{"id":12,"date":"2024-09-23T11:55:54","date_gmt":"2024-09-23T14:55:54","guid":{"rendered":"https:\/\/eventos.cmm.uchile.cl\/mmce2025\/?page_id=12"},"modified":"2025-12-24T07:50:20","modified_gmt":"2025-12-24T10:50:20","slug":"program","status":"publish","type":"page","link":"https:\/\/eventos.cmm.uchile.cl\/mmce2026\/program\/","title":{"rendered":"Program"},"content":{"rendered":"


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Day 1<\/h3>\n\n\n\n\n\n\n\n\n\n\n\n\n
Time<\/th>\nTopic<\/th>\nSpeaker<\/th>\nCategory<\/th>\n<\/tr>\n<\/thead>\n
09:00 \u2013 10:00<\/td>\nCourse Overview and Breakfast Meet & Greet (icebreaker activity)<\/td>\nAlejandro Maass, Luis Zapata<\/td>\nWelcome<\/td>\n<\/tr>\n
10:00 \u2013 11:00<\/td>\nIntro to mathematical modelling and data science in cancer evolution, covering cancer as an evolutionary process, motivation for studying cancer evolution, and examples such as adaptive therapy and driver gene identification.<\/td>\nLuis Zapata<\/td>\nLecture<\/td>\n<\/tr>\n
11:00 \u2013 12:30<\/td>\nData science in cancer evolution, including large-scale multi-omics analysis and mathematical principles for predictive modelling.<\/td>\nLuis Zapata<\/td>\nLecture<\/td>\n<\/tr>\n
12:30 \u2013 13:30<\/td>\nLunch<\/td>\n<\/td>\nBreak<\/td>\n<\/tr>\n
13:30 \u2013 15:00<\/td>\nIntroduction to mathematical modelling of cancer evolution using ordinary differential equations (ODEs), including tumour growth models, phenotype transitions, and tumour\u2013immune interactions.<\/td>\nChloe Colson<\/td>\nLecture<\/td>\n<\/tr>\n
15:00 \u2013 15:30<\/td>\nCoffee break<\/td>\n<\/td>\nBreak<\/td>\n<\/tr>\n
15:30 \u2013 17:00<\/td>\nPractical session on simulating ODE models in R\/Python, focusing on qualitative behaviour and steady-state analysis.<\/td>\nChloe Colson<\/td>\nPractical<\/td>\n<\/tr>\n
17:00 \u2013 18:00<\/td>\nGroup project and presentation assignment, including research paper discussion and participant research presentations.<\/td>\nLuis Zapata<\/td>\nPractical<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n

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Day 2<\/h3>\n\n\n\n\n\n\n\n\n\n\n\n\n
Time<\/th>\nTopic<\/th>\nSpeaker<\/th>\nCategory<\/th>\n<\/tr>\n<\/thead>\n
09:00 \u2013 10:30<\/td>\nDiscrete stochastic models of cancer evolution, including branching\/birth\u2013death processes for genetic evolution (mutations and selection) and stochastic models for phenotypic evolution.<\/td>\nChloe Colson<\/td>\nLecture<\/td>\n<\/tr>\n
10:30 \u2013 11:00<\/td>\nCoffee break<\/td>\n<\/td>\nBreak<\/td>\n<\/tr>\n
11:00 \u2013 12:30<\/td>\nPractical on stochastic genetic evolution models: simulation under neutrality vs driver mutations, VAF spectrum visualisation, and mutation-rate estimation from VAF distributions.<\/td>\nChloe Colson<\/td>\nPractical<\/td>\n<\/tr>\n
12:30 \u2013 13:30<\/td>\nLunch<\/td>\n<\/td>\nBreak<\/td>\n<\/tr>\n
13:30 \u2013 15:00<\/td>\nStatistical inference of parameters, covering maximum likelihood estimation and Bayesian inference (likelihood- and simulation-based approaches).<\/td>\nGiulio Caravagna<\/td>\nLecture<\/td>\n<\/tr>\n
15:00 \u2013 15:30<\/td>\nCoffee break<\/td>\n<\/td>\nBreak<\/td>\n<\/tr>\n
15:30 \u2013 17:00<\/td>\nPractical: parameter inference case studies, including estimating mutation and growth rates from single timepoint snapshots and from longitudinal data.<\/td>\nGiulio Caravagna<\/td>\nPractical<\/td>\n<\/tr>\n
17:00 \u2013 18:00<\/td>\nKeynote talk I<\/td>\nAlejandro Maass \/ Steffen<\/td>\n<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n

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Day 3<\/h3>\n\n\n\n\n\n\n\n\n\n\n\n
Time<\/th>\nTopic<\/th>\nSpeaker<\/th>\nCategory<\/th>\n<\/tr>\n<\/thead>\n
09:00 \u2013 10:30<\/td>\nMeasuring selection in cancer genomes, including genomic signals of positive\/negative selection and Bayesian\/frequentist approaches for quantifying selection.<\/td>\nLuis Zapata<\/td>\nLecture<\/td>\n<\/tr>\n
10:30 \u2013 11:00<\/td>\nCoffee break<\/td>\n<\/td>\nBreak<\/td>\n<\/tr>\n
11:00 \u2013 12:30<\/td>\nPractical: measuring selection in cancer genomes, including driver\/essential gene identification using functional impact, recurrence, and dN\/dS.<\/td>\nLuis Zapata<\/td>\nPractical<\/td>\n<\/tr>\n
12:30 \u2013 13:30<\/td>\nLunch<\/td>\n<\/td>\nBreak<\/td>\n<\/tr>\n
13:30 \u2013 15:00<\/td>\nSubclonal deconvolution of tumours: estimation of allele frequencies, purity, and copy number as inputs for subclonal reconstruction.<\/td>\nGiulio Caravagna<\/td>\nLecture<\/td>\n<\/tr>\n
15:30 \u2013 16:00<\/td>\nCoffee break<\/td>\n<\/td>\nBreak<\/td>\n<\/tr>\n
15:30 \u2013 17:00<\/td>\nPractical: subclonal deconvolution tools and workflows, including approaches for subclonal evolution and neutrality testing (e.g., MOBSTER, Battenberg, PyClone).<\/td>\nGiulio Caravagna<\/td>\nPractical<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n

