Using graph convolutional neural networks to learn a representation for glycans.
Burkholz R, Quackenbush J, Bojar D.
Cell Rep. 2021 Jun 15. 35(11):109251. PMID: 34133929
Professor
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
Gene Targeting in Disease Networks.
Weighill D, Ben Guebila M, Glass K, Platig J, Yeh JJ, Quackenbush J.
Front Genet. 2021. 12:649942. PMID: 33968133
BRCA1 and RNAi factors promote repair mediated by small RNAs and PALB2-RAD52.
Hatchi E, Goehring L, Landini S, Skourti-Stathaki K, DeConti DK, Abderazzaq FO, Banerjee P, Demers TM, Wang YE, Quackenbush J, Livingston DM.
Nature. 2021 Mar. 591(7851):665-670. PMID: 33536619
Multi-omic regulatory networks capture downstream effects of kinase inhibition in Mycobacterium tuberculosis.
Young AT, Carette X, Helmel M, Steen H, Husson RN, Quackenbush J, Platig J.
NPJ Syst Biol Appl. 2021 01 29. 7(1):8. PMID: 33514755
Genome-Wide Sex and Gender Differences in Cancer.
Lopes-Ramos CM, Quackenbush J, DeMeo DL.
Front Oncol. 2020. 10:597788. PMID: 33330090
Histone deacetylase 6-mediated selective autophagy regulates COPD-associated cilia dysfunction.
Lam HC, Cloonan SM, Bhashyam AR, Haspel JA, Singh A, Sathirapongsasuti JF, Cervo M, Yao H, Chung AL, Mizumura K, An CH, Shan B, Franks JM, Haley KJ, Owen CA, Tesfaigzi Y, Washko GR, Quackenbush J, Silverman EK, Rahman I, Kim HP, Mahmood A, Biswal SS, Ryter SW, Choi AM.
J Clin Invest. 2020 11 02. 130(11):6189. PMID: 33136096
Transparency and reproducibility in artificial intelligence.
Haibe-Kains B, Adam GA, Hosny A, Khodakarami F, Waldron L, Wang B, McIntosh C, Goldenberg A, Kundaje A, Greene CS, Broderick T, Hoffman MM, Leek JT, Korthauer K, Huber W, Brazma A, Pineau J, Tibshirani R, Hastie T, Ioannidis JPA, Quackenbush J, Aerts HJWL.
Nature. 2020 Oct. 586(7829):E14-E16. PMID: 33057217
Paenibacillus infection with frequent viral coinfection contributes to postinfectious hydrocephalus in Ugandan infants.
Paulson JN, Williams BL, Hehnly C, Mishra N, Sinnar SA, Zhang L, Ssentongo P, Mbabazi-Kabachelor E, Wijetunge DSS, von Bredow B, Mulondo R, Kiwanuka J, Bajunirwe F, Bazira J, Bebell LM, Burgoine K, Couto-Rodriguez M, Ericson JE, Erickson T, Ferrari M, Gladstone M, Guo C, Haran M, Hornig M, Isaacs AM, Kaaya BN, Kangere SM, Kulkarni AV, Kumbakumba E, Li X, Limbrick DD, Magombe J, Morton SU, Mugamba J, Ng J, Olupot-Olupot P, Onen J, Peterson MR, Roy F, Sheldon K, Townsend R, Weeks AD, Whalen AJ, Quackenbush J, Ssenyonga P, Galperin MY, Almeida M, Atkins H, Warf BC, Lipkin WI, Broach JR, Schiff SJ.
Sci Transl Med. 2020 09 30. 12(563). PMID: 32998967
PUMA: PANDA Using MicroRNA Associations.
Kuijjer ML, Fagny M, Marin A, Quackenbush J, Glass K.
Bioinformatics. 2020 09 15. 36(18):4765-4773. PMID: 32860050
Sex Differences in Gene Expression and Regulatory Networks across 29 Human Tissues.
Lopes-Ramos CM, Chen CY, Kuijjer ML, Paulson JN, Sonawane AR, Fagny M, Platig J, Glass K, Quackenbush J, DeMeo DL.
Cell Rep. 2020 06 23. 31(12):107795. PMID: 32579922
News
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…
How so-called 'junk DNA' affects cancer risk
January 29, 2020 – John Quackenbush, Henry Pickering Walcott Professor of Computational Biology and Bioinformatics and chair of the Department of Biostatistics, is trying to understand how our genes influence cancer risk. In a recent research paper, he…
Fong Wang Clow receives 2019 Lagakos Distinguished Alumni Award
October 8, 2019 – A biostatistician who has helped bring numerous lifesaving drugs to market is the recipient of the 2019 Lagakos Distinguished Alumni Award. The award, given to Fong Wang Clow, senior vice president and head of…
