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Research: A systems level predictive model for global gene regulation of methanogenesis in a hydrogenotrophic methanogen
- Sung Ho Yoon,
- Serdar Turkarslan,
- David J. Reiss,
- Min Pan,
- June A. Burn,
- Kyle C. Costa,
- Thomas J. Lie,
- Joseph Slagel,
- Robert L. Moritz,
- Murray Hackett,
- John A. Leigh,
- and Nitin S. Baliga
Genome Res. November 2013 23: 1839-1851; Published in Advance October 2, 2013, doi:10.1101/gr.153916.112
...-producing step (called methanogenesis) in the anaerobic decomposition of organic matter. Here, we present the first predictive model of global gene regulation of methanogenesis in a hydrogenotrophic methanogen, Methanococcus maripaludis. We generated a comprehensive list of genes (protein-coding and noncoding...
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ARTICLE: A systems view of haloarchaeal strategies to withstand stress from transition metals
- Amardeep Kaur,
- Min Pan,
- Megan Meislin,
- Marc T. Facciotti,
- Raafat El-Gewely,
- and Nitin S. Baliga
Genome Res. July 2006 16: 841-854; Published in Advance June 2, 2006, doi:10.1101/gr.5189606
...on experimentally verified regulatory mechanisms. Finally, through comparisons across global transcriptional responses to different metals, we provide insights into putative in vivo metal selectivity of metalloregulatory proteins and demonstrate that a systems approach can help rapidly unravel novel metabolic...
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Methods: Identification of genomic features using microsyntenies of domains: Domain teams
- Sophie Pasek,
- Anne Bergeron,
- Jean-Loup Risler,
- Alexandra Louis,
- Emmanuelle Ollivier,
- and Mathieu Raffinot
Genome Res. June 2005 15: 867-874; Published in Advance May 17, 2005, doi:10.1101/gr.3638405
...Abstract The detection, across several genomes, of local conservation of gene content and proximity considerably helps the prediction of features of interest, such as gene fusions or physical and functional interactions. Here, we want to process realistic models of chromosomes, in which genes (or genomic...
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Method: Characterization of network hierarchy reflects cell state specificity in genome organization
- Jingyao Wang,
- Yue Xue,
- Yueying He,
- Hui Quan,
- Jun Zhang,
- and Yi Qin Gao
Genome Res. February 2023 33: 247-260; Published in Advance February 24, 2023, doi:10.1101/gr.277206.122
...). A large and diverse set of gene regulatory elements in chromatin are found to regulate transcription through long-range interactions. For example, promoter–enhancer interactions regulate the dynamic activation of genes (Cloney 2016), whereas insulators and repressors play the opposite roles (Yang...
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Research: Intergenic ORFs as elementary structural modules of de novo gene birth and protein evolution
- Chris Papadopoulos,
- Isabelle Callebaut,
- Jean-Christophe Gelly,
- Isabelle Hatin,
- Olivier Namy,
- Maxime Renard,
- Olivier Lespinet,
- and Anne Lopes
Genome Res. December 2021 31: 2303-2315; Published in Advance November 22, 2021, doi:10.1101/gr.275638.121
...on its diffusion in the cytosol, where positively charged proteins get caught in nonspecific interactions with the abundant negatively charged ribosomes (Schavemaker et al. 2017). We show that the frequency of negatively charged residues of the yeast cytoplasmic proteins is strongly correlated...
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Method: A Bayesian inference transcription factor activity model for the analysis of single-cell transcriptomes
- Shang Gao,
- Yang Dai,
- and Jalees Rehman
Genome Res. July 2021 31: 1296-1311; Published in Advance June 30, 2021, doi:10.1101/gr.265595.120
...; Duren et al. 2018; Lopez et al. 2018; Wang and Gu 2018; Wu et al. 2018; Jung et al. 2019; Linderman et al. 2019; Moon et al. 2019). However, the identification of cell clusters based on the proximity of individual cells in lower dimensional space does not take into account the biological context...
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Perspective: Applications of single-cell genomics and computational strategies to study common disease and population-level variation
- Benjamin J. Auerbach,
- Jian Hu,
- Muredach P. Reilly,
- and Mingyao Li
Genome Res. October 2021 31: 1728-1741; doi:10.1101/gr.275430.121
...of many variables, such as chromatin conformation, DNA methylation, histone modifications, etc., to take on unique cell states. These cell states, such as those associated with our common notions of cell types, enable cells to perform specific functions. Through the interaction of cells within local...
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Research: MicroRNA, mRNA, and protein expression link development and aging in human and macaque brain
- Mehmet Somel,
- Song Guo,
- Ning Fu,
- Zheng Yan,
- Hai Yang Hu,
- Ying Xu,
- Yuan Yuan,
- Zhibin Ning,
- Yuhui Hu,
- Corinna Menzel,
- Hao Hu,
- Michael Lachmann,
- Rong Zeng,
- Wei Chen,
- and Philipp Khaitovich
Genome Res. September 2010 20: 1207-1218; Published in Advance July 20, 2010, doi:10.1101/gr.106849.110
...was performed by singular value decomposition, using the ‘‘prcomp’’ function in the R ‘‘stats’’ package, with each gene scaled to unit variance before analysis. The numbers represent each individual’s age in years. The proportion of variance explained by each principal component is shown in parentheses. For m...
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Letter: Complete genome of the cellulolytic thermophile Acidothermus cellulolyticus 11B provides insights into its ecophysiological and evolutionary adaptations
- Ravi D. Barabote,
- Gary Xie,
- David H. Leu,
- Philippe Normand,
- Anamaria Necsulea,
- Vincent Daubin,
- Claudine Médigue,
- William S. Adney,
- Xin Clare Xu,
- Alla Lapidus,
- Rebecca E. Parales,
- Chris Detter,
- Petar Pujic,
- David Bruce,
- Celine Lavire,
- Jean F. Challacombe,
- Thomas S. Brettin,
- and Alison M. Berry
Genome Res. June 2009 19: 1033-1043; Published in Advance March 6, 2009, doi:10.1101/gr.084848.108
...of three laterally acquired genomic islands of likely ecophysiological value. Efforts are under way worldwide to develop renewable energy sources as alternatives to fossil fuels. Microorganisms capable of breaking down lignocellulosic plant matter, a bioenergy source, are of enormous interest in the global...

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