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Author Details

John Quackenbush
Harvard T. H. Chan School of Public Health
1989
336
87
PMIDPaper TitleJournal TitlePublished Year
36909563Biologically informed NeuralODEs for genome-wide regulatory dynamics.bioRxiv2024
36909563Biologically informed NeuralODEs for genome-wide regulatory dynamics.bioRxiv2024
36894939The Network Zoo: a multilingual package for the inference and analysis of gene regulatory networks.Genome Biol2023
38014256Bayesian Optimized sample-specific Networks Obtained By Omics data (BONOBO).bioRxiv2023
37790409Gene regulatory Networks Reveal Sex Difference in Lung Adenocarcinoma.bioRxiv2023
36894939The Network Zoo: a multilingual package for the inference and analysis of gene regulatory networks.Genome Biol2023
36993392Biologically informed NeuralODEs for genome-wide regulatory dynamics.Res Sq2023
36533448DRAGON: Determining Regulatory Associations using Graphical models on multi-Omic Networks.Nucleic Acids Res2023
38014256Bayesian Optimized sample-specific Networks Obtained By Omics data (BONOBO).bioRxiv2023
37790409Gene regulatory Networks Reveal Sex Difference in Lung Adenocarcinoma.bioRxiv2023
36993392Biologically informed NeuralODEs for genome-wide regulatory dynamics.Res Sq2023
36533448DRAGON: Determining Regulatory Associations using Graphical models on multi-Omic Networks.Nucleic Acids Res2023
34508353GRAND: a database of gene regulatory network models across human conditions.Nucleic Acids Res2022
35459940An online notebook resource for reproducible inference, analysis and publication of gene regulatory networks.Nat Methods2022
35759080Proceedings of the fifth international Molecular Pathological Epidemiology (MPE) meeting.Cancer Causes Control2022
35637906Connectivity in eQTL networks dictates reproducibility and genomic properties.Cell Rep Methods2022
35715807Blood gene expression risk profiles and interstitial lung abnormalities: COPDGene and ECLIPSE cohort studies.Respir Res2022
34508353GRAND: a database of gene regulatory network models across human conditions.Nucleic Acids Res2022
35156023gpuZoo: Cost-effective estimation of gene regulatory networks using the Graphics Processing Unit.NAR Genom Bioinform2022
35637906Connectivity in eQTL networks dictates reproducibility and genomic properties.Cell Rep Methods2022
35759080Proceedings of the fifth international Molecular Pathological Epidemiology (MPE) meeting.Cancer Causes Control2022
35459940An online notebook resource for reproducible inference, analysis and publication of gene regulatory networks.Nat Methods2022
35715807Blood gene expression risk profiles and interstitial lung abnormalities: COPDGene and ECLIPSE cohort studies.Respir Res2022
35156023gpuZoo: Cost-effective estimation of gene regulatory networks using the Graphics Processing Unit.NAR Genom Bioinform2022
34133929Using graph convolutional neural networks to learn a representation for glycans.Cell Rep2021
33968133Gene Targeting in Disease Networks.Front Genet2021
33536619BRCA1 and RNAi factors promote repair mediated by small RNAs and PALB2-RAD52.Nature2021
33514755Multi-omic regulatory networks capture downstream effects of kinase inhibition in Mycobacterium tuberculosis.NPJ Syst Biol Appl2021
34133929Using graph convolutional neural networks to learn a representation for glycans.Cell Rep2021
34409295Analysis of morphological characteristics of IDH-mutant/wildtype brain tumors using whole-lesion phenotype analysis.Neurooncol Adv2021
34573415Environmental Influences Measured by Epigenetic Clock and Vulnerability Components at Birth Impact Clinical ASD Heterogeneity.Genes (Basel)2021
34493595Regulatory Network of PD1 Signaling Is Associated with Prognosis in Glioblastoma Multiforme.Cancer Res2021
34887443Constructing gene regulatory networks using epigenetic data.NPJ Syst Biol Appl2021
34707916Gene regulatory network inference as relaxed graph matching.Proc AAAI Conf Artif Intell2021
33514755Multi-omic regulatory networks capture downstream effects of kinase inhibition in Mycobacterium tuberculosis.NPJ Syst Biol Appl2021
33536619BRCA1 and RNAi factors promote repair mediated by small RNAs and PALB2-RAD52.Nature2021
