- Erwin G*, Lee H* et al. “Whole-genome variant detection in long-read sequencing data from ultra-low input tumor samples” (In preparation)
- Hayan Lee, James Gurtowski, Shinjae Yoo, Maria Nattestad, Shoshana Marcus, Sara Goodwin, W. Richard McCombie, and Michael Schatz, The resurgence of reference quality genome, http://qb.cshl.edu/asm_model/predict.html, http://biorxiv.org/content/early/2016/04/13/048603 (preprint)
Please search for the full publications: Google Scholar, ORCID: 0000-0003-0571-3192
Publications
Gerhard GS, Allard JB, Kaniper S, Lynch D, Lee H, Kumar S. Genome Assembly of Arctica islandica, the Longest-Lived Non-Colonial Animal Species. Animals. Multidisciplinary Digital Publishing Institute; 2025 Feb 27;15(5):690.
Zhu Y, Lee H, White S, Weimer AK, Monte E, Horning A, Nevins SA, Esplin ED, Paul K, Krieger G, Shipony Z, Chiu R, Laquindanum R, Karathanos TV, Chua MWY, Mills M, Ladabaum U, Longacre T, Shen J, Jaimovich A, Lipson D, Kundaje A, Greenleaf WJ, Curtis C, Ford JM, Snyder MP. Global loss of promoter-enhancer connectivity and rebalancing of gene expression during early colorectal cancer carcinogenesis. Nat Cancer. Nature Publishing Group; 2024 Oct 30;1–16. PMID: 39478119
Esplin ED, Hanson C, Wu S, Horning AM, Barapour N, Nevins SA, Jiang L, Contrepois K, Lee H, Guha TK, Hu Z, Laquindanum R, Mills MA, Chaib H, Chiu R, Jian R, Chan J, Ellenberger M, Becker WR, Bahmani B, Khan A, Michael B, Weimer AK, Esplin DG, Shen J, Lancaster S, Monte E, Karathanos TV, Ladabaum U, Longacre TA, Kundaje A, Curtis C, Greenleaf WJ, Ford JM, Snyder MP. Multiomic analysis of familial adenomatous polyposis reveals molecular pathways associated with early tumorigenesis. Nat Cancer. 2024 Nov;5(11):1737–1753. PMCID: PMC11584401
Sharma A, Lee H, Statistical analysis of methylation reveals epigenetic biomarkers for high-functioning autism spectrum disorder. Journal of Student Research. 2024.
Gray ZH, Chakraborty D, Duttweiler RR, Alekbaeva GD, Murphy SE, Chetal K, Ji F, Ferman BI, Honer MA, Wang Z, Myers C, Sun R, Kaniskan HÜ, Toma MM, Bondarenko EA, Santoro JN, Miranda C, Dillingham ME, Tang R, Gozani O, Jin J, Skorski T, Duy C, Lee H, Sadreyev RI, Whetstine JR. Epigenetic balance ensures mechanistic control of MLL amplification and rearrangement. Cell. 2023 Oct 12;186(21):4528–4545.e18. PMCID: PMC10591855
Tricarico R, Madzo J, Scher G, Cohen M, Jelinek J, Maegawa S, Nagarathinam R, Scher C, Chang WC, Nicolas E, Slifker M, Zhou Y, Devarajan K, Cai KQ, Kwok T, Nakajima P, Xu J, Mancuso P, Doneddu V, Bagella L, Williams R, Balachandran S, Maskalenko N, Campbell K, Ma X, Cañadas I, Viana-Errasti J, Moreno V, Valle L, Grivennikov S, Peshkova I, Kurilenko N, Mazitova A, Koltsova E, Lee H, Walsh M, Duttweiler R, Whetstine JR, Yen TJ, Issa JP, Bellacosa A. TET1 and TDG Suppress Inflammatory Response in Intestinal Tumorigenesis: Implications for Colorectal Tumors With the CpG Island Methylator Phenotype. Gastroenterology. 2023 Feb 8:S0016-5085(23)00112-9. doi: 10.1053/j.gastro.2023.01.039. Epub ahead of print. PMID: 36764492.
Lin J, Lee H, Snyder M. Deep Neural Network Classifier for Alzheimer’s Disease. J Stud Res 2022;11.
Lee H, Feng G, Esplin E & Snyder M. Predictive Signatures for Lung Adenocarcinoma Prognostic Trajectory by Multiomics Data Integration and Ensemble Learning. in Mathematical and Computational Oncology 9–23 (Springer International Publishing, 2021)
International Symposium on Mathematical and Computational Oncology (ISMCO), 2021 (Best Paper Award)
Roodgar M, Good BH, Garud NR, Martis S, Avula M, Zhou W, Lee H, et al. Longitudinal linked-read sequencing reveals ecological and evolutionary responses of a human gut microbiome during antibiotic treatment. Genome Res. 2021;31:1433–46.
