Deciphering the signaling network of breast cancer improves drug sensitivity prediction

Why geneticists stole cancer research even though cancer is primarily a signaling disease

(2019) Michael B. Yaffe   Science Signaling

Personalization of Logical Models With Multi-Omics Data Allows Clinical Stratification of Patients

(2019) Jonas Béal et al.   Frontiers in Physiology

Dynamics of breast-cancer relapse reveal late-recurring ER-positive genomic subgroups

(2019) Oscar M. Rueda et al.   NATURE

Analysis of the Human Kinome and Phosphatome by Mass Cytometry Reveals Overexpression-Induced Effects on Cancer-Related Signaling

(2019) Xiao-Kang Lun et al.   MOLECULAR CELL

Next-generation characterization of the Cancer Cell Line Encyclopedia

(2019) Mahmoud Ghandi et al.   NATURE

Functional linkage of gene fusions to cancer cell fitness assessed by pharmacological and CRISPR-Cas9 screening

(2019) Gabriele Picco et al.   Nature Communications

EP300 and SIRT1/6 Co-Regulate Lapatinib Sensitivity Via Modulating FOXO3-Acetylation and Activity in Breast Cancer

(2019) Zimam Mahmud et al.   Cancers

Silencinglnc-ASAH2B-2Inhibits Breast Cancer Cell Growthviathe mTOR Pathway

(2018) JINGJING LI et al.   ANTICANCER RESEARCH

A Map of Protein-Metabolite Interactions Reveals Principles of Chemical Communication

(2018) Ilaria Piazza et al.   CELL

Oncogenic Signaling Pathways in The Cancer Genome Atlas

(2018) Francisco Sanchez-Vega et al.   CELL

Linking drug target and pathway activation for effective therapy using multi-task learning

(2018) Mi Yang et al.   Scientific Reports

GOATOOLS: A Python library for Gene Ontology analyses

(2018) D. V. Klopfenstein et al.   Scientific Reports

Compensation of Signal Spillover in Suspension and Imaging Mass Cytometry

(2018) Stéphane Chevrier et al.   Cell Systems

The germline genetic component of drug sensitivity in cancer cell lines

(2018) Michael P. Menden et al.   Nature Communications

Cell-to-Cell Heterogeneity in p38-Mediated Cross-Inhibition of JNK Causes Stochastic Cell Death

(2018) Haruko Miura et al.   Cell Reports

Efficient Parameter Estimation Enables the Prediction of Drug Response Using a Mechanistic Pan-Cancer Pathway Model

(2018) Fabian Fröhlich et al.   Cell Systems

MEK inhibitors under development for treatment of non-small-cell lung cancer

(2017) Chul Kim et al.   EXPERT OPINION ON INVESTIGATIONAL DRUGS

Buparlisib plus fulvestrant versus placebo plus fulvestrant in postmenopausal, hormone receptor-positive, HER2-negative, advanced breast cancer (BELLE-2): a randomised, double-blind, placebo-controlled, phase 3 trial

(2017) José Baselga et al.   LANCET ONCOLOGY

Influence of node abundance on signaling network state and dynamics analyzed by mass cytometry

(2017) Xiao-Kang Lun et al.   NATURE BIOTECHNOLOGY

Accelerating Live Single-Cell Signalling Studies

(2017) Sam Cooper et al.   TRENDS IN BIOTECHNOLOGY

Apobec-1 complementation factor regulates cell migration and apoptosis through Dickkopf1 by acting on its 3′ untranslated region in MCF7 cells

(2017) Xin Yan et al.   TUMOR BIOLOGY

Functional Genomic Landscape of Human Breast Cancer Drivers, Vulnerabilities, and Resistance

(2016) Richard Marcotte et al.   CELL

A Landscape of Pharmacogenomic Interactions in Cancer

(2016) Francesco Iorio et al.   CELL

A Biobank of Breast Cancer Explants with Preserved Intra-tumor Heterogeneity to Screen Anticancer Compounds

(2016) Alejandra Bruna et al.   CELL

Phase II Randomized Preoperative Window-of-Opportunity Study of the PI3K Inhibitor Pictilisib Plus Anastrozole Compared With Anastrozole Alone in Patients With Estrogen Receptor–Positive Breast Cancer

