Integrated Proteogenomic Characterization across Major Histological Types of Pediatric Brain Cancer

Proteogenomic Characterization of Endometrial Carcinoma

(2020) Yongchao Dou et al.   CELL

Interpreting pathways to discover cancer driver genes with Moonlight

(2020) Antonio Colaprico et al.   Nature Communications

The mutational constraint spectrum quantified from variation in 141,456 humans

(2020) Konrad J. Karczewski et al.   NATURE

Quantitative proteomic landscape of metaplastic breast carcinoma pathological subtypes and their relationship to triple-negative tumors

(2020) Sabra I. Djomehri et al.   Nature Communications

Proteogenomic Characterization Reveals Therapeutic Vulnerabilities in Lung Adenocarcinoma

(2020) Michael A. Gillette et al.   CELL

Philosopher: a versatile toolkit for shotgun proteomics data analysis

(2020) Felipe da Veiga Leprevost et al.   NATURE METHODS

WNT/β-catenin pathway activation correlates with immune exclusion across human cancers

(2019) Jason J. Luke et al.   CLINICAL CANCER RESEARCH

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

(2019) Xuran Wang et al.   Nature Communications

Comprehensive gene expression meta-analysis identifies signature genes that distinguish microglia from peripheral monocytes/macrophages in health and glioma

(2019) Verena Haage et al.   Acta Neuropathologica Communications

New functionalities in the TCGAbiolinks package for the study and integration of cancer data from GDC and GTEx

(2019) Mohamed Mounir et al.   PLoS Computational Biology

Selumetinib in paediatric patients with BRAF-aberrant or neurofibromatosis type 1-associated recurrent, refractory, or progressive low-grade glioma: a multicentre, phase 2 trial

(2019) Jason Fangusaro et al.   LANCET ONCOLOGY

TMT labeling for the masses: A robust and cost-efficient, in-solution labeling approach

(2019) Jana Zecha et al.   MOLECULAR & CELLULAR PROTEOMICS

Graph algorithms for condensing and consolidating gene set analysis results

(2019) Sara R. Savage et al.   MOLECULAR & CELLULAR PROTEOMICS

Blocking Antibodies Targeting the CD39/CD73 Immunosuppressive Pathway Unleash Immune Responses in Combination Cancer Therapies

(2019) Ivan Perrot et al.   Cell Reports

Wild-Type IDH Enzymes as Actionable Targets for Cancer Therapy

(2019) Elisa Bergaggio et al.   Cancers

PTMProphet: Fast and Accurate Mass Modification Localization for the Trans-Proteomic Pipeline

(2019) David D. Shteynberg et al.   JOURNAL OF PROTEOME RESEARCH

Insights into impact of DNA copy number alteration and methylation on the proteogenomic landscape in human ovarian cancer via a multi-omics integrative analysis

(2019) Xiaoyu Song et al.   MOLECULAR & CELLULAR PROTEOMICS

Electrical and synaptic integration of glioma into neural circuits

(2019) Humsa S. Venkatesh et al.   NATURE

Glutamatergic synaptic input to glioma cells drives brain tumour progression

(2019) Varun Venkataramani et al.   NATURE

BRAF Mutations and the Utility of RAF and MEK Inhibitors in Primary Brain Tumors

(2019) Karisa C. Schreck et al.   Cancers

Integrated Proteogenomic Characterization of Clear Cell Renal Cell Carcinoma

(2019) David J. Clark et al.   CELL

Necroptotic astrocytes contribute to maintaining stemness of disseminated medulloblastoma through CCL2 secretion

(2019) Hailong Liu et al.   NEURO-ONCOLOGY

LINCS Data Portal 2.0: next generation access point for perturbation-response signatures

(2019) Vasileios Stathias et al.   NUCLEIC ACIDS RESEARCH

Glutamine blockade induces divergent metabolic programs to overcome tumor immune evasion

(2019) Robert D. Leone et al.   SCIENCE

Tumour compartment transcriptomics demonstrates the activation of inflammatory and odontogenic programmes in human adamantinomatous craniopharyngioma and identifies the MAPK/ERK pathway as a novel therapeutic target

(2018) John R. Apps et al.   ACTA NEUROPATHOLOGICA

A new method for constructing tumor specific gene co-expression networks based on samples with tumor purity heterogeneity

