Curriculum vitae
Personal information
| First name, Surname: | Peter, Horvath | ||
| Date of birth: | 11th October, 1980 | Sex: | male |
| Nationality: | Hungarian | ||
| Researcher unique identifier(s) (ORCID, ResearcherID, etc.): | 0000-0002-4492-1798 | ||
| URL for personal website: | Peter Horvath Laboratory (u-szeged.hu) | ||
Education
| Year | Faculty/department – University/institution – Country |
| 2023 | DSc. – Hungary |
| 2008 | Ph.D. : Digital image analysis – University of Nice, Sophia Antipolis – France |
| 2003 | MSc: Computer Science, Mathematics – University of Szeged – Hungary |
Positions – current and previous
| Year | Job title – Employer – Country |
| 2023- | Senior Researcher – Helmholtz Munich, AI4Health Institute, Germany |
| 2018 – | Director – Institute of Biochemistry, Biological Research Centre (BRC) – Hungary |
| 2017 -2023 | Director – FIMM High-Content Analysis Facility (FIMM-HCA HELMI) – Finland |
| 2016 – | CEO, Single-Cell Technologies Ltd., Szeged, Hungary |
| 2014 -2023 | Distinguished Professor Fellow – FIMM, University of Helsinki – Finland |
| 2014 – | Research group leader – Biological Research Center, Szeged – Hungary |
| 2007- 2013 | Senior Scientist, docent – ETH, Zurich – Switzerland |
Project management experience
| Year | Project owner – Project – Role – Funder |
| 2019 – 2023 | BRC – Artificial intelligence driven machines for biological discoveries – PI role – HAS Momentum starting Grant |
| 2021 -2022 | BRC – Nerve cell phenotyping and examining their communication using artificial intelligence and the automated patch clamp system – PI role – ELKH Consortium |
| 2021 – 2023 | BRC -The proteogenomic map of tumour cell division – PI role – ELKH Excellence Programme |
| 2021 – 2024 | BRC – Intelligent inference system to support biological discovery and its application in cancer research – coPI – OTKA SNN, NRDIO |
| 2022 – 2025 | BRC – Artificial intelligence-based single cell analysis – from basic research to the bedside – PI role – Thematic Excellence Programme Grant |
| 2022 – 2025 | BRC – Discovering the cellular landscape of the airways and the lung (DisvovAIR) – coPI role – H2020 HCA Seeding |
| 2022 – 2026 | BRC – Deep learning-based methods for automatically performing patch-clamp recording on multiple neurons – coPI- NAP3 NRDIO |
| 2022 – 2025 | BRC – BIALYMP (Bispecific antibodies in Lymphoma: Microenvironmental profiling to predict treatment response and uncover immunogenic resistance mechanisms)- coPI – EU Horizon 2020, TRANSCAN2021 |
| 2022 – 2025 | BRC- Fast Infrared Coherent Harmonic Microscopy ( FAIR CHARM)– coPI – EU Horizon 2020 |
| 2023 – 2026 | BRC – Swept laser enabled non-invasive Diagnostic tools (SWEEPICS) – coPI – EU Horizon |
| 2025 – 2027 | HUN-REN BRC – TKCS-2024/73; Towards the deep molecular map of cellular state transitions – PI |
Supervision of students
| Master’s students | Ph.D. students | University/institution – Country |
| 3 | 7 | Institute of Biochemistry, Biological Research Centre (BRC) – Hungary |
Other relevant professional experiences
| Year | Description – Role |
| 2024 – | ELLIS Membership |
| 2023 – | KEPAF (Hungarian Association for Image Processing and Pattern Recognition) – President |
| 2018 | Organized the NEUBIAS 2018 Szeged conference (250 participants, the largest bioimage informatics conference worldwide) |
| 2014 – 2016 | Councillor (Member of the Board of Directors) for the Society of Biomolecular Imaging and Informatics (SBI2 |
| 2010 – | Chair of the European Cell-based Assays Interest Group (EUCAI) |
| 2008 – | Organizer and Session chair of numerous conferences, meetings, and workshops |
- Peter Horvath has published 140 peer reviewed scientific articles, with an h-index of 47, cumulative impact factor of 1416, 227 and 14 572 citations (Google scholar – Peter Horvath).
