Hayan Lee, PhD

1. Gray Z, Chakraborty D, Duttweiller R, Alekbaeva G, Murphy S, Chetal K, Ji F, Wang Z, Myers C, Sun
M, Kaniskan HU, Dillingham M, Tang R, Gozani O, Jin J, Duy C, Lee H, Sadreyev R, and Whetstine
J, Histone 3 lysine 9 methylation balance controls site-specific DNA amplification and genomic
rearrangements of the Mixed Lineage Leukemia (MLL) gene. (submitted)

2. Sorscher S, LoPiccolo J, Heald B, Chen D, Bristow SL, Michalski ST, Nielsen SM, Lacoste A, Keyder
E, Lee H, Nussbaum RL, Martins R, Esplin ED, Rate of pathogenic germline variants in patients with
lung cancer. (submitted)

3. 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). Best Paper Award!

4. 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. PMCID: PMC8327913

5. Cao W*, Lee H*, Wu W*, Zaman A*, McCorkle S, Yan M, Chen J, Xing Q, Sinnott-Armstrong N, Xu
H, Sailani MR, Tang W, Cui Y, Liu J, Guan H, Lv P, Sun X, Sun L, Han P, Lou Y, Chang J, Wang J,
Gao Y, Guo J, Schenk G, Shain AH, Biddle FG, Collisson E, Snyder M, Bivona TG. Multi-faceted
epigenetic dysregulation of gene expression promotes esophageal squamous cell carcinoma. Nat
Commun. 2020 Jul 22;11(1):3675. PMCID: PMC7376194

6. Sailani MR, Jahanbani F, Abbott CW, Lee H, Zia A, Rego S, Winkelmann J, Hopfner F, Khan TN,
Katsanis N, Müller SH, Berg D, Lyman KM, Mychajliw C, Deuschl G, Bernstein JA, Kuhlenbäumer G,
Snyder MP. Candidate variants in TUB are associated with familial tremor. PLoS Genet. 2020
Sep;16(9):e1009010. PMCID: PMC7529431

7. Roodgar M, Babveyh A, Nguyen LH, Zhou W, Sinha R, Lee H, Hanks JB, Avula M, Jiang L, Jian R,
Lee H, Song G, Chaib H, Weissman IL, Batzoglou S, Holmes S, Smith DG, Mankowski JL, Prost S,
Snyder MP. Chromosome-level de novo assembly of the pig-tailed macaque genome using linked-read
sequencing and HiC proximity scaffolding. Gigascience. 2020 Jul 1;9(7). PMCID: PMC7350979

8. Sailani MR, Halling JF, Møller HD, Lee H, Plomgaard P, Pilegaard H, Snyder MP, Regenberg B.
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. 2019. PMCID: PMC6397284

9. Souza GM, Van Sluys M-A, Lembke CG, Lee H, Margarido GRA, Hotta CT, Gaiarsa JW, Diniz AL,
Oliveira M de M, Ferreira S de S, Nishiyama MY, Ten-Caten F, Ragagnin GT, Andrade P de M, de
Souza RF, Nicastro GG, Pandya R, Kim C, Guo H, Durham AM, Carneiro MS, Zhang J, Zhang X,
Zhang Q, Ming R, Schatz MC, Davidson B, Paterson AH, Heckerman D. Assembly of the 373k gene
space of the polyploid sugarcane genome reveals reservoirs of functional diversity in the world’s
leading biomass crop. Gigascience. 2019 Dec 1;8(12). PMCID: PMC6884061

10. HuBMAP Consortium. The human body at cellular resolution: the NIH Human Biomolecular Atlas
Program. Nature. 2019 Oct;574(7777):187–192. PMCID: PMC6800388

11. Sedlazeck FJ, Lee H, Darby CA, Schatz MC. Piercing the dark matter: bioinformatics of long-range
sequencing and mapping. Nat Rev Genet. 2018 Jun;19(6):329–346. PMID: 29599501

12. Miller JR, Zhou P, Mudge J, Gurtowski J, Lee H, Ramaraj T, Walenz BP, Liu J, Stupar RM, Denny R,
Song L, Singh N, Maron LG, McCouch SR, McCombie WR, Schatz MC, Tiffin P, Young ND,
Silverstein KAT. Hybrid assembly with long and short reads improves discovery of gene family
expansions. BMC Genomics. 2017 Jul 19;18(1):541. PMCID: PMC5518131
 

13. Ming R, VanBuren R, Wai CM, Tang H, Schatz MC, Bowers JE, Lyons E, Wang M-L, Chen J, Biggers
E, Zhang J, Huang L, Zhang L, Miao W, Zhang J, Ye Z, Miao C, Lin Z, Wang H, Zhou H, Yim WC,
Priest HD, Zheng C, Woodhouse M, Edger PP, Guyot R, Guo H-B, Guo H, Zheng G, Singh R, Sharma
A, Min X, Zheng Y, Lee H, Gurtowski J, Sedlazeck FJ, Harkess A, McKain MR, Liao Z, Fang J, Liu J,
Zhang X, Zhang Q, Hu W, Qin Y, Wang K, Chen L-Y, Shirley N, Lin Y-R, Liu L-Y, Hernandez AG,
Wright CL, Bulone V, Tuskan GA, Heath K, Zee F, Moore PH, Sunkar R, Leebens-Mack JH, Mockler
T, Bennetzen JL, Freeling M, Sankoff D, Paterson AH, Zhu X, Yang X, Smith JAC, Cushman JC, Paull
RE, Yu Q. The pineapple genome and the evolution of CAM photosynthesis. Nat Genet. 2015
Dec;47(12):1435–1442. PMCID: PMC4867222

14. Marcus S, Lee H, Schatz MC. SplitMEM: a graphical algorithm for pan-genome analysis with suffix
skips. Bioinformatics. 2014 Dec 15;30(24):3476–3483. PMCID: PMC4253837

15. Schatz MC, Maron LG, Stein JC, Hernandez Wences A, Gurtowski J, Biggers E, Lee H, Kramer M,
Antoniou E, Ghiban E, Wright MH, Chia J-M, Ware D, McCouch SR, McCombie WR. Whole-genome
de novo assemblies of three divergent strains of rice, Oryza sativa, document novel gene space of aus
and indica. Genome Biol. 2014;15(11):506. PMCID: PMC4268812

16. Kim S, Jeong K, Bhutani K, Lee J, Patel A, Scott E, Nam H, Lee H, Gleeson JG, Bafna V. Virmid:
accurate detection of somatic mutations with sample impurity inference. Genome Biol. 2013 Aug
29;14(8):R90. PMCID: PMC4054681

17. Lee H, Schatz MC. Genomic dark matter: the reliability of short read mapping illustrated by the
genome mappability score. Bioinformatics. 2012 Aug 15;28(16):2097–2105. PMCID: PMC3413383

18. Lee H, Tsai H-M, Tonguz OK. On the Security of Intra-Car Wireless Sensor Networks. IEEE 70th
Vehicular Technology Conference. 2009. Available from:
http://dx.doi.org/10.1109/vetecf.2009.5378964