A proteomic landscape of pharmacologic perturbations for functional relevance

[1]  Devin K. Schweppe,et al.  A proteome-wide atlas of drug mechanism of action , 2023, Nature Biotechnology.

[2]  Andy Liaw,et al.  A mass spectrometry-based proteome map of drug action in lung cancer cell lines , 2020, Nature Chemical Biology.

[3]  P. Spellman,et al.  Large-scale Characterization of Drug Responses of Clinically Relevant Proteins in Cancer Cell Lines , 2020, bioRxiv.

[4]  Bin Liu,et al.  The novel cereblon modulator CC-885 inhibits mitophagy via selective degradation of BNIP3L , 2020, Acta Pharmacologica Sinica.

[5]  E. Robert McDonald,et al.  Quantitative Proteomics of the Cancer Cell Line Encyclopedia , 2020, Cell.

[6]  Roman A. Zubarev,et al.  ProTargetMiner as a proteome signature library of anticancer molecules for functional discovery , 2019, Nature Communications.

[7]  Qing‐Yu He,et al.  Benzethonium chloride suppresses lung cancer tumorigenesis through inducing p38-mediated cyclin D1 degradation. , 2019, American journal of cancer research.

[8]  Guo Ci Teo,et al.  Integrated Proteogenomic Characterization of Clear Cell Renal Cell Carcinoma , 2019, Cell.

[9]  Ying Zhu,et al.  High-Throughput Single Cell Proteomics Enabled by Multiplex Isobaric Labelling in a Nanodroplet Sample Preparation Platform. , 2019, Analytical chemistry.

[10]  Qing‐Yu He,et al.  Proteomic Analysis Reveals that Odoroside A Triggers G2/M Arrest and Apoptosis in Colorectal Carcinoma Through ROS‐p53 Pathway , 2019, Proteomics.

[11]  R. Raggiaschi,et al.  Moonlighting Proteins and Cardiopathy in the Spatial Response of MCF‐7 Breast Cancer Cells to Tamoxifen , 2019, Proteomics. Clinical applications.

[12]  Natalie S. Fox,et al.  The Proteogenomic Landscape of Curable Prostate Cancer. , 2019, Cancer cell.

[13]  C. Ludwig,et al.  Analyzing bioactive effects of the minor hop compound xanthohumol C on human breast cancer cells using quantitative proteomics , 2019, PloS one.

[14]  Harald Mischak,et al.  Proteomics in Drug Development: The Dawn of a New Era? , 2019, Proteomics. Clinical applications.

[15]  U. Aryal,et al.  Proteomic Analysis Reveals That an Extract of the Plant Lippia origanoides Suppresses Mitochondrial Metabolism in Triple-Negative Breast Cancer Cells. , 2018, Journal of proteome research.

[16]  Min Huang,et al.  Targeting Epigenetic Crosstalk as a Therapeutic Strategy for EZH2-Aberrant Solid Tumors , 2018, Cell.

[17]  B. Ebert,et al.  Thalidomide promotes degradation of SALL4, a transcription factor implicated in Duane Radial Ray syndrome , 2018, eLife.

[18]  Fan Zhang,et al.  Integrative Analysis of Proteome and Ubiquitylome Reveals Unique Features of Lysosomal and Endocytic Pathways in Gefitinib‐Resistant Non‐Small Cell Lung Cancer Cells , 2018, Proteomics.

[19]  Peter W. Laird,et al.  Cell-of-Origin Patterns Dominate the Molecular Classification of 10,000 Tumors from 33 Types of Cancer , 2018, Cell.

[20]  Zhiwei Wu,et al.  Ultradeep Lysine Crotonylome Reveals the Crotonylation Enhancement on Both Histones and Nonhistone Proteins by SAHA Treatment. , 2017, Journal of proteome research.

[21]  Michael J. MacCoss,et al.  A Library of Phosphoproteomic and Chromatin Signatures for Characterizing Cellular Responses to Drug Perturbations , 2017, bioRxiv.

[22]  Antoine de Weck,et al.  Project DRIVE: A Compendium of Cancer Dependencies and Synthetic Lethal Relationships Uncovered by Large-Scale, Deep RNAi Screening , 2017, Cell.

[23]  Phillip G. Montgomery,et al.  Defining a Cancer Dependency Map , 2017, Cell.

[24]  Ann E. Sizemore,et al.  Computational correction of copy-number effect improves specificity of CRISPR-Cas9 essentiality screens in cancer cells , 2017, Nature Genetics.

[25]  M. Prunotto,et al.  Opportunities and challenges in phenotypic drug discovery: an industry perspective , 2017, Nature Reviews Drug Discovery.

[26]  Qing‐Yu He,et al.  Isodeoxyelephantopin induces protective autophagy in lung cancer cells via Nrf2-p62-keap1 feedback loop , 2017, Cell Death & Disease.

[27]  Angela N. Brooks,et al.  A Next Generation Connectivity Map: L1000 Platform and the First 1,000,000 Profiles , 2017, Cell.

[28]  Yi Wang,et al.  Quantitative proteomics profiling reveals activation of mTOR pathway in trastuzumab resistance , 2017, Oncotarget.

[29]  I. Amelio,et al.  Polypharmacology of Approved Anticancer Drugs. , 2017, Current drug targets.

[30]  Hui Zhang,et al.  Proteomics analyses of prostate cancer cells reveal cellular pathways associated with androgen resistance , 2017, Proteomics.

