iTHEMS生物学セミナー
257 イベント
生物学に関連する様々なトピックを扱ったセミナーを定期的に開催しています。生物学と数学・物理学との境界を低くし、接点を見つけ出すことで、新しい学際的な研究のアイデアが生まれることを期待しています。
詳細はiTHEMS生物学セミナースタディーグループのページをご覧下さい。
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セミナー
Rare k-mers reveal centromere haplogroups underlying human diversity and cancer translocation
2026年11月26日(木) 13:00 - 14:00
白石 友一 (国立がん研究センター研究所 ゲノム解析基盤開発分野 分野長)
Centromeres are highly variable and rapidly evolving regions of the human genome, and are frequently implicated in various cancers. Human centromeres consist of highly repetitive DNA sequences known as α-satellite higher-order repeats (HORs), which makes their analysis using conventional genome sequencing approaches extremely challenging. Although long-read sequencing technologies now enable near-complete sequencing of centromeres, applying these methods to large numbers of samples remains difficult. As a result, our understanding of centromere diversity across populations and its role in chromosomal rearrangements in cancer has remained limited. In this study, by focusing on rare k-mer markers, we demonstrate that α-satellite HOR haplotypes cluster into genetically related haplogroups. We further developed a software tool, ascairn, to accurately infer these haplogroups from common short-read whole-genome sequencing (WGS) data. Applying our approach to a dataset of more than 3,300 human samples revealed extensive centromere diversity and geographic variation. We also applied the rare k-mer–based approach to centromere sequences from 104 Japanese individuals generated as part of the Japanese Pangenome Project. This analysis revealed characteristic patterns of centromere evolution in the Japanese population and provided new insights into Japanese-specific centromere variation. In addition, we used this method to investigate class-defining chromosomal translocations, specifically der(1;19), also known as 1p/19q co-deletion, in oligodendrogliomas. By analyzing 142 samples from TCGA, we hypothesized that the breakpoints occurred on the p-arm side of D1Z7 and the q-arm side of D19Z3. This hypothesis was subsequently validated through extensive long-read sequencing in two cases, indicating that der(1;19) results in a dicentric chromosome containing two functional centromeres. We also observed that chromosomal rearrangements preferentially occurred in haplotypes with longer repetitive arrays on either the q-arm or p-arm side of the centromere. Furthermore, we identified specific centromere haplogroups associated with either increased or decreased likelihoods of der(1;19) translocations. Our findings show that rare k-mer analysis is a powerful approach for investigating centromere complexity and clarifying the mechanisms underlying centromere-associated abnormalities in cancer.
会場: via Zoom / セミナー室 (359号室)
イベント公式言語: 英語
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セミナーObservability-based causal inference in linear stochastic systems with hidden inputs
2026年10月22日(木) 13:00 - 14:00
關澤 太樹 (理化学研究所 脳神経科学研究センター (CBS) 数理脳科学研究チーム 基礎科学特別研究員)
Causal inference from neural time series is confounded by correlations induced by hidden common inputs, a problem that is especially acute because the full set of variables shaping neural activity is rarely accessible. Prediction based measures such as Granger causality can therefore falsely attribute such dependencies to causal influence. Delay coordinate reconstruction, which is also closely connected to observability in control theory, provides a complementary route: in deterministic systems, downstream delays can reconstruct upstream causes, whereas the reverse does not generally hold. This asymmetry provides a signature of causal direction, as exploited by convergent cross mapping. In stochastic dynamics, however, dynamical and observation noise enter delay coordinates and prevent exact trajectory reconstruction. Here, we develop data driven criteria that extend this observability principle to partially observed stochastic systems. First, we show that observability can be tested by regression of time lagged covariance matrices, which removes direct noise contributions while preserving the observability relation. Second, we show that causal direction can be tested through inclusion of stochastic Koopman eigenvalues estimated from upstream and downstream delay coordinates, because downstream observations generically contain the dynamical components observable upstream. Numerical examples show that the proposed criteria recover causal direction and reject spurious dependencies induced by unobserved common inputs, including cases in which Granger causality and convergent cross mapping fail to distinguish common input from causal influence. Although motivated by neural recordings, the framework applies broadly to partially observed stochastic dynamical systems beyond neuroscience.
