John Quackenbush

Publication Activity (10 Years)

Years Active: 2016-2024
Publications (10 Years): 49

Top Topics

Mycobacterium Tuberculosis

Network Analysis

Dna Methylation

Top Venues

bioRxiv : the preprint server for biology

Nucleic acids research

Genome research

This page only lists publications with an associated author ORCID identifier.

Publications

Enakshi Saha, Marouen Ben Guebila, Viola Fanfani, Katherine H Shutta, Dawn L DeMeo, John Quackenbush, Camila M Lopes-Ramos
Aging-associated Alterations in the Gene Regulatory Network Landscape Associate with Risk, Prognosis and Response to Therapy in Lung Adenocarcinoma. bioRxiv : the preprint server for biology (2024)
Panagiotis Mandros, Ian Gallagher, Viola Fanfani, Chen Chen, Jonas Fischer, Anis Ismail, Lauren Hsu, Enakshi Saha, Derrick K DeConti, John Quackenbush
node2vec2rank: Large Scale and Stable Graph Differential Analysis via Multi-Layer Node Embeddings and Ranking. bioRxiv : the preprint server for biology (2024)
Enakshi Saha, Viola Fanfani, Panagiotis Mandros, Marouen Ben Guebila, Jonas Fischer, Katherine H Shutta, Dawn L DeMeo, Camila M Lopes-Ramos, John Quackenbush
Bayesian inference of sample-specific coexpression networks. Genome research (2024)
Panagiotis Mandros, Ian Gallagher, Viola Fanfani, Chen Chen, Jonas Fischer, Anis Ismail, Lauren Hsu, Enakshi Saha, Derrick K DeConti, John Quackenbush
node2vec2rank: Large Scale and Stable Graph Differential Analysis via Multi-Layer Node Embeddings and Ranking. bioRxiv : the preprint server for biology (2024)
Enakshi Saha, Marouen Ben Guebila, Viola Fanfani, Katherine H Shutta, Dawn L DeMeo, John Quackenbush, Camila M Lopes-Ramos
Aging-associated Alterations in the Gene Regulatory Network Landscape Associate with Risk, Prognosis and Response to Therapy in Lung Adenocarcinoma. bioRxiv : the preprint server for biology (2024)
Stefan Schrod, Niklas Lück, Robert Lohmayer, Stefan Solbrig, Dennis Völkl, Tina Wipfler, Katherine H Shutta, Marouen Ben Guebila, Andreas Schäfer, Tim Beißbarth, Helena U Zacharias, Peter J Oefner, John Quackenbush, Michael Altenbuchinger
Spatial Cellular Networks from omics data with SpaCeNet. Genome research (2024)
Enakshi Saha, Viola Fanfani, Panagiotis Mandros, Marouen Ben Guebila, Jonas Fischer, Katherine H Shutta, Dawn L DeMeo, Camila M Lopes-Ramos, John Quackenbush
Bayesian inference of sample-specific coexpression networks. Genome research (2024)
Katherine L Stone, John Platig, John Quackenbush, Maud Fagny
Complex Traits Heritability is Highly Clustered in the eQTL Bipartite Network. bioRxiv : the preprint server for biology (2024)
Enakshi Saha, Marouen Ben Guebila, Viola Fanfani, Katherine H Shutta, Dawn L DeMeo, John Quackenbush, Camila M Lopes-Ramos
Aging-associated Alterations in the Gene Regulatory Network Landscape Associate with Risk, Prognosis and Response to Therapy in Lung Adenocarcinoma. bioRxiv : the preprint server for biology (2024)
Panagiotis Mandros, Ian Gallagher, Viola Fanfani, Chen Chen, Jonas Fischer, Anis Ismail, Lauren Hsu, Enakshi Saha, Derrick K DeConti, John Quackenbush
node2vec2rank: Large Scale and Stable Graph Differential Analysis via Multi-Layer Node Embeddings and Ranking. bioRxiv : the preprint server for biology (2024)
Panagiotis Mandros, Ian Gallagher, Viola Fanfani, Chen Chen, Jonas Fischer, Anis Ismail, Lauren Hsu, Enakshi Saha, Derrick K DeConti, John Quackenbush
