SEAM is a spatial single nuclear metabolomics method for dissecting tissue microenvironment

Integrating microarray-based spatial transcriptomics and single-cell RNA-seq reveals tissue architecture in pancreatic ductal adenocarcinomas

(2020) Reuben Moncada et al.   NATURE BIOTECHNOLOGY

SciPy 1.0: fundamental algorithms for scientific computing in Python

(2020) Pauli Virtanen et al.   NATURE METHODS

Novel specialized cell state and spatial compartments within the germinal center

(2020) Domenick E. Kennedy et al.   NATURE IMMUNOLOGY

Metabolomics and mass spectrometry imaging reveal channeled de novo purine synthesis in cells

(2020) Vidhi Pareek et al.   SCIENCE

Coordinated Cellular Neighborhoods Orchestrate Antitumoral Immunity at the Colorectal Cancer Invasive Front

(2020) Christian M. Schürch et al.   CELL

Single-cell metabolic profiling of human cytotoxic T cells

(2020) Felix J. Hartmann et al.   NATURE BIOTECHNOLOGY

Feature-based molecular networking in the GNPS analysis environment

(2020) Louis-Félix Nothias et al.   NATURE METHODS

Systematic classification of unknown metabolites using high-resolution fragmentation mass spectra

(2020) Kai Dührkop et al.   NATURE BIOTECHNOLOGY

Integrative single-cell analysis

(2019) Tim Stuart et al.   NATURE REVIEWS GENETICS

Transcriptome-scale super-resolved imaging in tissues by RNA seqFISH+

(2019) Chee-Huat Linus Eng et al.   NATURE

Multiplexed In Situ Imaging Mass Cytometry Analysis of the Human Endocrine Pancreas and Immune System in Type 1 Diabetes

(2019) Yue J. Wang et al.   Cell Metabolism

Evaluation of Distance Metrics and Spatial Autocorrelation in Uniform Manifold Approximation and Projection Applied to Mass Spectrometry Imaging Data

(2019) Tina Smets et al.   ANALYTICAL CHEMISTRY

Spatial heterogeneity in the mammalian liver

(2019) Shani Ben-Moshe et al.   Nature Reviews Gastroenterology & Hepatology

Transmission-mode MALDI-2 mass spectrometry imaging of cells and tissues at subcellular resolution

(2019) M. Niehaus et al.   NATURE METHODS

High-definition spatial transcriptomics for in situ tissue profiling

(2019) Sanja Vickovic et al.   NATURE METHODS

Spatial transcriptome profiling by MERFISH reveals subcellular RNA compartmentalization and cell cycle-dependent gene expression

(2019) Chenglong Xia et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Resolving the fibrotic niche of human liver cirrhosis at single-cell level

(2019) P. Ramachandran et al.   NATURE

MIBI-TOF: A multiplexed imaging platform relates cellular phenotypes and tissue structure

(2019) Leeat Keren et al.   Science Advances

High Spatial Resolution Imaging of Mouse Pancreatic Islets Using Nanospray Desorption Electrospray Ionization Mass Spectrometry

(2018) Ruichuan Yin et al.   ANALYTICAL CHEMISTRY

ChemDistiller: an engine for metabolite annotation in mass spectrometry

(2018) Ivan Laponogov et al.   BIOINFORMATICS

Liver sinusoidal endothelial cells — gatekeepers of hepatic immunity

(2018) Shishir Shetty et al.   Nature Reviews Gastroenterology & Hepatology

Single-cell transcriptomics of the mouse kidney reveals potential cellular targets of kidney disease

(2018) Jihwan Park et al.   SCIENCE

A Structured Tumor-Immune Microenvironment in Triple Negative Breast Cancer Revealed by Multiplexed Ion Beam Imaging

(2018) Leeat Keren et al.   CELL

Spatial Reconstruction of Single Enterocytes Uncovers Broad Zonation along the Intestinal Villus Axis

(2018) Andreas E. Moor et al.   CELL

Dimensionality reduction for visualizing single-cell data using UMAP

(2018) Etienne Becht et al.   NATURE BIOTECHNOLOGY

GENCODE reference annotation for the human and mouse genomes

(2018) Adam Frankish et al.   NUCLEIC ACIDS RESEARCH

Spatially resolved metabolomics to discover tumor-associated metabolic alterations

(2018) Chenglong Sun et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Epigenomic map of human liver reveals principles of zonated morphogenic and metabolic control

