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Book Chapters
Hannenhalli S, Hubbell E, Lipshutz R, Pevzner P.  2002.  Combinatorial Algorithms for Design of DNA Arrays. Chip TechnologyChip Technology. 77
Hannenhalli S, Hubbell E, Lipshutz R, Pevzner P.  2002.  Combinatorial Algorithms for Design of DNA Arrays. Chip TechnologyChip Technology. 77
Hannenhalli S, Hubbell E, Lipshutz R, Pevzner P.  2002.  Combinatorial Algorithms for Design of DNA Arrays. Chip TechnologyChip Technology. 77
Hannenhalli S, Hubbell E, Lipshutz R, Pevzner P.  2002.  Combinatorial Algorithms for Design of DNA Arrays. Chip TechnologyChip Technology. 77
Hannenhalli S, Hubbell E, Lipshutz R, Pevzner P.  2002.  Combinatorial Algorithms for Design of DNA Arrays. Chip TechnologyChip Technology. 77
Roe A., Weller S., Baixeras J., Brown J.W, Cummings MP, Davis D.R, Horak M., Kawahara A.Y, Mitter C., Parr C.S et al..  2010.  Evolutionary framework for Lepidoptera model systems. Genetics and Molecular Biology of LepidopteraGenetics and Molecular Biology of Lepidoptera.
Otto S.P, Cummings MP, Wakeley J..  1996.  Inferring phylogenies from DNA sequence data: The effects of sampling. New Uses for New PhylogeniesNew Uses for New Phylogenies.
Kim Y, Patro R, Ip CYiu, O'Leary DP, Anishkin A, Sukharev S, Varshney A.  2009.  Salient Frame Detection for Molecular Dynamics Simulations. Scientific VisualizationScientific Visualization.
Books
Khan Z, Balch T, Dellaert F.  2004.  Lecture Notes in Computer ScienceComputer Vision - ECCV 2004An MCMC-Based Particle Filter for Tracking Multiple Interacting Targets. 3024:279-290.
Khan Z, Balch T, Dellaert F.  2004.  Lecture Notes in Computer ScienceComputer Vision - ECCV 2004An MCMC-Based Particle Filter for Tracking Multiple Interacting Targets. 3024:279-290.
Conference Papers
Balch T, Khan Z, Veloso M.  2001.  Automatically tracking and analyzing the behavior of live insect colonies. the fifth international conferenceProceedings of the fifth international conference on Autonomous agents - AGENTS '01.
Conference Proceedings
Shneiderman B, Colwell RR, Diamond S, Greenhalgh P, Wulf W.  2007.  Bridging art and science with creativity support tools. Proceedings of the 6th ACM SIGCHI conference on Creativity & cognition.
Kingsford C, Zaslavsky E., Singh M..  2006.  A compact mathematical programming formulation for DNA motif finding. Combinatorial Pattern Matching.
Hannenhalli S, Perumalla K., Chandrasekharan N., Sridhar R..  1993.  A distributed algorithm for ear decomposition. Fifth International Conference on Computing and Information, 1993. Proceedings ICCI '93.
Hochheiser H., Baehrecke E.H, Mount SM, Shneiderman B.  2003.  Dynamic querying for pattern identification in microarray and genomic data. 2003 International Conference on Multimedia and Expo, 2003. ICME '03. Proceedings. 3
Shahri HHaidarian, Namata G, Navlakha S, Deshpande A, Roussopoulos N.  2007.  A graph-based approach to vehicle tracking in traffic camera video streams. Proceedings of the 4th workshop on Data management for sensor networks: in conjunction with 33rd International Conference on Very Large Data Bases.
Samet H, Phillippy A, Sankaranarayanan J.  2007.  Knowledge discovery using the sand spatial browser. Proceedings of the 8th annual international conference on Digital government research: bridging disciplines & domains.
Samet H, Phillippy A, Sankaranarayanan J.  2007.  Knowledge discovery using the sand spatial browser. Proceedings of the 8th annual international conference on Digital government research: bridging disciplines & domains.
Journal Article
Khan Z, Amini S, Bloom JS, Ruse C, Caudy AA, Kruglyak L, Singh M, Perlman DH, Tavazoie S.  2011.  Accurate proteome-wide protein quantification from high-resolution 15N mass spectra. Genome Biology. 12(12):R122.
Lee S.H, Kalejta R.F, Kerry J., Semmes O.J, O'Connor C.M, Khan Z., Garcia B.A, Shenk T., Murphy E..  2012.  BclAF1 restriction factor is neutralized by proteasomal degradation and microRNA repression during human cytomegalovirus infection. Proceedings of the National Academy of Sciences. 109(24):9575-9580.
Lee S.H, Kalejta R.F, Kerry J., Semmes O.J, O'Connor C.M, Khan Z., Garcia B.A, Shenk T., Murphy E..  2012.  BclAF1 restriction factor is neutralized by proteasomal degradation and microRNA repression during human cytomegalovirus infection. Proceedings of the National Academy of Sciences. 109(24):9575-9580.
Kanodia J.S, Kim Y., Tomer R., Khan Z., Chung K., Storey J.D, Lu H., Keller P.J, Shvartsman S.Y.  2011.  A computational statistics approach for estimating the spatial range of morphogen gradients. Development. 138(22):4867-4874.
Kanodia J.S, Kim Y., Tomer R., Khan Z., Chung K., Storey J.D, Lu H., Keller P.J, Shvartsman S.Y.  2011.  A computational statistics approach for estimating the spatial range of morphogen gradients. Development. 138(22):4867-4874.
Mukherjee R., Singh L.NS, Evans P., Hannenhalli S.  2013.  Correlated evolution of positions within mammalian cis elements . Plos One. 8:e55521.
Pop M, Walker AW, Paulson J, Lindsay B, Antonio M, M Hossain A, Oundo J, Tamboura B, Mai V, Astrovskaya I et al..  2014.  Diarrhea in young children from low-income countries leads to large-scale alterations in intestinal microbiota composition.. Genome Biol. 15(6):R76.

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