Publications by Anush Chiappino-Pepe

A workflow for annotating the knowledge gaps in metabolic reconstructions using known and hypothetical reactions

Vassily Hatzimanikatis, Noushin Hadadi, Jasmin Maria Hafner, Meriç Ataman, Anush Chiappino-Pepe, Homa Mohammadi Peyhani, Evangelia Vagena

Advances in medicine and biotechnology rely on a deep understanding of biological processes. Despite the increasingly available types and amounts of omics data, significant knowledge gaps remain, with current approaches to identify and curate missing annot ...

National Academy of Sciences2022

NICEdrug.ch, a workflow for rational drug design and systems-level analysis of drug metabolism

Vassily Hatzimanikatis, Noushin Hadadi, Jasmin Maria Hafner, Anush Chiappino-Pepe, Homa Mohammadi Peyhani

The discovery of a drug requires over a decade of intensive research and financial investments – and still has a high risk of failure. To reduce this burden, we developed the NICEdrug.ch resource, which incorporates 250,000 bioactive molecules, and studied ...

2021

Mechanistic insights into bacterial metabolic reprogramming from omics-integrated genome-scale models

Florence Mehl, Noushin Hadadi, Merten Morales, Anush Chiappino-Pepe, Vikash Kumar Pandey

Understanding the adaptive responses of individual bacterial strains is crucial for microbiome engineering approaches that introduce new functionalities into complex microbiomes, such as xenobiotic compound metabolism for soil bioremediation. Adaptation re ...

NATURE PUBLISHING GROUP2020

Functional and Computational Genomics Reveal Unprecedented Flexibility in Stage-Specific Toxoplasma Metabolism

Vassily Hatzimanikatis, Damien Lionel Nicolas, Dominique Soldati-Favre, Anush Chiappino-Pepe, Aarti Krishnan, Matteo Lunghi

To survive and proliferate in diverse host environments with varying nutrient availability, the obligate intracellular parasite Toxoplasma gondii reprograms its metabolism. We have generated and curated a genome-scale metabolic model (iTgo) for the fast-re ...

CELL PRESS2020

Genome-Scale Identification of Essential Metabolic Processes for Targeting the Plasmodium Liver Stage

Vassily Hatzimanikatis, Dominique Soldati-Favre, Anush Chiappino-Pepe, Vikash Kumar Pandey

Plasmodium gene functions in mosquito and liver stages remain poorly characterized due to limitations in the throughput of phenotyping at these stages. To fill this gap, we followed more than 1,300 barcoded P. berghei mutants through the life cycle. We dis ...

2019

Analysis of cellular and drug action mechanisms in the malaria parasites using systems biology approaches

Anush Chiappino-Pepe

Malaria puts at risk of infection half of the world population and still kills around half a million people every year. The rapid and worrisome rise of drug-resistant malaria parasites hinders the treatment of malaria and calls for a global collaboration t ...

EPFL2018

Bioenergetics-based modeling of Plasmodium falciparum metabolism reveals its essential genes, nutritional requirements, and thermodynamic bottlenecks

Vassily Hatzimanikatis, Stepan Tymoshenko, Dominique Soldati-Favre, Meriç Ataman, Anush Chiappino-Pepe

Novel antimalarial therapies are urgently needed for the fight against drug-resistant para- sites. The metabolism of malaria parasites in infected cells is an attractive source of drug targets but is rather complex. Computational methods can handle this co ...

Public Library of Science2017

Integration of Metabolic, Regulatory and Signaling Networks Towards Analysis of Perturbation and Dynamic Responses

Vassily Hatzimanikatis, Meriç Ataman, Anush Chiappino-Pepe, Vikash Kumar Pandey

The expanding generation of dynamic biological data requires approaches that integrate and analyze information from different types of cellular processes –metabolism, regulation, and signaling–, and ultimately increase our insights into the cell behavior u ...

2017