(2018) Mario Brosch et al.   Nature Communications

On Wasserstein Two-Sample Testing and Related Families of Nonparametric Tests

(2017) Aaditya Ramdas et al.   Entropy

Single-cell spatial reconstruction reveals global division of labour in the mammalian liver

(2017) Keren Bahar Halpern et al.   NATURE

The 3D OrbiSIMS—label-free metabolic imaging with subcellular lateral resolution and high mass-resolving power

(2017) Melissa K Passarelli et al.   NATURE METHODS

Visualization and analysis of single-cell RNA-seq data by kernel-based similarity learning

(2017) Bo Wang et al.   NATURE METHODS

Spatial transcriptomic analysis of cryosectioned tissue samples with Geo-seq

(2017) Jun Chen et al.   Nature Protocols

Immunofluorescence identifies distinct subsets of endothelial cells in the human liver

(2017) Otto Strauss et al.   Scientific Reports

Metabolic zonation of the liver: The oxygen gradient revisited

(2017) Thomas Kietzmann   Redox Biology

FDR-controlled metabolite annotation for high-resolution imaging mass spectrometry

(2016) Andrew Palmer et al.   NATURE METHODS

Atmospheric pressure MALDI mass spectrometry imaging of tissues and cells at 1.4-μm lateral resolution

(2016) Mario Kompauer et al.   NATURE METHODS

Data-driven identification of prognostic tumor subpopulations using spatially mapped t-SNE of mass spectrometry imaging data

(2016) Walid M. Abdelmoula et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Lysosomal amino acid transporter SLC38A9 signals arginine sufficiency to mTORC1

(2015) S. Wang et al.   SCIENCE

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

The betaine/GABA transporter and betaine: roles in brain, kidney, and liver

(2014) Stephen A. Kempson et al.   Frontiers in Physiology

Representation Learning: A Review and New Perspectives

(2013) Y. Bengio et al.   IEEE TRANSACTIONS ON PATTERN ANALYSIS AND MACHINE INTELLIGENCE

SLC17: A functionally diverse family of organic anion transporters

(2013) Richard J. Reimer   MOLECULAR ASPECTS OF MEDICINE

Microenvironmental regulation of tumor progression and metastasis

(2013) Daniela F Quail et al.   NATURE MEDICINE

Lipidomic and Spatio-Temporal Imaging of Fat by Mass Spectrometry in Mice Duodenum during Lipid Digestion

(2013) Alexandre Seyer et al.   PLoS One

Three-Dimensional Atlas of Iron, Copper, and Zinc in the Mouse Cerebrum and Brainstem

(2012) Dominic J. Hare et al.   ANALYTICAL CHEMISTRY

Hyperspectral Visualization of Mass Spectrometry Imaging Data

(2012) Judith M. Fonville et al.   ANALYTICAL CHEMISTRY

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Fiji: an open-source platform for biological-image analysis

(2012) Johannes Schindelin et al.   NATURE METHODS

clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters

(2012) Guangchuang Yu et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

SLC36A4 (hPAT4) Is a High Affinity Amino Acid Transporter When Expressed inXenopus laevisOocytes

(2010) Samyuktha Muralidharan Pillai et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Lipid mapping of colonic mucosa by cluster TOF-SIMS imaging and multivariate analysis incftrknockout mice

(2010) Marc Brulet et al.   JOURNAL OF LIPID RESEARCH

In SituLipidomic Analysis of Nonalcoholic Fatty Liver by Cluster TOF-SIMS Imaging

(2009) Delphine Debois et al.   ANALYTICAL CHEMISTRY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Lipid imaging of human skeletal muscle using TOF-SIMS with bismuth cluster ion as a primary ion source

(2008) Ylva Magnusson et al.   CLINICAL PHYSIOLOGY AND FUNCTIONAL IMAGING

Stem Cell Niche: Microenvironment and Beyond

(2008) Jiwang Zhang et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Network-based global inference of human disease genes

(2008) Xuebing Wu et al.   Molecular Systems Biology

Representational Power of Restricted Boltzmann Machines and Deep Belief Networks

(2008) Nicolas Le Roux et al.   NEURAL COMPUTATION

TOF-SIMS Analysis of Lipid Accumulation in the Skeletal Muscle of ob/ob Mice

(2008) Ylva K. Magnusson et al.   Obesity

Brain micro-ecologies: neural stem cell niches in the adult mammalian brain

(2007) P. A Riquelme et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES