Publications
Manuscripts authored (*first author)Peer-reviewed publications
1.
Maden, S. K.*, B. Walsh, K. Ellrott, K. D. Hansen, R. F. Thompson, A. Nellore. Recountmethylation enables flexible analysis of public blood DNA methylation array data. Bioinformatics Advances 3, no. 1 (January 1, 2023): vbad020. https://doi.org/10.1093/bioadv/vbad020.
2.
David, J. K.*, S. K. Maden*, M. A. Wood, R. F. Thompson, A. Nellore. Retained introns in long RNA-seq reads are not reliably detected in sample-matched short reads. Genome Biology 23, 240 (2022).
3.
Maden, S. K.*, R. F. Thompson, K. D. Hansen, A. Nellore. Human methylome variation across Infinium 450K data on the Gene Expression Omnibus. NAR Genomics and Bioinformatics 3, lqab025 (2021).
4.
David, J. K.*, S. K. Maden, B. R. Weeder, R. F. Thompson, A. Nellore. Putatively cancer-specific exon–exon junctions are shared across patients and present in developmental and other non-cancer cells. NAR Cancer 2, zcaa001 (2020).
5.
Nguyen, A.*, J. K. David, S. K. Maden, M. A. Wood, B. R. Weeder, A. Nellore, R. F. Thompson. Human Leukocyte Antigen Susceptibility Map for Severe Acute Respiratory Syndrome Coronavirus 2. Journal of Virology 94, e00510–20.
6.
Wang, T.*, S. K. Maden, G. E. Luebeck, L. I. Christopher, P. A. Newcomb, C. M. Ulrich, J. E. Joo, D. D. Buchanan, R. L. Milne, M. C. Southey, K. T. Carter, A. R. Willbanks, Y. Luo, M. Yu, W. M. Grady. Dysfunctional epigenetic aging of the normal colon and colorectal cancer risk. Clinical Epigenetics 12, 5 (2020).
7.
Luebeck, G. E.*, W. D. Hazelton, K. Curtius, S. K. Maden, M. Yu, K. T. Carter, W. Burke, P. D. Lampe, C. I. Li, C. M. Ulrich, P. A. Newcomb, M. Westerhoff, A. M. Kaz, Y. Luo, J. M. Inadomi, W. M. Grady. Implications of Epigenetic Drift in Colorectal Neoplasia. Cancer Research 79, 495–504 (2019).
8.
Yu, M.*, Maden, S. K.*, Stachler M. S.*, A. M. J. Ayers, Y. Guo, K. T. Carter, A. Willbanks, T. J. Heinzerling, R. M. O'Leary, X. Xu, A. Bass, A. K. Chandar, A. Chak, R. Elliott, J. E. Willis, S. D. Markowitz, W. M. Grady. Subtypes of Barrett’s oesophagus and oesophageal adenocarcinoma based on genome-wide methylation analysis. Gut 68, 389–399 (2019).
9.
Luebeck, G. E.*, K. Curtius, W. D. Hazelton, S. Maden, M. Yu, P. N. Thota, D. T. Patil, A. Chak, J. E. Willis, W. M. Grady. Identification of a key role of widespread epigenetic drift in Barrett’s esophagus and esophageal adenocarcinoma. Clinical Epigenetics 9, 113 (2017).
10.
Kim, D. S.*, S. K. Maden, A. A. Burt, J. E. Ranchalis, C. E. Furlong, G. P. Jarvik. 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, 183 (2013).
Preprint publications
11.
Maden, S. K.*, S. H. Kwon, L. A. Huuki-Myers, L. Collado-Torres, S. C. Hicks, K. R. Maynard. Challenges and opportunities to computationally deconvolve heterogeneous tissue with varying cell sizes using single cell RNA-sequencing datasets. (2023) doi:10.48550/arXiv.2305.06501.
12.
Smith, J.*, S. K. Maden*, D. Lee*, R. Buie, V. Peddu, R. Shean, B. Busby. Consensus Machine Learning for Gene Target Selection in Pediatric AML Risk. 632166 https://www.biorxiv.org/content/10.1101/632166v1 (2019) doi:10.1101/632166.