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Umeå University
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Staff photo Johan Trygg

Johan Trygg

Research focus on advanced data analytics and chemometrics where large-scale ('omics) datasets are used to understand, prevent and treat human diseases to achieve improved global health.

Research qualifications: Docent

Contact

E-mail
johan.trygg@umu.se
Phone
+46 90 786 69 17, +46 730 64 71 37

Works at

Affiliation
Professor at Department of Chemistry
Location
KB.B4, Linnaeus väg 10, (rum: C4.13.19) Umeå universitet, 901 87 Umeå
A novel data mining framework to investigate causes of boiler failures in waste-to-energy plants
Processes, MDPI 2024, Vol. 12, (7)
Wang, Dong; Jiang, Lili; Kjellander, Måns; et al.
A scalable, data analytics workflow for image-based morphological profiles
Chemometrics and Intelligent Laboratory Systems, Elsevier 2024, Vol. 254
Forsgren, Edvin; Cloarec, Olivier; Jonsson, Pär; et al.
Bounding box is all you need: learning to segment cells in 2D microscopic images via box annotations
Medical image understanding and analysis: 28th annual conference, MIUA 2024, Manchester, UK, July 24–26, 2024, proceedings, part I, Cham: Springer 2024 : 314-328
Khalid, Nabeel; Caroprese, Maria; Lovell, Gillian; et al.
CellGenie: an end-to-end pipeline for synthetic cellular data generation and segmentation: a use case for cell segmentation in microscopic images
Medical image understandingand analysis: 28th Annual Conference, MIUA 2024, Manchester, UK, July 24–26, 2024, Proceedings, part 1, Springer Nature 2024 : 387-401
Khalid, Nabeel; Koochali, Mohammadmahdi; Leon, Duway Nicolas Lesmes; et al.
CellSpot: deep learning-based efficient cell center detection in microscopic images
Artificial Neural Networks and Machine Learning – ICANN 2024: 33rd International Conference on Artificial Neural Networks, Lugano, Switzerland, September 17–20, 2024, Proceedings, Part VIII, Springer Nature 2024 : 215-229
Khalid, Nabeel; Caroprese, Maria; Lovell, Gillian; et al.
Feasibility and performance of cross-clone Raman calibration models in CHO cultivation
Biotechnology Journal, John Wiley & Sons 2024, Vol. 19, (1)
Machleid, Rafael; Hoehse, Marek; Scholze, Steffi; et al.
Deep learning architectures for the prediction of YY1-mediated chromatin loops
Bioinformatics research and applications: 19th international symposium, ISBRA 2023, Wrocław, Poland, October 9–12, 2023, proceedings, Springer 2023 : 72-84
Abbasi, Ahtisham Fazeel; Asim, Muhammad Nabeel; Trygg, Johan; et al.
Near-infrared hyperspectral image analysis for monitoring the cheese-ripening process
Journal of Dairy Science, Elsevier 2023, Vol. 106, (11) : 7407-7418
Alinaghi, Masoumeh; Nilsson, David; Singh, Nikita; et al.
PACE: point annotation-based cell segmentation for efficient microscopic image analysis
Artificial Neural Networks and Machine Learning – ICANN 2023: 32nd International Conference on Artificial Neural Networks, Heraklion, Crete, Greece, September 26–29, 2023, Proceedings, Part II, Springer Nature 2023 : 545-557
Khalid, Nabeel; Froes, Tiago Comassetto; Caroprese, Maria; et al.
BoT-Net: a lightweight bag of tricks-based neural network for efficient LncRNA–miRNA interaction prediction
Interdisciplinary Sciences: Computational Life Sciences, Springer 2022, Vol. 14, (4) : 841-862
Asim, Muhammad Nabeel; Ibrahim, Muhammad Ali; Zehe, Christoph; et al.
DeepMuCS: A framework for co-culture microscopic image analysis: from generation to segmentation
2022 IEEE-EMBS International Conference on Biomedical and Health Informatics (BHI), IEEE 2022 : 1-4
Khalid, Nabeel; Koochali, Mohammadmahdi; Rajashekar, Vikas; et al.
EL-RMLocNet: An explainable LSTM network for RNA-associated multi-compartment localization prediction
Computational and Structural Biotechnology Journal, Elsevier 2022, Vol. 20 : 3986-4002
Asim, Muhammad Nabeel; Ibrahim, Muhammad Ali; Malik, Muhammad Imran; et al.
Hierarchical time-series analysis of dynamic bioprocess systems
Biotechnology Journal, John Wiley & Sons 2022, Vol. 17, (12)
Alinaghi, Masoumeh; Surowiec, Izabella; Scholze, Steffi; et al.
Perinatal risk factors for mortality in very preterm infants: A nationwide, population-based discriminant analysis
