John Quackenbush - Publications

Affiliations: 
Biostatistics Harvard Chan School of Public Health 

40 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2020 Lopes-Ramos CM, Quackenbush J, DeMeo DL. Genome-Wide Sex and Gender Differences in Cancer. Frontiers in Oncology. 10: 597788. PMID 33330090 DOI: 10.3389/fonc.2020.597788  0.56
2020 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, ... ... Quackenbush J, et al. infection with frequent viral coinfection contributes to postinfectious hydrocephalus in Ugandan infants. Science Translational Medicine. 12. PMID 32998967 DOI: 10.1126/scitranslmed.aba0565  0.56
2020 Kuijjer ML, Fagny M, Marin A, Quackenbush J, Glass K. PUMA: PANDA Using MicroRNA Associations. Bioinformatics (Oxford, England). PMID 32860050 DOI: 10.1093/Bioinformatics/Btaa571  0.56
2020 Lopes-Ramos CM, Chen CY, Kuijjer ML, Paulson JN, Sonawane AR, Fagny M, Platig J, Glass K, Quackenbush J, DeMeo DL. Sex Differences in Gene Expression and Regulatory Networks across 29 Human Tissues. Cell Reports. 31: 107795. PMID 32579922 DOI: 10.1016/J.Celrep.2020.107795  0.56
2020 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, ... ... Quackenbush J, et al. Molecular networks in Network Medicine: Development and applications. Wiley Interdisciplinary Reviews. Systems Biology and Medicine. e1489. PMID 32307915 DOI: 10.1002/Wsbm.1489  0.56
2020 Morrow JD, Make B, Regan E, Han M, Hersh CP, Tal-Singer R, Quackenbush J, Choi AMK, Silverman EK, DeMeo DL. DNA Methylation is Predictive of Mortality in Current and Former Smokers. American Journal of Respiratory and Critical Care Medicine. PMID 31995399 DOI: 10.1164/rccm.201902-0439OC  0.44
2019 Fagny M, Platig J, Kuijjer ML, Lin X, Quackenbush J. Nongenic cancer-risk SNPs affect oncogenes, tumour-suppressor genes, and immune function. British Journal of Cancer. PMID 31806877 DOI: 10.1038/S41416-019-0614-3  0.56
2019 Kuijjer ML, Hsieh PH, Quackenbush J, Glass K. lionessR: single sample network inference in R. Bmc Cancer. 19: 1003. PMID 31653243 DOI: 10.1186/S12885-019-6235-7  0.56
2019 Campbell PT, Ambrosone CB, Nishihara R, Aerts HJWL, Bondy M, Chatterjee N, Garcia-Closas M, Giannakis M, Golden JA, Heng YJ, Kip NS, Koshiol J, Liu XS, Lopes-Ramos CM, Mucci LA, ... ... Quackenbush J, et al. Proceedings of the fourth international molecular pathological epidemiology (MPE) meeting. Cancer Causes & Control : Ccc. PMID 31069578 DOI: 10.1007/s10552-019-01177-z  0.56
2019 Lopes-Ramos CM, Kuijjer ML, Ogino S, Fuchs CS, DeMeo DL, Glass K, Quackenbush J. Correction: Gene Regulatory Network Analysis Identifies Sex-Linked Differences in Colon Cancer Drug Metabolism. Cancer Research. 79: 2084. PMID 30987980 DOI: 10.1158/0008-5472.Can-19-0678  0.56
2019 Kuijjer ML, Tung MG, Yuan G, Quackenbush J, Glass K. Estimating Sample-Specific Regulatory Networks. Iscience. 14: 226-240. PMID 30981959 DOI: 10.1016/J.Isci.2019.03.021  0.56
2018 Lopes-Ramos CM, Kuijjer ML, Ogino S, Fuchs CS, DeMeo DL, Glass K, Quackenbush J. Gene Regulatory Network Analysis Identifies Sex-Linked Differences in Colon Cancer Drug Metabolism. Cancer Research. 78: 5538-5547. PMID 30275053 DOI: 10.1158/0008-5472.Can-18-0454  0.56
2018 Barry JD, Fagny M, Paulson JN, Aerts HJWL, Platig J, Quackenbush J. Histopathological Image QTL Discovery of Immune Infiltration Variants. Iscience. 5: 80-89. PMID 30240647 DOI: 10.1016/J.Isci.2018.07.001  0.56
2018 Kuijjer ML, Paulson JN, Salzman P, Ding W, Quackenbush J. Cancer subtype identification using somatic mutation data. British Journal of Cancer. PMID 29765148 DOI: 10.1038/S41416-018-0109-7  0.56
