Yongyu Long,
- and Ying Wang
Genome Res. January 2026 36: 142-158; Published in Advance October 9, 2025, doi:10.1101/gr.280757.125
..., and interpretable exploration of causal GRNs with prior knowledge and multi-omics data.Gene regulatory networks (GRNs), which encapsulate the complex interactions among transcription factors (TFs), target genes, and various regulatory elements, constitute the core machinery of gene regulation (Levine and Davidson...
Select this article
Research: Integrating genetic variation with deep learning provides context for variants impacting transcription factor binding during embryogenesis
- Olga M. Sigalova,
- Mattia Forneris,
- Frosina Stojanovska,
- Bingqing Zhao,
- Rebecca R. Viales,
- Adam Rabinowitz,
- Fayrouz Hammal,
- Benoît Ballester,
- Judith B. Zaugg,
- and Eileen E.M. Furlong
Genome Res. May 2025 35: 1138-1153; Published in Advance April 15, 2025, doi:10.1101/gr.279652.124
...variants occur in the noncoding (Edwards et al. 2013; Buniello et al. 2019) and likely affect gene regulation (Claringbould and Zaugg 2021). One mechanism by which mutations impact transcriptional programs is through the disruption of transcription factor (TF) binding sites within regulatory elements...
OPEN ACCESS ARTICLE
Select this article
Method: Biosurfer for systematic tracking of regulatory mechanisms leading to protein isoform diversity
- Mayank Murali,
- Jamie Saquing,
- Senbao Lu,
- Ziyang Gao,
- Emily F. Watts,
- Ben Jordan,
- Zachary Peters Wakefield,
- Ana Fiszbein,
- David R. Cooper,
- Peter J. Castaldi,
- Dmitry Korkin,
- and Gloria M. Sheynkman
Genome Res. April 2025 35: 1012-1024; Published in Advance March 14, 2025, doi:10.1101/gr.279317.124
...isoforms using BiosurferThe principal and alternative isoforms were defined using the APPRIS annotation of genes (Rodriguez et al. 2013). First, the set of APPRIS isoforms is identified for each gene from the input data (GENCODE v42, basic annotation [Frankish et al. 2021]) by extracting the key transcript...

For checked items

view abstracts
download to citation manager

Searching journal content for articles similar to Bates et al. 36 (3): 433.

Search Results

Modify Results

This search

Preprint Server

Current Issue

In This Issue

Citation format:
Results / page:
Results order: