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List of works by Nitin S Baliga

<i>Mycobacterium abscessus</i> biofilms produce an extracellular matrix and have a distinct mycolic acid profile

scientific article published on 06 April 2021

A Major Role for Nonenzymatic Antioxidant Processes in the Radioresistance of Halobacterium salinarum ⬇️

scientific article published on January 28, 2011

A genome wide dosage suppressor network reveals genomic robustness.

scientific article

A high-resolution network model for global gene regulation in Mycobacterium tuberculosis

scientific article

A miRNA-regulatory network explains how dysregulated miRNAs perturb oncogenic processes across diverse cancers.

scientific article

A predictive model for transcriptional control of physiology in a free living cell.

scientific article published in December 2007

A refined genome-scale reconstruction of Chlamydomonas metabolism provides a platform for systems-level analyses

scientific article

A role for programmed cell death in the microbial loop

scientific article

A single transcription factor regulates evolutionarily diverse but functionally linked metabolic pathways in response to nutrient availability

scientific article published on 16 June 2009

A system-level model for the microbial regulatory genome

scientific article

A systems level predictive model for global gene regulation of methanogenesis in a hydrogenotrophic methanogen

scientific article published on 02 October 2013

A systems view of haloarchaeal strategies to withstand stress from transition metals

scientific article published on 2 June 2006

A systems-level gene regulatory network model for Plasmodium falciparum

scientific article published on 01 May 2021

An evolutionarily conserved RNase-based mechanism for repression of transcriptional positive autoregulation

scientific article

An integrated systems approach for understanding cellular responses to gamma radiation

scientific article published on 12 September 2006

Antibody-recruiting protein-catalyzed capture agents to combat antibiotic-resistant bacteria

scientific article published on 12 February 2020

Architecture for interoperable software in biology

scientific article

Bicluster Sampled Coherence Metric (BSCM) provides an accurate environmental context for phenotype predictions.

scientific article published on 15 April 2015

CTCF physically links cohesin to chromatin

scientific article

Causal Mechanistic Regulatory Network for Glioblastoma Deciphered Using Systems Genetics Network Analysis.

scientific article published on 14 July 2016

Combining inferred regulatory and reconstructed metabolic networks enhances phenotype prediction in yeast

scientific article

Comprehensive de novo structure prediction in a systems-biology context for the archaea Halobacterium sp. NRC-1

scientific article

Coordinate regulation of energy transduction modules in Halobacterium sp. analyzed by a global systems approach

scientific article

Coordination of frontline defense mechanisms under severe oxidative stress ⬇️

scientific article published on July 1, 2010

Crippling life support for SARS-CoV-2 and other viruses through synthetic lethality

scientific article published on 01 October 2020

Cytoscape: a software environment for integrated models of biomolecular interaction networks

scientific article

Data-driven integration of genome-scale regulatory and metabolic network models

scientific article

Diurnally entrained anticipatory behavior in archaea

scientific article published in 2009

Effects of H2 and formate on growth yield and regulation of methanogenesis in Methanococcus maripaludis

scientific article published on 18 January 2013

Evolution of context dependent regulation by expansion of feast/famine regulatory proteins

scientific article

GTC: A web server for integrating systems biology data with web tools and desktop applications

scientific article (publication date: 13 July 2010)

General transcription factor specified global gene regulation in archaea

scholarly article

Genome sequence of Haloarcula marismortui: a halophilic archaeon from the Dead Sea

scientific article

Genome-wide CRISPR-Cas9 Screens Reveal Loss of Redundancy between PKMYT1 and WEE1 in Glioblastoma Stem-like Cells

scientific article

Global analysis of mRNA stability in Mycobacterium tuberculosis ⬇️

scientific article published on November 3, 2012

Halobacterium salinarum NRC-1 PeptideAtlas: toward strategies for targeted proteomics and improved proteome coverage

scientific article published on 25 July 2008

Harnessing the power of human tumor-derived cell lines for the rational design of cancer therapies.

