Thursday, March 9, 2023

2023-03-13 / 11:00 ~ 12:00

by ()

The morphological method – based on the topology and singularity theory and originally developed for the analysis of the scattering experiments – was extended to be applicable for the analysis of biological data. The usefulness of the topological viewpoint was demonstrated by quantification of the changes of collagen fiber straightness in the human colon mucosa (healthy mucosa, colorectal cancer, and uninvolved mucosa far from cancer). This has been done by modeling the distribution of collagen segment angles by the polymorphic beta-distribution. Its shapes were classified according to the number and type of critical points. We found that biologically relevant shapes could be classified as shapes without any preferable orientation (i.e. shapes without local extrema), transitional forms (i.e. forms with one broad local maximum), and highly oriented forms (i.e. forms with two minima at both ends and one very narrow maximum between them). Thus, changes in the fiber organization were linked to the metamorphoses of the beta-distribution forms. The obtained classification was used to define a new, shape-aware/based, measure of the collagen straightness, which revealed a slight, and moderate increase of the straightness in mucosa samples taken 20 cm and 10 cm away from the tumor. The largest increase of collagen straightness was found in samples of cancer tissue. Samples of the healthy individuals have a uniform distribution of beta-distribution forms. We found that this distribution has the maximal information entropy. At 20 cm and 10 cm away from cancer, the transition forms redistribute into unoriented and highly oriented forms. Closer to cancer the number of unoriented forms decreases rapidly leaving only highly oriented forms present in the samples of the cancer tissue, whose distribution has minimal information entropy. The polarization of the distribution was followed by a significant increase in the number of quasi-symmetrical forms in samples 20 cm away from cancer which decreases closer to cancer. This work shows that the evolution of the distribution of the beta-distribution forms – an abstract construction of the mind – follows the familiar laws of statistical mechanics. Additionally, the polarization of the beta-distribution forms together with the described change in the number of quasi-symmetrical forms, clearly visible in the parametric space of the beta-distribution and very difficult to notice in the observable space, can be a useful indicator of the early stages in the development of colorectal cancer.

2023-03-15 / 16:00 ~ 17:00

IBS-KAIST 세미나 - 수리생물학:

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Multi-omics technologies, and in particular those with single-cell and spatial resolution, provide unique opportunities to study the deregulation of intra- and inter-cellular signaling processes in disease. I will present recent methods and applications from our group toward this aim, focusing on computational approaches that combine data with biological knowledge within statistical and machine learning methods. This combination allows us to increase both the statistical power of our analyses and the mechanistic interpretability of the results. These approaches allow us to identify key processes, that can be in turn studied in detailed with dynamic mechanistic models. I will then present how cell-specific logic models, trained with measurements upon perturbations, can provides new biomarkers and treatment opportunities. Finally, I will show how, using novel microfluidics-based technologies, this approach can also be applied directly to biopsies, allowing to build mechanistic models for individual cancer patients, and use these models to prose new therapies.

2023-03-10 / 14:00 ~ 16:00

IBS-KAIST 세미나 - 수리생물학:

by ()

A key goal of synthetic biology is to establish functional biochemical modules with network-independent properties. Antithetic integral feedback (AIF) is a recently developed control module in which two control species perfectly annihilate each other’s biological activity. The AIF module confers robust perfect adaptation to the steady-state average level of a controlled intracellular component when subjected to sustained perturbations. Recent work has suggested that such robustness comes at the unavoidable price of increased stochastic fluctuations around average levels. We present theoretical results that support and quantify this trade-off for the commonly analyzed AIF variant in the idealized limit with perfect annihilation. However, we also show that this trade-off is a singular limit of the control module: Even minute deviations from perfect adaptation allow systems to achieve effective noise suppression as long as cells can pay the corresponding energetic cost. We further show that a variant of the AIF control module can achieve significant noise suppression even in the idealized limit with perfect adaptation. This atypical configuration may thus be preferable in synthetic biology applications.

2023-03-10 / 10:00 ~ 11:00

IBS-KAIST 세미나 - 수리생물학:

by ()

Cooperation means that one individual pays a cost for another to receive a benefit. Cooperation can be at variance with natural selection. Why should you help competitors? Yet cooperation is abundant in nature and is important component of evolutionary innovation. Cooperation can be seen as the master architect of evolution and as the third fundamental principle of evolution beside mutation and selection. I will present five mechanisms for the evolution of cooperation: direct reciprocity, indirect reciprocity, spatial selection, group selection and kin selection. Global cooperation and the cooperation with future generations is necessary to ensure the survival of our species. Further reading: Nowak MA (2006). Evolutionary Dynamics. Harvard University Press Nowak MA & Highfield R (2011) SuperCooperators. Simon & Schuster. Hauser OP, Rand DG, Peysakhovich A & Nowak MA (2014). Cooperating with the future. Nature 511: 220-223 Hilbe C, Šimsa Š, Chatterjee K & Nowak MA (2018). Evolution of cooperation in stochastic games. Nature 559: 246-249 Hauser OP, Hilbe C, Chatterjee K & Nowak MA (2019). Social dilemmas among unequals. Nature 572: 524-527

2023-03-16 / 11:50 ~ 12:40

대학원생 세미나 - 대학원생 세미나:

by 장원용(카이스트)

For complex number $\alpha$, let $ A = \begin{bmatrix} 1 & 1 \\ 0 & 1 \end{bmatrix}$ and $B = \begin{bmatrix} 1 & 0 \\ \alpha & 1 \end{bmatrix} $ be two parabolic matrices and let $G_\alpha$ be the group generated by these two matrices. Determining whether $G_\alpha$ is the free group rank 2 or not, is one of the important problems. In this talk, I will introduce a geometric aspect of the group $G_\alpha$ and give previous results of the problem. Next, I will introduce my work joint with KyeongRo Kim.

2023-03-14 / 16:30 ~ 17:30

IBS-KAIST 세미나 - 이산수학: Recent progress on the Union-closed conjecture and related

by Stijn Cambie(IBS 극단조합및확률그룹)

We give a summary on the work of the last months related to Frankl's Union-Closed conjecture and its offsprings. The initial conjecture is stated as a theorem in extremal set theory; when a family F is union-closed (the union of sets of F is itself a set of $\mathcal F$), then $\mathcal F$ contains an (abundant) element that belongs to at least half of the sets. Meanwhile, there are many related versions of the conjecture due to Frankl. For example, graph theorists may prefer the equivalent statement that every bipartite graph has a vertex that belongs to no more than half of the maximal independent sets. While even proving the ε-Union-Closed Sets Conjecture was out of reach, Poonen and Cui & Hu conjectured already stronger forms. At the end of last year, progress was made on many of these conjectures. Gilmer proved the ε-Union-Closed Sets Conjecture using an elegant entropy-based method which was sharpened by many others. Despite a sharp approximate form of the union-closed conjecture as stated by Chase and Lovett, a further improvement was possible. In a different direction, Kabela, Polak and Teska constructed union-closed family sets with large sets and few abundant elements. This talk will keep the audience up-to-date and give them insight in the main ideas. People who would like more details, can join the Ecopro-reading session on the 7th of March (10 o'clock, B332) as well. Here we go deeper in the core of the proofs and discuss possible directions for the full resolution.

Events for the 취소된 행사 포함