iTHEMS Biology Seminar

We are holding regular seminars and other activities on topics related to biology. Our aim is to lower the boundaries between biology and mathematics/physics, to identify common grounds between biology and mathematics/physics, and to develop ideas for new research topics at the intersection of biology and mathematics or physics.

For further details see iTHEMS Biology Seminar Study Group page.

Seminar

iTHEMS Biology Seminar

The rheotaxis mechanism of swimming ciliates

April 22 at 10:00 - 11:00, 2021

Dr. Yukinori Nishigami (Research Institute for Electronic Science, Hokkaido University)

The swimming unicellular organisms, which live in freshwater, need to resist currents in the environment. Without this ability, their habitat changes with the flow, and they cannot survive in nature f...more

Venue: via Zoom

Event Official Language: English

Seminar

iTHEMS Biology Seminar

Liquid condensates in cell nucleus

April 15 at 10:00 - 11:00, 2021

Dr. Kyosuke Adachi (Special Postdoctoral Researcher, iTHEMS)

I will give a talk in a journal club style. I will introduce recent papers regarding liquid-liquid phase separation in cells. In cell biology, several types of liquid condensates of proteins/RNAs h...more

Venue: via Zoom

Event Official Language: English

Seminar

iTHEMS Biology Seminar

Simple models of cancer growth, MCMC parameter estimation and identifiability

April 8 at 10:00 - 11:00, 2021

Prof. Catherine Beauchemin (Deputy Program Director, iTHEMS)

I would like to introduce some basic concepts about (very simple) mathematical model of cancer growth, the basic math behind parameter estimation via Markov chain Monte Carlo (MCMC) based on Bayes' th...more

Venue: via Zoom

Event Official Language: English

Seminar

iTHEMS Biology Seminar

Structural reduction of chemical reaction networks based on topology

April 1 at 10:00 - 11:00, 2021

Dr. Yuji Hirono (Assistant Professor, Asia Pacific Center for Theoretical Physics, Republic of Korea)

Chemical reactions form a complex network in living cells and they play vital roles for physiological functions. An amusing question is how the structure of a reaction network is linked to its chemica...more

Venue: via Zoom

Event Official Language: English

Seminar

iTHEMS Biology Seminar

Evolutionary conservativeness and diversification of cycads: Understanding the evolution of living fossils

March 25 at 10:00 - 11:00, 2021

Dr. Jose Said Gutiérrez-Ortega (Assistant Professor, Institute for Excellence in Educational Innovation, Chiba University)

The cycads are a lineage of gymnosperms that represent an example of biological stasis success. Despite their early origin in the seed plant evolution, they survived multiple events of mass extinction...more

Venue: via Zoom

Event Official Language: English

Seminar

iTHEMS Biology Seminar

Microeconomics of metabolism

March 10 at 10:00 - 11:00, 2021

Mr. Jumpei Yamagishi (Kaneko Laboratory, University of Tokyo)

Metabolic behaviors of proliferating cells are often explained as a rational choice to optimize cellular growth rate. In contrast, microeconomics formulates consumption behaviors as optimization probl...more

Venue: via Zoom

Event Official Language: English

Seminar

iTHEMS Biology Seminar

Origin of non-linearity of large deformation on DNA stretched

February 25 at 10:00 - 11:00, 2021

Dr. Hiroshi Yokota (Postdoctoral Researcher, iTHEMS)

Since DNA in a cell is mechanically stretched or rotated by many proteins, the mechanical response of DNA in vitro is expected to be basic point for understanding its behavior. When DNA is stretched b...more

Venue: via Zoom

Event Official Language: English

Seminar

iTHEMS Biology Seminar

High-throughput laboratory evolution with machine learning reveals constraints for drug resistance evolution

February 18 at 10:00 - 11:00, 2021

Mr. Junichiro Iwasawa (Doctoral course, Department of Physics, Graduate School of Science, The University of Tokyo)

The understanding of evolution is crucial to tackle the problem of antibiotic resistance which is a growing health concern. Although the lack of sufficient data has long hindered the mechanism of evol...more

Venue: via Zoom

Event Official Language: English

Seminar

iTHEMS Biology Seminar

A machine learning approach for prediction of mitochondrial proteins in non-model organisms

February 12 at 10:00 - 11:00, 2021

Dr. Keitaro Kume (Assistant professor, Faculty of Medicine, University of Tsukuba)

The evolution of the repertoire of proteins localized to organelles is important for understanding the evolutionary process of organelles. However, experimental methods for identifying organelle-local...more

Venue: via Zoom

Event Official Language: English

Seminar

iTHEMS Biology Seminar

System identification of mechano-chemical epithelial sheet dynamics

February 4 at 10:00 - 11:00, 2021

Mr. Yoshifumi Asakura (3rd year doctoral program, Graduate School of BIOSTUDIES, Kyoto University)