scientific article

Inference of Bacterial Small RNA Regulatory Networks and Integration with Transcription Factor-Driven Regulatory Networks

scientific article published on 02 June 2020

Inference of expanded Lrp-like feast/famine transcription factor targets in a non-model organism using protein structure-based prediction

scientific article

Integrated biclustering of heterogeneous genome-wide datasets for the inference of global regulatory networks

scientific article

Integration and visualization of systems biology data in context of the genome

scientific article

Intricate Genetic Programs Controlling Dormancy in Mycobacterium tuberculosis

scientific article published on 01 April 2020

Large scale physiological readjustment during growth enables rapid, comprehensive and inexpensive systems analysis

scientific article

Low-pass sequencing for microbial comparative genomics

scientific article

Mapping and manipulating the Mycobacterium tuberculosis transcriptome using a transcription factor overexpression-derived regulatory network

scientific article

Mathematical models to study the biology of pathogens and the infectious diseases they cause

publication published on 15 March 2022

Mechanism for microbial population collapse in a fluctuating resource environment.

scientific article published on 20 March 2017

Metallochaperones regulate intracellular copper levels

scientific article

MiR-155-regulated molecular network orchestrates cell fate in the innate and adaptive immune response to Mycobacterium tuberculosis

scientific article published on 28 September 2016

Model-based deconvolution of genome-wide DNA binding

scientific article published on December 2007

Molecular mechanisms of system responses to novel stimuli are predictable from public data

scientific article

Network portal: a database for storage, analysis and visualization of biological networks.

scientific article

Niche adaptation by expansion and reprogramming of general transcription factors.

scientific article published on 22 November 2011

Parallel evolution of transcriptome architecture during genome reorganization

scientific article

Path-seq identifies an essential mycolate remodeling program for mycobacterial host adaptation

scientific article published on 04 March 2019

Prevalence of transcription promoters within archaeal operons and coding sequences.

scientific article published on 16 June 2009

Proteomic analysis of an extreme halophilic archaeon, Halobacterium sp. NRC-1.

scientific article published on 18 July 2003

Quantitative prediction of conditional vulnerabilities in regulatory and metabolic networks using PRIME

scientific article published on 06 December 2021

Selective Translation of Low Abundance and Upregulated Transcripts in Halobacterium salinarum

scientific article published on 28 July 2020

Sense overlapping transcripts in IS1341-type transposase genes are functional non-coding RNAs in archaea

scientific article published on January 2015

Structure-based predictions broadly link transcription factor mutations to gene expression changes in cancers

scientific article

Synergistic epistasis enhances the co-operativity of mutualistic interspecies interactions

scientific article published on 21 February 2021

Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1

scientific article

The DNA-binding network of Mycobacterium tuberculosis

scientific article

The Firegoose: two-way integration of diverse data from different bioinformatics web resources with desktop applications

scientific article

The Gaggle: an open-source software system for integrating bioinformatics software and data sources

scientific article

The Inferelator: an algorithm for learning parsimonious regulatory networks from systems-biology data sets de novo

scientific article

The Transcription Factor Nfatc2 Regulates β-Cell Proliferation and Genes Associated with Type 2 Diabetes in Mouse and Human Islets

scientific article

The anatomy of microbial cell state transitions in response to oxygen

scientific article

The role of predictive modelling in rationally re-engineering biological systems

scientific article (publication date: April 2009)

Transcription start site associated RNAs (TSSaRNAs) are ubiquitous in all domains of life

scientific article published in 2014

Transcriptional program for nitrogen starvation-induced lipid accumulation in Chlamydomonas reinhardtii

scientific article

Transcriptional regulatory networks underlying gene expression changes in Huntington's disease

scientific article published on 26 March 2018

Transcriptome signature of cell viability predicts drug response and drug interaction in Mycobacterium tuberculosis

scientific article published on 06 December 2021

Two transcription factors are necessary for iron homeostasis in a salt-dwelling archaeon ⬇️

scientific article published on November 24, 2010

Visualization of omics data for systems biology

scientific article

cMonkey2: Automated, systematic, integrated detection of co-regulated gene modules for any organism

scientific article published on 14 April 2015

metaXCMS: second-order analysis of untargeted metabolomics data

scientific article

miRvestigator: web application to identify miRNAs responsible for co-regulated gene expression patterns discovered through transcriptome profiling.

scientific article

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