CellO: comprehensive and hierarchical cell type classification of human cells with the Cell Ontology

Regenerative lineages and immune-mediated pruning in lung cancer metastasis

(2020) Ashley M. Laughney et al.   NATURE MEDICINE

Alignment of Cell Lineage Trees Elucidates Genetic Programs for the Development and Evolution of Cell Types

(2020) Meng Yuan et al.   iScience

Reference-based analysis of lung single-cell sequencing reveals a transitional profibrotic macrophage

(2019) Dvir Aran et al.   NATURE IMMUNOLOGY

Challenges in unsupervised clustering of single-cell RNA-seq data

(2019) Vladimir Yu Kiselev et al.   NATURE REVIEWS GENETICS

RNA-Seq Signatures Normalized by mRNA Abundance Allow Absolute Deconvolution of Human Immune Cell Types

(2019) Gianni Monaco et al.   Cell Reports

scMatch: a single-cell gene expression profile annotation tool using reference datasets

(2019) Rui Hou et al.   BIOINFORMATICS

CHETAH: a selective, hierarchical cell type identification method for single-cell RNA sequencing

(2019) Jurrian K de Kanter et al.   NUCLEIC ACIDS RESEARCH

SingleCellNet: A Computational Tool to Classify Single Cell RNA-Seq Data Across Platforms and Across Species

(2019) Yuqi Tan et al.   Cell Systems

Supervised classification enables rapid annotation of cell atlases

(2019) Hannah A. Pliner et al.   NATURE METHODS

Probabilistic cell-type assignment of single-cell RNA-seq for tumor microenvironment profiling

(2019) Allen W. Zhang et al.   NATURE METHODS

nVenn: generalized, quasi-proportional Venn and Euler diagrams

(2018) José G Pérez-Silva et al.   BIOINFORMATICS

Pervasive Correlated Evolution in Gene Expression Shapes Cell and Tissue Type Transcriptomes

(2018) Cong Liang et al.   Genome Biology and Evolution

Pro-tumorigenic roles of fibroblast activation protein in cancer: back to the basics

(2018) Ellen Puré et al.   ONCOGENE

OUP accepted manuscript

(2018)   NUCLEIC ACIDS RESEARCH

CaSTLe – Classification of single cells by transfer learning: Harnessing the power of publicly available single cell RNA sequencing experiments to annotate new experiments

(2018) Yuval Lieberman et al.   PLoS One

Massively parallel digital transcriptional profiling of single cells

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

Molecular Diversity of Midbrain Development in Mouse, Human, and Stem Cells

(2016) Gioele La Manno et al.   CELL

Single-Cell Transcriptome Profiling of Human Pancreatic Islets in Health and Type 2 Diabetes

(2016) Åsa Segerstolpe et al.   Cell Metabolism

Near-optimal probabilistic RNA-seq quantification

(2016) Nicolas L Bray et al.   NATURE BIOTECHNOLOGY

The origin and evolution of cell types

(2016) Detlev Arendt et al.   NATURE REVIEWS GENETICS

Update of the FANTOM web resource: high resolution transcriptome of diverse cell types in mammals

(2016) Marina Lizio et al.   NUCLEIC ACIDS RESEARCH

The BLUEPRINT Data Analysis Portal

(2016) José María Fernández et al.   Cell Systems

Robust enumeration of cell subsets from tissue expression profiles

(2015) Aaron M Newman et al.   NATURE METHODS

ENCODE data at the ENCODE portal

(2015) Cricket A. Sloan et al.   NUCLEIC ACIDS RESEARCH

Massively Parallel Single-Cell RNA-Seq for Marker-Free Decomposition of Tissues into Cell Types

(2014) D. A. Jaitin et al.   SCIENCE

Ontology-aware classification of tissue and cell-type signals in gene expression profiles across platforms and technologies

(2013) Young-suk Lee et al.   BIOINFORMATICS

An expression atlas of human primary cells: inference of gene function from coexpression networks

(2013) Neil A Mabbott et al.   BMC GENOMICS

Explainers: Expert Explorations with Crafted Projections

(2013) Michael Gleicher   IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS

Human dendritic cell subsets

(2013) Matthew Collin et al.   IMMUNOLOGY

Smart-seq2 for sensitive full-length transcriptome profiling in single cells

(2013) Simone Picelli et al.   NATURE METHODS

Uberon, an integrative multi-species anatomy ontology

(2012) Christopher J Mungall et al.   GENOME BIOLOGY

DDX4 (VASA) Is Conserved in Germ Cell Development in Marsupials and Monotremes1

(2011) Danielle E. Hickford et al.   BIOLOGY OF REPRODUCTION

The BRENDA Tissue Ontology (BTO): the first all-integrating ontology of all organisms for enzyme sources

(2010) M. Gremse et al.   NUCLEIC ACIDS RESEARCH

The Sequence Read Archive

(2010) R. Leinonen et al.   NUCLEIC ACIDS RESEARCH

Neuregulin 1 in neural development, synaptic plasticity and schizophrenia

(2008) Lin Mei et al.   NATURE REVIEWS NEUROSCIENCE

Consistent probabilistic outputs for protein function prediction

(2008) Guillaume Obozinski et al.   GENOME BIOLOGY