Single cell proteomics in biomedicine: High-dimensional data acquisition, visualization, and analysis

Protein Counting in Single Cancer Cells

(2016) Stephanie M. Schubert et al.   ANALYTICAL CHEMISTRY

Single-Cell, Multiplexed Protein Detection of Rare Tumor Cells Based on a Beads-on-Barcode Antibody Microarray

(2016) Liu Yang et al.   ANALYTICAL CHEMISTRY

Assay of Genome-Wide Transcriptome and Secreted Proteins on the Same Single Immune Cells by Microfluidics and RNA Sequencing

(2016) Justin George et al.   ANALYTICAL CHEMISTRY

Single-Cell Phosphoproteomics Resolves Adaptive Signaling Dynamics and Informs Targeted Combination Therapy in Glioblastoma

(2016) Wei Wei et al.   CANCER CELL

Mass Cytometry: Single Cells, Many Features

(2016) Matthew H. Spitzer et al.   CELL

Single-cell gene expression profiling and cell state dynamics: collecting data, correlating data points and connecting the dots

(2016) Carsten Marr et al.   CURRENT OPINION IN BIOTECHNOLOGY

Emerging single-cell technologies for functional proteomics in oncology

(2016) Jun Wang et al.   Expert Review of Proteomics

A Thermodynamic-Based Interpretation of Protein Expression Heterogeneity in Different Glioblastoma Multiforme Tumors Identifies Tumor-Specific Unbalanced Processes

(2016) Nataly Kravchenko-Balasha et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Supramolecular Probes for Assessing Glutamine Uptake Enable Semi-Quantitative Metabolic Models in Single Cells

(2016) Min Xue et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Digital Quantification of Proteins and mRNA in Single Mammalian Cells

(2016) Cem Albayrak et al.   MOLECULAR CELL

Wishbone identifies bifurcating developmental trajectories from single-cell data

(2016) Manu Setty et al.   NATURE BIOTECHNOLOGY

Expansion microscopy with conventional antibodies and fluorescent proteins

(2016) Tyler J Chozinski et al.   NATURE METHODS

Automated mapping of phenotype space with single-cell data

(2016) Nikolay Samusik et al.   NATURE METHODS

Highly multiplexed simultaneous detection of RNAs and proteins in single cells

(2016) Andreas P Frei et al.   NATURE METHODS

Single cell–resolution western blotting

(2016) Chi-Chih Kang et al.   Nature Protocols

Intercellular signaling through secreted proteins induces free-energy gradient-directed cell movement

(2016) Nataly Kravchenko-Balasha et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Critical Points in Tumorigenesis: A Carcinogen-Initiated Phase Transition Analyzed via Single-Cell Proteomics

(2016) Suresh Kumar Poovathingal et al.   Small

Single-Cell Codetection of Metabolic Activity, Intracellular Functional Proteins, and Genetic Mutations from Rare Circulating Tumor Cells

(2015) Yu Zhang et al.   ANALYTICAL CHEMISTRY

Diffusion maps for high-dimensional single-cell analysis of differentiation data

(2015) Laleh Haghverdi et al.   BIOINFORMATICS

Data-Driven Phenotypic Dissection of AML Reveals Progenitor-like Cells that Correlate with Prognosis

(2015) Jacob H. Levine et al.   CELL

Evaluating the efficiency of isotope transmission for improved panel design and a comparison of the detection sensitivities of mass cytometer instruments

(2015) Sabine Tricot et al.   CYTOMETRY PART A

FlowSOM: Using self-organizing maps for visualization and interpretation of cytometry data

(2015) Sofie Van Gassen et al.   CYTOMETRY PART A

Categorical Analysis of Human T Cell Heterogeneity with One-Dimensional Soli-Expression by Nonlinear Stochastic Embedding

(2015) Yang Cheng et al.   JOURNAL OF IMMUNOLOGY

Chemical Methods for the Simultaneous Quantitation of Metabolites and Proteins from Single Cells

(2015) Min Xue et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Reproducibility crisis: Blame it on the antibodies

