Searching journal content for articles similar to Ehrenberg et al. 13 (11): 2377.

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  1. Research: Timescale and genetic linkage explain the variable impact of defense systems on horizontal gene transfer
    • Yang Liu,
    • João Botelho,
    • and Jaime Iranzo
    Genome Res. February 2025 35: 268-278; Published in Advance January 10, 2025, doi:10.1101/gr.279300.124
    ..., Spain; 3Institute for Biocomputation and Physics of Complex Systems (BIFI), University of Zaragoza, 50018, Zaragoza, Spain Corresponding author: jaime.iranzo@cab.inta-csic.esAbstractProkaryotes have evolved a wide repertoire of defense systems to prevent invasion by mobile genetic elements (MGEs...
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  2. Research: A systems genetics approach reveals environment-dependent associations between SNPs, protein coexpression, and drought-related traits in maize
    • Mélisande Blein-Nicolas,
    • Sandra Sylvia Negro,
    • Thierry Balliau,
    • Claude Welcker,
    • Llorenç Cabrera-Bosquet,
    • Stéphane Dimitri Nicolas,
    • Alain Charcosset,
    • and Michel Zivy
    Genome Res. November 2020 30: 1593-1604; Published in Advance October 15, 2020, doi:10.1101/gr.255224.119
    ...makes the design of new drought-tolerant varieties a difficult task that would greatly benefit from a better understanding of the genotype–phenotype relationship. To provide novel insight into this relationship, we applied a systems genetics approach integrating high-throughput phenotypic, proteomic...
  3. Research: Systems analysis reveals complex biological processes during virus infection fate decisions
    • Jordi Argilaguet,
    • Mireia Pedragosa,
    • Anna Esteve-Codina,
    • Graciela Riera,
    • Enric Vidal,
    • Cristina Peligero-Cruz,
    • Valentina Casella,
    • David Andreu,
    • Tsuneyasu Kaisho,
    • Gennady Bocharov,
    • Burkhard Ludewig,
    • Simon Heath,
    • and Andreas Meyerhans
    Genome Res. June 2019 29: 907-919; Published in Advance May 28, 2019, doi:10.1101/gr.241372.118
    ...equally to this work. ↵13 Present address: Department of Immunology, Weizmann Institute of Science, Rehovot, 76100, Israel Corresponding author: andreas.meyerhans@upf.eduAbstractThe processes and mechanisms of virus infection fate decisions that are the result of a dynamic virus-immune system interaction...
  4. Research: Chimeras taking shape: Potential functions of proteins encoded by chimeric RNA transcripts
    • Milana Frenkel-Morgenstern,
    • Vincent Lacroix,
    • Iakes Ezkurdia,
    • Yishai Levin,
    • Alexandra Gabashvili,
    • Jaime Prilusky,
    • Angela del Pozo,
    • Michael Tress,
    • Rory Johnson,
    • Roderic Guigo,
    • and Alfonso Valencia
    Genome Res. July 2012 22: 1231-1242; Published in Advance May 15, 2012, doi:10.1101/gr.130062.111
    ...Chimeras taking shape: Potential functions of proteins encoded by chimeric RNA transcripts Milana Frenkel-Morgenstern 1 , Vincent Lacroix 2 , Iakes Ezkurdia 1 , Yishai Levin 3 , Alexandra Gabashvili 3 , Jaime Prilusky 4...
