Publications
Includes research articles and reviews published in peer-reviewed journal publications and preprint manuscripts.
1. Maden et al 2023, "lute: estimating the cell composition of heterogeneous tissue with varying cell sizes using gene expression". BioArxiv.
Maden, S.K., Huuki-Myers, L.A., Kwon, S.H., Collado-Torres, L., Maynard, K.R., & Hicks, S.C. (2024). lute: estimating the cell composition of heterogeneous tissue with varying cell sizes using gene expression. bioRxiv. Available at: https://doi.org/10.1101/2024.04.04.588105.
2. Huuki-Meyers et al 2024, "Benchmark of cellular deconvolution methods using a multi-assay reference dataset from postmortem human prefrontal cortex". BioArxiv.
Benchmark of cellular deconvolution methods using a multi-assay reference dataset from postmortem human prefrontal cortex Louise A. Huuki-Myers, Kelsey D. Montgomery, Sang Ho Kwon, Sophia Cinquemani, Nicholas J. Eagles, Daianna Gonzalez-Padilla, Sean K. Maden, Joel E. Kleinman, Thomas M. Hyde, Stephanie C. Hicks, Kristen R. Maynard, Leonardo Collado-Torres bioRxiv 2024.02.09.579665; doi: https://doi.org/10.1101/2024.02.09.579665
3. Maden et al 2023, "Challenges and opportunities to computationally deconvolve heterogeneous tissue with varying cell sizes using single-cell RNA-sequencing datasets". Genome Biology
Maden, S.K., Kwon, S.H., Huuki-Myers, L.A., Collado-Torres, L., Hicks, S.C., and Maynard, K.R. (2023) ‘Challenges and opportunities to computationally deconvolve heterogeneous tissue with varying cell sizes using single-cell RNA-sequencing datasets’, Genome Biology, 24(1), pp. 1-15. doi: 10.1186/s13059-023-03123-4.
4. Maden et al 2023, "recountmethylation enables flexible analysis of public blood DNA methylation array data". Bioinformatics Advances.
Sean K Maden, Brian Walsh, Kyle Ellrott, Kasper D Hansen, Reid F Thompson, Abhinav Nellore, recountmethylation enables flexible analysis of public blood DNA methylation array data, Bioinformatics Advances, Volume 3, Issue 1, 2023, vbad020, https://doi.org/10.1093/bioadv/vbad020
5. David and Sean et al 2022, "Retained introns in long RNA‑seq reads are not reliably detected in sample‑matched short reads". Genome Biology.
David, J.K., Maden, S.K., Wood, M.A., Thompson, R.F., and Nellore, A. (2022) ‘Retained introns in long RNA-seq reads are not reliably detected in sample-matched short reads’, Genome Biology. doi: 10.1186/s13059-022-02789-6.
6. Maden et al 2021, "Human methylome variation across Infinium 450K data on the Gene Expression Omnibus". Nucleic Acids Research Genomics and Bioinformatics
Sean K Maden, Reid F Thompson, Kasper D Hansen, Abhinav Nellore, Human methylome variation across Infinium 450K data on the Gene Expression Omnibus, NAR Genomics and Bioinformatics, Volume 3, Issue 2, June 2021, lqab025, https://doi.org/10.1093/nargab/lqab025
7. David et al 2020, "Putatively cancer-specific exon–exon junctions are shared across patients and present in developmental and other non-cancer cells". Nucleic Acids Research Cancer
Julianne K David, Sean K Maden, Benjamin R Weeder, Reid F Thompson, Abhinav Nellore, Putatively cancer-specific exon–exon junctions are shared across patients and present in developmental and other non-cancer cells, NAR Cancer, Volume 2, Issue 1, March 2020, zcaa001, https://doi.org/10.1093/narcan/zcaa001
8. Nguyen et al 2020, "Human Leukocyte Antigen Susceptibility Map for Severe Acute Respiratory Syndrome Coronavirus 2". Journal of Virology.
Nguyen A, David JK, Maden SK, Wood MA, Weeder BR, Nellore A, Thompson RF 2020. Human Leukocyte Antigen Susceptibility Map for Severe Acute Respiratory Syndrome Coronavirus 2. J Virol 94:10.1128/jvi.00510-20. https://doi.org/10.1128/jvi.00510-20
9. Wang et al 2020, "Dysfunctional epigenetic aging of the normal colon and colorectal cancer risk". Clinical Epigenetics.