- Selected publications in major national or international peer-reviewed journals:
- Learning representations for image-based profiling of perturbations, , Moshkov, N., Bornholdt, M., Benoit, S., Smith, M., McQuin, C., Horvath, P., …, Carpenter, A. E., Singh, S., Caicedo, J. C., Nature Communications, 15 (1), 1594, 2024
- Segmentation metric misinterpretations in bioimage analysis, Hirling, D., Tasnadi, E., Caicedo, J., Caroprese, MV., …, Koos, K., Horvath, P., Nature methods,1-4, 2023
- An integrated cell atlas of the lung in health and disease; Sikkema, L., Ramírez-Suástegui, C., Strobl, C.D., Gillett, T. E., Zappia, L., Madissoon, E., …, HCA Lung Biological Network (Horvath, P.), …, Nawijn, M.C., Luecken, M.D., Theis, F., Nature Medicine 29, 1563-1577,2023
- Predicting compound activity from phenotypic profiles and chemical structures; Moshkov, N., Becker, T., Yang, K., Horvath, P., Dancik, V., …, Carpenter, A. E., Caicedo, J. C., Nature Communications 14, 1967,2023
- Cell Segmentation and Representation with Shape Priors, Hirling, D., Horvath, P., Computational and Structural Biotechnology Journal 21, 742-750, 2023
- Nucleus segmentation: towards automated solutions; Hollandi, R., Moshkov, N., Paavolainen L., Tasnadi, E., Piccinini, F., Horvath, P. ; Trends in Cell Biology, (32) 4, 2022
- Deep Visual Proteomics defines cell identity and heterogeneity ; Mund, A., Coscia, F., Hollandi, R., Kovacs, F., Kriston, A., Brunner, A-D., Bzorek, M., Naimy, S., Gjerdrum, L. M. R., Dyring-Andersen, B., Bulkescher, J., Lukas, C., Gnann, C., Lundberg, E., Horvath, P., Mann, M., Nature Biotechnology 40, 1231-1240, 2022
- Regression plane concept for analysing continuous cellular processes with machine learning; A Szkalisity, F Piccinini, A Beleon, T Balassa, IG Varga, E Migh, C Molnar, …, P. Horvath; Nature communications 12 (1), 1-9, 2021
- Chronic lung diseases are associated with gene expression programs favoring SARS-CoV-2 entry and severity; Bui, L. T., Winters, N. I., Chung, M. I., Joseph, C., Gutierrez, A. J., …, HCA Lung Biological Network (P. Horvath) Nature communications12: 4314, 2021
- Single-cell meta-analysis of SARS-CoV-2 entry genes across tissues and demographics; C Muus, MD Luecken, G Eraslan, L Sikkema, A Waghray, G Heimberg, … , P. Horvath, …; Nature medicine 27 (3), 546-559 188* 2021
- Automatic deep learning-driven label-free image-guided patch clamp system; K Koos, G Oláh, T Balassa, N Mihut, M Rózsa, A Ozsvár, E Tasnadi, … P. Horvath; Nature communications 12 (1), 1-11 2*, 2021
- The human melanoma proteome atlas—Defining the molecular pathology; LH Betancourt, J Gil, Y Kim, V Doma, U Çakır, A Sanchez, JR Murillo, … , P. Horvath, …; Clinical and Translational Medicine 11 (7), 2021
- Neuropilin-1 is a host factor for SARS-CoV-2 infection; JL Daly, B Simonetti, K Klein, KE Chen, MK Williamson, C Antón-Plágaro, …P. Horvath, …; Science 370 (6518), 861-865, 2020
- AnnotatorJ: an ImageJ plugin to ease hand annotation of cellular compartments; R Hollandi, Á Diósdi, G Hollandi, N Moshkov, P Horváth; Molecular biology of the cell 31 (20), 2179-2186, 2020
- SARS-CoV-2 receptor ACE2 is an interferon-stimulated gene in human airway epithelial cells and is detected in specific cell subsets across tissues; CGK Ziegler, SJ Allon, SK Nyquist, IM Mbano, VN Miao, CN Tzouanas, …P. Horvath, …; Cell 181 (5), 1016-1035. e19, 2020
- Software Tools
- Advanced Cell Classifier v1.0 (Horvath et.al.), v2.0 (Balassa et.al.), v3.0 (Szkalisity et.al.)
- CellTracker v0.6 (Kiss et.al.), v1.1 (Piccinini et.al.)
- FindMyCells v1.0 (Suleymanova et.al.)
- NucleAIzer (Hollandi et.al.)
- Patents
- PHASECIRCLE – software deposited to the APP under the number IDDN-FR-001-280029-000-S-C-2007-000-21000, and transferred to the Joint Research Center (JRC) of the European Union.
