Bioinformatics · Montpellier, France

Mohammad SalmaPhD

Senior Bioinformatician & Data Scientist

I analyse sequencing data to understand blood disorders and gene regulation. I also build tools that make genomic analysis easier to use.

Explore my work Get in touch

Research & tools

Recent research · 2026

A better control for ATAC-seq

We showed that using whole-genome sequencing as a control improves ATAC-seq peak calling.

NAR Genomics and Bioinformatics

Explore the publications

Variant analysis

Var|Decrypt

Explore and prioritise variants in whole-exome sequencing data.

Nanopore sequencing

ONTdeCIPHER

An amplicon-based sequencing pipeline for tracking pathogen variants.

About Me

Bioinformatician and data scientist working on sequencing data since 2018, at IGMM, Institut Imagine and IRCM.

Much of my work concerns how red blood cells are made and what goes wrong in inherited blood disorders: single-cell analysis of CD34+ cells in sickle cell anaemia, a Myb enhancer deletion in β-thalassaemia, and the ZEB1–GATA2–KLF1 switch published in Nucleic Acids Research in 2026. At IRCM, I also worked on cancer genomics.

I also develop machine-learning methods for gene regulation. RegFiT (manuscript in preparation) reconstructs enhancer-based gene regulatory networks from paired ATAC-seq and RNA-seq data, from as few as two experimental conditions. Applied to eight stages of erythroid differentiation, it identified a functional interaction between the erythroid transcription factor KLF1 and ZEB1, which was then validated experimentally.

I have supervised bioinformatics engineers and doctoral students, and managed bioinformatics and data science projects at Institut Imagine from 2025 to 2026. Since October 2026 I am back at IGMM, and I continue to collaborate with members of the GR-Ex Laboratory of Excellence (InIdex GR-Ex).

PhD in Biotechnology

University of Montpellier

Experience Since 2018

Bioinformatics & Data Science

18 Publications

267 Citations, h-index: 8

Professional Experience

October 2026 - Present

Senior Bioinformatics & Data Scientist

IGMM - Institut de Génétique Moléculaire de Montpellier (CNRS)

Montpellier, France

  • Continuing collaboration with members of the Laboratory of Excellence GR-Ex (InIdex GR-Ex)
  • Coordinated multidisciplinary teams and project deliverables
  • Implemented genomic analysis workflows
June 2025 - September 2026

Project Manager

Institut Imagine | Bioinformatics & Data Science

Montpellier, France

  • Led bioinformatics and data science projects for genetic disease research
  • Coordinated multidisciplinary teams and project deliverables
  • Implemented 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

NGS Analysis

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

Programming

Python R Bash PHP JavaScript

Development

Flask Streamlit RShiny GitHub GitLab

Selected Publications

2026

Controlling for DNA dosage with whole-genome sequencing improves ATAC-seq peak calling

Christophe Vroland, Mohammad Salma, Artemy Zhigulev, Pelin Sahlen, Eric Soler, Laurent Bréhélin and Charles-Henri Lecellier

NAR Genomics and Bioinformatics (2026)

View Publication
2026
NAR Breakthrough Article Co-First Author

ZEB1 drives terminal erythroid maturation by controlling the GATA2–KLF1 regulatory switch

Alexia Kinoo, Virginie Deleuze, Mohammad Salma, Noémie Legoff, Jérémie Candotti, Pedro Gonzalez-Menendez, Axel Joly, Jérémy Galtier, Julie Charmeaux-Goulot, Sanjay Chahar, Peggy Raynaud, Haoyang Zheng, Betty Rouaisnel, Quentin Bouvier, Céline Faux, Frédérique Verdier, Dominique Helmlinger, Sara El Hoss, Thiago Trovati Maciel, Naomi Taylor, Olivier Hermine, Sandrina Kinet, Charlotte Andrieu-Soler and Eric Soler

Nucleic Acids Research (2026)

Selected as an NAR Breakthrough Article — the journal's highest distinction, reserved for the top 1–2% of papers. Alexia Kinoo, Virginie Deleuze and Mohammad Salma contributed equally as co-first authors.

