- Erwin G*, Lee H* et al. “Whole-genome variant detection in long-read sequencing data from ultra-low input tumor samples” (In preparation)
- Horning A, Esplin E, Wu S, Hanson C, Bararpour N, Nevins SA, Jiang L, Contrepois K, Lee H, …, Michael P. Snyder, Multi-omic Analysis of Familial Adenomatous Polyposis Reveals Molecular Pathways and Polyclonal Spreading Associated with Early Tumorigenesis (In revision)
- 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)
Publications
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/
Lee Lab 