34887443Constructing gene regulatory networks using epigenetic data.NPJ Syst Biol Appl2021
34707916Gene regulatory network inference as relaxed graph matching.Proc AAAI Conf Artif Intell2021
34409295Analysis of morphological characteristics of IDH-mutant/wildtype brain tumors using whole-lesion phenotype analysis.Neurooncol Adv2021
34493595Regulatory Network of PD1 Signaling Is Associated with Prognosis in Glioblastoma Multiforme.Cancer Res2021
34573415Environmental Influences Measured by Epigenetic Clock and Vulnerability Components at Birth Impact Clinical ASD Heterogeneity.Genes (Basel)2021
33968133Gene Targeting in Disease Networks.Front Genet2021
32157112MicroRNA-mRNA networks define translatable molecular outcome phenotypes in osteosarcoma.Sci Rep2020
35372952Initial Validation of a Machine Learning-Derived Prognostic Test (KidneyIntelX) Integrating Biomarkers and Electronic Health Record Data To Predict Longitudinal Kidney Outcomes.Kidney3602020
36329870Clustering Sparse Data With Feature Correlation With Application to Discover Subtypes in Cancer.IEEE Access2020
31639475Gaussian and Mixed Graphical Models as (multi-)omics data analysis tools.Biochim Biophys Acta Gene Regul Mech2020
32416095Reverse transcriptase kinetics for one-step RT-PCR.Anal Biochem2020
32307915Molecular networks in Network Medicine: Development and applications.Wiley Interdiscip Rev Syst Biol Med2020
31995399DNA Methylation Is Predictive of Mortality in Current and Former Smokers.Am J Respir Crit Care Med2020
31871106The Impact of Stroma Admixture on Molecular Subtypes and Prognostic Gene Signatures in Serous Ovarian Cancer.Cancer Epidemiol Biomarkers Prev2020
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Collaborators

Benjamin Haibe-Kains
Princess Margaret Cancer Centre, University Health Network
Co-authored papers 27
Razvan Sultana
John A. Burns School of Medicine, University of Hawaii at Manoa
Co-authored papers 21
Aedin C Culhane
Dana-Farber Cancer Institute & Harvard School of Public Health
Co-authored papers 19
Jessica C Mar
Australian Institute for Bioengineering and Nanotechnology, University of Queensland
Co-authored papers 17
Camila M Lopes-Ramos
Harvard T. H. Chan School of Public Health
Co-authored papers 16
Edwin K Silverman
Brigham and Women's Hospital
Co-authored papers 16
Christian J Stoeckert
Perelman School of Medicine, University of Pennsylvania
Co-authored papers 13
Hugo J W L Aerts
Harvard Medical School
Co-authored papers 13
Catherine A Ball
Co-authored papers 12
Alvis Brazma
European Bioinformatics Institute
Co-authored papers 12
Craig P Hersh
Co-authored papers 12
Helen Parkinson
European Bioinformatics Institute
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Ivana V Yang
Co-authored papers 10
Christine A Wells
The University of Melbourne
Co-authored papers 9
Martin Ringwald
Max-Planck-Institut fur Immunbiologie
Co-authored papers 9
Yoshihide Hayashizaki
Center for Integrative Medical Sciences
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Guo-Cheng Yuan
Dana-Farber Cancer Institute, Harvard School of Public Health
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Piero Carninci
RIKEN Center for Integrative Medical Sciences
Co-authored papers 8
David A Schwartz
Co-authored papers 8
Charles M Perou
Co-authored papers 8
Steven L Salzberg
Center for Computational Biology, Johns Hopkins University
Co-authored papers 8
Michael H Cho
Brigham and Women's Hospital Channing Division of Network Medicine
Co-authored papers 8
Rafael A Irizarry
Dana-Farber Cancer Institute
Co-authored papers 8
David A Hume
Mater Research Institute-UQ, Translational Research Institute
Co-authored papers 8
Paul T Spellman
Oregon Health & Science University Hospital.
Co-authored papers 7
Andrew H Beck
Beth Israel Deaconess Medical Center, Harvard Medical School
Co-authored papers 7
Susanna-Assunta Sansone
Oxford e-Research Centre, University of Oxford
Co-authored papers 7
Takeya Kasukawa
RIKEN Center for Integrative Medical Sciences
Co-authored papers 7
Yasushi Okazaki
Intractable Disease Research Center, Graduate School of Medicine, Juntendo University
Co-authored papers 7
Masaaki Furuno
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Release 1.2