Major Publications

(in chronological order, 25 total publications, 8,253 combined citations, h-index=15, courtesy of Google Scholar)

First and Last Author

(*equal contribution, #project lead, @senior author)

• Becker T*, Lee WP*, Leone J, Zhu Q, Zhang C, Sargent J, Shanker K, Mil-homens A, Cerveira E, Romanovitch M, Cha J, Navarro FCP, Galeev T, Gerstein M, Mills RE, Shin DG, Lee C, Malhotra A@, "FusorSV: An algorithm for optimally combining data from multiple structural variation detection methods", Genome Biology, Accepted 

• Chaisson MJP*, Sanders AD*, Zhao X*, Malhotra A#,…..Human Genome Structural Variation Consortium, “Multi platform discovery of haplotype-resolved structural variation in human genomes”, In review (1 citation) 

• Plewczynski D, Gruca S, Szałaj P, Gulik K, de Oliveira SF, Malhotra A@, “Analysis of Structural Chromosome Variants by Next Generation Sequencing Methods”, in Book “Clinical Applications for Next-Generation Sequencing” published by Elsevier, September 2015 

• Malhotra A*, Wang Y*, Waters J, Chen K, Meric-Bernstam F, Hall IM, Navin N, “Ploidy-Seq: Inferring mutational chronology by sequencing polyploidy tumor subpopulations”, Genome Medicine, January 2015 (5 citations) 

• Malhotra A*, Shibata Y*, Dutta A, “Chromosomal structural variations during progression of a prostate epithelial cell line to a malignant, metastatic state inactivate the NF2, NIPSNAP1, UGT2B17 and LPIN2 genes”, Cancer Biology and Therapy, July 2013 (Sole computational biologist) (8 citations) 

• Malhotra A, Lindberg M, Faust G, Leibowitz ML, Clark RA, Layer R, Quinlan AR, and Hall IM, “Breakpoint profiling of 64 cancer genomes reveals numerous complex rearrangements spawned by homology-independent mechanisms”, Genome Research, Feb 2013 (117 citations) 

• Shibata Y*, Malhotra A*, Dutta A, “Detection of BCR-ABL translocation by Anchored ChromPET: A powerful, cost efficient technology to detect chromosomal breakpoints”, Genome Medicine, September 2010 (Sole computational biologist) (Article was featured on the cover page) (20 citations) 

• Shibata Y*, Malhotra A*, Dutta A, “Yeast genome analysis by ChromPET technology identifies sites of translocation and several sites of Ty element insertion”, Nucleic Acids Research, August 2009 (Sole computational biologist) (12 citations) 

Other Publications 

(*equal contribution, #project lead, @senior author)

• G David Poznik, Yali Xue, Fernando L Mendez, Thomas F Willems, Andrea Massaia, Melissa A Wilson Sayres, Qasim Ayub, Shane A McCarthy, Apurva Narechania, Seva Kashin, Yuan Chen, Ruby Banerjee, Juan L Rodriguez-Flores, Maria Cerezo, Haojing Shao, Melissa Gymrek, Ankit Malhotra, Sandra Louzada, Rob Desalle, Graham R S Ritchie, Eliza Cerveira, Tomas W Fitzgerald, Erik Garrison, Anthony Marcketta, David Mittelman, Mallory Romanovitch, Chengsheng Zhang, Xiangqun Zheng-Bradley, Gonçalo R Abecasis, Steven A McCarroll, Paul Flicek, Peter A Underhill, Lachlan Coin, Daniel R Zerbino, Fengtang Yang, Charles Lee, Laura Clarke, Adam Auton, Yaniv Erlich, Robert E Handsaker, The 1000 Genomes Project Consortium, Carlos D Bustamante & Chris Tyler-Smith, “Punctuated bursts in human male demography inferred from 1,244 worldwide Y-chromosome sequences”, Nature Genetics, June 2016 (73 citations) 

• Menghi F, Inaki K, Woo X, Kumar PA, Grzeda KR, Malhotra A, Yadav V, Kim H, Marquez EJ, Ucar D, Shreckengast PT, Wagner JP, MacIntyre G, Murthy Karuturi KR, Scully R, Keck J, Chuang JH, Liu ET, “The tandem duplicator phenotype as a distinct genomic configuration in cancer”, Proc Natl Acad Sci USA. April 2016 (21 citations) 

