Sandrine Dudoit

Division of Biostatistics and Department of Statistics, University of California, Berkeley
United States

http://www.stat.berkeley.edu/~sandrine

Presentation Title: Identification of Novel Cell Types in the Brain Using Single-Cell Transcriptome Sequencing
Time: Monday, July 11th 9:00 am - 10:00 am
Introduction by: Janet Kelso
Room: Northern Hemisphere BCD, Dolphin Hotel

Abstract

Single-cell transcriptome sequencing (scRNA-Seq), which combines high-throughput single-cell extraction and sequencing capabilities, enables the transcriptome of large numbers of individual cells to be assayed efficiently. Profiling of gene expression at the single-cell level for a large sample of cells is crucial for addressing many biologically relevant questions, such as, the investigation of rare cell types or primary cells (e.g., early development, where each of a small number of cells may have a distinct function) and the examination of subpopulations of cells from a larger heterogeneous population (e.g., classifying cells in brain tissues).

I will discuss some of the statistical analysis issues that have arisen in the context of a collaboration funded by the Brain Research through Advancing Innovative Neurotechnologies (BRAIN) Initiative, with the aim of classifying neuronal cells in the mouse somatosensory cortex. These issues, ranging from so-called low-level to high-level analyses, include: experimental design, exploratory data analysis (EDA) of scRNA-Seq reads, quality assessment/control (QA/QC), normalization to account for nuisance technical effects, cluster analysis to identify novel cell types, and differential expression analysis to derive gene expression signatures for the cell types.

Biography

Sandrine Dudoit is Professor of Biostatistics and Statistics and Chair of the Graduate Group in Biostatistics at the University of California, Berkeley.  Her methodological research interests regard high-dimensional inference and include exploratory data analysis (EDA), visualization, loss-based estimation with cross-validation, and multiple hypothesis testing. Her methodological work is motivated by statistical inference questions arising in biological research and, in particular, the design and analysis of high-throughput microarray and sequencing gene expression experiments. She is also interested in statistical computing and reproducible research. She is a founding core developer of the Bioconductor Project.

Professor Dudoit is a co-author of the book "Multiple Testing Procedures with Applications to Genomics" and a co-editor of the book "Bioinformatics and Computational Biology Solutions Using R and Bioconductor".  She was named Fellow of the American Statistical Association in 2010 and Elected Member of the International Statistical Institute in 2014.

Professor Dudoit obtained a Bachelor's degree (1992) and a Master's degree (1994) in Mathematics from Carleton University, Ottawa, Canada, and a PhD degree (1999) in Statistics from UC Berkeley. Before joining the Faculty at UC Berkeley in July 2001, she underwent two years of postdoctoral training in the laboratory of Professor Patrick O. Brown, Department of Biochemistry, Stanford University. 

Sarah Teichmann

EMBL-EBI and Head of Cellular Genetics at Wellcome Trust Sanger Institute
Hinxton, United Kingdom

website: https://www.ebi.ac.uk/research/teichmann

Presentation Title: Understanding Cellular Heterogeneity
Time: Monday, July 11th, 4:40 pm - 5:40 pm
Introduction by: Christine Orengo
Room: Northern Hemisphere BCD, Dolphin Hotel

From techniques such as microscopy and FACS analysis, we know that many cell populations harbour heterogeneity in morphology and protein expression. With the advent of high throughput single cell RNA-sequencing, we can now quantify transcriptomic cell-to-cell variation. I will discuss technical advances and biological insights into understanding cellular heterogeneity in T cells and ES cells using single cell RNA-sequencing.

Sarah Teichmann is interested in global principles of protein interactions and gene expression. In particular, her research focuses on structural bioinformatics and biophysics of protein complexes, and genome biology to study genetic switches in T cells. Sarah did her PhD at the MRC Laboratory of Molecular Biology, Cambridge, UK and was a Beit Memorial Fellow at University College London. She started a group at the MRC Laboratory of Molecular Biology in 2001. In 2013, she moved to the Wellcome Trust Genome Campus in Hinxton/Cambridge, where her group is joint between the EMBL-European Bioinformatics Institute and the Sanger Institute. Sarah is an EMBO member and fellow of the Academy of Medical Sciences, and her work has been recognized by a number of prizes, including the Lister Prize, Biochemical Society Colworth Medal, Royal Society Crick Lecture and EMBO Gold Medal.

She is an ISCB’s vice-president, a member of its Board of Directors, and is active in the Conference and Education committees and the ISCB Students’ council. She served as the Chair of the European Conference in Computational Biology, and a member of the steering committees of RECOMB and ECCB.

Ruth Nussinov

ISCB Fellows Keynote

Leidos Biomedical Research, Inc., National Cancer Institute
Frederick, United States;
Sackler School of Medicine, Tel Aviv University
Israel

https://ccr.cancer.gov/ruth-nussinov

Presentation Title: Ras signaling: a challenge to the biological sciences
Time: Sunday, July 10th, 9:00 am - 10:00 am
Introduction by: Teresa Przytycka
Room: Northern Hemisphere BCD, Dolphin Hotel

Abstract:

Ras proteins are classical members of small GTPases that function as molecular switches by alternating between inactive GDP-bound and active GTP-bound states. Ras activation is regulated by guanine nucleotide exchange factors that catalyze the exchange of GDP by GTP, and inactivation is terminated by GTPase-activating proteins that accelerate the intrinsic GTP hydrolysis rate by orders of magnitude. Ras has multiple partners, signals through several key pathways and fulfills critical functions in the cell life. Mutations in Ras are common in a variety of cancers; yet it is still undruggable. Consequently, it is at the center of an NCI initiative. In my talk, I will provide the background on Ras and an overview of our recent work, highlighting how it may help in elucidating vital questions in Ras biology and hopefully contribute to therapeutic strategies.

Biography:

Ruth Nussinov received her Ph.D. in 1977 from Rutgers University and did post-doctoral work in the Structural Chemistry Department of the Weizmann Institute.  Subsequently she was at the Chemistry Department at Berkeley, the Biochemistry Department at Harvard, and the NIH.  In 1984 she joined the Department of Human Genetics, at the Medical School at Tel Aviv University. In 1985, she accepted a concurrent position at the National Cancer Institute of the NIH, Leidos Biomedical Research, where she is a Senior Principal Scientist and Principle Investigator heading the Computational Structural Biology Group at the NCI. She has authored over 500 scientific papers. She is the Editor-in-Chief in PLoS Computational Biology and Associate Editor and on the Editorial Boards of a number of journals. She is a frequent speaker in Domestic and International meetings, symposia and academic institutions, and won several awards. Her National Cancer Institute website gives further details about her scientific work. https://ccr.cancer.gov/ruth-nussinov