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X-WR-CALDESC:Events for Department of Bioengineering
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DTSTART:20230101T000000
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DTSTART;TZID=UTC:20230703T160000
DTEND;TZID=UTC:20230703T170000
DTSTAMP:20260407T233850
CREATED:20230604T223620Z
LAST-MODIFIED:20230605T030515Z
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SUMMARY:Seminar by Dr. Sudin Bhattacharya titled Deep Generative Learning of Single Cell Gene Expression to predict Dose-Dependent Chemical Perturbations
DESCRIPTION:The Centre for BioSystems Science and Engineering (BSSE) cordially invites you to attend a departmental seminar. \nSpeaker: Dr. Sudin Bhattacharya \nDepartment of Biomedical Engineering\, Department of Pharmacology and Toxicology \nInstitute for Quantitative Health Science & Engineering \nMichigan State University \nAbstract:  \nSingle cell RNA-sequencing allows us to study cell-type specificity and heterogeneity of biological responses to chemical perturbations. However\, experimentally testing all relevant combinations of cell types\, chemicals\, and doses is a near-impossible task. A deep learning formalism called variational autoencoders (VAEs) has been shown to be effective in computationally predicting single-cell gene expression perturbations. We have developed single cell Variational Inference of Dose-Response (scVIDR)\, a VAE-based tool to predict the trajectory of cellular dose-response\, which achieves better dose-response predictions than existing models. We show that scVIDR can predict dose-dependent gene expression changes across cell types and interpret the latent space of the autoencoder model in terms of biological pathways.
URL:https://be.iisc.ac.in/event/seminar-by-dr-sudin-bhattacharya-titled-deep-generative-learning-of-single-cell-gene-expression-to-predict-dose-dependent-chemical-perturbations/
LOCATION:CES Seminar Hall\, CES Seminar Hall\, 3rd Floor\, Biological Science Building
CATEGORIES:Seminar
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DTSTART;TZID=UTC:20230711T160000
DTEND;TZID=UTC:20230711T170000
DTSTAMP:20260407T233850
CREATED:20230608T221509Z
LAST-MODIFIED:20230608T221509Z
UID:4393778-1689091200-1689094800@be.iisc.ac.in
SUMMARY:Special Seminar by Prof. Yamuna Krishnan titled Intracellular electrophysiology
DESCRIPTION:The Centre for BioSystems Science and Engineering (BSSE) cordially invites you to attend a special seminar: \nSpeaker: Prof. Yamuna Krishnan \nDepartment of Chemistry\, \nInstitute for Biophysical Dynamics\, \nGrossman Institute for Neuroscience \nUniversity of Chicago \nTitle: Intracellular electrophysiology \nAbstract:  \nI have been interested in exploring how the ionic milieu within an organelle facilitates organelle function. To map these lumenal chemistries\, my lab developed a DNA-based\, fluorescent reporter technology to quantitatively map ions such as H+\, Cl- and Ca2+ within organelles (1). It can be applied to organelles of cells in culture\, in live organisms (2) and in human patient cells (3\,4). Our most recent reporter for absolute membrane potential ended a previous misconception by showing that many organelles do in fact\, have membrane potential (4). Today I will discuss two new reporters for organellar Na+ and K+ : the final pieces needed to build an electrochemical model for organelle membranes (5\,6). The only existing electrochemical model of a biological membrane is that of the cell membrane\, first developed by Hodgkin and Huxley in 1952 for neurons (7). To accomplish this for organelles we will need input from physicists\, cell biologists and electrophysiologists. \nReferences: \n\nKrishnan\, Y. et. al. “Quantitative imaging of biochemistry in situ and at the nanoscale.” ACS Cent. Sci.\, 2020\, 6\, 1938–1954.\nNarayanaswamy\, N. et. al. “A pH-correctable\, DNA-based fluorescent reporter for organellar Calcium.” Nature Methods\, 2019\, 16\, 95-102.\nLeung\, K.\, et. al. “A DNA Nanomachine chemically resolves lysosomes in live cells.” Nature Nanotechnology\, 2019\, 14\, 176-183.\nSaminathan\, A.\, et. al. “A DNA-based voltmeter for organelles.” Nature Nanotechnology\, 2021\, 16\, 96-103.\nAnees\, P. et al. “DNA nanodevices for measuring the organelle-specific activity of potassium channels.” 2023\, in revision.\nZou\, J. et al. “A DNA nanodevice maps sodium at single organelle resolution” 2023\, in revision.\nHodgkin A.L.\, Huxley A.F. “A quantitative description of membrane current and its application to conduction and excitation in nerve”. J. Physiol. 1952\, 117\, 500–44.
URL:https://be.iisc.ac.in/event/special-seminar-by-prof-yamuna-krishnan-titled-intracellular-electrophysiology/
LOCATION:Biological Sciences Auditorium
CATEGORIES:Seminar
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