Sophie Abby received a bi-disciplinary education in biology and computer sciences. She is an evolutionary biologist, particularly interested in the mechanisms of diversification of archaea and bacteria. She studies these at different scales: from enzymes and metabolic pathways, to macromolecular complexes and genome dynamics in response to environmental adaptations. She also develops methods in the field of comparative genomics and phylogenomics, in particular for genome annotation.
Elise Amblard joined the lab as a post-doctoral researcher in early 2022. During her doctoral work, she worked on scRNAseq datasets with two focuses in mind. She was trying to characterize how immune cells were modified from a healthy tissue to a tumoral one, while also working on improving bioinformatical tools for the analysis of scRNAseq data in general. She is now working in the team on how to benchmark and improve algorithms to deconvolve bulk data across various omics.
Victor Bañon Garcia is a PHD student working on “Systematic study of inverted repeated sequences in prokaryotic genomes” under the supervision of Ivan Junier and Nelle Varoquaux.
Sophie-Carole Chobert is a PhD candidate trained in bioinformatics. She is interested in the evolution of microorganisms and their adaptation to their environment. Her thesis focuses on a family of molecules with a key role in respiratory chains of most living organisms: the isoprenoid quinones. She aims at deciphering the origins and diversification of their biosynthetic pathways. She is supervised by Sophie Abby and Fabien Pierrel.
My name is Quentin FERNANDEZ DE GRADO, and I am currently in the second year of my PhD at TIMC, within the MAGe team. My thesis aims to enhance our knowledge of the evolutionary mechanisms impacting an organism’s journey toward adaptation. First, we will study the selective pressures that shape the order of genes in operons. Second, we will investigate the evolutionary mechanisms that affect the evolution of a population’s mutation rate, and the impact on the genome organization.
Antoine is a research faculty who does cool stuff!
Flora Gaudillière is a PhD student working on the role of insertion sequences in the evolution and adaptation of prokaryotic genomes. She combines bioinformatic approaches with wet lab experiments. She is supervised by Ivan Junier and Thomas Hindré.
Ivan Junier is the resident biophycist expert. He works on rationalising the tinkering that has shaped the content, organisation and structuring of bacterial genomes. To this end, he develops quantitative, biophysical models of DNA in interaction with various fundamental proteins and molecular machineries that are crucial for gene expression, chromosome replication and chromosome segregation. To navigate in the (sometimes dark) space of bacterial genomes, he uses comparative genomics and statistical methods to distinguish between universal and idiosyncratic features.
Sandy Frank Kwamou Ngaha is a PHD student working on the Detection of new secretion systems in collaboration with experts in these systems under the supervisions of Nelle VAROQUAUX and Sophie ABBY
Lucie Lamothe is a research engineer working on improving deconvolution methods for Pancreatic ductal adenocarcinoma (PDAC) data by creating a single-cell RNA-seq atlas, as well as generate data for data challenges. She joined the Bigre in january 2024. Now part of the Aptikal Team at LIG (Laboratoire d’informatique de Grenoble).
[Nicolas Louviaux] is a PhD student that arrived in TIMC laboratory in february 2024. His research subject is about the interactions between migrating cells and their surrounding environment (the extra-cellular matrix). In order to displace their nucleus, cells anchor to the substrate and contract their cytoskeleton yielding traction forces exerted on the matrix. Those forces deform the substrate and modify its mechanical properties (such as stiffness), which in turn bias the direction of motion of cells, for example in the direction of higher stiffness (e.g. durotaxis). The objective of the thesis is to study a long range communication between migrating cells through the matrix deformations using a bio-mechanical model of cell coupled with a deformable substrate modelled using finite elements method.
Magali Richard was initially trained in biology (experimental genetics and cell biology). During her postdoc, she joined a multidisciplinary team made up of biologists, computer scientists and statisticians to learn how to develop biostatistical approaches to analyse high-throughput omic data. Then she became interested in the evolution of tumor as a complex heterogeneous ecosystem. In 2025, she joined the LIG (team ’APTIKAL’) as a CNRS researcher to tackle this question through the development of novel dedicated computational approaches.
Morgane Roger-Margueritat is a PhD student working on the impact of quinone exchanges on the gut microbiota. She combines experimental and bioinformatic approaches. She is supervised by Fabien Pierrel and Sophie Abby.
Timothée SALZAT-HERVOUETTE is a PhD student researching the evolution and distribution of phototrophy in Pseudomonadota. He holds a degree in Bioinformatics from the University of Nantes and specializes in gene cluster detection, phylogeny, and comparative genomics. His work also involves analyzing public datasets from NCBI, GTDB, and IMG/PR. He is supervised by Sophie Abby and Fabien Pierrel
Zakaria Tougui is a PhD student working on the quantitative characterisation of the human gut microbiome, with a focus on the small intestine, combining publicly available data with data obtained from collaborators at TIMC using a newly developped non-invasive sampling method. This thesis is supervised by Antoine Frénoy, Nelle Varoquaux and Philippe Cinquin
