4.5 Article

Opportunities for pharmacoproteomics in biomarker discovery

Related references

Note: Only part of the references are listed.
Article Multidisciplinary Sciences

Machine learning for multi-omics data integration in cancer

Zhaoxiang Cai et al.

Summary: This article reviews the application of machine learning in multi-omics data analysis, including both general-purpose and task-specific methods. By benchmarking the performance of five machine learning approaches using data from the Cancer Cell Line Encyclopedia, recommendations are provided for method selection in specific applications. The importance of this research lies in promoting the development of novel machine learning methodologies, which will be critical for drug discovery, clinical trial design, and personalized treatments.

ISCIENCE (2022)

Article Multidisciplinary Sciences

Benchmarking of analysis strategies for data-independent acquisition proteomics using a large-scale dataset comprising inter-patient heterogeneity

Klemens Froehlich et al.

Summary: This study presents a benchmark dataset for evaluating DIA data analysis workflows in clinical settings, using real-world inter-patient heterogeneity. The results demonstrate the effectiveness of gas-phase fractionated spectral libraries and non-parametric permutation-based statistical tests for correctly identifying differentially abundant proteins in DIA analysis.

NATURE COMMUNICATIONS (2022)

Article Oncology

Pan-cancer proteomic map of 949 human cell lines

Emanuel Goncalves et al.

Summary: The study analyzes the proteomes of multiple cancer cell lines through mass spectrometry and reveals thousands of cancer protein biomarkers that are not significant at the transcript level, demonstrating that the proteome has predictive power for drug response similar to the transcriptome.

CANCER CELL (2022)

Review Biochemistry & Molecular Biology

Computational estimation of quality and clinical relevance of cancer cell lines

Lucia Trastulla et al.

Summary: Immortal cancer cell lines (CCLs) are widely used in cancer biology research and preclinical development of oncology therapies. However, there are limitations to using CCLs as tumor proxies, and it is important to develop more accurate in vitro models. This article discusses the limitations of CCLs and reviews computational methods for evaluating their suitability as tumor proxies, as well as identifying the best in vitro patient representative models.

MOLECULAR SYSTEMS BIOLOGY (2022)

Article Multidisciplinary Sciences

HarmonizR enables data harmonization across independent proteomic datasets with appropriate handling of missing values

Hannah Voss et al.

Summary: HarmonizR is an efficient tool for missing data tolerant experimental variance reduction, which does not require data imputation and can be easily adjusted for individual dataset properties and user preferences. It demonstrated successful data harmonization for different tissue preservation techniques, LC-MS/MS instrumentation setups, and quantification approaches, and outperformed data imputation methods in detecting significant proteins.

NATURE COMMUNICATIONS (2022)

Review Biochemical Research Methods

A review of COVID-19 biomarkers and drug targets: resources and tools

Francesca P. Caruso et al.

Summary: The bioinformatics community has responded to the outbreak emergency by providing tools and resources to identify biomarkers and drug targets for COVID-19. The topics selected cover a range of areas from machine learning and artificial intelligence for disease characterization to vaccine development and therapeutic target identification. The global cooperation and unprecedented example of knowledge, data, and tools generated so far signify a long road ahead to defeat the pandemic.

BRIEFINGS IN BIOINFORMATICS (2021)

Article Multidisciplinary Sciences

A genome-scale CRISPR screen reveals factors regulating Wnt-dependent renewal of mouse gastric epithelial cells

Kazuhiro Murakami et al.

Summary: Safe utilization of the regenerative potential of adult stem cells for clinical applications requires a comprehensive understanding of the regulatory mechanisms. Epithelial organoid cultures accurately mimic in vivo stem cell-driven epithelial renewal, offering a great ex vivo platform for studying key regulatory mechanisms. Through genome-scale CRISPR knockout screening, Alk, Bclaf3, and Prkra were identified as potential regulators of gastric epithelial differentiation and could suppress stemness/proliferation.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2021)

Review Biochemistry & Molecular Biology

The next horizon in precision oncology: Proteogenomics to inform cancer diagnosis and treatment

Henry Rodriguez et al.

Summary: Proteogenomics plays a crucial role in precision oncology, offering more accurate methods for the diagnosis and treatment of tumors. The full integration of proteogenomics into clinical trials and patient care is necessary for precision oncology to deliver the right cancer treatment to the right patient at the right dose and at the right time.
Review Biochemistry & Molecular Biology

Large-scale pharmacogenomic studies and drug response prediction for personalized cancer medicine

Fangyoumin Feng et al.

Summary: The response rate of most anti-cancer drugs is limited due to cancer heterogeneity and complex drug mechanisms. Personalized treatment using molecular biomarkers shows promise. Advances in pharmacogenomics, especially computational methods in drug response prediction, have been successful and increasingly utilized in personalized cancer medicine.

