Thomas Wim Hamelryck
Professor
Computational and RNA Biology
Ole Maaløes Vej 5
2200 København N.
Programming Languages and Theory of Computing
Universitetsparken 5
2100 København Ø
ORCID: 0000-0003-2917-3602
Date of Birth: 24/06/1971
Contact: +45 23960613, thamelry@bio.ku.dk
Webpage: https://thamelry.github.io
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 |
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)
Publication overview
- 48 publications in PubMed
- 26 as communicating author
- Highlights: PNAS (2), Mol. Biol. Evol., PLoS Comp. Biol. (2), ICML, ICLR
- 79 publications in ORCID (0000-0003-2917-3602)
- H-index and number of citations (Google Scholar): 31 / 7723.
- Two most cited articles: 4078 and 750 citations.
- Textbook: “Bayesian methods in structural bioinformatics”, 386 pages, Springer, 2012.
- 36.000 downloads since 2012 on springer.com
Supervision
- Supervised 8 postdocs and 15 PhD students.
- Current group : 2 postdocs, 3 PhD students
Current teaching
- Introduction to data science (DIKU), 7.5 ECTS
- Structural bioinformatics (BIO), 7.5 ECTS
- Python programming for data science (BIO-DIKU), 7.5 ECTS
- Probabilistic machine learning (DIKU, 7.5 ECTS)
- Bioinformatics individual projects (BIO), 7.5 ECTS
Recent outreach
- Researchers develop AI tool to combat coronavirus variants of the future. KU press release, 2021
- Flere unge skal have en fremtid med AI og machine learning. TechSavvy, 2018.
ID: 5765
Most downloads
-
2308
downloads
Protein structure validation and refinement using amide proton chemical shifts derived from quantum mechanics
Research output: Contribution to journal › Journal article › Research › peer-review
Published -
1788
downloads
Parallel GPGPU Evaluation of Small Angle X-ray Scattering Profiles in a Markov Chain Monte Carlo Framework
Research output: Chapter in Book/Report/Conference proceeding › Book chapter › Research › peer-review
Published -
1469
downloads
A probabilistic model of RNA conformational space
Research output: Contribution to journal › Journal article › Research › peer-review
Published