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Si-Han Chen

Curriculum Vitae Page 1

Si-Han Chen

Address: Academia Sinica, Taiwan Lab: +886-2-27855696 ext 7031
Institute of Biological Chemistry, Room 703 Home: +886-2-29691262
No. 128, Sec. 2, Academia Road, Nankang, E-mail: r93B46005@ntu.edu.tw
Taipei City 115, Taiwan, ROC. Website: http://niwhu.blogspot.com/

RESEARCH INTERESTS & GOALS

My main research interests include the binding energetics of biomolecules, their
structural dynamics, and their diffusive motion in living cells or cell-like environment. I
am applying for biophysics programs at the PhD level as I hope to learn more about
single-molecular techniques such as near-field, time-resolved fluorescence and cryo-
electron microscopes that would allow us to better understand the dynamics and
energetics of biomolecules in a scale-free manner. My past research experience
involves thermodynamics of biomolecular recognition, characterization of DNA-protein
complexes, and structural analysis of triple helical and G-quadruplex DNA, all of which
support the extension of my research interests. As for laboratory skills, I use molecular
cloning, site-directed mutagenesis, and other basic molecular biology techniques for
my daily benchwork. I specialize in isothermal titration calorimetry (ITC) and am
experienced in differential scanning calorimetry (DSC), analytical ultracentrifugation
(AUC), circular dichroism (CD), and fluorescence anisotropy. I am also familiar with
surface plasmon resonance (SPR) and dynamic light scattering (DLS).

EDUCATION

National Taiwan University, Taipei, Taiwan, R.O.C.
Master of Science, Biochemical Sciences (9/2004-6/2006)
Thesis: Thermodynamic Characterization of DNA-binding Activity of Human Lon
Protease
Advisor: Prof. Shih-Hsiung Wu
Overall GPA: 4.00/4.00, Class Rank: 2/27 (7%)
National Dong Hwa University, Hualien, Taiwan, R.O.C.
Bachelor of Science, Life Science (9/2000-6/2004)
Advisor: Prof. Chia-Ching Chang, Department of Physics, NDHU
Co-advisor: Dr. Lou-Sing Kan, Institute of Chemistry, Academia Sinica
Overall GPA: 3.94/4.00; Science GPA: 3.97/4.00, Class Rank: 1/61 (2%)

WORK EXPERIENCE

Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan, R.O.C.
Research Assistant (2006~present)
- Investigating the dynamics of rat mitochondrial nucleoid and the involved protein-
protein/protein-DNA interactions
- Analyzing the structural properties of mitochondrial DNA replicative intermediates
- Sub-cloning of human lon and defining its DNA-binding domain
Si-Han Chen
Curriculum Vitae Page 2

PUBLICATIONS

JOURNAL ARTICLES
Nucleic Acids Research (2008) 36(4):1273-1287
Chen SH, Suzuki CK, and Wu SH, “Thermodynamic Characterization of Specific
Interactions between the Human Lon Protease and G-quartet DNA”

CONFERENCE PAPERS
Mitochondria Minisymposium: Mitochondria and their Proteomics, Bethesda,
Maryland, USA (2008)
Suzuki CK, Lu B, Santos J, Tian B, Chen SH and Wu SH, “Multitasking in the
Mitochondrion by the Lon Protease in Protein and mtDNA Quality Control”
5th East Asian Biophysics Symposium, Okinawa, Japan (2006)
Chen SH and Wu SH, “Thermodynamic Characterization of DNA-binding Activity of
Human Lon Protease”
11th Symposium on Recent Advances in Biophysics, Taipei, Taiwan (2006)
Chen SH and Wu SH, “Thermodynamic Characterization of DNA-binding Activity of
Human Lon Protease”
48th Biophysical Annual Meeting, Baltimore, Maryland, USA (2004)
Chen SH and Kan LS, “The Effect of pH and Double Helix Association on
Pyrimidine Motif Triplex Formation: Thermodynamic and Kinetic Studies”
4th East Asian Biophysics Symposium, Taipei, Taiwan (2003)
Chen SH and Kan LS, “The Effect of pH and Double Helix Association on
Pyrimidine Motif Triplex Formation: Thermodynamic and Kinetic Studies”

BOOKS

Master Thesis, National Taiwan University (2006)
Chen SH, “Thermodynamic Characterization of DNA-binding Activity of Human Lon
Protease”