(2015) Monya Baker   NATURE

Assessment of a method to characterize antibody selectivity and specificity for use in immunoprecipitation

(2015) Edyta Marcon et al.   NATURE METHODS

Trajectories of cell-cycle progression from fixed cell populations

(2015) Gabriele Gut et al.   NATURE METHODS

Single-cell analysis tools for drug discovery and development

(2015) James R. Heath et al.   NATURE REVIEWS DRUG DISCOVERY

Entropy, Ergodicity, and Stem Cell Multipotency

(2015) Sonya J. Ridden et al.   PHYSICAL REVIEW LETTERS

Nanotechnologies for biomedical science and translational medicine

(2015) James R. Heath   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Highly multiplexed profiling of single-cell effector functions reveals deep functional heterogeneity in response to pathogenic ligands

(2015) Yao Lu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

An interactive reference framework for modeling a dynamic immune system

(2015) M. H. Spitzer et al.   SCIENCE

Highly multiplexed imaging of single cells using a high-throughput cyclic immunofluorescence method

(2015) Jia-Ren Lin et al.   Nature Communications

Microfluidics-Based Single-Cell Functional Proteomics for Fundamental and Applied Biomedical Applications

(2014) Jing Yu et al.   Annual Review of Analytical Chemistry

Single-Cell Trajectory Detection Uncovers Progression and Regulatory Coordination in Human B Cell Development

(2014) Sean C. Bendall et al.   CELL

Environmental sensing, information transfer, and cellular decision-making

(2014) Clive G Bowsher et al.   CURRENT OPINION IN BIOTECHNOLOGY

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

(2014) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

High-dimensional analysis of the murine myeloid cell system

(2014) Burkhard Becher et al.   NATURE IMMUNOLOGY

Multiplexed ion beam imaging of human breast tumors

(2014) Michael Angelo et al.   NATURE MEDICINE

Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry

(2014) Charlotte Giesen et al.   NATURE METHODS

Single-cell western blotting

(2014) Alex J Hughes et al.   NATURE METHODS

Single-cell in situ RNA profiling by sequential hybridization

(2014) Eric Lubeck et al.   NATURE METHODS

Glioblastoma cellular architectures are predicted through the characterization of two-cell interactions

(2014) N. Kravchenko-Balasha et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Surprisal analysis characterizes the free energy time course of cancer cells undergoing epithelial-to-mesenchymal transition

(2014) S. Zadran et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Automated identification of stratifying signatures in cellular subpopulations

(2014) Robert V. Bruggner et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Bifurcation analysis of single-cell gene expression data reveals epigenetic landscape

(2014) Eugenio Marco et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Conditional density-based analysis of T cell signaling in single-cell data

(2014) S. Krishnaswamy et al.   SCIENCE

Clinical recovery from surgery correlates with single-cell immune signatures

(2014) B. Gaudilliere et al.   Science Translational Medicine

Cancer Cell Profiling by Barcoding Allows Multiplexed Protein Analysis in Fine-Needle Aspirates

(2014) A. V. Ullal et al.   Science Translational Medicine

Normalization of mass cytometry data with bead standards

(2013) Rachel Finck et al.   CYTOMETRY PART A

viSNE enables visualization of high dimensional single-cell data and reveals phenotypic heterogeneity of leukemia

(2013) El-ad David Amir et al.   NATURE BIOTECHNOLOGY

Single-cell analysis and sorting using droplet-based microfluidics

(2013) Linas Mazutis et al.   Nature Protocols

Hypoxia induces a phase transition within a kinase signaling network in cancer cells

(2013) W. Wei et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Automatic Classification of Cellular Expression by Nonlinear Stochastic Embedding (ACCENSE)

(2013) K. Shekhar et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Quantum dot imaging platform for single-cell molecular profiling

(2013) Pavel Zrazhevskiy et al.   Nature Communications

Multifunctional T-cell Analyses to Study Response and Progression in Adoptive Cell Transfer Immunotherapy

(2013) Chao Ma et al.   Cancer Discovery

hARACNe: improving the accuracy of regulatory model reverse engineering via higher-order data processing inequality tests

