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Methods: A SILAC-based DNA protein interaction screen that identifies candidate binding proteins to functional DNA elements
- Gerhard Mittler,
- Falk Butter,
- and Matthias Mann
Genome Res. February 2009 19: 284-293; Published in Advance November 17, 2008, doi:10.1101/gr.081711.108
...A SILAC-based DNA protein interaction screen that identifies candidate binding proteins to functional DNA elements Gerhard Mittler 1 , 2 , 4 , Falk Butter 3 and Matthias Mann 3 , 5 1 Center for Experimental Bioinformatics, University...
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Method: Putting genetic interactions in context through a global modular decomposition
- Jeremy Bellay,
- Gowtham Atluri,
- Tina L. Sing,
- Kiana Toufighi,
- Michael Costanzo,
- Philippe Souza Moraes Ribeiro,
- Gaurav Pandey,
- Joshua Baller,
- Benjamin VanderSluis,
- Magali Michaut,
- Sangjo Han,
- Philip Kim,
- Grant W. Brown,
- Brenda J. Andrews,
- Charles Boone,
- Vipin Kumar,
- and Chad L. Myers
Genome Res. August 2011 21: 1375-1387; Published in Advance June 29, 2011, doi:10.1101/gr.117176.110
..., while theunstructuredhubs tend to exhibit fitness defects even when independently deleted. The distinction between structured and unstructured hubs is reminiscent of date and party hubs defined on protein interaction networks and coexpression data [debated in a number of papers, including Han et al...
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ARTICLE: Extensive low-affinity transcriptional interactions in the yeast genome
- Amos Tanay
Genome Res. August 2006 16: 962-972; Published in Advance June 29, 2006, doi:10.1101/gr.5113606
...at the characterization of transcriptional networks on a genomic scale. The ultimate goal of many of these studies is to construct networks associating transcription factors with genes via well-defined binding sites. Weaker regulatory interactions other than those occurring at high-affinity binding sites are largely...
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ARTICLE: Tandem Clusters of Membrane Proteins in Complete Genome Sequences
- Daisuke Kihara and
- Minoru Kanehisa
Genome Res. June 1, 2000 10: 731-743; doi:10.1101/gr.10.6.731
...of ATP hydrolysis by SecA and proton motive force ( Tokuda 1994 ). Another involves the signal recognition particle (SRP) that interacts with the hydrophobic signal peptide of a nascent protein. The two translocation pathways seem to use the common translocon ( Valent et al. 1998 ). It has been shown...
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LETTER: B-ZIP Proteins Encoded by the Drosophila Genome: Evaluation of Potential Dimerization Partners
- Jan Fassler,
- David Landsman,
- Asha Acharya,
- Jonathan R. Moll,
- Maria Bonovich,
- and Charles Vinson
Genome Res. August 1, 2002 12: 1190-1200; doi:10.1101/gr.67902
...attractive or repulsive g↔e‘ pairs as is observed for canonical leucine zippers. This indicates either that they are not real B-ZIP proteins or are a group of new B-ZIP proteins that have evolved in the insects. The observation that sisA, an insoluble protein, interacts in a yeast two-hybrid screen with two...
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Resource: Interspecies systems biology links bacterial metabolic pathways to nematode gene expression, chemotaxis behavior, and survival
- Marina Athanasouli,
- Tobias Loschko,
- and Christian Rödelsperger
Genome Res. October 2025 35: 2363-2374; Published in Advance August 5, 2025, doi:10.1101/gr.280848.125
...). Based on the strongest enrichment patterns, we connected 50 of the processed 60 modules with biological processes and protein domains, allowing the functional labeling of the majority of the modules (Supplemental Table S8).View larger version: In this window In a new window Figure 6. Interactions...
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Mini-Review: Revisiting models of enhancer–promoter communication in gene regulation
- Gilad Barshad and
- Charles G. Danko
Genome Res. June 2025 35: 1277-1286; doi:10.1101/gr.278389.123
...: the structural bridge model, in which enhancers and promoters come into close proximity through stable, protein-mediated interactions, and the hub model, in which dynamic clusters of transcription-associated proteins facilitate communication over variable distances. Emerging evidence suggests that although...
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Research: Single-cell spatial transcriptomics reveals a dystrophic trajectory following a developmental bifurcation of myoblast cell fates in facioscapulohumeral muscular dystrophy
- Lujia Chen,
- Xiangduo Kong,
- Kevin G. Johnston,
- Ali Mortazavi,
- Todd C. Holmes,
- Zhiqun Tan,
- Kyoko Yokomori,
- and Xiangmin Xu
Genome Res. May 2024 34: 665-679; Published in Advance May 22, 2024, doi:10.1101/gr.278717.123
...(Gawriyski et al. 2023), and the NCOA3 protein was found to interact with LEUTX protein (Gawriyski et al. 2023), supporting the connection. SOX9 has been shown to be upregulated by DUX4, but the mechanism is unclear (Resnick et al. 2019). SMCHD1, a FSHD modifier gene also linked to FSHD2, binds to D4Z4...
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Research: Estrogen receptor 1 chromatin profiling in human breast tumors reveals high inter-patient heterogeneity with enrichment of risk SNPs and enhancer activity at most-conserved regions
- Stacey E.P. Joosten,
- Sebastian Gregoricchio,
- Suzan Stelloo,
- Elif Yapıcı,
- Chia-Chi Flora Huang,
- Kerim Yavuz,
- Maria Donaldson Collier,
- Tunç Morova,
- Umut Berkay Altintaş,
- Yongsoo Kim,
- Sander Canisius,
- Cathy B. Moelans,
- Paul J. van Diest,
- Gozde Korkmaz,
- Nathan A. Lack,
- Michiel Vermeulen,
- Sabine C. Linn,
- and Wilbert Zwart
Genome Res. April 2024 34: 539-555; Published in Advance May 6, 2024, doi:10.1101/gr.278680.123
...biotin-labeled and pulled through an MCF-7 lysate to detect interacting proteins via mass spectrometry in an unbiased fashion (Supplemental Table S5; Vermeulen 2012). For rs11695384 and rs11665924, we were unable to confirm differential binding of ESR1, leaving rs9952980 for further study.rs9952980...
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Resource: Tracking pre-mRNA maturation across subcellular compartments identifies developmental gene regulation through intron retention and nuclear anchoring
- Kyu-Hyeon Yeom,
- Zhicheng Pan,
- Chia-Ho Lin,
- Han Young Lim,
- Wen Xiao,
- Yi Xing,
- and Douglas L. Black
Genome Res. June 2021 31: 1106-1119; Published in Advance April 8, 2021, doi:10.1101/gr.273904.120
...TTG and GTT triplets in the 5′ intron segment were predictive of Group C over D. The predictive power of intron sequence conservation and of multiple triplets indicate that particular RNA/protein interactions likely determine the retention properties of these groups.IR and chromatin association...

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