(2018) Francesca Petralia et al.   BIOINFORMATICS

PD2/PAF1 at the Crossroads of the Cancer Network

(2018) Saswati Karmakar et al.   CANCER RESEARCH

Comprehensive Characterization of Cancer Driver Genes and Mutations

(2018) Matthew H. Bailey et al.   CELL

Machine Learning Identifies Stemness Features Associated with Oncogenic Dedifferentiation

(2018) Tathiane M. Malta et al.   CELL

Streamlined Tandem Mass Tag (SL-TMT) Protocol: An Efficient Strategy for Quantitative (Phospho)proteome Profiling Using Tandem Mass Tag-Synchronous Precursor Selection-MS3

(2018) José Navarrete-Perea et al.   JOURNAL OF PROTEOME RESEARCH

The landscape of genomic alterations across childhood cancers

(2018) Susanne N. Gröbner et al.   NATURE

DNA methylation-based classification of central nervous system tumours

(2018) David Capper et al.   NATURE

Strelka2: fast and accurate calling of germline and somatic variants

(2018) Sangtae Kim et al.   NATURE METHODS

Multiplexed immunofluorescence reveals potential PD-1/PD-L1 pathway vulnerabilities in craniopharyngioma

(2018) Shannon Coy et al.   NEURO-ONCOLOGY

A Multiplexed Mass Spectrometry-Based Assay for Robust Quantification of Phosphosignaling in Response to DNA Damage

(2018) Jeffrey R. Whiteaker et al.   RADIATION RESEARCH

Controlling the Immune Suppressor: Transcription Factors and MicroRNAs Regulating CD73/NT5E

(2018) Theresa Kordaß et al.   Frontiers in Immunology

A Library of Phosphoproteomic and Chromatin Signatures for Characterizing Cellular Responses to Drug Perturbations

(2018) Lev Litichevskiy et al.   Cell Systems

Targeting adenosine for cancer immunotherapy

(2018) Robert D. Leone et al.   Journal for ImmunoTherapy of Cancer

Proteomic analysis of Medulloblastoma reveals functional biology with translational potential

(2018) Samuel Rivero-Hinojosa et al.   Acta Neuropathologica Communications

How to reprogram microglia toward beneficial functions

(2018) Marta Fumagalli et al.   GLIA

CBTRUS Statistical Report: Primary Brain and Other Central Nervous System Tumors Diagnosed in the United States in 2011–2015

(2018) Quinn T Ostrom et al.   NEURO-ONCOLOGY

Role of MCM2–7 protein phosphorylation in human cancer cells

(2018) Liangru Fei et al.   Cell and Bioscience

Single-cell transcriptome analysis of lineage diversity in high-grade glioma

(2018) Jinzhou Yuan et al.   Genome Medicine

Investigation of frequent somatic mutations of MTND5 gene in gastric cancer cell lines and tissues

(2018) Lian Li et al.   Mitochondrial DNA Part B-Resources

A curcumin derivative hydrazinobenzoylcurcumin suppresses stem-like features of glioblastoma cells by targeting Ca2+ /calmodulin-dependent protein kinase II

(2018) Hee Jeong Shin et al.   JOURNAL OF CELLULAR BIOCHEMISTRY

Simultaneous overexpression of human E5NT and ENTPD1 protects porcine endothelial cells against H 2 O 2 -induced oxidative stress and cytotoxicity in vitro

(2017) Elisa Chisci et al.   FREE RADICAL BIOLOGY AND MEDICINE

The Human Gene Mutation Database: towards a comprehensive repository of inherited mutation data for medical research, genetic diagnosis and next-generation sequencing studies

(2017) Peter D. Stenson et al.   HUMAN GENETICS

The TREM2-APOE Pathway Drives the Transcriptional Phenotype of Dysfunctional Microglia in Neurodegenerative Diseases

(2017) Susanne Krasemann et al.   IMMUNITY

The whole-genome landscape of medulloblastoma subtypes

(2017) Paul A. Northcott et al.   NATURE

MSFragger: ultrafast and comprehensive peptide identification in mass spectrometry–based proteomics

