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Viacheslav Fofanov

Graduate Student

Department of Statistics, Rice University

DH 2105

(713) 348 - 6075

vfofanov@rice.edu

 

Personal Information

 

I am a PhD Candidate at Rice Bioinformatics Group headed by Professor Marek Kimmel.  The primary area of my research is Bioinformatics, with a focus on the application of computational, mathematical, and statistical tools to the complex problems in the areas of genomics and proteomics.  My Curriculum Vitae can be found here, with research statement available upon request. 

 

Refereed Publications

 

  1. C. Reed, V.Y. Fofanov, C. Putonti, S. Chumakov, T. Slezak, Y. Fofanov.  Effect of the Mutation Rate and Background Size on the Quality of Pathogen Identification. Bioinformatics. In Press.
  2. A. Skewes, M. Quance, C. Putoni, V.Y. Fofanov, Y. Fofanov.  Statistical Properties of Short n-mers Located in One Mismatch Area of Microbial Genomes. In Proceedings of the International Conference on Bioinformatics and Computational Biology (BIOCOMP) 2007.  In Press.
  3. B.Y. Chen, D.H. Bryant, A.E. Cruess, J.H. Bylund, V.Y. Fofanov, D.M. Kristensen, , M. Kimmel, O. Lichtarge, L.E. Kavraki.  Composite Motifs Integrating Multiple Protein Structures Increase Sensitivity for Function Prediction.  In Proceedings of Computational Systems Bioinformatics Conference (CSB) 2007.  In Press.
  4. B.Y. Chen, D.H. Bryant, V.Y. Fofanov, D.M. Kristensen, A.E. Cruess, M. Kimmel, O. Lichtarge, L.E. Kavraki.  Cavity Scaling: Automated Refinement of Cavity Aware Motifs in Protein Function Prediction.  Journal of Bioinformatics and Computational Biology 2007, 5(2a):353-382.
  5. B.Y. Chen, D.H. Bryant, V.Y. Fofanov, D.M. Kristensen, A.E. Cruess, M. Kimmel, O. Lichtarge, L.E. Kavraki.  Cavity-Aware Motifs Reduce False Positives in Protein Function Prediction.  Computational Systems Bioinformatics Conference (CSB) 2006, 311-323.
  6. D.M. Kristensen, B.Y. Chen, V.Y. Fofanov, R.M. Ward, A.M. Lisewski, M. Kimmel, O. Lichtarge, L.E. Kavraki.  Recurrent Use of Evolutionary Importance for Functional Annotation of Proteins Based on Local Structural Similarity.  Protein Science 2006, 15(6):1530-1536.
  7. B.Y. Chen*, V.Y. Fofanov*, D.H. Bryant, B.D. Dodson, D.M. Kristensen, A.M. Lisewski, M. Kimmel, O. Lichtarge, L.E. Kavraki.  Geometric Sieving: Automated Distributed Optimization of 3D Motifs for Protein Function Prediction. In Proceedings of International Conference on Research in Computational Molecular Biology (RECOMB) 2006, 500-515.
  8. B.Y. Chen*, V.Y. Fofanov*, D.M. Kristensen, M. Kimmel, O. Lichtarge, L.E. Kavraki.  Algorithms for Structural Comparison and Statistical Analysis of 3D Protein Motifs.  In Proceedings of the Pacific Symposium on Biocomputing (PSB) 2005, 10:334-345.

9.       Y. Fofanov, Y. Luo, C. Katili, J. Wang, Y. Belosludtsev, T. Powdrill, C. Belapurkar, V.Y. Fofanov, T. Li, S. Chumakov, B.M. Pettitt. How Independent are the Appearances of n-mers in Different Genomes?  Bioinformatics 2004, 20(15):2421-2428.

 

* equal contribution

Research

Year

Description

2006 – present

Research Assistant,

 

Cancer Research Laboratories,

 

Texas Children’s Hospital, Houston, TX.

 

 

2003 – present

Research Assistant,

 

Rice Bioinformatics Group,

 

Rice University, Houston, TX.

 

 

2004 – 2006

VIGRE Graduate Researcher,

 

Department of Statistics,

 

Rice University, Houston, TX.

 

 

2001 – 2002

Research Assistant,

 

Bioinformatics Lab,

 

University of Houston, Houston, TX.

 

Teaching

Year

Location

Description

Spring 2006

Department of Statistics,

Lecturer

 

Rice University, Houston, TX.

Introduction to Statistics (STAT 280)

 

 

 

Fall 2002 – Fall 2003

Department of Statistics,

Teaching Assistant,

 

Rice University, Houston, TX.

Introduction to Statistics (STAT 280),

 

 

 

Fall 2001 – Spring 2002

Department of Computer Science,

Lecturer,

 

Montgomery County Community College, Conroe, TX.

Introduction to Programming Logic

 

 

 

Summer 2001

Summer scholars program for gifted children

Lecturer

 

Pacific Lutheran University, Tacoma, WA.

Introduction to C++

 

 

 

2000 – 2001

Department of Computer Science,

Lecturer,

 

Renton Technical College, Renton, WA.

Introduction to C++,

 

 

Advanced C++

 

Hobbies

 

Flying single engine airplanes