사람이 어떻게 만들어지고 각 기관이 어떻게 발달하는지에 대한 질문은 아주 오래전부터 있었습니다. 체외수정(IVF)의 고유의 장점으로 인해 과학자들이 수정란을 외부에서 관찰할 수 있게 되었습니다. 하지만, 1979년도에 제정된 14일 규정(the 14-day rule)으로 인해, 수정 후 최대 14일까지의 배아 만의 연구가 가능합니다. 따라서, 이 14일 규정은 발생 생물학자들이 사람 발생학 연구에 있어서 수정 후 2주 이상(신경계 발달, 기관 형성 등)에 나타나는 현상을 연구하고자 할 경우 다른 방향을 모색할 수밖에 없게 되었습니다. 본 연구는 이 지점에서부터 시작합니다. 연구진들은 세포 분열 때 우연히 발생하는 생리학적 체세포 변이(Post-zygotic Variants)를 추적하여 각 세포들의 운명을 재구성하였습니다. 특히 사망 후 기증된 시신에서 단일 세포를 배양하고, 최근 개발된 차세대 염기서열 분석 기술을 사용하여 인간 발생 연구의 후향적 혈통 추적(Retrospective Lineage Tracing)을 수행하는 과정을 발표하고자 합니다. 이번 발표를 통해서 이런 방법론이 어떻게 가능했는지에 대한 생물학적 및 과학적 배경과 인간 발생학의 미래에서 해결해야 할 과제와 가설을 강조할 예정입니다. 추가로, 이 과정에서 필요한 수학적인 해석이 필요한 질문들에 대해서도 논의할 예정입니다. 여러분들의 참신한 시각과 질문을 크게 환영합니다. 1) Park, S., Mali, N.M., Kim, R. et al. Clonal dynamics in early human embryogenesis inferred from somatic mutation. Nature 597, 393–397 (2021). https://doi.org/10.1038/s41586-021-03786-8 2) Kwon, S.G., Bae, G.H., Choi, J.H. et al. Asymmetric Contribution of Blastomere Lineages of First Division of the Zygote to Entire Human Body Using Post-Zygotic Variants. Tissue Eng Regen Med 19, 809–821 (2022). https://doi.org/10.1007/s13770-022-00443-7

Various types of independent sets have been studied for decades. As an example, the minimum number of maximal independent sets in a connected graph of given order is easy to determine (hint; the answer is written in the stars). When considering this question for twin-free graphs, it becomes less trivial and one discovers some surprising behaviour. The minimum number of maximal independent sets turns out to be; logarithmic in the number of vertices for arbitrary graphs, linear for bipartite graphs and exponential for trees. Finally, we also have a sneak peek on the 69-conjecture, part of an unpublished work on an inverse problem on the number of independent sets. In this talk, we will focus on the basic concepts, the intuition behind the statements and sketch some proof ideas. The talk is based on joint work with Stephan Wagner, with the main chunk being available at arXiv:2211.04357.

Absolute Concentration Robustness (ACR) was introduced by Shinar and Feinberg (Science 327:1389-1391, 2010) as robustness of equilibrium species concentration in a mass action dynamical system. Their aim was to devise a mathematical condition that will ensure robustness in the function of the biological system being modeled. The robustness of function rests on what we refer to as empirical robustness — the concentration of a species remains unvarying, when measured in the long run, across arbitrary initial conditions. Even simple examples show that the ACR notion introduced in Shinar and Feinberg (here referred to as static ACR) is neither necessary nor sufficient for empirical robustness. To make a stronger connection with empirical robustness, we define dynamic ACR, a property related to long-term, global dynamics, rather than only to equilibrium behavior. We discuss general dynamical systems with dynamic ACR properties as well as parametrized families of dynamical systems related to reaction networks. In particular, we find necessary and sufficient conditions for dynamic ACR in complex balanced reaction networks, a class of networks that is central to the theory of reaction networks.This is joint work with Badal Joshi (CSUSM)

TBA

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ZOOM ID: 997 8258 4700 (Biomedical Mathematics Online Colloquium), (pw: 1234)