Acta Paediatrica, John Wiley & Sons 2022, Vol. 111, (8) : 1526-1535
Norman, Mikael; Nilsson, David; Trygg, Johan; et al.
Point2Mask: A Weakly Supervised Approach for Cell Segmentation Using Point Annotation
Medical image understanding and analysis: 26th annual conference, MIUA 2022, Cambridge, UK, July 27–29, 2022, proceedings, Springer 2022 : 139-153
Khalid, Nabeel; Schmeisser, Fabian; Koochali, Mohammadmahdi; et al.
Serine protease inhibitors restrict host susceptibility to SARS-CoV-2 infections
mBio, American Society for Microbiology 2022, Vol. 13, (3)
Rosendal, Ebba; Mihai, Ionut Sebastian; Becker, Miriam; et al.
Toward Delicate Anomaly Detection of Energy Consumption for Buildings: Enhance the Performance From Two Levels
IEEE Access, IEEE 2022, Vol. 10 : 31649-31659
Wang, Dong; Enlund, Therese; Trygg, Johan; et al.
Towards better process management in wastewater treatment plants: Process analytics based on SHAP values for tree-based machine learning methods
Journal of Environmental Management, Elsevier 2022, Vol. 301
Wang, Dong; Thunéll, Sven; Lindberg, Ulrika; et al.
A machine learning framework to improve effluent quality control in wastewater treatment plants
Science of the Total Environment, Elsevier 2021, Vol. 784
Wang, Dong; Thunéll, Sven; Lindberg, Ulrika; et al.
A robust and precise convnet for small non-coding rna classification (rpc-snrc)
IEEE Access, Vol. 9 : 19379-19390
Asim, Muhammad Nabeel; Malik, Muhammad Imran; Zehe, Christoph; et al.
An Introduction to Some Basic Chemometric Tools
Chemometrics and Cheminformatics in Aquatic Toxicology, John Wiley & Sons 2021 : 71-88
Eriksson, Lennart; Johansson, Erik; Trygg, Johan
DeepCeNS: An end-to-end Pipeline for Cell and Nucleus Segmentation in Microscopic Images
Proceedings of the International Joint Conference on Neural Networks
Khalid, Nabeel; Munir, Mohsin; Edlund, Christoffer; et al.
DeepCIS: An end-to-end Pipeline for Cell-type aware Instance Segmentation in Microscopic Images
2021 IEEE EMBS International Conference on Biomedical and Health Informatics, Proceedings
Khalid, Nabeel; Munir, Mohsin; Edlund, Christoffer; et al.
L2S-MirLoc: A Lightweight Two Stage MiRNA Sub-Cellular Localization Prediction Framework
Proceedings of the International Joint Conference on Neural Networks
Asim, Muhammad Nabeel; Ibrahim, Muhammad Ali; Zehe, Christoph; et al.
LIVECell: a large-scale dataset for label-free live cell segmentation
Nature Methods, Nature Publishing Group 2021, Vol. 18, (9) : 1038-1045
Edlund, Christoffer; Jackson, Timothy R.; Khalid, Nabeel; et al.
Multiblock variable influence on orthogonal projections (MB-VIOP) for enhanced interpretation of total, global, local and unique variations in OnPLS models
BMC Bioinformatics, BioMed Central 2021, Vol. 22, (1)
Galindo-Prieto, Beatriz; Geladi, Paul; Trygg, Johan
Out-of-Distribution Example Detection in Deep Neural Networks using Distance to Modelled Embedding
Sjögren, Rickard; Trygg, Johan
Overexpression of vesicle-associated membrane protein PttVAP27-17 as a tool to improve biomass production and the overall saccharification yields in Populus trees
Biotechnology for Biofuels, BioMed Central 2021, Vol. 14, (1)
Gandla, Madhavi Latha; Mähler, Niklas; Escamez, Sacha; et al.
Statistical analysis in metabolic phenotyping
Nature Protocols, Nature Publishing Group 2021, Vol. 16, (9) : 4299-4326
Blaise, Benjamin J.; Correia, Gonçalo D. S.; Haggart, Gordon A.; et al.
A whole-genome sequenced control population in northern Sweden reveals subregional genetic differences
PLOS ONE, Public Library Science 2020, Vol. 15, (9)
Svensson, Daniel; Rentoft, Matilda; Dahlin, Anna M.; et al.
Analysis of Plant Cell Walls Using High-Throughput Profiling Techniques with Multivariate Methods
The Plant Cell Wall: Methods and Protocols, Humana Press 2020 : 327-337
Moore, John P.; Gao, Yu; Zietsman, Anscha J. J.; et al.
Application of multiblock analysis on a small metabolomic multi-tissue dataset
Metabolites, MDPI 2020, Vol. 10, (7)
Torell, Frida; Skotare, Tomas; Trygg, Johan
MirLocPredictor: A ConvNet-Based Multi-Label MicroRNA Subcellular Localization Predictor by Incorporating k-Mer Positional Information
Genes, MDPI 2020, Vol. 11, (12)
