SCANGEN: Single-Cell Cancer Genomics

Workshop at ISMB 2018


The first workshop on single-cell cancer genomics (SCANGEN) will take place on July 10th at ISMB 2018 in Chicago, USA. The workshop aims to cover computational and statistical methods, models, and applications in single-cell cancer genomics.


  • Modelling cancer evolution: phylogenetic inference from single-cell data; inference of evolutionary processes from single-cell data; identifying single-cell cancer signatures; inference of fitness from single-cell analysis of population dynamics
  • Integrative analyses of multi-modal data: modelling of joint measurement assays (such as G&T-seq); relating and interpreting measurements from different technologies
  • Scalable inference at the single-cell level: scalable statistical inference for single-cell data using methods such as stochastic optimization; computational tools for dealing with large single-cell datasets
  • Interactions and perturbations at the single-cell level: how cells interact with their microenvironment; how cells respond to and resist chemotherapeutic interventions; how transcriptional programming and clonal selection are affected by genomic perturbations such as CRISPR


Start End Presenter Title
8:358:40 Introduction / Welcome
8:409:00Jean Fan, Harvard University (invited) Integrated genetic and transcriptional analysis at the single-cell level
9:009:20Kieran O'Neill, BC Cancer AgencyDeterming the Mechanism of 5-Azacytidine Response in Myeloid Malignancies Using Single-cell DNA Methylation Sequencing Paired With Flow Cytometry
9:209:40Sombeet Sahu, Mission BioMethods for Identifying Tumor Heterogeneity and Rare Subclones in Single Cell DNA Sequence Data
10:1510:20 Welcome Back
10:2010:40Chris Yau, University of Birmingham (invited)Scalable Bayesian Tensor Factorization for single-cell Genomics
10:4011:00Huidong Chen, Massachusetts General Hospital Research InstituteSTREAM: Single-cell Trajectories Reconstruction, Exploration And Mapping of omics data
11:0011:20Sahar Ansari, University of MichiganLeveraging transcription factor networks to identify cell types from single-cell transcriptomes
11:2011:40Xun Zhu, University of Hawaii Cancer CenterGranatum X: A community engaging and flexible scRNA-Seq analysis environment connecting tool developers to bench scientists
11:4012:00Wei Vivian Li, University of California, Los AngelesscImpute: An accurate and robust imputation method for single-cell RNA-seq data
12:0012:20Davis McCarthy, EMBL-EBI (invited)An approach to studying clonal cell populations using bulk exome and single-cell RNA sequencing data
12:2012:40Simone Ciccolella, Università degli studi Milano BicoccaInferring Cancer Progression from Single Cell Sequencing while allowing loss of mutations
  Lunch and posters
14:0014:20Florian Markowetz, CRUK Cambridge Institute (invited)Inferring cancer evolution and mutational processes
14:2014:40Mohammed El-Kebir, University of Illinois at Urbana-ChampaignSPhyR: Tumor Phylogeny Estimation from Single-Cell Sequencing Data under Loss and Error
14:4015:00Violeta Beleva Guthrie, Johns Hopkins UniversitySingle-cell sequencing analysis of pancreatic cancer precursor lesions reveals convergent evolution and polyclonal origins
15:0015:20Haoyun Lei, Carnegie Mellon UniversityDeconvolution of tumor copy number data using bulk and single-cell sequencing data
15:2015:40Katharina Jahn, ETH Zurich (invited)Modelling tumour evolution from single-cell sequencing data
15:4016:00Bojan Losic, Icahn Institute for Muliscale BiologyRegulatory underpinnings of intra-tumor heterogeneity in HCC liver cancer
16:0016:20Sumon Ahmed, University of Manchester Investigating Haematopoietic Stem Cells development by single cell sequencing
16:2016:40Rui Kuang, University of Minnesota Twin CitiesA multitask learning approach for clustering multiple single cell RNA-seq datasets

Call for submissions

The call for submissions is now closed.

Travel award for early career researchers

We are pleased to offer two travel awards of $1000USD to PhD students and postdocs, generously supported by Memorial Sloan Kettering Cancer Centre. To apply, first submit your work to SCANGEN then email kicampbell _at_ bccrc _dot_ ca indicating that you wish to be considered for an award.

Workshop info

The workshop is co-located at ISMB 2018 in Chicago, USA. It will be held on July 10th. For information on the venue, hotels, registration, and travel, see the main ISMB conference page.


  • Kieran R Campbell, Postdoctoral Fellow, University of British Columbia kicampbell _at_ bccrc _dot_ ca
  • Sohrab P Shah, Canada Research Chair in Computational Cancer Biology, University of British Columbia