New paper on the dynamics of biological networks in PNAS

This work (pdf) was done during my postdoc at the BarabasiLab. We investigated the role of network topology in accurately predicting perturbation patterns in biological network. Indeed, the development of high-throughput technologies has allowed mapping a significant proportion of interactions between biochemical entities in the cell. In short, we begin to have a good mapping of the subcellular “interacotme”. However, it is unclear how much information is lost given the lack of measurements on the kinetic parameters governing the dynamics of these interactions. Using biochemical networks with experimentally measured kinetic parameters, we show that a knowledge of the network topology offers 65–80% accuracy in predicting the impact of perturbation patterns. In other words, we can use the increasingly accurate topological models to approximate perturbation patterns, bypassing expensive kinetic constant measurement. These results could open new avenues in modeling drug action and in identifying drug targets relying on the human interactome only.

New paper on the topological impact of micro-RNAs in JCI insight

This paper (pdf) is a result of a collaboration between the Sharma Lab at Harvard Medical School and the Renz group at Philipps University Marburg. In this work, I developed IDEAL, a method to predict the role of micro-RNAs (miRNAs) in a disease based on their topological impact in the interactome, and not on their fold-change. The method was applied in the case of asthma, based on an experimental setup and validation done by Ayşe Kılıç (a massive work!). We found that a cocktail of 5 miRNAs identified as having large topological impact, but not large expression fold-change, led to a sharp reduction of the asthmatic Th2 phenotype.

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The NetMed18 satellite

The network medicine satellite “NetMed18: Personalized Medicine in the Era of Big Data” at the NetSci18 conference was a success! With talks ranging from interactome and patient network approaches, social media and word embedding, brain stimulation, genetics and molecular biology… The multi-faceted approaches to network medicine were well represented! Can’t wait for next year 🙂

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New paper on personalized medicine for heart failure in the news!

Our paper “A personalized, multiomics approach identifies genes involved in cardiac hypertrophy and heart failure” is in the news! I still remember the first time Alain Karma told me about this project, almost 5 years ago when I was finishing my PhD… A few months later I would be in Boston working on it, and there we are 4 years later. A great adventure, and many ideas for follow-ups!

Coexpression networks in HF
Co-expression network built from gene expression correlation across 100+ mouse strains. Newly discovered personalized FC genes constitute a separate module compare to the traditional population-wide SAM genes.

 

Positions available!

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Note: the application process is now over! However, if you are interested in the project and would like to do an internship, do not hesitate to contact me!

We are looking for postdoctoral associates and PhD candidates in the area of Network Science and Science of Science to join us at the Center for Research and Interdisciplinarity (CRI) in Paris. We seek curious, motivated, autonomous, ambitious individuals with strong analytical skills, network science or data science experience and interest in applying it towards social systems. The ideal candidate has a physics, computer science, bioinformatics, data science, network science, computational social science or mathematics background with coding experience, and thrives in inter/anti-disciplinarity dynamic environments, is inspired and motivated by daily interactions with diverse peers, comfortably mixes disciplines and wishes to explore uncharted domains.

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