Quackenbush, John

Decoding tumour phenotype by noninvasive imaging using a quantitative radiomics approach

Aerts, H. J. W. L., Velazquez, E. R., Leijenaar, R. T. H., Parmar, C., Grossmann, P., Carvalho, S., Bussink, J., Monshouwer, R., Haibe-Kains, B., Rietveld, D., et al. (2014) · Nature Communications

Radiomics and Machine Learning in Medical ImagingImage Retrieval and Classification Techniques

Cited by 5,132

TM4: a free, open-source system for microarray data management and analysis

Saeed, A. I., Sharov, V., White, J., Li, J., Liang, W., Bhagabati, N., Braisted, J., Klapa, M., Currier, T., Thiagarajan, M., et al. (2003) · BioTechniques

Gene expression and cancer classificationGenomics and Phylogenetic Studies

Cited by 4,837

Minimum information about a microarray experiment (MIAME)-toward standards for microarray data

Brazma, A., Hingamp, P., Quackenbush, J., Sherlock, G., Spellman, P., Stoeckert, C., Aach, J., Ansorge, W., Ball, C. A., Causton, H. C., et al. (2001) · Nature Genetics

Gene expression and cancer classificationResearch Data Management Practices

Cited by 4,109

Artificial intelligence in radiology

Hosny, A., Parmar, C., Quackenbush, J., Schwartz, L. H., & Aerts, H. J. W. L. (2018) · Nature Reviews Cancer

AI in cancer detectionArtificial Intelligence in Healthcare and Education

Cited by 3,803

The complete genome sequence of the gastric pathogen Helicobacter pylori

Tomb, J.-F., White, O., Kerlavage, A. R., Clayton, R. A., Sutton, G. G., Fleischmann, R. D., Ketchum, K. A., Klenk, H. P., Gill, S., Dougherty, B. A., et al. (1997) · Nature

Helicobacter pylori-related gastroenterology studiesBacterial Genetics and Biotechnology

Cited by 3,529

Microarray data normalization and transformation

Quackenbush, J. (2002) · Nature Genetics

Gene expression and cancer classificationBioinformatics and Genomic Networks

Cited by 1,975

Genesis: cluster analysis of microarray data

Sturn, A., Quackenbush, J., & Trajanoski, Z. (2002) · Bioinformatics

Gene expression and cancer classificationBioinformatics and Genomic Networks

Cited by 1,761

Multiple-laboratory comparison of microarray platforms

Irizarry, R. A., Warren, D., Spencer, F., Kim, I. F., Biswal, S., Frank, B. C., Gabrielson, E., Garcia, J. G. N., Geoghegan, J., Germino, G., et al. (2005) · Nature Methods

Gene expression and cancer classificationMolecular Biology Techniques and Applications

Cited by 862

Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project

Taylor, C. F., Field, D., Sansone, S.-A., Aerts, J., Apweiler, R., Ashburner, M., Ball, C. A., Binz, P.-A., Bogue, M., Booth, T., et al. (2008) · Nature Biotechnology

Research Data Management PracticesScientific Computing and Data Management

Cited by 558

Transparency and reproducibility in artificial intelligence

Haibe-Kains, B., Adam, G. A., Hosny, A., Khodakarami, F., Massive Analysis Quality Control (MAQC) Society Board of Directors, Shraddha, T., Kusko, R., Sansone, S.-A., Tong, W., Wolfinger, R. D., et al. (2020) · Nature

Explainable Artificial Intelligence (XAI)Ethics and Social Impacts of AI

Cited by 540

Inconsistency in large pharmacogenomic studies

Haibe-Kains, B., El-Hachem, N., Birkbak, N. J., Jin, A. C., Beck, A. H., Aerts, H. J. W. L., & Quackenbush, J. (2013) · Nature

Computational Drug Discovery MethodsCancer Genomics and Diagnostics

Cited by 499

Interpreting cancer genomes using systematic host network perturbations by tumour virus proteins

Rozenblatt-Rosen, O., Deo, R. C., Padi, M., Adelmant, G., Calderwood, M. A., Rolland, T., Grace, M., Dricot, A., Askenazi, M., Tavares, M., et al. (2012) · Nature

Bioinformatics and Genomic NetworksViral-associated cancers and disorders

Cited by 378

A function for cyclin D1 in DNA repair uncovered by protein interactome analyses in human cancers

