Summary

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.

Scope:

• 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

Programme

Start	End	Presenter	Title
8:35	8:40		Introduction / Welcome
8:40	9:00	Jean Fan, Harvard University (invited)	Integrated genetic and transcriptional analysis at the single-cell level
9:00	9:20	Kieran O'Neill, BC Cancer Agency	Determing the Mechanism of 5-Azacytidine Response in Myeloid Malignancies Using Single-cell DNA Methylation Sequencing Paired With Flow Cytometry
9:20	9:40	Sombeet Sahu, Mission Bio	Methods for Identifying Tumor Heterogeneity and Rare Subclones in Single Cell DNA Sequence Data
10:15	10:20		Welcome Back
10:20	10:40	Chris Yau, University of Birmingham (invited)	Scalable Bayesian Tensor Factorization for single-cell Genomics
10:40	11:00	Huidong Chen, Massachusetts General Hospital Research Institute	STREAM: Single-cell Trajectories Reconstruction, Exploration And Mapping of omics data
11:00	11:20	Sahar Ansari, University of Michigan	Leveraging transcription factor networks to identify cell types from single-cell transcriptomes
11:20	11:40	Xun Zhu, University of Hawaii Cancer Center	Granatum X: A community engaging and flexible scRNA-Seq analysis environment connecting tool developers to bench scientists
11:40	12:00	Wei Vivian Li, University of California, Los Angeles	scImpute: An accurate and robust imputation method for single-cell RNA-seq data
12:00	12:20	Davis McCarthy, EMBL-EBI (invited)	An approach to studying clonal cell populations using bulk exome and single-cell RNA sequencing data
12:20	12:40	Simone Ciccolella, Università degli studi Milano Bicocca	Inferring Cancer Progression from Single Cell Sequencing while allowing loss of mutations
			Lunch and posters
14:00	14:20	Florian Markowetz, CRUK Cambridge Institute (invited)	Inferring cancer evolution and mutational processes
14:20	14:40	Mohammed El-Kebir, University of Illinois at Urbana-Champaign	SPhyR: Tumor Phylogeny Estimation from Single-Cell Sequencing Data under Loss and Error
14:40	15:00	Violeta Beleva Guthrie, Johns Hopkins University	Single-cell sequencing analysis of pancreatic cancer precursor lesions reveals convergent evolution and polyclonal origins
15:00	15:20	Haoyun Lei, Carnegie Mellon University	Deconvolution of tumor copy number data using bulk and single-cell sequencing data
15:20	15:40	Katharina Jahn, ETH Zurich (invited)	Modelling tumour evolution from single-cell sequencing data
15:40	16:00	Bojan Losic, Icahn Institute for Muliscale Biology	Regulatory underpinnings of intra-tumor heterogeneity in HCC liver cancer
16:00	16:20	Sumon Ahmed, University of Manchester	Investigating Haematopoietic Stem Cells development by single cell sequencing
16:20	16:40	Rui Kuang, University of Minnesota Twin Cities	A 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.

Organizers

• 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