(2013) I. S. Jang et al.   Interface Focus

Microchip platforms for multiplex single-cell functional proteomics with applications to immunology and cancer research

(2013) Wei Wei et al.   Genome Medicine

Sequential Application of Anticancer Drugs Enhances Cell Death by Rewiring Apoptotic Signaling Networks

(2012) Michael J. Lee et al.   CELL

Photocleavable DNA Barcode–Antibody Conjugates Allow Sensitive and Multiplexed Protein Analysis in Single Cells

(2012) Sarit S. Agasti et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Functional single-cell analysis of T-cell activation by supported lipid bilayer-tethered ligands on arrays of nanowells

(2012) Alexis J. Torres et al.   LAB ON A CHIP

Quantitating Cell–Cell Interaction Functions with Applications to Glioblastoma Multiforme Cancer Cells

(2012) Jun Wang et al.   NANO LETTERS

A gene ontology inferred from molecular networks

(2012) Janusz Dutkowski et al.   NATURE BIOTECHNOLOGY

On a fundamental structure of gene networks in living cells

(2012) N. Kravchenko-Balasha et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Predicting rates of cell state change caused by stochastic fluctuations using a data-driven landscape model

(2012) D. R. Sisan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Computational Approaches for Analyzing Information Flow in Biological Networks

(2012) B. Kholodenko et al.   Science Signaling

Protein Signaling Networks from Single Cell Fluctuations and Information Theory Profiling

(2011) Young Shik Shin et al.   BIOPHYSICAL JOURNAL

Microproteomic analysis of 10,000 laser captured microdissected breast tumor cells using short-range sodium dodecyl sulfate-polyacrylamide gel electrophoresis and porous layer open tubular liquid chromatography tandem mass spectrometry

(2011) Dipak Thakur et al.   JOURNAL OF CHROMATOGRAPHY A

Extracting a cellular hierarchy from high-dimensional cytometry data with SPADE

(2011) Peng Qiu et al.   NATURE BIOTECHNOLOGY

A clinical microchip for evaluation of single immune cells reveals high functional heterogeneity in phenotypically similar T cells

(2011) Chao Ma et al.   NATURE MEDICINE

Single-cell proteomic chip for profiling intracellular signaling pathways in single tumor cells

(2011) Q. Shi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Single-Cell Mass Cytometry of Differential Immune and Drug Responses Across a Human Hematopoietic Continuum

(2011) S. C. Bendall et al.   SCIENCE

The Potential Landscape of Genetic Circuits Imposes the Arrow of Time in Stem Cell Differentiation

(2010) Jin Wang et al.   BIOPHYSICAL JOURNAL

Cellular Heterogeneity: Do Differences Make a Difference?

(2010) Steven J. Altschuler et al.   CELL

Chemistries for Patterning Robust DNA MicroBarcodes Enable Multiplex Assays of Cytoplasm Proteins from Single Cancer Cells

(2010) Young Shik Shin et al.   CHEMPHYSCHEM

Rare Cell Proteomic Reactor Applied to Stable Isotope Labeling by Amino Acids in Cell Culture (SILAC)-based Quantitative Proteomics Study of Human Embryonic Stem Cell Differentiation

(2010) Ruijun Tian et al.   MOLECULAR & CELLULAR PROTEOMICS

Single-molecule enzyme-linked immunosorbent assay detects serum proteins at subfemtomolar concentrations

(2010) David M Rissin et al.   NATURE BIOTECHNOLOGY

Information-theoretic analysis of phenotype changes in early stages of carcinogenesis

(2010) F. Remacle et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Publishing flow cytometry data

(2009) D. F. Alvarez et al.   AMERICAN JOURNAL OF PHYSIOLOGY-LUNG CELLULAR AND MOLECULAR PHYSIOLOGY

Elite and stochastic models for induced pluripotent stem cell generation

(2009) Shinya Yamanaka   NATURE

Nature, Nurture, or Chance: Stochastic Gene Expression and Its Consequences

(2008) Arjun Raj et al.   CELL