2018 Carette X, Platig J, Young DC, Helmel M, Young AT, Wang Z, Potluri LP, Moody CS, Zeng J, Prisic S, Paulson JN, Muntel J, Madduri AVR, Velarde J, Mayfield JA, ... ... Quackenbush J, et al. Multisystem Analysis ofReveals Kinase-Dependent Remodeling of the Pathogen-Environment Interface. Mbio. 9. PMID 29511081 DOI: 10.1128/Mbio.02333-17  0.56
2018 Morrow JD, Cho MH, Platig J, Zhou X, DeMeo DL, Qiu W, Celli B, Marchetti N, Criner GJ, Bueno R, Washko GR, Glass K, Quackenbush J, Silverman EK, Hersh CP. Ensemble genomic analysis in human lung tissue identifies novel genes for chronic obstructive pulmonary disease. Human Genomics. 12: 1. PMID 29335020 DOI: 10.1186/S40246-018-0132-Z  0.56
2018 Morrow JD, Glass K, Cho MH, Hersh CP, Pinto-Plata V, Celli B, Marchetti N, Criner G, Bueno R, Washko G, Choi AMK, Quackenbush J, Silverman EK, DeMeo DL. Human Lung DNA Methylation Quantitative Trait Loci Colocalize with COPD Genome-wide Association Loci. American Journal of Respiratory and Critical Care Medicine. PMID 29313708 DOI: 10.1164/Rccm.201707-1434Oc  0.56
2017 Driesbaugh KH, Branchetti E, Grau JB, Keeney SJ, Glass K, Oyama MA, Rioux N, Ayoub S, Sacks MS, Quackenbush J, Levy RJ, Ferrari G. Serotonin receptor 2B signaling with interstitial cell activation and leaflet remodeling in degenerative mitral regurgitation. Journal of Molecular and Cellular Cardiology. PMID 29291394 DOI: 10.1016/J.Yjmcc.2017.12.014  0.56
2017 Schlauch D, Glass K, Hersh CP, Silverman EK, Quackenbush J. Estimating drivers of cell state transitions using gene regulatory network models. Bmc Systems Biology. 11: 139. PMID 29237467 DOI: 10.1186/S12918-017-0517-Y  0.56
2017 Sonawane AR, Platig J, Fagny M, Chen CY, Paulson JN, Lopes-Ramos CM, DeMeo DL, Quackenbush J, Glass K, Kuijjer ML. Understanding Tissue-Specific Gene Regulation. Cell Reports. 21: 1077-1088. PMID 29069589 DOI: 10.1016/J.Celrep.2017.10.001  0.56
2017 Hicks SC, Okrah K, Paulson JN, Quackenbush J, Irizarry RA, Bravo HC. Smooth quantile normalization. Biostatistics (Oxford, England). PMID 29036413 DOI: 10.1093/Biostatistics/Kxx028  0.56
2017 Paulson JN, Chen CY, Lopes-Ramos CM, Kuijjer ML, Platig J, Sonawane AR, Fagny M, Glass K, Quackenbush J. Tissue-aware RNA-Seq processing and normalization for heterogeneous and sparse data. Bmc Bioinformatics. 18: 437. PMID 28974199 DOI: 10.1186/S12859-017-1847-X  0.56
2017 Lopes-Ramos CM, Paulson JN, Chen CY, Kuijjer ML, Fagny M, Platig J, Sonawane AR, DeMeo DL, Quackenbush J, Glass K. Regulatory network changes between cell lines and their tissues of origin. Bmc Genomics. 18: 723. PMID 28899340 DOI: 10.1186/S12864-017-4111-X  0.56
2017 Fagny M, Paulson JN, Kuijjer ML, Sonawane AR, Chen CY, Lopes-Ramos CM, Glass K, Quackenbush J, Platig J. Exploring regulation in tissues with eQTL networks. Proceedings of the National Academy of Sciences of the United States of America. PMID 28851834 DOI: 10.1073/Pnas.1707375114  0.56
2017 Qiu W, Guo F, Glass K, Guo Cheng Yuan, Quackenbush J, Zhou X, Tantisira KG. Differential Connectivity of Gene Regulatory Networks Distinguishes Corticosteroid Response in Asthma. The Journal of Allergy and Clinical Immunology. PMID 28736268 DOI: 10.1016/J.Jaci.2017.05.052  0.56
2017 Nishihara R, Glass K, Mima K, Hamada T, Nowak JA, Qian ZR, Kraft P, Giovannucci EL, Fuchs CS, Chan AT, Quackenbush J, Ogino S, Onnela JP. Biomarker correlation network in colorectal carcinoma by tumor anatomic location. Bmc Bioinformatics. 18: 304. PMID 28623901 DOI: 10.1186/S12859-017-1718-5  0.56
2017 Hill KE, Kelly AD, Kuijjer ML, Barry W, Rattani A, Garbutt CC, Kissick H, Janeway K, Perez-Atayde A, Goldsmith J, Gebhardt MC, Arredouani MS, Cote G, Hornicek F, Choy E, ... ... Quackenbush J, et al. An imprinted non-coding genomic cluster at 14q32 defines clinically relevant molecular subtypes in osteosarcoma across multiple independent datasets. Journal of Hematology & Oncology. 10: 107. PMID 28506242 DOI: 10.1186/S13045-017-0465-4  0.56