会場: 研究本館 3階 359号室とZoomのハイブリッド開催 / via Zoom
イベント公式言語: 英語
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セミナー
Finding your rhythm in a complex acoustic environment
2026年10月14日(水) 13:00 - 14:00
Kim Hoke (Professor, Department of Biology, Colorado State University, USA)
My lab integrates genetic, transcriptomic, morphological, and physiological mechanisms to understand the striking diversity of behavior. This talk will focus on recent work on frog acoustic communication. Although the basic acoustic features of frog calls differ reliably among species, individual males of the same species differ in some acoustic properties and female frogs use those male-male differences in mate choice. And for many species, this communication is occurring in very dense choruses which can reach hundreds of males! Our current work assesses which features of calls are characteristic of individuals and how males adjust their calling based on their social environments. We hope to trace how overall chorus dynamics emerge from individual call strategies playing out in time and space, and link those individual strategies to neurobiological mechanisms. We also address the complementary question of female preferences: how do females integrate over a series of signals in this cacophony to make mate choice decisions? Together these lines of research adopt a systems approach to understand how the robust genetic and developmental processes that produce species-specific behaviors have evolved to generate the striking diversity of communication strategies frogs employ.
会場: セミナー室 (359号室) / via Zoom
イベント公式言語: 英語
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セミナー
Adaptive Regulation through Model-Observation Mismatch: From Process Control to Cognitive Neurorobotics
2026年10月8日(木) 13:00 - 14:00
Henrique Oyama (沖縄科学技術大学院大学 (OIST) 認知脳ロボティクス研究ユニット ポスドク研究員)
Adaptive behavior requires biological and artificial systems to respond when their internal models no longer match what they observe. How can such discrepancies be used not only to correct predictions, but also to regulate how a system interacts with its environment? In this talk, I will explore this question across two research directions spanning process control and cognitive neurorobotics. First, I will introduce a model predictive control framework in which a controller actively guides a nonlinear process toward informative conditions to distinguish among competing models while maintaining safe operation. I will then move to cognitive neurorobotics, where brain-inspired computational principles are used to investigate perception, prediction, and action in embodied artificial agents. In physical human-robot interaction, I will show how a predictive-coding-inspired recurrent neural network enables a humanoid robot to regulate the balance between its learned expectations and sensory information arising from human-guided movements. In particular, recent mismatches between sensory observations and the robot's internal model are used to regulate how strongly it relies on its learned dynamics or accommodates ongoing interaction. Together, these studies illustrate how model-observation mismatch can provide a general signal for adaptive regulation, connecting ideas from control engineering, artificial intelligence, neuroscience, and embodied cognition.
会場: 研究本館 3階 359号室とZoomのハイブリッド開催 / via Zoom
イベント公式言語: 英語
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セミナー
Coexistence and hybridization in plant communities - lessons from mediterranean shrublands
2026年10月1日(木) 13:00 - 14:00
Carmelo Gómez Martínez (Postdoctoral Researcher, Global Change Research Institute, Universidad Rey Juan Carlos, Spain)
This talk explores how two closely related Mediterranean shrubs, the rockroses Cistus ladanifer and Cistus laurifolius, share the same habitat despite being direct competitors for soil, light and pollinators. Hybridization – the natural interbreeding of two related species – often produces offspring that blend both parents' traits, and is surprisingly common in plants, including the Cistus genus. Fieldwork across Spain's Iberian Central System combining genomics, flowering timing and soil experiments shows that no single factor by itself – not genetics, climate or soil – fully explains these dynamics. The next step is to study how pollination shapes hybridization, and for that, we are developing and agent-based model that simulates bee foraging across realistic landscapes to predict new hybrid outcomes under environmental change.