The disjoint paths logic, FOL+DP,  is an extension of First Order Logic (FOL) with the extra atomic predicate $\mathsf{dp}_k(x_1,y_1,\ldots,x_k,y_k),$ expressing the existence of internally vertex-disjoint paths between $x_i$ and $y_i,$ for $i\in \{1,\ldots, k\}$. This logic can express a wide variety of problems that escape the expressibility potential of FOL. We prove that for every minor-closed graph class, model-checking for FOL+DP can be done in quadratic time. We also introduce an extension of FOL+DP, namely the scattered disjoint paths logic, FOL+SDP, where we further consider the atomic predicate $\mathsf{s-sdp}_k(x_1,y_1,\ldots,x_k,y_k),$ demanding that the disjoint paths are within distance bigger than some fixed value $s$. Using the same technique we prove that model-checking for FOL+SDP can be done in quadratic time on classes of graphs with bounded Euler genus. Joint work with Petr A. Golovach and Dimitrios M. Thilikos.

The ability to reliably engineer the mammalian cell will impact a variety of applications in a disruptive way, including cell fate control and reprogramming, targeted drug delivery, and regenerative medicine. However, our current ability to engineer mammalian genetic circuits that behave as predicted remains limited. These circuits depend on the intra and extra cellular environment in ways that are difficult to anticipate, and this fact often hampers genetic circuit performance. This lack of robustness to poorly known and often variable cellular environment is the subject of this talk. Specifically, I will describe control engineering approaches that make the performance of genetic devices robust to context. I will show a feedforward controller that makes gene expression robust to variability in cellular resources and, more generally, to changes in intra-cellular context linked to differences in cell type. I will then show a feedback controller that uses bacterial two component signaling systems to create a quasi-integral controller that makes the input/output response of a genetic device robust to a variety of perturbations that affect gene expression. These solutions support rational and modular design of sophisticated genetic circuits and can serve for engineering biological circuits that are more robust and predictable across changing contexts.

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ZOOM ID: 997 8258 4700 (Biomedical Mathematics Online Colloquium), (pw: 1234)

TBA

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ZOOM ID: 997 8258 4700 (Biomedical Mathematics Online Colloquium), (pw: 1234)

Fano varieties are algebraic varieties with positive curvature; they are basic building blocks of algebraic varieties. Great progress has been recently made by Xu et al. to construct moduli spaces of Fano varieties by using K-stability (which is related to the existence of Kähler-Einstein metrics). These moduli spaces are called K-moduli. In this talk I will explain how to easily deduce some geometric properties of K-moduli by using toric geometry and deformation theory. In particular, I will show how to construct a 1-dimensional component of K-moduli which parametrises certain K-polystable del Pezzo surfaces. * ZOOM information will not be provided. Please send an email to Jinhyung Park if you are interested in.

TBD

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ZOOM ID: 997 8258 4700 (Biomedical Mathematics Online Colloquium), (pw: 1234)

A linear $3$-graph is called a (3-)hypertree if there exists exactly one path between each pair of two distinct vertices.  A linear $3$-graph is called a Steiner triple system if each pair of two distinct vertices belong to a unique edge. A simple greedy algorithm shows that every $n$-vertex Steiner triple system $G$ contains all hypertrees $T$ of order at most $\frac{n+3}{2}$. On the other hand, it is not immediately clear whether one can always find larger hypertrees in $G$. In 2011, Goodall and de Mier proved that a Steiner triple system $G$ contains at least one spanning tree. However, one cannot expect the Steiner triple system to contain all possible spanning trees, as there are many Steiner triple systems that avoid numerous spanning trees as subgraphs. Hence it is natural to wonder how much one can improve the bound from the greedy algorithm. Indeed, Elliott and Rödl conjectured that an $n$-vertex Steiner triple system $G$ contains all hypertrees of order at most $(1-o(1))n$. We prove the conjecture by Elliott and Rödl. This is joint work with Jaehoon Kim, Joonkyung Lee, and Abhishek Methuku.