Wang, T., Maden, S.K., Luebeck, G.E., Li, C.I., Newcomb, P.A., Ulrich, C.M., Joo, J.E., Buchanan, D.D., Milne, R.L., Southey, M.C., Carter, K.T., Willbanks, A.R., Luo, Y., Yu, M. and Grady, W.M., 2020. Dysfunctional epigenetic aging of the normal colon and colorectal cancer risk. Clinical Epigenetics, 12(1), p.5. DOI: 10.1186/s13148-019-0801-3.
10. Luebeck et al 2018, "Implications of Epigenetic Drift in Colorectal Neoplasia"
Luebeck GE, Hazelton WD, Curtius K, Maden SK, Yu M, Carter KT, Burke W, Lampe PD, Li CI, Ulrich CM, Newcomb PA, Westerhoff M, Kaz AM, Luo Y, Inadomi JM, Grady WM. “Implications of Epigenetic Drift in Colorectal Neoplasia.” Cancer Research 79, 495–504. 2019.
11. Yu and Maden and Stachler et al 2019, "Subtypes of Barrett’s Esophagus and Esophageal Adenocarcinoma Based on Genome-wide Methylation Analysis". Gut.
Guo, Y., Ayers, J.L., Carter, K.T., Wang, T., Maden, S.K., Edmond, D., Newcomb, P.P., Li, C., Ulrich, C., Yu, M., & Grady, W.M. (2019). Senescence‐associated tissue microenvironment promotes colon cancer formation through the secretory factor GDF15. Aging Cell, 18(6). doi:10.1111/acel.13013.
12. Smith and Maden and Lee et al 2019, "Consensus Machine Learning for Gene Target Selection in Pediatric AML Risk". BioArxiv.
Consensus Machine Learning for Gene Target Selection in Pediatric AML Risk. Jenny Smith, Sean K. Maden, David Lee, Ronald Buie, Vikas Peddu, Ryan Shean, Ben Busby. bioRxiv 632166; doi: https://doi.org/10.1101/632166
13. Barault et al 2018, "Discovery Of Methylated Circulating DNA Biomarkers For Comprehensive Non-Invasive Monitoring Of Treatment Response In Metastatic Colorectal Cancer". Gut.
Barault, L., Amatu, A., Siravegna, G., Ponzetti, A., Moran, S., Cassingena, A., Mussolin, B., Falcomatà, C., Binder, A.M., Cristiano, C., Oddo, D., Guarrera, S., Cancelliere, C., Bustreo, S., Bencardino, K., Maden, S., Vanzati, A., Zavattari, P., Matullo, G., Truini, M., Grady, W.M., Racca, P., Michels, K.B., Siena, S., Esteller, M., Bardelli, A., Sartore-Bianchi, A., & Di Nicolantonio, F. (2017). Discovery of methylated circulating DNA biomarkers for comprehensive non-invasive monitoring of treatment response in metastatic colorectal cancer. Gut, 67(11), 1995-2005. doi:10.1136/gutjnl-2016-313372.
14. Guo et al 2018, "Senescence‐associated tissue microenvironment promotes colon cancer formation through the secretory factor GDF15". Aging Cell.
Guo, Y., Ayers, J.L., Carter, K.T., Wang, T., Maden, S.K., Edmond, D., Newcomb, P.P., Li, C., Ulrich, C., Yu, M. and Grady, W.M., 2019. Senescence-associated tissue microenvironment promotes colon cancer formation through the secretory factor GDF15. Aging Cell, 18(6). Available at: http://dx.doi.org/10.1111/acel.13013.
15. Luebeck et al 2017, "Identification of a key role of widespread epigenetic drift in Barrett’s esophagus and esophageal adenocarcinoma". Clinical Epigenetics.
Luebeck, E.G., Curtius, K., Hazelton, W.D., Maden, S., Yu, M., Thota, P.N., Patil, D.T., Chak, A., Willis, J.E. and Grady, W.M. (2017) ‘Identification of a key role of widespread epigenetic drift in Barrett’s esophagus and esophageal adenocarcinoma’, Clinical Epigenetics, 9(1), p.113. doi:10.1186/s13148-017-0409-4.
16. Kim et al 2013, "Dietary fatty acid intake is associated with paraoxonase 1 activity in a cohort-based analysis of 1,548 subjects". Lipids in Health and Disease.
Kim, D.S., Maden, S.K., Burt, A.A., Ranchalis, J.E., Furlong, C.E., & Jarvik, G.P. (2013) ‘Dietary fatty acid intake is associated with paraoxonase 1 activity in a cohort-based analysis of 1,548 subjects’, Lipids in Health and Disease, 12, Article number: 183. doi:10.1186/1476-511X-12-183.