会場: セミナー室 (359号室) 3階 359号室とZoomのハイブリッド開催 / via Zoom
イベント公式言語: 英語
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セミナー
How fungi generate one of the highest pressures in biology: the cell wall as a living nanoporous material
2026年9月7日(月) 14:00 - 15:00
熊倉 直祐 (理化学研究所 環境資源科学研究センター (CSRS) 上級研究員)
Many devastating crop diseases, including anthracnose and rice blast, begin when a fungal pathogen builds a single infection cell called an appressorium. This single cell generates up to ~8 megapascals of turgor pressure (roughly 40 times a car tire’s air pressure), among the highest documented in any living organism, to physically rupture the plant's tough surface. This pressure arises because the cell wall acts as a semipermeable membrane, retaining internal osmolytes such as glycerol while allowing water to pass. What confers this selective permeability had remained unknown for decades: melanin was long assumed responsible, but turgor still forms in melanin-deficient mutants. Using genome editing and direct biochemical analysis of these fungi, we identified two enzymes, PKS2 and PBG13, that synthesize a novel polymer from dihydroxyhexanoic acid (DHHA), which narrows cell-wall pore size at the nanometer scale and is required for turgor generation (Kumakura* et al., Science, 2026). I will frame this system as a living adaptive porous material and discuss questions open to mathematical and physical modeling, including how pore geometry sets the limits of selective permeability.
会場: セミナー室 (359号室) 3階 359号室とZoomのハイブリッド開催
イベント公式言語: 英語
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セミナー
Computational demands shape seizure susceptibility in recurrent neural networks
2026年9月3日(木) 13:00 - 14:00
Sebastian Eydam (理化学研究所 脳神経科学研究センター (CBS) 神経回路計算研究ユニット 研究員)
Why do some brain areas slip into seizures more readily than others? Anatomy and physiology are part of the story, but in this talk we argue that the computation a network performs is itself a determinant of its vulnerability. Working in the language of recurrent neural networks and attractor dynamics, we contrast two computational regimes: networks that represent continuous variables (e.g. tracking a continuous position in space) establish barrier-free state manifolds, whereas networks that store discrete memories have to separate different states by establishing deep wells. A simple energy-landscape picture suggests that continuous networks can amplify perturbations into runaway activity more easily while discrete networks contain them. We test this idea across three systems: handcrafted spiking attractor networks, recurrent networks trained on continuous or discrete computational tasks, and in vivo Neuropixels recordings comparing medial entorhinal cortex (continuous, grid-cell dynamics) with hippocampal CA3 (discrete memory). Under a shared disinhibitory "seizure perturbation," the continuous systems destabilize sooner and drive stronger epileptiform activity, and causal silencing shows this depends on intact entorhinal output. Together, these results establish a direct link between the computation a network is built to perform and its susceptibility to seizures, showing that the very features that enable a network to process information also shape its vulnerability to pathological transitions.
会場: via Zoom / セミナー室 (359号室) 3階 359号室
イベント公式言語: 英語
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セミナー
Multistability in Biochemical Reaction Systems: Structural Approach
2026年8月27日(木) 16:00 - 17:00
岡田 崇 (広島大学 大学院統合生命科学研究科 数理生命科学プログラム 准教授)
In living cells, biochemical reactions form intricate networks that can exhibit multistability, allowing a single system to maintain multiple stable states under identical conditions. However, determining theoretically whether a given reaction system can exhibit multistability is challenging because detailed kinetic parameters are often unknown. In this presentation, we introduce a structural framework that decomposes biochemical networks into subnetworks based solely on network topology. For each subnetwork, we define a scalar quantity, and an index-theoretic argument shows that the sign of this quantity determines whether the subnetwork can contribute to multistability. Our method identifies indicator species whose concentrations distinguish all steady states without detailed kinetic information, thereby enabling efficient measurement design in large networks.
