Age K. Smilde

Multi-omics data analysis reveals a novel beneficial role for strigolactones in tomato

This study identifies strigolactones as nitrogen-responsive rhizosphere signals in tomato that recruit beneficial bacteria under nitrogen limitation.

Supervised restricted data fusion with common, local & distinct components

PESCAR improves detection of subtle response-related patterns in multi-omics data by integrating response information into multiblock decomposition.

Extracting host-specific developmental signatures from longitudinal microbiome data

The paper introduces PARAFAC2 to model subject-specific temporal patterns in longitudinal microbiome data, outperforming CP in capturing individual variations and enabling replicable pattern discovery.

ACMTF-R: supervised multi-omics data integration uncovering shared and distinct outcome-associated variation

ACMTF-R integrates multi-omics data to identify shared and distinct outcome-associated variation, outperforming existing methods in simulated and real-world datasets.

parafac4microbiome: Exploratory analysis of longitudinal microbiome data using Parallel Factor Analysis

This paper introduces PARAFAC for analyzing longitudinal microbiome data, demonstrating its effectiveness in identifying temporal patterns across three studies.

MASCARA: coexpression analysis in data from designed experiments

MASCARA improves coexpression analysis in designed experiments by removing experimental variance to detect pathway-related coexpression patterns.

Longitudinal metabolomics data analysis informed bymechanistic models

The paper introduces a method combining simulated and real metabolomics data using tensor factorization to improve pattern discovery, showing better performance in males for BMI-related phenotypes.

Multi-way modelling of oral microbial dynamics and host-microbiome interactions during induced gingivitis

This study uses PARAFAC to analyze oral microbiome and metabolome dynamics during experimental gingivitis, identifying microbial subcommunities and metabolic pathways linked to inflammation.

A Strategy for Differential Abundance Analysis of Sparse Microbiome Data with Group-wise Structured Zeros

The paper proposes a combined differential abundance analysis method for sparse microbiome data with group-wise zeros, validated through simulations and applied to plant microbiome datasets.

Characterizing human postprandial metabolic response using multiway data analysis

This study uses multiway data analysis to characterize postprandial metabolic responses in humans, revealing BMI-related differences in metabolite groups and temporal profiles between males.

Analyzing postprandial metabolomics data using multiway models: A simulation study

This study evaluates CP models for analyzing postprandial metabolomics data through simulations, showing their effectiveness in revealing metabolic patterns and group differences.

Gut microbiome and its cofactors are linked tolipoprotein distribution profiles

The paper links gut microbiome composition and its metabolic traits to lipoprotein distribution profiles in healthy individuals.

Human blood lipoprotein predictions from 1H NMR spectra: protocol, model performances and cage of covariance

The paper develops partial least squares regression models to predict human blood lipoprotein subfractions from 1H NMR spectra, achieving high accuracy in independent cohorts.

Kernel integration by Graphical LASSO

The paper introduces a method for integrating heterogeneous biological data using a graphical LASSO framework and applies it to study asthma and eczema risk factors in children.

Corruption of the Pearson correlation coefficient by measurement error: estimation, bias, and correction under different error models

The paper examines how measurement errors affect Pearson correlation coefficients and discusses methods to improve their estimation under various error models.

iTOP: Inferring the Topology of Omics Data

iTOP infers relationships between omics datasets using partial matrix correlations and identifies gene expression as a mediator between other datasets and drug response.