Quantitative single-cell proteomics as a tool to characterize cellular hierarchies

An improved Boosting to Amplify Signal with Isobaric Labeling (iBASIL) strategy for precise quantitative single-cell proteomics

(2020) Chia-Feng Tsai et al.   MOLECULAR & CELLULAR PROTEOMICS

Single-cell analysis targeting the proteome

(2020) Mahmoud Labib et al.   Nature Reviews Chemistry

Defining the carrier proteome limit for single-cell proteomics

(2020) Tommy K. Cheung et al.   NATURE METHODS

Unravelling Intratumoral Heterogeneity through High-Sensitivity Single-Cell Mutational Analysis and Parallel RNA Sequencing

(2019) Alba Rodriguez-Meira et al.   MOLECULAR CELL

Single-Cell RNA-Seq Reveals AML Hierarchies Relevant to Disease Progression and Immunity

(2019) Peter van Galen et al.   CELL

The Proteogenomic Landscape of Curable Prostate Cancer

(2019) Ankit Sinha et al.   CANCER CELL

A stemness screen reveals C3orf54/INKA1 as a promoter of human leukemia stem cell latency

(2019) Kerstin B. Kaufmann et al.   BLOOD

Characterization and Optimization of Multiplexed Quantitative Analyses Using High-Field Asymmetric-Waveform Ion Mobility Mass Spectrometry

(2019) Devin K. Schweppe et al.   ANALYTICAL CHEMISTRY

Microsampling Capillary Electrophoresis Mass Spectrometry Enables Single-Cell Proteomics in Complex Tissues: Developing Cell Clones in Live Xenopus laevis and Zebrafish Embryos

(2019) Camille Lombard-Banek et al.   ANALYTICAL CHEMISTRY

Efficient integration of heterogeneous single-cell transcriptomes using Scanorama

(2019) Brian Hie et al.   NATURE BIOTECHNOLOGY

Single Cell Proteomics by Data-Independent Acquisition To Study Embryonic Asymmetry in Xenopus laevis

(2019) Anumita Saha-Shah et al.   ANALYTICAL CHEMISTRY

Somatic mutations and cell identity linked by Genotyping of Transcriptomes

(2019) Anna S. Nam et al.   NATURE

High-Throughput Single Cell Proteomics Enabled by Multiplex Isobaric Labeling in a Nanodroplet Sample Preparation Platform

(2019) Maowei Dou et al.   ANALYTICAL CHEMISTRY

TMTpro: Design, Synthesis, and Initial Evaluation of a Proline-Based Isobaric 16-Plex Tandem Mass Tag Reagent Set

(2019) Andrew Thompson et al.   ANALYTICAL CHEMISTRY

Sphingolipid Modulation Activates Proteostasis Programs to Govern Human Hematopoietic Stem Cell Self-Renewal

(2019) Stephanie Z. Xie et al.   Cell Stem Cell

Decoding human fetal liver haematopoiesis

(2019) Dorin-Mirel Popescu et al.   NATURE

Single-cell proteomics reveals changes in expression during hair-cell development

(2019) Ying Zhu et al.   eLife

Nanodroplet processing platform for deep and quantitative proteome profiling of 10–100 mammalian cells

(2018) Ying Zhu et al.   Nature Communications

Differences in Cell Cycle Status Underlie Transcriptional Heterogeneity in the HSC Compartment

(2018) Felicia Kathrine Bratt Lauridsen et al.   Cell Reports

The stem cell-associated gene expression signature allows risk stratification in pediatric acute myeloid leukemia

(2018) Nicolas Duployez et al.   LEUKEMIA

A Myc enhancer cluster regulates normal and leukaemic haematopoietic stem cell hierarchies

(2018) Carsten Bahr et al.   NATURE

A Cancer Cell Program Promotes T Cell Exclusion and Resistance to Checkpoint Blockade

(2018) Livnat Jerby-Arnon et al.   CELL

The PRIDE database and related tools and resources in 2019: improving support for quantification data