会場: via Zoom
イベント公式言語: 英語
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セミナー
Theoretical Approaches for Cell Deaths
2026年8月6日(木) 13:00 - 14:00
姫岡 優介 (東京大学 生物普遍性研究機構 助教)
Understanding the boundary between cell life and death is a fundamental challenge and a highly important theme in biology. In this talk, focusing on microbial cell death, I would like to discuss how "cell death" can be understood from the perspective of mathematical sciences. Research on microbial cell death has progressed by identifying the molecular mechanisms that drive relevant biochemical processes, which are identified based on empirically known cell death markers. However, there has been little discussion on what death actually is in the first place, or how it can be "defined." Furthermore, recent reports have shown that commonly used live/dead assays—such as dead-cell staining and metabolic activity measurements—can yield conflicting results regarding cell viability, highlighting the growing need to discuss what criteria we should use to define "death." In this study, we propose a definition: a cell is "dead" if it cannot return to a predetermined "representative point of the living state," no matter how gene expression levels or external nutrient concentrations are controlled. Plant seeds may appear "dead" at first glance due to their lack of apparent biochemical activity, yet they germinate when watered. Our proposal in this study is to determine the life or death of a cell based on whether an operation equivalent to "watering" exists [1]. Of course, it is experimentally impossible to prove that a cell cannot regain activity under any operation; however, it is theoretically possible using mathematical models. We developed a method called "Stoichiometric Rays" to calculate the controllability of metabolic reaction systems. Using this, we calculated states that cannot be controlled back to the "representative point of the living state" regardless of how enzyme levels and external nutrient concentrations are manipulated. Consequently, we succeeded in quantifying the separating hyperplane between the "living state" and the "dead state" in a mathematical model of metabolism [2], which we call the Separating Alive and Non-life Zone (SANZ) Hypersurface. In this talk, I will outline the theory, the quantification of the SANZ hypersurface, and its biological interpretation. In addition, through our research [3], we have partially identified a class of models that do not exhibit "death" in the sense described above. I would also like to discuss the relationship between the absence of "death" in these models and the autonomy of life.
会場: セミナー室 (359号室) 3階 359号室 (メイン会場) / via Zoom
イベント公式言語: 英語
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セミナー
Visual system and (social) behavior in zebrafish
2026年7月16日(木) 13:00 - 14:00
久保 郁 (理化学研究所 脳神経科学研究センター (CBS) 知覚運動統合機構研究チーム チームディレクター)
Animals make decisions about their actions using sensory information from the external world. Our lab investigates how the brain processes visual information and generates appropriate behavior using the vertebrate model organism, zebrafish. Our research has uncovered the neural circuits required for processing optic flow, a visual cue that animals use to estimate their own motion. We employ a diverse range of techniques, including behavioral tracking, live imaging of neural activity, and molecular and genetic characterization of neuronal cell types. More recently, our research has focused on social behavior, in which groups of animals collectively generate behavioral decisions. In this seminar, I will present our recent work investigating behavioral contagion in zebrafish.
会場: セミナー室 (359号室) 3階 359号室とZoomのハイブリッド開催
イベント公式言語: 英語
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セミナー
Toward an understanding of microbial circulation in the Mongolian nomadic ecosystem
2026年7月6日(月) 13:00 - 14:00
篠田 あかり (岡山大学 環境生命自然科学学域)
I have been studying microorganisms in the Mongolian nomadic ecosystem from several perspectives. First, I seek to characterize the microbial communities in traditional fermented dairy products—most notably airag (fermented mare's milk)—and their features. Second, I am analyzing the relationship between the traditional Mongolian diet and the gut microbiome. Third, focusing on environmental microorganisms (bioaerosols) in regions undergoing desertification, I aim to trace their origins and atmospheric transport. In the course of these studies, I have come to suspect that microorganisms may circulate among humans, livestock, fermented foods, and the environment. In this research, I aim to understand such microbial circulation by combining approaches from each of these perspectives and by investigating the relationships among these elements. In this talk, I will provide an overview of each topic and discuss the potential of an interdisciplinary approach that connects them.
会場: セミナー室 (359号室) (メイン会場) / via Zoom
イベント公式言語: 英語
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セミナー
Genome Structural Variation and the Evolutionary Potential of Sex in the Unicellular Green Alga Closterium
2026年7月2日(木) 13:00 - 14:00
川口 也和子 (国立遺伝学研究所 分子生命史研究室 博士研究員)
Genome size varies widely among eukaryotes, even between closely related species and within species. However, we still know relatively little about where such variation originates, how organisms tolerate its potential negative effects, and whether it can contribute to adaptation. In this seminar, I will present our studies on the unicellular green alga Closterium peracerosum–strigosum–littorale complex. I will first show that genome size variation in this alga is largely explained by extensive genome-wide copy number variation, and that gene expression can be buffered against changes in gene copy number. I will then show that a single episode of sexual reproduction can generate substantial variation in population growth rates under dual environmental stressors, with some F1 populations growing even when both parental strains decline. Finally, I will discuss how sexual reproduction may drive rapid evolutionary change not only by reshuffling alleles, but also by rearranging genome structure.
