List of works - Kiran R Patil

A new class of IMP dehydrogenase with a role in self-resistance of mycophenolic acid producing fungi

scientific article

Adaptive laboratory evolution of microbial co-cultures for improved metabolite secretion

scientific article published on 01 August 2021

Antibiotics-induced monodominance of a novel gut bacterial order

scientific article published on 18 January 2019

Architecture of transcriptional regulatory circuits is knitted over the topology of bio-molecular interaction networks

scientific article

BioMet Toolbox: genome-wide analysis of metabolism

scientific article published on 18 May 2010

Bioaccumulation of therapeutic drugs by human gut bacteria

scientific article published in 2021

Bioactivity assessment of natural compounds using machine learning models trained on target similarity between drugs

scientific article published on 25 April 2022

CRISPRi screens reveal genes modulating yeast growth in lignocellulose hydrolysate

scientific article published on 10 February 2021

Computational tools for modeling xenometabolism of the human gut microbiota

scientific article

Conjugative transposition of the vancomycin resistance carrying Tn1549: enzymatic requirements and target site preferences.

scientific article published on 22 December 2017

Contribution of network connectivity in determining the relationship between gene expression and metabolite concentration changes

scientific article

Do genome-scale models need exact solvers or clearer standards?

scientific article published on 14 October 2015

Draft Genome Sequence of Corynebacterium kefirresidentii SB, Isolated from Kefir.

scientific article published on 14 September 2017

Draft Genome Sequences of Three Novel Low-Abundance Species Strains Isolated from Kefir Grain.

scientific article published on 28 September 2017

Enhancing sesquiterpene production in Saccharomyces cerevisiae through in silico driven metabolic engineering.

scientific article published on 18 July 2009

Evolutionary programming as a platform for in silico metabolic engineering

scientific article

Extensive impact of non-antibiotic drugs on human gut bacteria

scientific article published on 19 March 2018

Fast automated reconstruction of genome-scale metabolic models for microbial species and communities

article published in 2018

Flux coupling and transcriptional regulation within the metabolic network of the photosynthetic bacterium Synechocystis sp. PCC6803.

scientific article published on 11 January 2011

Freeing Yeast from Alcohol Addiction (Just) to Make (It) Fat Instead

scientific article published on 01 September 2018

Global transcriptional and physiological responses of Saccharomyces cerevisiae to ammonium, L-alanine, or L-glutamine limitation

scientific article

Global transcriptional response of Saccharomyces cerevisiae to the deletion of SDH3.

scientific article

Hap4 is not essential for activation of respiration at low specific growth rates in Saccharomyces cerevisiae.

scientific article published on 7 March 2006

Identification of metabolic engineering targets through analysis of optimal and sub-optimal routes

scientific article (publication date: 2013)

Impact of Stoichiometry Representation on Simulation of Genotype-Phenotype Relationships in Metabolic Networks ⬇️

scientific article published on January 1, 2012

Improved vanillin production in baker's yeast through in silico design

scientific article

Industrial systems biology of Saccharomyces cerevisiae enables novel succinic acid cell factory

scientific article

Integration of Biomass Formulations of Genome-Scale Metabolic Models with Experimental Data Reveals Universally Essential Cofactors in Prokaryotes

scientific article

Integration of metabolome data with metabolic networks reveals reporter reactions

scientific article

Involvement of a natural fusion of a cytochrome P450 and a hydrolase in mycophenolic acid biosynthesis

scientific article published on 27 April 2012

Laboratory evolution reveals regulatory and metabolic trade-offs of glycerol utilization in Saccharomyces cerevisiae.

scientific article

MEMOTE for standardized genome-scale metabolic model testing

scientific article published on 01 March 2020

Memote: A community-driven effort towards a standardized genome-scale metabolic model test suite

Metabolic anchor reactions for robust biorefining

scientific article

Metabolic cooperation and spatiotemporal niche partitioning in a kefir microbial community

scientific article published in 2021

Metabolic dependencies drive species co-occurrence in diverse microbial communities

scientific article published on 4 May 2015

Metabolic interactions in microbial communities: untangling the Gordian knot

scientific article

Metabolic memory underlying minimal residual disease in breast cancer

scientific article published on 01 October 2021

Metabolic models and gene essentiality data reveal essential and conserved metabolism in prokaryotes

article

Metabolic network topology reveals transcriptional regulatory signatures of type 2 diabetes

scientific article

Metabolic shifts in residual breast cancer drive tumor recurrence

scientific article published on 15 May 2017

Model-guided development of an evolutionarily stable yeast chassis

scientific article published on 01 July 2021

Model-guided identification of gene deletion targets for metabolic engineering in Saccharomyces cerevisiae

scientific article published in January 2014

Multiplexed electron microscopy by fluorescent barcoding allows screening for ultrastructural phenotype

