Mohammad Salma, PhD

Senior Bioinformatician & Data Scientist

Transforming complex genomic data into actionable insights through advanced bioinformatics, machine learning, and innovative pipeline development

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About Me

Senior Bioinformatician and Data Scientist with extensive expertise in analyzing next-generation sequencing (NGS) data and developing cutting-edge bioinformatics pipelines.

My journey combines a strong foundation in genomics with advanced skills in artificial intelligence and machine learning. I specialize in translating complex biological data into meaningful insights for oncology and rare disease research.

Throughout my career, I have supervised bioinformatics engineers and doctoral students, refining my expertise in project management and team leadership. I am passionate about innovation, particularly in applying AI/ML methods to genomics to improve diagnostics and research in fields such as oncology and rare diseases.

PhD in Biotechnology

University of Montpellier

6+ Years Experience

Bioinformatics & Data Science

19+ Publications

223 Citations, h-index: 7

Professional Experience

June 2025 - Present

Project Manager

Institut Imagine | Bioinformatics & Data Science

Montpellier, France

  • Leading bioinformatics and data science projects for genetic disease research
  • Coordinating multidisciplinary teams and project deliverables
  • Implementing advanced genomic analysis workflows
December 2023 - May 2025

Senior Bioinformatics & Data Scientist

IRCM - Institut de Recherche en Cancérologie de Montpellier

Montpellier, France

  • Supervised bioinformatics engineers and provided technical leadership
  • Implemented advanced AI/ML algorithms for cancer genomics analysis
  • Mentored doctoral student in bioinformatics (since October 2022)
  • Developed robust pipelines for ATAC-Seq, RNA-Seq, and multi-omics integration
Single Cell Sequencing ATAC-Seq Machine Learning
November 2021 - September 2023

Bioinformatics & Data Scientist

Institut Imagine | Laboratory of Excellence GR-Ex | Université Paris Cité

Paris, France

  • Developed custom tools and pipelines for complex genomic data analysis
  • Applied machine learning with TensorFlow and scikit-learn for biomarker identification
  • Supervised doctoral student providing pedagogical and scientific mentorship
Exome-Seq RNA-Seq TensorFlow
September 2018 - October 2021

Bioinformatics & Data Scientist

IGMM - Institut de Génétique Moléculaire de Montpellier (CNRS)

Montpellier, France

  • Implemented NGS workflows for DNA, RNA, and epigenome analysis
  • Conducted variant detection, functional annotation, and automated reporting
  • Collaborated with multidisciplinary teams of biologists and data scientists
ChIP-Seq ATAC-Seq Variant Calling

Skills & Expertise

Programming

Python R Bash PHP JavaScript

NGS Analysis

DNA-Seq RNA-Seq scRNA-Seq ATAC-Seq ChIP-Seq Exome-Seq Cut&Run CaptureC-Seq Spatial Transcriptomics

AI & Machine Learning

TensorFlow scikit-learn Random Forest LASSO Deep Learning

Workflows & Tools

Snakemake Nextflow nf-core Docker Singularity

Data Management

MySQL MongoDB HPC

Development

Flask Streamlit RShiny GitHub GitLab

Selected Publications

2025

The methyl-CpG-binding protein 2 inhibits cGAS-associated signaling

Chamma H, Guha S, Eloiflin RJ, Augereau A, Le Hars P, et al.

Nature Communications (2025)

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2025

VEXAS syndrome anemia is a mosaic erythroblastopenia

François Rodrigues and Giulia Hardouin and Sara El Hoss and Aya Ghoul and Emilie-Fleur Gautier and Michaël Dussiot and Maria A Lizarralde-Iragorri and Annalisa Santini and Sandy Peltier and Pascal Amireault and Vanessa Soldan and Annarita Miccio and Mounia Debili and Vincent Jachiet and Thiago Trovati Maciel and Julien Rossignol and Eric Allemand and Arsène Mekinian and Sophie Georgin-Lavialle and Mohammad Salma and Eric Soler and Pierre-Emmanuel Gleizes and Marie-Françoise O’Donohue and Olivier Kosmider and Manuel S Rodriguez and Olivier Hermine

Blood (2025)

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2025

MMS22L is a novel key actor of normal and pathological erythropoiesis

Elia Colin and Ivan Ferrer‐Vicens and Dror Brook and Mohammad Salma and Charlotte Andrieu‐Soler and Elisa Bayard and Alicia Fernandes and Chantal Brouzes and Carine Lefèvre and Romain Duval and Michaël Dussiot and Thiago Trovati and Geneviève Courtois and Slim Azouzi and Mohammed Zarhrate and Anne Lambilliotte and Sophie Park and Benjamin Carpentier and Martin Colard and Sandra Manceau and Despina Moshous and Patrick Mayeux and Emilie‐Fleur Gautier and Annarita Miccio and Jean Soulier and William Vainchenker and Liran Shlush and Lydie Da Costa and Jan Frayne and Eric Soler and Olivier Hermine and Lucile Couronné

