Software Engineer Design

Joyce Huang Address: **

Tulip Hill Ln, Centereach, NY 11720

E-mail: ***********@*****.*** Cell: 631-***-****

Professional Summary:

. Over 6 years of experience in object-oriented programming on

supercomputers

. Extensive knowledge in C++, python, shell scripting, Unix, and Linux

. Expertise knowledge in C++ objected-oriented concepts, standard

template library, and data structures

. Experience in parallel computing (multi-core, multi-processor, MPI)

. Participation in full development life cycle (requirements, design,

architecture, development, testing)

. Experience in equity and fixed income modeling and optimization

Object:

Seeking a position in software design/development, data analysis and

modeling.

Technical Skills:

Languages: C/C++, Python/IPython, PERL, SQL, and Shell-scripting

Platforms: Linux, Windows, Mac, IBM Blue Gene Light (BG/L) Supercomputer,

and Brookhaven Linux Cluster (BLC)

Software and Tools: Matlab, vim, Valgrind, g++, gcc, gdb, Mosek, LOQO, APT,

AMPL, DOCK, and AMBER

Education

2007 -2013 Ph.D. in Computational Biology (CUM GPA: 3.5)

Dept of Applied Math and Statistics, SUNY-Stony Brook

University

2003 - 2007 B.S. in Bioinformatics (Major GPA: 3.96)

Dept of Life Science, Soochow

University, China

Employment

07/2013 - present Intern, Computer Science Group, Computational

Sciences Center,

Brookhaven National Laboratory

05/2013 - 07/2013 Intern Software Engineer, Niche Trading LLC

06/2008 - 05/2013 Research Assistant, Dept. of Applied Math and

Statistics, Stony Brook University

Research Experiences

07/2013 - present Accelerating Differential Phase Contrast imaging for

data analysis. Three implementations in Matlab, Python and C++ were

compared for their performance.

. Implemented non-linear fitting and Fourier transformation operations

involved in the algorithm

. Designed a parallel algorithm for computing on a batch-queue based

multi-core servers cluster.

Environment: C++, Python/IPython, Matlab

05/2013 - 07/2013 Market structure forecasts using a range of risk

models. Risk models were used to forecast the volatilities of multiple

asset classes and commodities.

. Compared model volatility and correlation forecasts for a number of

indices across time

. Explored how the efficient frontier shifts when adding unlisted assets

. Performed yield curve and principal component analysis

. Carried out quadratic programming

Environment: C/C++, AMPL, LOQO, Mosek

06/2008 - 04/2013 Design and development of software package DOCK.

The drug design software has been written in a modular format (C++) on IBM

Blue Gene Light (BG/L) Supercomputer for easy implementation of new

algorithm and analysis tools.

. Developed full software life-cycle (SDLC) of extension modules in

C/C++ as a team member

. Incorporated parallelization of the algorithm through an external

library

. Used Linux profiler Valgrind for single processor optimization

. Profiled C++ code for optimization and memory management

. Tested the software by virtual screening, clustering and sorting

ligands on BG/L 512 block and 32 block

. Mentored junior members of the team with the software development

methodologies used in the project

Environment: Linux, C++, Shell Scripting, MPI

08/2008 - 12/2012 Quantitative modeling of protein-drug/protein-

protein interactions and time-series analysis. Binding energy between the

protein and the ligands has been calculated and drug specificity and

resistance has been revealed which provide insight for future drug

discovery.

. Implemented the python pipeline for integrating numerical results of

thermodynamic integration

. Simulated protein-drug interactions using molecular dynamics in

parallel on BG 512 block

. Explored protein-protein interactions over time based on differential

equations (ODE)

. Analyzed autocorrelation functions and block-averaged standard errors

of the mean

Environment: Linux, Python, Matlab, Shell Scripting, MPI

Honors and Awards

2011 Walk-for-Beauty Foundation Award (The Village Times Herald, and Long

Island Business)

2007 Excellent Student in Soochow University, China (top 1%)

2006 Second Prize National English Contest for college students, China

2005 Excellent prize for National Math Contest for Non-Math Major College

Students, China

2004 - 2006 First-Class Scholarship in Soochow University, China (top 1%)

2002 Second Prize in the Olympic Biological Contest in Jiangsu Province,

China

Selected Publications and Presentations

1. Huang, Y.; Rizzo, R. C. A Water-Based Mechanism of Specificity and

Resistance for Lapatinib with ErbB Family Kinases. Biochemistry. 2012,

51, 2390-2406. dx.doi.org/10.1021/bi2016553

2. Huang, Y.; Rizzo, R. C. Free Energy of Binding calculations for ErbB and

IGF-IR Tyrosine

Kinases. Workshop on Free Energy Methods in Drug Design, Cambridge, MA

2012 (conference).

3. Huang, Y.; Rizzo, R. C. Prediction of Lapatinib Selectivity with Kinases

in the ErbB family. The

240th ACS National Meeting, Boston, MA. 2010 (conference)

4. Huang, Y.; Rizzo, R. C. Targeted design of dual kinase inhibitors for

breast cancer. The 238th ACS National Meeting and Exposition. Washington,

D.C. 2009 (conference)

5. Mukherjee, S.; Goyal, R.; Huang, Y.; Rizzo, R. C. Construction of a Test

Set to Evaluate Binding Pose Prediction: Cross-docking and Family-

specific Analysis. The 22nd Annual Meeting of AIDS-Related Systems.

National Institutes of Health, Bethesda, MD. 2008 (conference)

6. Huang, Y.; Gao, G.; Xue, R.; Gong, C. Sequence and Molecular

Evolution of Baculovirus Based on Gene p35. Chinese Sericulture, 2006,

3, 13-22. (ISSN: 1007-0982 CN: 32-1421/S)

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