John Quackenbush

73.8k citations

293 papers · 29.2k indexed · 10 hit papers · h-index 75

Impact in

Health Informatics top 0.02%
Radiology, Nuclear Medicine and Imaging top 0.05%
- Radiomics and Machine Learning in Medical Imaging

Papers in

Molecular Biology 212
- Gene expression and cancer classification 93
- Bioinformatics and Genomic Networks 85
- Molecular Biology Techniques and Applications 33
- Gene Regulatory Network Analysis 28
- Genomics and Phylogenetic Studies 22
- RNA modifications and cancer 22
- Genomics and Chromatin Dynamics 17
Cancer Research 45
- Cancer-related molecular mechanisms research 20

Co-authors: Hugo J.W.L. Aerts Chintan Parmar Zlatko Trajanoski Alexander Sturn Ahmed Hosny Benjamin Haibe‐Kains Lawrence H. Schwartz Joseph White
Journals: Bioinformatics (19 papers)Genomics (13 papers)Cancer Research (12 papers)PLoS ONE (11 papers)Genome biology (9 papers)
Partner nations: United States United Kingdom Canada

In The Last Decade

John Quackenbush

287 papers receiving 28.6k citations

Hit Papers

10 papers align trajectories log scale

Artificial intelligence in radiology 2018 · 2.3k citations

What are hit papers?

Hit papers significantly outperform the citation benchmark for their cohort. A paper qualifies if any of the following hold:

it has ≥500 total citations;
it reaches ≥1.5× the top-1% citation threshold for papers in the same subfield and year (the threshold is the minimum needed to enter the top 1%, not the average within it);
it reaches the top citation threshold in at least one of its specific research topics.

2018 Nature reviews. Cancer
2017 Cancer Research
2016 Frontiers in Oncology
2014 Nature Communications
2006 Methods in enzymology on CD-ROM/Methods in enzymology
2003 Bioinformatics
2002 Bioinformatics
2002 Nature Genetics
2001 Nature Reviews Genetics
2000 BioTechniques

Peers

Countries citing papers authored by John Quackenbush

Since Specialization

Citations

This map shows the geographic impact of John Quackenbush's research. It shows the number of citations coming from papers published by authors working in each country. You can also color the map by specialization and compare the number of citations received by John Quackenbush with the expected number of citations based on a country's size and research output (numbers larger than one mean the country cites John Quackenbush more than expected).

Fields of papers citing papers by John Quackenbush

Since Specialization

Physical SciencesHealth SciencesLife SciencesSocial Sciences

This network shows the impact of papers produced by John Quackenbush. Nodes represent research fields, and links connect fields that are likely to share authors. Colored nodes show fields that tend to cite the papers produced by John Quackenbush. The network helps show where John Quackenbush may publish in the future.

Co-authors

The 25 scholars most cited alongside John Quackenbush, linked wherever they have co-authored with each other. Click a name or a connecting line to browse the papers they share.

Border = papers with John Quackenbush Line = papers co-authored together John Quackenbush links everyone, so they are left out of the graph.

