Presentation:

This will be an intensive course targeted to students from the M. Sc. to post-doctoral levels with either biological or exact sciences backgrounds who wish to acquire skills in Computational Biology. It will have four main components:

  • Introductory lectures on mathematics and physics for biologists, and biology for exact sciences students (parallel tracks),
  • courses on specialized Computational Biology topics ranging from the molecular level to integrated physiological systems,
  • seminars on recent developments,
  • mini-research projects where the students will have opportunity to apply the acquired skills to realistic research problems.

Illustrative applications will emphasize biomedical problems.

Topics covered:

  • Core knowledge for modeling biological systems
  • Molecular dynamics for lipid membranes and proteins
  • Protein-ligand interactions and drug discovery
  • Data Science in Biology
  • Transcriptomics to characterize cellular mechanisms
  • Kinetic modeling of metabolic and signaling processes
  • Modeling of physiological systems

Key dates:

Application deadline: May 31, 2024
Acceptance announcement: June 6
Registration/payment deadline: June 30
Registration confirmation announcement: July 15

Lecturers and tutors

  • Armindo Salvador* (Center for Neuroscience and Cell Biology and Coimbra Chemistry Center, University of Coimbra)
  • Conceição Egas* (Center for Neuroscience and Cell Biology, University of Coimbra and Genoinseq)
  • Joel P. Arrais* (CISUC, Informatics Engineering Department, University of Coimbra)
  • Rui Travasso* (CFisUC, Physics Department, University of Coimbra)
  • Maryam Abbasi, (CISUC, Informatics Engineering Department, University of Coimbra)
  • Luana Afonso (Center for Neuroscience and Cell Biology, University of Coimbra)
  • Adérito Araújo (CMUC, Mathematics Department, University of Coimbra)
  • Tiago Azevedo (CFisUC, Physics Department, University of Coimbra)
  • Martín Calvelo (ITQB NOVA, NOVA University of Lisbon)
  • Beatriz Caniceiro (Center for Neuroscience and Cell Biology, University of Coimbra)
  • João Carvalho (CFisUC, Physics Department, University of Coimbra)
  • Ana Luísa Carvalho (Center for Neuroscience and Cell Biology, University of Coimbra)
  • Filipe Duarte (Center for Neuroscience and Cell Biology, University of Coimbra)
  • José Augusto Ferreira (CMUC, Mathematics Department, University of Coimbra)
  • Luís Loura (Coimbra Chemistry Center, and Faculty of Pharmacy, University of Coimbra )
  • Rita Paiva Melo (Center for Nuclear Science and Technology, University of Lisbon)
  • Irina Moreira (Center for Neuroscience and Cell Biology, University of Coimbra)
  • Alexandre Oliveira (Coimbra Chemistry Center, University of Coimbra )
  • Paulo Oliveira (Center for Neuroscience and Cell Biology, University of Coimbra)
  • Matilde Sá (CFisUC, Physics Department, University of Coimbra)
  • * coordinators

Venue and accommodation

Coimbra
The University of Coimbra
The Computational Biology Network at the University of Coimbra
The organization is able to provide affordable accommodation to the participants in the Summer School. Further information will be provided upon registration.

Application and registration

There is a limited number of places available!

Please use the following form to apply https://forms.gle/3APzzE2bEUtEpzAT6 no later than May 31.

Please also mention which of the parallel tracks you will attend:
A. Mathematics and physics for students with a life sciences background;
B. Biology for students with an exact sciences background.

Registration fee: 100€

Invited Speakers

Christopher Quince

Chris Quince has pioneered techniques to reduce sequencing noise and the application of methods such as shotgun metagenomics to microbial communities. This cutting-edge approach fragments and sequences all of the genomes in a microbiome – quite literally taking a shotgun approach – and these are then reconstructed using sophisticated computational approaches. The methods to reconstruct sequence fragments back into metagenome assembled genomes (MAGs) have been significantly advanced by Quince.

Pedro Beltrão

Pedro Beltrao has a Biochemistry degree from University of Coimbra (2002) and a PhD in Biology from the University of Aveiro for research conducted at EMBL-Heidelberg under the supervision of Luis Serrano (2007). He did his postdoctoral research at the University of California San Francisco under the supervision of Prof. Nevan Krogan (2008-2012). He was a group leader at EMBL-EBI from 2013 to 2021 and he is now an Associate Professor at the Department of Biology, ETH Zurich from Jan 2022

Tomás Alarcón

I obtained my PhD in Theoretical Physics from the University of Barcelona in 2000. After that, I spent many wonderful years working as a postdoc at the University of Oxford, UK (2001-2003), University College London, UK (2003-2006), and Imperial College London, UK (2006-2009). I briefly held a senior researcher and group leader position at BCAM, Bilbao, Spain (2009-2010), after which I moved to the Centre Recerca Matematica in Barcelona, Spain, where I lead the Cancer Modelling Group. I have also held visiting fellowships at the Universidad Complutense de Madrid, IIMAS (UNAM, Mexico DF), OCCAM (University of Oxford, UK), the Mathematical Institute (University of Oxford, UK), the Mathematical Biosciences Institute (Columbus, Ohio, USA), and the Isaac Newton Institute for Mathematical Sciences (Cambridge, UK). In October 2015, I was appointed to an ICREA Research Professorship at the Centre de Recerca Matematica.

Manuel Santos

Multidisciplinary Institute of Aging (MIA), University of Coimbra, Portugal

Aging is a gradual, degenerative and complex process characterized by a decline in physiological function and increased vulnerability to disease. Gene and protein expression play crucial roles in this degenerative process, serving as mechanisms that modulate its processes and pathways and, for these reasons, are excellent proxies to understand the underlying biology of aging. To understand gene expression dynamics and regulatory mechanisms during aging, we analysed data from the transcriptome, proteome, transcription factors and miRNAs during aging in the mouse in a way that allowed us to unveil specific time points, protein solubility and aggregation variables that change across the lifespan. By mapping transcriptomic and proteomic changes we have advanced on the identification of true biomarkers of aging to monitor the impact of therapeutic interventions on biological age.

Sílvia Barbeiro

Sílvia Barbeiro is an Associate Professor at the Department of Mathematics of the University of Coimbra, member of the Numerical Analysis and Optimization group of the Centre for Mathematics of University of Coimbra. She studied at the University of Coimbra and at the Technical University of Berlin and she received her PhD degree in Applied Mathematics in 2005 from the University of Coimbra. She was awarded a L'Oréal Portugal Medal of Honor for Women in Science 2010, a prize promoted by the Foundation for Science and Technology, the L'Oréal Portugal and the UNESCO National Commission. Her research interests are in numerical analysis and computational mathematics, including modeling and the development and analysis of numerical methods for partial differential equations and integro-differential equations. Her research focuses on theory and applications, namely problems in biomathematics, engineering, geosciences and medical imaging.

Provisional programme