iTHEMS Biology Seminar

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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

Seminar

iTHEMS Biology Seminar

Basics of population genomic data analysis

October 29 at 10:00 - 11:00, 2020

Dr. Jeffrey Fawcett (Senior Research Scientist, iTHEMS)

In recent years, it has become possible to obtain the DNA sequence data of a large number of individuals of the same species. This data set is basically a M (number of samples) x N (number of genomic ...more

Venue: via Zoom

Event Official Language: English

Seminar

iTHEMS Biology Seminar

Bayesian nonparametric estimation of Random Dynamical Systems

October 21 at 14:00 - 15:00, 2020

Dr. Christos Merkatas (Postdoctoral Researcher, Aalto University, Finland)

In this talk, a Bayesian nonparametric framework for the estimation and prediction, from observed time series data, of discretized random dynamical systems is presented [1]. The size of the observed t...more

Venue: via Zoom

Event Official Language: English

Seminar

iTHEMS Biology Seminar

A PDE model for the localization and spread of flu in the human respiratory tract

October 14 at 10:00 - 11:00, 2020

Mr. Christian Quirouette (PhD student, Department of Medical Physics, Ryerson University, Canada)

Within the human respiratory tract (HRT), virus diffuses through the periciliary fluid (PCF) bathing the epithelium. But it also undergoes advection: as the mucus layer sitting atop the PCF is pushed ...more

Venue: via Zoom

Event Official Language: English

Seminar

iTHEMS Biology Seminar

Phase Transitions in Biological Systems

September 23 at 10:00 - 11:00, 2020

Dr. Kyosuke Adachi (Special Postdoctoral Researcher, iTHEMS)

Biological systems are built hierarchically by DNA, proteins, cells, tissues, organs, individuals, etc. Recent experiments have clarified the existence of interesting mesoscale phenomena inside cells,...more

Venue: via Zoom

Event Official Language: English

Seminar

iTHEMS Biology Seminar

Eco-evolutionary dynamics with novel mutations

September 16 at 10:00 - 11:00, 2020

Dr. Hye Jin Park (Junior Research Group Leader, Statistical physics of ecology and evolution group, Asia Pacific Center for Theoretical Physics, Korea (the Democratic People's Republic of))

Evolution is driven by individual birth and death that are determined by interactions between individuals. Hence studying interactions is crucial to understand the population evolution. However, tradi...more

Venue: via Zoom

Event Official Language: English

Seminar

iTHEMS Biology Seminar

Singular point implies coexistence in adaptive dynamics

September 9 at 10:00 - 11:00, 2020

Dr. Masashi Tachikawa (Visiting Scientist (Academia), iTHEMS)

Adaptive dynamics is a relatively new mathematical framework for studying evolution(~1990s). Under the influence of the mathematical ecology and the game theory, adaptive dynamics considers the effect...more

Venue: via Zoom

Event Official Language: English

Seminar

iTHEMS Biology Seminar

The hitch-hiker’s guide to 
the concept of 
adaptive dynamics

September 2 at 10:00 - 10:30, 2020

Dr. Ryosuke Iritani (Research Scientist, iTHEMS)

Adaptation is of multi-causality, composed of mutation and selection processes. I will talk about how we model adaptation on the basis of the adaptive dynamics framework. This is a very quick, concept...more

Venue: via Zoom

Event Official Language: English

Seminar

iTHEMS Biology Seminar

Modeling biological timing

August 26 at 10:00 - 11:00, 2020

Dr. Gen Kurosawa (Senior Research Scientist, iTHEMS)

Under stay-at-home situation, some of you may suffer from sleep disorder. Efficacy of a drug often depends on the timing of its prescription. We know this fact about our "timing", but we don't know wh...more

Venue: via Zoom

Event Official Language: English

Seminar

iTHEMS Biology Seminar

Heavy tails in the brain

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

Dr. Lukasz Kusmierz (research scientist, RIKEN Center for Brain Science)

In my talk I will discuss the relation between two seemingly unrelated measures in the brain that exhibit heavy tails: neuronal avalanches, i.e. bursts of activity with power-law distributions of size...more

Venue: via Zoom

Event Official Language: English

Seminar

iTHEMS Biology Seminar

Time-dependent bias emerges in population models with broad offspring number distributions

July 29 at 10:00 - 11:00, 2020

Dr. Takashi Okada (Senior Research Scientist, iTHEMS)

It has been increasingly recognized that natural populations exhibit broad offspring number distributions, either because offspring numbers are strongly variable (e.g. marine organisms) or because ran...more

Venue: via Zoom

Event Official Language: English