All Works

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20 of 20 papers shown

#	Work
1	Gene regulatory networks reveal sex difference in lung adenocarcinoma Biology of Sex Differences ·Enakshi Saha, Marouen Ben Guebila, Viola Fanfani, Jonas Fischer, Katherine H. Shutta, Panagiotis Mandros, Dawn L. DeMeo, John Quackenbush, Camila M. Lopes‐Ramos	2024	6
2	Bayesian inference of sample-specific coexpression networks Genome Research ·Enakshi Saha, Viola Fanfani, Panagiotis Mandros, Marouen Ben Guebila, Jonas Fischer, Katherine H. Shutta, Dawn L. DeMeo, Camila M. Lopes‐Ramos, John Quackenbush	2024	2
3	Predicting genotype-specific gene regulatory networks Genome Research ·Deborah Weighill, Marouen Ben Guebila, Kimberly Glass, John Quackenbush, John Platig	2022	6
4	PUMA: PANDA Using MicroRNA Associations Bioinformatics ·Marieke L. Kuijjer, Maud Fagny, Alessandro Marin, John Quackenbush, Kimberly Glass	2020	16
5	The Impact of Stroma Admixture on Molecular Subtypes and Prognostic Gene Signatures in Serous Ovarian Cancer Cancer Epidemiology Biomarkers & Prevention ·Matthew Schwede, Levi Waldron, Samuel C. Mok, Wei Wei, Azfar Basunia, Melissa A. Merritt, Constantine S. Mitsiades, Giovanni Parmigiani, David P. Harrington, John Quackenbush, Michael J. Birrer, Aedín C. Culhane	2019	24
6	Gene Regulatory Network Analysis Identifies Sex-Linked Differences in Colon Cancer Drug Metabolism Cancer Research ·Camila M. Lopes‐Ramos, Marieke L. Kuijjer, Shuji Ogino, Charles S. Fuchs, Dawn L. DeMeo, Kimberly Glass, John Quackenbush	2018	63
7	High-Throughput Sequencing in Respiratory, Critical Care, and Sleep Medicine Research. An Official American Thoracic Society Workshop Report Annals of the American Thoracic Society ·Craig P. Hersh, Ian M. Adcock, Juan C. Celedón, Michael H. Cho, David C. Christiani, Blanca E. Himes, Naftali Kaminski, Rasika A. Mathias, Deborah A. Meyers, John Quackenbush, Susan Redline, Katrina Steiling, Holly K. Tabor, Martin D. Tobin, Mark M. Wurfel, Ivana V. Yang, Gerard H. Koppelman	2018	7
8	WebMeV: A Cloud Platform for Analyzing and Visualizing Cancer Genomic Data Cancer Research ·Yaoyu E. Wang, Lev Kutnetsov, Antony Partensky, Jalil Farid, John Quackenbush	2017	39
9	Somatic Mutations Drive Distinct Imaging Phenotypes in Lung Cancer Cancer Research ·Emmanuel Rios Velazquez, Chintan Parmar, Ying Liu, Thibaud Coroller, Gisele Cruz, Olya Stringfield, Zhaoxiang Ye, Mike Makrigiorgos, Fiona Fennessy, Raymond H. Mak, Robert J. Gillies, John Quackenbush, Hugo J.W.L. Aerts Hit paper breakdown →	2017	304
10	Differential connectivity of gene regulatory networks distinguishes corticosteroid response in asthma Journal of Allergy and Clinical Immunology ·Weiliang Qiu, Feng Guo, Kimberly Glass, Guo Yuan, John Quackenbush, Xiaobo Zhou, Kelan G. Tantisira	2017	26
11	BatchQC: interactive software for evaluating sample and batch effects in genomic data Bioinformatics ·Solaiappan Manimaran, Heather Marie Selby, Kwame Okrah, Claire Ruberman, Jeffrey T. Leek, John Quackenbush, Benjamin Haibe‐Kains, Héctor Corrada Bravo, W. Evan Johnson	2016	45
12	Enhancing Reproducibility in Cancer Drug Screening: How Do We Move Forward? Cancer Research ·Christos Hatzis, Philippe L. Bédard, Nicolai J. Birkbak, Andrew H. Beck, Hugo J.W.L. Aerts, David F. Stern, Leming Shi, Robert Clarke, John Quackenbush, Benjamin Haibe‐Kains	2014	67
13	A Genome-Wide Aberrant RNA Splicing in Patients with Acute Myeloid Leukemia Identifies Novel Potential Disease Markers and Therapeutic Targets Clinical Cancer Research ·Sophia Adamia, Benjamin Haibe‐Kains, Patrick M. Pilarski, Michal Bar‐Natan, Samuel Pevzner, Hervé Avet‐Loiseau, Laurence Lodé, Sigitas Verselis, Edward A. Fox, John P. Burke, Ilene Galinsky, Ibiayi Dagogo‐Jack, Martha Wadleigh, David P. Steensma, Gabriela Motyckova, Daniel J. DeAngelo, John Quackenbush, Richard M. Stone, James D. Griffin	2013	79
14	Sequential Binary Gene Ratio Tests Define a Novel Molecular Diagnostic Strategy for Malignant Pleural Mesothelioma Clinical Cancer Research ·Assunta De Rienzo, William G. Richards, Beow Y. Yeap, Melissa H. Coleman, Peter E. Sugarbaker, Lucian R. Chirieac, Yaoyu E. Wang, John Quackenbush, Roderick V. Jensen, Raphael Bueno	2013	17
15	Expression Profiling of Archival Tumors for Long-term Health Studies Clinical Cancer Research ·Levi Waldron, Shuji Ogino, Yujin Hoshida, Kaori Shima, Amy E. McCart Reed, Peter T. Simpson, Yoshifumi Baba, Katsuhiko Nosho, Nicola Segata, Ana Cristina Vargas, Margaret C. Cummings, Sunil R. Lakhani, Gregory J. Kirkner, Edward L. Giovannucci, John Quackenbush, Todd R. Golub, Charles S. Fuchs, Giovanni Parmigiani, Curtis Huttenhower	2012	25
16	Identification of Novel Kinase Targets for the Treatment of Estrogen Receptor–Negative Breast Cancer Clinical Cancer Research ·Corey Speers, Anna Tsimelzon, K. Sexton, Ashley M. Herrick, Carolina Gutiérrez, Aedín C. Culhane, John Quackenbush, Susan G. Hilsenbeck, Jenny C. Chang, Powel H. Brown	2009	77
17	Epithelial Progeny of Estrogen-Exposed Breast Progenitor Cells Display a Cancer-like Methylome Cancer Research ·Alfred S.L. Cheng, Aedín C. Culhane, Michael W.Y. Chan, Chinnambally Venkataramu, Mathias Ehrich, Aejaz Nasir, Blanca Rodríguez, Joseph K. Liu, Pearlly S. Yan, John Quackenbush, Kenneth P. Nephew, Timothy J. Yeatman, Tim H-M. Huang	2008	112
18	Molecular fingerprints and mechanisms of chemoresistance in ovarian cancer Cancer Research ·John Quackenbush, Jian‐Bing Fan, Michelle S. Hirsch, Kristina M. Holton, Renee Rubio, Craig April, Jing Chen, Eliza Wickham‐Garcia, Joyce F. Liu, Aedín C. Culhane, Ronny Drapkin, Ursula A. Matulonis	2008	1
19	Marked Genomic Differences Characterize Primary and Secondary Glioblastoma Subtypes and Identify Two Distinct Molecular and Clinical Secondary Glioblastoma Entities Cancer Research ·Elizabeth A. Maher, Cameron Brennan, Patrick Y. Wen, Laura Durso, Keith L. Ligon, Aaron Richardson, Deepak Khatry, Bin Feng, Raktim Sinha, David N. Louis, John Quackenbush, Peter McL. Black, Lynda Chin, Ronald A. DePinho	2006	140
20	Knowledge-Based Access to the Bio-Medical Literature Ontologically-Grounded Experiments for the TREC 2003 Genomics Track Text REtrieval Conference ·Richard M. Tong, John Quackenbush, Mark Snuffin	2003	2