node2vec2rank: Large Scale and Stable Graph Differential Analysis via Multi-Layer Node Embeddings and Ranking. bioRxiv : the preprint server for biology (2024)
Katherine L Stone, John Platig, John Quackenbush, Maud Fagny
Complex Traits Heritability is Highly Clustered in the eQTL Bipartite Network. bioRxiv : the preprint server for biology (2024)
Katherine L Stone, John Platig, John Quackenbush, Maud Fagny
Complex Traits Heritability is Highly Clustered in the eQTL Bipartite Network. bioRxiv : the preprint server for biology (2024)
Katherine L Stone, John Platig, John Quackenbush, Maud Fagny
Complex Traits Heritability is Highly Clustered in the eQTL Bipartite Network. bioRxiv : the preprint server for biology (2024)
Marouen Ben Guebila, Tian Wang, Camila M Lopes-Ramos, Viola Fanfani, Des Weighill, Rebekka Burkholz, Daniel Schlauch, Joseph N Paulson, Michael Altenbuchinger, Katherine H Shutta, Abhijeet R Sonawane, James Lim, Genis Calderer, David G P van IJzendoorn, Daniel Morgan, Alessandro Marin, Cho-Yi Chen, Qi Song, Enakshi Saha, Dawn L DeMeo, Megha Padi, John Platig, Marieke L Kuijjer, Kimberly Glass, John Quackenbush
The Network Zoo: a multilingual package for the inference and analysis of gene regulatory networks. Genome biology 24 (1) (2023)
Marouen Ben Guebila, Tian Wang, Camila M Lopes-Ramos, Viola Fanfani, Des Weighill, Rebekka Burkholz, Daniel Schlauch, Joseph N Paulson, Michael Altenbuchinger, Katherine H Shutta, Abhijeet R Sonawane, James Lim, Genis Calderer, David G P van IJzendoorn, Daniel Morgan, Alessandro Marin, Cho-Yi Chen, Qi Song, Enakshi Saha, Dawn L DeMeo, Megha Padi, John Platig, Marieke L Kuijjer, Kimberly Glass, John Quackenbush
The Network Zoo: a multilingual package for the inference and analysis of gene regulatory networks. Genome biology 24 (1) (2023)
Intekhab Hossain, Viola Fanfani, John Quackenbush, Rebekka Burkholz
Biologically informed NeuralODEs for genome-wide regulatory dynamics. bioRxiv : the preprint server for biology (2023)
Katherine H Shutta, Deborah A Weighill, Rebekka Burkholz, Marouen Ben Guebila, Dawn L DeMeo, Helena U Zacharias, John Quackenbush, Michael Altenbuchinger
DRAGON: Determining Regulatory Associations using Graphical models on multi-Omic Networks. Nucleic acids research 51 (3) (2023)
Katherine H Shutta, Deborah A Weighill, Rebekka Burkholz, Marouen Ben Guebila, Dawn L DeMeo, Helena U Zacharias, John Quackenbush, Michael Altenbuchinger
DRAGON: Determining Regulatory Associations using Graphical models on multi-Omic Networks. Nucleic acids research 51 (3) (2023)
Enakshi Saha, Viola Fanfani, Panagiotis Mandros, Marouen Ben-Guebila, Jonas Fischer, Katherine Hoff-Shutta, Kimberly Glass, Dawn Lisa DeMeo, Camila Lopes-Ramos, John Quackenbush
Bayesian Optimized sample-specific Networks Obtained By Omics data (BONOBO). bioRxiv : the preprint server for biology (2023)
Marouen Ben Guebila, Tian Wang, Camila M Lopes-Ramos, Viola Fanfani, Des Weighill, Rebekka Burkholz, Daniel Schlauch, Joseph N Paulson, Michael Altenbuchinger, Katherine H Shutta, Abhijeet R Sonawane, James Lim, Genis Calderer, David G P van IJzendoorn, Daniel Morgan, Alessandro Marin, Cho-Yi Chen, Qi Song, Enakshi Saha, Dawn L DeMeo, Megha Padi, John Platig, Marieke L Kuijjer, Kimberly Glass, John Quackenbush
