Searching journal content for articles similar to Rivera-Mulia et al. 29 (9): 1415.

Displaying results 1-10 of 131

For checked items

view abstracts
download to citation manager

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. April 2026 36: 802-813; Published in Advance March 19, 2026, doi:10.1101/gr.281532.125
..., Wilson KA, Marchal C, Lyu X, Zhao PA, Li B, Poulet A, Bartlett DA, Rivera-Mulia JC, Qin ZS, et al. 2019. Rapid irreversible transcriptional reprogramming in human stem cells accompanied by discordance between replication timing and chromatin compartment. Stem Cell Reports 13: 193–206. doi:10.1016/j...
OPEN ACCESS ARTICLE
Select this article
Resource: Binding profiles for 961 Drosophila and C. elegans transcription factors reveal tissue-specific regulatory relationships
- Michelle Kudron,
- Louis Gevirtzman,
- Alec Victorsen,
- Bridget C. Lear,
- Jiahao Gao,
- Jinrui Xu,
- Swapna Samanta,
- Emily Frink,
- Adri Tran-Pearson,
- Chau Huynh,
- Dionne Vafeados,
- Ann Hammonds,
- William Fisher,
- Martha Wall,
- Greg Wesseling,
- Vanessa Hernandez,
- Zhichun Lin,
- Mary Kasparian,
- Kevin White,
- Ravi Allada,
- Mark Gerstein,
- LaDeana Hillier,
- Susan E. Celniker,
- Valerie Reinke,
- and Robert H. Waterston
Genome Res. December 2024 34: 2319-2334; Published in Advance October 22, 2024, doi:10.1101/gr.279037.124
...authors: watersto@uw.edu, valerie.reinke@yale.eduAbstractA catalog of transcription factor (TF) binding sites in the is critical for deciphering regulatory relationships. Here, we present the culmination of the efforts of the modENCODE (model organism Encyclopedia of DNA Elements) and modERN (model...
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. April 2026 36: 695-712; Published in Advance March 4, 2026, doi:10.1101/gr.280838.125
...chose 28 hpf as the earliest time point to ensure robust detection of all three fluorescent proteins. To verify that our sorting strategy enriched for endodermal cells in the sox17E population, we performed bulk RNA-seq on 28-hpf samples. This revealed strong enrichment for transcripts expressed...
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
..., hinging on the precise binding of transcription factors (TFs) and cofactors to gene regulatory elements such as promoters and enhancers. Although it is relatively routine to profile -wide DNA binding landscapes of proteins, identifying the specific proteins that bind to, and regulate the transcription of...
OPEN ACCESS ARTICLE
Select this article
Method: Aggregation of recount3 RNA-seq data improves inference of consensus and tissue-specific gene coexpression networks
- Prashanthi Ravichandran,
- Princy Parsana,
- Rebecca Keener,
- Kasper D. Hansen,
- and Alexis Battle
Genome Res. September 2025 35: 2087-2103; Published in Advance July 17, 2025, doi:10.1101/gr.280808.125
...-specific networks. Central genes in consensus networks are enriched for evolutionarily constrained genes and ubiquitous biological pathways, whereas context-specific central nodes include tissue-specific transcription factors. The increased statistical power from data aggregation facilitates the derivation...
OPEN ACCESS ARTICLE
Select this article
Resource: Integrated single-cell multiome analysis reveals muscle fiber-type gene regulatory circuitry modulated by endurance exercise
- Aliza B. Rubenstein,
- Gregory R. Smith,
- Zidong Zhang,
- Xi Chen,
- Toby L. Chambers,
- Frederique Ruf-Zamojski,
- Natalia Mendelev,
- Wan Sze Cheng,
- Michel Zamojski,
- Mary Anne S. Amper,
- Venugopalan D. Nair,
- Andrew R. Marderstein,
- Stephen B. Montgomery,
- Olga G. Troyanskaya,
- Elena Zaslavsky,
- Todd Trappe,
- Scott Trappe,
- and Stuart C. Sealfon
Genome Res. July 2025 35: 1664-1677; Published in Advance May 20, 2025, doi:10.1101/gr.280051.124
...were normalized by the mean of the pre-exercise samples. (C) Network plot reveals the cell-type-specific target genes (blue) of PPARD (orange) identified by the integrated regulatory circuit analysis. Selected GO terms enriched in the target genes are annotated below. (D,E) Log2 fold-change (log2FC...
Select this article
Research: Oxygen-induced stress reveals context-specific gene regulatory effects in human brain organoids
- Benjamin D. Umans and
- Yoav Gilad
Genome Res. August 2025 35: 1689-1700; Published in Advance June 2, 2025, doi:10.1101/gr.280219.124
...brain organoids to hypoxic and hyperoxic conditions, we identify hundreds of gene regulatory changes that are undetectable under baseline conditions, with 148 trait-associated genes showing regulatory effects only in response to oxygen stress. To capture more nuanced transcriptional patterns, we employ...
OPEN ACCESS ARTICLE
Select this article
Research: Developmental transcriptomics in Pristionchus reveals the environmental responsiveness of a plasticity gene-regulatory network
- Shelley Reich,
- Tobias Loschko,
- Julie Jung,
- Samantha Nestel,
- Ralf J. Sommer,
- and Michael S. Werner
Genome Res. July 2025 35: 1560-1573; Published in Advance June 9, 2025, doi:10.1101/gr.279783.124
..., indicating that nodes in plasticity networks are under temporal regulatory constraint.Third, regulatory circuits exist between genes that code for enzymes with different functions (e.g., nag-1/nag-2, eud-1, seud-1/sult-1, and lsy-12). Some of these links, like nag-1/nag-2 and eud-1, were known through...
OPEN ACCESS ARTICLE
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
...genetic variation impacts transcription factor (TF) binding remains a major challenge, limiting our ability to model disease-associated variants. Here, we used a highly controlled system of F1 crosses with extensive genetic diversity to profile allele-specific binding of four TFs at several time points...
OPEN ACCESS ARTICLE
Select this article
Research: Allele-specific control of replication timing and genome organization during development
- Juan Carlos Rivera-Mulia,
- Andrew Dimond,
- Daniel Vera,
- Claudia Trevilla-Garcia,
- Takayo Sasaki,
- Jared Zimmerman,
- Catherine Dupont,
- Joost Gribnau,
- Peter Fraser,
- and David M. Gilbert
Genome Res. June 2018 28: 800-811; Published in Advance May 7, 2018, doi:10.1101/gr.232561.117
...(Hiratani et al. 2010; Rivera-Mulia et al. 2015), and can be exploited to characterize complex circuits of gene regulatory networks (Rivera-Mulia et al. 2017b). Hence, RT constitutes a functional readout of organization and function.Chromosome homologs replicate highly synchronously, with very few...

For checked items

view abstracts
download to citation manager

Searching journal content for articles similar to Rivera-Mulia et al. 29 (9): 1415.

Search Results

Modify Results

This search

Preprint Server

Current Issue

In This Issue

Citation format:
Results / page:
Results order: