EGRIN (Environment and Gene Regulatory Influence Network). We have developed an approach for data-driven inference of a systems-scale predictive GRN model for any organism that can be cultured in the laboratory. The computational framework is comprised of two algorithms: cMonkey […]


cMonkey2 – Python port of the cMonkey biclustering algorithm Description This is the Python implementation of the cMonkey algorithm based on the original R implementation by David J. Reiss, Institute for Systems Biology. Documentation A complete set of documentation for installation and […]


You have reached the updated cMonkey site with a new R package, installation and running instructions, and additional information. If you are looking for the original cMonkey site, you can find it here. The original cMonkey algorithm was published with the manuscript “Integrated biclustering of heterogeneous genome-wide datasets for the inference […]

Halobacterium species NRC-1 Genome

Search SBEAMS Database Select attributes All AttributesGene SymbolORF NameFull Gene NameEC Number Enter Keywords Action Search   Show all domain search results in SBEAMS for Halobacterium sp. NRC-1 (new window)   Explore data with the Halobacterium Gaggle (new window)   […]

Systems Education Experiences

The Systems Education Experiences (SEE) program provides an integrative approach to help all participants internalize systems biology methods and thinking.Our Vision is for all students to be engaged in using systems-level, scientific thinking to better understand and participate in solving […]


A human crisis of unprecedented proportions is in the making. Diminishing arable land, water shortage, and expected population growth to 10 billion portend a catastrophic food security crisis by 2030. This threat requires a dramatic reduction of the environmental footprint […]

Single Cell Network Inference

Development of multicellular organisms from a single cell is arguably one of the most fascinating phenomena in biology. Mechanistic understanding of such a complex process is an important scientific challenge. Our single cell work aligns with the development of a systems […]


We previously constructed an “Environment and Gene Regulatory Influence Network” (EGRIN) for Halobacterium salinarum NRC‐1 (Bonneau et al, 2007). This model was constructed in two steps. First, modular organization of gene regulation was deciphered through semi‐supervised biclustering of gene expression, guided […]

Genetic Programs Controlling Responses of MTB

When MTB infects a human host, a menagerie of immune cells swarm around the pathogens and restrict their access to oxygen and nutrients, whereafter the bacteria cease to replicate and slow their metabolism to a crawl, entering into a latent […]

Network Portal

The Network Portal is a database of gene transcription regulatory networks and enables exploration, annotation and comparative analysis.Deciphering the complexity of biological systems requires a systems-level view of regulatory players and their interactions. However, inference of these complex interactions is […]

Persister MTB cells

More than 10 million people fall ill from Mycobacterium tuberculosis infection every year. Putting up a fight against the pathogen is posed with recurrent infections worldwide which is the consequence of resistance and tolerance strains among population. Resistance develop due […]

Synthetic Communities

Nitrate is a key contaminant and electron acceptor and its transformations link together the nitrogen cycle, the carbon cycle, and the fate of various contaminants. By designing environmentally-relevant synthetic communities composed of isolates from the field, we can study nitrate […]