Identifying multicellular spatiotemporal organization of cells with SpaceFlow

massNet: integrated processing and classification of spatially resolved mass spectrometry data using deep learning for rapid tumor delineation

(2022) Walid M Abdelmoula et al.   BIOINFORMATICS

Spatial components of molecular tissue biology

(2022) Giovanni Palla et al.   NATURE BIOTECHNOLOGY

Spatial-CUT&Tag: Spatially resolved chromatin modification profiling at the cellular level

(2022) Yanxiang Deng et al.   SCIENCE

Deciphering tissue structure and function using spatial transcriptomics

(2022) Benjamin L. Walker et al.   Communications Biology

Anomalous collapses of Nares Strait ice arches leads to enhanced export of Arctic sea ice

(2021) G. W. K. Moore et al.   Nature Communications

Spatially aware clustering of ion images in mass spectrometry imaging data using deep learning

(2021) Wanqiu Zhang et al.   ANALYTICAL AND BIOANALYTICAL CHEMISTRY

Transcriptome-scale spatial gene expression in the human dorsolateral prefrontal cortex

(2021) Kristen R. Maynard et al.   NATURE NEUROSCIENCE

Spatiotemporal single-cell RNA sequencing of developing chicken hearts identifies interplay between cellular differentiation and morphogenesis

(2021) Madhav Mantri et al.   Nature Communications

Inferring biologically relevant molecular tissue substructures by agglomerative clustering of digitized spatial transcriptomes with multilayer

(2021) Julien Moehlin et al.   Cell Systems

Integrated analysis of multimodal single-cell data

(2021) Yuhan Hao et al.   CELL

Characterizing spatial gene expression heterogeneity in spatially resolved single-cell transcriptomic data with nonuniform cellular densities

(2021) Brendan F. Miller et al.   GENOME RESEARCH

Exploring tissue architecture using spatial transcriptomics

(2021) Anjali Rao et al.   NATURE

Spatial transcriptomics at subspot resolution with BayesSpace

(2021) Edward Zhao et al.   NATURE BIOTECHNOLOGY

SC-MEB: spatial clustering with hidden Markov random field using empirical Bayes

(2021) Yi Yang et al.   BRIEFINGS IN BIOINFORMATICS

SpaGCN: Integrating gene expression, spatial location and histology to identify spatial domains and spatially variable genes by graph convolutional network

(2021) Jian Hu et al.   NATURE METHODS

Midkine Prevents Calcification of Aortic Valve Interstitial Cells via Intercellular Crosstalk

(2021) Qian Zhou et al.   Frontiers in Cell and Developmental Biology

Spatially Resolved Transcriptomes—Next Generation Tools for Tissue Exploration

(2020) Michaela Asp et al.   BIOESSAYS

Neurogranin: A Potential Biomarker of Neurological and Mental Diseases

(2020) Yang Xiang et al.   Frontiers in Aging Neuroscience

The Roles of Matrix Metalloproteinases and Their Inhibitors in Human Diseases

(2020) Griselda A Cabral-Pacheco et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution

(2019) Samuel G. Rodriques et al.   SCIENCE

Gene expression cartography

(2019) Mor Nitzan et al.   NATURE

Slingshot: cell lineage and pseudotime inference for single-cell transcriptomics

(2018) Kelly Street et al.   BMC GENOMICS

Multiscale Visualization and Exploration of Large Bipartite Graphs

(2018) Nicola Pezzotti et al.   COMPUTER GRAPHICS FORUM

Identification of spatial expression trends in single-cell gene expression data

(2018) Daniel Edsgärd et al.   NATURE METHODS

SpatialDE: identification of spatially variable genes

(2018) Valentine Svensson et al.   NATURE METHODS

Knockdown of IFI27 inhibits cell proliferation and invasion in oral squamous cell carcinoma

(2018) Hong Wang et al.   World Journal of Surgical Oncology

RNA velocity of single cells

(2018) Gioele La Manno et al.   NATURE

BrainScope: interactive visual exploration of the spatial and temporal human brain transcriptome

(2017) Sjoerd M.H. Huisman et al.   NUCLEIC ACIDS RESEARCH

Visual analysis of mass cytometry data by hierarchical stochastic neighbour embedding reveals rare cell types

(2017) Vincent van Unen et al.   Nature Communications

Massively parallel digital transcriptional profiling of single cells

(2017) Grace X. Y. Zheng et al.   Nature Communications

Spatial Autocorrelation in Mass Spectrometry Imaging

(2016) Alberto Cassese et al.   ANALYTICAL CHEMISTRY

Hierarchical Stochastic Neighbor Embedding

(2016) N. Pezzotti et al.   COMPUTER GRAPHICS FORUM

Diffusion pseudotime robustly reconstructs lineage branching

(2016) Laleh Haghverdi et al.   NATURE METHODS

In Situ Transcription Profiling of Single Cells Reveals Spatial Organization of Cells in the Mouse Hippocampus

(2016) Sheel Shah et al.   NEURON

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

Spatially resolved, highly multiplexed RNA profiling in single cells

(2015) K. H. Chen et al.   SCIENCE

Functional Receptors and Intracellular Signal Pathways of Midkine (MK) and Pleiotrophin (PTN)

(2014) Chuanying Xu et al.   BIOLOGICAL & PHARMACEUTICAL BULLETIN

The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells

(2014) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Area-specific substratification of deep layer neurons in the rat cortex

(2012) Akiya Watakabe et al.   JOURNAL OF COMPARATIVE NEUROLOGY

Mechanisms of CaMKII action in long-term potentiation

(2012) John Lisman et al.   NATURE REVIEWS NEUROSCIENCE

Postnatal characterization of cells in the accessory olfactory bulb of wild type and reeler mice

(2012) Eduardo Martín-López et al.   Frontiers in Neuroanatomy

A long nuclear-retained non-coding RNA regulates synaptogenesis by modulating gene expression

(2010) Delphine Bernard et al.   EMBO JOURNAL

Extra-embryonic syndecan 2 regulates organ primordia migration and fibrillogenesis throughout the zebrafish embryo

(2009) C. B. Arrington et al.   DEVELOPMENT

Wnt signaling in heart valve development and osteogenic gene induction

(2009) Christina M. Alfieri et al.   DEVELOPMENTAL BIOLOGY

Clustering of spatial gene expression patterns in the mouse brain and comparison with classical neuroanatomy

(2009) Jason W. Bohland et al.   METHODS

Hepatitis C virus ARFP/F protein interacts with cellular MM-1 protein and enhances the gene trans-activation activity of c-Myc

(2008) Hsin-Chieh Ma et al.   JOURNAL OF BIOMEDICAL SCIENCE