S Misra and N Harris (2005). Using Apollo to Browse and Edit Genome Annotations. Current Protocols in Bioinformatics, Unit 9.5, published by John Wiley & Sons, Inc.
S Lewis, M Gibson, N Harris, C Wiel, J Richter, M Wilkinson, D Block, W Crosby, M Clamp and S Searle (2004). Genquire and Apollo: Construction of a genome 'sandbox'. Computational Genomics: Theory and Application, Horizon Bioscience.
SE Lewis, SMJ Searle, N Harris, M Gibson, V Iyer, J Richter, C Wiel, L Bayraktaroglu, E Birney, MA Crosby, JS Kaminker, BB Matthews, SE Prochnik, CD Smith, JL Tupy, GM Rubin, S Misra, CJ Mungall and ME Clamp (2002). Apollo: a sequence annotation editor. Genome Biology 3(12):research0082
CJ Mungall, S Misra, BP Berman, J Carlson, E Frise, N Harris, B Marshall, S Shu, JS Kaminker, SE Prochnik, CD Smith, E Smith, JL Tupy, C Wiel, GM Rubin and SE Lewis (2002). An integrated computational pipeline and database to support whole-genome sequence annotation. Genome Biology 3(12):research0081
S Misra, MA Crosby, CJ Mungall, BB Matthews, KS Campbell, P Hradecky, Y Huang, JS Kaminker, GH Millburn, SE Prochnik, CD Smith, JL Tupy, EJ Whitfield, L Bayraktaroglu, BP Berman, BR Bettencourt, SE Celniker, ADNJ de Grey, RA Drysdale, NL Harris, J Richter, S Russo, AJ Schroeder, SQ Shu, M Stapleton, C Yamada, M Ashburner, WM Gelbart, GM Rubin and SE Lewis (2002). Annotation of the Drosophila melanogaster euchromatic genome: a systematic review. Genome Biology 3(12):research0083
N.L. Harris (2000). Annotating sequence data using Genotator. Molecular Biotechnology 16:3, 221-232.
C. Upton, D. Hogg, D. Perrin, M. Boone, and N.L. Harris (2000). Viral genome organizer: a system for analyzing complete viral genomes. Virus Research 70, 55-64.
M.G. Reese, G. Hartzell, N.L. Harris, U. Ohler, J.F. Abril, and S.E. Lewis (2000). Genome Annotation Assessment in Drosophila melanogaster. Genome Research 10(4):483-501.
M.D. Adams, S.E. Celniker, R.A. Holt, C.A. Evans, J.D. Gocayne, Amanatides, Scherer, Li, Hoskins, Galle, George, Lewis, Richards, Ashburner, Henderson, Sutton, Wortman, Yandell, Zhang, Chen, Brandon, Rogers, Blazej, Champe, Pfeiffer, Wan, Doyle, Baxter, Helt, Nelson, Gabor, Miklos, Abril, Agbayani, An, Andrews-Pfannkoch, Baldwin, Ballew, Basu, Baxendale, Bayraktaroglu, Beasley, Beeson, Benos, Berman, Bhandari, Bolshakov, Borkova, Botchan, Bouck, Brokstein, Brottier, Burtis, Busam, Butler, Cadieu, Center, Chandra, Cherry, Cawley, Dahlke, Davenport, Davies, Pablos, Delcher, Deng, Mays, Dew, Dietz, Dodson, Doup, Downes, Dugan-Rocha, Dunkov, Dunn, Durbin, Evangelista, Ferraz, Ferriera, Fleischmann, Fosler, Gabrielian, Garg, Gelbart, Glasser, Glodek, Gong, Gorrell, Gu, Guan, M. Harris, N.L.Harris, Harvey, Heiman, Hernandez, Houck, Hostin, Houston, Howland, Wei, Ibegwam, Jalali, Kalush, Karpen, Ke, Kennison, Ketchum, Kimmel, Kodira, Kraft, Kravitz, Kulp, Lai, Lasko, Lei, Levitsky, Li, Li, Liang, Lin, Liu, Mattei, McIntosh, McLeod, McPherson, Merkulov, Milshina, Mobarry, Morris, Moshrefi, Mount, Moy, Murphy, Murphy, Muzny, Nelson, Nelson, Nelson, Nixon, Nusskern, Pacleb, Palazzolo, Pittman, Pan, Pollard, Puri, Reese, Reinert, Remington, Saunders, Scheeler, Shen, Shue, Sidén-Kiamos, Simpson, Skupski, Smith, Spier, Spradling, Stapleton, Strong, Sun, Svirskas, Tector, Turner, Venter, Wang, Wang, Wang, Wassarman, Weinstock, Weissenbach, Williams, Woodage, Worley, Wu, Yang, Yao, Ye, Yeh, Zaveri, Zhan, Zhang, Zhao, Zheng, Zheng, Zhong, Zhong, Zhou, Zhu, Zhu, H.O. Smith, R.A. Gibbs, E.W. Myers, G.M. Rubin, and J.C. Venter (2000). "The Genome Sequence of Drosophila melanogaster". Science 287(5461):2185.
