Society for Systems Biology & Translational Research (SSBTR) is a registered (and also both 12A & 80G certified) not-for-profit scientific society organizes an International Webinar Series Lectures.
TRUTH ALWAYS BELONGS TO MINORITY - Raja Rammohan Roy
All are cordially invited. For date, time and link and other details aas below:
GOOGLE MEET Link: url (https://meet.google.com/qjb-utgp-ymk)
Day: 2021-Jan-12 (Tuesday) Time: IST 12:45 Hour
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Speaker: Prof. Olivier Gandrillon, Ecole Normale Superieure de Lyon at IST 13:00
Hour
Title:
Toward a dynamical network view on a differentiation process
Abstract:
A recent view emerged that stochastic dynamics governing the
switching of cells from one differentiation state to another could be
characterized by a peak in gene expression variability at the point
of fate commitment. We have tested this hypothesis at the single-cell
level by analyzing primary chicken erythroid progenitors through
their differentiation process and measuring the expression of
selected genes at six sequential time-points after induction of
differentiation. In contrast to population-based expression data,
single-cell gene expression data revealed a high cell-to-cell
variability, which was masked by averaging. Shannon entropy was used
as as a measure of the cell-to-cell variability in gene expression.
Entropy values showed a significant increase, reaching a peak between
8 and 24 h, before decreasing to significantly lower values. We
observed that the previous point of maximum entropy precedes an
irreversible commitment to differentiation between 24 and 48 h. In
conclusion, when analyzed at the single cell level, the
differentiation process looks very different from its classical
population average view. New observables (like entropy) can be
computed, the behavior of which is fully compatible with the idea
that differentiation is not a “simple” program that all cells
execute identically but results from the dynamical behavior of the
underlying molecular network.
Bio-sketch:
Dr. Olivier Gandrillon received PhD degree in biology in 1989. After
a two years post-doctoral stay at Caltech, he was appointed a
permanent research position at Ecole Normale Supérieure de Lyon in
1989 and started his own team as an independent group leader in 1999
in Université Claude Bernard. He was awarded research director at
CNRS in 2009. He moved back to ENS in 2015, where he is now heading a
group entitled "Systems Biology of Decision Making". He has
a long experience in multidisciplinary projects and interactions
between Computer Science, Life Sciences and Mathematics. He is a
member of the Dracula Inria team that is devoted to developing
mathematical tools for multiscale modeling. He was elected director
of the BioSyL research federation since 2011 when the federation was
founded. He is the founder of the modeling seminar “Semovi” and
of the international conference series “Integrative Post Genomics”
(2001-2010) and “LyonSysBio” (since 2014). He was the co-chair of
the very successful ICSB2018 conference. He co-authored 72 original
publications in a very large range of different disciplinary fields.
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Speaker: Dr. Bishwajit Das, SSBTR at IST 14:00
Hour
Title:
Information Theoretic Multivariate Dependence Analysis of HLA Immune-gene Regulation
Abstract: Cell
surface expression of Human
Leukocytic Antigen (HLA) plays a significant role in immune recognition. HLA
molecules are classified into two – class I and class II. In different cancers
including leukemia, HLA (both class I and II) down-regulation is frequently
reported. Regarding its regulation, different transcription factors (TFs) are
responsible for its constitutive expression; however, it is also regulated by
several inducible TFs. Using 1st order information theory based
analysis for HLA and its associated TFs (human) gene expression data reveals
that RFXB, an inducible controlling TF plays a major role in both myeloid and
lymphoid types of leukemia; however, in lymphoid leukemia CREB1, another
inducible TF may play an important role. Application of MaxEnt based
multivariate dependence information theory for higher order analysis confirm
the same finding along with an indication of the regulatory role of another
combination of two TFs namely CIITA and IRF1 for myeloid type leukmic cells.
However through this analysis no alteration is noted for HLA class II gene
regulation.
Bio-sketch: Dr. Bishwajit Das, is an Investigator of SSBTR. He received his Ph.D. degree in 2021 from West Bengal State University. The field of his research is to understand HLA gene regulation in different non-communicable complex diseases by using different quantitative and analytical methods. He is interested in the development of different analytical tools for immune-informatics. He extensively used Information Theoretic approach in his doctoral thesis. So far eight international research papers are to his credits. He has presented his works in different International conferences and reviewer of leading bioinformatics review journal (Briefings in Bioinformatics).
Event Photos: Day 2021 Jan 12 (Tuesday)
Day: 2021-Jan-24 (Sunday) Time: IST 17:45 Hour
# Speaker: Dr. Jianhua
Xing, University
of Pittsburgh at IST 18:00 Hour
Title : Reconstructing
cell phenotypic transition dynamics from single cell data
Abstract : Recent
advances in single-cell techniques catalyze an emerging field of
studying how cells convert from one phenotype to another, i.e., cell
phenotypic transitions (CPTs). Two grand technical challenges,
however, impede further development of the field. Fixed cell-based
approaches can provide snapshots of high-dimensional expression
profiles but have fundamental limits on revealing temporal
information, and fluorescence-based live cell imaging approaches
provide temporal information but are technically challenging for
multiplex long- term imaging. My
lab is tackling these grand challenges from two directions, with the
ultimate goal of integrating the two directions to reconstruct the
spatial-temporal dynamics of CPTs. In one direction, we developed a
live-cell imaging platform that tracks cellular status change in a
composite multi-dimensional cell feature space that include cell
morphological and texture features readily through fluorescent and
transmission light imaging.