(2017) Andy T Kong et al.   NATURE METHODS

Diffuse high-grade gliomas with H3 K27M mutations carry a dismal prognosis independent of tumor location

(2017) Michael Karremann et al.   NEURO-ONCOLOGY

NGSCheckMate: software for validating sample identity in next-generation sequencing studies within and across data types

(2017) Sejoon Lee et al.   NUCLEIC ACIDS RESEARCH

The Reactome Pathway Knowledgebase

(2017) Antonio Fabregat et al.   NUCLEIC ACIDS RESEARCH

Exon 3 mutations of CTNNB1 drive tumorigenesis: a review

(2017) Chao Gao et al.   Oncotarget

Overcoming resistance to single-agent therapy for oncogenic BRAF gene fusions via combinatorial targeting of MAPK and PI3K/mTOR signaling pathways

(2017) Payal Jain et al.   Oncotarget

Metabotropic glutamate receptors as a new therapeutic target for malignant gliomas

(2017) Mery Stefani Leivas Pereira et al.   Oncotarget

Deregulated expression and activity of Farnesyl Diphosphate Synthase (FDPS) in Glioblastoma

(2017) Mario Abate et al.   Scientific Reports

Single-Cell RNA-Seq Analysis of Infiltrating Neoplastic Cells at the Migrating Front of Human Glioblastoma

(2017) Spyros Darmanis et al.   Cell Reports

Cancer-Associated IDH1 Promotes Growth and Resistance to Targeted Therapies in the Absence of Mutation

(2017) Andrea E. Calvert et al.   Cell Reports

Analysis of 100,000 human cancer genomes reveals the landscape of tumor mutational burden

(2017) Zachary R. Chalmers et al.   Genome Medicine

iCAVE: an open source tool for visualizing biomolecular networks in 3D, stereoscopic 3D and immersive 3D

(2017) Vaja Liluashvili et al.   GigaScience

Molecular, phenotypic, and sample-associated data to describe pluripotent stem cell lines and derivatives

(2017) Kenneth Daily et al.   Scientific Data

Nucleophosmin: from structure and function to disease development

(2016) Joseph K. Box et al.   BMC MOLECULAR BIOLOGY

Integrated Proteogenomic Characterization of Human High-Grade Serous Ovarian Cancer

(2016) Hui Zhang et al.   CELL

Epithelial-Mesenchymal Transition Is Associated with a Distinct Tumor Microenvironment Including Elevation of Inflammatory Signals and Multiple Immune Checkpoints in Lung Adenocarcinoma

(2016) Y. Lou et al.   CLINICAL CANCER RESEARCH

Microglial Physiology and Pathophysiology: Insights from Genome-wide Transcriptional Profiling

(2016) Andrea Crotti et al.   IMMUNITY

New Method for Joint Network Analysis Reveals Common and Different Coexpression Patterns among Genes and Proteins in Breast Cancer

(2016) Francesca Petralia et al.   JOURNAL OF PROTEOME RESEARCH

A Tale of the Good and Bad: Remodeling of the Microtubule Network in the Brain by Cdk5

(2016) Kavita Shah et al.   MOLECULAR NEUROBIOLOGY

Divergent clonal selection dominates medulloblastoma at recurrence

(2016) A. Sorana Morrissy et al.   NATURE

Proteogenomics connects somatic mutations to signalling in breast cancer

(2016) Philipp Mertins et al.   NATURE

Differential Expression of Stem Cell Markers in Human Adamantinomatous Craniopharyngioma and Pituitary Adenoma

(2016) Claudia Veiga Chang et al.   NEUROENDOCRINOLOGY

Open Targets: a platform for therapeutic target identification and validation

(2016) Gautier Koscielny et al.   NUCLEIC ACIDS RESEARCH

KEGG: new perspectives on genomes, pathways, diseases and drugs

(2016) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Characterizing and targeting PDGFRA alterations in pediatric high-grade glioma

(2016) Carl Koschmann et al.   Oncotarget

CNVkit: Genome-Wide Copy Number Detection and Visualization from Targeted DNA Sequencing

(2016) Eric Talevich et al.   PLoS Computational Biology

Integrated Genomic Analysis of Diverse Induced Pluripotent Stem Cells from the Progenitor Cell Biology Consortium