Wei Cao*, Hayan Lee*, Wei Wu*, Aubhishek Zaman*, Sean McCorkle, Ming Yan, Justin Chen, Qinghe Xing, Nasa Sinnott-Armstrong, Hongen Xu, M. Reza Sailani, Wenxue Tang, Yuanbo Cui, Jia liu, Hongyan Guan, Pengju Lv, Xiaoyan Sun, Lei Sun, Pengli Han, Yanan Lou, Jing Chang, Jinwu Wang, Yuchi Gao, Jiancheng Guo, Gundolf Schenk, Alan Hunter Shain, Fred G. Biddle, Eric Collisson, Michael Snyder & Trever G. Bivona
Multi-faceted epigenetic dysregulation of gene expression promotes esophageal squamous cell carcinoma
Nature Communications volume 11, Article number: 3675 (2020)
doi: 10.1038/s41598-018-37895-8
HuBMAP Consortium*
The human body at cellular resolution: the NIH Human Biomolecular Atlas Program
Nature 574:187–192 (2019)
doi: 10.1038/s41598-018-37895-8
Glaucia Mendes Souza, Marie-Anne Van Sluys, Carolina Gimiliani Lembke, Hayan Lee, Gabriel Rodrigues Alves Margarido, Carlos Takeshi Hotta, Jonas Weissmann Gaiarsa, Augusto Lima Diniz, Mauro de Medeiros Oliveira, Savio de Siqueira Ferreira, Milton Yutaka Nishiyama, Jr, Felipe ten-Caten, Geovani Tolfo Ragagnin, Pablo de Morais Andrade, Robson Francisco de Souza, Gianlucca Gonc¸alves Nicastro, Ravi Pandya, Changsoo Kim, Hui Guo, Alan Mitchell Durham, Monalisa Sampaio Carneiro, Jisen Zhang, Xingtan Zhang, Qing Zhang, Ray Ming, Michael C. Schatz, Bob Davidson, Andrew H. Paterson and David Heckerman
Assembly of the 373k gene space of the polyploid sugarcane genome reveals reservoirs of functional diversity in the world’s leading biomass crop
GigaScience, Volume 8, Issue 12, December 2019,
doi: 10.1038/s41598-018-37895-8
M. Reza Sailani, Jens Frey Halling, Henrik Devitt Møller, Hayan Lee, Peter Plomgaard, Henriette Pilegaard, Michael P. Snyder & Birgitte Regenberg
Lifelong physical activity is associated with promoter hypomethylation of genes involved in metabolism, myogenesis, contractile properties and oxidative stress resistance in aged human skeletal muscle
Scientific Reports 9, Article number: 3272 (2019)
doi: 10.1038/s41598-018-37895-8
Fritz J. Sedlazeck, Hayan Lee, Charlotte A. Darby & Michael C. Schatz (2018)
Piercing the dark matter: bioinformatics of long-range sequencing and mapping
Nature Reviews Genetics 19, 329–346 (2018)
doi: 10.1038/s41576-018-0003-4
Jason Miller et al. (2017)
Hybrid assembly with long and short reads improves discovery of gene family expansions
BMC Genomics 18:541
doi: 10.1186/s12864-017-3927-8
Ray Ming et al.
The pineapple genome reveals the evolution of CAM photosynthesis
Nature Genetics47,1435–1442(2015)
doi:10.1038/ng.3435
Shoshana Marcus, Hayan Lee, and Michael Schatz (2014)
SplitMEM: Graphical pan-genome analysis with suffix skips
Bioinformatics (2014) 30 (24):3476-3483.
doi:10.1093/bioinformatics/btu756
Michael C Schatz, Lyza G Maron, Joshua C Stein, Alejandro H Wences, James Gurtowski, Eric Biggers, Hayan Lee, Melissa Kramer, Eric Antonio, Elena Ghiban, Mark H Wright, Jer-ming Chia, Doreen Ware, Susan R McCouch and William R McCombie (2014) New whole genome de novo assemblies of three divergent strains of rice (O. sativa) documents novel gene space of aus and indica, Genome Biology 2014, 15(11):506, doi:10.1186/s13059-014-0506-z
Sangwoo Kim, Kyowon Jeong, Kunal Bhutani, Jeong Ho Lee, Anand Patel, Eric Scott, Hojung Nam, Hayan Lee, Joseph G Gleeson and Vineet Bafna (2013)
Virmid: accurate detection of somatic mutations with sample impurity inference, Genome Biology 2013, 14(8):R90
doi:10.1186/gb-2013-14-8-r90
Hayan Lee, Michael C. Schatz (2012)
Genomic Dark Matter: The reliability of short read mapping illustrated by the Genome Mappability Score
Bioinformatics (2012) 28 (16):2097-2105.
doi:10.1093/bioinformatics/bts330
Hayan Lee, H.-M. Tsai and O. Tonguz (2009)
On the Security of Intra-Car Wireless Sensor Networks
Proc. 70th IEEE Vehicular Technology Conference, Anchorage, Alaska, USA, September 2009.
https://sourceforge.net/p/gma-bio/wiki/Home/
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