Searching journal content for articles similar to Margulies et al. 11 (10): 1686.

Displaying results 1-10 of 6178

For checked items

view abstracts
download to citation manager

Select this article
Research: Functional genomics analysis of developing zebrafish and human endoderm reveals highly conserved cis-regulatory modules acting during vertebrate organogenesis
- Daniela M. Riley,
- Randa Elsayed,
- Mark D. Walsh,
- Simaran Johal,
- Ying Lin,
- Harry Walton,
- Till Bretschneider,
- Sascha Ott,
- and Andrew C. Nelson
Genome Res. March 4, 2026 ; Published in Advance March 4, 2026, doi:10.1101/gr.280838.125
...by the conservation of critical genes governing embryonic development. However, for conserved genes to deliver consistent developmental outcomes between species, similar gene regulatory programs and gene expression patterns must also be maintained. The endoderm germ layer makes major contributions to the respiratory...
Select this article
Method: Gene duplication is associated with gene diversification and potential neofunctionalization in lung cancer evolution
- Paul Ashford,
- Alexander M. Frankell,
- Zofia Piszka,
- Camilla S.M. Pang,
- Mahnaz Abbasian,
- Maise Al Bakir,
- Mariam Jamal-Hanjani,
- Nicholas McGranahan,
- Charles Swanton,
- and Christine A. Orengo
Genome Res. March 2026 36: 561-577; Published in Advance February 19, 2026, doi:10.1101/gr.278663.123
...functional diversification during evolution. In this study, we seek to identify the diversification and potential gene neofunctionalization of lung tumors in the TRACERx cohort. We develop a novel computational protocol to identify preduplication and postduplication mutations predicted to affect protein...
OPEN ACCESS ARTICLE
Select this article
Method: Analysis of coding gene expression from small RNA sequencing
- Aygun Azadova,
- Anthonia Ekperuoh,
- Greg N. Brooke,
- and Antonio Marco
Genome Res. March 2026 36: 611-618; Published in Advance February 10, 2026, doi:10.1101/gr.281364.125
...), and the development of microarrays first (Schena et al. 1995) and high-throughput sequencing later (Margulies et al. 2005) boosted our capacity to analyze transcriptomes. Nowadays, the most common technique to analyze gene expression is RNA sequencing (RNA-seq). This technique consists of first isolating RNA from...
Select this article
Method: Parallel analysis of replication timing, gene expression, and copy number with PARTAGE
- Lakshana Sruthi Sadu Murari,
- Quinn Dickinson,
- Silvia Meyer-Nava,
- and Juan Carlos Rivera-Mulia
Genome Res. March 19, 2026 ; Published in Advance March 19, 2026, doi:10.1101/gr.281532.125
...into functional compartments that replicate at specific times during S-phase. This temporal program, referred to as replication timing (RT), is coregulated with the 3D organization, is cell type–specific, and changes during development in coordination with gene expression. Moreover, RT alterations are linked...
OPEN ACCESS ARTICLE
Select this article
Resource: Cell type–specific gene regulatory atlas prioritizes drug targets and repurposable medicines in Alzheimer's disease
- Yunxiao Ren,
- Ming Hu,
- Yang E. Li,
- Andrew A. Pieper,
- Jeffrey Cummings,
- and Feixiong Cheng
Genome Res. March 2026 36: 645-659; Published in Advance January 21, 2026, doi:10.1101/gr.280436.125
...occurring in the early stages of the disease and to inform the development of therapeutics aimed at halting AD progression. Additionally, we presented the distribution of limbic-predominant age-related TDP-43 encephalopathy (LATE) stage, apolipoprotein E (APOE) gene carrier status, sex, and age at death...
OPEN ACCESS ARTICLE
Select this article
Method: Robust and efficient annotation of cell states through gene signature scoring
- Laure Ciernik,
- Agnieszka Kraft,
- Florian Barkmann,
- Josephine Yates,
- and Valentina Boeva
Genome Res. March 2026 36: 630-644; Published in Advance February 18, 2026, doi:10.1101/gr.280926.125
...score stability and cross-signature comparability, achieving cell-state annotation accuracy comparable to supervised methods. We demonstrate the practical utility of ANS by developing and validating a gene signature to differentiate cancer-associated fibroblasts from malignant cells undergoing...
OPEN ACCESS ARTICLE
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
...a crucial role in differentiation and development (Furlong and Levine 2018). Mutations in CREs contribute to various diseases by disrupting the regular expression of their target genes (Nasser et al. 2021). Decoding how CREs regulate gene expression may reveal the mechanisms of gene regulation and provide...
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. March 4, 2026 ; Published in Advance March 4, 2026, doi:10.1101/gr.281113.125
...genes that may represent age-related risk factors for PD development. By integrating our mouse data with human PD single-cell RNA-seq data sets, we identified a subset of genes that were differentially expressed during aging and also dysregulated in PD. Among these, Hsp90aa1 and Hsp90ab1, both members...
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
..., such as “regulation of pri-miRNA transcription by RNA polymerase II” and “epithelial cell development,” both of which are critically involved in the regulatory functions of A549 cells (Foster et al. 1998; Lin and Gregory 2015). The GO enrichment analysis results for genes from cluster 1 to cluster 9 are also...
Select this article
Review: A systematic guide for identifying transcription factors that directly regulate the expression of a gene of interest
- Andrew D. Bates,
- Dawid Grzela,
- Maciej Studzian,
- Louise Brennan,
- Moli Williams,
- Conor Fawcett,
- Beth Hammond,
- Manreen Grewal,
- Marcin Ratajewski,
- Lukasz Pulaski,
- and Urszula L. McClurg
Genome Res. March 2026 36: 433-459; Published in Advance February 17, 2026, doi:10.1101/gr.281154.125
...emergent transcripts at the single-cell (or sometimes single-GOI) level (Salataj et al. 2023). Recently, a sophisticated method of quasi-immediate visualization of transcribed genes has been developed in the form of nascent RNA tagging. This method requires the GOI modification (endogenous or exogenously...
OPEN ACCESS ARTICLE

For checked items

view abstracts
download to citation manager

Searching journal content for articles similar to Margulies et al. 11 (10): 1686.

Search Results

Modify Results

This search

Preprint Server

Current Issue

In This Issue

Citation format:
Results / page:
Results order: