Year 2020
Oral Presentations:
- M Gauthier gave a talk at the online ISCB Conference
- L Villain gave a talk at the online ISCB Conference
- B Hejblum gave a talk at the SMPGD 2020 annual workshop in Paris
Scientific progress:
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Completed:
- implementation and validation of a method for differential gene expression analysis in single-cell RNA-seq data relying on the estimation of the conditional cumulative distribution function in the ccdf R package
- extension of Gene Set Analysis methods for RNA-seq data to time-to-event outcomes
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Ongoing:
- develoement of a new method for doubly-robust evaluation of high-dimensional surrogate markers
- development of a new framework for optimal surrogacy analysis in vaccine development (R21 application to NIH)
Supervision:
- Master thesis: Gene Set Analysis of RNA-seq data for time-to-event response by Benjamin Hivert
- Master thesis: Meta-analysis over the results of Generalized-Berk Jones and dearseq applied on 18 studies on Breast cancer to identify the gene sets linked to a tumor grade by Arulmani Thiyagarajan
Year 2019
Oral Presentations:
- B. Hejblum gave an invited talk at the EcoSta Conference in Taïchung (Taïwan)
- B. Hejblum gave an talk at the Joint Statistical Meeting in Denver (USA)
- L. Villain gave a talk at the Journées Statistiques et Santé meeting in Paris (France)
- M. Gauthier will give a talk at the StatOmique meeting in Paris (France)
Scientific progress:
-
Completed:
- preprint introducing dearseq method for robust gene-wise analysis of RNA-seq data
- implementation of the above method in the dearseq R package (publicly available)
- development of a method for differential gene expression analysis in single-cell RNA-seq data relying on the estimation of the conditional cumulative distribution function
-
Ongoing:
- implementation and validation of the above method for scRNA-seq
- surrogacy analysis in high-dimensional setting for quantifying how much of the immune response can be explained from gene expression RNA-seq measurements in vaccine trials (R21 application to NIH)
- extension of Gene Set Analysis methods for RNA-seq data to time-to-event outcomes
Visits:
- SWAGR strategic meeting at the RAND Corporation in Boston (USA) in November 2019 (1 week – work agenda)
Supervision:
- Post-doctoral project: Gene Set Analysis of RNA-seq data for time-to-event response by Laura Villain
Year 2018
Oral Presentations:
- B. Hejblum talk at the International Biometric Conference in Barcelona
- D. Agniel talk at the Joint Statistical Meeting in Vancouver
- B. Hejblum invited talk at the Genotoul Biostat Biofinfo day 2018 in Toulouse
Scientific progress:
-
Completed:
- simulation study examplifying the lack of Type-I error and FDR control from state-of-the-art RNA-seq differential expression methods
- varseq method for gene-wise analysis of bulk RNA-seq data
- Effective FDR control method for discrete p-values arising from permutation tests (useful for small sample size studies)
- implementation of the above method in the tcgsaseq R package
Visits:
- SWAGR meeting at the RAND Corporation in Santa Monica in July 2018 (10 days)
Supervision:
- Master 2 thesis: Test en composante de variance pour l’analyse de données RNA-seq by Marine Gauthier