会場: セミナー室 (359号室) (メイン会場) / via Zoom
イベント公式言語: 英語
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セミナー
Improving data analysis in biology and in general with Tensor Decomposition
2026年6月18日(木) 13:00 - 14:30
リュカ・ソール (理化学研究所 数理創造研究センター (iTHEMS) 数理基礎部門 数理遺伝学理研ECL研究ユニット 特別研究員)
This talk will provide an introduction to the basic principles of tensor decomposition methods, especially CANDECOMP/PARAFAC (CP) decomposition. I will explain how such methods can be used to extract meaningful and interpretable patterns from high-dimensional tensor-structured data, which commonly arises in biology, as well as in a broad range of other scientific domains. These patterns can then be used to gain a better understanding of the phenomena under study. I will also briefly discuss how tensor decomposition methods can be extended for various types of data, focusing in particular on how I have been trying to better model longitudinal data.
会場: via Zoom / セミナー室 (359号室)
イベント公式言語: 英語
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セミナー
Mode Estimation in the Space of Phylogenetic Trees with Applications to Species Tree Reconstruction
2026年6月11日(木) 13:00 - 14:00
髙澤 祐槻 (東京大学 大学院情報理工学系研究科 特任助教)
Analyzing samples of phylogenetic trees arises in many settings, including bootstrap tree sets, Bayesian posterior samples, and collections of gene trees. The Billera–Holmes–Vogtmann (BHV) tree space provides a geometric framework in which such samples can be viewed as point clouds in a common metric space. A fundamental summary in this space is the Fréchet mean, but it has a property known as stickiness: mean trees tend to lie on lower-dimensional boundaries of the space, corresponding to unresolved, non-binary trees. This behavior can be undesirable, as the mean may then fail to represent the center of interest. In this talk, I will introduce the BHV tree space framework and discuss mode estimation as an alternative way to summarize distributions of phylogenetic trees. After motivating the use of the mode, I will present simple approaches to mode estimation and discuss their consistency and robustness properties. I will then discuss how these ideas can be applied to species tree reconstruction from conflicting gene trees. To handle larger taxon sets, I will use quartet-based aggregation, in which local modal summaries are constructed from trees restricted to sets of four taxa and then combined to reconstruct a species tree. This approach provides a scalable way to apply mode estimation to trees with many taxa and helps reduce the influence of contamination in gene tree collections, as illustrated in simulation studies.
会場: セミナー室 (359号室) (メイン会場) / via Zoom
イベント公式言語: 英語
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セミナー
Membrane Geometry Regulates Phase Morphology in Postsynaptic Condensates
2026年6月4日(木) 14:00 - 15:00
山田 莉彩 (京都大学 大学院理学研究科 生物科学専攻 博士課程)
Biomolecular condensates are generally regarded as membrane-less organelles formed through liquid–liquid phase separation (LLPS). However, some condensates in living cells emerge in close proximity to biological membranes, where spatial confinement and surface geometry can critically influence their organization and function. In this talk, I will discuss recent advances in understanding how membrane association regulates the phase behavior of postsynaptic density (PSD) condensates. Using mesoscale molecular simulations constrained by experimental interaction data, our study reproduced the distinct condensate architectures observed in solution and on membranes. In three-dimensional solution, AMPA receptor/PSD-95 complexes form the condensate core, whereas NMDA receptor/CaMKII complexes localize to the shell. Strikingly, this organization becomes reversed in membrane-associated two-dimensional systems. The analysis revealed that this transition arises from the competition between CaMKII’s large excluded volume and its highly multivalent interactions. While excluded-volume effects dominate in solution, membrane confinement favors specific multivalent interactions, stabilizing distinct receptor nanodomains. These results provide a physical framework for understanding how spatial dimensionality and molecular architecture regulate biomolecular condensates and synaptic organization.