About John Quackenbush

John Quackenbush is a scholar working on Molecular Biology, Cancer Research, Reproductive Medicine, Genetics and Pulmonary and Respiratory Medicine, having authored 293 papers that have together received 29.2k indexed citations. Recurring topics across this work include Gene expression and cancer classification (93 papers), Bioinformatics and Genomic Networks (85 papers), Molecular Biology Techniques and Applications (33 papers), Gene Regulatory Network Analysis (28 papers), Genomics and Phylogenetic Studies (22 papers), RNA modifications and cancer (22 papers), Cancer-related molecular mechanisms research (20 papers) and Genomics and Chromatin Dynamics (17 papers). The work is most often cited by research in Health Informatics (1.1k citations), Radiology, Nuclear Medicine and Imaging (6.0k citations), Cancer Research (3.3k citations), Molecular Biology (13.9k citations) and Oncology (3.4k citations). John Quackenbush has collaborated with scholars based in United States, United Kingdom and Canada. Frequent co-authors include Hugo J.W.L. Aerts, Chintan Parmar, Zlatko Trajanoski, Alexander Sturn, Ahmed Hosny, Benjamin Haibe‐Kains, Lawrence H. Schwartz, Joseph White, Eleanor Howe and Philippe Lambin. Their work appears in journals such as Bioinformatics, Genomics, Cancer Research, PLoS ONE and Genome biology.

Rankless uses publication and citation data sourced from OpenAlex, an open and comprehensive bibliographic database. While OpenAlex provides broad and valuable coverage of the global research landscape, it—like all bibliographic datasets—has inherent limitations. These include incomplete records, variations in author disambiguation, differences in journal indexing, and delays in data updates. As a result, some metrics and network relationships displayed in Rankless may not fully capture the entirety of a scholar's output or impact.

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