HemaSphere (2025)

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2025

IFN-I-Mediated Transcriptional Reprogramming Drives Myeloid-skewed Hematopoiesis in Sickle Cell Anemia

Marion Serra and Marine Aglave and Mohammad Salma and Steven Akkaya and Patricia Hermand and Carine Lefevre and Romain Duval and Jade Merrer and Fallou Leye and Joelle Magne and Isabelle Plo and Lionel Blanc and Eric Soler and Slim Azouzi and Berengere Koehl

(2025)

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2025

In vivo deletion of a GWAS-identified Myb distal enhancer acts on Myb expression, globin switching, and clinical erythroid parameters in β-thalassemia

Virginie Deleuze and Tharshana Stephen and Mohammad Salma and Cédric Orfeo and Ruud Jorna and Alex Maas and Vilma Barroca and Marie-Laure Arcangeli and Charles-Henri Lecellier and Charlotte Andrieu-Soler and Frank Grosveld and Eric Soler

Scientific Reports (2025)

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2023

Efficient genome editing in erythroid cells unveils novel MYB target genes and regulatory functions

Virginie Deleuze and Leonor Garcia and Betty Rouaisnel and Mohammad Salma and Alexia Kinoo and Charlotte Andrieu-Soler and Eric Soler

IScience (2023)

View Publication
2023
Featured Tool

Var|Decrypt: a novel and user-friendly tool to explore and prioritize variants in whole-exome sequencing data

Salma M, et al.

Epigenetics & Chromatin (2023)

Developed a web-based tool that significantly streamlines WES data analysis, offering extensive gene and variant filtering, clustering, and enrichment tools without requiring complex bioinformatics skills.

View Publication
2023

High-throughput methods for the analysis of transcription factors and chromatin modifications

Salma M, et al.

Blood Cells, Molecules, and Diseases (2023)

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2022

ONTdeCIPHER: an amplicon-based nanopore sequencing pipeline for tracking pathogen variants

Cherif E, Thiam FS, Salma M, Rivera-Ingraham G, et al.

Bioinformatics (2022)

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2021

PPARγ agonists promote the resolution of myelofibrosis in preclinical models

Lambert J, Saliba J, Calderon C, Sii-Felice K, Salma M, et al.

Journal of Clinical Investigation (2021)

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2021
Most Cited - 86 Citations

p53 activation during ribosome biogenesis regulates normal erythroid differentiation

Le Goff S, Boussaid I, Floquet C, Raimbault A, Hatin I, Andrieu-Soler C, Salma M, et al.

Blood (2021)

Demonstrates how p53 activation during ribosome biogenesis plays a crucial role in regulating normal erythroid differentiation processes.

View Publication
2014

Comparison of droplet-vitrification and D-cryoplate for cryopreservation of date palm polyembryonic masses

Salma M, Fki L, Engelmann-Sylvestre I, Niino T, Engelmann F

Scientia Horticulturae (2014) - 39 Citations

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2014

Effect of the successive steps of a cryopreservation protocol on the structural integrity of Rubia akane Nakai hairy roots

Salma M, Engelmann-Sylvestre I, Collin M, Escoute J, Lartaud M, Yi JY, Kim HH, Verdeil JL, Engelmann F

Protoplasma (2014) - 21 Citations

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2017

Cryopreservation of Date Palm Pro-Embryonic Masses Using the D Cryo-plate Technique

Salma M, Engelmann F

Methods in Molecular Biology (2017)

View Publication
View All Publications on Google Scholar

19+

Publications

223

Citations

7

h-index

6

i10-index

Notable Projects

Var|Decrypt

A web-based tool for exploring and prioritizing variants in whole-exome sequencing data. Features extensive filtering, clustering, and enrichment capabilities without requiring complex bioinformatics skills.

Python Flask Exome-Seq
Learn More

ONTdeCIPHER

Nanopore-based pipeline for tracking pathogenic variants. Developed for real-time monitoring of SARS-CoV-2 and other pathogen variants using Oxford Nanopore sequencing.

Nanopore Snakemake Variant Calling
Learn More

NGS Analysis Pipelines

Comprehensive suite of bioinformatics pipelines for multi-omics analysis including RNA-Seq, ATAC-Seq, ChIP-Seq, and single-cell sequencing with automated QC and reporting.

Snakemake Nextflow Docker

ML for Genomics

Machine learning models for biomarker identification and predictive analysis in cancer genomics using TensorFlow and scikit-learn frameworks.

TensorFlow scikit-learn Python

Get in Touch

I'm always interested in discussing new opportunities, collaborations, and innovative projects in bioinformatics and data science.

Professional Email

mohammad.salma@igmm.cnrs.fr

Location

Montpellier, France