2017 Schlauch D, Paulson JN, Young A, Glass K, Quackenbush J. Estimating Gene Regulatory Networks with pandaR. Bioinformatics (Oxford, England). PMID 28334344 DOI: 10.1093/Bioinformatics/Btx139  0.56
2017 Morrow JD, Zhou X, Lao T, Jiang Z, DeMeo DL, Cho MH, Qiu W, Cloonan S, Pinto-Plata V, Celli B, Marchetti N, Criner GJ, Bueno R, Washko GR, Glass K, ... Quackenbush J, et al. Functional interactors of three genome-wide association study genes are differentially expressed in severe chronic obstructive pulmonary disease lung tissue. Scientific Reports. 7: 44232. PMID 28287180 DOI: 10.1038/Srep44232  0.56
2017 Campbell PT, Rebbeck TR, Nishihara R, Beck AH, Begg CB, Bogdanov AA, Cao Y, Coleman HG, Freeman GJ, Heng YJ, Huttenhower C, Irizarry RA, Kip NS, Michor F, Nevo D, ... ... Quackenbush J, et al. Proceedings of the third international molecular pathological epidemiology (MPE) meeting. Cancer Causes & Control : Ccc. PMID 28097472 DOI: 10.1007/s10552-016-0845-z  0.32
2016 Platig J, Castaldi PJ, DeMeo D, Quackenbush J. Bipartite Community Structure of eQTLs. Plos Computational Biology. 12: e1005033. PMID 27618581 DOI: 10.1371/Journal.Pcbi.1005033  0.56
2016 Morrow JD, Cho MH, Hersh CP, Pinto-Plata V, Celli B, Marchetti N, Criner G, Bueno R, Washko G, Glass K, Choi AM, Quackenbush J, Silverman EK, DeMeo DL. DNA methylation profiling in human lung tissue identifies genes associated with COPD. Epigenetics. 0. PMID 27564456 DOI: 10.1080/15592294.2016.1226451  0.56
2016 Vargas AJ, Quackenbush J, Glass K. Diet-induced weight loss leads to a switch in gene regulatory network control in the rectal mucosa. Genomics. PMID 27524493 DOI: 10.1016/J.Ygeno.2016.08.001  0.56
2016 van IJzendoorn DG, Glass K, Quackenbush J, Kuijjer ML. PyPanda: a Python package for gene regulatory network reconstruction. Bioinformatics (Oxford, England). PMID 27402905 DOI: 10.1093/Bioinformatics/Btw422  0.56
2016 Cloonan SM, Glass K, Laucho-Contreras ME, Bhashyam AR, Cervo M, Pabón MA, Konrad C, Polverino F, Siempos II, Perez E, Mizumura K, Ghosh MC, Parameswaran H, Williams NC, Rooney KT, ... ... Quackenbush J, et al. Mitochondrial iron chelation ameliorates cigarette smoke-induced bronchitis and emphysema in mice. Nature Medicine. PMID 26752519 DOI: 10.1038/Nm.4021  0.56
2015 Glass K, Quackenbush J, Spentzos D, Haibe-Kains B, Yuan GC. A network model for angiogenesis in ovarian cancer. Bmc Bioinformatics. 16: 115. PMID 25888305 DOI: 10.1186/S12859-015-0551-Y  0.56
2015 Lao T, Glass K, Qiu W, Polverino F, Gupta K, Morrow J, Mancini JD, Vuong L, Perrella MA, Hersh CP, Owen CA, Quackenbush J, Yuan GC, Silverman EK, Zhou X. Haploinsufficiency of Hedgehog interacting protein causes increased emphysema induced by cigarette smoke through network rewiring. Genome Medicine. 7: 12. PMID 25763110 DOI: 10.1186/S13073-015-0137-3  0.56
2014 Glass K, Quackenbush J, Silverman EK, Celli B, Rennard SI, Yuan GC, DeMeo DL. Sexually-dimorphic targeting of functionally-related genes in COPD. Bmc Systems Biology. 8: 118. PMID 25431000 DOI: 10.1186/S12918-014-0118-Y  0.56
2013 Glass K, Huttenhower C, Quackenbush J, Yuan GC. Passing messages between biological networks to refine predicted interactions. Plos One. 8: e64832. PMID 23741402 DOI: 10.1371/Journal.Pone.0064832  0.56
2012 Waldron L, Ogino S, Hoshida Y, Shima K, McCart Reed AE, Simpson PT, Baba Y, Nosho K, Segata N, Vargas AC, Cummings MC, Lakhani SR, Kirkner GJ, Giovannucci E, Quackenbush J, et al. Expression profiling of archival tumors for long-term health studies. Clinical Cancer Research : An Official Journal of the American Association For Cancer Research. 18: 6136-46. PMID 23136189 DOI: 10.1158/1078-0432.Ccr-12-1915  0.32
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