会場: セミナー室 (359号室) 3階 359号室とZoomのハイブリッド開催
イベント公式言語: 英語
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セミナー
Towards rock-solid evolutionary genomics
2026年5月28日(木) 13:00 - 14:00
シュパイデル 玲雄 (理化学研究所 数理創造研究センター (iTHEMS) 数理基礎部門 数理遺伝学理研ECL研究ユニット 理研ECL研究ユニットリーダー)
I will present an overview of ongoing and future projects in our lab. We aim to understand how human genomes retain information about our evolutionary past; a central goal is to reconstruct a high-resolution history of humans, pushing the limits of what we can learn about our origins, past migrations, and adaptation to changing environments and survival pressures. Our genomes reveal events that would otherwise be lost to history, revealing how evolutionary forces have shaped genetic variation and influence our health today. How can we confidently infer events that occurred tens of thousands of years ago? I will discuss how converging and independent lines of genomic evidence can provide “rock-solid” support for major evolutionary events, including archaic admixture, large-scale migrations across continents, and population bottlenecks, and how we aim to extend these approaches to study the evolutionary history and origins of humans and other species.
会場: via Zoom / セミナー室 (359号室)
イベント公式言語: 英語
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セミナー
Stochastic Thermodynamics: noise and energetics of nanoscale systems
2026年5月21日(木) 13:00 - 14:00
Jean-Charles Delvenne (Professor, Applied Mathematics, Université Catholique de Louvain, Belgium)
Stochastic thermodynamics, initiated three decades ago, aims at quantifying the fluctuations of physical observables in relation with thermodynamic quantities (such as heat or entropy production). A typical result is the Thermodynamic Uncertainty Relation, which states that a high entropy production is required to obtain a favorable noise-to-signal ratio for some observables (such as displacement of a molecular motor) in stationary out-of-equilibrium systems. It is especially relevant for nanoscale systems, where the fluctuations cannot be neglected. This includes biological systems (e.g. biological motors such as kinesin along a microtubule), electronic systems (transistor-based memories), chemical reactions, etc. The talk will be both a tutorial on some basic results or applications, and a presentation of some recent results and perspectives.
会場: via Zoom / セミナー室 (359号室)
イベント公式言語: 英語
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セミナー
Sexual conflict over floral receptivity? — theory-guided experiments of evolutionary ecology
2026年5月14日(木) 16:00 - 17:00
京極 大助 (奈良女子大学 研究院自然科学系 准教授)
The theory of evolutionary biology predicts that the interests (in terms of adaptation) of different individuals can conflict with one another. Specifically, mating partners can have different optima in traits such as mating rates, number of mates, number of offspring, and resource allocation to the offspring. Botanists have long recognized that pollination induces floral closure or wilting, which is typically seen as the adaptation of the pollen recipients (i.e., getting rid of costly flowers after achieving their function). However, it is also possible that floral closure or wilting is, at least in part, the outcome of the manipulation by selfish pollen. For example, pollen may secure their paternity by preventing additional pollination. Fewer seed production by the recipients can result in so much allocation of maternal resources to each fertilized egg cell that is maternally maladaptive (but paternally adaptive). Being guided by these theoretical predictions, I have been testing the hypothesis using both Taraxacum dandelions and Arabidopsis. In this talk, I will show our recent (mostly unpublished) results. Although the projects are halfway, results so far generally support the hypothesis. The ideas of related future projects and the philosophy behind the projects may also be discussed.
会場: セミナー室 (359号室) 3階 359号室とZoomのハイブリッド開催
イベント公式言語: 英語
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セミナー
Cautionary tales in data analysis from gravitational-wave astronomy
2026年4月23日(木) 13:00 - 14:00
キップ・カンノン (東京大学 ビッグバン宇宙国際センター (RESCEU) 教授)
We'll look at signal detection in noisy data, and at Bayesian inference in astrophysical inverse problems. We'll look at the form these problems take in the context of gravitational-wave astronomy, but we'll focus on where attempts at solutions have gone wrong. The mistakes we make transcend disciplines, and hopefully by shining light on them others can be helped to avoid making them as well.
会場: 研究本館 3階 359号室とZoomのハイブリッド開催
イベント公式言語: 英語
257 イベント