Genome-Wide Sex and Gender Differences in Cancer.
Lopes-Ramos CM, Quackenbush J, DeMeo DL.
Front Oncol. 2020. 10:597788. PMID: 33330090
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
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 Nov 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 Sep 30. 12(563). PMID: 32998967
PUMA: PANDA Using MicroRNA Associations.
Kuijjer ML, Fagny M, Marin A, Quackenbush J, Glass K.
Bioinformatics. 2020 Sep 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
DNA Methylation Is Predictive of Mortality in Current and Former Smokers.
Morrow JD, Make B, Regan E, Han M, Hersh CP, Tal-Singer R, Quackenbush J, Choi AMK, Silverman EK, DeMeo DL.
Am J Respir Crit Care Med. 2020 05 01. 201(9):1099-1109. PMID: 31995399
Molecular networks in Network Medicine: Development and applications.
Silverman EK, Schmidt HHHW, Anastasiadou E, Altucci L, Angelini M, Badimon L, Balligand JL, Benincasa G, Capasso G, Conte F, Di Costanzo A, Farina L, Fiscon G, Gatto L, Gentili M, Loscalzo J, Marchese C, Napoli C, Paci P, Petti M, Quackenbush J, Tieri P, Viggiano D, Vilahur G, Glass K, Baumbach J.
Wiley Interdiscip Rev Syst Biol Med. 2020 Nov. 12(6):e1489. PMID: 32307915
MicroRNA-mRNA networks define translatable molecular outcome phenotypes in osteosarcoma.
Lietz CE, Garbutt C, Barry WT, Deshpande V, Chen YL, Lozano-Calderon SA, Wang Y, Lawney B, Ebb D, Cote GM, Duan Z, Hornicek FJ, Choy E, Petur Nielsen G, Haibe-Kains B, Quackenbush J, Spentzos D.
Sci Rep. 2020 03 10. 10(1):4409. PMID: 32157112
The Impact of Stroma Admixture on Molecular Subtypes and Prognostic Gene Signatures in Serous Ovarian Cancer.
Schwede M, Waldron L, Mok SC, Wei W, Basunia A, Merritt MA, Mitsiades CS, Parmigiani G, Harrington DP, Quackenbush J, Birrer MJ, Culhane AC.
Cancer Epidemiol Biomarkers Prev. 2020 02. 29(2):509-519. PMID: 31871106
News
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…
Q&A: Why Sex Matters (in Disease Susceptibility)
John Quackenbush and colleagues have been turning over a boulder of faulty assumptions about how sex differences affect disease risk and progression.
