Publications by Vikash Kumar Pandey

3D fluorescence molecular tomography utilizing a novel SPAD camera

Edoardo Charbon, Claudio Bruschini, Arin Can Ülkü, Vikash Kumar Pandey

3D Fluorescence Molecular Tomography (FMT) is an important pre-clinical tool for quantifying and characterizing molecular markers for different diseases. Herein, we demonstrate, for the first time, 3D K-Space FMT reconstructions using a large time-gated SP ...

SPIE2024

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

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

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

Enhanced flux prediction by integrating relative expression and relative metabolite abundance into thermodynamically consistent metabolic models

Vassily Hatzimanikatis, Noushin Hadadi, Vikash Kumar Pandey

The ever-increasing availability of transcriptomic and metabolomic data can be used to deeply analyze and make ever-expanding predictions about biological processes, as changes in the reaction fluxes through genome-wide pathways can now be tracked. Current ...

2019

Investigating the deregulation of metabolic tasks via Minimum Network Enrichment Analysis (MiNEA) as applied to nonalcoholic fatty liver disease using mouse and human omics data

Vassily Hatzimanikatis, Vikash Kumar Pandey

Nonalcoholic fatty liver disease (NAFLD) is associated with metabolic syndromes spanning a wide spectrum of diseases, from simple steatosis to the more complex nonalcoholic steatohepatitis. To identify the deregulation that occurs in metabolic processes at ...

2019

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

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

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

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

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

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