ANKIT MALHOTRA Dept of Biochemistry and Molecular Genetics, University of Virginia 1232 Jordan Hall, Charlottesville, VA 22903 Ph. (434) 924 2466, Fax: (434) 924 5069, Email: [at] virginia [dot] edu EDUCATION Jan'07- Dept. of Biochemistry and Molecular Genetics, University of Virginia Ph.D. Candidate, expected graduation May 2009 Title: "A Computational Study of Chromosome Structure and Instability" Advisor: Dr. Anindya Dutta Committee Members: Dr. Amy Bouton, Dr. Stefan Bekiranov, Dr. Ira Hall Aug'03-Jan'07, Dept. of Computer Science, University of Virginia, Master of Computer Science, G.P.A.: 3.6/4.0 Title: "Computational Infrastructure for High Throughput RNAi screening experiments" Advisor(s): Dr. Gabriel Robins, Dr. Anindya Dutta Committee Members: Dr. Worthy Martin Jul'99-May'03 Dept. of Computer Science, Hans Raj College, University of Delhi, India Bachelor of Information Science, Class Rank: 2nd RESEARCH INTERESTS Bioinformatics, Computational Biology, High Throughput Sequencing, Microarray Analysis, High Performance Algorithms, Genomics, Sequence Analysis, Statistics, Artificial Intelligence, Operating Systems PUBLICATIONS Lee YS, Malhotra A, Dutta A, "A novel class of small RNAs, tRNA-derived RNA fragments (tRFs), is highly expressed in proliferating cells and required for cell proliferation", Communicated to Genes and Development Shibata Y*, Malhotra A*, Dutta A, "Yeast genome analysis by ChromPET technology identifies sites of translocation and several sites of Ty element insertion", Communicated to Genome Research (* co-first authors) Lee YS, Malhotra A, Sun D, Kim HK, Matecic M, Evans C, Dutta A, "miRNAs in the androgen-independence and androgen regulation of prostate epithelial cell lines", Communicated to RNA Karnani N, Taylor CM, Malhotra A, Dutta A, "High-throughput mapping of nascent DNA to identify efficient origins of DNA replication in human chromosomes", Communicated to Genome Research Dutta A, Karnani N, Malhotra A, Robins G, Taylor CM. "Extraction of Human DNA Replication Timing Patterns from Discrete Microarray Data" 3rd IAPR International Conference on Pattern Recognition in Bioinformatics (PRIB 2008), Melbourne, Australia, October 2008. Karnani N, Taylor CM, Malhotra A, Dutta A. "Pan-s replication patterns and chromosomal domains defined by genome-tiling arrays of ENCODE genomic areas". Genome Res. 2007 Jun;17(6):865-76. The ENCODE consortium. "Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project", Nature. 2007 Jun 14; 447(7146):799-816 (Article was featured on the cover page) (I was one of the two bioinformaticians from UVA) Kim HK, Lee YS, Sivaprasad U, Malhotra A, Dutta A, "Muscle-specific microRNA miR-206 promotes muscle differentiation", Journal of Cell Biology, 2006; 174, 677-687 (Article was featured on the cover page) Machida Y, Chen Y, Malhotra A, Machida Y, Dutta A,"Targeted Comparative RNAi (TARCOR) Analysis Reveals Differential Requirement of Genes Essential for Cell Proliferation", Mol Biol Cell. 2006 Nov;17(11):4837-45 Malhotra A, Kaur H, Bedi P, "Fuzzy Dimension to Databases", 37th National Convention of Computer Society of India, Bangalore, India, 2002, Nov PATENTS 2008 U.S. Provisional Patent (#61/099,943) "Anchored Chrompets for Identifying Chromosomal Translocations n Disease" Inventors: Dr. Anindya Dutta, Ankit Malhotra, Yoshiyuki Shibata 2008 U.S. Provisional Patent (#61/100,048) "Yeast Genome Analysis by ChromPET Technology Identifies Sites of Translocation and Several Sites of Ty Element Insertion" Inventors: Dr. Anindya Dutta, Ankit Malhotra, Yoshiyuki Shibata INVITED TALK Dec'08 "Yeast genome analysis by ChromPET technology identifies sites of translocation and several sites of Ty element insertion", Annual Structural, Computational Biology and Biophysics (SCBB'08) retreat, University