학과 세미나 및 콜로퀴엄




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“Semi-supervised Bayesian integration of multiple spatial proteomics dataset”, bioRxiv (2024) will be discussed in this Journal Club. The subcellular localisation of proteins is a key determinant of their function. High-throughput analyses of these localisations can be performed using mass spectrometry-based spatial proteomics, which enables us to examine the localisation and relocalisation of proteins. Furthermore, complementary data sources can provide additional sources of functional or localisation information. Examples include protein annotations and other high-throughput ‘omic assays. Integrating these modalities can provide new insights as well as additional confidence in results, but existing approaches for integrative analyses of spatial proteomics datasets are limited in the types of data they can integrate and do not quantify uncertainty. Here we propose a semi-supervised Bayesian approach to integrate spatial proteomics datasets with other data sources, to improve the inference of protein sub-cellular localisation. We demonstrate our approach outperforms other transfer learning methods and has greater flexibility in the data it can model. To demonstrate the flexibility of our approach, we apply our method to integrate spatial proteomics data generated for the parasite Toxoplasma gondii with time-course gene expression data generated over its cell cycle. Our findings suggest that proteins linked to invasion organelles are associated with expression programs that peak at the end of the first cell-cycle. Furthermore, this integrative analysis divides the dense granule proteins into heterogeneous populations suggestive of potentially different functions. Our method is disseminated via the mdir R package available on the lead author’s Github. If you want to participate in the seminar, you need to enter IBS builiding (https://www.ibs.re.kr/bimag/visiting/). Please contact if you first come IBS to get permission to enter IBS building.
Host: Jae Kyoung Kim     영어     2024-03-04 13:38:19
Let $\mathcal{G}$ and $\mathcal{H}$ be minor-closed graphs classes. The class $\mathcal{H}$ has the Erdős-Pósa property in $\mathcal{G}$ if there is a function $f : \mathbb{N} \to \mathbb{N}$ such that every graph $G$ in $\mathcal{G}$ either contains (a packing of) $k$ disjoint copies of some subgraph minimal graph $H \not\in \mathcal{H}$ or contains (a covering of) $f(k)$ vertices, whose removal creates a graph in $\mathcal{H}$. A class $\mathcal{G}$ is a minimal EP-counterexample for $\mathcal{H}$ if $\mathcal{H}$ does not have the Erdős-Pósa property in $\mathcal{G}$, however it does have this property for every minor-closed graph class that is properly contained in $\mathcal{G}$. The set $\frak{C}_{\mathcal{H}}$ of the subset-minimal EP-counterexamples, for every $\mathcal{H}$, can be seen as a way to consider all possible Erdős-Pósa dualities that can be proven for minor-closed classes. We prove that, for every $\mathcal{H}$, $\frak{C}_{\mathcal{H}}$ is finite and we give a complete characterization of it. In particular, we prove that $|\frak{C}_{\mathcal{H}}| = 2^{\operatorname{poly}(\ell(h))}$, where $h$ is the maximum size of a minor-obstruction of $\mathcal{H}$ and $\ell(\cdot)$ is the unique linkage function. As a corollary of this, we obtain a constructive proof of Thomas' conjecture claiming that every minor-closed graph class has the half-integral Erdős-Pósa property in all graphs. This is joint work with Christophe Paul, Dimitrios Thilikos, and Sebastian Wiederrecht.
Host: Sang-il Oum     영어     2024-03-05 22:57:39
"Solving the time-dependent protein distributions for autoregulated bursty gene expression using spectral decomposition", J. Chem. Phys. (2024) will be discussed in this Journal Club. In this study, we obtain an exact time-dependent solution of the chemical master equation (CME) of an extension of the two-state telegraph model describing bursty or non-bursty protein expression in the presence of positive or negative autoregulation. Using the method of spectral decomposition, we show that the eigenfunctions of the generating function solution of the CME are Heun functions, while the eigenvalues can be determined by solving a continued fraction equation. Our solution generalizes and corrects a previous time-dependent solution for the CME of a gene circuit describing non-bursty protein expression in the presence of negative autoregulation [Ramos et al., Phys. Rev. E 83, 062902 (2011)]. In particular, we clarify that the eigenvalues are generally not real as previously claimed. We also investigate the relationship between different types of dynamic behavior and the type of feedback, the protein burst size, and the gene switching rate. If you want to participate in the seminar, you need to enter IBS builiding (https://www.ibs.re.kr/bimag/visiting/). Please contact if you first come IBS to get permission to enter IBS building.