The Network Zoo: a multilingual package for the inference and analysis of gene regulatory networks. Genome biology 24 (1) (2023)
Intekhab Hossain, Viola Fanfani, John Quackenbush, Rebekka Burkholz
Biologically informed NeuralODEs for genome-wide regulatory dynamics. Research square (2023)
Enakshi Saha, Marouen Ben Guebila, Viola Fanfani, Jonas Fischer, Katherine H Shutta, Panagiotis Mandros, Dawn L DeMeo, John Quackenbush, Camila M Lopes-Ramos
Gene regulatory Networks Reveal Sex Difference in Lung Adenocarcinoma. bioRxiv : the preprint server for biology (2023)
Marouen Ben Guebila, Tian Wang, Camila M Lopes-Ramos, Viola Fanfani, Des Weighill, Rebekka Burkholz, Daniel Schlauch, Joseph N Paulson, Michael Altenbuchinger, Katherine H Shutta, Abhijeet R Sonawane, James Lim, Genis Calderer, David G P van IJzendoorn, Daniel Morgan, Alessandro Marin, Cho-Yi Chen, Qi Song, Enakshi Saha, Dawn L DeMeo, Megha Padi, John Platig, Marieke L Kuijjer, Kimberly Glass, John Quackenbush
The Network Zoo: a multilingual package for the inference and analysis of gene regulatory networks. Genome biology 24 (1) (2023)
Katherine H Shutta, Deborah A Weighill, Rebekka Burkholz, Marouen Ben Guebila, Dawn L DeMeo, Helena U Zacharias, John Quackenbush, Michael Altenbuchinger
DRAGON: Determining Regulatory Associations using Graphical models on multi-Omic Networks. Nucleic acids research (2022)
Deborah A Weighill, Marouen Ben Guebila, Kimberly Glass, John Quackenbush, John Platig
Predicting genotype-specific gene regulatory networks. Genome research 32 (3) (2022)
Katherine H Shutta, Deborah A Weighill, Rebekka Burkholz, Marouen Ben Guebila, Dawn L DeMeo, Helena U Zacharias, John Quackenbush, Michael Altenbuchinger
DRAGON: Determining Regulatory Associations using Graphical models on multi-Omic Networks. Nucleic acids research (2022)
Marouen Ben Guebila, Deborah Weighill, Camila M Lopes-Ramos, Rebekka Burkholz, Romana T Pop, Kalyan Palepu, Mia Shapoval, Maud Fagny, Daniel Schlauch, Kimberly Glass, Michael Altenbuchinger, Marieke Lydia Kuijjer, John Platig, John Quackenbush
An online notebook resource for reproducible inference, analysis and publication of gene regulatory networks. Nature methods 19 (5) (2022)
Marouen Ben Guebila, Daniel C Morgan, Kimberly Glass, Marieke Lydia Kuijjer, Dawn L DeMeo, John Quackenbush
gpuZoo: Cost-effective estimation of gene regulatory networks using the Graphics Processing Unit. NAR genomics and bioinformatics 4 (1) (2022)
Albert T Young, Xavier Carette, Michaela Helmel, Hanno Steen, Robert N Husson, John Quackenbush, John Platig
Multi-omic regulatory networks capture downstream effects of kinase inhibition in Mycobacterium tuberculosis. NPJ systems biology and applications 7 (1) (2021)
Abhijeet Rajendra Sonawane, Dawn L DeMeo, John Quackenbush, Kimberly Glass
Constructing gene regulatory networks using epigenetic data. NPJ systems biology and applications 7 (1) (2021)
Joseph N Paulson, Brent L Williams, Christine Hehnly, Nischay Mishra, Shamim A Sinnar, Lijun Zhang, Paddy Ssentongo, Edith Mbabazi-Kabachelor, Dona S S Wijetunge, Benjamin von Bredow, Ronnie Mulondo, Julius Kiwanuka, Francis Bajunirwe, Joel Bazira, Lisa M Bebell, Kathy Burgoine, Mara Couto-Rodriguez, Jessica E Ericson, Tim Erickson, Matthew J Ferrari, Melissa J Gladstone, Cheng Guo, Murali Haran, Mady Hornig, Albert M Isaacs, Brian Nsubuga Kaaya, Sheila M Kangere, Abhaya V Kulkarni, Elias Kumbakumba, Xiaoxiao Li, David D Limbrick, Joshua Magombe, Sarah U Morton, John Mugamba, James Ng, Peter Olupot-Olupot, Justin Onen, Mallory R Peterson, Farrah Roy, Kathryn E Sheldon, Reid Townsend, Andrew D Weeks, Andrew J Whalen, John Quackenbush, Peter Ssenyonga, Michael Y Galperin, Mathieu Almeida, Hannah M Atkins, Benjamin C Warf, W Ian Lipkin, James R Broach, Steven J Schiff
