PhD position :  Next-generation diagnosis of imprinting disorders: multi-omic approaches and machine learning for integrated and predictive analysis.

We offer a 3-year position for a PhD Student. The position starts on November 2026. You will work under the supervision of Dr. Frederic Brioude at Inserm Centre de Recherche Saint-Antoine (Paris, France)

Imprinting Disorders (ID) affect ~1:5000 newborns and require lifelong disease management. IDs are caused by abnormal activity of imprinted genes: the ~ 200 human genes with mono-allelic activity based on parental-origin. Mono-allelic activity of imprinted genes is determined by differential DNA methylation at Differentially Methylated Regions (DMRs) and, at 11p15, further involves DNA-methylation dependent binding of the CTCF insulator proteins to create topologically associated domains (TADs) of gene regulation. Patients with epigenetic alterations in a DMR may also present with epimutations in other imprinted DMRs, whether or not these are associated with a disease; this is known as multilocus imprinting disturbances (MLID). A rarer mechanism involves copy number variations (CNVs) within DMRs. This mechanism remains particularly difficult to interpret due to the variable content of imprinted genes, DMRs and regulatory elements. Current molecular diagnosis for SRS and BWS relies on the detection of DNA methylation and CNVs at the 11p15 ICRs. This non-comprehensive approach frequently results in diagnostic gridlocks and provides scattered insights into broader perturbations. Moreover, it’s poorly capable to predict the severity of phenotype and to distinguish SRS and BWS from Multi Locus Imprinting Disturbance (MLID), an increasingly recognized cause of IDs were multiple ICRs are perturbed.

Your project: We are offering a 3-year position for a PhD Student. The position will start on November 2026. You will work under the supervision of  Dr. Frederic Brioude at Inserm Centre de Recherche Saint-Antoine (Paris, France). Your project is part of an ANR project - Next-generation diagnosis of imprinting disorders: multi-omic approaches and
machine learning for integrated and predictive analysis. This project aims at 1. identification of BWS and SRS patients with MLID and correlation with their clinical features; 2. further characterization of the epigenetic and genetic changes through the use of several techniques including whole-genome methylation analysis, exome and whole-genome sequencing as well as nanopore sequencing; 3. characterize the impact of epigenetic defects on chromatin organization (topopologiccaly associated domains, TADs) with the help of machine learning technologies. To achieve this objective, this translational project will be led by a consortium of three teams bringing together experts in parental imprinting from clinical and diagnostic perspectives, multi-omic approaches in the context of parental imprinting, artificial intelligence and machine learning. As a PhD student, you will be responsible for the methylation studies part. You will work closely with the those recruited in the two other teams (bioinfomatics, TAD studies, machine learning processes...)

Dr. Frederic Brioude (https://www.crsa.fr/fiche-brioude-frederic.html), established within the Sant Antoine Research Centre, Inserm-Sorbonne Université (Paris, FR), focus on the study of the molecular bases of IDs and on the role that genetic variants play in their pathogenesis.

Your qualifications: We are looking for someone who is curious, independent and creative, with a strong background and interest in molecular biology. You should have a university Master degree in biology or an equivalent field and have good skills in state of the art molecular biology. Knowledge of methods of statistical and bioinformatic analysis of high-throughput generated data will be highly advantageous.

Eligibility Criteria :

- Academic degree: Applicants shall have a master degree or equivalent corresponding to the second level of studies.

- Mobility rule: There will be no nationality restrictions. Applicants can be from any Country.

Evaluation Criteria

- Curriculum assessment concerning: a) the degree thesis (the degree pertinence with the Ph.D. scientific topics, the degree final grade); b) knowledge of English language and other certified skills. Knowledge of French language is a plus; c) research and study stages; d) scholarships; e) post graduate qualifications; f) other documents if relevant for a full assessment (for example publications, conference abstracts, reference letters written by professors of the foreign university where candidates are/have been enrolled).

- Oral examinations concerning your previous research experience and the project specific to the position offered. The interview can be done in videoconference via Skype if requested.