[31]  Rodrigo Dienstmann,et al.  Genomic Determinants of Protein Abundance Variation in Colorectal Cancer Cells , 2016, bioRxiv.

[32]  Jordi Mestres,et al.  Polypharmacology in Precision Oncology: Current Applications and Future 
Prospects , 2016, Current pharmaceutical design.

[33]  A. Cifuentes,et al.  Nano-liquid Chromatography-orbitrap MS-based Quantitative Proteomics Reveals Differences Between the Mechanisms of Action of Carnosic Acid and Carnosol in Colon Cancer Cells* , 2016, Molecular & Cellular Proteomics.

[34]  Alejandro Cifuentes,et al.  Comprehensive Proteomic Study of the Antiproliferative Activity of a Polyphenol-Enriched Rosemary Extract on Colon Cancer Cells Using Nanoliquid Chromatography-Orbitrap MS/MS. , 2016, Journal of proteome research.

[35]  Michael L. Gatza,et al.  Proteogenomics connects somatic mutations to signaling in breast cancer , 2016, Nature.

[36]  Richard H. Baltz,et al.  Natural product discovery: past, present, and future , 2016, Journal of Industrial Microbiology & Biotechnology.

[37]  S. Gygi,et al.  Proteomic Profiling of Paclitaxel Treated Cells Identifies a Novel Mechanism of Drug Resistance Mediated by PDCD4. , 2015, Journal of proteome research.

[38]  O. Jensen,et al.  Modulation of Cell Metabolic Pathways and Oxidative Stress Signaling Contribute to Acquired Melphalan Resistance in Multiple Myeloma Cells , 2015, PloS one.

[39]  P. Bork,et al.  Histone Deacetylase Inhibitors (HDACi) Cause the Selective Depletion of Bromodomain Containing Proteins (BCPs)* , 2015, Molecular & Cellular Proteomics.

[40]  Ya-xin Lou,et al.  YSY01A, a Novel Proteasome Inhibitor, Induces Cell Cycle Arrest on G2 Phase in MCF-7 Cells via ERα and PI3K/Akt Pathways , 2015, Journal of Cancer.

[41]  M. Kinch,et al.  An overview of FDA-approved new molecular entities: 1827-2013. , 2014, Drug discovery today.

[42]  Arnold L. Demain,et al.  Importance of microbial natural products and the need to revitalize their discovery , 2014, Journal of Industrial Microbiology & Biotechnology.

[43]  Christopher J. Ott,et al.  The Myeloma Drug Lenalidomide Promotes the Cereblon-Dependent Destruction of Ikaros Proteins , 2014, Science.

[44]  S. Carr,et al.  Lenalidomide Causes Selective Degradation of IKZF1 and IKZF3 in Multiple Myeloma Cells , 2014, Science.

[45]  T. Kunoh,et al.  A novel tamoxifen derivative, ridaifen-F, is a nonpeptidic small-molecule proteasome inhibitor. , 2014, European journal of medicinal chemistry.

[46]  P. Johnston,et al.  Cancer drug resistance: an evolving paradigm , 2013, Nature Reviews Cancer.

[47]  D. Newman,et al.  Microbial natural products: molecular blueprints for antitumor drugs , 2013, Journal of Industrial Microbiology & Biotechnology.

[48]  Weiqing Wang,et al.  Perturbation Biology: Inferring Signaling Networks in Cellular Systems , 2013, PLoS Comput. Biol..

[49]  J. Peters.  Polypharmacology - foe or friend? , 2013, Journal of medicinal chemistry.

[50]  Syreeta L. Tilghman,et al.  Proteomic Signatures of Acquired Letrozole Resistance in Breast Cancer: Suppressed Estrogen Signaling and Increased Cell Motility and Invasiveness* , 2013, Molecular & Cellular Proteomics.

[51]  Brian L Hood,et al.  Mitochondrial proteomic analysis of cisplatin resistance in ovarian cancer. , 2012, Journal of proteome research.

[52]  Xinning Jiang,et al.  Quantitative proteomic analysis revealed lovastatin-induced perturbation of cellular pathways in HL-60 cells. , 2011, Journal of proteome research.

[53]  David M. Simcha,et al.  Tackling the widespread and critical impact of batch effects in high-throughput data , 2010, Nature Reviews Genetics.

[54]  Toshihiko Ogura,et al.  Identification of a Primary Target of Thalidomide Teratogenicity , 2010, Science.

[55]  P. Leeson,et al.  The influence of drug-like concepts on decision-making in medicinal chemistry , 2007, Nature Reviews Drug Discovery.

[56]  Jeremy R. Greenwood,et al.  Epik: a software program for pKa prediction and protonation state generation for drug-like molecules , 2007, J. Comput. Aided Mol. Des..

[57]  Paul A Clemons,et al.  The Connectivity Map: Using Gene-Expression Signatures to Connect Small Molecules, Genes, and Disease , 2006, Science.

[58]  Di Chen,et al.  Dietary flavonoids as proteasome inhibitors and apoptosis inducers in human leukemia cells. , 2005, Biochemical pharmacology.

[59]  V. Jordan,et al.  Tamoxifen: a most unlikely pioneering medicine , 2003, Nature Reviews Drug Discovery.

[60]  Jacob D. Jaffe,et al.  Next-generation characterization of the Cancer Cell Line Encyclopedia , 2019, Nature.

[61]  S. Dutta.  Natural sources as potential anti-cancer agents: A review , 2015 .

[62]  Cheng Li,et al.  Adjusting batch effects in microarray expression data using empirical Bayes methods. , 2007, Biostatistics.