of Virginia. POSTER PRESENTATIONS July'06 Malhotra A, Taylor CM, Karnani N, Boyle P, Dutta A, "Transition Zones in Replication Timing predict Chromosomal Domains", 3nd ENCODE Consortium Meeting Sept'05 Machida Y, Chen Y, Malhotra A, Machida Y, Dutta A, "Targeted Comparitive RNAi (TARCOR) Analysis of essential genes in human cell lines", RNAi-2005 Jul'05 Taylor CM, Malhotra A, Karnani N, Dutta A, "Computational Analysis of DNA Replication Data", 2nd ENCODE Consortium Meeting Jul'05 Karnani N, Taylor CM, Malhotra A, Dutta A, "Replication Profiling of ENCODE regions in HeLa", 2nd ENCODE Consortium Meeting Oct'04 Taylor CM, Malhotra A, Jeon Y, Bekiranov S, Karnani N, Kapranov P, Ghosh S, Gingeras TR, Dutta A, Robins G, "Temporal Profile of replication of human chromosomes", 7th Annual Conference on Computational Genomics RESEARCH EXPERIENCE 2003 Ð Present Graduate Research Assistant, Dr. Anindya Dutta, University of Virginia Identification of chromosomal rearrangements in cancer using deep sequencing Analysis of DNA Replication dynamics in Humans Functional Profiling of miRNA's Computational Infrastructure for High Throughput TARCOR Screens 2005 Graduate Project, Dr. Jae K Lee, University of Virginia Combinatorial Regulation by miRNA's 2004 Graduate Project, Dr. Andrew Grimshaw, University of Virginia A Study of Parallel Sockets on TCP Performance 2004 Graduate Project, Dr. Kevin Skadron, Dr. Dave Luebke, University of Virginia Exploring Specialization for Rasterization Hardware 2003 Graduate Project, Dr. John A. Stankovic, University of Virginia A Divide and Conquer Approach for Localization in Wireless Sensor Networks 2003 Research Assistant, Dr. P.R. Panda, Indian Institute of Technology, Delhi Performance Estimation through Floorplan Generation for VLSI Circuits 2002 - 2003 Undergraduate Research, Dr. Harmeet Kaur, University of Delhi Intelligent Agents and Electronic Marketplace Fuzzified Relational Database Model WORK EXPERIENCE 2004 Graduate Teaching Assistant, Dept of Computer Science, University of Virginia CS-654, Computer Architecture 2003 Graduate Teaching Assistant, Dept of Computer Science, University of Virginia CS-101, Introduction to computing 2001 Intern, Videsh Sanchar Nigam Limited (VSNL), New Delhi, India VSNL was India's sole carrier for overseas telephony till 2002, and it provides bandwidth for internet service providers COMPUTER SKILLS Programming Languages Java, C, C++, Perl, Assembly Language Statistical Languages R, Minitab Bioinformatics Software BLAST, Maq, BLAT, MEME, YMF, Clover, Clustal package, Multalign NovoAlign, BioConductor Software Packages Jbuilder, JDBC, MPI, Apache, Microsoft Office Scripting Languages HTML, DHTML, JavaScript, CGI, Scripting under UNIX Database Systems MySQL, Microsoft Access, Oracle, PL/SQL Operating Systems Windows 95/98/2000/XP/Vista, Mac OS X, Linux, SunOS, Solaris, Windows 3.x, DOS HONORS AND ACCOMPLISHMENTS 1997 Meritorious Scholarship, All India Talent Scholarship Award Examination, organized by Children's Education Trust of India. 1997 Meritorious Scholarship for standing among the top 0.1% of appeared students in Mathematics in the All India Senior Secondary Examination (A.I.S.S.E.), awarded by the Central Board of Secondary Education 1996 Meritorious Certificate, University of New South Wales, Talent Search for Science & Maths (Placed 99th and 78th percentile all India respectively) 1996 Meritorious Certificate in Maths Olympiad. 1996 18th rank, Delhi Science Open Merit test, organized by Delhi State Science Teachers Forum 1991 Meritorious Scholarship, All India Talent Scholarship Award Examination, organized by Children's Education Trust of India. BIOGRAPHICAL INFORMATION Citizen of India, currently holding F1 visa in US REFERENCES Available on request.