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SynBio Forum: Genetics, Vision & Machine Learning in Biological Systems

Join us for our termly SynBio Forum- insightful talks by distinguished speakers, dinner, drinks and networking opportunities.
When Feb 12, 2019
from 05:30 PM to 07:30 PM
Where Old Divinity School, St Johns Street, Cambridge
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Free registration>>>

 

Schedule

5:30-6:15pm Ricardo Henriques (UCL) + Q&A

6:15-7:00pm Brenda Andrews (Univ. of Toronto) + Q&A

7:00pm onwards Dinner buffet + drinks reception

There will also be a showcase of projects created through the Biomaker Winter Challenge - a computing challenge at the intersection of biology, engineering and computer science. (https://www.biomaker.org/)

 

Democratising live-cell high-speed super resolution microscopy

Dr. Ricardo Henriques (UCL)

Abstract: Dr. Ricardo Henriques established his lab at the MRC Laboratory for Molecular Cell Biology, UCL to undertake research combining cell biology, optical physics and biochemistry. His group focuses on biological problems that cannot be addressed with current imaging technology, and thus aims to develop analytical, optical and biochemical approaches to address these questions.

In cell biology they aim to understand how viruses enter cells by probing and remodelling membranes, and what are the structural changes viruses undergo during cell-entry, uncoating and morphogenesis. To do so, the group is developing new classes of fluorescent probes, high-speed cell friendly Super-Resolution (SR) methods and computational modelling approaches that, although designed to answer questions of interest in the lab, will have broad applications in cell biology research.

Ricardo and his lab have developed robust fluidics approaches to automate complex sequences of treatment, labelling and imaging of live and fixed cells. Their open-source NanoJ-Fluidics system is based on low-cost LEGO hardware controlled by ImageJ-based software and can be directly adapted to any microscope, providing easy-to-implement high-content, multimodal imaging with high reproducibility.

Bio: Dr. Ricardo Henriques is a group leader since 2013 at both the University College London and The Francis Crick Institute in the UK. His group undergoes research in optical and computational biophysics, with a special interest in super-resolution microscopy and host-pathogen interactions. He graduated in Physics, specialising in biophotonics and robotics. He finished his PhD In 2011 on the topic of advancing super-resolution microscopy technologies (Musa Mhlanga lab). He then pursued postdoc research at Institut Pasteur Paris, studying HIV-1 T-cell infection through nanoscale imaging (Christophe Zimmer lab).

 

Machine Learning and Computer Vision Approaches for Phenotypic Profiling in Yeast

Dr. Brenda Andrews (University of Toronto)

Abstract: A powerful method to study the genotype-to-phenotype relationship is the systematic assessment of mutant phenotypes using high-content screening and automated image analysis. We have developed a combined experimental-computational pipeline for analysis of the effect of genetic perturbations on subcellular compartments in yeast. Our approach involves using Synthetic Genetic Array (SGA) analysis, which automates yeast genetics, to introduce markers of various subcellular compartments into yeast mutant arrays, in order to identify comprehensive lists of genes involved in subcellular morphology. Quantitative analysis of these large image datasets requires computational approaches such as image recognition, feature extraction and machine learning. We have developed a general computational pipeline for single cell image analysis to quantify penetrance of perturbations affecting the sub-cellular morphology of 18 sub-cellular compartments. To develop the pipeline, we first focused on surveying the yeast genome for genes required for proper formation and maintenance of the early, intermediate and late endocytic compartments. This analysis revealed that mutation of 13% of the screened genes caused a morphological phenotype with a penetrance of 50% or greater for at least one of the four screened markers. Mutation of hundreds more genes, mostly connected to more distant bioprocesses, caused moderate but still significant defects in at least one of the major compartments involved in endocytosis. This analysis will allow for the identification of connections between biological processes, the prediction of novel gene function, and the generation of a clearer understanding of basic eukaryotic cell biology.

Bio: Dr. Brenda Andrews is the Charles H Best Chair of Medical Research, Director of the Donnelly Centre for Cellular and Biomolecular Research, and University Professor in Molecular Genetics at the University of Toronto.

She obtained her BSc and PhD from the University of Toronto, then studied at the University of California, San Francisco before returning to Toronto to start her own lab in the Department of Medical Genetics (now Molecular Genetics). She became Chair of the Department in 1999, a position she held for 5 years before assuming her position as inaugural Director of the Donnelly Centre, an interdisciplinary research facility designed to promote collaborative research at the forefront of biomedicine.

Dr. Andrews was recently named a Companion of the Order of Canada for her “globally significant research in systems biology and for developing and nurturing prominent scientific communities in molecular genetics”. Dr. Andrews is also an elected Fellow of the Royal Society of Canada, the American Association for the Advancement of Science and the American Academy of Microbiology. She was inaugural Director of the Genetic Networks program of the Canadian Institute for Advanced Research, and remains a Senior Fellow.

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The Synthetic Biology Strategic Research Initiative provides a hub for anyone interested in Synthetic Biology at the University of Cambridge, as well as commercial partners and external collaborators.