Asim, Muhammad Nabeel; Malik, Muhammad Imran; Zehe, Christoph; et al.
Multivariate patent analysis: using chemometrics to analyze collections of chemical and pharmaceutical patents
Journal of Chemometrics, John Wiley & Sons 2020, Vol. 34, (1)
Sjögren, Rickard; Stridh, Kjell; Skotare, Tomas; et al.
Overexpression of VviPGIP1 and NtCAD14 in Tobacco Screened Using Glycan Microarrays Reveals Cell Wall Reorganisation in the Absence of Fungal Infection
Vaccines, MDPI 2020, Vol. 8, (3)
Weiller, Florent; Gerber, Lorenz; Trygg, Johan; et al.
Subspace Based Model Identification for an Industrial Bioreactor: Handling Infrequent Sampling Using Missing Data Algorithms
Processes, MDPI 2020, Vol. 8, (12)
Patel, Nikesh; Corbett, Brandon; Trygg, Johan; et al.
A geographically matched control population efficiently limits the number of candidate disease-causing variants in an unbiased whole-genome analysis
PLOS ONE, Public Library of Science 2019, Vol. 14, (3)
Rentoft, Matilda; Svensson, Daniel; Sjödin, Andreas; et al.
Cytokine Profiles in Autoantibody Defined Subgroups of Systemic Lupus Erythematosus
Journal of Proteome Research, American Chemical Society (ACS) 2019, Vol. 18, (3) : 1208-1217
Torell, Frida; Eketjäll, Susanna; Idborg, Helena; et al.
doepipeline: a systematic approach to optimizing multi-level and multi-step data processing workflows
BMC Bioinformatics, BioMed Central 2019, Vol. 20, (1)
Svensson, Daniel; Sjögren, Rickard; Sundell, David; et al.
Joint and unique multiblock analysis for integration and calibration transfer of NIR instruments
Analytical Chemistry, Washington: American Chemical Society (ACS) 2019, Vol. 91, (5) : 3516-3524
Skotare, Tomas; Nilsson, David; Xiong, Shaojun; et al.
Joint and unique multiblock analysis of biological data: multiomics malaria study
Faraday discussions, Cambridge: Royal Society of Chemistry 2019, Vol. 218 : 268-283
Surowiec, Izabella; Skotare, Tomas; Sjögren, Rickard; et al.
Metabolic profiling of zebrafish embryo development from blastula period to early larval stages
PLOS ONE, San Francisco: Public Library of Science 2019, Vol. 14, (5)
Dhillon, Sundeep S.; Torell, Frida; Donten, Magdalena; et al.
Ultrasound imaging of dorsal neck muscles with speckle tracking analyses: the relationship between muscle deformation and force
Scientific Reports, Nature Publishing Group 2019, Vol. 9
Peterson, Gunnel; O'Leary, Shaun; Nilsson, David; et al.
A multi-omics approach reveals function of Secretory Carrier-Associated Membrane Proteins in wood formation of​ ​​Populus​​ ​trees
BMC Genomics, Springer Publishing Company 2018, Vol. 19
Obudulu, Ogonna; Mähler, Niklas; Skotare, Tomas; et al.
Alterations in the Mechanical Response of Deep Dorsal Neck Muscles in Individuals Experiencing Whiplash-Associated Disorders Compared to Healthy Controls: An Ultrasound Study
American Journal of Physical Medicine & Rehabilitation, LIPPINCOTT WILLIAMS & WILKINS 2018, Vol. 97, (2) : 75-82
Rahnama, Leila; Peterson, Gunnel; Kazemnejad, Anoshirvan; et al.
Kynurenine pathway is altered in patients with SLE and associated with severe fatigue
Lupus Science and Medicine, BMJ Publishing Group Ltd 2018, Vol. 5, (1)
Åkesson, Karolina; Pettersson, Susanne; Stahl, Sara; et al.
Metabolic Profiling of Multiorgan Samples: Evaluation of MODY5/RCAD Mutant Mice
Journal of Proteome Research, American Chemical Society (ACS) 2018, Vol. 17, (7) : 2293-2306
Torell, Frida; Bennet, Kate; Cereghini, Silvia; et al.
Neck-specific exercise improves impaired interactions between ventral neck muscles in chronic whiplash: A randomized controlled ultrasound study
Scientific Reports, Nature Publishing Group 2018, Vol. 8
Peterson, Gunnel; Nilsson, David; Trygg, Johan; et al.
OnPLS-Based Multi-Block Data Integration: A Multivariate Approach to Interrogating Biological Interactions in Asthma
Analytical Chemistry, AMER CHEMICAL SOC 2018, Vol. 90, (22) : 13400-13408
Reinke, Stacey N.; Galindo-Prieto, Beatriz; Skotare, Tomas; et al.
Quantification of run order effect on chromatography: mass spectrometry profiling data
Journal of Chromatography A, Vol. 1568 : 229-234
Surowiec, Izabella; Johansson, Erik; Stenlund, Hans; et al.
View publications in DiVA

Research groups

Head of research
Johan Trygg Chemometrics Lab