Evidence of ability to identify, critically analyze, and research a problem, and of written communication skills, in the form of two or more items authored by the student and reviewed by doctoral level scholars. The first item (literature review) is required; at least one of the remainder must be supplied.

1. Written Literature Review in the proposed area of study of 20-30 pages, following the graduate division dissertation format and reviewing at least 20 published works. (The student may elect to change the area of study at the proposal stage).
• "Literature Review on Time Series Indexing"
  

1. Thesis by the student from MS Plan A.
• For my thesis I've developed a software package aiming numerical simulation of interstellar grain chemistry, while the thesis "MCMC simulation of interstellar grain chemistry" is available for download in PDF format from here, the source code hosted at http://code.google.com/p/iclouds/
  
  
2. Publication(s) in reviewed journals or conferences. Evidence of quality such as acceptance rates or citation indexing should be provided.
• While working at LANL/JGI I have developed the metagenomics data processing pipeline which was used for analysis of the GOS expedition data. This work resulted in publication and was presented at the conference:
• Assembling the marine metagenome, one cell at a time, PLoS ONE, April 23, 2009.
  Tanja Woyke, Gary Xie, Alex Copeland, José M. González, Cliff Han, Hajnalka Kiss, Jimmy Saw, Pavel Senin, Chi Yang, Sourav Chatterji, Jan-Fang Cheng, Jonathan A. Eisen, Michael E. Sieracki and Ramunas Stepanauskas
  http://dx.plos.org/10.1371/journal.pone.0005299.
  
• Poster, Fragment recruitment of Flavobacteria sequences from the Global Ocean Sampling expedition data.
  Jimmy H Saw, Pavel Senin, Tanja Woyke, Ramunas Stepanauskas
  Finishing in the future conference, Santa Fe, NM, May, 2008.
  
• Experiences with Hackystat as a service-oriented architecture
  Philip Johnson, Shaoxuan Zhang, Pavel Senin.
  Submitted for IEEE Service cup 2009
• I've developed the database and web-site for the Oral metagenome data:
• Poster, Oral Metagenome Database at Los Alamos National Laboratory
  Pavel Senin, Gary Xie, Jimmy Saw
  IADR/AADR 37th Annual Meeting and Exhibition, Dallas, TX, April 2008.
• Poster, Oral Metagenome Database at Los Alamos National Laboratory
  Pavel Senin, Gary Xie, Jimmy Saw
  Next Generation Sequencing Symposium, Santa Fe, NM, March 6‐7, 2008.
  
• While working in Advanced Studies in Genomics, Proteomics and Bioinformatics I have developed the genome assembly and annotation pipeline which was used for assembling papaya genome and led to the next publication:
  The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus)
  Ray Ming, Shaobin Hou, Yun Feng, Qingyi Yu, Alexandre Dionne-Laporte, Jimmy H. Saw, Pavel Senin, Wei Wang, Benjamin V. Ly, Kanako L. T. Lewis, Steven L. Salzberg, Lu Feng, Meghan R. Jones, Rachel L. Skelton, Jan E. Murray, Cuixia Chen, Wubin Qian, Junguo Shen, Peng Du, Moriah Eustice, Eric Tong, Haibao Tang, Eric Lyons, Robert E. Paull, Todd P. Michael, Kerr Wall, Danny W. Rice, Henrik Albert, Ming-Li Wang, Yun J. Zhu, Michael Schatz, Niranjan Nagarajan, Ricelle A. Acob, Peizhu Guan, Andrea Blas, Ching Man Wai, Christine M. Ackerman, Yan Ren, Chao Liu, Jianmei Wang, Jianping Wang, Jong-Kuk Na, Eugene V. Shakirov, Brian Haas, Jyothi Thimmapuram, David Nelson, Xiyin Wang, John E. Bowers, Andrea R. Gschwend, Arthur L. Delcher, Ratnesh Singh, Jon Y. Suzuki, Savarni Tripathi, Kabi Neupane, Hairong Wei, Beth Irikura, Maya Paidi, Ning Jiang, Wenli Zhang, Gernot Presting, Aaron Windsor, Rafael Navajas-Perez, Manuel J. Torres, F. Alex Feltus, Brad Porter, Yingjun Li, A. Max Burroughs, Ming-Cheng Luo, Lei Liu, David A. Christopher, Stephen M. Mount, Paul H. Moore, Tak Sugimura, Jiming Jiang, Mary A. Schuler, Vikki Friedman, Thomas Mitchell-Olds, Dorothy E. Shippen, Claude W. dePamphilis, Jeffrey D. Palmer, Michael Freeling, Andrew H. Paterson, Dennis Gonsalves, Lei Wang and Maqsudul Alam
  Nature 452, 991-996 (24 April 2008)
  
• With some modification the same pipeline was used for microbial genomes and next two papers resulted from this work:
• Methane oxidation by an extremely acidophilic bacterium of the phylum Verrucomicrobia
  Peter F. Dunfield, Anton Yuryev, Pavel Senin, Angela V. Smirnova, Matthew B. Stott, Shaobin Hou, Binh Ly, Jimmy H. Saw, Zhemin Zhou, Yan Ren, Jianmei Wang, Bruce W. Mountain, Michelle A. Crowe, Tina M. Weatherby, Paul L. E. Bodelier, Werner Liesack, Lu Feng, Lei Wang & Maqsudul Alam
  Nature 450, 879-882 (6 December 2007)
•  Complete genome sequence of the extremely acidophilic methanotroph isolate V4, "Methylacidiphilum infernorum", a representative of the bacterial phylum Verrucomicrobia
  Shaobin Hou, Kira S. Makarova, Jimmy H. W Saw, Pavel Senin, Benjamin V. Ly, Zhemin Zhou, Yan Ren, Jianmei Wang, Michael Y. Galperin, Marina V. Omelchenko, Yuri I. Wolf, Natalya Yutin, Eugene V. Koonin, Matthew B. Stott, Bruce W. Mountain, Michelle A. Crowe, Angela V. Smirnova, Peter F. Dunfield, Lu Feng, Lei Wang and Maqsudul Alam
  Biology Direct 2008, 3:26, 1 July 2008.
  
  
3. Technical report(s) on research project(s) that were supervised by a faculty member and read and approved by two other faculty members. ICS 699 projects may be included.
• DTW application to the Hackystat telemetry streams alignment.
  Technical report and software implementation for ICS 699 course, Fall 2008.
  I've developed a plugin for the ProjectBrowser module of Hackystat which allows to align telemetry streams using DTW. In this work I've extensively studied the DTW algorithm background, it's applications and existing extensions.
  The report is here: Dynamic Time Warping Algorithm Review, the source code is embedded in the project browser code.
  
• Bayesian image segmentation using reversible jump Markov chain Monte Carlo and Simulated Annealing.
  Technical report and software implementation for Pattern Classification course by Kyungim Baek. Fall 2006.
  In this project I’ve implemented software which does automatic image segmentation by following the algorithm published by Z. Kato "Bayesian color image segmentation using reversible jump Markov chain Monte Carlo". Probability, Networks and Algorithms, February, 28, 1999. CWI, Amsterdam.
  The code hosted at http://code.google.com/p/rjimage/
• Classification of microarray data using penalized logistic regression.
  Technical report and software implementation for Machine Learning course by Will Gersch, Spring 2006.
  In this project I’ve designed and developed computational software which uses R and Bioconductor along with attached supportvector machines C code in order to classify DNA microarrays of Human acute leukemias. The implemented leukemia class discovery procedure automatically determines leukemia classes through selection of responsible genes expression without any prior knowledge about classes.