Oz Single Cell - Cell type, cell state, or cell artefact? Finding the biology in your single cell data

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Thursday, September 17, 2020

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10:00 AM AEST - 11:30 AM AEST



About the Webinar

Cell classification – is it really all that difficult? How do you deconvolute 1000s of single cells into a meaningful biology? Should we re-think how a cell is 'classified'? Is there really a difference between cell type and cell state? Hear from the inventor of SingleCellNet, Dr Patrick Cahan, Johns Hopkins University, USA, to learn about the latest computational approaches to cell classification. Jose Alquicira-Hernandez (Garvan) provides an update on his classification method, scPred, while Sean Wilson (MCRI), and Nadia Rajab (UoM) discuss the challenges of classifying stem cell models of their biology. 

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A/ Professor Patrick Cahan – John Hopkins University, Department of Biomedical Engineering

Patrick Cahan grew up in St. Louis, MO. He received a B.S. in Computer Science from University of Maryland, Baltimore County, where he got his first research experience working on Information Retrieval systems. While working in Chile as a programmer, Patrick became interested in Computational Biology and returned to the US to pursue a M.S. in Genomics and Bioinformatics at GWU in Washington D.C., and then a Ph.D. in Computational Biology from Washington University in St. Louis, where he investigated the impact of DNA copy number variation on gene expression in Dr. Timothy Graubert's lab. 

His postdoctoral work in the lab of Dr. George Daley at Harvard Medical School and Boston Children's Hospital included the development and experimental validation of computational methods to assess and improve engineered cells, such as those resulting from directed differentiation of pluripotent stem cells.

Jose Alquicira-Hernandez – Garvan Institute of Medical Research

Jose Alquicira Hernandez is a PhD student at the Garvan Institute of Medical Research supervised by Joseph Powell. Jose’s research interests include Human Genomics and Computational Biology, particularly on understanding the genetic control of gene expression and its role in disease at a single-cell resolution. In the first year of his PhD Jose developed a package called scPred to predict cell types at single-cell level. 

Jose obtained a bachelor degree in Genome Sciences from the National Autonomous University of Mexico. During the last year of the degree, he worked with Jeff Leek in the Department of Biostatistics at Johns Hopkins Bloomberg School of Public Health analysing RNA-seq data, and Julio Collado developing software to infer genetic ancestry from Mexican populations.

Nadia Rajab – The University of Melbourne

Nadia Rajab completed her BSc (Hons) in Immunology at the University of Glasgow before moving to Australia to undertake her doctoral research at the University of Melbourne and CSIRO Future Science Platform. Her research involves using human pluripotent stem cells to develop better human models to study macrophage biology. 

Her interests centre around innate memory, and the requirements for cellular responsiveness. Her research work will hopefully enable the development of our understanding of the requirements for protection against infection. 

Nadia has diverse experience which include teaching, mentoring and outreach, in addition to having worked in diverse settings including the Industrial Biotechnology Innovation Centre in Scotland and hospital settings in Peru. She is actively sitting on the ECR leadership committee for Stem Cell Conversations.

Sean Wilson – Murdoch Children’s Research Institute

Sean Wilson joined Melissa Little’s laboratory at the Murdoch Children's Research Institute as a research assistant in 2015, working closely with Alex Combes on Six2 haploinsufficiency in mice. In 2017 he was transferring to the Stem Cells and Regeneration division of the lab, working closely with Jess Vanslambrouck and Sara Howden studying the processes that drive differentiation within stem cell derived kidney organoids. During that time, he developed a passion for utilising stem cell technology, kidney organoids and bioinformatics analysis approaches in understanding kidney development, function and disease. This led to Sean undertaking a PhD in 2019 under the supervision of Melissa Little and Sara Howden to map morphogenesis in kidney organoids and improve the in vitro nephrogenic niche dynamics in this system. This has included a focus on classifying and comparing the cell types within human fetal kidney and kidney organoids using single cell RNA sequencing.


Professor Christine Wells – The University of Melbourne

Professor Christine Wells is the Founding Director of the University of Melbourne Centre for Stem Cell Systems. As the architect of the Stemformatics.org platform, Christine leads program of research in biological data integration and visualization for the stem cell community. Stemformatics.org is a collaboration platform which hosts a large curated compendium of stem cell data, including reference atlases for human hematopoiesis and myelopoiesis. This resource is used to generate definitive molecular signatures of stem cell subsets and their differentiated progeny.

Associate Professor Joseph Powell - Garvan Institute of Medical Research

Associate Professor Joseph Powell is the Director of the Garvan-Weizmann Centre for Cellular Genomics. The Garvan-Weizmann Centre is a research centre focused on the use of cellular genomics technology to address critical medical research questions. Joseph’s research oil focused on how genetic causes of disease act at a cellular level, bringing together the fields of statistical genetics and cellular genomics to do so. His contributions have been recognised with numerous awards, including the youngest ever recipient of the Commonwealth Health Minister's Medal, NHMRC Research Excellence Medal, and the Munro Fox Medal.

This episode is brought to you by AGRF & Missionbio