Searching journal content for articles similar to McGuire et al. 10 (6): 744.

Displaying results 1-10 of 92

For checked items

view abstracts
download to citation manager

Select this article
Method: Designing realistic regulatory DNA with autoregressive language models
- Avantika Lal,
- David Garfield,
- Tommaso Biancalani,
- and Gokcen Eraslan
Genome Res. September 2024 34: 1411-1420; Published in Advance September 25, 2024, doi:10.1101/gr.279142.124
...94080, USA Corresponding authors: lal.avantika@gene.com, eraslan.gokcen@gene.comAbstractCis-regulatory elements (CREs), such as promoters and enhancers, are DNA sequences that regulate the expression of genes. The activity of a CRE is influenced by the order, composition, and spacing of sequence motifs...
OPEN ACCESS ARTICLE
Select this article
Resource: Quadrupia provides a comprehensive catalog of G-quadruplexes across genomes from the tree of life
- Nikol Chantzi,
- Akshatha Nayak,
- Fotis A. Baltoumas,
- Eleni Aplakidou,
- Shiau Wei Liew,
- Jesslyn Elvaretta Galuh,
- Michail Patsakis,
- Austin Montgomery,
- Camille Moeckel,
- Ioannis Mouratidis,
- Saiful Arefeen Sazed,
- Wilfried Guiblet,
- Panagiotis Karmiris-Obratański,
- Guliang Wang,
- Apostolos Zaravinos,
- Karen M. Vasquez,
- Chun Kit Kwok,
- Georgios A. Pavlopoulos,
- and Ilias Georgakopoulos-Soares
Genome Res. November 2025 35: 2578-2600; Published in Advance August 26, 2025, doi:10.1101/gr.279790.124
...). Such experimental approaches have enabled the derivation of patterns enabling the prediction of sequences that can adopt G4 DNA structures.Early computational studies showed that conserved sequence motifs can accurately capture a significant proportion of potential G4-forming regions (Huppert and Balasubramanian...
OPEN ACCESS ARTICLE
Select this article
Research: Modeling alternative translation initiation sites in plants reveals evolutionarily conserved cis-regulatory codes in eukaryotes
- Ting-Ying Wu,
- Ya-Ru Li,
- Kai-Jyun Chang,
- Jhen-Cheng Fang,
- Daisuke Urano,
- and Ming-Jung Liu
Genome Res. February 2024 34: 272-285; Published in Advance March 13, 2024, doi:10.1101/gr.278100.123
...also helped characterize novel cis-regulatory DNA elements and their combined effects in regulating transcription and associating genetic variation with differential gene expression and phenotypic diversity (Azodi et al. 2020a,b). Therefore, integrating high-throughput translation initiation sequencing...
OPEN ACCESS ARTICLE
Select this article
Research: Conserved noncoding sequences provide insights into regulatory sequence and loss of gene expression in maize
- Baoxing Song,
- Edward S. Buckler,
- Hai Wang,
- Yaoyao Wu,
- Evan Rees,
- Elizabeth A. Kellogg,
- Daniel J. Gates,
- Merritt Khaipho-Burch,
- Peter J. Bradbury,
- Jeffrey Ross-Ibarra,
- Matthew B. Hufford,
- and M. Cinta Romay
Genome Res. July 2021 31: 1245-1257; Published in Advance May 27, 2021, doi:10.1101/gr.266528.120
...may have a diversity of functions.In terms of DNA methylation, the cis pan-And-CNSs showed a low DNA methylation ratio, which supports the previous observation that putative cis-regulatory sequences correspond to a low DNA methylation ratio in plants (Zhang et al. 2006, 2012; Zilberman et al. 2007...
Select this article
Research: Evolutionary conservation of Y Chromosome ampliconic gene families despite extensive structural variation
- Wesley A. Brashear,
- Terje Raudsepp,
- and William J. Murphy
Genome Res. December 2018 28: 1841-1851; Published in Advance October 31, 2018, doi:10.1101/gr.237586.118
...) and is highly amplified across the domestic cat Y.Although the transcriptional content of the ampliconic region of the domestic cat MSY has been previously explored, the actual DNA sequence, structure, and regulatory architecture have not been determined. Sequencing and assembling these regions are important...
