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.
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, and data generation for data challenges. She joined the Methods and Algorithm for Genomics (MAGe) team in january 2024.
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 2018, she joined the team ’Methods and Algorithm for Genomics (MAGe)’ 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.
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
