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- Publications
- Influence
Cytoscape: a software environment for integrated models of biomolecular interaction networks.
- P. Shannon, Andrew Markiel, +6 authors T. Ideker
- Medicine, Biology
- Genome research
- 1 November 2003
Cytoscape is an open source software project for integrating biomolecular interaction networks with high-throughput expression data and other molecular states into a unified conceptual framework.… Expand
Genome sequence of Halobacterium species NRC-1.
- W. Ng, S. Kennedy, +40 authors S. Dassarma
- Biology, Medicine
- Proceedings of the National Academy of Sciences…
- 24 October 2000
We report the complete sequence of an extreme halophile, Halobacterium sp. NRC-1, harboring a dynamic 2,571,010-bp genome containing 91 insertion sequences representing 12 families and organized into… Expand
The Inferelator: an algorithm for learning parsimonious regulatory networks from systems-biology data sets de novo
- R. Bonneau, D. Reiss, +4 authors V. Thorsson
- Biology, Medicine
- Genome Biology
- 10 May 2006
We present a method (the Inferelator) for deriving genome-wide transcriptional regulatory interactions, and apply the method to predict a large portion of the regulatory network of the archaeon… Expand
Peroxiredoxins are conserved markers of circadian rhythms
- R. Edgar, E. Green, +16 authors A. B. Reddy
- Biology, Medicine
- Nature
- 16 May 2012
Cellular life emerged ∼3.7 billion years ago. With scant exception, terrestrial organisms have evolved under predictable daily cycles owing to the Earth’s rotation. The advantage conferred on… Expand
CTCF physically links cohesin to chromatin
- E. Rubio, D. Reiss, +6 authors A. Krumm
- Biology, Medicine
- Proceedings of the National Academy of Sciences
- 17 June 2008
Cohesin is required to prevent premature dissociation of sister chromatids after DNA replication. Although its role in chromatid cohesion is well established, the functional significance of cohesin's… Expand
Genome sequence of Haloarcula marismortui: a halophilic archaeon from the Dead Sea.
- N. Baliga, R. Bonneau, +12 authors W. Ng
- Biology, Medicine
- Genome research
- 1 November 2004
We report the complete sequence of the 4,274,642-bp genome of Haloarcula marismortui, a halophilic archaeal isolate from the Dead Sea. The genome is organized into nine circular replicons of varying… Expand
Catabolite control protein A (CcpA) contributes to virulence and regulation of sugar metabolism in Streptococcus pneumoniae.
- R. Iyer, N. Baliga, A. Camilli
- Biology, Medicine
- Journal of bacteriology
- 15 December 2005
We characterized the role of catabolite control protein A (ccpA) in the physiology and virulence of Streptococcus pneumoniae. S. pneumoniae has a large percentage of its genome devoted to sugar… Expand
The DNA-binding network of Mycobacterium tuberculosis
- Kyle J. Minch, T. Rustad, +12 authors D. Sherman
- Biology, Medicine
- Nature communications
- 12 January 2015
Mycobacterium tuberculosis (MTB) infects 30% of all humans and kills someone every 20–30 s. Here we report genome-wide binding for ~80% of all predicted MTB transcription factors (TFs), and assayed… Expand
A systems view of haloarchaeal strategies to withstand stress from transition metals.
- Amardeep Kaur, M. Pan, M. Meislin, M. Facciotti, Raafat El-Gewely, N. Baliga
- Biology, Medicine
- Genome research
- 1 July 2006
Given that transition metals are essential cofactors in central biological processes, misallocation of the wrong metal ion to a metalloprotein can have resounding and often detrimental effects on… Expand