• Sudmant PH, Rausch T, Gardner EJ, Handsaker RE, Abyzov A, Huddleston J, Zhang Y, Ye K, Jun G, Hsi-Yang Fritz M, Konkel MK, Malhotra A, Stütz AM, Shi X, Paolo Casale F, Chen J, Hormozdiari F, Dayama G, Chen K, Malig M, Chaisson MJ, Walter K, Meiers S, Kashin S, Garrison E, Auton A, Lam HY, Jasmine Mu X, Alkan C, Antaki D, Bae T, Cerveira E, Chines P, Chong Z, Clarke L, Dal E, Ding L, Emery S, Fan X, Gujral M, Kahveci F, Kidd JM, Kong Y, Lameijer EW, McCarthy S, Flicek P, Gibbs RA, Marth G, Mason CE, Menelaou A, Muzny DM, Nelson BJ, Noor A, Parrish NF, Pendleton M, Quitadamo A, Raeder B, Schadt EE, Romanovitch M, Schlattl A, Sebra R, Shabalin AA, Untergasser A, Walker JA, Wang M, Yu F, Zhang C, Zhang J, Zheng-Bradley X, Zhou W, Zichner T, Sebat J, Batzer MA, McCarroll SA; 1000 Genomes Project Consortium, Mills RE, Gerstein MB, Bashir A, Stegle O, Devine SE, Lee C, Eichler EE, Korbel JO. "An integrated map of structural variation in 2,504 human genomes", Nature, October 2015 (401 citations) 

• 1000 Genomes Project Consortium,…..Malhotra A#…..Auton A, Brooks LD, Durbin RM, Garrison EP, Kang HM, Korbel JO, Marchini JL, McCarthy S, McVean GA, Abecasis GR. "A global reference for human genetic variation", Nature, October 2015 (1684 citations) 

• Inaki K, Menghi F, Woo XY, Wagner JP, Jacques PE, Lee YF, Shreckengast PT, Soon WW, Malhotra A, Teo ASM, Hillmer AM, Khng AJ, Ruan X, Ong SH, Bertrand D, Nagarajan N, Karuturi RKM, Miranda, AH and Liu ET, “Systems consequences of amplicon formation in human breast cancer”, Genome Research, Oct 2014 (18 citations) 

• Sun D, Lee YS, Malhotra A, Kim HK, Matecic M, Evans C, Dutta A, “miR-99 family of microRNAs suppresses the expression of prostate-specific antigen and prostate cancer cell proliferation”, Cancer Research, January 2011 (Sole computational biologist) (177 citations) 

• Lee YS*, Shibata Y*, Malhotra A, Dutta A, “A novel class of small RNAs: tRNA-derived RNA fragments (tRFs)”, Genes and Development, November 2009 (Sole computational biologist) (466 citations) 

• The ENCODE consortium. “Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project”, Nature. June 2007 (Article was featured on the cover page) (I was one of the two bioinformaticians from UVA) (4264 citations) 

• Kim HK, Lee YS, Sivaprasad U, Malhotra A, Dutta A, “Muscle-specific microRNA miR-206 promotes muscle differentiation”, Journal of Cell Biology, August 2006 (Article was featured on the cover page) (Sole computational biologist) (657 citations) 

Software Developed

• fusorSV: An ensemble based computational framework for calling structural variations from whole genome sequencing datasets

• AbCNV: A software package to analyze CNV in a single genome, or a matched pair of genomes using paired or single reads from Illumina Solexa sequencing platform

Invited Talks

• 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.

Posters

• May’12 Malhotra A, Lindberg M, Clark RA, Leibowitz M, Faust G, Layer R, Shumiliana S, Quinlan AR, Hall IM, “Characterizing complex structural variation in cancer genomes”, Biology of Genomes, 2012, Cold Spring Harbor Laboratories

• Apr’12 Wang Y, Malhotra A, Leung M, Waters J, Chen K, Hall IM, Navin N, “Inferring mutational chronology in breast cancer by deep-sequencing intra-tumor subpopulations”, American Association for Cancer Research (AACR), 2012

• Nov’11 Malhotra A, Quinlan AR, Lindberg M, Clark RA, Leibowitz M, Faust G, Shumiliana S, Hall IM, “Complex structural variation in germline and somatic genomes”, Genome Informatics, 2011, Cold Spring Harbor Laboratories

• May’09 Malhotra A, Shibata Y, Dutta A, “AbLink: High throughput study of genomic structural variation”, Biology of Genomes, 2009, Cold Spring Harbor Laboratories

• Jul’06 Malhotra A, Taylor CM, Karnani N, Boyle P, Dutta A, “Transition zones in replication timing predict chromosomal domains”, 3nd ENCODE Consortium Meeting

• Sep’05 Machida Y, Chen Y, Malhotra A, Machida Y, Dutta A, “Targeted comparative 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