Jirawatnotai, S., Hu, Y., Michowski, W., Elias, J. E., Becks, L., Bienvenu, F., Zagozdzon, A., Goswami, T., Wang, Y. E., Clark, A. B., et al. (2011) · Nature

DNA Repair MechanismsCancer-related Molecular Pathways

Cited by 333

Histone deacetylase 6–mediated selective autophagy regulates COPD-associated cilia dysfunction

Lam, H. C., Cloonan, S. M., Bhashyam, A. R., Haspel, J. A., Singh, A., Sathirapongsasuti, J. F., Cervo, M., Yao, H., Chung, A. L., Mizumura, K., et al. (2013) · Journal of Clinical Investigation

Autophagy in Disease and TherapyCystic Fibrosis Research Advances

Cited by 307

Passing Messages between Biological Networks to Refine Predicted Interactions

Glass, K., Huttenhower, C., Quackenbush, J., & Yuan, G.-C. (2013) · PLoS ONE

Gene Regulatory Network AnalysisBioinformatics and Genomic Networks

Cited by 266

What would you do if you could sequence everything?

Kahvejian, A., Quackenbush, J., & Thompson, J. F. (2008) · Nature Biotechnology

Genomics and Phylogenetic StudiesGenomics and Rare Diseases

Cited by 189

Genome-wide siRNA screen for mediators of NF-κB activation

Gewurz, B. E., Towfic, F., Mar, J. C., Shinners, N. P., Takasaki, K., Zhao, B., Cahir-McFarland, E. D., Quackenbush, J., Xavier, R. J., & Kieff, E. (2012) · Proceedings of the National Academy of Sciences

NF-κB Signaling PathwaysSignaling Pathways in Disease

Cited by 108

A genome-wide aberrant RNA splicing in patients with acute myeloid leukemia identifies novel potential disease markers and therapeutic targets

Adamia, S., Haibe-Kains, B., Pilarski, P. M., Bar-Natan, M., Pevzner, S., Avet-Loiseau, H., Lode, L., Verselis, S., Fox, E. A., Burke, J., et al. (2014) · Clinical Cancer Research

RNA Research and SplicingAcute Myeloid Leukemia Research

Cited by 106

Sources of variation in baseline gene expression levels from toxicogenomics study control animals across multiple laboratories

Boedigheimer, M. J., Wolfinger, R. D., Bass, M. B., Bushel, P. R., Chou, J. W., Cooper, M., Corton, J. C., Fostel, J., Hester, S., Lee, J. S., et al. (2008) · BMC Genomics

Gene expression and cancer classificationBioinformatics and Genomic Networks

Cited by 85

Identification of Src transformation fingerprint in human colon cancer

Malek, R. L., Irby, R. B., Guo, Q. M., Lee, K., Wong, S., He, M., Tsai, J., Frank, B., Liu, E. T., Quackenbush, J., et al. (2002) · Oncogene

Cancer Mechanisms and TherapyProtein Kinase Regulation and GTPase Signaling

Cited by 81

Multisystem Analysis of Mycobacterium tuberculosis Reveals Kinase-Dependent Remodeling of the Pathogen-Environment Interface

Carette, X., Platig, J., Young, D. C., Helmel, M., Young, A. T., Wang, Z., Potluri, L.-P., Moody, C. S., Zeng, J., Prisic, S., et al. (2018) · mBio

Tuberculosis Research and EpidemiologyBacterial Genetics and Biotechnology

Cited by 65

Using a Single Daytime Performance Test to Identify Most Individuals at High-Risk for Performance Impairment during Extended Wake

St. Hilaire, M. A., Kristal, B. S., Rahman, S. A., Sullivan, J. P., Quackenbush, J., Duffy, J. F., Barger, L. K., Gooley, J. J., Czeisler, C. A., & Lockley, S. W. (2019) · Scientific Reports

Sleep and Work-Related FatigueSleep and Wakefulness Research

Cited by 14

SINGLE CELL ANALYSIS, WHAT IS IN THE FUTURE?

Garmire, L. X., Yuan, G.-C., Fan, R., Yeo, G. W., & Quackenbush, J. (2018) · Biocomputing 2019

Single-cell and spatial transcriptomicsAdvanced Fluorescence Microscopy Techniques

Cited by 2