SCANGEN: Single-Cell Cancer Genomics

Workshop at ISMB 2020


The second workshop on single-cell cancer genomics (SCANGEN) will take place virtually on Tuesday, July 14th 2pm-5.30pm ET at ISMB 2020. The workshop aims to cover computational and statistical methods, models, and applications in single-cell cancer genomics.

Contributed talks and posters are now closed.


  • 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 (ET) End (ET) Presenter Title
14:0014:20Smita Krishnaswamy, Yale (invited) Deep Representation Learning for Problems in Biology
14:2014:40Laura Richards, TorontoGradient of developmental and injury-response transcriptional states define roots of glioblastoma heterogeneity
14:4015:00Claudia Kleinman, McGill (invited)Inferring the origins of pediatric brain tumors by single-cell analysis of the normal developing brain
15:0015:20 Break
15:2015:40Ben Raphael, Princeton (invited)Copy number aberrations from single-cell sequencing
15:4016:00Xiangqi Bai, Chinese Academy of SciencesJoint Inference of Clonal Structure using Single-cell DNA-Seq and RNA-Seq data
16:0016:20Yingxin Lin, University of Sydney Integrative analysis of breast cancer survival based on spatial features
17:0017:20Sohrab Shah, MSKCC (Invited) Single cell whole genome sequencing for studying cancer evolution
17:2017:40Lingfei Wang, Broad InstituteNormalisr: inferring single-cell differential and co-expression with linear association testing

Invited speakers

  • Smita Krishnaswamy, Yale
  • Sohrab Shah, Memorial Sloan Kettering Cancer Center
  • Claudia Kleinman, McGill
  • Ben Raphael, Princeton

Workshop info

The workshop is co-located at ISMB 2020. Due to the ongoing Covid-19 situation, the entire conference will now be held virtually, on Tuesday July 14th. For information on registration, see the main ISMB conference page.


Kieran R Campbell, Principal Investigator, Lunenfeld-Tanenbaum Research Institute & University of Toronto

kierancampbell _at_ lunenfeld _dot_ ca

Previous meetings