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LETTER: Reconciling Gene Expression Data With Known Genome-Scale Regulatory Network Structures
- Markus J. Herrgård,
- Markus W. Covert,
- and Bernhard ø. Palsson
Genome Res. November 2003 13: 2423-2434; Published in Advance January 1, 2003, doi:10.1101/gr.1330003
.... The results suggest that targeted gene expression profiling data can be used to refine and expand particular subcomponents of known regulatory networks that are sufficiently decoupled from the rest of the network. Footnotes [Supplemental material is available online at www...
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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
...that even mild water deficit induced a profound remodeling of the proteome, which affected the structure of the protein coexpression network, and a reprogramming of the genetic control of the abundance of many proteins, including those involved in stress response. Colocalizations between pQTLs and QTLs...
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Method: Linking the signaling cascades and dynamic regulatory networks controlling stress responses
- Anthony Gitter,
- Miri Carmi,
- Naama Barkai,
- and Ziv Bar-Joseph
Genome Res. February 2013 23: 365-376; Published in Advance October 11, 2012, doi:10.1101/gr.138628.112
..., and the affected genes. The signaling and regulatory components of our networks are linked via a set of common transcription factors that serve as targets in the signaling network and as regulators of the transcriptional response network. Detailed case studies of stress responses in budding yeast demonstrate...
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Method: Model-driven mapping of transcriptional networks reveals the circuitry and dynamics of virulence regulation
- Ezekiel J. Maier,
- Brian C. Haynes,
- Stacey R. Gish,
- Zhuo A. Wang,
- Michael L. Skowyra,
- Alyssa L. Marulli,
- Tamara L. Doering,
- and Michael R. Brent
Genome Res. May 2015 25: 690-700; Published in Advance February 2, 2015, doi:10.1101/gr.184101.114
...of each TF is based on the degree to which its NetProphet-predicted targets are enriched for genes associated with the phenotype of interest. We demonstrate the power of combining NetProphet and PhenoProphet by mapping the network that regulates the major virulence factor of a pathogenic yeast...
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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
...retention of WGD pairs while disfavoring the fixation of TD. Indeed, empirical data in yeast and Arabidopsis demonstrate that genes involved in signal transduction and transcription are more likely to be retained following a WGD but less likely to be retained in tandem (Seoighe and Gehring 2004; Davis...
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Research: Microsporidian genome analysis reveals evolutionary strategies for obligate intracellular growth
- Christina A. Cuomo,
- Christopher A. Desjardins,
- Malina A. Bakowski,
- Jonathan Goldberg,
- Amy T. Ma,
- James J. Becnel,
- Elizabeth S. Didier,
- Lin Fan,
- David I. Heiman,
- Joshua Z. Levin,
- Sarah Young,
- Qiandong Zeng,
- and Emily R. Troemel
Genome Res. December 2012 22: 2478-2488; Published in Advance July 18, 2012, doi:10.1101/gr.142802.112
...deep sequencing of transcripts from a time course of N. parisii infection. Examination of pathogen gene expression revealed compact transcripts and a dramatic takeover of host cells by Nematocida . We also performed phylogenomic analyses of Nematocida and other microsporidian genomes to refine...
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Letter: Comparative genomics of the fungal pathogens Candida dubliniensis and Candida albicans
- Andrew P. Jackson,
- John A. Gamble,
- Tim Yeomans,
- Gary P. Moran,
- David Saunders,
- David Harris,
- Martin Aslett,
- Jamie F. Barrell,
- Geraldine Butler,
- Francesco Citiulo,
- David C. Coleman,
- Piet W.J. de Groot,
- Tim J. Goodwin,
- Michael A. Quail,
- Jacqueline McQuillan,
- Carol A. Munro,
- Arnab Pain,
- Russell T. Poulter,
- Marie-Adèle Rajandream,
- Hubert Renauld,
- Martin J. Spiering,
- Adrian Tivey,
- Neil A.R. Gow,
- Barclay Barrell,
- Derek J. Sullivan,
- and Matthew Berriman
Genome Res. December 2009 19: 2231-2244; Published in Advance September 10, 2009, doi:10.1101/gr.097501.109
...yeast species in humans. However, despite both species sharing many phenotypic characteristics, including the ability to form true hyphae, C. dubliniensis is a significantly less virulent and less versatile pathogen. Therefore, to identify C. albicans -specific genes that may be responsible...
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ARTICLE: Coping with cold: The genome of the versatile marine Antarctica bacterium Pseudoalteromonas haloplanktis TAC125
- Claudine Médigue,
- Evelyne Krin,
- Géraldine Pascal,
- Valérie Barbe,
- Andreas Bernsel,
- Philippe N. Bertin,
- Frankie Cheung,
- Stéphane Cruveiller,
- Salvino D'Amico,
- Angela Duilio,
- Gang Fang,
- Georges Feller,
- Christine Ho,
- Sophie Mangenot,
- Gennaro Marino,
- Johan Nilsson,
- Ermenegilda Parrilli,
- Eduardo P.C. Rocha,
- Zoé Rouy,
- Agnieszka Sekowska,
- Maria Luisa Tutino,
- David Vallenet,
- Gunnar von Heijne,
- and Antoine Danchin
Genome Res. October 2005 15: 1325-1335; Published in Advance September 16, 2005, doi:10.1101/gr.4126905
...not possess at the moment a reference set of annotations for the of bacteria thriving in such conditions. The present sequence was therefore carefully annotated manually, and annotation will be, as much as possible, continuously refined. We endeavored to post to the community reference databases, allowing...

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