Gene regulatory Networks Reveal Sex Difference in Lung Adenocarcinoma.
Saha E, Guebila MB, Fanfani V, Fischer J, Shutta KH, Mandros P, DeMeo DL, Quackenbush J, Lopes-Ramos CM.
bioRxiv. 2023 Sep 24. PMID: 37790409
Primary Faculty
John Quackenbush
Henry Pickering Walcott Professor of Computational Biology and Bioinformatics
Biostatistics
Other Positions
Chair, Department of Biostatistics
Biostatistics
Harvard T.H. Chan School of Public Health
Overview
John Quackenbush is Professor of Computational Biology and Bioinformatics and Chair of the Department of Biostatistics at the Harvard T.H. Chan School of Public Health, Professor in the Channing Division of Network Medicine, and Professor at the Dana-Farber Cancer Institute. John's PhD was in Theoretical Physics, but in 1992 he received a fellowship to work on the Human Genome Project. This led him through the Salk Institute, Stanford, The Institute for Genomic Research (TIGR), and to Harvard in 2005. John uses massive data to probe how many small effects combine to influence human health and disease. He has more than 300 scientific papers and over 73,000 citations. Among his honors is recognition in 2013 as a White House Open Science Champion of Change.
Bibliography
Supervised Risk Predictor of Breast Cancer Based on Intrinsic Subtypes.
Parker JS, Mullins M, Cheang MCU, Leung S, Voduc D, Vickery T, Davies S, Fauron C, He X, Hu Z, Quackenbush JF, Stijleman IJ, Palazzo J, Marron JS, Nobel AB, Mardis E, Nielsen TO, Ellis MJ, Perou CM, Bernard PS.
J Clin Oncol. 2023 Sep 10. 41(26):4192-4199. PMID: 37672882
Biologically informed NeuralODEs for genome-wide regulatory dynamics.
Hossain I, Fanfani V, Quackenbush J, Burkholz R.
Res Sq. 2023 Mar 14. PMID: 36993392
The Network Zoo: a multilingual package for the inference and analysis of gene regulatory networks.
Ben Guebila M, Wang T, Lopes-Ramos CM, Fanfani V, Weighill D, Burkholz R, Schlauch D, Paulson JN, Altenbuchinger M, Shutta KH, Sonawane AR, Lim J, Calderer G, van IJzendoorn DGP, Morgan D, Marin A, Chen CY, Song Q, Saha E, DeMeo DL, Padi M, Platig J, Kuijjer ML, Glass K, Quackenbush J.
Genome Biol. 2023 03 09. 24(1):45. PMID: 36894939
Biologically informed NeuralODEs for genome-wide regulatory dynamics.
Hossain I, Fanfani V, Quackenbush J, Burkholz R.
bioRxiv. 2023 Feb 27. PMID: 36909563
DRAGON: Determining Regulatory Associations using Graphical models on multi-Omic Networks.
Shutta KH, Weighill D, Burkholz R, Guebila MB, DeMeo DL, Zacharias HU, Quackenbush J, Altenbuchinger M.
Nucleic Acids Res. 2023 02 22. 51(3):e15. PMID: 36533448
Proceedings of the fifth international Molecular Pathological Epidemiology (MPE) meeting.
Yao S, Campbell PT, Ugai T, Gierach G, Abubakar M, Adalsteinsson V, Almeida J, Brennan P, Chanock S, Golub T, Hanash S, Harris C, Hathaway CA, Kelsey K, Landi MT, Mahmood F, Newton C, Quackenbush J, Rodig S, Schultz N, Tearney G, Tworoger SS, Wang M, Zhang X, Garcia-Closas M, Rebbeck TR, Ambrosone CB, Ogino S.
Cancer Causes Control. 2022 Aug. 33(8):1107-1120. PMID: 35759080
Blood gene expression risk profiles and interstitial lung abnormalities: COPDGene and ECLIPSE cohort studies.
Moll M, Hobbs BD, Menon A, Ghosh AJ, Putman RK, Hino T, Hata A, Silverman EK, Quackenbush J, Castaldi PJ, Hersh CP, McGeachie MJ, Sin DD, Tal-Singer R, Nishino M, Hatabu H, Hunninghake GM, Cho MH.
Respir Res. 2022 Jun 17. 23(1):157. PMID: 35715807
Connectivity in eQTL networks dictates reproducibility and genomic properties.
Gaynor SM, Fagny M, Lin X, Platig J, Quackenbush J.
Cell Rep Methods. 2022 05 23. 2(5):100218. PMID: 35637906
An online notebook resource for reproducible inference, analysis and publication of gene regulatory networks.
Ben Guebila M, Weighill D, Lopes-Ramos CM, Burkholz R, Pop RT, Palepu K, Shapoval M, Fagny M, Schlauch D, Glass K, Altenbuchinger M, Kuijjer ML, Platig J, Quackenbush J.
Nat Methods. 2022 05. 19(5):511-513. PMID: 35459940
News
Wafaie Fawzi, Vikram Patel, John Quackenbush elected to National Academy of Medicine
Harvard Chan School faculty members Wafaie Fawzi, Vikram Patel, and John Quackenbush were elected to the National Academy of Medicine.
Artificial Intelligence’s Promise and Peril
As algorithms analyze mammograms and smartphones capture lived experiences, researchers are debating the use of ai in public health.
To address remote learning challenges, hybrid program brings international students back to campus
A new hybrid program is helping first-year international students, who were facing challenges with taking remote classes from thousands of miles away. The program brought a group of students to Boston, where they take both online and once-a-week…
A call for greater transparency, reproducibility in use of artificial intelligence in medicine
For immediate release: October 14, 2020 Boston, MA – Scientists working at the intersection of Artificial Intelligence (AI) and cancer care need to be more transparent about their methods and publish research that is reproducible, according to a…
Study sheds light on sex-based differences in gene regulation
New research from Harvard T.H. Chan School of Public Health and Brigham and Women’s Hospital has uncovered sex-based differences in networks that regulate gene expression in a large number of human tissues. The finding is important because it…