JOURNAL OF GENETICS AND GENOMICS (2021)

Article Biochemistry & Molecular Biology

Artificial intelligence to deep learning: machine intelligence approach for drug discovery

Rohan Gupta et al.

Summary: Drug designing and development faces challenges in terms of low efficacy, high cost, and complexity of data. However, artificial intelligence and machine learning technologies play a crucial role in overcoming these challenges and advancing the field.

MOLECULAR DIVERSITY (2021)

Article Biochemical Research Methods

Improved identification and quantification of peptides in mass spectrometry data via chemical and random additive noise elimination (CRANE)

Akila J. Seneviratne et al.

Summary: This study introduces a novel technique for denoising raw ESI-LC-MS data using 2D undecimated wavelet transform, which is applied to proteomics data acquired by DIA-MS, leading to improved peptide identification and quantification in complex biological samples.

BIOINFORMATICS (2021)

Article Multidisciplinary Sciences

SARS-CoV-2 RNAemia and proteomic trajectories inform prognostication in COVID-19 patients admitted to intensive care

Clemens Gutmann et al.

Summary: Prognostic characteristics for ICU COVID-19 patients can be determined using blood samples, with RNAemia and pentraxin-3 identified as predictors of 28-day ICU mortality. Additionally, galectin-3-binding protein is found to interact with the SARS-CoV-2 spike glycoprotein and exhibit antiviral properties.

NATURE COMMUNICATIONS (2021)

Article Biochemistry & Molecular Biology

A time-resolved proteomic and prognostic map of COVID-19

Vadim Demichev et al.

Summary: This study investigates the time-dependent progression of COIVD-19 inpatients by measuring diagnostic parameters and plasma proteomes, revealing an initial spike in inflammatory response followed by tissue repair and immunomodulation. Prognostic marker signatures for treatment strategies were identified and machine learning models based on proteome show transferability to independent cohorts.

CELL SYSTEMS (2021)

Article Multidisciplinary Sciences

Identification of serum prognostic biomarkers of severe COVID-19 using a quantitative proteomic approach

Yayoi Kimura et al.

Summary: The COVID-19 pandemic poses a significant threat to global health, and accurately predicting disease progression is crucial for determining the best treatment options. Using proteomic approaches, researchers have identified potential serum proteins associated with COVID-19 prognosis. The findings suggest that CHI3L1 and IGFALS could serve as highly sensitive prognostic markers, aiding in the diagnosis and treatment of severe COVID-19 cases.

SCIENTIFIC REPORTS (2021)

Article Biochemical Research Methods

DIA-NN: neural networks and interference correction enable deep proteome coverage in high throughput

Vadim Demichev et al.

NATURE METHODS (2020)

Article Biochemistry & Molecular Biology

Quantitative Proteomics of the Cancer Cell Line Encyclopedia

David P. Nusinow et al.

Article Biochemical Research Methods

High-throughput screening of human induced pluripotent stem cell-derived brain organoids

Madel Durens et al.

JOURNAL OF NEUROSCIENCE METHODS (2020)

Article Computer Science, Artificial Intelligence

Explainable Artificial Intelligence (XAI): Concepts, taxonomies, opportunities and challenges toward responsible AI

Alejandro Barredo Arrieta et al.

INFORMATION FUSION (2020)

Article Biochemistry & Molecular Biology

Drug mechanism-of-action discovery through the integration of pharmacological andCRISPRscreens

Emanuel Goncalves et al.

MOLECULAR SYSTEMS BIOLOGY (2020)

Review Cell Biology

Human organoids: model systems for human biology and medicine

Jihoon Kim et al.

NATURE REVIEWS MOLECULAR CELL BIOLOGY (2020)

Article Multidisciplinary Sciences

Proteome activity landscapes of tumor cell lines determine drug responses

Martin Frejno et al.

NATURE COMMUNICATIONS (2020)

Article Multidisciplinary Sciences

Strategies to enable large-scale proteomics for reproducible research

Rebecca C. Poulos et al.

NATURE COMMUNICATIONS (2020)

Article Biochemical Research Methods

diaPASEF: parallel accumulation-serial fragmentation combined with data-independent acquisition

Florian Meier et al.

NATURE METHODS (2020)

Article Multidisciplinary Sciences

Next-generation characterization of the Cancer Cell Line Encyclopedia

Mahmoud Ghandi et al.

NATURE (2019)

Article Biochemistry & Molecular Biology

PDX Finder: A portal for patient-derived tumor xenograft model discovery

Nathalie Conte et al.

NUCLEIC ACIDS RESEARCH (2019)

Article Multidisciplinary Sciences

Quantitative Proteome Landscape of the NCI-60 Cancer Cell Lines

Tiannan Guo et al.

