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Method: A novel synthetic-genetic-array–based yeast one-hybrid system for high discovery rate and short processing time
- Chung-Shu Yeh,
- Zhifeng Wang,
- Fang Miao,
- Hongyan Ma,
- Chung-Ting Kao,
- Tzu-Shu Hsu,
- Jhong-He Yu,
- Er-Tsi Hung,
- Chia-Chang Lin,
- Chen-Yu Kuan,
- Ni-Chiao Tsai,
- Chenguang Zhou,
- Guan-Zheng Qu,
- Jing Jiang,
- Guifeng Liu,
- Jack P. Wang,
- Wei Li,
- Vincent L. Chiang,
- Tien-Hsien Chang,
- and Ying-Chung Jimmy Lin
Genome Res. August 2019 29: 1343-1351; Published in Advance June 11, 2019, doi:10.1101/gr.245951.118
...AJ. 2006b. Gateway-compatible yeast one-hybrid screens. CSH Protoc 2006. doi:10.1101/pdb.prot4590 ↵French S, Mangat C, Bharat A, Côté JP, Mori H, Brown ED. 2016. A robust platform for chemical genomics in bacterial systems. Mol Biol Cell 27: 1015–1025. doi:10.1091/mbc.E15-08-0573 ↵Fuxman Bass JI...
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Research: Evolution at two levels of gene expression in yeast
- Carlo G. Artieri and
- Hunter B. Fraser
Genome Res. March 2014 24: 411-421; Published in Advance December 6, 2013, doi:10.1101/gr.165522.113
...of Saccharomyces yeast and their interspecific hybrid in order to assess the relative contributions of changes in mRNA abundance and translation to regulatory evolution. We report that both cis- and trans -acting regulatory divergence in translation are abundant, affecting at least 35% of genes. The majority...
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Perspective: What does our genome encode?
- John A. Stamatoyannopoulos
Genome Res. September 2012 22: 1602-1611; doi:10.1101/gr.146506.112
..., Stamatoyannopoulos Stamatoyannopoulos John A. J.A. Stamatoyannopoulos Stamatoyannopoulos, John A John Stamatoyannopoulos John A Stamatoyannopoulos John JA Stamatoyannopoulos J Stamatoyannopoulos John A genome;22/9/1602 10.1101/gr.146506.112 1088-9051 What does our genome encode? Perspective What does our encode...
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PERSPECTIVE: The mouse genome
- Jean Louis Guénet
Genome Res. December 2005 15: 1729-1740; doi:10.1101/gr.3728305
..., the last fifteen years have been crucial for the development of mouse genetics, and they have certainly paved the way for a few decades to come. View this table: In this window In a new window Table 1. Some useful Web sites Sequencing of the mouse and its consequences The recent publication of the nearly...
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PERSPECTIVE: Determinants of the success of whole-genome association testing
- Andrew G. Clark,
- Eric Boerwinkle,
- James Hixson,
- and Charles F. Sing
Genome Res. November 2005 15: 1463-1467; doi:10.1101/gr.4244005
..., or a metabolic or physiological pathway? We almost never know the answer initially, and thus a proper study must allow for flexibility in interpretation of the unit of gene function. In model organisms, it seems that whenever a study is designed to detect gene–gene interactions, they are nearly always present...
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Research: After the bottleneck: Genome-wide diversification of the Mycobacterium tuberculosis complex by mutation, recombination, and natural selection
- Amine Namouchi,
- Xavier Didelot,
- Ulrike Schöck,
- Brigitte Gicquel,
- and Eduardo P.C. Rocha
Genome Res. April 2012 22: 721-734; Published in Advance February 29, 2012, doi:10.1101/gr.129544.111
...After the bottleneck: Genome-wide diversification of the Mycobacterium tuberculosis complex by mutation, recombination, and natural selection Amine Namouchi 1 , 7 , Xavier Didelot 2 , Ulrike Schöck 3 , Brigitte Gicquel 1 , 6 and Eduardo P...
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PERSPECTIVE: Structure and function of the human genome
- Peter F.R. Little
Genome Res. December 2005 15: 1759-1766; doi:10.1101/gr.4560905
...DNA sequence. The past decade in biological research has surely been the decade of research—from the scientific perspective, in the public imagination, and even in the minds of international politicians. It is therefore timely to use this 10th anniversary of Genome Research to take stock of where we...
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PERSPECTIVE: Insights on biology and evolution from microbial genome sequencing
- Claire M. Fraser-Liggett
Genome Res. December 2005 15: 1603-1610; doi:10.1101/gr.3724205
.... Bacteriol. 185 : 155 -164. ↵ Dolinski, K. and Botstein, D. 2005 . Changing perspectives in yeast research nearly a decade after the sequence. Genome Res. (this issue). ↵ Doolittle, W.F. 1999 . Phylogenetic classification and the universal tree. Science 284 : 2124 -2129. ↵ Douglas, S., Zauner, S., Fraunholz...
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Research: The chromatin landscape of the histone-possessing Bacteriovorax bacteria
- Georgi K. Marinov,
- Benjamin Doughty,
- Anshul Kundaje,
- and William J. Greenleaf
Genome Res. January 2025 35: 109-123; Published in Advance November 21, 2024, doi:10.1101/gr.279418.124
...proposed to exhibit a range of divergent features compared with histones in archaea and eukaryotes. However, no functional genomic studies of the properties of Bdellovibrionota chromatin have been carried out. In this work, we map the landscape of chromatin accessibility, active transcription, and three...
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Research: Genomic analysis of Rad26 and Rad1–Rad10 reveals differences in their dependence on Mediator and RNA polymerase II
- Diyavarshini Gopaul,
- Cyril Denby Wilkes,
- Arach Goldar,
- Nathalie Giordanengo Aiach,
- Marie-Bénédicte Barrault,
- Elizaveta Novikova,
- and Julie Soutourina
Genome Res. August 2022 32: 1516-1528; Published in Advance June 23, 2022, doi:10.1101/gr.276371.121
.... In this work, we analyzed the -wide distribution of Rad26/ERCC6(CSB) and Rad1–Rad10/ERCC4(XPF)-ERCC1, addressing the question of a potential link of these proteins with Mediator and Pol II in yeast Saccharomyces cerevisiae. Our genomic analyses reveal that Rad1–Rad10 and Rad26 are present on the yeast...

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