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Method: Whole-genome analysis of noncoding genetic variations identifies multiscale regulatory element perturbations associated with Hirschsprung disease
- Alexander Xi Fu,
- Kathy Nga-Chu Lui,
- Clara Sze-Man Tang,
- Ray Kit Ng,
- Frank Pui-Ling Lai,
- Sin-Ting Lau,
- Zhixin Li,
- Maria-Mercè Garcia-Barcelo,
- Pak-Chung Sham,
- Paul Kwong-Hang Tam,
- Elly Sau-Wai Ngan,
- and Kevin Y. Yip
Genome Res. November 2020 30: 1618-1632; Published in Advance September 18, 2020, doi:10.1101/gr.264473.120
...TFs regulate gene expression through both promoters and enhancers.The recurrent TFs form an extensive network by way of physical protein-protein interactions (PPIs), with MYC and SMAD proteins acting as interaction hubs (Fig. 4A). The premigratory NC pool size regulators ZBTB17 and MYC...
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Research: Contrasting patterns of evolution following whole genome versus tandem duplication events in Populus
- Eli Rodgers-Melnick,
- Shrinivasrao P. Mane,
- Palitha Dharmawardhana,
- Gancho T. Slavov,
- Oswald R. Crasta,
- Steven H. Strauss,
- Amy M. Brunner,
- and Stephen P. DiFazio
Genome Res. January 2012 22: 95-105; Published in Advance October 5, 2011, doi:10.1101/gr.125146.111
...compared gene duplicates resulting from a recent whole genome duplication to a set of tandemly duplicated genes in the model forest tree Populus trichocarpa . We used a combination of microarray expression analyses of a diverse set of tissues and functional annotation to assess factors related...
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Research: Positionally biased gene loss after whole genome duplication: Evidence from human, yeast, and plant
- Takashi Makino and
- Aoife McLysaght
Genome Res. December 2012 22: 2427-2435; Published in Advance July 26, 2012, doi:10.1101/gr.131953.111
...paralogon are preferentially retained in cis after WGD. We compare the number of protein–protein interactions (PPIs) between linked singletons within a paralogon (defined as cis -PPIs) with that of PPIs between singletons across paralogon pairs (defined as trans -PPIs). We find that paralogons in which...
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Resource: Automated identification of conserved synteny after whole-genome duplication
- Julian M. Catchen,
- John S. Conery,
- and John H. Postlethwait
Genome Res. August 2009 19: 1497-1505; Published in Advance May 22, 2009, doi:10.1101/gr.090480.108
.... 1999) or their exon structure (Altschmied et al. 2002), or their activities (Zhang et al. 2002; Zhang 2003), and such changes can alter protein–protein interactions or subsequent developmental or physiological functions. 3Corresponding author. E-mail jpostle@uoneuro.uoregon.edu; fax (541) 346...
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LETTER: The extensive and condition-dependent nature of epistasis among whole-genome duplicates in yeast
- Gabriel Musso,
- Michael Costanzo,
- ManQin Huangfu,
- Andrew M. Smith,
- Jadine Paw,
- Bryan-Joseph San Luis,
- Charles Boone,
- Guri Giaever,
- Corey Nislow,
- Andrew Emili,
- and Zhaolei Zhang
Genome Res. July 2008 18: 1092-1099; Published in Advance May 7, 2008, doi:10.1101/gr.076174.108
...a sister gene, how extensive this epistasis is, and how adaptable it is toward alternate environmental states. To this end, we have performed a comprehensive experimental analysis of epistasis as indicated by aggravating genetic interactions between paralogs resulting from an ancient whole-genome...
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Letter: Evolution of gene function and regulatory control after whole-genome duplication: Comparative analyses in vertebrates
- Karin S. Kassahn,
- Vinh T. Dang,
- Simon J. Wilkins,
- Andrew C. Perkins,
- and Mark A. Ragan
Genome Res. August 2009 19: 1404-1418; Published in Advance May 13, 2009, doi:10.1101/gr.086827.108
...1970; Lynch 2002) but also by several rounds of whole duplication (WGD) (Jaillon et al. 2004; Dehal and Boore 2005), which were typically followed by extensive gene loss. These WGD events would thus have had significant effects on gene regulatory control and protein–protein interactions. Nonetheless...
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Method: Gene duplication is associated with gene diversification and potential neofunctionalization in lung cancer evolution
- Paul Ashford,
- Alexander M. Frankell,
- Zofia Piszka,
- Camilla S.M. Pang,
- Mahnaz Abbasian,
- Maise Al Bakir,
- Mariam Jamal-Hanjani,
- Nicholas McGranahan,
- Charles Swanton,
- and Christine A. Orengo
Genome Res. March 2026 36: 561-577; Published in Advance February 19, 2026, doi:10.1101/gr.278663.123
...studies have sought to catalog driver events occurring in hundreds of cancer genes across different tumor types (Martincorena and Campbell 2015; Chung et al. 2016; Tokheim and Karchin 2019; Dietlein et al. 2020; Kumar et al. 2020; The ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium 2020...
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LETTER: Whole-genome Trees Based on the Occurrence of Folds and Orthologs: Implications for Comparing Genomes on Different Levels
- Jimmy Lin and
- Mark Gerstein
Genome Res. June 1, 2000 10: 808-818; doi:10.1101/gr.10.6.808
...Whole-genome Trees Based on the Occurrence of Folds and Orthologs: Implications for Comparing Genomes on Different Levels Jimmy Lin 1 and Mark Gerstein 1 , 2 1Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520 USA...
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Method: A general calculus of fitness landscapes finds genes under selection in cancers
- Teng-Kuei Hsu,
- Jennifer Asmussen,
- Amanda Koire,
- Byung-Kwon Choi,
- Mayur A. Gadhikar,
- Eunna Huh,
- Chih-Hsu Lin,
- Daniel M. Konecki,
- Young Won Kim,
- Curtis R. Pickering,
- Marek Kimmel,
- Lawrence A. Donehower,
- Mitchell J. Frederick,
- Jeffrey N. Myers,
- Panagiotis Katsonis,
- and Olivier Lichtarge
Genome Res. May 2022 32: 916-929; Published in Advance March 17, 2022, doi:10.1101/gr.275811.121
...to known cancer drivers in the STRING protein–protein interaction network (n = 55, P-value = 2 × 10−5) (Supplemental Fig. S6E; Shin et al. 2007; Lisewski et al. 2014; Szklarczyk et al. 2015), and a nonsynonymous-to-synonymous mutation ratio, dN/dS, greater than one and consistent with positive selection (n...
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Research: Global deceleration of gene evolution following recent genome hybridizations in fungi
- Sira Sriswasdi,
- Masako Takashima,
- Ri-ichiroh Manabe,
- Moriya Ohkuma,
- Takashi Sugita,
- and Wataru Iwasaki
Genome Res. August 2016 26: 1081-1090; Published in Advance July 20, 2016, doi:10.1101/gr.205948.116
...with transcription and translation, gene-loss events will be concentrated among interaction partners of single-copy genes, where stoichiometry is disrupted. However, permutation tests on the protein–protein interaction networks involving these complexes revealed that this is not the case (Methods). Also...

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