4.3 Article

Proteomic and phosphoproteomic measurements enhance ability to predict ex vivo drug response in AML

Related references

Note: Only part of the references are listed.
Article Hematology

Clinical relevance of proteomic profiling in de novo pediatric acute myeloid leukemia: a Children's Oncology Group study

Fieke W. Hoff et al.

Summary: This study investigated the proteomic landscape of pediatric acute myeloid leukemia (AML) and identified nine protein expression signatures associated with cytogenetics, mutational state, and prognosis. The study also found certain proteins that were significantly differentially expressed from normal, potentially forming a platform for personalized medicine.

HAEMATOLOGICA (2022)

Article Hematology

Venetoclax combines synergistically with FLT3 inhibition to effectively target leukemic cells in FLT3-ITD+ acute myeloid leukemia models

Raghuveer Singh Mali et al.

Summary: The combination of FLT3-ITD inhibition with venetoclax demonstrates impressive anti-tumor activity in FLT3-ITD+ AML preclinical models, highlighting the strong mechanistic rationale for clinical studies.

HAEMATOLOGICA (2021)

Article Oncology

Proteogenomic insights into the biology and treatment of HPV-negative head and neck squamous cell carcinoma

Chen Huang et al.

Summary: This study presents a proteogenomic analysis of HPV-negative HNSCCs, identifying potential therapeutic targets and uncovering tumor characteristics such as immune status and resistance mechanisms. The findings suggest new strategies for stratifying HNSCC and improving treatment outcomes.

CANCER CELL (2021)

Article Biochemistry & Molecular Biology

The STRING database in 2021: customizable protein-protein networks, and functional characterization of user-uploaded gene/measurement sets

Damian Szklarczyk et al.

Summary: The STRING database integrates various associations between proteins, including physical interactions and functional associations, by collecting evidence from sources such as literature, databases, computational predictions, and systematic transfers. STRING aims for wide coverage and provides extensive user interface features and querying methods for experimental data.

NUCLEIC ACIDS RESEARCH (2021)

Article Oncology

Proteogenomic and metabolomic characterization of human glioblastoma

Liang-Bo Wang et al.

Summary: Understanding the molecular pathogenesis of glioblastoma is crucial for improving diagnosis and treatment. Integrated analysis of genomic, proteomic, and metabolomic data on treatment-naive glioblastomas has identified key phosphorylation events and potential targets for specific tumor alterations. Immune subtypes with distinct immune cell types were discovered, and specific histone acetylation patterns were correlated with these subtypes, providing insights for stratification of patients for more effective treatment.

CANCER CELL (2021)

Article Biochemical Research Methods

leapR: An R Package for Multiomic Pathway Analysis

Vincent Danna et al.

Summary: The goal of high-throughput data studies is to identify functional mechanisms underlying biological phenomena, which requires time-consuming evaluation of various statistical methods. The leapR package allows rapid assessment of biological pathway activity, facilitating integration of multisource data.

JOURNAL OF PROTEOME RESEARCH (2021)

Article Multidisciplinary Sciences

Drug ranking using machine learning systematically predicts the efficacy of anti-cancer drugs

Henry Gerdes et al.

Summary: The DRUML approach uses omics data to rank drugs by their efficacy in cancer cell proliferation, with machine learning models trained on normalized drug response metrics. The method accurately predicts drug responses in independent validation datasets and shows prognostic value in clinical samples.

NATURE COMMUNICATIONS (2021)

Article Oncology

The AML microenvironment catalyzes a stepwise evolution to gilteritinib resistance

Sunil K. Joshi et al.

Summary: The study reveals that the bone marrow microenvironment protects residual AML cells and AML cells develop resistance mechanisms over time. By integrating multiple methods, early resistant cells were found to undergo metabolic reprogramming and depend on AURKB, while late resistant cells are characterized by expansion of pre-existing NRAS mutant subclones and metabolic reprogramming.

CANCER CELL (2021)

Article Biochemistry & Molecular Biology

Quantitative Proteomics of the Cancer Cell Line Encyclopedia

David P. Nusinow et al.

Article Biochemistry & Molecular Biology

Proteogenomic Characterization of Endometrial Carcinoma

Yongchao Dou et al.

Article Biochemical Research Methods

Phosphotyrosine-based Phosphoproteomics for Target Identification and Drug Response Prediction in AML Cell Lines

Carolien van Alphen et al.

MOLECULAR & CELLULAR PROTEOMICS (2020)

Article Oncology

Leukemia incidence trends at the global, regional, and national level between 1990 and 2017

Ying Dong et al.

EXPERIMENTAL HEMATOLOGY & ONCOLOGY (2020)

Article Multidisciplinary Sciences

Proteome activity landscapes of tumor cell lines determine drug responses

Martin Frejno et al.

