Aug 24, 2021: [Publication] Our CHIPIN method accepted in BMC Bioinformatics

Please welcome a simple but super-effective method to normalize ChIP-seq data without Spike-ins when you have matched RNA-seq: Link to the paper
CHIPIN uses averaged ChIP-seq profiles along 10% of constant genes (user-defined) from all gene expression categories.

Aug 11, 2021: [Internship offer - Bachelor, Master theses, long/short research projects] Open internship positions

We are looking for Bachelor students and Master students at ETH Zurich (D-INFK, D-BSSE, D-BIOL, D-MATH, but also mobility students from EPFL are welcome to apply). Please check this page for more information!

April 22, 2021: [Internship offer - Bachelor, Master theses, long/short research projects] We are looking for Bachelor students and Master students at ETH Zurich (D-INFK, D-BSSE, D-BIOL, D-MATH, but also mobility students from EPFL are welcome to apply)

Our team is looking for students to work on several topics including:

1. Infering ploidy and purity of cancer samples [machine learning, C/C++]
2. Neural networks for signal deconvolution in cancer transcriptomics data [machine learning]
3. Detection of shared transcriptional programs from single cell transcriptomics data in cancer [machine learning]
4. Multi-omics data integration for cancer patients' survival [biomedicine, data analysis, machine learning]
5. Deconvolution of epigenetic data from mixed tumor samples [deconvolution, computational methods]
6. Analysis of ChIP-seq data in adrenocortical carcinoma [data analysis, biology]
7. Transcriptional heterogeneity in mesothelioma [data analysis, biology]
8. Reconstruction of gene regulatory interactions using machine learning [machine learning]
9. Prediction of intratumoral heterogeneity using bulk transcriptional data from cancer samples [deconvolution, machine learning]
10. Digging deep into intratumoral heterogeneity in melanoma and neuroblastoma using scRNA-seq data [data analysis]
11. Analysis of genomic events driving transcriptional programs in cancer [data analysis]
12. Analysis of tumor microenvironmnet in melanoma [data analysis, biology]

To get more information, please, contact Valentina Boeva directly.

May 19, 2020: [Internship offer] We are looking for Bachelor students and Master students at ETH Zurich

Our team is looking for students to work on several projects including:

1. Neural networks for signal deconvolution in cancer transcriptomics data [machine learning]
2. Combination of pathway databases for use in ML survival models [biomedicine, machine learning]
3. Analysis of H&E staining images for cancer biomarkers [image analysis, machine learning]
4. Multi-omics data integration for cancer patients' survival [biomedicine, data analysis, machine learning]
5. Detection of chimeric genes from transcriptional data with genomic prior [computational methods]
6. Deconvolution of epigenetic data from mixed tumor samples [deconvolution, computational methods]
7. Intergrative analysis of genomic, transcriptomic and epigenetic data in cholangiocarcinoma (collaboration with Mayo Clinics) [data analysis, biology]
8. Analysis of ChIP-seq data in adrenocortical carcinoma [data analysis, biology]
9. Characterization of the DNA hypermethylation phenotype in the pan-cancer context [data analysis, machine learning]
10. Transcriptional heterogeneity in mesothelioma [data analysis, biology]
11. Embedding in low dimensions for population migration tracking [data analysis, machine learning]

To get more information, please, contact Valentina Boeva Valentina Boeva directly.

Oct 1, 2019: [Hiring] Welcome to talented postdocs and visiting PhD!

Dr Gabriela Malenova, Dr Daniel Rowson and Ms Agnieszka Kraft

Aug 22, 2019: [Conference] Do not miss the conference we organize in the Swiss Alps!
Genomic Regulation 2020: Focus on Cancer

Please, check the conference website for more information, abstract submission and registration! Keep in mind that the number of pre-booked hotel rooms is limited. First come, first served.

July 30, 2019: [Internship offer] We are looking for Master students at ETH Zurich

Our team is looking for Master students to work on several master projects including:

1. Reconstruction of gene regulatory interactions using machine learning [machine learning]
2. Adaptation of group lasso to survival analysis [machine learning]
3. Infering ploidy and purity of cancer samples [machine learning]
4. Prediction of intratumoral heterogeneity using bulk transcriptional data from cancer samples [deconvolution, machine learning]
5. Analysis of H&E staining images for cancer biomarkers [image analysis, machine learning]
6. Detection of chimeric genes from transcriptional data with genomic prior [computational methods]
7. Deconvolution of epigenetic data from mixed tumor samples [deconvolution, computational methods]
8. Digging deep into intratumoral heterogeneity in melanoma and neuroblastoma using scRNA-seq data [data analysis]
9. Intergrative analysis of genomic, transcriptomic and epigenetic data in cholangiocarcinoma (collaboration with Mayo Clinics) [data analysis]
10. Analysis of genomic events driving transcriptional programs in cancer [data analysis]

To get more information, please, contact Valentina Boeva Valentina Boeva directly.

April 6, 2019: [Job offer] We are looking for post-doctoral researchers (Zurich, 1 year contract renewable)

Our team is looking for post-doctoral researchers to work on Machine learning methods applied to cancer epigenetics.
You can find more details and apply for the position here.