(2016) Peter Schmid et al.   JOURNAL OF CLINICAL ONCOLOGY

Pictilisib for oestrogen receptor-positive, aromatase inhibitor-resistant, advanced or metastatic breast cancer (FERGI): a randomised, double-blind, placebo-controlled, phase 2 trial

(2016) Ian E Krop et al.   LANCET ONCOLOGY

EGFR Is Regulated by TFAP2C in Luminal Breast Cancer and Is a Target for Vandetanib

(2016) J. P. De Andrade et al.   MOLECULAR CANCER THERAPEUTICS

Landscape of somatic mutations in 560 breast cancer whole-genome sequences

(2016) Serena Nik-Zainal et al.   NATURE

OmniPath: guidelines and gateway for literature-curated signaling pathway resources

(2016) Dénes Türei et al.   NATURE METHODS

DisGeNET: a comprehensive platform integrating information on human disease-associated genes and variants

(2016) Janet Piñero et al.   NUCLEIC ACIDS RESEARCH

HER Specific TKIs Exert Their Antineoplastic Effects on Breast Cancer Cell Lines through the Involvement of STAT5 and JNK

(2016) Daphne Gschwantler-Kaulich et al.   PLoS One

The somatic mutation profiles of 2,433 breast cancers refines their genomic and transcriptomic landscapes

(2016) Bernard Pereira et al.   Nature Communications

Proteomic maps of breast cancer subtypes

(2016) Stefka Tyanova et al.   Nature Communications

System-wide Clinical Proteomics of Breast Cancer Reveals Global Remodeling of Tissue Homeostasis

(2016) Yair Pozniak et al.   Cell Systems

Tailoring therapies—improving the management of early breast cancer: St Gallen International Expert Consensus on the Primary Therapy of Early Breast Cancer 2015

(2015) A. S. Coates et al.   ANNALS OF ONCOLOGY

MEK-independent ERK activation in human neutrophils and its impact on functional responses

(2015) F. A. Simard et al.   JOURNAL OF LEUKOCYTE BIOLOGY

Ranking Fragment Ions Based on Outlier Detection for Improved Label-Free Quantification in Data-Independent Acquisition LC–MS/MS

(2015) Aivett Bilbao et al.   JOURNAL OF PROTEOME RESEARCH

Extending the Limits of Quantitative Proteome Profiling with Data-Independent Acquisition and Application to Acetaminophen-Treated Three-Dimensional Liver Microtissues

(2015) Roland Bruderer et al.   MOLECULAR & CELLULAR PROTEOMICS

Palladium-based mass tag cell barcoding with a doublet-filtering scheme and single-cell deconvolution algorithm

(2015) Eli R Zunder et al.   Nature Protocols

Signaling pathway models as biomarkers: Patient-specific simulations of JNK activity predict the survival of neuroblastoma patients

(2015) D. Fey et al.   Science Signaling

Signaling pathway models as biomarkers: Patient-specific simulations of JNK activity predict the survival of neuroblastoma patients

(2015) D. Fey et al.   Science Signaling

MSstats: an R package for statistical analysis of quantitative mass spectrometry-based proteomic experiments

(2014) Meena Choi et al.   BIOINFORMATICS

Rapamycin: One Drug, Many Effects

(2014) Jing Li et al.   Cell Metabolism

Natural genetic variation impacts expression levels of coding, non-coding, and antisense transcripts in fission yeast

(2014) M. Clement-Ziza et al.   Molecular Systems Biology

A community effort to assess and improve drug sensitivity prediction algorithms

(2014) James C Costello et al.   NATURE BIOTECHNOLOGY

Making models match measurements: Model optimization for morphogen patterning networks

(2014) J.B. Hengenius et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

Normalization of mass cytometry data with bead standards

(2013) Rachel Finck et al.   CYTOMETRY PART A

Network quantification of EGFR signaling unveils potential for targeted combination therapy

(2013) B. Klinger et al.   Molecular Systems Biology

Protein kinase C and cancer: what we know and what we do not

(2013) R Garg et al.   ONCOGENE

Profiles of Basal and Stimulated Receptor Signaling Networks Predict Drug Response in Breast Cancer Lines