Paenibacillus infection with frequent viral coinfection contributes to postinfectious hydrocephalus in Ugandan infants. Science translational medicine 12 (563) (2021)
Elodie Hatchi, Liana Goehring, Serena Landini, Konstantina Skourti-Stathaki, Derrick K DeConti, Fieda O Abderazzaq, Priyankana Banerjee, Timothy M Demers, Yaoyu E Wang, John Quackenbush, David M Livingston
BRCA1 and RNAi factors promote repair mediated by small RNAs and PALB2-RAD52. Nature 591 (7851) (2021)
Marouen Ben Guebila, Camila M Lopes-Ramos, Deborah A Weighill, Abhijeet Rajendra Sonawane, Rebekka Burkholz, Behrouz Shamsaei, John Platig, Kimberly Glass, Marieke Lydia Kuijjer, John Quackenbush
GRAND: a database of gene regulatory network models across human conditions. Nucleic acids research (2021)
Camila M Lopes-Ramos, Tatiana Belova, Tess H Brunner, Marouen Ben Guebila, Daniel Osorio, John Quackenbush, Marieke Lydia Kuijjer
Regulatory Network of PD1 Signaling Is Associated with Prognosis in Glioblastoma Multiforme. Cancer research 81 (21) (2021)
Edwin K Silverman, Harald H H W Schmidt, Eleni Anastasiadou, Lucia Altucci, Marco Angelini, Lina Badimón, Jean-Luc Balligand, Giuditta Benincasa, Giovambattista Capasso, Federica Conte, Antonella Di Costanzo, Lorenzo Farina, Giulia Fiscon, Laurent Gatto, Michele Gentili, Joseph Loscalzo, Cinzia Marchese, Claudio Napoli, Paola Paci, Manuela Petti, John Quackenbush, Paolo Tieri, Davide Viggiano, Gemma Vilahur, Kimberly Glass, Jan Baumbach
Molecular networks in Network Medicine: Development and applications. Wiley interdisciplinary reviews. Systems biology and medicine 12 (6) (2020)
Craig P Hersh, Issssswan M Adcock, Juan C Celedón, Michael H Cho, David Chistopher Christiani, Blanca E Himes, Naftali Kaminski, Rasika A Mathias, Deborah A Meyers, John Quackenbush, Susan Redline, Katrina A Steiling, Holly K Tabor, Martin D Tobin, Mark M Wurfel, Ivana V Yang, Gerard H Koppelmann
High-Throughput Sequencing in Respiratory, Critical Care, and Sleep Medicine Research. An Official American Thoracic Society Workshop Report. Annals of the American Thoracic Society 16 (1) (2020)
Jipeng Qiang, Wei Ding, Marieke Lydia Kuijjer, John Quackenbush, Ping Chen
Clustering Sparse Data With Feature Correlation With Application to Discover Subtypes in Cancer. IEEE access : practical innovations, open solutions 8 (2020)
Benjamin Haibe-Kains, George Alexandru Adam, Ahmed Hosny, Farnoosh Khodakarami, null null, Levi Waldron, Bo Wang, Chris McIntosh, Anna Goldenberg, Anshul Kundaje, Casey S Greene, Tamara Broderick, Michael M Hoffman, Jeffrey T Leek, Keegan Korthauer, Wolfgang Huber, Alvis Brazma, Joelle Pineau, Robert Tibshirani, Trevor Hastie, John P A Ioannidis, John Quackenbush, Hugo J W L Aerts
Transparency and reproducibility in artificial intelligence. Nature 586 (7829) (2020)