Host: Jae Kyoung Kim     영어     2024-03-04 13:48:08
Bollobás proved that for every $k$ and $\ell$ such that $k\mathbb{Z}+\ell$ contains an even number, an $n$-vertex graph containing no cycle of length $\ell \bmod k$ can contain at most a linear number of edges. The precise (or asymptotic) value of the maximum number of edges in such a graph is known for very few pairs $\ell$ and $k$. We precisely determine the maximum number of edges in a graph containing no cycle of length $0 \bmod 4$. This is joint work with Ervin Győri, Binlong Li, Nika Salia, Kitti Varga and Manran Zhu.
Host: Sang-il Oum     영어     2024-01-08 14:52:31

ZOOM ID: 997 8258 4700(pw: 1234)
Host: 김재경 교수     Contact: 채송지 (042-878-8244)     영어     2024-02-29 11:15:36
"Reduced model for female endocrine dynamics: Validation and functional variations", Mathematical Biosciences (2023) will be discussed in this Journal Club. A normally functioning menstrual cycle requires significant crosstalk between hormones originating in ovarian and brain tissues. Reproductive hormone dysregulation may cause abnormal function and sometimes infertility. The inherent complexity in this endocrine system is a challenge to identifying mechanisms of cycle disruption, particularly given the large number of unknown parameters in existing mathematical models. We develop a new endocrine model to limit model complexity and use simulated distributions of unknown parameters for model analysis. By employing a comprehensive model evaluation, we identify a collection of mechanisms that differentiate normal and abnormal phenotypes. We also discover an intermediate phenotype—displaying relatively normal hormone levels and cycle dynamics—that is grouped statistically with the irregular phenotype. Results provide insight into how clinical symptoms associated with ovulatory disruption may not be detected through hormone measurements alone. If you want to participate in the seminar, you need to enter IBS builiding (https://www.ibs.re.kr/bimag/visiting/). Please contact if you first come IBS to get permission to enter IBS building.
Host: Jae Kyoung Kim     영어     2024-03-04 13:15:43
We prove a conjecture of Bonamy, Bousquet, Pilipczuk, Rzążewski, Thomassé, and Walczak, that for every graph $H$, there is a polynomial $p$ such that for every positive integer $s$, every graph of average degree at least $p(s)$ contains either $K_{s,s}$ as a subgraph or contains an induced subdivision of $H$. This improves upon a result of Kühn and Osthus from 2004 who proved it for graphs whose average degree is at least triply exponential in $s$ and a recent result of Du, Girão, Hunter, McCarty and Scott for graphs with average degree at least singly exponential in $s$. As an application, we prove that the class of graphs that do not contain an induced subdivision of $K_{s,t}$ is polynomially $\chi$-bounded. In the case of $K_{2,3}$, this is the class of theta-free graphs, and answers a question of Davies. Along the way, we also answer a recent question of McCarty, by showing that if $\mathcal{G}$ is a hereditary class of graphs for which there is a polynomial $p$ such that every bipartite $K_{s,s}$-free graph in $\mathcal{G}$ has average degree at most $p(s)$, then more generally, there is a polynomial $p'$ such that every $K_{s,s}$-free graph in $\mathcal{G}$ has average degree at most $p'(s)$. Our main new tool is an induced variant of the Kővári-Sós-Turán theorem, which we find to be of independent interest. This is joint work with Romain Bourneuf (ENS de Lyon), Matija Bucić (Princeton), and James Davies (Cambridge),
Host: Sang-il Oum     영어     2024-02-15 17:31:02