Searching journal content for articles similar to Herrgård et al. 13 (11): 2423.

Displaying results 1-10 of 14

For checked items

view abstracts
download to citation manager

Select this article
Research: Genome-wide determinants of sequence-specific DNA binding of general regulatory factors
- Matthew J. Rossi,
- William K.M. Lai,
- and B. Franklin Pugh
Genome Res. April 2018 28: 497-508; Published in Advance March 21, 2018, doi:10.1101/gr.229518.117
...Matthew J. Rossi, William K.M. Lai and B. Franklin Pugh Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA Corresponding author: bfp2@psu.eduAbstractGeneral regulatory factors (GRFs...
OPEN ACCESS ARTICLE
Select this article
Methods: Genome-Scale In Silico Models of E. coli Have Multiple Equivalent Phenotypic States: Assessment of Correlated Reaction Subsets That Comprise Network States
- Jennifer L. Reed and
- Bernhard Ø. Palsson
Genome Res. September 2004 14: 1797-1805; doi:10.1101/gr.2546004
.... 2003 . Experimental determination and system level analysis of essential genes in Escherichia coli MG1655. J. Bacteriol. 185 : 5673 -5684. ↵ Herrgard, M.J., Covert, M.W., and Palsson, B.Ø. 2003 . Reconciling gene expression data with known -scale regulatory network structures. Genome Res. 13 : 2423...
Select this article
Resource: Isoform- and pathway-specific regulation of post-transcriptional RNA processing in human cells
- Ishwarya Venkata Narayanan,
- Karan Bedi,
- Brian Magnuson,
- Ariel McShane,
- Mario Ashaka,
- Michelle Paulsen,
- Thomas E Wilson,
- and Mats Ljungman
Genome Res. March 26, 2026 gr.280892.125; Published in Advance March 26, 2026, doi:10.1101/gr.280892.125
...dynamics in controlling gene expression, allowing for the 35 precise coordination of cellular functions. 36 37 INTRODUCTION 38 Gene expression is regulated at many levels in mammalian cells. Transcription initiation 39 is directed by epigenetic marks allowing regulatory DNA elements to be accessible to 40...
- Abstract
- Full Text (PDF)
OPEN ACCESS ARTICLEACCEPTED MANUSCRIPT
Select this article
Research: Derepression of Polycomb targets during pancreatic organogenesis allows insulin-producing beta-cells to adopt a neural gene activity program
- Joris van Arensbergen,
- Javier García-Hurtado,
- Ignasi Moran,
- Miguel Angel Maestro,
- Xiaobo Xu,
- Mark Van de Casteele,
- Anouchka L. Skoudy,
- Matteo Palassini,
- Harry Heimberg,
- and Jorge Ferrer
Genome Res. June 2010 20: 722-732; Published in Advance April 15, 2010, doi:10.1101/gr.101709.109
...of common developmental origin. Beta-cells selectively lack PcG repression in a neural regulatory program We next attempted to reconcile the paradox that in beta-cells a H3K27me3 repression signature shared with endoderm tissues is associated with a neural-like gene activity profile. We hypothesized...
Select this article
Method: Linear-time cluster ensembles of large-scale single-cell RNA-seq and multimodal data
- Van Hoan Do,
- Francisca Rojas Ringeling,
- and Stefan Canzar
Genome Res. April 2021 31: 677-688; Published in Advance February 24, 2021, doi:10.1101/gr.267906.120
...based on commonalities and differences in -wide expression patterns, reconstruct the heterogeneous composition of cell populations in tumors and their microenvironment, and unveil regulatory programs that govern the dynamic changes in gene expression along developmental trajectories.One of the most...
Select this article
Methods: High-resolution nucleosome mapping reveals transcription-dependent promoter packaging
- Assaf Weiner,
- Amanda Hughes,
- Moran Yassour,
- Oliver J. Rando,
- and Nir Friedman
Genome Res. January 2010 20: 90-100; Published in Advance October 21, 2009, doi:10.1101/gr.098509.109
...). Nucleosomes influence the expression of a huge fraction of yeast genes (Wyrick et al. 1999) and the precise positioning of nucleosomes relative to underlying DNA, controls access to protein-binding sites, and thereby affects regulatory programs (Stunkel et al. 1997; Lomvardas and Thanos 2002; Lam et al. 2008...
OPEN ACCESS ARTICLE
Select this article
LETTER: Principles of transcriptional regulation and evolution of the metabolic system in E. coli
- Aswin S.N. Seshasayee,
- Gillian M. Fraser,
- M. Madan Babu,
- and Nicholas M. Luscombe
Genome Res. January 2009 19: 79-91; Published in Advance October 3, 2008, doi:10.1101/gr.079715.108
.... 2000 ; Ravasz et al. 2002 ; Ibarra et al. 2003 ; Almaas et al. 2004 , 2005 ). Control of metabolic activity can be studied by overlaying a transcriptional regulatory network in which edges represent regulatory interactions from transcription factors (TFs) to target genes. Data for the best...
Select this article
Research: Identification of FMR1-regulated molecular networks in human neurodevelopment
- Meng Li,
- Junha Shin,
- Ryan D. Risgaard,
- Molly J. Parries,
- Jianyi Wang,
- Deborah Chasman,
- Shuang Liu,
- Sushmita Roy,
- Anita Bhattacharyya,
- and Xinyu Zhao
Genome Res. March 2020 30: 361-374; Published in Advance March 16, 2020, doi:10.1101/gr.251405.119
...results show that studying FMR1 at multiple regulatory levels through our network-based approach can identify components of important cellular functions regulated by FMR1 in human neural cells. These network clusters and gene hubs validate some of the animal studies and point to novel functional targets...
Select this article
Research: ATAC-seq reveals regional differences in enhancer accessibility during the establishment of spatial coordinates in the Drosophila blastoderm
- Marta Bozek,
- Roberto Cortini,
- Andrea Ennio Storti,
- Ulrich Unnerstall,
- Ulrike Gaul,
- and Nicolas Gompel
Genome Res. May 2019 29: 771-783; Published in Advance April 8, 2019, doi:10.1101/gr.242362.118
...propose that differential accessibility is a signature of patterning cis-regulatory elements in the Drosophila blastoderm and discuss potential mechanisms by which accessibility of enhancers may be modulated by activator and repressor TFs.Embryonic development is controlled by gene regulatory networks...
OPEN ACCESS ARTICLE
Select this article
Resource: Early genome activation in Drosophila is extensive with an initial tendency for aborted transcripts and retained introns
- Jamie C. Kwasnieski,
- Terry L. Orr-Weaver,
- and David P. Bartel
Genome Res. July 2019 29: 1188-1197; Published in Advance June 24, 2019, doi:10.1101/gr.242164.118
...to a major wave, in which many more genes are activated (Tadros and Lipshitz 2009).The onset of activation takes place in a unique regulatory paradigm in which some genes must be activated in the context of an otherwise quiescent . For animals whose embryos undergo external development, such as zebrafish...

For checked items

view abstracts
download to citation manager

Searching journal content for articles similar to Herrgård et al. 13 (11): 2423.

Search Results

Modify Results

This search

Preprint Server

Current Issue

In This Issue

Citation format:
Results / page:
Results order: