Searching journal content for articles similar to Draghici et al. 17 (10): 000.

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  1. Resource: A systems view on DNA damage response kinetics in Tetrahymena
    • Emily Nischwitz,
    • Vivien Schoonenberg,
    • Rachel Mullner,
    • Albert Fradera-Sola,
    • Susanne Zimbelmann,
    • Joshua J Smith,
    • and Falk Butter
    Genome Res. January 28, 2026 gr.281000.125; Published in Advance January 28, 2026, doi:10.1101/gr.281000.125
    ...Systems Biology of Signal Transduction, German Cancer 15 Research Center (DKFZ), 69120 Heidelberg, Germany 16 8 These authors contributed equally. Either author can be listed first. 17 * Correspondence: falk.butter@fli.de (FB) 18 19 Abstract 20 A tightly regulated DNA damage response is critical...
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  2. Resource: Interspecies systems biology links bacterial metabolic pathways to nematode gene expression, chemotaxis behavior, and survival
    • Marina Athanasouli,
    • Tobias Loschko,
    • and Christian Rödelsperger
    Genome Res. October 2025 35: 2363-2374; Published in Advance August 5, 2025, doi:10.1101/gr.280848.125
    ..., Germany Corresponding author: christian.roedelsperger@tuebingen.mpg.deAbstractAll animals live in tight association with complex microbial communities, yet studying the effects of individual bacteria remains challenging. Bacterial feeding nematodes are powerful systems to study host-microbe interactions...
  3. 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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  4. Research: Systems genetics of the Drosophila metabolome
    • Shanshan Zhou,
    • Fabio Morgante,
    • Matthew S. Geisz,
    • Junwu Ma,
    • Robert R.H. Anholt,
    • and Trudy F.C. Mackay
    Genome Res. March 2020 30: 392-405; Published in Advance November 6, 2019, doi:10.1101/gr.243030.118
    ...@clemson.eduAbstractHow effects of DNA sequence variants are transmitted through intermediate endophenotypes to modulate organismal traits remains a central question in quantitative genetics. This problem can be addressed through a systems approach in a population in which genetic polymorphisms, gene expression traits...
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  5. 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
    ...: mkirst@ufl.eduAbstractDespite the growing resources and tools for high-throughput characterization and analysis of genomic information, the discovery of the genetic elements that regulate complex traits remains a challenge. Systems genetics is an emerging field that aims to understand the flow...
  6. 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...
  7. 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...
  8. Erratum: Erratum: Ultralow-input single-tube linked-read library method enables short-read second-generation sequencing systems to routinely generate highly accurate and economical long-range sequencing information
    • Zhoutao Chen,
    • Long Pham,
    • Tsai-Chin Wu,
    • Guoya Mo,
    • Yu Xia,
    • Peter L. Chang,
    • Devin Porter,
    • Tan Phan,
    • Huu Che,
    • Hao Tran,
    • Vikas Bansal,
    • Justin Shaffer,
    • Pedro Belda-Ferre,
    • Greg Humphrey,
    • Rob Knight,
    • Pavel Pevzner,
    • Son Pham,
    • Yong Wang,
    • and Ming Lei
    Genome Res. May 2021 31: 934; doi:10.1101/gr.275614.121
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  9. Method: Ultralow-input single-tube linked-read library method enables short-read second-generation sequencing systems to routinely generate highly accurate and economical long-range sequencing information
    • Zhoutao Chen,
    • Long Pham,
    • Tsai-Chin Wu,
    • Guoya Mo,
    • Yu Xia,
    • Peter L. Chang,
    • Devin Porter,
    • Tan Phan,
    • Huu Che,
    • Hao Tran,
    • Vikas Bansal,
    • Justin Shaffer,
    • Pedro Belda-Ferre,
    • Greg Humphrey,
    • Rob Knight,
    • Pavel Pevzner,
    • Son Pham,
    • Yong Wang,
    • and Ming Lei
    Genome Res. June 2020 30: 898-909; Published in Advance June 15, 2020, doi:10.1101/gr.260380.119
    ...and require micrograms of DNA for library construction, which is very challenging to obtain for many real-world samples or applications.One (sequencing) system for all (applications) is the desire of the customer but requires a significant breakthrough of an enabling technology on either second- or third...
  10. 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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