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:

• 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

• 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