About Me


Shantao Li


I am a third year Ph.D student in the Computational Biology and Bioinformatics Program, Yale University. My thesis advisor is Professor Mark Gerstein. I work on next-generation sequencing processing, large-scale data mining, algorithm development and implementation in bioinformatics.

Before graduate school, I obtained B.Sci. degree from Fudan University.


Structural Variation in Human Genome

Structural variation (SV) refers to genomic variation that involves large pieces of DNA. Some common examples are deletion, insertion, duplication, inversion and translocation. 

Structural variations can produce huge impacts on human genome. Studies have showed de novo structural variations are associated with autism (Marshall et al., 2008), schizophrenia and bipolar disorder (ISC, 2009). Moreover, somatic structural variations potentially lead to cancer development. The target of a famous drug, Imatinib(Gleevec), is a chimeric kinase product resulting from a translocation event in CML patients.

My research involves developing computational tools for structural variation discovery. As the sequencing datasets are growing, my research focuses on both computational complexity and accuracy.

Meanwhile, I work on structural variation analysis. I hope to unveil mechanisms of structural variant events using computational approaches.


Biological Network Analysis

There are many networks in biology: protein interaction, transcription regulation, metabolism and many more. While flowing around in these networks, information gets processed and integrated. Since creatures are often facing a constantly changing environment, they have developed sophisticated network structures to efficiently process signal inputs from the outside world.

I am interested in understanding the underlying structures of networks and how they help organisms to achieve rapid response and adaption to the environment. Also, using graphical models, I study network perturbation and rewiring, in both physiological (adaptive) and pathological (disruptive) situations. 

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Beyond Biology...

Although biology is already a huge fascinating world, I am intrigued by many problems in other fields as well. Especially, I would like to apply the lessons we have learnt in biology to the world at large, and vice versa. 

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Yale University
Ph.D in Computational Bioinformatics (conc. in Comp. Sci.)
Advisor: Mark Gerstein
2012 – 2017 (expected)

Fudan University
B.Sci. (with Honors) in Biological Science
GPA: 3.83, Rank: 1/126
2008 – 2012

UCLA-DOE Institute for Genomics and Proteomics
CSST Fellow in Eisenberg Lab
Research Evaluation: A+
2011 Summer

The Chinese University of Hong Kong
Exchange student
2010 Fall

Harvard Summer School
2010 Summer

Friedrich-Glück-Schule Grundschule, Oberensingen Germany
Burgschule, Plochingen Germany

Primary School, Grade 2 – 4
Accepted by Gymnasium, Plochigen
1998 – 2001

Selected Honors and Awards

Yale University Fellowship
2012 - 2015

UCLA Cross-disciplinary Scholar in Science & Technology (CSST) Fellow
2011 Summer

Hui-Chun Chin and Tsung-Dao Lee Chinese Undergraduate Research Endowment(CURE) Fellow
2011 – 2012

National Scholarship (Ministry of Education, 2%)
Fudan Alumni Scholarship (3%)
Fosun Pharma Scholarship, First(1%)
Fude Scholarship (2%)

Work Experience

Yale University
Teaching Assistant
2013 Fall & 2014 Spring

Bristol-Myers Squibb
Software Engineer Intern, Automation Dept.
2013 Summer

ZS Associates
Part-time Associate (Data Analysis)
2012 Spring

Huang Lab, Fudan University
Undergraduate Research Assistant (Comp. Bio.)
2011.1 – 2012.6

Computer Expertise

Programming Languages: C/C++, Python, OpenMPI/OpenMP, MatLab, CUDA
Data Analysis: R
Others: Shell, LaTex, SQL, HTML, JS


Chinese (Native)


You can link my Linkedin to know more about me.

Also, you are always welcomed to contact me via email. Please send me emails to shantao dot li at yale dot edu.

Thank you!

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