(2016) Nathan Salomonis et al.   Stem Cell Reports

Integrative random forest for gene regulatory network inference

(2015) Francesca Petralia et al.   BIOINFORMATICS

From big data analysis to personalized medicine for all: challenges and opportunities

(2015) Akram Alyass et al.   BMC Medical Genomics

Mathematical analysis predicts imbalanced IDH1/2 expression associates with 2-HG-inactivating β-oxygenation pathway in colorectal cancer

(2015) JUN KOSEKI et al.   INTERNATIONAL JOURNAL OF ONCOLOGY

Loss of PTPN12 Stimulates Progression of ErbB2-Dependent Breast Cancer by Enhancing Cell Survival, Migration, and Epithelial-to-Mesenchymal Transition

(2015) Juan Li et al.   MOLECULAR AND CELLULAR BIOLOGY

Comprehensive, Integrative Genomic Analysis of Diffuse Lower-Grade Gliomas

(2015)   NEW ENGLAND JOURNAL OF MEDICINE

TCGAbiolinks: an R/Bioconductor package for integrative analysis of TCGA data

(2015) Antonio Colaprico et al.   NUCLEIC ACIDS RESEARCH

Gap junctions modulate glioma invasion by direct transfer of microRNA

(2015) Xiaoting Hong et al.   Oncotarget

The Molecular Signatures Database Hallmark Gene Set Collection

(2015) Arthur Liberzon et al.   Cell Systems

RNA-sequencing reveals oligodendrocyte and neuronal transcripts in microglia relevant to central nervous system disease

(2014) Anne C. Solga et al.   GLIA

Glutamate and its receptors in cancer

(2014) Andrzej Stepulak et al.   JOURNAL OF NEURAL TRANSMISSION

Ischemia in Tumors Induces Early and Sustained Phosphorylation Changes in Stress Kinase Pathways but Does Not Affect Global Protein Levels

(2014) Philipp Mertins et al.   MOLECULAR & CELLULAR PROTEOMICS

Proteogenomic characterization of human colon and rectal cancer

(2014) Bing Zhang et al.   NATURE

Exome sequencing identifies BRAF mutations in papillary craniopharyngiomas

(2014) Priscilla K Brastianos et al.   NATURE GENETICS

PhosphoSitePlus, 2014: mutations, PTMs and recalibrations

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

Reduction of Phosphorylated Synapsin I (Ser-553) Leads to Spatial Memory Impairment by Attenuating GABA Release after Microwave Exposure in Wistar Rats

(2014) Simo Qiao et al.   PLoS One

Learning-induced and stathmin-dependent changes in microtubule stability are critical for memory and disrupted in ageing

(2014) Shusaku Uchida et al.   Nature Communications

MS-GF+ makes progress towards a universal database search tool for proteomics

(2014) Sangtae Kim et al.   Nature Communications

MODMatcher: Multi-Omics Data Matcher for Integrative Genomic Analysis

(2014) Seungyeul Yoo et al.   PLoS Computational Biology

Robust and tissue-independent gender-specific transcript biomarkers

(2013) Frank Staedtler et al.   BIOMARKERS

GSVA: gene set variation analysis for microarray and RNA-Seq data

(2013) Sonja Hänzelmann et al.   BMC BIOINFORMATICS

hnRNP U Enhances Caspase-9 Splicing and Is Modulated by AKT-dependent Phosphorylation of hnRNP L

(2013) Ngoc T. Vu et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Identification of a unique TGF-β–dependent molecular and functional signature in microglia

(2013) Oleg Butovsky et al.   NATURE NEUROSCIENCE

Inferring tumour purity and stromal and immune cell admixture from expression data

(2013) Kosuke Yoshihara et al.   Nature Communications

Late Recruitment of Synapsin to Nascent Synapses Is Regulated by Cdk5

(2013) Courtney Easley-Neal et al.   Cell Reports

The many roles of the conserved eukaryotic Paf1 complex in regulating transcription, histone modifications, and disease states

(2012) Brett N. Tomson et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Copy Number Gain of 1q25 Predicts Poor Progression-Free Survival for Pediatric Intracranial Ependymomas and Enables Patient Risk Stratification: A Prospective European Clinical Trial Cohort Analysis on Behalf of the Children's Cancer Leukaemia Group (CCLG), Societe Francaise d'Oncologie Pediatrique (SFOP), and International Society for Pediatric Oncology (SIOP)