We applied the framework to study human
A549 cells undergoing TGF-β induced epithelial-to-mesenchymal
transition (EMT).
In
another direction, we aim at reconstructing single cell dynamics and
governing equations from single cell genomics data. We developed a
procedure of learning the analytical form of the vector field F(x)
and the equation dx/dt
= F(x)
in the Reproducing Kernel Hilbert Space. Further differential
geometry analysis on the vector field reveals rich information on
gene regulations and dynamics of various CPT processes.
Bio-sketch :Dr Xing received B.S. in Chemistry from Peking University, M.S. in
Chemical Physics from University of Minnesota, and PhD in Theoretical
Chemistry from UC Berkeley. After being a postdoc researcher in
theoretical biophysics at UC Berkeley and an independent fellow at
Lawrence Livermore National Laboratory, he assumed his first faculty
position at Virginia Tech, then moved to University of Pittsburgh in
2015. Currently Dr Xing is
an Associate Professor in the Computational and Systems Biology
Department, School of Medicine, a founding member of Center for
Systems Immunology, and an affiliated faculty member of Department of
Physics, University of Pittsburgh. He is also an affiliated member of
University of Pittsburgh Hillman Cancer Center. Dr Xing’s research
uses statistical and chemical physics, dynamical systems theory,
mathematical/computational modeling in combination with quantitative
measurements to study the dynamics and mechanics of biological
processes. Recently his lab focuses on reconstructing information of
cell phenotypic transition dynamics from live cell time-lapse images
and snapshot high-throughput single cell data. Another related
direction is to study how three-dimensional chromosome structure and
dynamics, epigenetic modification, and gene regulation are coupled.
# Speaker: Dr. Mohit
Kumar Jolly, Indian
Institute of Science, Bangalore at IST 19:00 Hour
Title : Systems
biology of cancer metastasis: how do cancer cells coordinate,
communicate, and cooperate?
Abstract : Metastasis
(the spread of cancer cells from one organ to another) and therapy
resistance cause above 90% of all cancer-related deaths. Despite
extensive ongoing efforts in cancer genomics, no unique genetic or
mutational signature has emerged for metastasis. However, a hallmark
that has been observed in metastasis is adaptability or phenotypic
plasticity – the ability of a cell to reversibly switch among
different phenotypes in response to various internal or external
stimuli. Phenotypic plasticity has also been recently implicated in
enabling the emergence of resistance for many cancers across multiple
therapies. However, a mechanistic understanding of these processes
from a dynamical systems perspective remains incomplete. This
talk will describe how mechanism-based mathematical models for
phenotypic plasticity can enable our improved understanding of
cellular decision-making at individual and population levels from
these perspectives: a) Multistability (how many cell states exist en
route?),
b) Reversibility (do cells come across a ‘tipping point’ at
specific time and/or dose of inducers beyond which they do not
revert?), and c) Cell-cell communication (how do cells affect
tendency of their neighbors to exhibit plasticity?). Collectively,
our work highlights how an iterative crosstalk between mathematical
modeling and experiments can both generate novel insights into the
emergent nonlinear dynamics of cellular transitions and uncover
previously unknown accelerators of metastasis and therapy resistance.
Bio-sketch : Dr.
Mohit Kumar Jolly received his B.Tech. and M.Tech. degree in Bio-engineering from IIT Kanpur and Ph.D. in Bio-engineering from Rice University He leads the Cancer Systems Biology group at the
Centre for BioSystems Science and Engineering, Indian Institute of
Science. He has made seminal contributions to decoding the emergent
dynamics of epithelial-mesenchymal plasticity (EMP) in cancer
metastasis, through mathematical modeling of regulatory networks
implicated in EMP; his work has featured on the cover of Journal of
Clinical Medicine, Cancer Research, and Molecular and Cellular
Biology, and he won the 2016 iBiology Young Scientist Seminar Series
– a coveted award for communicating one’s research to a diverse
audience. Currently, his lab focuses on decoding mechanisms and
implications of non-genetic heterogeneity in cancer metastasis and
therapy resistance, with specific focus on mechanism-based and
data-based mathematical modeling in close collaboration with
experimental cancer biologists and clinicians. He is an elected
fellow of Indian National Young Academy of Sciences (INYAS), and
serves as Secretary of The International Epithelial-Mesenchymal
Transition Association (TEMTIA).
Event Photos: Day 2021 Jan 24 (Sunday)
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Dr. Durjoy Majumder
Organizing Secretary, SSBTR International Webinar Lecture Series