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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
...aberrations in cell-cycle control. In non-small-cell lung cancer (NSCLC), instability occurs early in tumor growth, resulting in pronounced intratumor heterogeneity, including changes in gene copy number, and whole- doubling (WGD) in ∼75% of tumors. Gene duplication, genetic drift, and selection mediate...
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Letter: Pervasive, genome-wide positive selection leading to functional divergence in the bacterial genus Campylobacter
- Tristan Lefébure and
- Michael J. Stanhope
Genome Res. July 2009 19: 1224-1232; Published in Advance March 20, 2009, doi:10.1101/gr.089250.108
...Pervasive, genome-wide positive selection leading to functional divergence in the bacterial genus Campylobacter Tristan Lefébure and Michael J. Stanhope , 1 Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell...
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Method: Integration of high-throughput proteomic data and complementary omics layers with PriOmics
- Robin Kosch,
- Katharina Limm,
- Annette M. Staiger,
- Nadine S. Kurz,
- Nicole Seifert,
- Bence Oláh,
- Stefan Solbrig,
- Viola Poeschel,
- Gerhard Held,
- Marita Ziepert,
- Norbert Schmitz,
- Emil Chteinberg,
- Reiner Siebert,
- Rainer Spang,
- Helena U. Zacharias,
- German Ott,
- Peter J. Oefner,
- and Michael Altenbuchinger
Genome Res. January 2026 36: 197-213; Published in Advance November 18, 2025, doi:10.1101/gr.279487.124
...variablesWe evaluated PriOmics and the competing methods for a fixed number of 75 (i.e., 150) duplicated continuous, 50 nonduplicated continuous, and 30 discrete variables for different sample sizes n (n ∈ {100, 175, 250, 375, 500, 750, 1000, 1500, 2000}), in which the subsets were always drawn from...
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Research: High sensitivity to aligner and high rate of false positives in the estimates of positive selection in the 12 Drosophila genomes
- Penka Markova-Raina and
- Dmitri Petrov
Genome Res. June 2011 21: 863-874; Published in Advance March 10, 2011, doi:10.1101/gr.115949.110
...High sensitivity to aligner and high rate of false positives in the estimates of positive selection in the 12 Drosophila genomes Penka Markova-Raina 1 and Dmitri Petrov Department of Biology, Stanford University, Stanford, California 94305, USA...
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Resource: Comprehensive, integrated, and phased whole-genome analysis of the primary ENCODE cell line K562
- Bo Zhou,
- Steve S. Ho,
- Stephanie U. Greer,
- Xiaowei Zhu,
- John M. Bell,
- Joseph G. Arthur,
- Noah Spies,
- Xianglong Zhang,
- Seunggyu Byeon,
- Reenal Pattni,
- Noa Ben-Efraim,
- Michael S. Haney,
- Rajini R. Haraksingh,
- Giltae Song,
- Hanlee P. Ji,
- Dimitri Perrin,
- Wing H. Wong,
- Alexej Abyzov,
- and Alexander E. Urban
Genome Res. March 2019 29: 472-484; Published in Advance February 8, 2019, doi:10.1101/gr.234948.118
...(blue), and a 163-kb tandem duplication (green). This rearrangement resides on the nonduplicated haplotype of this triploid region. ORC6 is located entirely within the 63-kb inversion on 16q11.2 and is “deleted” by the left breakpoint of the 125-kb inversion, which also inverts MYLK3. C16orf8...
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Letter: Adaptive evolution of young gene duplicates in mammals
- Mira V. Han,
- Jeffery P. Demuth,
- Casey L. McGrath,
- Claudio Casola,
- and Matthew W. Hahn
Genome Res. May 2009 19: 859-867; doi:10.1101/gr.085951.108
...be responsible for many differences in phenotypes between species. However, recent work searching for the targets of positive selection in humans has largely ignored duplicated genes due to complications in orthology assignment. Here we find that a high proportion of young gene duplicates in the human, macaque...
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Method: Ultraconserved elements are novel phylogenomic markers that resolve placental mammal phylogeny when combined with species-tree analysis
- John E. McCormack,
- Brant C. Faircloth,
- Nicholas G. Crawford,
- Patricia Adair Gowaty,
- Robb T. Brumfield,
- and Travis C. Glenn
Genome Res. April 2012 22: 746-754; Published in Advance December 29, 2011, doi:10.1101/gr.125864.111
....e., probes overlapped by 60 bp). If UCEs were <180 bp in total length,we selected a single probe from the center of theUCE. We conducted a BLAST search of in silico probes against themselves to identify and remove duplicates arising as a result of probe design, andwe selected a reduced set of 2560...

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