- Endocitózist kiváltó peptidek sejtbe történő bejuttatáshoz; 19483/19, 2020
- P2100295 – MINI-IFA – Image-based & machine learning-guided multiplexed serology test for SARS-CoV-2
- BIAS (Biological Image Analysis Software) – software developed by Single-Cell Technologies Inc. for single cell image analysis.
- P2200213 – Lemezösszeállítás és eljárás annak alkalmazására minták gyors, automatikus, nagy behatolási mélységgel való vizsgálatára light-sheet mikroszkóppal
- U2200088 – Lemezösszeállítás minták gyors, automatikus, nagy behatolási mélységgel való vizsgálatára lightsheet mikroszkóppal
- P2300224 – Eljárás biológiai mintákban lévő objektumok automatizált, skálázható, nagy áteresztőképességű detektálására és elemzésére, valamint rendszer annak végrehajtására –
- P2300149 – Eljárások biológiai minták gyors, automatizált, nagy áteresztőképességű vizsgálatára, valamint azok végrehajtására szolgáló rendszer
- P2300390 – Microscope device, microscope system and methods
- SE 22513 – Method for full body melanoma screening for melanoma detection
- SE 22513 – Method for melanoma screening and artificial intelligence scoring
- SE 22513 – “Hope-AI” method for profiling a cancer on a cellular and molecular level by artificial intelligence and molecular pathology
- Teaching merits
- Overall 16 years academic teaching experience.
- Courses: Programming, Image Processing, Algorithms and data structures, programming languages, introduction to informatics, MatLab, Image analysis for Biologists, Protein and cell dynamics, Microscopy image analysis.
- Institutions: ETH Zurich, University of Harvard, Max Planck Institute, Trinity College Dublin, University of Helsinki, University of Szeged.
- Awards and honours
- Member of Academia Europaea (2024)
- Szent-Györgyi Talentum Prize (2019)
- Bolyai plaquette (2018); Bolyai Fellowship (2014)
- Various scientific grants by the NRDIO (National Research Development and Innovation Office)
- Pfizer Research Award (2016, Banerjee etal. Science)
- Selected and nominated by the HBS for the EBSA (European Biophysical Societies’ Association) Young Investigators’ Medal and Prize (2015)
- NAP-B brain research grant for research group establishment (4 years, Szeged, BRC)
- Finland Distinguished Professor award and fellowship for research group establishment (5 years, University of Helsinki, Finland)
- CEEPUS – Central European Exchange Program (2002, 6 months, Johannes Kepler University, Linz, Austria)
- Marie Curie Fellowship (2007, 6 months PhD scholarship, Sophia Antipolis, France)
- International roles:
- Chair of the European Cell-based Assays Interest Group (EUCAI)
- Councilor (Board of Directors Member) for the Society of Biomolecular Imaging and Informatics (SBI2)
- Organizer and Session chair of numerous conferences, meetings, and workshops
- Main organizer of the NEUBIAS 2018 Szeged conference
- Major collaborations:
- ETH Zurich (Prof Ulrike Kutay, Prof Ari Helenius, Prof Yves Barral, Prof Jean-Pierre Bourquin)
- INRIA (Prof Josiane Zerubia, Dr Ian Jermyn)
- Harvard University/Broad Institute (Prof Anne Carpenter, Prof Matthias Mann)
- Trinity Dublin (Dr Anthony Davies)
- FIMM University of Helsinki (Prof Olli Kallioniemi, Prof Johan Lundin, Prof Päivi Ojala, Dr Vilja Pietiäinen, Dr Päivi Östling, Dr Caroline Heckman)
- BRC (Prof Laszlo Vigh, Dr Csaba Pal, Dr Balazs Papp, Dr Lajos Haracska)
- University of Szeged (Prof Gabor Tamas, Prof Zoltan Kato)
- DKFZ (Dr. Sina Oppermann)
- Lund University (Prof Dr Marko- Varga György)
- UCPH Novo Nordisk Foundation Center (Prof. Andreas Mund)
- COMMISSIONS OF TRUST
Scientific journal and conference reviews (frequency article/year)
- Nature Methods (2), Nature Communications (2), eLife (1), BMC Bioinformatics (2), Oxford J. of Bioinformatics (1), Frontiers in BioEngineering (2), J. of Biomolecular Screening (3-4), J. of Microscopy (2), PLoS One (2-3), Pattern Recognition (2), IEEE Transactions in Medical Imaging (1)
- IEEE ICPR (3), KEPAF (3), IEEE ISBI (3)
- Grant proposal reviews
- Cancer Research UK, Israel Science Foundation, Sciex, Various Hungarian Grants