Identifying temporal and spatial patterns of variation from multimodal data using MEFISTO

Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation

(2021) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

Statistical analysis of spatial expression patterns for spatially resolved transcriptomic studies

(2020) Shiquan Sun et al.   NATURE METHODS

What Is the Evolutionary Fingerprint in Neutrophil Granulocytes?

(2020) Leonie Fingerhut et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

A sensitive assay for dNTPs based on long synthetic oligonucleotides, EvaGreen dye and inhibitor-resistant high-fidelity DNA polymerase

(2020) Janne Purhonen et al.   NUCLEIC ACIDS RESEARCH

Context-aware dimensionality reduction deconvolutes gut microbial community dynamics

(2020) Cameron Martino et al.   NATURE BIOTECHNOLOGY

A longitudinal big data approach for precision health

(2019) Sophia Miryam Schüssler-Fiorenza Rose et al.   NATURE MEDICINE

Comprehensive Integration of Single-Cell Data

(2019) Tim Stuart et al.   CELL

Evolution of the human cold/menthol receptor, TRPM8

(2019) Samuel Blanquart et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Gene expression across mammalian organ development

(2019) Margarida Cardoso-Moreira et al.   NATURE

Modeling Cell-Cell Interactions from Spatial Molecular Data with Spatial Variance Component Analysis

(2019) Damien Arnol et al.   Cell Reports

Multi-omics profiling of mouse gastrulation at single-cell resolution

(2019) Ricard Argelaguet et al.   NATURE

Insulin-like growth factor 2 mRNA-binding protein 1 (IGF2BP1) in cancer

(2018) Xinwei Huang et al.   Journal of Hematology & Oncology

Multi‐Omics Factor Analysis—a framework for unsupervised integration of multi‐omics data sets

(2018) Ricard Argelaguet et al.   Molecular Systems Biology

SpatialDE: identification of spatially variable genes

(2018) Valentine Svensson et al.   NATURE METHODS

Clustering gene expression time series data using an infinite Gaussian process mixture model

(2018) Ian C. McDowell et al.   PLoS Computational Biology

Tensor decomposition for multiple-tissue gene expression experiments

(2016) Victoria Hore et al.   NATURE GENETICS

Visualization and analysis of gene expression in tissue sections by spatial transcriptomics

(2016) P. L. Stahl et al.   SCIENCE

Natural history of the infant gut microbiome and impact of antibiotic treatment on bacterial strain diversity and stability

(2016) Moran Yassour et al.   Science Translational Medicine

Antibiotics, birth mode, and diet shape microbiome maturation during early life

(2016) Nicholas A. Bokulich et al.   Science Translational Medicine

Fast Nonparametric Clustering of Structured Time-Series

(2015) James Hensman et al.   IEEE TRANSACTIONS ON PATTERN ANALYSIS AND MACHINE INTELLIGENCE

Computational assignment of cell-cycle stage from single-cell transcriptome data

(2015) Antonio Scialdone et al.   METHODS

Ensembl 2016

(2015) Andrew Yates et al.   NUCLEIC ACIDS RESEARCH

A Linear Mixed Model Spline Framework for Analysing Time Course ‘Omics’ Data

(2015) Jasmin Straube et al.   PLoS One

Computing and Visualizing Dynamic Time Warping Alignments inR: ThedtwPackage

(2015) Toni Giorgino   Journal of Statistical Software

A multivariate approach to the integration of multi-omics datasets

(2014) Chen Meng et al.   BMC BIOINFORMATICS

Hierarchical Bayesian modelling of gene expression time series across irregularly sampled replicates and clusters

(2013) James Hensman et al.   BMC BIOINFORMATICS

The Reactome pathway knowledgebase

(2013) David Croft et al.   NUCLEIC ACIDS RESEARCH

Deciphering Signatures of Mutational Processes Operative in Human Cancer

(2013) Ludmil B. Alexandrov et al.   Cell Reports

The accessible chromatin landscape of the human genome

(2012) Robert E. Thurman et al.   NATURE

Using probabilistic estimation of expression residuals (PEER) to obtain increased power and interpretability of gene expression analyses

(2012) Oliver Stegle et al.   Nature Protocols

Organogenesis relies on SoxC transcription factors for the survival of neural and mesenchymal progenitors

(2010) Pallavi Bhattaram et al.   Nature Communications

A penalized matrix decomposition, with applications to sparse principal components and canonical correlation analysis

(2009) D. M. Witten et al.   BIOSTATISTICS

Delayed Parturition and Altered Myometrial Progesterone Receptor Isoform A Expression in Mice Null for Krüppel-Like Factor 91

(2008) Zhaoyang Zeng et al.   BIOLOGY OF REPRODUCTION