(2013) M. Niepel et al.   Science Signaling

Overexpression of MACC1 and Its significance in human Breast Cancer Progression

(2013) Yongbo Huang et al.   Cell and Bioscience

Global Proteome Analysis of the NCI-60 Cell Line Panel

(2013) Amin Moghaddas Gholami et al.   Cell Reports

CellNOptR: a flexible toolkit to train protein signaling networks to data using multiple logic formalisms

(2012) Camille Terfve et al.   BMC Systems Biology

Differential expression of immune-related markers in breast cancer by molecular phenotypes

(2012) Junjeong Choi et al.   BREAST CANCER RESEARCH AND TREATMENT

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

(2012) Michael J. Lee et al.   CELL

PIK3CA/PTEN Mutations and Akt Activation As Markers of Sensitivity to Allosteric mTOR Inhibitors

(2012) F. Meric-Bernstam et al.   CLINICAL CANCER RESEARCH

Targeted Data Extraction of the MS/MS Spectra Generated by Data-independent Acquisition: A New Concept for Consistent and Accurate Proteome Analysis

(2012) Ludovic C. Gillet et al.   MOLECULAR & CELLULAR PROTEOMICS

Systematic identification of genomic markers of drug sensitivity in cancer cells

(2012) Mathew J. Garnett et al.   NATURE

The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity

(2012) Jordi Barretina et al.   NATURE

Comprehensive molecular portraits of human breast tumours

(2012) Daniel C. Koboldt et al.   NATURE

The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups

(2012) Christina Curtis et al.   NATURE

Multiplexed mass cytometry profiling of cellular states perturbed by small-molecule regulators

(2012) Bernd Bodenmiller et al.   NATURE BIOTECHNOLOGY

The E3 ligase RNF8 regulates KU80 removal and NHEJ repair

(2012) Lin Feng et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Genomics of Drug Sensitivity in Cancer (GDSC): a resource for therapeutic biomarker discovery in cancer cells

(2012) Wanjuan Yang et al.   NUCLEIC ACIDS RESEARCH

Resistance to HER2-directed antibodies and tyrosine kinase inhibitors

(2011) Joan T. Garrett et al.   CANCER BIOLOGY & THERAPY

The proliferation rate paradox in antimitotic chemotherapy

(2011) Timothy J. Mitchison   MOLECULAR BIOLOGY OF THE CELL

Combating trastuzumab resistance by targeting SRC, a common node downstream of multiple resistance pathways

(2011) Siyuan Zhang et al.   NATURE MEDICINE

mProphet: automated data processing and statistical validation for large-scale SRM experiments

(2011) Lukas Reiter et al.   NATURE METHODS

Subtype and pathway specific responses to anticancer compounds in breast cancer

(2011) L. M. Heiser et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Data-driven assessment of eQTL mapping methods

(2010) Jacob J Michaelson et al.   BMC GENOMICS

Lapatinib in breast cancer: clinical experiences and future perspectives

(2010) M. Giampaglia et al.   CANCER TREATMENT REVIEWS

BCR-ABL tyrosine kinase inhibitors in the treatment of Philadelphia chromosome positive chronic myeloid leukemia: A review

(2010) Xin An et al.   LEUKEMIA RESEARCH

PPM1D gene amplification and overexpression in breast cancer: a qRT-PCR and chromogenic in situ hybridization study

(2010) Maryou B Lambros et al.   MODERN PATHOLOGY

COSMIC: mining complete cancer genomes in the Catalogue of Somatic Mutations in Cancer

(2010) S. A. Forbes et al.   NUCLEIC ACIDS RESEARCH

Transforming Boolean models to continuous models: methodology and application to T-cell receptor signaling

(2009) Dominik M Wittmann et al.   BMC Systems Biology

Differential activation of p38MAPK isoforms by MKK6 and MKK3

(2009) Gaëlle Remy et al.   CELLULAR SIGNALLING

Detection and interpretation of expression quantitative trait loci (eQTL)

(2009) Jacob J. Michaelson et al.   METHODS

The Identification of 2-(1H-Indazol-4-yl)-6-(4-methanesulfonyl-piperazin-1-ylmethyl)-4-morpholin-4-yl-thieno[3,2-d]pyrimidine (GDC-0941) as a Potent, Selective, Orally Bioavailable Inhibitor of Class I PI3 Kinase for the Treatment of Cancer†

(2008) Adrian J. Folkes et al.   JOURNAL OF MEDICINAL CHEMISTRY