ISCIENCE (2019)

Article Biochemistry & Molecular Biology

DrugBank 5.0: a major update to the DrugBank database for 2018

David S. Wishart et al.

NUCLEIC ACIDS RESEARCH (2018)

Review Biochemical Research Methods

Automated Cell Culture Systems and Their Applications to Human Pluripotent Stem Cell Studies

Maciej Daniszewski et al.

SLAS TECHNOLOGY (2018)

Review Oncology

The Generation and Application of Patient-Derived Xenograft Model for Cancer Research

Jaeyun Jung et al.

CANCER RESEARCH AND TREATMENT (2018)

Review Biochemistry & Molecular Biology

Data-independent acquisition-based SWATH-MS for quantitative proteomics: a tutorial

Christina Ludwig et al.

MOLECULAR SYSTEMS BIOLOGY (2018)

Article Biochemical Research Methods

TCGA-assembler 2: software pipeline for retrieval and processing of TCGA/CPTAC data

Lin Wei et al.

BIOINFORMATICS (2018)

Review Biochemistry & Molecular Biology

Integrating Pharmacoproteomics into Early-Phase Clinical Development: State-of-the-Art, Challenges, and Recommendations

Savita Nandal et al.

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2017)

Article Oncology

Personalized In Vitro and In Vivo Cancer Models to Guide Precision Medicine

Chantal Pauli et al.

CANCER DISCOVERY (2017)

Editorial Material Chemistry, Medicinal

The Promises of Quantitative Proteomics in Precision Medicine

Bhagwat Prasad et al.

JOURNAL OF PHARMACEUTICAL SCIENCES (2017)

Review Oncology

Tumor-Derived Cell Lines as Molecular Models of Cancer Pharmacogenomics

Andrew Goodspeed et al.

MOLECULAR CANCER RESEARCH (2016)

Article Multidisciplinary Sciences

Can we open the black box of AI?

Davide Castelvecchi

NATURE (2016)

Article Biochemistry & Molecular Biology

Prospective Derivation of a Living Organoid Biobank of Colorectal Cancer Patients

Marc van de Wetering et al.

Article Biochemical Research Methods

The CPTAC Data Portal: A Resource for Cancer Proteomics Research

Nathan J. Edwards et al.

JOURNAL OF PROTEOME RESEARCH (2015)

Article Multidisciplinary Sciences

Pharmacogenomic agreement between two cancer cell line data sets

Nicolas Stransky et al.

NATURE (2015)

Review Multidisciplinary Sciences

Machine learning: Trends, perspectives, and prospects

M. I. Jordan et al.

SCIENCE (2015)

Letter Biotechnology & Applied Microbiology

OpenSWATH enables automated, targeted analysis of data-independent acquisition MS data

Hannes L. Roest et al.

NATURE BIOTECHNOLOGY (2014)

Article Multidisciplinary Sciences

A repository of assays to quantify 10,000 human proteins by SWATH-MS

George Rosenberger et al.

SCIENTIFIC DATA (2014)

Article Oncology

Significance of immunohistochemistry in breast cancer

Dana Carmen Zaha

WORLD JOURNAL OF CLINICAL ONCOLOGY (2014)

Article Biochemistry & Molecular Biology

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

Wanjuan Yang et al.

NUCLEIC ACIDS RESEARCH (2013)

Article Cell Biology

Global Proteome Analysis of the NCI-60 Cell Line Panel

Amin Moghaddas Gholami et al.

CELL REPORTS (2013)

Review Oncology

Cancer biomarkers

N. Lynn Henry et al.

MOLECULAR ONCOLOGY (2012)

Article Multidisciplinary Sciences

Systematic identification of genomic markers of drug sensitivity in cancer cells

Mathew J. Garnett et al.

NATURE (2012)

Article Medicine, General & Internal

Improved Survival with Vemurafenib in Melanoma with BRAF V600E Mutation

Paul B. Chapman et al.

NEW ENGLAND JOURNAL OF MEDICINE (2011)

Article Oncology

Supervised Risk Predictor of Breast Cancer Based on Intrinsic Subtypes

Joel S. Parker et al.

JOURNAL OF CLINICAL ONCOLOGY (2009)

Review Biochemistry & Molecular Biology

The role of drug-metabolising enzymes in clinical responses to chemotherapy

Charity D. Scripture et al.

EXPERT OPINION ON DRUG METABOLISM & TOXICOLOGY (2006)

Correction Biochemical Research Methods

UPLC/MSE; a new approach for generating molecular fragment information for biomarker structure elucidation (vol 20, pg 1989, 2006)

Robert S. Plumb et al.

RAPID COMMUNICATIONS IN MASS SPECTROMETRY (2006)

Review Genetics & Heredity

Pharmacoproteomics in drug development

FA Witzmann et al.

PHARMACOGENOMICS JOURNAL (2003)