TBA

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ZOOM ID: 997 8258 4700 (Biomedical Mathematics Online Colloquium), (pw: 1234)

In this talk, we will introduce the absolute coregularity of Fano varieties. The coregularity measures the singularities of the anti-pluricanonical sections. Philosophically, most Fano varieties have coregularity 0. In the talk, we will explain some theorems that support this philosophy. We will show that a Fano variety of coregularity 0 admits a non-trivial section in |-2K_X|, independently of the dimension of X. This is joint work with Fernando Figueroa, Stefano Filipazzo, and Junyao Peng. * ZOOM information will not be provided. Please send an email to Jinhyung Park if you are interested in.

By a seminal result of Valiant, computing the permanent of (0, 1)-matrices is, in general, #P-hard. In 1913 Pólya asked for which (0, 1)-matrices A it is possible to change some signs such that the permanent of A equals the determinant of the resulting matrix. In 1975, Little showed these matrices to be exactly the biadjacency matrices of bipartite graphs excluding $K_{3,3}$ as a matching minor. This was turned into a polynomial time algorithm by McCuaig, Robertson, Seymour, and Thomas in 1999. However, the relation between the exclusion of some matching minor in a bipartite graph and the tractability of the permanent extends beyond K3,3. Recently it was shown that the exclusion of any planar bipartite graph as a matching minor yields a class of bipartite graphs on which the permanent of the corresponding (0, 1)-matrices can be computed efficiently. In this paper we unify the two results above into a single, more general result in the style of the celebrated structure theorem for single-crossing minor-free graphs. We identify a class of bipartite graphs strictly generalising planar bipartite graphs and $K_{3,3}$ which includes infinitely many non-Pfaffian graphs. The exclusion of any member of this class as a matching minor yields a structure that allows for the efficient evaluation of the permanent. Moreover, we show that the evaluation of the permanent remains #P-hard on bipartite graphs which exclude $K_{5,5}$ as a matching minor. This establishes a first computational lower bound for the problem of counting perfect matchings on matching minor closed classes. As another application of our structure theorem, we obtain a strict generalisation of the algorithm for the k-vertex disjoint directed paths problem on digraphs of bounded directed treewidth. This is joint work with Archontia Giannopoulou and Dimitrios Thilikos.

Wearable analytics hold far more potential than sleep tracking or step counting. In recent years, a number of applications have emerged which leverage the massive quantities of data being amassed by wearables around the world, such as real-time mood detection, advanced COVID screening, and heart rate variability analysis. Yet packaging insights from research for success in the consumer market means prioritizing design and understandability, while also seamlessly managing the sometimes-unreliable stream of data from the device. In this presentation, I will discuss my own experiences building apps which interface with wearable data and process the data using mathematical modeling, as well as recent work extending to other wearable streams and environmental controls.

Cells make individual fate decisions through linear and nonlinear regulation of gene network, generating diverse dynamics from a single reaction pathway. In this colloquium, I will present two topics of our recent work on signaling dynamics at cellular and patient levels. The first example is about the initial value of the model, as a mechanism to generate different dynamics from a single pathway in cancer and the use of the dynamics for stratification of the patients [1-3]. Models of ErbB receptor signaling have been widely used in prediction of drug sensitivity for many types of cancers. We trained the ErbB model with the data obtained from cancer cell lines and predicted the common parameters of the model. By simulation of the ErbB model with those parameters and individual patient transcriptome data as initial values, we were able to classify the prognosis of breast cancer patients and drug sensitivity based on their in silico signaling dynamics. This result raises the question whether gene expression levels, rather than genetic mutations, might be better suited to classify the disease. Another example is about the regulation of transcription factors, the recipients of signal dynamics, for target gene expression [4-6]. By focusing on the NFkB transcription factor, we found that the opening and closing of chromatin at the DNA regions of the putative transcription factor binding sites and the cooperativity in their interaction significantly influenced the cell-to cell heterogeneity in gene expression levels. This study indicates that the noise in gene expression is rather strongly regulated by the DNA side, even though the signals are similarly regulated in a cell population. Overall these mechanisms are important in our understanding the cell as a system for encoding and decoding signals for fate decisions and its application to human diseases.

