Evolutionary programming as a platform for in silico metabolic engineering. - Kiran Raosaheb Patil; Isabel Rocha; Jochen Förster; Jens Nielsen (BMC Bioinform., 2005)

Natural computation meta-heuristics for the in silico optimization of microbial strains. - Miguel Rocha 001; Paulo Maia; Rui Mendes 001; José P. Pinto; Eugénio C. Ferreira; Jens Nielsen; Kiran Raosaheb Patil; Isabel Rocha (BMC Bioinform., 2008)

Architecture of transcriptional regulatory circuits is knitted over the topology of bio-molecular interaction networks. - Ana Oliveira; Kiran Raosaheb Patil; Jens Nielsen (BMC Syst. Biol., 2008)

Global transcriptional response of Saccharomyces cerevisiae to the deletion of SDH3. - Donatella Cimini; Kiran Raosaheb Patil; Chiara Schiraldi; Jens Nielsen (BMC Syst. Biol., 2009)

Reconstruction and analysis of genome-scale metabolic model of a photosynthetic bacterium. - Arnau Montagud; Emilio Navarro; Pedro Fernández de Córdoba; Javier F. Urchueguía; Kiran Raosaheb Patil (BMC Syst. Biol., 2010)

OptFlux: an open-source software platform for in silico metabolic engineering. - Isabel Rocha; Paulo Maia; Pedro Evangelista; Paulo Vilaça; Simão Soares; José P. Pinto; Jens Nielsen; Kiran Raosaheb Patil; Eugénio C. Ferreira; Miguel Rocha 001 (BMC Syst. Biol., 2010)

BioMet Toolbox: genome-wide analysis of metabolism. - Marija Cvijovic; Roberto Olivares-Hernández; Rasmus Agren; Niklas Dahr; Wanwipa Vongsangnak; Intawat Nookaew; Kiran Raosaheb Patil; Jens Nielsen (Nucleic Acids Res., 2010)

Metabolic Network Topology Reveals Transcriptional Regulatory Signatures of Type 2 Diabetes. - Aleksej Zelezniak; Tune H. Pers; Simão Soares; Mary Elizabeth Patti; Kiran Raosaheb Patil (PLoS Comput. Biol., 2010)

PHUSER (Primer Help for USER): a novel tool for USER fusion primer design. - Lars Rønn Olsen; Niels Bjørn Hansen; Mads Tvillinggaard Bonde; Hans Jasper Genee; Dorte Koefoed Holm; Simon Carlsen; Bjarne Gram Hansen; Kiran Raosaheb Patil; Uffe Hasbro Mortensen; Rasmus Wernersson (Nucleic Acids Res., 2011)

Random sampling of elementary flux modes in large-scale metabolic networks. - Daniel Machado; Zita Soons; Kiran Raosaheb Patil; Eugénio C. Ferreira; Isabel Rocha (Bioinform., 2012)

Impact of Stoichiometry Representation on Simulation of Genotype-Phenotype Relationships in Metabolic Networks. - Ana Rita Brochado; Sergej Andrejev; Costas D. Maranas; Kiran Raosaheb Patil (PLoS Comput. Biol., 2012)

Contribution of Network Connectivity in Determining the Relationship between Gene Expression and Metabolite Concentration Changes. - Aleksej Zelezniak; Steven Sheridan; Kiran Raosaheb Patil (PLoS Comput. Biol., 2014)

Extensive impact of non-antibiotic drugs on human gut bacteria. - Lisa Maier; Mihaela Pruteanu; Michael Kuhn 004; Georg Zeller; Anja Telzerow; Exene Erin Anderson; Ana Rita Brochado; Keith Conrad Fernandez; Hitomi Dose; Hirotada Mori; Kiran Raosaheb Patil; Peer Bork; et al. (Nat., 2018)

Metabolic models and gene essentiality data reveal essential and conserved metabolism in prokaryotes. - Joana C. Xavier; Kiran Raosaheb Patil; Isabel Rocha (PLoS Comput. Biol., 2018)

Bioactivity assessment of natural compounds using machine learning models trained on target similarity between drugs. - Vinita Periwal; Stefan Bassler; Sergej Andrejev; Natalia Gabrielli; Kaustubh Raosaheb Patil; Athanasios Typas; Kiran Raosaheb Patil (PLoS Comput. Biol., 2022)