MASQOT: a method for cDNA microarray spot quality control. - Max Bylesjö; Daniel Eriksson; Andreas Sjödin; Michael Sjöström; Stefan Jansson; Henrik Antti; Johan Trygg (BMC Bioinform., 2005)

MASQOT-GUI: spot quality assessment for the two-channel microarray platform. - Max Bylesjö; Andreas Sjödin; Daniel Eriksson; Henrik Antti; Thomas Moritz; Stefan Jansson; Johan Trygg (Bioinform., 2006)

Orthogonal projections to latent structures as a strategy for microarray data normalization. - Max Bylesjö; Daniel Eriksson; Andreas Sjödin; Stefan Jansson; Thomas Moritz; Johan Trygg (BMC Bioinform., 2007)

K-OPLS package: Kernel-based orthogonal projections to latent structures for prediction and interpretation in feature space. - Max Bylesjö; Mattias Rantalainen; Jeremy K. Nicholson; Elaine Holmes; Johan Trygg (BMC Bioinform., 2008)

Piecewise multivariate modelling of sequential metabolic profiling data. - Mattias Rantalainen; Olivier Cloarec; Timothy M. D. Ebbels; Torbjörn Lundstedt; Jeremy K. Nicholson; Elaine Holmes; Johan Trygg (BMC Bioinform., 2008)

Modelling human musculoskeletal functional movements using ultrasound imaging. - Michael Peolsson; Tommy Löfstedt; Susanna Vogt; Hans Stenlund; Anton Arndt; Johan Trygg (BMC Medical Imaging, 2010)

Dynamic ultrasound imaging - A multivariate approach for the analysis and comparison of time-dependent musculoskeletal movements. - Tommy Löfstedt; Olof Ahnlund; Michael Peolsson; Johan Trygg (BMC Medical Imaging, 2012)

doepipeline: a systematic approach to optimizing multi-level and multi-step data processing workflows. - Daniel Svensson; Rickard Sjögren; David Sundell; Andreas Sjödin; Johan Trygg (BMC Bioinform., 2019)

DeepCIS: An end-to-end Pipeline for Cell-type aware Instance Segmentation in Microscopic Images. - Nabeel Khalid; Mohsin Munir; Christoffer Edlund; Timothy R. Jackson; Johan Trygg; Rickard Sjögren; Andreas Dengel 001; Sheraz Ahmed (BHI, 2021)

L2S-MirLoc: A Lightweight Two Stage MiRNA Sub-Cellular Localization Prediction Framework. - Muhammad Nabeel Asim; Muhammad Ali Ibrahim; Christoph Zehe; Olivier Cloarec; Rickard Sjögren; Johan Trygg; Andreas Dengel 001; Sheraz Ahmed (IJCNN, 2021)

DeepCeNS: An end-to-end Pipeline for Cell and Nucleus Segmentation in Microscopic Images. - Nabeel Khalid; Mohsin Munir; Christoffer Edlund; Timothy R. Jackson; Johan Trygg; Rickard Sjögren; Andreas Dengel 001; Sheraz Ahmed (IJCNN, 2021)

A Robust and Precise ConvNet for Small Non-Coding RNA Classification (RPC-snRC). - Muhammad Nabeel Asim; Muhammad Imran Malik; Christoph Zehe; Johan Trygg; Andreas Dengel 001; Sheraz Ahmed (IEEE Access, 2021)

Multiblock variable influence on orthogonal projections (MB-VIOP) for enhanced interpretation of total, global, local and unique variations in OnPLS models. - Beatriz Galindo-Prieto; Paul Geladi; Johan Trygg (BMC Bioinform., 2021)

Out-of-Distribution Example Detection in Deep Neural Networks using Distance to Modelled Embedding. - Rickard Sjögren; Johan Trygg (CoRR, 2021)

DeepMuCS: A Framework for Co-culture Microscopic Image Analysis: From Generation to Segmentation. - Nabeel Khalid; Mohammadmahdi Koochali; Vikas Rajashekar; Mohsin Munir; Christoffer Edlund; Timothy R. Jackson; Johan Trygg; Rickard Sjögren; Andreas Dengel 001; Sheraz Ahmed (BHI, 2022)

Point2Mask: A Weakly Supervised Approach for Cell Segmentation Using Point Annotation. - Nabeel Khalid; Fabian Schmeisser; Mohammadmahdi Koochali; Mohsin Munir; Christoffer Edlund; Timothy R. Jackson; Johan Trygg; Rickard Sjögren; Andreas Dengel 001; Sheraz Ahmed (MIUA, 2022)

Toward Delicate Anomaly Detection of Energy Consumption for Buildings: Enhance the Performance From Two Levels. - Dong Wang; Therese Enlund; Johan Trygg; Mats Tysklind; Lili Jiang 002 (IEEE Access, 2022)

PACE: Point Annotation-Based Cell Segmentation for Efficient Microscopic Image Analysis. - Nabeel Khalid; Tiago Comassetto Fróes; Maria Caroprese; Gillian Lovell; Johan Trygg; Andreas Dengel 001; Sheraz Ahmed (ICANN (2), 2023)

Deep Learning Architectures for the Prediction of YY1-Mediated Chromatin Loops. - Ahtisham Fazeel Abbasi; Muhammad Nabeel Asim; Johan Trygg; Andreas Dengel 001; Sheraz Ahmed (ISBRA, 2023)

CellSpot: Deep Learning-Based Efficient Cell Center Detection in Microscopic Images. - Nabeel Khalid; Maria Caroprese; Gillian Lovell; Johan Trygg; Andreas Dengel 001; Sheraz Ahmed (ICANN (8), 2024)

Bounding Box Is All You Need: Learning to Segment Cells in 2D Microscopic Images via Box Annotations. - Nabeel Khalid; Maria Caroprese; Gillian Lovell; Daniel A. Porto; Johan Trygg; Andreas Dengel 001; Sheraz Ahmed (MIUA (1), 2024)

CellGenie: An End-to-End Pipeline for Synthetic Cellular Data Generation and Segmentation: A Use Case for Cell Segmentation in Microscopic Images. - Nabeel Khalid; Mohammadmahdi Koochali; Duway Nicolas Lesmes-Leon; Maria Caroprese; Gillian Lovell; Daniel A. Porto; Johan Trygg; Andreas Dengel 001; Sheraz Ahmed (MIUA (1), 2024)

SAT: Segment and Track Anything for Microscopy. - Nabeel Khalid; Mohammadmahdi Koochali; Khola Naseem; Maria Caroprese; Gillian Lovell; Daniel A. Porto; Johan Trygg; Andreas Dengel 001; Sheraz Ahmed (ICAART (2), 2025)

OPLS-Based Multiclass Classification and Data-Driven Interclass Relationship Discovery. - Edvin Forsgren; Benny Björkblom; Johan Trygg; Pär Jonsson (J. Chem. Inf. Model., 2025)