Christopher E Lietz, Cassandra Garbutt, William T Barry, Vikram Deshpande, Yen-Lin Chen, Santiago A Lozano Calderón, Yaoyu Wang, Brian Lawney, David Ebb, Gregory M Cote, Zhenfeng Duan, Francis J Hornicek, Edwin Choy, G Petur Nielsen, Benjamin Haibe-Kains, John Quackenbush, Dimitrios Spentzos
MicroRNA-mRNA networks define translatable molecular outcome phenotypes in osteosarcoma. Scientific reports 10 (1) (2020)
Ahmed Hosny, Chintan Parmar, John Quackenbush, Lawrence H Schwartz, Hugo J W L Aerts
Artificial intelligence in radiology. Nature reviews. Cancer 18 (8) (2019)
Camila M Lopes-Ramos, Marieke Lydia Kuijjer, Shuji Ogino, Charles S Fuchs, Dawn L DeMeo, Kimberly Glass, John Quackenbush
Gene Regulatory Network Analysis Identifies Sex-Linked Differences in Colon Cancer Drug Metabolism. Cancer research 78 (19) (2019)
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, Aedin C Culhane
The Impact of Stroma Admixture on Molecular Subtypes and Prognostic Gene Signatures in Serous Ovarian Cancer. Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology 29 (2) (2019)
Maud Fagny, John Platig, Marieke Lydia Kuijjer, Xihong Lin, John Quackenbush
Nongenic cancer-risk SNPs affect oncogenes, tumour-suppressor genes, and immune function. British journal of cancer 122 (4) (2019)
Melissa A St Hilaire, Bruce S Kristal, Shadab A Rahman, Jason P Sullivan, John Quackenbush, Jeanne F Duffy, Laura K Barger, Joshua J Gooley, Charles A Czeisler, Steven W Lockley
Using a Single Daytime Performance Test to Identify Most Individuals at High-Risk for Performance Impairment during Extended Wake. Scientific reports 9 (1) (2019)
Valeriy Domenyuk, Zoran Gatalica, Radhika Santhanam, Xixi Wei, Adam Stark, Patrick Kennedy, Brandon Toussaint, Symon Levenberg, Jie Wang, Nianqing Xiao, Richard Greil, Gabriel Rinnerthaler, Simon P Gampenrieder, Amy B Heimberger, Donald A Berry, Anna Barker, John Quackenbush, John L Marshall, George Poste, Jeffrey L Vacirca, Gregory A Vidal, Lee S Schwartzberg, David D Halbert, Andreas Voss, Daniel Magee, Mark R Miglarese, Michael Famulok, Günter Mayer, David Spetzler
Poly-ligand profiling differentiates trastuzumab-treated breast cancer patients according to their outcomes. Nature communications 9 (1) (2018)
Maud Fagny, Joseph N Paulson, Marieke L Kuijjer, Abhijeet R Sonawane, Cho-Yi Chen, Camila M Lopes-Ramos, Kimberly Glass, John Quackenbush, John Platig
Exploring regulation in tissues with eQTL networks. Proceedings of the National Academy of Sciences of the United States of America 114 (37) (2017)
Suzanne M Cloonan, Kimberly Glass, Maria E Laucho-Contreras, Abhiram R Bhashyam, Morgan Cervo, Maria A Pabón, Csaba Konrad, Francesca Polverino, Ilias I Siempos, Elizabeth Perez, Kenji Mizumura, Manik C Ghosh, Harikrishnan Parameswaran, Niamh C Williams, Kristen T Rooney, Zhi-Hua Chen, Monica P Goldklang, Guo-Cheng Yuan, Stephen C Moore, Dawn L Demeo, Tracey A Rouault, Jeanine M D'Armiento, Eric A Schon, Giovanni Manfredi, John Quackenbush, Ashfaq Mahmood, Edwin K Silverman, Caroline A Owen, Augustine M K Choi
Mitochondrial iron chelation ameliorates cigarette smoke-induced bronchitis and emphysema in mice. Nature medicine 22 (2) (2016)
Christian Berrios, Megha Padi, Mark A Keibler, Donglim Esther Park, Vadim Molla, Jingwei Cheng, Soo Mi Lee, Gregory Stephanopoulos, John Quackenbush, James A Decaprio
Merkel Cell Polyomavirus Small T Antigen Promotes Pro-Glycolytic Metabolic Perturbations Required for Transformation. PLoS pathogens 12 (11) (2016)