Thomas Wim Hamelryck

Professor

Computational and RNA Biology
Ole Maaløes Vej 5
2200 København N.
- thamelry@bio.ku.dk
- https://www1.bio.ku.dk/english/research/scarb/
- http://thamelry.github.io
Phone: +4523960613Mobile: +4523960613
Programming Languages and Theory of Computing
Universitetsparken 5
2100 København Ø
- thamelry@bio.ku.dk
Phone: +4523960613Mobile: +4523960613

Date of Birth: 24/06/1971

Contact: +45 23960613, thamelry@bio.ku.dk

Scientific focus areas: protein structure prediction, structural biology,, Bayesian statistics, machine learning, data science, deep probabilistic programming

Education

Academic degree	University	Year
PhD (protein crystallography)	Free University of Brussels (VUB), BE	1999
Masters (bio-engineer)	Free University of Brussels (VUB), BE	1994

Positions

Position	Place	From	To
Visiting associate professor (50%)	DIKU	2016	Now
Visiting professor	University of Leeds, UK	2011	2016
Associate professor	University of Copenhagen, DK	2007	now
Assistant professor	University of Copenhagen, DK	2004	2007
Postdoc - Head bioinformatics research initiative VUB	Free University of Brussels (VUB), BE	2002	2004
Postdoc	Free University of Brussels (VUB), BE and University of Århus, DK	1999	2002

Selected offices, Academic Service, Professional activities 2012- 2016

Task	Event	From	To
Senior associate editor	ACM Transactions on Probabilistic Machine Learning	2023	Now
Main conference organizer	Conference: Machine learning and molecules (190 participants, 13 international speakers)	2017
Main book editor	Book: “Bayesian Methods in Structural Bioinformatics”. Springer Verlag. 386 pages.	2012
Conference organizer	Conference: Machine Learning in Structural Bioinformatics (150 participants, 8 international speakers)	2008
Software developer	Mocapy and Mocapy++: Machine learning library for dynamic Bayesian networks.	2008
Software developer	Bio.PDB package in Biopython. Bio.PDB article cited 260 times. Biopython article cited 4110 times. Bio.PDB is still (in 2023) a standard and widely-used tool for structural bioinformatics.	2004

Academic awards and honours

Award/honour	Year
Ishango prize for young scientists in Brussels capital region.	2002
DSM Science & Technology Award Europe - 2nd prize.	1999

Current funding

Principal Investigator (PI) / Partner	Funding Source & Amount of Money	Project title	From	To
PI	Villum Fonden - Villum EXPERIMENT, 1.837.956 DKK	Predicting protein structure, mutations and dynamics with deep generative models.	2023	2025
Partner. PI: Prof. Anders Lund, BRIC.	Independent Research Fund Denmark-FNU, 2.863.996 DKK	Identification and Characterization of Specialized Ribosome Subtypes	2022	2025
PI (Co-applicant: Prof. Fritz Henglein, DIKU)	Independent Research Fund Denmark-FTP, 5.901.438 DKK	Deep probabilistic programming for protein structure prediction	2020	2024
PI	GKN Aerospace, Sweden, 2.053.400 DKK	Application of deep learning in aerospace industry manufacturing.	2019	2023

Current international collaborators

Prof. Jotun Hein, U. Oxford, UK (protein evolution)
Prof. John T. Kent and Prof. Kanti V. Mardia, U. Leeds, UK (directional statistics)
Assoc. Prof. Christophe Ley, U. Luxembourg (statistics, machine learning)
Assoc. Prof. Douglas Theobald, U. Brandeis, USA (protein evolution)
Assist. Prof. Eric Nalisnick, U. Amsterdam (probabilistic machine learning)