RESEARCH SUMMARY

Proteomics and Interactomics of Mitochondrial Nucleoid* (2008~present)
- Designed original research into the dynamics of mitochondrial nucleoid,
including the characterization of its component proteins, the interaction network of
these proteins, possible association with mitochondrial DNA (mtDNA), and the
dynamics of interested nucleoid proteins. An independent research project under
the direction of Prof. Shih-Hsiung Wu. Proposal abstract available at http://
niwhu.blogspot.com/2008/10/proposal-summary.html
- Techniques employed: blue native/SDS 2D PAGE, mass spectroscopy, time-
resolved fluorescence microscopy
Structural Profiling of Mitochondrial DNA* (2008~present)
- Designed an original study into possible secondary structures (e.g. G-
quadruplexes) of mtDNA replicative intermediates, especially on the mtDNA
displacement-loop (D-loop) region. An extended research idea of previous work
“Biophysical Characterization of Lon Protease and Its DNA-binding Activity”, in
which I discovered specific association between human Lon and G-quartet DNA
Si-Han Chen
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- Techniques employed: 2D agarose gel electrophoresis, Southern blotting, and
fluorescence imaging
Biophysical Characterization of Lon Protease and Its DNA-binding Activity
(2004~2007)
- Designed and conducted original research into properties of human Lon (hLon)
and its association with different DNA substrates. Analyzed the types of
thermodynamic driving forces responsible for each binding reaction, and thereby
gaining the information about specificity and affinity. Calculated the changes of
hLon heat capacity in response to forming a complex with its DNA substrates. As
well as characterized structural properties and thermal stability of hLon, DNA
molecules, and their complexes
- Partially for the fulfilment of my master thesis, under the guidance of Prof. Shih-
Hsiung Wu and in collaboration with Dr. Carolyn K. Suzuki
- Research results published in Nucleic Acids Research, article available at http://
nar.oxfordjournals.org/cgi/content/abstract/gkm1140v1?ck=nck. Platform paper
also available at http://niwhu.blogspot.com/2008/10/selected-conference-
paper.html
- Techniques employed: ITC (isothermal titration calorimetry), DSC (differential
scanning calorimetry), fluorescence anisotropy, SPR (surface plasmon resonance)/
Biacore, AUC (analytical ultracentrifugation), DLS (dynamic light scattering), CD
(circular dichroism) spectroscopy, UV/VIS spectrophotometry, native and
denaturing PAGE
Physical Properties of Triplex DNA Formation (2003~2004)
- Wrote an undergraduate research grant proposal and conducted this project
under the supervision of Profs. Chia-Ching Chang and Lou-Sing Kan. As an
“Undergraduate Research Participation Program” funded by National Science
Council
- Investigated the effects of double strand dynamics and nucleotide replacement on
the formation of pyrimidine motif triplexes
- Techniques employed: ITC (isothermal titration calorimetry), SPR (surface
plasmon resonance)/Biacore, CD (circular dichroism) spectroscopy, UV/VIS
spectrophotometry, native and denaturing PAGE
* ongoing projects

HONORS & AWARDS

Travel Grant for the 5th East Asian Biophysics Symposium (2006)
- From The Biophysical Society of Japan
- With a cash prize of JPY 50,000
Best Poster Award in the 11th Symposium on Recent Advances in Biophysics
(2006)
- From The Biophysics Society of Taiwan
- Top 10% of posters presented in the poster session
- With a certificate and a cash prize of NTD 5,000
National Science Council Research Creativity Award (2004)
- The Republic of China National Science Council is the largest research fund/grant
provider in Taiwan. Its significance is equivalent to National Science Foundation in
the US.
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- The best 100 undergraduate research papers of all categories selected from the
recipients of NSC Undergraduate Research Fellowships
- With a certificate and a cash prize of NTD 20,000
- For awardees who continue their graduate studies in Taiwan will receive a
generous stipend from NSC
Graduate Academic Excellence Award, National Dong Hwa University (2004)
- Top 2 students in each graduate class, selected by the department
Outstanding Student Travel Grant for the 48th Biophysical Annual Meeting (2004)
- From Foundation for the Advancement of Outstanding Scholarships
Presidential Awards, National Dong Hwa University (Oct 2003, Mar 2003, Oct
2002, Mar 2002, Oct 2001 & Mar 2001; 6 times over 7 awards can be granted
during four year study)
- Top 5% of students in their classes, selected by each department
- With a certificate and a case prize of NTD 5,000
International Travel Award for the 48th Biophysical Annual Meeting (2004)
- From the Biophysical Society (US)
- Only 10 applicants awarded annually to attend the biophysical meeting
- With a certificate and a cash prize of USD 600
National Science Council Undergraduate Research Fellowship (Jul 2003~Feb
2004)
- Awarded Project “Physical Properties of Triplex DNA Formation” (#92-2815-
C-001-002-M)
- With a research allowance of NTD 32,000
Wu Chien-Shiung Memorial Award & Creative Poster Award at the 4th Wu
Chien-Shiung Science Camp (2001)
- From Wu Chien-Shiung Education Foundation, an non-profit organization as a
memorial to renowned physicist Dr. Chien-Shiung Wu
- Wu Chien-Shiung Memorial Award for the top 5 female students who show the
potentials of developing a career in research, with a certificate and a cash prize of
NTD 5,000
- Creative Poster Award for the best 3 teamwork posters, with a certificate and a
cash prize of NTD 5,000/team

FELLOWSHIPS & SCHOLARSHIPS

Government Fellowship for Overseas Graduate Studies (2008)
- Awarded by Ministry of Education, ROC
- Students who show strength in their research areas (on the basis of their complete
research proposals and academic performance) and will be pursuing doctorates
abroad. It is for a two-year period with a stipend of USD 12,000/yr and a tuition
defrayment of USD 13,000/yr.
- Awarded proposal “Dynamic Structures and Composition of Human
Mitochondrial Nucleoids: Biochemical and Biophysical Studies”
Master Thesis Scholarship from Archilife Research Foundation (2006)
- Top 24 graduate students with outstanding proposed projects, selected
nationwide
- With a certificate and a cash prize of NTD 75,000
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Xing Tian Gong Fellowship for Outstanding Students (2005~2006)
- Top 2 students selected in each academic realm
- With a financial support for tuition and living expenses up to NTD 150,000
annually
Taipei County Government Scholarships for Outstanding Students (2004 &
2002; twice)
- With a cash prize of NTD 20,000
Lin Hsiung-Chen Scholarship from Lin Hsiung-Chen Foundation (2003)
- Top 10 college students selected nationwide
- With a cash prize of NTD 100,000
Song Ying-Tan Scholarship from the People First Party (ROC) (2001)
- The best 20 college students selected nationwide whose parents are blue-collar
workers
- With a cash prize of NTD 30,000

PROFESSIONAL AFFILIATIONS

Biophysical Society (US) (2004~Present)