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Related publications (27)

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Quantifying and Localizing the Mitochondrial Proteome Across Five Tissues in A Mouse Population

Johan Auwerx, Dongryeol Ryu, Jun Yong Kim, Pooja Jha, Evan Graehl Williams

We have used SWATH mass spectrometry to quantify 3648 proteins across 76 proteomes collected from genetically diverse BXD mouse strains in two fractions (mitochondria and total cell) from five tissues: liver, quadriceps, heart, brain, and brown adipose (BA ...

AMER SOC BIOCHEMISTRY MOLECULAR BIOLOGY INC2018

ScienceWISE: Topic Modeling over Scientific Literature Networks

Paolo De Los Rios, Alessio Vincenzo Cardillo, Andrea Martini

We provide an up-to-date view on the knowledge management system ScienceWISE (SW) and address issues related to the automatic assignment of articles to research topics. So far, SW has been proven to be an effective platform for managing large volumes of te ...

2017

redGEM: Systematic reduction and analysis of genome-scale metabolic reconstructions for development of consistent core metabolic models

Vassily Hatzimanikatis, Meriç Ataman, Georgios Fengos, Daniel Federico Hernandez Gardiol

Genome-scale metabolic reconstructions have proven to be valuable resources in enhancing our understanding of metabolic networks as they encapsulate all known metabolic capabilities of the organisms from genes to proteins to their functions. However the co ...

2017

Transforming Growth Factor beta/Activin signaling in neurons increases susceptibility to starvation

Bruno Lemaitre, Xiaoxue Li, Wen Bin Chng

Animals rely on complex signaling network to mobilize its energy stores during starvation. We have previously shown that the sugar-responsive TGF beta/Activin pathway, activated through the TGF beta ligand Dawdle, plays a central role in shaping the post-p ...

2017

Reconstruction of biological pathways and metabolic networks from in silico labeled metabolites

Vassily Hatzimanikatis, Noushin Hadadi, Jasmin Maria Hafner, Keng Cher Soh

Reaction atom mappings track the positional changes of all of the atoms between the substrates and the products as they undergo the biochemical transformation. However, information on atom transitions in the context of metabolic pathways is not widely avai ...

Wiley-V C H Verlag Gmbh2017

Thermodynamics-based Metabolite Sensitivity Analysis in metabolic networks

Vassily Hatzimanikatis, Dimitrios Alexandros Kyparissidis

The increasing availability of large metabolomics datasets enhances the need for computational methodologies that can organize the data in a way that can lead to the inference of meaningful relationships. Knowledge of the metabolic state of a cell and how ...

Elsevier2017

From recommender systems to spatio-temporal dynamics with network science

Kirell Maël Benzi

Networks are data structures that are fundamental for capturing and analyzing complex interactions between objects. While they have been used for decades to solve problems in virtually all scientific fields, their usage for data analysis in real-world prac ...

EPFL2017