Applied Systems Biology

5MSc / PhD course at the Faculty of Information Technology and Bionics, Pázmány Péter Catholic University

4 credits 

Journal clubs on papers given by speakers: Tuesdays 15:15 - 17:00 (Hungarian local time) in room 134

Presentations by listed speakers: Thursdays 14:15 – 16:00 (Hungarian local time) online (unless stated below)

Organised by Attila Csikász-Nagy and Andrea Ciliberto

Lectures from earlier years can be found under 2021 vol1,  2022 vol2 and 2023 vol3

Planned lectures of the semester:

Sep 12 - Attila Csikász-Nagy,  Pazmany - in person -room 132

Feed-forward loops of the cell cycle

Papers to read in preparation and discussed on 10 Sept: 1: Milo et al, 2: Novak et al.

Sep 19 - John Tyson, Virginia Tech

Network Dynamics and Cell Physiology

Papers to read in preparation and discussed on 17 Sept: 1: Tyson et al. , 2: Problem set

Sep 26 - Laurence Calzone, Institute Curie

A multiscale modelling approach of tumour growth

Papers to read in preparation and discussed on 24 Sept: 1: Calzone et al.  , 2: Noel et al. 

Oct 3 - Gábor Szederkényi, Pázmány

Biochemical reaction networks: dynamical modeling of molecular processes and beyond

Papers to read in preparation and discussed on 1 Oct: 1: Angeli , 2: Szederkényi et al. 

Oct 10 - Orsolya Kapuy, Semmelweis

A systems-level study of autophagy regulation

Papers to read in preparation and discussed on 8 Oct: 1:  Tyson and Novak, 2: Hajdú et al. 

Oct 17 - Francesca Buffa, Oxford University

Machine Learning Meets Systems Biology: Inference through Gene Signatures and Omics

Papers to read in preparation and discussed on 15 Oct: 1: Dhawan 1. et al. , 2: Dhawan2 et al. , 3: 

Oct 24 - Marko Djordevic, University of Belgrade

Bridging Machine Learning and Mechanistic Modeling: From Populations to Cells

Papers to read in preparation and discussed on 22 Oct: 1: Markovic et al.  , 2: Djordevic et al. 

Oct 31 - Holiday Week

Nov 7 - János Szalma, Cytocast

Large Language Models in Biology

Papers to read in preparation and discussed on 5 Nov: 1:  Simon et al., 2: Ferrando et al. 

Nov 14 - Diego Di Bernardo, Tigem Naples 

Elucidation of gene regulation and signalling dynamics by microfluidics and mathematical modelling

Papers to read in preparation and discussed on 12 Nov: 1: Mangan et al. , 2: Lim et al., 

Nov 21 - Francesco Ginelli, University of Insubria

The Physics of Collective Motion

Papers to read in preparation and discussed on 19 Nov: 1:  Ramaswamy, 2: Giavazzi, 3: Ginelli

Nov 28 - Fabio Giavazzi, University of Milan

You can catch them if they move: capturing collective dynamics and phase transitions in cell collectives

Papers to read in preparation and discussed on 26 Nov: 1: Pinheiro , 2: Cerbino, 

Dec 5 - Gábor Balázsi, Stony Brook University 

Synthetic biology of cancer

Papers to read in preparation and discussed on 3 Dec: 1: Wu et al.  , 2: Wan PNAS , 3: Wan NCB