View Publication
2026

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

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

American Journal of Hematology (2026)

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2026

VEXAS anemia is a mosaic erythroblastopenia

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

Blood (2026)

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2025

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

Hanane Chamma, Soumyabrata Guha, Roger Junior Eloiflin, Adeline Augereau, Pierre Le Hars, Moritz Schüssler, Yasmine Messaoud-Nacer, Mohammad Salma, Joe McKellar, Joanna Re, Morgane Chemarin, Arnaud Carrier, Michael A Disyak, Clara Taffoni, Robin Charpentier, Zoé Husson, Emmanuel Valjent, Charlotte Andrieu-Soler, Eric Soler, Maria H Christensen, Søren R Paludan, Florian I Schmidt, Daniela Tropea, Karim Majzoub, Isabelle K Vila and Nadine Laguette

Nature Communications (2025)

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2025

MMS22L is a novel key actor of normal and pathological erythropoiesis

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

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

Scientific Reports (2025)

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2023

Single cell analysis and functional features of circulating CD34+ cells from patients with sickle cell anaemia unveil a defect in the myeloid lineage

Marion Serra, Patricia Hermand, Romain Duval, Carine Lefevre, Jade Merrer, Fallou Leye, Mohammad Salma, Marine Aglave, William Vainchenker, Caroline Le Van Kim, Slim Azouzi and Berengere Koehl

Blood (2023)

View Publication
2023

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

Virginie Deleuze, Leonor Garcia, Betty Rouaisnel, Mohammad Salma, Alexia Kinoo, 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

Mohammad Salma, Elina Alaterre, Jérôme Moreaux and Eric Soler

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

Mohammad Salma, Charlotte Andrieu-Soler, Virginie Deleuze and Eric Soler

Blood Cells, Molecules, and Diseases (2023)

View Publication
2022

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

Emira Cherif, Fatou Seck Thiam, Mohammad Salma, Georgina Rivera-Ingraham, Fabienne Justy, Theo Deremarque, Damien Breugnot, Jean-Claude Doudou, Rodolphe Elie Gozlan and Marine Combe

Bioinformatics (2022)

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2021

PPARγ agonists promote the resolution of myelofibrosis in preclinical models

Juliette Lambert, Joseph Saliba, Carolina Calderon, Karine Sii-Felice, Mohammad Salma, Valérie Edmond, Jean-Claude Alvarez, Marc Delord, Caroline Marty, Isabelle Plo, Jean-Jacques Kiladjian, Eric Soler, William Vainchenker, Jean-Luc Villeval, Philippe Rousselot and Stéphane Prost

Journal of Clinical Investigation (2021)

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2021
Most Cited - 95 Citations

p53 activation during ribosome biogenesis regulates normal erythroid differentiation

Salomé Le Goff, Ismael Boussaid, Celia Floquet, Anna Raimbault, Isabelle Hatin, Charlotte Andrieu-Soler, Mohammad Salma, Marjorie Leduc, Emilie-Fleur Gautier, Boris Guyot, Diane d’Allard, Nathalie Montel-Lehry, Sarah Ducamp, Amandine Houvert, Francois Guillonneau, Stephane Giraudier, Elisabeth Cramer-Borde, Francois Morle, Jean-Jacques Diaz, Olivier Hermine, Naomi Taylor, Sandrina Kinet, Frédérique Verdier, Rose-Ann Padua, Narla Mohandas, Pierre-Emmanuel Gleizes, Eric Soler, Patrick Mayeux and Michaela Fontenay

Blood (2021)

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

View Publication
2017

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

Mohammad Salma and Florent Engelmann

Methods in Molecular Biology (2017)

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2014

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

Mohammad Salma, Lotfi Fki, Isabelle Engelmann-Sylvestre, Takao Niino and Florent Engelmann

Scientia Horticulturae (2014) - 41 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

Mohammad Salma, Isabelle Engelmann-Sylvestre, Myriam Collin, Jacques Escoute, Marc Lartaud, Jung-Yoon Yi, Haeng-Hoon Kim, Jean-Luc Verdeil and Florent Engelmann

Protoplasma (2014) - 23 Citations

View Publication
2012

Improved cryopreservation using droplet-vitrification and histological changes associated with cryopreservation of Madder (Rubia akane Nakai)

Jung-Yoon Yi, Isabelle Sylvestre, Myriam Colin, Mohammad Salma, Sok-Young Lee, Haeng-Hoon Kim, Hong-Jae Park and Florent Engelmann

원예과학기술지 (2012)

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Google Scholar metrics as of .

18

Publications

267

Citations

8

h-index

7

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

Get in touch about collaborations on sequencing data, chromatin accessibility or gene regulatory networks, questions about Var|Decrypt or ONTdeCIPHER, or job opportunities.

Professional Email

mohammad.salma@igmm.cnrs.fr

Location

Montpellier, France