A spatial vascular transcriptomic, proteomic, and phosphoproteomic atlas unveils an angiocrine Tie–Wnt signaling axis in the liver

Preclinical validation of a novel metastasis‐inhibiting Tie1 function‐blocking antibody

(2020) Mahak Singhal et al.   EMBO Molecular Medicine

Mass-spectrometry-based draft of the Arabidopsis proteome

(2020) Julia Mergner et al.   NATURE

NASQAR: a web-based platform for high-throughput sequencing data analysis and visualization

(2020) Ayman Yousif et al.   BMC BIOINFORMATICS

Onco-fetal Reprogramming of Endothelial Cells Drives Immunosuppressive Macrophages in Hepatocellular Carcinoma

(2020) Ankur Sharma et al.   CELL

Commensal-driven immune zonation of the liver promotes host defence

(2020) Anita Gola et al.   NATURE

Central dogma rates and the trade-off between precision and economy in gene expression

(2019) Jean Hausser et al.   Nature Communications

Lineage Tracing Reveals the Bipotency of SOX9+ Hepatocytes during Liver Regeneration

(2019) Ximeng Han et al.   Stem Cell Reports

Tie2–FGFR1 Interaction Induces Adaptive PI3K Inhibitor Resistance by Upregulating Aurora A/PLK1/CDK1 Signaling in Glioblastoma

(2019) Xiaolong Li et al.   CANCER RESEARCH

LECT2, a Ligand for Tie1, Plays a Crucial Role in Liver Fibrogenesis

(2019) Meng Xu et al.   CELL

Landscape of Intercellular Crosstalk in Healthy and NASH Liver Revealed by Single-Cell Secretome Gene Analysis

(2019) Xuelian Xiong et al.   MOLECULAR CELL

A dream of single-cell proteomics

(2019) Vivien Marx   NATURE METHODS

Single-Cell Transcriptomics Uncovers Zonation of Function in the Mesenchyme during Liver Fibrosis

(2019) Ross Dobie et al.   Cell Reports

Arterial Venous Differentiation for Vascular Bioengineering

(2018) Laura Niklason et al.   Annual Review of Biomedical Engineering

Defeating Major Contaminants in Fe3+- Immobilized Metal Ion Affinity Chromatography (IMAC) Phosphopeptide Enrichment

(2018) Clement M. Potel et al.   MOLECULAR & CELLULAR PROTEOMICS

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update

(2018) Enis Afgan et al.   NUCLEIC ACIDS RESEARCH

Mechanosensing by β1 integrin induces angiocrine signals for liver growth and survival

(2018) Linda Lorenz et al.   NATURE

Paired-cell sequencing enables spatial gene expression mapping of liver endothelial cells

(2018) Keren Bahar Halpern et al.   NATURE BIOTECHNOLOGY

Coral: Clear and Customizable Visualization of Human Kinome Data

(2018) Kathleen S. Metz et al.   Cell Systems

The Role of Angiogenesis in Hepatocellular Carcinoma

(2018) Michael A. Morse et al.   CLINICAL CANCER RESEARCH

STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets

(2018) Damian Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

FOXO Signaling Pathways as Therapeutic Targets in Cancer

(2017) Mohd Farhan et al.   International Journal of Biological Sciences

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

(2017) Keren Bahar Halpern et al.   NATURE

20 years of the SMART protein domain annotation resource

(2017) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

Targeting the vascular and perivascular niches as a regenerative therapy for lung and liver fibrosis

(2017) Zhongwei Cao et al.   Science Translational Medicine

Opposing actions of angiopoietin-2 on Tie2 signaling and FOXO1 activation

(2016) Minah Kim et al.   JOURNAL OF CLINICAL INVESTIGATION

The Perseus computational platform for comprehensive analysis of (prote)omics data

(2016) Stefka Tyanova et al.   NATURE METHODS

The MaxQuant computational platform for mass spectrometry-based shotgun proteomics

(2016) Stefka Tyanova et al.   Nature Protocols

Immunosurveillance of the Liver by Intravascular Effector CD8 + T Cells

(2015) Luca G. Guidotti et al.   CELL

Spatiotemporal dynamics of effector CD8+ T cell responses within the liver

(2015) Donato Inverso et al.   JOURNAL OF LEUKOCYTE BIOLOGY

Self-renewing diploid Axin2+ cells fuel homeostatic renewal of the liver

(2015) Bruce Wang et al.   NATURE

High-yield and high-purity isolation of hepatic stellate cells from normal and fibrotic mouse livers

(2015) Ingmar Mederacke et al.   Nature Protocols

The Angiocrine Factor Rspondin3 Is a Key Determinant of Liver Zonation

(2015) Ana Sofia Rocha et al.   Cell Reports

PhosphoSitePlus, 2014: mutations, PTMs and recalibrations

(2014) Peter V. Hornbeck et al.   NUCLEIC ACIDS RESEARCH

The Eukaryotic Promoter Database: expansion of EPDnew and new promoter analysis tools

(2014) René Dreos et al.   NUCLEIC ACIDS RESEARCH

Endothelial Cell-Derived Angiopoietin-2 Controls Liver Regeneration as a Spatiotemporal Rheostat

(2014) J. Hu et al.   SCIENCE

Ten years of next-generation sequencing technology

(2014) Erwin L. van Dijk et al.   TRENDS IN GENETICS

Ultradeep Human Phosphoproteome Reveals a Distinct Regulatory Nature of Tyr and Ser/Thr-Based Signaling

(2014) Kirti Sharma et al.   Cell Reports

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

In vitro expansion of single Lgr5+ liver stem cells induced by Wnt-driven regeneration

(2013) Meritxell Huch et al.   NATURE

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Enrichment techniques employed in phosphoproteomics

(2011) Jan Fíla et al.   AMINO ACIDS

Global quantification of mammalian gene expression control

(2011) Björn Schwanhäusser et al.   NATURE

Gitools: Analysis and Visualisation of Genomic Data Using Interactive Heat-Maps

(2011) Christian Perez-Llamas et al.   PLoS One

A Tissue-Specific Atlas of Mouse Protein Phosphorylation and Expression

(2010) Edward L. Huttlin et al.   CELL

Abnormal embryonic lymphatic vessel development in Tie1 hypomorphic mice

(2010) X. Qu et al.   DEVELOPMENT

Ephrin-B2 controls VEGF-induced angiogenesis and lymphangiogenesis

(2010) Yingdi Wang et al.   NATURE

Phosphorylation Dynamics during Early Differentiation of Human Embryonic Stem Cells

(2009) Dennis Van Hoof et al.   Cell Stem Cell

FoxO transcription factors in the maintenance of cellular homeostasis during aging

(2008) Dervis AM Salih et al.   CURRENT OPINION IN CELL BIOLOGY

Interaction of CD44 and hyaluronan is the dominant mechanism for neutrophil sequestration in inflamed liver sinusoids

(2008) Braedon McDonald et al.   JOURNAL OF EXPERIMENTAL MEDICINE

A reproducible and well-tolerated method for 2/3 partial hepatectomy in mice

(2008) Claudia Mitchell et al.   Nature Protocols