Maria K. Jaakkola
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View article: Differential associations of subcutaneous and visceral fat with bone turnover markers: A study on bariatric surgery patients with severe obesity and individuals without obesity
Differential associations of subcutaneous and visceral fat with bone turnover markers: A study on bariatric surgery patients with severe obesity and individuals without obesity Open
Background Obesity suppresses bone turnover markers (BTMs) in circulation, and weight loss after metabolic and bariatric surgery (MBS) increases BTM levels. However, the relationship between regional fat distribution and BTMs has not been …
View article: Comparison of Automatic Segmentation and Preprocessing Approaches for Dynamic Total-Body 3D Pet Images with Different Pet Tracers
Comparison of Automatic Segmentation and Preprocessing Approaches for Dynamic Total-Body 3D Pet Images with Different Pet Tracers Open
Segmentation is a routine step in PET image analysis, and few automatic tools have been developed for it. However, excluding supervised methods with their own limitations, they are typically designed for older, small images and the impleme…
View article: Longitudinal pathway analysis using structural information with case studies in early type 1 diabetes
Longitudinal pathway analysis using structural information with case studies in early type 1 diabetes Open
View article: Quantitative evaluation of unsupervised clustering algorithms for dynamic total-body PET image analysis
Quantitative evaluation of unsupervised clustering algorithms for dynamic total-body PET image analysis Open
GMM, FCM, and ICA with mini batch K-means show promise for dynamic total-body PET analysis.
View article: Author Correction: Community assessment of methods to deconvolve cellular composition from bulk gene expression
Author Correction: Community assessment of methods to deconvolve cellular composition from bulk gene expression Open
View article: Differential Associations of Subcutaneous and Visceral Fat with Bone Turnover Markers: A Study on Bariatric Surgery Patients with Severe Obesity and Individuals Without Obesity
Differential Associations of Subcutaneous and Visceral Fat with Bone Turnover Markers: A Study on Bariatric Surgery Patients with Severe Obesity and Individuals Without Obesity Open
Backgrounds Obesity is associated with alterations in bone turnover markers (BTMs). However, the association between regional fat distribution and bone metabolism has received less attention. This study therefore aimed to identify which sp…
View article: Community assessment of methods to deconvolve cellular composition from bulk gene expression
Community assessment of methods to deconvolve cellular composition from bulk gene expression Open
We evaluate deconvolution methods, which infer levels of immune infiltration from bulk expression of tumor samples, through a community-wide DREAM Challenge. We assess six published and 22 community-contributed methods using in vitro and i…
View article: Segmentation of Dynamic Total-Body [18F]-FDG PET Images Using Unsupervised Clustering
Segmentation of Dynamic Total-Body [18F]-FDG PET Images Using Unsupervised Clustering Open
Clustering time activity curves of PET images have been used to separate clinically relevant areas of the brain or tumours. However, PET image segmentation in multiorgan level is much less studied due to the available total-body data being…
View article: Quantitative Perfusion Imaging with Total-Body PET
Quantitative Perfusion Imaging with Total-Body PET Open
Recently, PET systems with a long axial field of view have become the current state of the art. Total-body PET scanners enable unique possibilities for scientific research and clinical diagnostics, but this new technology also raises numer…
View article: SEGMENTATION OF DYNAMIC TOTAL-BODY [<sup>18</sup>F]-FDG PET IMAGES USING UNSUPERVISED CLUSTERING
SEGMENTATION OF DYNAMIC TOTAL-BODY [<sup>18</sup>F]-FDG PET IMAGES USING UNSUPERVISED CLUSTERING Open
A bstract Clustering time activity curves of PET images has been used to separate clinically relevant areas of the brain or tumours. However, PET image segmentation in multi-organ level is much less studied due to the available total-body …
View article: Gene expression signature predicts rate of type 1 diabetes progression
Gene expression signature predicts rate of type 1 diabetes progression Open
View article: Longitudinal pathway analysis using structural information with case studies in early type 1 diabetes
Longitudinal pathway analysis using structural information with case studies in early type 1 diabetes Open
Summary We introduce a new method for Pathway Analysis of Longitudinal data (PAL), which is suitable for complex study designs, such as longitudinal data. The main advantages of PAL are the use of pathway structures and the suitability of …
View article: Pancreas Whole Tissue Transcriptomics Highlights the Role of the Exocrine Pancreas in Patients With Recently Diagnosed Type 1 Diabetes
Pancreas Whole Tissue Transcriptomics Highlights the Role of the Exocrine Pancreas in Patients With Recently Diagnosed Type 1 Diabetes Open
Although type 1 diabetes (T1D) is primarily a disease of the pancreatic beta-cells, understanding of the disease-associated alterations in the whole pancreas could be important for the improved treatment or the prevention of the disease. W…
View article: Estimating cell type-specific differential expression using deconvolution
Estimating cell type-specific differential expression using deconvolution Open
View article: Crowdsourcing digital health measures to predict Parkinson’s disease severity: the Parkinson’s Disease Digital Biomarker DREAM Challenge
Crowdsourcing digital health measures to predict Parkinson’s disease severity: the Parkinson’s Disease Digital Biomarker DREAM Challenge Open
View article: Computational deconvolution to estimate cell type-specific gene expression from bulk data.
Computational deconvolution to estimate cell type-specific gene expression from bulk data. Open
Computational deconvolution is a time and cost-efficient approach to obtain cell type-specific information from bulk gene expression of heterogeneous tissues like blood. Deconvolution can aim to either estimate cell type proportions or abu…
View article: Crowdsourcing digital health measures to predict Parkinson’s disease severity: the <i>Parkinson’s Disease Digital Biomarker DREAM Challenge</i>
Crowdsourcing digital health measures to predict Parkinson’s disease severity: the <i>Parkinson’s Disease Digital Biomarker DREAM Challenge</i> Open
Mobile health, the collection of data using wearables and sensors, is a rapidly growing field in health research with many applications. Deriving validated measures of disease and severity that can be used clinically or as outcome measures…
View article: A crowdsourced analysis to identify ab initio molecular signatures predictive of susceptibility to viral infection
A crowdsourced analysis to identify ab initio molecular signatures predictive of susceptibility to viral infection Open
View article: PASI: A novel pathway method to identify delicate group effects
PASI: A novel pathway method to identify delicate group effects Open
Pathway analysis is a common approach in diverse biomedical studies, yet the currently-available pathway tools do not typically support the increasingly popular personalized analyses. Another weakness of the currently-available pathway met…
View article: Enterovirus-associated changes in blood transcriptomic profiles of children with genetic susceptibility to type 1 diabetes
Enterovirus-associated changes in blood transcriptomic profiles of children with genetic susceptibility to type 1 diabetes Open
View article: ROTS: An R package for reproducibility-optimized statistical testing
ROTS: An R package for reproducibility-optimized statistical testing Open
Differential expression analysis is one of the most common types of analyses performed on various biological data (e.g. RNA-seq or mass spectrometry proteomics). It is the process that detects features, such as genes or proteins, showing s…
View article: Comparison of methods to detect differentially expressed genes between single-cell populations
Comparison of methods to detect differentially expressed genes between single-cell populations Open
We compared five statistical methods to detect differentially expressed genes between two distinct single-cell populations. Currently, it remains unclear whether differential expression methods developed originally for conventional bulk RN…
View article: Empirical comparison of structure-based pathway methods
Empirical comparison of structure-based pathway methods Open
Multiple methods have been proposed to estimate pathway activities from expression profiles, and yet, there is not enough information available about the performance of those methods. This makes selection of a suitable tool for pathway ana…