Natural computation meta-heuristics for the in silico optimization of microbial strains

scientific article

Nutritional preferences of human gut bacteria reveal their metabolic idiosyncrasies

scientific article published on 19 March 2018

OptFlux: an open-source software platform for in silico metabolic engineering

scientific article

Optimal fed-batch cultivation when mass transfer becomes limiting

scientific article published in October 2007

Overexpression of O‐methyltransferase leads to improved vanillin production in baker's yeast only when complemented with model‐guided network engineering ⬇️

scientific article published on October 23, 2012

PHUSER (Primer Help for USER): a novel tool for USER fusion primer design

scientific article published on 26 May 2011

Prediction and identification of sequences coding for orphan enzymes using genomic and metagenomic neighbours

scientific journal article

Predictive evolution of metabolic phenotypes using model‐designed environments

scientific article published in 2022

Proteomic characterization of extracellular vesicles produced by several wine yeast species

scientific article published on 23 June 2020

Publisher Correction: MEMOTE for standardized genome-scale metabolic model testing

scientific article published on 01 April 2020

Random sampling of elementary flux modes in large-scale metabolic networks ⬇️

scientific article published on September 15, 2012

Reconstruction and analysis of genome-scale metabolic model of a photosynthetic bacterium

scientific article (publication date: 17 November 2010)

Saccharomyces cerevisiae metabolism in ecological context

scientific article published on 14 September 2016

Single-cell transcriptomics identifies CD44 as a marker and regulator of endothelial to haematopoietic transition

scientific article published on 29 January 2020

Systems biology perspectives on minimal and simpler cells

scientific article

The metabolic background is a global player in Saccharomyces gene expression epistasis

scientific article published on February 2016

The metabolic response of heterotrophic Arabidopsis cells to oxidative stress

scientific article published in 2007

Towards standards for human fecal sample processing in metagenomic studies.

scientific article

Uncovering transcriptional regulation of metabolism by using metabolic network topology

scientific article

Use of genome-scale microbial models for metabolic engineering

scientific article published on February 2004

Versatile enzyme expression and characterization system for Aspergillus nidulans, with the Penicillium brevicompactum polyketide synthase gene from the mycophenolic acid gene cluster as a test case

scientific article published on 11 March 2011

Vitamin D regulates microbiome-dependent cancer immunity

scientific article published on 26 April 2024

Yeast Creates a Niche for Symbiotic Lactic Acid Bacteria through Nitrogen Overflow

scientific article

Yeast metabolic chassis designs for diverse biotechnological products

scientific article published on 19 July 2016

List of works by Kiran R Patil

A new class of IMP dehydrogenase with a role in self-resistance of mycophenolic acid producing fungi

Adaptive laboratory evolution of microbial co-cultures for improved metabolite secretion

Antibiotics-induced monodominance of a novel gut bacterial order

Architecture of transcriptional regulatory circuits is knitted over the topology of bio-molecular interaction networks

BioMet Toolbox: genome-wide analysis of metabolism

Bioaccumulation of therapeutic drugs by human gut bacteria

Bioactivity assessment of natural compounds using machine learning models trained on target similarity between drugs

CRISPRi screens reveal genes modulating yeast growth in lignocellulose hydrolysate

Computational tools for modeling xenometabolism of the human gut microbiota

Conjugative transposition of the vancomycin resistance carrying Tn1549: enzymatic requirements and target site preferences.

Contribution of network connectivity in determining the relationship between gene expression and metabolite concentration changes

Do genome-scale models need exact solvers or clearer standards?

Draft Genome Sequence of Corynebacterium kefirresidentii SB, Isolated from Kefir.

Draft Genome Sequences of Three Novel Low-Abundance Species Strains Isolated from Kefir Grain.

Enhancing sesquiterpene production in Saccharomyces cerevisiae through in silico driven metabolic engineering.