Collective migration of epithelial cells is a fundamental process of multi-cellular organisms. Our recent study using live imaging with FRET-based biosensor discovered that cell migration within an ep...more

Venue: via Zoom

Event Official Language: English

Seminar

iTHEMS Biology Seminar

Numerical inference of the molecular origin of the cyanobacterial circadian rhythm

January 28 at 10:00 - 11:00, 2021

Dr. Shin-ichi Koda (Assistant professor, Institute for Molecular Science)

The cyanobacterial clock proteins, KaiA, KaiB, and KaiC, are known as the simplest biological clock; Just by mixing them with ATP in a test tube, self-sustaining oscillation with a nearly 24h temperat...more

Venue: via Zoom

Event Official Language: English

Seminar

iTHEMS Biology Seminar

Introduction to Boolean modeling and Boolean networks as information processing units

January 21 at 10:00 - 11:00, 2021

Dr. Takashi Okada (Senior Research Scientist, iTHEMS)

Boolean networks are widely used in physics, biology, social science, and computer science. In this talk, I will introduce the basics of Boolean networks and give an overview of Biological application...more

Venue: via Zoom

Event Official Language: English

Seminar

iTHEMS Biology Seminar

What are genes and how can we find them?

January 14 at 10:00 - 11:00, 2021

Dr. Jeffrey Fawcett (Senior Research Scientist, iTHEMS)

Although 'gene' is a word that is used frequently in the society, most people probably do not know what genes actually are. In fact, its definition is not so straightforward. In this talk, I will firs...more

Venue: via Zoom

Event Official Language: English

Seminar

iTHEMS Biology Seminar

From local resynchronization to global pattern recovery in the zebrafish segmentation clock

January 7 at 10:00 - 11:00, 2021

Dr. Koichiro Uriu (Assistant Professor, College of Science and Engineering, Kanazawa University)

Tissue-scale developmental patterns are often generated by local cellular interactions and global tissue deformation. An example is gene expression rhythms in vertebrate, termed the segmentation clock...more

Venue: via Zoom

Event Official Language: English

Seminar

iTHEMS Biology Seminar

Mathematical model-based quantitative data analysis for COVID-19

December 22 at 10:00 - 11:00, 2020

Dr. Shingo Iwami (Associate Professor, Department of Biology, Kyushu University)

The recent spread of corona threatens the health of people around the world. We urgently need strategies to reduce COVID-19 spread and to enhance antiviral drug development for individual patients. Ma...more

Venue: via Zoom

Event Official Language: English

Seminar

iTHEMS Biology Seminar

Autoimmune diseases initiated by pathogen infection: mathematical modeling

December 17 at 10:00 - 11:00, 2020

Ms. Akane Hara (Doctoral Course, Graduate School of Systems Life Sciences, Kyushu University)

The pathogen with proteins similar to host’s proteins is likely to cause autoimmunity, which is called “molecular mimicry”. To understand the mechanism of autoimmunity development caused by pathogen i...more

Venue: via Zoom

Event Official Language: English

Seminar

iTHEMS Biology Seminar

How to obtain the large amount of sequence data from the eukaryote

December 10 at 10:00 - 11:00, 2020

Dr. Yuki Yazaki (Postdoctoral Researcher, iTHEMS)

Most of the modern biology is supported by genetic sequence data. Recent advances in sequencing technology have made it possible to obtain comprehensive and large numbers of sequence data from a small...more

Venue: via Zoom

Event Official Language: English

Seminar

iTHEMS Biology Seminar

Rotifer can be a good model organism for theoretical biology

November 27 at 10:00 - 11:00, 2020

Dr. Yuri Kominami (Specially Appointed Assistant Professor, Graduate School of Agricultural and Life Sciences, The University of Tokyo)

Rotifers are cylindrical zooplankton which constitute the phylum Rotifera. They have organs and tissues including ganglia, muscles, digestive organs, ovaries, and sensory organs in their <1mm body. Ro...more

Venue: via Zoom

Event Official Language: English

Seminar

iTHEMS Biology Seminar

Symmetry and conservation laws in neural networks

November 20 at 10:00 - 11:00, 2020

Dr. Hidenori Tanaka (Group Leader & Senior Scientist, Physics & Informatics Laboratories, NTT Research, Inc., USA / Visiting Scholar, Stanford University, USA)

Symmetry is the central guiding principle in the exploration of the physical world but has been underutilized in understanding and engineering neural networks. We first identify simple yet powerful ge...more

Venue: via Zoom

Event Official Language: English

Seminar

iTHEMS Biology Seminar

Evolution of a peak of genetic divergence driven by local adaptation

November 5 at 10:00 - 11:00, 2020

Dr. Takahiro Sakamoto (Postdoctoral Researcher, The Graduate University for Advanced Studies, SOKENDAI)

In species that are distributed in various environments, each subpopulation adapts to the local environment. In general, when there is migration between subpopulations, genetic divergence does not pro...more

Venue: via Zoom

Event Official Language: English