G.M. Rubin, M.D. Yandell, Wortman, Gabor, Miklos, Nelson, Hariharan, Fortini, Li, Apweiler, Fleischmann, Cherry, Henikoff, Skupski, Misra, Ashburner, Birney, Boguski, Brody, Brokstein, Celniker, Chervitz, Coates, Cravchik, Gabrielian, Galle, Gelbart, George, Goldstein, Gong, Guan, N.L. Harris, Hay, Hoskins, Li, Li, Hynes, Jones, Kuehl, Lemaitre, Littleton, Morrison, Mungall, O'Farrell, Pickeral, Shue, Vosshall, Zhang, Zhao, Zheng, Zhong, Zhong, R. Gibbs, J.C. Venter, M.D. Adams, and S. Lewis (2000). "Comparative Genomics of the Eukaryotes". Science 287(5461):2204.
Harris, N., Reese, M., Hartzell, G., and Lewis, S. (1999). "The Genome Annotation Assessment Project". Invited tutorial at the Third Annual Conference on Computational Genomics, Baltimore, Maryland.
Reese, M., Harris, N., Hartzell, G., Ohler, U., and Lewis, S. (1999). "The challenge of annotating a complete eukaryotic genome: A case study in Drosophila melanogaster". Tutorial at ISMB 99, August 6, Heidelberg, Germany.
Harris, N.L. (1999). "Annotating sequence data using Genotator." Chapter in Methods in Molecular Biology, vol 132: Bioinformatics Methods and Protocols, edited by S. Misener and S. Krawetz, Humana Press, Totowa, NJ, pp. 259-276.
Ashburner, Misra, Roote, Lewis, Blazej, Davis, Doyle, Galle, George, Harris, Harvey, Hong, Houston, Hoskins, Martin, Moshrefi, Palazzolo, Spradling, Tsang, Wan, Whitelaw, Kimmel, Celniker, and Rubin (1999). "An exploration of the sequence of a 2.9-megabase region of the genome of Drosophila melanogaster--The Adh region." Genetics 153: 179-219.
Lewis, S.E., Harris, N.L., Helt, G.A., Misra, S., and Rubin, G.M. (1998). "An intelligent system for interpretation of sequence alignment results." Second Annual Conference on Computational Genomics, Reston, VA. [Talk]
Harris, N.L. (1997). "Genotator: A workbench for sequence annotation." Genome Research 7(7):754-762.
Harris, N.L., Reese, M.G., and Eeckman, F.H. (1996). "Genotater: A workbench for sequence annotation." Eighth International Genome Sequencing and Analysis Conference, Hilton Head, SC. [Talk]
Harris, N.L., Reese, M.G.,
Helt, G.A.,
and Eeckman, F.H. (1996).