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Day 4<\/h3>\n\n\n\n\n\n\n\n\n\n\n\n\n\n
Time<\/th>\nTopic<\/th>\nSpeaker<\/th>\nCategory<\/th>\n<\/tr>\n<\/thead>\n
09:00 \u2013 10:30<\/td>\nMachine learning for tumour profiling: unsupervised analysis to uncover subtypes, multi-omic integration with MOFA to expose latent axes, and phenotype prediction using PARETO.<\/td>\nAlex Di Genova<\/td>\nLecture<\/td>\n<\/tr>\n
10:30 \u2013 11:00<\/td>\nCoffee break<\/td>\n<\/td>\nBreak<\/td>\n<\/tr>\n
11:00 \u2013 12:30<\/td>\nPractical: machine learning for tumour profiling, including hands-on applications (Google Colab).<\/td>\nAlex Di Genova<\/td>\nPractical<\/td>\n<\/tr>\n
12:30 \u2013 13:30<\/td>\nLunch<\/td>\n<\/td>\nBreak<\/td>\n<\/tr>\n
13:30 \u2013 15:00<\/td>\nIntroduction to mathematical modelling of cancer evolution using partial differential equations (PDEs), including tumour cell growth\/movement and phenotype evolution along continuous state spaces.<\/td>\nChlo\u00e9 Colson<\/td>\nLecture<\/td>\n<\/tr>\n
15:00 \u2013 15:30<\/td>\nCoffee break<\/td>\n<\/td>\nBreak<\/td>\n<\/tr>\n
15:30 \u2013 17:00<\/td>\nPractical: visualising PDE model simulations.<\/td>\nChlo\u00e9 Colson<\/td>\nPractical<\/td>\n<\/tr>\n
17:00 \u2013 18:00<\/td>\nKeynote talk III<\/td>\n<\/td>\n<\/td>\n<\/tr>\n
18:00 \u2013 late<\/td>\nFree evening<\/td>\n<\/td>\n<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n

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Day 5<\/h3>\n\n\n\n\n\n\n\n\n\n\n\n\n
Time<\/th>\nTopic<\/th>\nSpeaker<\/th>\nCategory<\/th>\n<\/tr>\n<\/thead>\n
09:00 \u2013 10:30<\/td>\nContinue: applications of data science and genomics for cancer treatment.<\/td>\nLuis Zapata<\/td>\nLecture<\/td>\n<\/tr>\n
10:30 \u2013 11:00<\/td>\nCoffee break<\/td>\n<\/td>\nBreak<\/td>\n<\/tr>\n
11:00 \u2013 12:30<\/td>\nContinue: machine learning in genomics.<\/td>\nAlex Di Genova<\/td>\nPractical<\/td>\n<\/tr>\n
12:30 \u2013 13:30<\/td>\nLunch<\/td>\n<\/td>\nBreak<\/td>\n<\/tr>\n
13:30 \u2013 15:00<\/td>\nFlash talks: participants\u2019 own research.<\/td>\n<\/td>\nPractical<\/td>\n<\/tr>\n
15:00 \u2013 15:30<\/td>\nCoffee break<\/td>\n<\/td>\nBreak<\/td>\n<\/tr>\n
15:30 \u2013 17:00<\/td>\nFlash talks: research papers.<\/td>\n<\/td>\nPractical<\/td>\n<\/tr>\n
17:00 \u2013 18:00<\/td>\nWrap-up discussion and course debrief.<\/td>\n<\/td>\n<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<\/div>\n

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Day 1 Time Topic Speaker Category 09:00 \u2013 10:00 Course Overview and Breakfast Meet & Greet (icebreaker activity) Alejandro Maass, Luis Zapata Welcome 10:00 \u2013 11:00 Intro to mathematical modelling and data science in cancer evolution, covering cancer as an evolutionary process, motivation for studying cancer evolution, and examples such as adaptive therapy and driver … Continue reading Program<\/span> →<\/span><\/a><\/p>\n","protected":false},"author":2,"featured_media":0,"parent":0,"menu_order":2,"comment_status":"closed","ping_status":"closed","template":"","meta":{"inline_featured_image":false,"footnotes":""},"class_list":["post-12","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/eventos.cmm.uchile.cl\/mmce2026\/wp-json\/wp\/v2\/pages\/12","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/eventos.cmm.uchile.cl\/mmce2026\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/eventos.cmm.uchile.cl\/mmce2026\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/eventos.cmm.uchile.cl\/mmce2026\/wp-json\/wp\/v2\/users\/2"}],"replies":[{"embeddable":true,"href":"https:\/\/eventos.cmm.uchile.cl\/mmce2026\/wp-json\/wp\/v2\/comments?post=12"}],"version-history":[{"count":20,"href":"https:\/\/eventos.cmm.uchile.cl\/mmce2026\/wp-json\/wp\/v2\/pages\/12\/revisions"}],"predecessor-version":[{"id":152,"href":"https:\/\/eventos.cmm.uchile.cl\/mmce2026\/wp-json\/wp\/v2\/pages\/12\/revisions\/152"}],"wp:attachment":[{"href":"https:\/\/eventos.cmm.uchile.cl\/mmce2026\/wp-json\/wp\/v2\/media?parent=12"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}