Evolutionary programming as a platform for in silico metabolic engineering

Extensive impact of non-antibiotic drugs on human gut bacteria

Fast automated reconstruction of genome-scale metabolic models for microbial species and communities

Flux coupling and transcriptional regulation within the metabolic network of the photosynthetic bacterium Synechocystis sp. PCC6803.

Freeing Yeast from Alcohol Addiction (Just) to Make (It) Fat Instead

Global transcriptional and physiological responses of Saccharomyces cerevisiae to ammonium, L-alanine, or L-glutamine limitation

Global transcriptional response of Saccharomyces cerevisiae to the deletion of SDH3.

Hap4 is not essential for activation of respiration at low specific growth rates in Saccharomyces cerevisiae.

Identification of metabolic engineering targets through analysis of optimal and sub-optimal routes

Impact of Stoichiometry Representation on Simulation of Genotype-Phenotype Relationships in Metabolic Networks ⬇️

Improved vanillin production in baker's yeast through in silico design

Industrial systems biology of Saccharomyces cerevisiae enables novel succinic acid cell factory

Integration of Biomass Formulations of Genome-Scale Metabolic Models with Experimental Data Reveals Universally Essential Cofactors in Prokaryotes

Integration of metabolome data with metabolic networks reveals reporter reactions

Involvement of a natural fusion of a cytochrome P450 and a hydrolase in mycophenolic acid biosynthesis

Laboratory evolution reveals regulatory and metabolic trade-offs of glycerol utilization in Saccharomyces cerevisiae.

MEMOTE for standardized genome-scale metabolic model testing

Memote: A community-driven effort towards a standardized genome-scale metabolic model test suite

Metabolic anchor reactions for robust biorefining

Metabolic cooperation and spatiotemporal niche partitioning in a kefir microbial community

Metabolic dependencies drive species co-occurrence in diverse microbial communities

Metabolic interactions in microbial communities: untangling the Gordian knot

Metabolic memory underlying minimal residual disease in breast cancer

Metabolic models and gene essentiality data reveal essential and conserved metabolism in prokaryotes

Metabolic network topology reveals transcriptional regulatory signatures of type 2 diabetes

Metabolic shifts in residual breast cancer drive tumor recurrence

Model-guided development of an evolutionarily stable yeast chassis

Model-guided identification of gene deletion targets for metabolic engineering in Saccharomyces cerevisiae

Multiplexed electron microscopy by fluorescent barcoding allows screening for ultrastructural phenotype

Natural computation meta-heuristics for the in silico optimization of microbial strains

Nutritional preferences of human gut bacteria reveal their metabolic idiosyncrasies

OptFlux: an open-source software platform for in silico metabolic engineering

Optimal fed-batch cultivation when mass transfer becomes limiting

Overexpression of O‐methyltransferase leads to improved vanillin production in baker's yeast only when complemented with model‐guided network engineering ⬇️

PHUSER (Primer Help for USER): a novel tool for USER fusion primer design

Prediction and identification of sequences coding for orphan enzymes using genomic and metagenomic neighbours

Predictive evolution of metabolic phenotypes using model‐designed environments

Proteomic characterization of extracellular vesicles produced by several wine yeast species

Publisher Correction: MEMOTE for standardized genome-scale metabolic model testing

Random sampling of elementary flux modes in large-scale metabolic networks ⬇️

Reconstruction and analysis of genome-scale metabolic model of a photosynthetic bacterium

Saccharomyces cerevisiae metabolism in ecological context

Single-cell transcriptomics identifies CD44 as a marker and regulator of endothelial to haematopoietic transition

Systems biology perspectives on minimal and simpler cells

The metabolic background is a global player in Saccharomyces gene expression epistasis

The metabolic response of heterotrophic Arabidopsis cells to oxidative stress

Towards standards for human fecal sample processing in metagenomic studies.

Uncovering transcriptional regulation of metabolism by using metabolic network topology

Use of genome-scale microbial models for metabolic engineering

Versatile enzyme expression and characterization system for Aspergillus nidulans, with the Penicillium brevicompactum polyketide synthase gene from the mycophenolic acid gene cluster as a test case

Vitamin D regulates microbiome-dependent cancer immunity

Yeast Creates a Niche for Symbiotic Lactic Acid Bacteria through Nitrogen Overflow

Yeast metabolic chassis designs for diverse biotechnological products