High Performance Computational Biology Group with Srinivas Aluru
I designed and implemented scalable parallel algorithms for exact and heuristic structure learning of Bayesian networks. I apply these algorithms in the reconstruction and analyses of moderate scale and whole-genome scale gene networks from microarray expression data of the model plant Arabidopsis. Currently, I am working on network-centered analysis of RNA-Seq expression data of maize recombinant inbred lines of the intermated B73-Mo17 population. I am also beginning to apply these methods for temperature-dependent sex determination in turtles. I am especially excited about a novel large-scale BN structure learning via speculative execution.
Machine Learning and Perception Group with Chris Bishop
At MSR I worked on automated modeling of causal effects in childhood asthma and allergy intervention trial. I also worked on investigating genetic-environmental interactions via a genome-wide association study. I used Infer.NET.
Computational Genomics with Patrick Schnable
Investigated correlations between gene expression profiles and gene location on the chromosome using cDNA microarray gene expression data and genetic and physical high-density maps in maize
Computational Metabolomics with Di Cook
LC/MS stands for Liquid Chromatography/Mass Spectrometry, which is an efficient analytical chemistry technique for identifying different chemical components in mixtures. Our goal is to build a pipeline for LC/MS data processing, including the pre-processing component, which we have found to be problematic in the somewhat new field of metabolomics. Software packages exist to solve the problem in proteomics but we have shown that metabolomics requires a new statistical approach for adequate peak detection, retention time correction, peak quantification, etc. Besides learning about metabolomics, this project introduced me to some new (to me) statistical approaches and the basics of R.
Computational Genomics with Volker Brendel
I tested and evaluated The GenomeThreader (GTH) gene prediction software using zebrafish genomic data as a testing ground. My goal was to investigate the feasibility of using human/mouse homologs for zebrafish gene structure prediction.
Mathematical Biology Undergraduate Research Program with Jon Beck
Designed and developed an interactive database with a web-based interface for the annotation, curation, and analysis of maize shoot apical meristem (See my project).
Information Technology Services - Web Integration Team
Developed new and maintained existing dynamic web applications, and provided instruction to staff and faculty
Small-scale dynamic web and internal application development and maintenance
- James Cornette Research Fellowship in Bioinformatics and Computational Biology, Iowa State University (2012)
- Professional Advancement Grant, Iowa State University (2011)
- Travel Award, Women in Machine Learning, Vancouver, Canada (2010)
- Volunteer Registration Fee Award, Neural Information Processing Systems, Vancouver, Canada (2010)
- All-paid expenses, CRA-W Grad Cohort, San Mateo, California (2009)
- All-paid expenses, CRA-W Grad Cohort, Seattle, Washington (2008)
- All-paid expenses, CRA-W Grad Cohort, San Francisco, California (2007)
- Google Scholarship, ACM Conference Grace Hopper Celebration of Women in Computing, San Diego, California (2006)
- Google Scholarship, ACM Conference Grace Hopper Celebration of Women in Computing, Chicago, Illinois (2004)
- Outstanding Student in Computer Science Award (2006):
Awarded to the top student in each field upon graduation, based on scholastic achievement. This award is one of the highest academic honors at Truman State University
- Mathematics and Computer Science Departmental Honors (2006)
- President's Honorary Scholarship (2003-2006)
- Boeing Scholars Award (2005-2006)
- Mathematics and Computer Science Division Scholarship (2005-2006)
- International Excellence Scholarship (2005-2006)
Familiar with Matlab, Infer.NET, SAS, PHP, Python, Prolog
- Technologies: Linux/Unix, Windows, SVN, MySQL, ASP, ASP.NET, Visual Studio.NET, Adobe Photoshop, Adobe Illustrator
- Grid computing and Supercomputers: TeraGrid/XSEDE, BlueGene, Linux clusters
Fluent in English, Bulgarian (native), and Russian (native)
Intermediate knowledge of German
- Membership: ACM, IEEE, ISCB
- Journal of Parallel and Distributed Computing (JPDC)
- IEEE Intl. Workshop on High Performance Computational Biology (HiCOMB) in concurrence with the IEEE Intl. Parallel and Distributed Processing Symposium (IPDPS)
- Intl. Conf. on Bioinformatics and Computational Biology (BICoB)
- IEEE Intl. Conf. on Computational Advances in Biological and Medical Sciences (ICCABS)
- Intl. Conf. on Intelligent Systems for Molecular Biology (ISMB): Student Symposium
- Consulting: BCB Laboratory (BCB Lab), student-driven bioinformatics consulting group at ISU (2007-2008)
- ISU Committees:
Graduate and Professional Student Senate (2010-2012),
Computation Advisory Committee (2010- 2012)
- Outreach: Volunteer in a science outreach program for middle school children
- Statistics 500. Statistical Methods.
- CprE 626. Advanced Parallel Algorithms and Scientific Computing
- CprE 528X. Probabilistic Methods in Computer Engineering.
- BCB 570. Computational Functional Genomics & Systems Biology.
- BCB 568. Advanced Genome Informatics.
- CprE 526. Introduction to Parallel Algorithms and Programming.
- BCB 569. Structural Genome Informatics.
- Statistics 430X. Empirical Methods for Computer Science.
- BCB/ComS/CprE/Gen 548. Fundamentals of Genome Informatics
- GEN 411. Molecular Genetics.
- Biol 313. Principles of Genetics.
Wet Lab Experience: Introduction to proteomics, DNA, and protein techniques