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
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
c-MAF coordinates enterocyte zonation and nutrient uptake transcriptional programs.
González-Loyola A, Bernier-Latmani J, Roci I, (…), Zamboni N, Verdeil G, Petrova TV
The Journal of experimental medicine – 2022 Sep 19
Connexins orchestrate progression of breast cancer metastasis to the brain by promoting FAK activation.
Lorusso G, Wyss CB, Kuonen F, (…), Delorenzi M, Bikfalvi A, Rüegg C
Science translational medicine – 2022 Sep 7
Integrated multi-omics reveals cellular and molecular interactions governing the invasive niche of basal cell carcinoma.
Yerly L, Pich-Bavastro C, Di Domizio J, (…), Gilliet M, Werner S, Kuonen F
Nature communications – 2022 Aug 20
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
Gliadin-reactive vitamin D-sensitive proinflammatory ILCPs are enriched in celiac patients.
Ercolano G, Moretti A, Falquet M, (…), Salvatore S, Jandus C, Trabanelli S
Cell reports – 2022 Jun 14
Apelin-driven endothelial cell migration sustains intestinal progenitor cells and tumor growth.
Bernier-Latmani J, Cisarovsky C, Mahfoud S, (…), Delorenzi M, Sempoux C, Petrova TV
Nature cardiovascular research – 2022 May 16
c-Maf enforces cytokine production and promotes memory-like responses in mouse and human type 2 innate lymphoid cells.
Trabanelli S, Ercolano G, Wyss T, (…), Adotevi O, Jandus C, Verdeil G
The EMBO journal – 2022 Apr 25
The mitochondrial pyruvate carrier regulates memory T cell differentiation and antitumor function.
Wenes M, Jaccard A, Wyss T, (…), Lunt SY, Ho PC, Romero P
Cell metabolism – 2022 Apr 21
Tcf1 is essential for initiation of oncogenic Notch1-driven chromatin topology in T-ALL.
Antoszewski M, Fournier N, Ruiz Buendía GA, (…), Weng AP, Koch U, Radtke F
Blood – 2022 Apr 21
Loss of vascular endothelial notch signaling promotes spontaneous formation of tertiary lymphoid structures.
Fleig S, Kapanadze T, Bernier-Latmani J, (…), Haller H, Petrova TV, Limbourg FP
Nature communications – 2022 Apr 19