April 6, 2019: [Internship offer] We are looking for Master students

Our team is looking for Master students to work on Reconstruction of gene regulatory interactions using machine learning.
You can find more details here.

April 5, 2019: Starting a new lab at ETH Zurich: stronger focus on Computer Science

Starting from June 1st, 2019, we will open a second lab at ETH Zurich, Department of Computer Science. The PI, Valentina Boeva, got a position of assistant professor in biomedical informatics.

Oct 22, 2018: We are looking for a post-doctoral researcher (Paris, 2.5 years)

Our team is looking for a post-doctoral researcher to work on epigenetic heterogeneity and cell plasticity in neuroblastoma in the context of tumor aggressiveness and sensitivity to treatment.
You can find more details here. The deadline for the application: Dec 1, 2018.

Oct 20, 2018: We are looking for master students (enrolled in French University programs)

Apply if you want to learn more about cancer and about epigenetics! You will also improve you programming skills and learn new data analysis techniques. We are looking for Master student for two projects:

• Understanding transcriptional and epigenetic heterogeneity in human cancers - Link
• Reconstruction of transcriptional circuitries based on epigenetic data of cancer samples - Link

Please, contact the lab directly to get more details about the projects. Or check the www.sfbi.fr website.

Jul 20, 2018: Three grants accepted in only 2 weeks

We will be recruiting a postdoc and a research assistant to work in cancer bioinformatics projects very soon. Stay tuned!

Jul 15, 2018: France world champion 2018!

Watching the semi-final game with the team

Mar 5, 2018: Neuroblastoma copy number paper is online in the Journal of the National Cancer Institute

Genomic amplifications and distal 6q-loss: novel markers for poor survival in high-risk neuroblastoma patients. P. Depuydt, V. Boeva, T.D. Hocking, R. Cannoodt, I.M. Ambros, P.F. Ambros, S. Asgharzadeh, E.F. Attiyeh, V. Combaret, R. Defferrari, M. Fischer, B. Hero, M.D. Hogarty, M.S. Irwin, J. Koster, S. Kreissman, R. Ladenstein, E. Lapouble, G. Laureys, W.B. London, K. Mazzocco, A. Nakagawara, R. Noguera, M. Ohira, J.R. Park, U. Pötschger, J. Theissen, G.P. Tonini, D. Valteau-Couanet, L. Varesio, R. Versteeg, F. Speleman, J.M. Maris, G. Schleiermacher, K. De Preter. JNCI. Journal of the National Cancer Institute. 2018 Mar 5. doi: 10.1093/jnci/djy022. [Epub ahead of print]. PMID: 29514301 Link to the paper

Feb 3, 2018: Today we support Worldwide Cancer Research!

#livesturnedupsidedown #upsidedownselfie

Jan 13, 2018: QuantumClone paper is online in Bioinformatics

QuantumClone: Clonal assessment of functional mutations in cancer based on a genotype-aware method for clonal reconstruction. P. Deveau, L. Colmet Daage, D. Oldridge, V. Bernard, A. Bellini, M. Chicard, N. Clement, E. Lapouble, V. Combaret, A. Boland, V. Meyer, J.-F. Deleuze, I. Janoueix-Lerosey, E. Barillot, O. Delattre, J. Maris, G. Schleiermacher, and V. Boeva. Bioinformatics. Accepted for publication. Link to the paper

July 24, 2017: Neuroblastoma heterogeneity paper is online in Nature Genetics

Heterogeneity of neuroblastoma cell identity defined by transcriptional circuitries. V. Boeva, et al., Nature Genetics. published online July 24, 2017. PMID: 28740262. doi: 10.1038/ng.3921. Link to the paper

Juin 27, 2017: PhD defense of Paul Deveau

December 15, 2016: HMCan-diff paper has been accepted for publication in Nucleic Acids Research

HMCan-diff: a method to detect changes in histone modifications in cells with different genetic characteristics. H. Ashoor, C. Louis-Brennetot, I. Janoueix-Lerosey, V.B. Bajic, and V. Boeva. Nucleic Acids Research. Accepted for publication. Link to the method

November 28, 2016: PhD defense of Karel Brinda

October 28, 2016: Our Russian-French collaborative team has won the first phase of the ENCODE-DREAM Challenge for in vivo Transcription Factor Binding Site Prediction

We are hiring post-doctoral researchers

• Your background is in mathematics, statistics or bioinformatics, you have already developed statistical approaches to analyze biological data?
• Or you are a biologist who is interested in the generation and analysis of high-throughput datasets to understand changes in the genome and epigenome taking place in cancer?

• You want to work in Europe, contribute to cancer treatment and have access to patients data?

• And on the top of that you enjoy French wine and cheese, love picnics, bouldering and traveling?

• Then the Boeva lab is for you. Read the advertisement and apply!

We are looking for master students (enrolled in French University programs only)

Apply if you want to learn more about cancer and about epigenetics! You will also improve you programming skills and learn new data analysis techniques.
We are looking for Master student for two projects:

• Changes in the 3D structure of the chromatin in cancer.
• Role of the Spi1/PU.1 transcription factor in RNA and DNA regulation and leukemogenesis

Please, contact the lab directly to get more details about the projects.

July 23, 2016, we welcomed our wet lab technician: Marie-Ange Calmejane!

April 1, 2016: official lab openning!