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, Cell: (434) 227 6024, Email: <my-first-name> [at] virginia [dot] edu

 

Education

        

Jan’07 – May’09        Dept. of Biochemistry and Molecular Genetics, University of Virginia, USA

                                    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, USA,

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: 2^nd                                                                                                            

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” 3^rd 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”, 3^nd 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”, 2^nd ENCODE Consortium Meeting

 

Jul’05              Karnani N, Taylor CM, Malhotra A, Dutta A, “Replication Profiling of ENCODE regions in HeLa”, 2^nd 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”, 7^th Annual Conference on Computational Genomics

 

Research Experience

 

2003 - 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.