Translational Data Science – Facility
We work at the interface between data science and cancer immunology, with the goal to help scientists exploit large data efficiently. Our group provides the statistics, bioinformatics and computational expertise to molecular biology and applied research labs. We are part of the Swiss Institute of Bioinformatics and are physically located in the AGORA Cancer Research Center in Lausanne.
We actively participate in fundamental and translational research by providing expertise in data analysis of single-cell and bulk multi-omics, spatial transcriptomics, flow cytometry and various other sequencing and proteomics technologies. We have also proficiency in machine learning, multivariate regression, mixed-effect modeling, and longitudinal data analyses.
Our team is composed of highly motivated bioinformaticians with over 15 years of experience in cancer research, tumor microenvironment, but also vaccinology, virology, and other medical research topics. We are glad to hear from you, please contact us for questions and discussions
Our areas of expertise
- Single cell RNAseq, TCRseq, multiome and CITE-seq analysis
- Spatial transcriptomics
- Spectral Flow Cytometry, CyTOF
- Nanostring and protein arrays
- Bulk RNAseq, ChIPseq and ATACseq
- Functional analysis and transcriptional regulatory network
- Statistical analysis and modeling, longitudinal studies
- Machine learning and biomarker discovery
- Development and validation of prognostic and predictive signatures
- Exploration of publicly available databases
- Tailored pipeline development, shiny app
Our services
Our group offers a full support : from project planning and experimental design to data analysis and results interpretation. We produce publication ready figures and participate to manuscript and grant writing. We also provide expertise in the application of classic and new technologies in genomics to problems of clinical importance, such as development and assessment of the validity of biomarkers for diagnosis, prognosis or tumor profiling and classification. We propose statistical consulting, training (one-on-one, lectures, workshops), bioinformatics helpdesk.
We are also teaching statistics, single-cell / bulk RNAseq and functional analysis at the SIB Swiss Institute of Bioinformatics (https://www.sib.swiss/training/upcoming-training-courses).
Contact
Selected Publications
Fibrotic response to anti-CSF-1R therapy potentiates glioblastoma recurrence.
Watson SS, Zomer A, Fournier N, (…), Cossu G, Hottinger AF, Joyce JA
Cancer Cell – 2024 Sep 9
Interrogation of endothelial and mural cells in brain metastasis reveals key immune-regulatory mechanisms
Bejarano L, Kauzlaric A, Lamprou E, (…), Daniel RT, Hegi ME, Joyce JA
Cancer Cell – 2024 Jan 18
Cytokine-armed dendritic cell progenitors for antigen-agnostic cancer immunotherapy.
Ghasemi A, Martinez-Usatorre A, Li L, (…), Migliorini D, Heikenwalder M, De Palma M
Nature Cancer – 2023 Nov 23
The local microenvironment drives activation of neutrophils in human brain tumors.
Maas RR, Soukup K, Fournier N, (…), Roy DT, Hegi ME, Joyce JA
Cell – 2023 Sep 27
Reductive carboxylation epigenetically instructs T cell differentiation.
Jaccard A, Wyss T, Maldonado-Pérez N, (…), Romero P, Ho PC, Wenes M
Nature – 2023 Sep 20
Activation of the transcription factor NFAT5 in the tumor microenvironment enforces CD8(+) T cell exhaustion.
Tillé L, Cropp D, Charmoy M, (…), Carmona SJ, Held W, Verdeil G
Nature immunology – 2023 Sep 14
Resistance mechanism to Notch inhibition and combination therapy in human T-cell acute lymphoblastic leukemia.
Cao L, Ruiz Buendía GA, Fournier N, (…), Hamelin R, Pavlou M, Radtke F
Blood advances – 2023 Jun 26
Phenotypic diversity of T cells in human primary and metastatic brain tumors revealed by multiomic interrogation
Wischnewski V, Maas RR, Guerrero Aruffo P, (…), Hegi ME, Lugli E, Joyce JA
Nature Cancer – 2023 May 22
Bispecific PD1-IL2v and anti-PD-L1 break tumor immunity resistance by enhancing stem-like tumor-reactive CD8+ T cells and reprogramming macrophages
Tichet M, Wullschleger S, Chryplewicz A, (…), Umaña P, Klein C, Hanahan D
Immunity – 2023 Jan 10
Dendritic cells direct circadian anti-tumour immune responses.
Wang C, Barnoud C, Cenerenti M, (…), Pittet MJ, Jandus C, Scheiermann C
Nature – 2022 Dec 5
Aberrant hyperexpression of the RNA binding protein FMRP in tumors mediates immune evasion.
Zeng Q, Saghafinia S, Chryplewicz A, (…), Tichet M, Homicsko K, Hanahan D
Science – 2022 Nov 18
Multispectral fluorine-19 MRI enables longitudinal and noninvasive monitoring of tumor-associated macrophages
Croci D, Santalla Méndez R, Temme S, (…), Flögel U, van Heeswijk RB, Joyce JA
Science Translational Medicine – 2022 Oct 19
ADAMTS18(+) villus tip telocytes maintain a polarized VEGFA signaling domain and fenestrations in nutrient-absorbing intestinal blood vessels.
Bernier-Latmani J, Mauri C, Marcone R, (…), Delorenzi M, Brisken C, Petrova TV
Nature communications – 2022 Jul 9
