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Research: Complete genomes of Asgard archaea reveal diverse integrated and mobile genetic elements
- Luis E. Valentin-Alvarado,
- Ling-Dong Shi,
- Kathryn E. Appler,
- Alexander Crits-Christoph,
- Valerie De Anda,
- Benjamin A. Adler,
- Michael L. Cui,
- Lynn Ly,
- Pedro Leão,
- Richard J. Roberts,
- Rohan Sachdeva,
- Brett J. Baker,
- David F. Savage,
- and Jillian F. Banfield
Genome Res. October 2024 34: 1595-1609; Published in Advance October 15, 2024, doi:10.1101/gr.279480.124
...in uncultured microorganisms from complex environmental samples.ResultsComplete Atabeyarchaeia s contain integrated genetic mobile elementsShort- and long-read metagenomic data sets were generated from wetland soil sampled at a single local site (for details, see Methods). We mapped reads from 28 samples...
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Method: Systematic identification of interchromosomal interaction networks supports the existence of specialized RNA factories
- Borislav Hrisimirov Hristov,
- William Stafford Noble,
- and Alessandro Bertero
Genome Res. October 2024 34: 1610-1623; Published in Advance September 25, 2024, doi:10.1101/gr.278327.123
...that jointly interact in trans. This method, trans-C, initiates probabilistic random walks with restarts from a set of seed loci to traverse an input Hi-C contact network, thereby identifying sets of trans-contacting loci. We validate trans-C in three increasingly complex models of established trans contacts...
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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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Method: The discovery of integrated gene networks for autism and related disorders
- Fereydoun Hormozdiari,
- Osnat Penn,
- Elhanan Borenstein,
- and Evan E. Eichler
Genome Res. January 2015 25: 142-154; Published in Advance November 5, 2014, doi:10.1101/gr.178855.114
..., Ramani AK, Marcotte EM. 2006. How complete are current yeast and human protein-interaction networks? Genome Biol 7: 120. He X, Sanders SJ, Liu L, De Rubeis S, Lim ET, Sutcliffe JS, Schellenberg GD, Gibbs RA, Daly MJ, Buxbaum JD, et al. 2013. Integrated model of de novo and inherited genetic variants...
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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
...on the drought scenario, the phenological stage, the genetic makeup, and the general environmental conditions (Tardieu et al. 2018). Taken together, the multiplicity and versatility of the mechanisms involved explain the difficulty in selecting for drought tolerance.A better understanding of the genotype...
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Resource: Organ-level protein networks as a reference for the host effects of the microbiome
- Robert H. Mills,
- Jacob M. Wozniak,
- Alison Vrbanac,
- Anaamika Campeau,
- Benoit Chassaing,
- Andrew Gewirtz,
- Rob Knight,
- and David J. Gonzalez
Genome Res. February 2020 30: 276-286; Published in Advance January 28, 2020, doi:10.1101/gr.256875.119
..., spleens, hearts, small intestines, and colons of conventionally raised and GF mice, identifying associations to colonization state in over 7000 proteins. Highly ranked associations were constructed into protein–protein interaction networks and visualized onto an interactive 3D mouse model for user...
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Research: Replication timing networks reveal a link between transcription regulatory circuits and replication timing control
- Juan Carlos Rivera-Mulia,
- Sebo Kim,
- Haitham Gabr,
- Abhijit Chakraborty,
- Ferhat Ay,
- Tamer Kahveci,
- and David M. Gilbert
Genome Res. September 2019 29: 1415-1428; Published in Advance August 21, 2019, doi:10.1101/gr.247049.118
...values ranging from −0.9 to +0.9 (red and orange lines in Fig. 1C). Here, we used gene pairs in trans (from distinct chromosomes) as well as gene pairs in cis but separated by >500 kb (classified as colocated distant) to construct distinct models of RT networks (Fig. 1C). Figure 1, D and E, illustrates...
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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
...in expression that can explain the lack of simple patterns of pairwise redundancy. We propose a model in which gene families evolve to attain differential alliances in different tissues and in response to a range of environmental stresses. Footnotes ↵ 9 Corresponding authors E-mail heidi...
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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 signaling pathways that activate these networks. In addition to the general interaction data, SDREM uses condition-specific time-series data and a small set of proteins that are known to sense the environmental stress, interact with the infecting agent, or play some other role in initiating the response...
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Method: Identification of microRNA-regulated gene networks by expression analysis of target genes
- Vincenzo Alessandro Gennarino,
- Giovanni D'Angelo,
- Gopuraja Dharmalingam,
- Serena Fernandez,
- Giorgio Russolillo,
- Remo Sanges,
- Margherita Mutarelli,
- Vincenzo Belcastro,
- Andrea Ballabio,
- Pasquale Verde,
- Marco Sardiello,
- and Sandro Banfi
Genome Res. June 2012 22: 1163-1172; Published in Advance February 15, 2012, doi:10.1101/gr.130435.111
.... The network of miRNAs was displayed using Cytoscape (Shannon et al. 2003). In the graphical representation, only the interactions among miRNAs from the same community were kept. Gene Ontology (GO) analysis GO analysis was performed using the ‘‘database for annotation, visualization, and integrated discover...

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