NATURE COMMUNICATIONS (2020)

Article Biochemistry & Molecular Biology

Proteogenomic Landscape of Breast Cancer Tumorigenesis and Targeted Therapy

Karsten Krug et al.

Article Biochemical Research Methods

Dr.VAE: improving drug response prediction via modeling of drug perturbation effects

Ladislav Rampasek et al.

BIOINFORMATICS (2019)

Article Biochemistry & Molecular Biology

15 years of PhosphoSitePlus®: integrating post-translationally modified sites, disease variants and isoforms

Peter V. Hornbeck et al.

NUCLEIC ACIDS RESEARCH (2019)

Article Multidisciplinary Sciences

Genetic and transcriptional evolution alters cancer cell line drug response

Uri Ben-David et al.

NATURE (2018)

Article Multidisciplinary Sciences

Functional genomic landscape of acute myeloid leukaemia

Jeffrey W. Tyner et al.

NATURE (2018)

Article Biochemical Research Methods

Proteome Profiling Outperforms Transcriptome Profiling for Coexpression Based Gene Function Prediction

Jing Wang et al.

MOLECULAR & CELLULAR PROTEOMICS (2017)

Article Multidisciplinary Sciences

Molecularly targeted drug combinations demonstrate selective effectiveness for myeloid- and lymphoidderived hematologic malignancies

Stephen E. Kurtz et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2017)

Article Biochemical Research Methods

PCSF: An R-package for network-based interpretation of high-throughput data

Murodzhon Akhmedov et al.

PLOS COMPUTATIONAL BIOLOGY (2017)

Article Biochemistry & Molecular Biology

A Landscape of Pharmacogenomic Interactions in Cancer

Francesco Iorio et al.

Article Biochemical Research Methods

Network-Based Interpretation of Diverse High-Throughput Datasets through the Omics Integrator Software Package

Nurcan Tuncbag et al.

PLOS COMPUTATIONAL BIOLOGY (2016)

Article Biochemical Research Methods

Correcting systematic bias and instrument measurement drift with mzRefinery

Bryson C. Gibbons et al.

BIOINFORMATICS (2015)

Article Immunology

Dose-dependent role of the cohesin complex in normal and malignant hematopoiesis

Aaron D. Viny et al.

JOURNAL OF EXPERIMENTAL MEDICINE (2015)

Article Oncology

Harnessing Connectivity in a Large-Scale Small-Molecule Sensitivity Dataset

Brinton Seashore-Ludlow et al.

CANCER DISCOVERY (2015)

Article Biotechnology & Applied Microbiology

A community effort to assess and improve drug sensitivity prediction algorithms

James C. Costello et al.

NATURE BIOTECHNOLOGY (2014)

Article Multidisciplinary Sciences

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

Sangtae Kim et al.

NATURE COMMUNICATIONS (2014)

Article Chemistry, Multidisciplinary

Proteochemometric modeling in a Bayesian framework

Isidro Cortes-Ciriano et al.

JOURNAL OF CHEMINFORMATICS (2014)

Review Biotechnology & Applied Microbiology

Pharmacogenomics in clinical practice and drug development

Andrew R. Harper et al.

NATURE BIOTECHNOLOGY (2012)

Article Biotechnology & Applied Microbiology

clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters

Guangchuang Yu et al.

OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY (2012)

Article Multidisciplinary Sciences

Survey of Activated FLT3 Signaling in Leukemia

Ting-lei Gu et al.

PLOS ONE (2011)

Article Biochemistry & Molecular Biology

A User's Guide to the Encyclopedia of DNA Elements (ENCODE)

Richard M. Myers et al.

PLOS BIOLOGY (2011)

Article Computer Science, Interdisciplinary Applications

Regularization Paths for Generalized Linear Models via Coordinate Descent

Jerome Friedman et al.

JOURNAL OF STATISTICAL SOFTWARE (2010)

Article Biochemical Research Methods

Spectral probabilities and generating functions of tandem mass spectra: A strike against decoy databases

Sangtae Kim et al.

JOURNAL OF PROTEOME RESEARCH (2008)

Article Biochemistry & Molecular Biology

NetworKIN: a resource for exploring cellular phosphorylation networks

Rune Linding et al.

NUCLEIC ACIDS RESEARCH (2008)

Article Biotechnology & Applied Microbiology

A probability-based approach for high-throughput protein phosphorylation analysis and site localization

Sean A. Beausoleil et al.

NATURE BIOTECHNOLOGY (2006)

Article Statistics & Probability

Regularization and variable selection via the elastic net

H Zou et al.

JOURNAL OF THE ROYAL STATISTICAL SOCIETY SERIES B-STATISTICAL METHODOLOGY (2005)

Article Biochemistry & Molecular Biology

Cytoscape: A software environment for integrated models of biomolecular interaction networks

P Shannon et al.

GENOME RESEARCH (2003)