AdRoit is an accurate and robust method to infer complex transcriptome composition

SPOTlight: seeded NMF regression to deconvolute spatial transcriptomics spots with single-cell transcriptomes

(2021) Marc Elosua-Bayes et al.   NUCLEIC ACIDS RESEARCH

Droplet scRNA-seq is not zero-inflated

(2020) Valentine Svensson   NATURE BIOTECHNOLOGY

Cellular deconvolution of GTEx tissues powers discovery of disease and cell-type associated regulatory variants

(2020) Margaret K. R. Donovan et al.   Nature Communications

Molecular taxonomy of human ocular outflow tissues defined by single-cell transcriptomics

(2020) Gaurang Patel et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Accurate estimation of cell composition in bulk expression through robust integration of single-cell information

(2020) Brandon Jew et al.   Nature Communications

Single-cell and spatial transcriptomics enables probabilistic inference of cell type topography

(2020) Alma Andersson et al.   Communications Biology

Bulk tissue cell type deconvolution with multi-subject single-cell expression reference

(2019) Xuran Wang et al.   Nature Communications

Determining cell type abundance and expression from bulk tissues with digital cytometry

(2019) Aaron M. Newman et al.   NATURE BIOTECHNOLOGY

Cytokines for evaluation of chronic inflammatory status in ageing research: reliability and phenotypic characterisation

(2019) Liselot Koelman et al.   Immunity & Ageing

Single-Cell RNA-Seq Technologies and Related Computational Data Analysis

(2019) Geng Chen et al.   Frontiers in Genetics

Comprehensive Integration of Single-Cell Data

(2019) Tim Stuart et al.   CELL

Complete deconvolution of cellular mixtures based on linearity of transcriptional signatures

(2019) Konstantin Zaitsev et al.   Nature Communications

Accurate estimation of cell-type composition from gene expression data

(2019) Daphne Tsoucas et al.   Nature Communications

High-definition spatial transcriptomics for in situ tissue profiling

(2019) Sanja Vickovic et al.   NATURE METHODS

A systematic evaluation of single cell RNA-seq analysis pipelines

(2019) Beate Vieth et al.   Nature Communications

Improved cell composition deconvolution method of bulk gene expression profiles to quantify subsets of immune cells

(2019) Yen-Jung Chiu et al.   BMC Medical Genomics

CDSeq: A novel complete deconvolution method for dissecting heterogeneous samples using gene expression data

(2019) Kai Kang et al.   PLoS Computational Biology

Pseudotime Ordering of Single Human β-Cells Reveals States of Insulin Production and Unfolded Protein Response

(2018) Yurong Xin et al.   DIABETES

Maximum a posteriori estimators as a limit of Bayes estimators

(2018) Robert Bassett et al.   MATHEMATICAL PROGRAMMING

Molecular Architecture of the Mouse Nervous System

(2018) Amit Zeisel et al.   CELL

Roles of the immune system in cancer: from tumor initiation to metastatic progression

(2018) Hugo Gonzalez et al.   GENES & DEVELOPMENT

Scaling single-cell genomics from phenomenology to mechanism

(2017) Amos Tanay et al.   NATURE

Massively parallel digital transcriptional profiling of single cells

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

RNA Sequencing of Single Human Islet Cells Reveals Type 2 Diabetes Genes

(2016) Yurong Xin et al.   Cell Metabolism

Immune suppressive mechanisms in the tumor microenvironment

(2016) David H Munn et al.   CURRENT OPINION IN IMMUNOLOGY

Chemokine and cytokine levels in inflammatory bowel disease patients

(2016) Udai P. Singh et al.   CYTOKINE

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

(2016) P. L. Stahl et al.   SCIENCE

A Single-Cell Transcriptomic Map of the Human and Mouse Pancreas Reveals Inter- and Intra-cell Population Structure

(2016) Maayan Baron et al.   Cell Systems

fitdistrplus: AnRPackage for Fitting Distributions

(2015) Marie Laure Delignette-Muller et al.   Journal of Statistical Software

Robust enumeration of cell subsets from tissue expression profiles

(2015) Aaron M Newman et al.   NATURE METHODS

Structural similarities and differences between the human and the mouse pancreas

(2015) Jurij Dolenšek et al.   Islets

Alpha- and beta-cell abnormalities in haemoglobin A1c-defined prediabetes and type 2 diabetes

(2014) Salvatore Calanna et al.   ACTA DIABETOLOGICA

Chronic Inflammation and Cytokines in the Tumor Microenvironment

(2014) Glauben Landskron et al.   Journal of Immunology Research

TNF-α signalling and inflammation: interactions between old acquaintances

(2013) Hana Zelová et al.   INFLAMMATION RESEARCH

Beta Cell Dysfunction and Insulin Resistance

(2013) Marlon E. Cerf   Frontiers in Endocrinology

PERT: A Method for Expression Deconvolution of Human Blood Samples from Varied Microenvironmental and Developmental Conditions

(2012) Wenlian Qiao et al.   PLoS Computational Biology

The Relationship Between  -Cell Function and Glycated Hemoglobin: Results from the Veterans Administration Genetic Epidemiology Study

(2011) M. Kanat et al.   DIABETES CARE

Gene expression deconvolution in clinical samples

(2011) Yingdong Zhao et al.   Genome Medicine

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

mRNA-Seq whole-transcriptome analysis of a single cell

(2009) Fuchou Tang et al.   NATURE METHODS

Deconvolution of Blood Microarray Data Identifies Cellular Activation Patterns in Systemic Lupus Erythematosus

(2009) Alexander R. Abbas et al.   PLoS One

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS