Hayan Lee

Short Bio

I am a Ph.D. student of Computer Science Deptment in Stony Brook University. My interests are computational biology using Machine Learning. Currently I am advised by Prof. Michael Schatz, Simons Center for Quantitative Biology in Cold Spring Harbor Laboratory (CSHL). I received my Master's degree from Carnegie Mellon University. Master thesis is published at 70th IEEE Vehicular Technology Conference. My undergraduate degree with Cum Laude was received at Seoul National University in Korea and worked for 4 years at Ahnlab, Inc., where I programmed Windows kernel-level file system filter driver for V3 anti-virus program.

Research Interests

I am interested in developing methods (tools/software) using statistical machine learning for long reads produced by 3rd generation sequencing technology such as PacBio, Moleculo and Oxford Nanopre. This includes de-novo genome assembly, alternative splicing, population structure analysis in large scale to discover biological importance.
Key words : Computationsl Biology, Machin Learning (ML), Probabilistic Graphical Model (PGM), Cloud Computing; Operating System, Computer Security, Virtualization and Wireless Sensor Network

Latest News

I successfully presented my thesis proposal "Long Read Sequencing Technology, Altorithms and applications". (05/04/2015)
My presentation slide about "MLE and its recent application in computational biology" is posted. (03/17/2015)
I will give a presentation about "Sugarcane Genome De Novo Assemblly Challenges" at the Sugar Cane Sequencing Initiative workshop, PAG XXIII. (12/24/2014)
ReadSim1.6 is released with improved speed and a new feature, dnasim, which simulates heterozygous polyploidy genome. (11/21/2014)
My talk "Sugarcane genome de novo assembly challenges" is selected as a platform presentaion for data mining session, Biological Data Science Meeting, CSHL (11/05/2014-11/08/2014) All of the presentations and talks are listed I'll serve as a program comittee member for Cancer Panomics in Pacific Symposium on Biocomputing (PSB) 2015
My internship in Microsoft Research, Redmond, WA started. (June - Aug, 2014)
I'll serve as a program comittee member for Cancer Panomics in Pacific Symposium on Biocomputing (PSB) 2014

Software

Publications and Talks

Conferences/Journals
1. Hayan Lee*, James Gurtowski*, Shinjae Yoo, Shoshana Marcus, W. Richard McCombie, and Michael Schatz (2014)
  Error corection and assembly complexity of single molecule sequencing reads
  (PDF)
  In submission
1. Shoshana Marcus, Hayan Lee, and Michael Schatz (2014)
  SplitMEM: Graphical pan-genome analysis with suffix skips
  Bioinformatics 30 (24): 3476-3483, Oxford Journals
1. 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 15(11)
1. 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 14(8)
1. Hayan Lee, Michael C. Schatz (2012)
  Genomic Dark Matter: The reliability of short read mapping illustrated by the Genome Mappability Score
  Bioinformatics 28(16) cited by the papers
1. Hayan Lee, H.-M. Tsai and O. Tonguz
  ''On the Security of Intra-Car Wireless Sensor Networks'' in Proc. 70th IEEE Vehicular Technology Conference, Anchorage, Alaska, USA, September 2009.
  cited by the papers
Citations
- Stats
Posters/Talks
1. Hayan Lee "Long read sequencing technology; Algorithms and its applications", Thesis proposal, May 4, 2015
2. Hayan Lee "MLE and its recent application in computational biology" in Schatz Lab meeting, March 17, 2015
3. Hayan Lee, Ravi Pandya, Gabriel Margarido, Bob Davidson, Michael Schatz, David Heckerman, "Sugarcane De Novo genome assembly chllenges, Biological Data Science, Nov 5-8, 2014, Cold Spring Harbor Laboratory, NY, [slides]
4. Hayan Lee, James Gurtowski, Shinjae Yoo, Shoshana Marcus and Michael Schatz ''How long is long enough?'', in Quantitative Biology Seminar, Cold Spring Harbor, NY, Feburary 2014 [slides]
5. Sangwoo Kim, Kyowon Jeong, Kunal Bhutani, Hayan Lee, and Vineet Bafna, ''Computational Identification of Within Individual Contamination for Higher Sensitivity in Somatic Mutation Profiling'' Conference on High Throughput Sequencing Methods and Applications (HiTSeq 2012, Special Interest Group of ISMB 2012), accepted for oral presentation.
6. Hayan Lee and Michael C. Schatz ''Genomic Dark Matter: The reliability of short read mapping illustrated by the Genome Mappability Score (GMS)'' in Poster, The 16th Annual International Conference on Research in Computational Molecular Biology, iarcelona, Spain. April 2012.
7. Hayan Lee and Michael C. Schatz ''Limitations of short read mappings illustrated by the Genome Mappability Score(GMS)'' in Poster, The 4th Annual Meeting on Personal Genomes, Cold Spring Harbor, NY, September 2011.
8. Hayan Lee and Michael C. Schatz ''Genome Mappability Score'' in Quantitative Biology Seminar, Cold Spring Harbor, NY, September 2011 [slides]

Program Committee

Pacific Symposium on Biocomputing (PSB) - Cancer Panomics, 2015
Pacific Symposium on Biocomputing (PSB) - Cancer Panomics, 2014

Paper Review

Bioinformatics, Oxford Journals

Previous Projects

Libraray level virtualization using only graphic library beyond platforms with WINE at ECSL (Experimental Computer Systmes Lab)

Multimodal Wireless Sensor Networks for Buildings as a part of iCast project at CyLab, Carnegie Mellon University. Collaborated with and sponsored by ITRI, Tiwan. Advised by Prof. Virgil Gligor.

Patent applied and pendding (Lee-Chun Ko, Hayan Lee, Virgil Gligor)

Hayan Lee

Department of Computer Science
Stony Brook University
100 Nicolls Road
Stony Brook, NY 11794

Simons Center for Quantitative Biology
Cold Spring Harbor Laboratory
One Bungtown Road
Koch Building rm1123
Cold Spring Harbor, NY 11724