15 Result(s)
within
Nitin S. Baliga
English
Bioinformatics
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Article
Open AccessQuantitative prediction of conditional vulnerabilities in regulatory and metabolic networks using PRIME
The ability of Mycobacterium tuberculosis (Mtb) to adopt heterogeneous physiological states underlies its success in evading the immune system and tolerating antibiotic killing. Drug tolerant phenotypes are a maj...
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Article
EcoFABs: advancing microbiome science through standardized fabricated ecosystems
Microbiomes play critical roles in ecosystems and human health, yet in most cases scientists lack standardized and reproducible model microbial communities. The development of fabricated microbial ecosystems, ...
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Article
Open AccessBicluster Sampled Coherence Metric (BSCM) provides an accurate environmental context for phenotype predictions
Biclustering is a popular method for identifying under which experimental conditions biological signatures are co-expressed. However, the general biclustering problem is NP-hard, offering room to focus algorit...
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Article
Open AccessEvolution of context dependent regulation by expansion of feast/famine regulatory proteins
Expansion of transcription factors is believed to have played a crucial role in evolution of all organisms by enabling them to deal with dynamic environments and colonize new environments. We investigated how ...
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Article
Open AccessMap** and manipulating the Mycobacterium tuberculosis transcriptome using a transcription factor overexpression-derived regulatory network
Mycobacterium tuberculosis senses and responds to the shifting and hostile landscape of the host. To characterize the underlying intertwined gene regulatory network governed by approximately 200 transcription fac...
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Article
Open AccessIntegration and visualization of systems biology data in context of the genome
High-density tiling arrays and new sequencing technologies are generating rapidly increasing volumes of transcriptome and protein-DNA interaction data. Visualization and exploration of this data is critical to...
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Article
Open AccessGTC: A web server for integrating systems biology data with web tools and desktop applications
Gaggle Tool Creator (GTC) is a web application which provides access to public annotation, interaction, orthology, and genomic data for hundreds of organisms, and enables instant analysis of the data using man...
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Article
Open AccessLarge scale physiological readjustment during growth enables rapid, comprehensive and inexpensive systems analysis
Rapidly characterizing the operational interrelationships among all genes in a given organism is a critical bottleneck to significantly advancing our understanding of thousands of newly sequenced microbial and...
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Article
Visualization of omics data for systems biology
High-throughput studies of biological systems are rapidly accumulating a wealth of 'omics'-scale data. Visualization is a key aspect of both the analysis and understanding of these data, and users now have man...
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Article
Open AccessThe Firegoose: two-way integration of diverse data from different bioinformatics web resources with desktop applications
Information resources on the World Wide Web play an indispensable role in modern biology. But integrating data from multiple sources is often encumbered by the need to reformat data files, convert between nami...
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Chapter
Prokaryotic Systems Biology
Prokaryotic systems biology is a holistic biological approach that enables comprehensive understanding of an organism. However, two opposing strategies have been proposed to attain such understanding: the top-...
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Article
Open AccessIntegrated biclustering of heterogeneous genome-wide datasets for the inference of global regulatory networks
The learning of global genetic regulatory networks from expression data is a severely under-constrained problem that is aided by reducing the dimensionality of the search space by means of clustering genes int...
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Article
Open AccessThe Inferelator: an algorithm for learning parsimonious regulatory networks from systems-biology data sets de novo
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 Halobacterium NRC-...
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Article
Open AccessThe Gaggle: An open-source software system for integrating bioinformatics software and data sources
Systems biologists work with many kinds of data, from many different sources, using a variety of software tools. Each of these tools typically excels at one type of analysis, such as of microarrays, of metabol...
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Article
Comprehensive de novo structure prediction in a systems-biology context for the archaea Halobacterium sp. NRC-1
Large fractions of all fully sequenced genomes code for proteins of unknown function. Annotating these proteins of unknown function remains a critical bottleneck for systems biology and is crucial to understan...
