Searching journal content for articles similar to Snel and Huynen 14 (3): 391.

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  1. 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
    ...immune system and are associated with increased mutagenesis later in tumor evolution in many cancer types, including the lung (Roberts et al. 2013; Jamal-Hanjani et al. 2017).Increases in mutagenesis and mutational ITH allow a greater scope for novel drivers, which will be under dynamic selective...
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  2. Research: Xylem systems genetics analysis reveals a key regulator of lignin biosynthesis in Populus deltoides
    • Kelly M. Balmant,
    • Jerald D. Noble,
    • Filipe C. Alves,
    • Christopher Dervinis,
    • Daniel Conde,
    • Henry W. Schmidt,
    • Ana I. Vazquez,
    • William B. Barbazuk,
    • Gustavo de los Campos,
    • Marcio F.R. Resende, Jr.,
    • and Matias Kirst
    Genome Res. August 2020 30: 1131-1143; Published in Advance August 19, 2020, doi:10.1101/gr.261438.120
    ...1 µg of total RNA using poly(T) oligo–attached magnetic beads. The mRNA was further fragmented, reverse transcribed, and amplified for 12 cycles using dual indexes primers. The PCR products were purified with an AMPure XP system (Beckman Coulter). The libraries were quantified using a Qubit 2...
  3. Research: Cis-acting variation is common across regulatory layers but is often buffered during embryonic development
    • Swann Floc'hlay,
    • Emily S. Wong,
    • Bingqing Zhao,
    • Rebecca R. Viales,
    • Morgane Thomas-Chollier,
    • Denis Thieffry,
    • David A. Garfield,
    • and Eileen E.M. Furlong
    Genome Res. February 2021 31: 211-224; Published in Advance December 11, 2020, doi:10.1101/gr.266338.120
    ...Molecular, Structural and Computational Biology Division, Victor Chang Cardiac Research Institute, Darlinghurst, New South Wales 2010, Australia; 3School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Kensington, New South Wales 2052, Australia; 4European Molecular Biology Laboratory (EMBL...
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  4. LETTER: Novel specificities emerge by stepwise duplication of functional modules
    • José B. Pereira-Leal and
    • Sarah A. Teichmann
    Genome Res. April 2005 15: 552-559; doi:10.1101/gr.3102105
    ...-Lewis, S., and Seraphin, B. 1999 . Sm and Sm-like proteins assemble in two related complexes of deep evolutionary origin. EMBO J. 18 : 3451 -3462. ↵ Snel, B. and Huynen, M.A. 2004 . Quantifying modularity in the evolution of biomolecular systems. Genome Res. 14 : 391 -397. ↵ Takatsu, H., Futatsumori, M...
  5. Resource: Multiparameter functional diversity of human C2H2 zinc finger proteins
    • Frank W. Schmitges,
    • Ernest Radovani,
    • Hamed S. Najafabadi,
    • Marjan Barazandeh,
    • Laura F. Campitelli,
    • Yimeng Yin,
    • Arttu Jolma,
    • Guoqing Zhong,
    • Hongbo Guo,
    • Tharsan Kanagalingam,
    • Wei F. Dai,
    • Jussi Taipale,
    • Andrew Emili,
    • Jack F. Greenblatt,
    • and Timothy R. Hughes
    Genome Res. December 2016 26: 1742-1752; Published in Advance November 16, 2016, doi:10.1101/gr.209643.116
    ...Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada; 2Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada; 3Department of Biosciences and Nutrition, Karolinska Institutet, SE 141 83, Sweden...
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  6. LETTER: A systematic analysis of intronic sequences downstream of 5′ splice sites reveals a widespread role for U-rich motifs and TIA1/TIAL1 proteins in alternative splicing regulation
    • Isabel Aznarez,
    • Yoseph Barash,
    • Ofer Shai,
    • David He,
    • Julian Zielenski,
    • Lap-Chee Tsui,
    • John Parkinson,
    • Brendan J. Frey,
    • Johanna M. Rommens,
    • and Benjamin J. Blencowe
    Genome Res. August 2008 18: 1247-1258; Published in Advance May 2, 2008, doi:10.1101/gr.073155.107
    ...Department of Medical Research, Centre for Cellular and Biomolecular Research, Toronto, Ontario M5S 3E1, Canada ↵ 8 These authors contributed equally to this work. Abstract To identify human intronic sequences associated with 5′ splice site recognition, we performed a systematic...
  7. 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
    ...and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada; 2 Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada; 3 Department of Pharmaceutical Sciences, University of Toronto, Toronto, Ontario M5S 3M2, Canada Abstract...
  8. Research: Complex expression dynamics and robustness in C. elegans insulin networks
    • Ashlyn D. Ritter,
    • Yuan Shen,
    • Juan Fuxman Bass,
    • Sankarganesh Jeyaraj,
    • Bart Deplancke,
    • Arnab Mukhopadhyay,
    • Jian Xu,
    • Monica Driscoll,
    • Heidi A. Tissenbaum,
    • and Albertha J.M. Walhout
    Genome Res. June 2013 23: 954-965; Published in Advance March 28, 2013, doi:10.1101/gr.150466.112
    ...Mukhopadhyay 2 , 3 , 8 , Jian Xu 4 , Monica Driscoll 4 , Heidi A. Tissenbaum 2 , 3 , 9 and Albertha J.M. Walhout 1 , 3 , 9 1 Program in Systems Biology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA...
  9. Method: Identification of phenotype-specific networks from paired gene expression–cell shape imaging data
    • Charlie George Barker,
    • Eirini Petsalaki,
    • Girolamo Giudice,
    • Julia Sero,
    • Emmanuel Nsa Ekpenyong,
    • Chris Bakal,
    • and Evangelia Petsalaki
    Genome Res. April 2022 32: 750-765; Published in Advance February 23, 2022, doi:10.1101/gr.276059.121
    .... However, the exact regulatory systems that define these changes remain poorly characterized. In this study, we used a network-systems approach to integrate imaging data and RNA-seq expression data. Our workflow allowed the discovery of unbiased and context-specific gene expression signatures and cell...
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  10. Method: Fast and flexible bacterial genomic epidemiology with PopPUNK
    • John A. Lees,
    • Simon R. Harris,
    • Gerry Tonkin-Hill,
    • Rebecca A. Gladstone,
    • Stephanie W. Lo,
    • Jeffrey N. Weiser,
    • Jukka Corander,
    • Stephen D. Bentley,
    • and Nicholas J. Croucher
    Genome Res. February 2019 29: 304-316; Published in Advance January 24, 2019, doi:10.1101/gr.241455.118
    ...to quantify clustering similarity between all those permutations in which the final population to be integrated was the same; only those isolates in the most recent extension of the network were used. These values are shown separated according to the starting reference population (Massachusetts or Maela...
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