(2012) J.-P. Kilday et al.   CLINICAL CANCER RESEARCH

Ca2+-independent Activation of Ca2+/Calmodulin-dependent Protein Kinase II Bound to the C-terminal Domain of CaV2.1 Calcium Channels

(2012) Venkat G. Magupalli et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

MicroRNA-183 upregulates HIF-1α by targeting isocitrate dehydrogenase 2 (IDH2) in glioma cells

(2012) Hirotomo Tanaka et al.   JOURNAL OF NEURO-ONCOLOGY

Medulloblastoma exome sequencing uncovers subtype-specific somatic mutations

(2012) Trevor J. Pugh et al.   NATURE

Novel mutations target distinct subgroups of medulloblastoma

(2012) Giles Robinson et al.   NATURE

IDH Mutations in Human Glioma

(2012) Won Kim et al.   NEUROSURGERY CLINICS OF NORTH AMERICA

GSK3 as a Sensor Determining Cell Fate in the Brain

(2012) Adam R. Cole   Frontiers in Molecular Neuroscience

Molecular signatures database (MSigDB) 3.0

(2011) A. Liberzon et al.   BIOINFORMATICS

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

(2011) Bo Li et al.   BMC BIOINFORMATICS

Bioinformatic Prediction and Confirmation of β-Adducin as a Novel Substrate of Glycogen Synthase Kinase 3

(2011) Hovik Farghaian et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Ghrelin induces cell migration through GHS-R, CaMKII, AMPK, and NF-κB signaling pathway in glioma cells

(2011) Jia-Hong Chen et al.   JOURNAL OF CELLULAR BIOCHEMISTRY

β-Adducin Is Required for Stable Assembly of New Synapses and Improved Memory upon Environmental Enrichment

(2011) Ewa Bednarek et al.   NEURON

GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers

(2011) Craig H Mermel et al.   GENOME BIOLOGY

ConsensusClusterPlus: a class discovery tool with confidence assessments and item tracking

(2010) Matthew D. Wilkerson et al.   BIOINFORMATICS

The carboxyl tail of Cx43 augments p38 mediated cell migration in a gap junction-independent manner

(2010) Juliane Behrens et al.   EUROPEAN JOURNAL OF CELL BIOLOGY

Molecular Interaction and Functional Regulation of ClC-3 by Ca2+/Calmodulin-dependent Protein Kinase II (CaMKII) in Human Malignant Glioma

(2010) Vishnu Anand Cuddapah et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

The Genetic Landscape of the Childhood Cancer Medulloblastoma

(2010) D. W. Parsons et al.   SCIENCE

CTNNB1 Gene Mutations, Pituitary Transcription Factors, and MicroRNA Expression Involvement in the Pathogenesis of Adamantinomatous Craniopharyngiomas

(2010) Marina Lanciotti Campanini et al.   Hormones & Cancer

β-adducin (Add2) KO mice show synaptic plasticity, motor coordination and behavioral deficits accompanied by changes in the expression and phosphorylation levels of the α- and γ-adducin subunits

(2009) F. Porro et al.   GENES BRAIN AND BEHAVIOR

V600EBRAF is associated with disabled feedback inhibition of RAF-MEK signaling and elevated transcriptional output of the pathway

(2009) C. A. Pratilas et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Rab GTPases and their roles in brain neurons and glia

(2008) Ee Ling Ng et al.   BRAIN RESEARCH REVIEWS

MASIC: A software program for fast quantitation and flexible visualization of chromatographic profiles from detected LC–MS(/MS) features

(2008) Matthew E. Monroe et al.   COMPUTATIONAL BIOLOGY AND CHEMISTRY

Antiangiogenic therapy in brain tumors

(2008) Sajani S Lakka et al.   Expert Review of Neurotherapeutics

Spectral Probabilities and Generating Functions of Tandem Mass Spectra: A Strike against Decoy Databases

(2008) Sangtae Kim et al.   JOURNAL OF PROTEOME RESEARCH

Comprehensive genomic characterization defines human glioblastoma genes and core pathways

(2008) Roger McLendon et al.   NATURE