Select this article
Method: P-value-based regulatory motif discovery using positional weight matrices
- Holger Hartmann,
- Eckhart W. Guthöhrlein,
- Matthias Siebert,
- Sebastian Luehr,
- and Johannes Söding
Genome Res. January 2013 23: 181-194; Published in Advance September 18, 2012, doi:10.1101/gr.139881.112
...-Maximilians-Universität (LMU) München, Feodor-Lynen-Straße 25, 81377 Munich, Germany Abstract To analyze gene regulatory networks, the sequence-dependent DNA/RNA binding affinities of proteins and noncoding RNAs are crucial. Often, these are deduced from sets of sequences enriched in factor binding sites. Two...
Select this article
Method: Leveraging chromatin accessibility for transcriptional regulatory network inference in T Helper 17 Cells
- Emily R. Miraldi,
- Maria Pokrovskii,
- Aaron Watters,
- Dayanne M. Castro,
- Nicholas De Veaux,
- Jason A. Hall,
- June-Yong Lee,
- Maria Ciofani,
- Aviv Madar,
- Nick Carriero,
- Dan R. Littman,
- and Richard Bonneau
Genome Res. March 2019 29: 449-463; Published in Advance January 29, 2019, doi:10.1101/gr.238253.118
...(Barski et al. 2007) correlate with promoters, enhancers, and/or other locus control regions. These data can partially overcome limitations in a priori knowledge of cell-type–specific TF regulators if integrated with TF DNA-binding motifs (Pique-Regi et al. 2011). Large-scale efforts to characterize TF...
OPEN ACCESS ARTICLE
Select this article
LETTER: Functional conservation of Rel binding sites in drosophilid genomes
- Richard R. Copley,
- Maxim Totrov,
- Jane Linnell,
- Simon Field,
- Jiannis Ragoussis,
- and Irina A. Udalova
Genome Res. September 2007 17: 1327-1335; doi:10.1101/gr.6490707
...regulatory elements are poorly understood: Little is known about how the strength of transcription factor binding correlates with DNA sequence conservation, and whether transcription factor binding sites can evolve rapidly while retaining their function. Here we use the model of the NFKB/Rel-dependent gene...
OPEN ACCESS ARTICLE
Select this article
Research: Regulatory modules controlling maize inflorescence architecture
- Andrea L. Eveland,
- Alexander Goldshmidt,
- Michael Pautler,
- Kengo Morohashi,
- Christophe Liseron-Monfils,
- Michael W. Lewis,
- Sunita Kumari,
- Susumu Hiraga,
- Fang Yang,
- Erica Unger-Wallace,
- Andrew Olson,
- Sarah Hake,
- Erik Vollbrecht,
- Erich Grotewold,
- Doreen Ware,
- and David Jackson
Genome Res. March 2014 24: 431-443; Published in Advance December 4, 2013, doi:10.1101/gr.166397.113
...by a single zinc finger domain, implicated in bindingDNA through a consensus AGTsequence (Dathan et al. 2002). To determine whether additional sequences were associated with RA1 binding, we tested for enrichment of de novo motifs under high-confidence peaks in target gene promoters. Most notablewas a...
Select this article
LETTER: Genome-wide prediction of G4 DNA as regulatory motifs: Role in Escherichia coli global regulation
- Pooja Rawal,
- Veera Bhadra Rao Kummarasetti,
- Jinoy Ravindran,
- Nirmal Kumar,
- Kangkan Halder,
- Rakesh Sharma,
- Mitali Mukerji,
- Swapan Kumar Das,
- and Shantanu Chowdhury
Genome Res. May 2006 16: 644-655; doi:10.1101/gr.4508806
...Genome-wide prediction of G4 DNA as regulatory motifs: Role in Escherichia coli global regulation G4 DNA-mediated regulation in prokaryotes Pooja Rawal 1 , Veera Bhadra Rao Kummarasetti 1 , Jinoy Ravindran 1 , Nirmal Kumar 1 , Kangkan Halder 2...

For checked items

view abstracts
download to citation manager

Searching journal content for articles similar to McGuire et al. 10 (6): 744.

Search Results

Modify Results

This search

Preprint Server

Current Issue

In This Issue

Citation format:
Results / page:
Results order: