[ccp4bb] Funded PhD position near Paris, France: AI-powered prediction of protein-nucleic acid interactions

[ANDREANI Jessica]

Dear all,

please find below an announcement for a funded PhD position on the development 
of deep learning approaches to predict interactions between proteins and 
nucleic acids. The deadline for application is 30 April 2023.

Best regards,
Jessica Andreani

Scientific project
Interactions between proteins and nucleic acids have strong biological 
relevance and are often perturbed in diseases. This project aims to better 
understand the molecular mechanisms of protein-nucleic acid interactions. A 
large gap exists between vast amounts of high-throughput protein-nucleic acid 
interaction data and the scarcity of 3D structures of protein-nucleic acid 
complexes, triggering the need for computational methods to analyze and predict 
these structures. Recently, artificial intelligence (in particular deep 
learning in AlphaFold and related methods) has emerged as a revolutionary 
approach to predict protein and protein-protein interaction structures.
The present project aims to develop computational approaches for the analysis 
and prediction of protein-nucleic acid interactions, by building upon deep 
learning methodologies and integrating complementary data sources. We will also 
use an evolutionary perspective to provide crucial insights into the exquisite 
regulation of complex processes driven by protein-nucleic acid interactions.

Host team and environment for the PhD project
The doctoral research will take place in the “Molecular assemblies and genome 
integrity” team of I2BC (Institute for Integrative Biology of the Cell, UMR 
9198 CEA/CNRS/Université Paris-Saclay). I2BC is a research institute of 
Université Paris-Saclay that gathers 60 research teams covering a wide range of 
integrative biology projects. The “Molecular assemblies and genome integrity” 
team relies on a strong coupling between computational and experimental 
approaches to characterize, predict and inhibit macromolecular interactions. 
I2BC is localized in Gif sur Yvette (less than one hour from the center of 
Paris).
Our bioinformatics team has a strong expertise in macromolecular structure and 
evolution, macromolecular interaction prediction and heterogeneous data 
integration. In recent years, our team developed original approaches for the 
structural prediction of protein interactions using evolutionary information 
(Quignot et al, NAR 2021; Quignot et al, Bioinformatics 2021). We also have 
numerous collaborations with wet-lab biologists. We have access to relevant 
computational resources, including GPU cluster nodes.

Funding and benefits
CEA will provide 3 years PhD funding for this project to an excellent PhD 
candidate. The gross monthly salary for CEA doctoral students is €2,290 (as of 
October 2022). CEA doctoral students have access to the same benefits as other 
CEA employees (social security contributions, training opportunities, company 
canteen, paid leave, social benefits…). Expected start of the PhD position: 
October 2023.

Expected profile
We are looking for a highly motivated candidate with a Master's degree in 
bioinformatics, data science, machine learning or a related field. Proficiency 
in Python programming is necessary. Previous experience in deep learning and 
data science is highly desirable. (Structural) bioinformatics experience is a 
plus but not strictly required, provided the candidate has a strong interest in 
life sciences and molecular aspects.

Application process
Please send a CV, a motivation letter and contact details of two references 
(ideally, researchers who have supervised the candidate for relevant research 
projects) to Jessica Andreani: 
jessica.andre...@cea.fr
Deadline for application: 30 April 2023




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[ccp4bb] Call for papers "Web Tools for Modeling and Analysis of Biomolecular Interactions"

[ANDREANI Jessica]

Dear all,

together with Brian Jiménez-García (Utrecht University) and Masahito Ohue 
(Tokyo Institute of Technology), we are editing a Research Topic entitled "Web 
Tools for Modeling and Analysis of Biomolecular Interactions" for the journal 
"Frontiers in Molecular Biosciences".



Full details and links to participate and submit contributions can be found at

https://www.frontiersin.org/research-topics/17397



Our goal is to gather a collection of user-friendly tools (web servers and 
databases) useful for non-specialists. The collection is focused on 
biomolecular interactions and may therefore include resources for computational 
modeling, visualization, prediction, analysis of experimental (structural, 
proteomics, other -omics) data, analysis of interaction networks…



The abstract submission deadline is 15 January 2021 and the submission deadline 
for manuscripts is 28 May 2021. Please note that manuscripts will be peer 
reviewed, and if accepted for publication, are subject to publishing fees 
(https://www.frontiersin.org/about/publishing-fees). It is possible to apply 
for fees support.

If you are interested in participating or if you need any further information, 
please do not hesitate to contact me.

Best regards,



Jessica Andreani



---

Jessica Andreani

I2BC (Institute for Integrative Biology of the Cell)

Institut des Sciences du Vivant Frédéric Joliot

Bâtiment 144 - Point courrier 22

CEA

91191 Gif sur Yvette cedex

France

jessica.andre...@cea.fr<mailto:jessica.andre...@cea.fr>





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