(2018) Yasset Perez-Riverol et al.   NUCLEIC ACIDS RESEARCH

BloodSpot: a database of healthy and malignant haematopoiesis updated with purified and single cell mRNA sequencing profiles

(2018) Frederik Otzen Bagger et al.   NUCLEIC ACIDS RESEARCH

Double-slit photoelectron interference in strong-field ionization of the neon dimer

(2018) Maksim Kunitski et al.   Nature Communications

Extended Multiplexing of Tandem Mass Tags (TMT) Labeling Reveals Age and High Fat Diet Specific Proteome Changes in Mouse Epididymal Adipose Tissue

(2017) Deanna L. Plubell et al.   MOLECULAR & CELLULAR PROTEOMICS

Tracing the origins of relapse in acute myeloid leukaemia to stem cells

(2017) Liran I. Shlush et al.   NATURE

miR-126 Regulates Distinct Self-Renewal Outcomes in Normal and Malignant Hematopoietic Stem Cells

(2016) Eric R. Lechman et al.   CANCER CELL

Granulopoiesis and granules of human neutrophils

(2016) Jack B. Cowland et al.   IMMUNOLOGICAL REVIEWS

Improvement of Quantitative Measurements in Multiplex Proteomics Using High-Field Asymmetric Waveform Spectrometry

(2016) Sibylle Pfammatter et al.   JOURNAL OF PROTEOME RESEARCH

CONSTANd : A Normalization Method for Isobaric Labeled Spectra by Constrained Optimization

(2016) Evelyne Maes et al.   MOLECULAR & CELLULAR PROTEOMICS

A 17-gene stemness score for rapid determination of risk in acute leukaemia

(2016) Stanley W. K. Ng et al.   NATURE

Diffusion pseudotime robustly reconstructs lineage branching

(2016) Laleh Haghverdi et al.   NATURE METHODS

Combined tissue and fluid proteomics with Tandem Mass Tags to identify low-abundance protein biomarkers of disease in peripheral body fluid: An Alzheimer's Disease case study

(2016) Claire L. Russell et al.   RAPID COMMUNICATIONS IN MASS SPECTROMETRY

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

(2015) Laleh Haghverdi et al.   BIOINFORMATICS

Not All Created Equal: Lineage Hard-Wiring in the Production of Blood

(2015) Francois E. Mercier et al.   CELL

Transcriptional Heterogeneity and Lineage Commitment in Myeloid Progenitors

(2015) Franziska Paul et al.   CELL

Defining cell types and states with single-cell genomics

(2015) Cole Trapnell   GENOME RESEARCH

Proteome-wide quantitative multiplexed profiling of protein expression: carbon-source dependency in Saccharomyces cerevisiae

(2015) Joao A. Paulo et al.   MOLECULAR BIOLOGY OF THE CELL

Distinct routes of lineage development reshape the human blood hierarchy across ontogeny

(2015) F. Notta et al.   SCIENCE

MultiNotch MS3 Enables Accurate, Sensitive, and Multiplexed Detection of Differential Expression across Cancer Cell Line Proteomes

(2014) Graeme C. McAlister et al.   ANALYTICAL CHEMISTRY

Evolution of the Cancer Stem Cell Model

(2014) Antonija Kreso et al.   Cell Stem Cell

Reconstructing lineage hierarchies of the distal lung epithelium using single-cell RNA-seq

(2014) Barbara Treutlein et al.   NATURE

ForceAtlas2, a Continuous Graph Layout Algorithm for Handy Network Visualization Designed for the Gephi Software

(2014) Mathieu Jacomy et al.   PLoS One

Primate Transcript and Protein Expression Levels Evolve Under Compensatory Selection Pressures

(2013) Z. Khan et al.   SCIENCE

Insights into the regulation of protein abundance from proteomic and transcriptomic analyses

(2012) Christine Vogel et al.   NATURE REVIEWS GENETICS

Stem cell gene expression programs influence clinical outcome in human leukemia

(2011) Kolja Eppert et al.   NATURE MEDICINE