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  5. Research: Systems consequences of amplicon formation in human breast cancer
    • Koichiro Inaki,
    • Francesca Menghi,
    • Xing Yi Woo,
    • Joel P. Wagner,
    • Pierre-Étienne Jacques,
    • Yi Fang Lee,
    • Phung Trang Shreckengast,
    • Wendy WeiJia Soon,
    • Ankit Malhotra,
    • Audrey S.M. Teo,
    • Axel M. Hillmer,
    • Alexis Jiaying Khng,
    • Xiaoan Ruan,
    • Swee Hoe Ong,
    • Denis Bertrand,
    • Niranjan Nagarajan,
    • R. Krishna Murthy Karuturi,
    • Alfredo Hidalgo Miranda,
    • and Edison T. Liu
    Genome Res. October 2014 24: 1559-1571; Published in Advance September 3, 2014, doi:10.1101/gr.164871.113
    ...Systems consequences of amplicon formation in human breast cancer Koichiro Inaki 1 , 2 , 9 , Francesca Menghi 1 , 2 , 9 , Xing Yi Woo 1 , 9 , Joel P. Wagner 1 , 2 , 3 , Pierre-Étienne Jacques 4 , 5...
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  6. Perspective: Half dozen of one, six billion of the other: What can small- and large-scale molecular systems biology learn from one another?
    • Ian A. Mellis and
    • Arjun Raj
    Genome Res. October 2015 25: 1466-1472; doi:10.1101/gr.190579.115
    ...’s evolved circuits. Take, for example, the standard formula for a small-scale systems biology paper: Start with an interesting phenomenon and make some quantitative measurements. Develop a mechanistic model, often mathematical, to explain the data. Mine this model for a prediction. Make a perturbation...
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  7. Research: A systems-level approach to parental genomic imprinting: the imprinted gene network includes extracellular matrix genes and regulates cell cycle exit and differentiation
    • Hala Al Adhami,
    • Brendan Evano,
    • Anne Le Digarcher,
    • Charlotte Gueydan,
    • Emeric Dubois,
    • Hugues Parrinello,
    • Christelle Dantec,
    • Tristan Bouschet,
    • Annie Varrault,
    • and Laurent Journot
    Genome Res. March 2015 25: 353-367; Published in Advance January 22, 2015, doi:10.1101/gr.175919.114
    ...A systems-level approach to parental genomic imprinting: the imprinted gene network includes extracellular matrix genes and regulates cell cycle exit and differentiation Hala Al Adhami 1 , 2 , 3 , 4 , 6 , Brendan Evano 1 , 2 , 3 , 4 , 7...
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  8. Research: Emergence of male-biased genes on the chicken Z-chromosome: Sex-chromosome contrasts between male and female heterogametic systems
    • Hans Ellegren
    Genome Res. December 2011 21: 2082-2086; Published in Advance August 25, 2011, doi:10.1101/gr.119065.110
    ...Emergence of male-biased genes on the chicken Z-chromosome: Sex-chromosome contrasts between male and female heterogametic systems Hans Ellegren 1 Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala...
  9. Methods: Quality scores and SNP detection in sequencing-by-synthesis systems
    • William Brockman,
    • Pablo Alvarez,
    • Sarah Young,
    • Manuel Garber,
    • Georgia Giannoukos,
    • William L. Lee,
    • Carsten Russ,
    • Eric S. Lander,
    • Chad Nusbaum,
    • and David B. Jaffe
    Genome Res. May 2008 18: 763-770; Published in Advance January 22, 2008, doi:10.1101/gr.070227.107
    ...Quality scores and SNP detection in sequencing-by-synthesis systems William Brockman 1 , 3 , 4 , Pablo Alvarez 1 , 3 , 5 , Sarah Young 1 , Manuel Garber 1 , Georgia Giannoukos 1 , William L. Lee 1 , Carsten Russ 1...
  10. Methods: A systems biology approach for pathway level analysis
    • Sorin Draghici,
    • Purvesh Khatri,
    • Adi Laurentiu Tarca,
    • Kashyap Amin,
    • Arina Done,
    • Calin Voichita,
    • Constantin Georgescu,
    • and Roberto Romero
    Genome Res. October 2007 17: 1537-1545; Published in Advance September 4, 2007, doi:10.1101/gr.6202607
    ...in a given experiment. Here, we show that the existing pathway analysis methods fail to take into consideration important biological aspects and may provide incorrect results in certain situations. By using a systems biology approach, we developed an impact analysis that includes the classical statistics...
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