Microscopic examination of spatial transcriptome using Seq-Scope

Method of the Year: spatially resolved transcriptomics

(2021) Vivien Marx   NATURE METHODS

Macrophage Phenotype and Function in Liver Disorder

(2020) Lang Dou et al.   Frontiers in Immunology

Spatially Resolved Transcriptomes—Next Generation Tools for Tissue Exploration

(2020) Michaela Asp et al.   BIOESSAYS

Polyploidy in liver development, homeostasis and disease

(2020) Romain Donne et al.   Nature Reviews Gastroenterology & Hepatology

Seamless integration of image and molecular analysis for spatial transcriptomics workflows

(2020) Joseph Bergenstråhle et al.   BMC GENOMICS

Evolution and new frontiers of histology in bio‐medical research

(2020) Maria Mazzarini et al.   MICROSCOPY RESEARCH AND TECHNIQUE

Holistic characterization of single-hepatocyte transcriptome responses to high-fat diet

(2020) Sung Rye Park et al.   AMERICAN JOURNAL OF PHYSIOLOGY-ENDOCRINOLOGY AND METABOLISM

High-Spatial-Resolution Multi-Omics Sequencing via Deterministic Barcoding in Tissue

(2020) Yang Liu et al.   CELL

Highly sensitive spatial transcriptomics at near-cellular resolution with Slide-seqV2

(2020) Robert R. Stickels et al.   NATURE BIOTECHNOLOGY

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

(2019) Samuel G. Rodriques et al.   SCIENCE

Spatial heterogeneity in the mammalian liver

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

A human liver cell atlas reveals heterogeneity and epithelial progenitors

(2019) Nadim Aizarani et al.   NATURE

High-definition spatial transcriptomics for in situ tissue profiling

(2019) Sanja Vickovic et al.   NATURE METHODS

Concurrent activation of growth factor and nutrient arms of mTORC1 induces oxidative liver injury

(2019) Chun-Seok Cho et al.   Cell Discovery

Integrating single-cell transcriptomic data across different conditions, technologies, and species

(2018) Andrew Butler et al.   NATURE BIOTECHNOLOGY

RNA velocity of single cells

(2018) Gioele La Manno et al.   NATURE

Dimensionality reduction for visualizing single-cell data using UMAP

(2018) Etienne Becht et al.   NATURE BIOTECHNOLOGY

Barcoded solid-phase RNA capture for Spatial Transcriptomics profiling in mammalian tissue sections

(2018) Fredrik Salmén et al.   Nature Protocols

A single-cell survey of the small intestinal epithelium

(2017) Adam L. Haber et al.   NATURE

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

(2017) Keren Bahar Halpern et al.   NATURE

Designing Randomized DNA Sequences Free of Restriction Enzyme Recognition Sites

(2017) Audra J. Storm et al.   Biotechnology Journal

A single-cell resolution map of mouse hematopoietic stem and progenitor cell differentiation

(2016) S. Nestorowa et al.   BLOOD

The human intestinal B-cell response

(2016) J Spencer et al.   Mucosal Immunology

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

(2016) P. L. Stahl et al.   SCIENCE

Tumor suppressive role of sestrin2 during colitis and colon carcinogenesis

(2016) Seung-Hyun Ro et al.   eLife

EpCAM and the biology of hepatic stem/progenitor cells

(2015) Laurent Dollé et al.   AMERICAN JOURNAL OF PHYSIOLOGY-GASTROINTESTINAL AND LIVER PHYSIOLOGY

Nuclear Retention of mRNA in Mammalian Tissues

(2015) Keren Bahar Halpern et al.   Cell Reports

Osteopontin: a new player in regulating hepatic ductular reaction and hepatic progenitor cell responses during chronic liver injury

(2014) Mario Strazzabosco et al.   GUT

The mucus and mucins of the goblet cells and enterocytes provide the first defense line of the gastrointestinal tract and interact with the immune system

(2014) Thaher Pelaseyed et al.   IMMUNOLOGICAL REVIEWS

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Intestinal Epithelial Serum Amyloid A Modulates Bacterial Growth In Vitro and Pro-Inflammatory Responses in Mouse Experimental Colitis

(2010) Erik RM Eckhardt et al.   BMC GASTROENTEROLOGY

Invading macrophages play a major role in the liver progenitor cell response to chronic liver injury

(2010) Cornelia S. Viebahn et al.   JOURNAL OF HEPATOLOGY

Cellular organization of normal mouse liver: a histological, quantitative immunocytochemical, and fine structural analysis

(2009) Janie L. Baratta et al.   HISTOCHEMISTRY AND CELL BIOLOGY

Decreased Expression of Colonic Slc26a3 and Carbonic Anhydrase IV as a Cause of Fatal Infectious Diarrhea in Mice

(2009) D. Borenshtein et al.   INFECTION AND IMMUNITY

Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt

(2009) Steffen Durinck et al.   Nature Protocols

BioVenn – a web application for the comparison and visualization of biological lists using area-proportional Venn diagrams

(2008) Tim Hulsen et al.   BMC GENOMICS

Accurate whole human genome sequencing using reversible terminator chemistry

(2008) David R. Bentley et al.   NATURE