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ZOOM ID: 997 8258 4700 (Biomedical Mathematics Online Colloquium), (pw: 1234)

Shift workers experience profound circadian disruption due to the nature of their work, which often has them working at times when their internal clock is sending a strong signal for sleep. Mathematical models can be used to generate recommendations for shift workers that shift their body’s clock to better align with their work schedules, to help them sleep, feel, and perform better. In this talk, I will discuss our recent mobile app, Shift, which pulls wearable data from user’s devices and generates personalized recommendations to help them manage shift work schedules. I will also discuss how this product was designed, how it can interface with Internet of Things devices, and how its insights can be useful for other groups beyond shift workers.

Let $\mathcal{F}$ be a family of graphs, and let $p$ and $r$ be nonnegative integers. The $(p,r,\mathcal{F})$-Covering problem asks whether for a graph $G$ and an integer $k$, there exists a set $D$ of at most $k$ vertices in $G$ such that $G^p\setminus N_G^r[D]$ has no induced subgraph isomorphic to a graph in $\mathcal{F}$, where $G^p$ is the $p$-th power of $G$ and $N^r_G[D]$ is the set of all vertices in $G$ at distance at most $r$ from $D$ in $G$. The $(p,r,\mathcal{F})$-Packing problem asks whether for a graph $G$ and an integer $k$, $G^p$ has $k$ induced subgraphs $H_1,\ldots,H_k$ such that each $H_i$ is isomorphic to a graph in $\mathcal{F}$, and for distinct $i,j\in \{1, \ldots, k\}$, the distance between $V(H_i)$ and $V(H_j)$ in $G$ is larger than $r$. The $(p,r,\mathcal{F})$-Covering problem generalizes Distance-$r$ Dominating Set and Distance-$r$ Vertex Cover, and the $(p,r,\mathcal{F})$-Packing problem generalizes Distance-$r$ Independent Set and Distance-$r$ Matching. By taking $(p',r',\mathcal{F}')=(pt, rt, \mathcal{F})$, we may formulate the $(p,r,\mathcal{F})$-Covering and $(p, r, \mathcal{F})$-Packing problems on the $t$-th power of a graph. Moreover, $(1,0,\mathcal{F})$-Covering is the $\mathcal{F}$-Free Vertex Deletion problem, and $(1,0,\mathcal{F})$-Packing is the Induced-$\mathcal{F}$-Packing problem. We show that for every fixed nonnegative integers $p,r$ and every fixed nonempty finite family $\mathcal{F}$ of connected graphs, the $(p,r,\mathcal{F})$-Covering problem with $p\leq2r+1$ and the $(p,r,\mathcal{F})$-Packing problem with $p\leq2\lfloor r/2\rfloor+1$ admit almost linear kernels on every nowhere dense class of graphs, and admit linear kernels on every class of graphs with bounded expansion, parameterized by the solution size $k$. We obtain the same kernels for their annotated variants. As corollaries, we prove that Distance-$r$ Vertex Cover, Distance-$r$ Matching, $\mathcal{F}$-Free Vertex Deletion, and Induced-$\mathcal{F}$-Packing for any fixed finite family $\mathcal{F}$ of connected graphs admit almost linear kernels on every nowhere dense class of graphs and linear kernels on every class of graphs with bounded expansion. Our results extend the results for Distance-$r$ Dominating Set by Drange et al. (STACS 2016) and Eickmeyer et al. (ICALP 2017), and the result for Distance-$r$ Independent Set by Pilipczuk and Siebertz (EJC 2021). This is joint work with Jinha Kim and O-joung Kwon.

The classification of terminal Fano 3-folds has been tackled from different directions: for instance, using the Minimal Model Program, via explicit Birational Geometry, and via Graded Rings methods. In this talk I would like to introduce the Graded Ring Database - an upper bound to the numerics of Fano 3-folds - and discuss the role it plays in the classification and construction of codimension 4 Fano 3-folds having Fano index 2.

Castelnuovo-Mumford regularity, simply regularity, is one of the most interesting invariants in projective algebraic geometry, and the regularity conjecture due to Eisenbud and Goto says that the regularity can be controlled by the degree for any projective variety. But counterexamples to the conjecture have been constructed by some methods. In this talk we review the counterexample constructions including the Rees-like algebra method by McCullough and Peeva and the unprojection method.