"Towards Automatic Recognition of Exons.'' Intelligent Systems for Molecular Biology '96, St. Louis, MO. [Poster]
Abstract
Reese, M.G., Harris, N.L. and Eeckman, F.H. (1996). "Large scale sequencing specific neural networks for promoter and splice site recognition.'' Proceedings of the Pacific Symposium on Biocomputing, 1996, edited by L. Hunter and T. Klein. [Poster]
Chapman, D., Harris, N., Park, J., and Critchlow, R.E. (1995). "Navigator: Tools for informal structure-activity relationship discovery.'' Journal of Molecular Graphics 13:242-249.
Jain, A.N., Harris, N., and Park, J. (1995). "Quantitative binding site model generation: Compass applied to multiple chemotypes targeting the 5-HT1A receptor,'' Journal of Medicinal Chemistry.
Spiegelhalter, D.J., Harris, N.L., Bull, K., and Franklin, R.C.G. (1994). "Empirical evaluation of prior beliefs about frequencies: Methodology and a case study in congenital heart disease,'' Journal of the American Statistical Association, 89:426, 435-443.
Harris, N.L., Presnell, S.R., and Cohen, F.E. (1994). "Four helix bundle diversity in globular proteins,'' Journal of Molecular Biology, Vol. 236.
States, D.J., Harris, N., and Hunter, L. (1993). "Computationally efficient representation of classes in protein sequence megaclassification," Proc Int Syst Mol Biol, 1:387-394.
Harris, N.L., States, D.J., and Hunter, L. (1993). "ClassX: A browsing tool for protein sequence megaclassifications,'' Twenty-sixth Annual Hawaii International Conference on System Sciences, Maui, HI, January, 1993.
Harris, N.L., Hunter, L., and States, D.J. (1992). "Megaclassification: Discovering motifs in massive datastreams,'' Tenth National Conference on Artificial Intelligence, San Jose, CA, July, 1992.
Hunter, L., Harris, N.L., and States, D.J. (1992). "Efficient classification of massive, unsegmented datastreams,'' Ninth International Machine Learning Conference, Aberdeen, Scotland, July, 1992.
Harris, N.L., and Jones, R. (1991). "Protein structure comparison on the Connection Machine,'' at AAAI-91 Workshop on AI Approaches to Classification and Pattern Recognition in Molecular Biology, Anaheim, CA, July, 1991.
Harris, N.L., Spiegelhalter, D.J., Bull, K., and Franklin, R.C.G. (1990). "Criticizing conditional probabilities in belief networks,'' in Randolph A. Miller (Ed.), 14th Symposium on Computer Applications in Medical Care, Washington DC, 805-809.
Harris, N.L. (1990). "Probabilistic belief networks for genetic counseling,'' Computer Methods and Programs in Biomedicine, 32:1, 37-44.
Harris, N.L., and Senapathy, P. (1990). "Distribution and consensus of branch point signals in eukaryotic genes: A computerized statistical analysis,'' Nucleic Acids Research 18:10, 3015-3019.
Harris, N.L. (1989). "Probabilistic reasoning in the domain of genetic counseling,'' TR-460, Laboratory for Computer Science, Massachusetts Institute of Technology.
Senapathy, P., Shapiro, M., and Harris, N.L. (1989). "Splice junctions, branch point sites, and exons: sequence statistics, identification, and applications to genome project'', Molecular Evolution: Computer Analysis of Protein and Nucleic Acid Sequences (Vol. 183 of Methods in Enzymology), 252-278.
September, 2003: Co-organizer, Generic Model Organism Database (GMOD) meeting.
November, 2001: Organizing Committee, Fifth Annual Conference on Computational Genomics.
July, 2001: Organizing Committee, Second Bioinformatics Open Source Conference (BOSC2001).
November, 2000: Organizing Committee, Fourth Annual Conference on Computational Genomics.
August, 2000: Organizing Committee, Bioinformatics Open Source Conference (BOSC2000).
June, 1998: Program Committee, Intelligent Systems for Molecular Biology '98.
October 8, 1996: Session Chair, Sequence Analysis and Annotation, Eighth International Genome Sequencing and Analysis Conference, Hilton Head, SC.
June, 1996: Program Committee, Intelligent Systems for Molecular Biology '96.
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