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• Oh, J., Fung, E., Price, M.N., Dehal, P.S., Davis, R.W., Giaever, G., Nislow, C., Arkin, A.P., and Deutschbauer, A. (2010) A universal TagModule collection for parallel genetic analysis of microorganisms. Nucleic Acids Research, doi:10.1093/nar/gkq419.
  Freely available at NAR.

• He, Q., He, Z., Joyner, D.C., Joachimiak, M., Price, M.N., Yang, Z.K., Yen, H.C., Hemme, C.L., Chen, W., Fields, M.M., Stahl, D.A., Keasling, J.D., Keller, M., Arkin, A.P., Hazen, T.C., Wall, J.D., and Zhou J. (2010) Impact of elevated nitrate on sulfate-reducing bacteria: a comparative Study of Desulfovibrio vulgaris. ISME J doi:10.1038/ismej.2010.59.
  See ISME J or PubMed.

• Price, M.N., Dehal, P.S., and Arkin, A.P. (2010) FastTree 2 -- Approximately Maximum-Likelihood Trees for Large Alignments. PLoS ONE, 5(3):e9490. doi:10.1371/journal.pone.0009490.
  Freely available at PLoS ONE. Also see the FastTree software page

• Dehal, P.S., Joachimiak, M.P., Price, M.N., Bates, J.T., Baumohl, J.K., Chivian, D., Friedland, G.D., Huang, K.H., Keller, K., Novichkov, P.S., Dubchak, I.L., Alm, E.J., Arkin, A.P. (2009) MicrobesOnline: an integrated portal for comparative and functional genomics. Nucleic Acids Research, database issue.
  Freely available at NAR; also see MicrobesOnline

• Price, M.N., Dehal, P.S., and Arkin, A.P. (2009) FastTree: Computing Large Minimum-Evolution Trees with Profiles instead of a Distance Matrix. Molecular Biology and Evolution 26:1641-1650, doi:10.1093/molbev/msp077.
  Freely available at MBE
  Also see the FastTree software page

• Price, M.N., Dehal, P.S., and Arkin, A.P. (2008) FastBLAST: Homology relationships for millions of proteins. PLoS ONE 3(10): e3589.
  Freely available at PLoS ONE.
  Also see the FastHMM/FastBLAST software page.

• Price, M.N., Dehal, P.S., and Arkin, A.P. (2008) Horizontal gene transfer and the evolution of transcriptional regulation in Escherichia coli. Genome Biology 9:R4.
  Freely available at Genome Biology
  You can also download the automatically identified HGT and ORFan genes in E. coli K12

• Price, M.N., Dehal, P.S., and Arkin, A.P. (2007) Orthologous transcription factors in bacteria have different functions and regulate different genes. PLoS Computational Biology, 3(9): e175.
  Freely available at PLoS, PubMed or as PDF

• Price, M.N., Arkin, A.P. and Alm, E.J. (2006) The Life-cycle of Operons. PLoS Genetics 2(6):e96.
  See a diagram of the lifecycle, or the open-access paper at PLoS or PubMed

• Price, M.N., Arkin, A.P. and Alm, E.J. (2006) OpWise: Operons aid the identification of differentially expressed genes in bacterial microarray experiments. BMC Bioinformatics 7:19.
  Freely available at BMC. OpWise is available here

• Price, M.N., Alm, E.J. and Arkin, A.P. (2006) The Histidine Operon is Ancient. J. Molecular Evolution, DOI: 10.1007/s00239-005-0191-3
  Available here

• Price, M.N., Alm, E.J. and Arkin, A.P. (2005) Interruptions in gene expression drive highly expressed operons to the leading strand of DNA replication. Nucleic Acids Research 33:3224-34.
  Freely available at NAR or as PDF

• Price, M.N., Huang, K.H., Arkin, A.P. and Alm, E.J. (2005) Operon Formation is Driven by Co-Regulation and Not by Horizontal Gene Transfer. Genome Research 15:809-819.
  Freely available at Genome Research or as PDF

• Alm, E.J., Huang, K.H., Price, M.N., Koche, R.P., Keller, K., Dubchak, I.L. and Arkin, A.P. (2005) The MicrobesOnline Website for Comparative Genomics. Genome Research 15:1015-1022.
  See MicrobesOnline.org web site; paper freely available at Genome Research or as PDF

• Price, M.N., Huang, K.H., Alm, E.J., and Arkin, A.P. (2005) A Novel Method for Accurate Operon Predictions in All Sequenced Prokaryotes. Nucleic Acids Research 33(3):880-892
  See Pubmed, NAR, or supplementary information or see MicrobesOnline.org for operon predictions for over 500 genomes and source code

• Price, M.N. and Rieffel, E. (2004) Finding Coexpressed Genes in Counts-Based Data: An Improved Measure and Validation Experiments. Bioinformatics 20(6):945-52.
  See PubMed, Bioinformatics, or supplementary information.

• Shipman, F., Price, M., Marshall, C., and Golovchinsky, G. Identifying Useful Passages in Documents based on Annotation Patterns. 7th European Conference on Research and Advanced Technology for Digital Libraries (ECDL 2003) Trondheim, Norway, August 17-22, 2003., August 17, 2003.
  See abstract or PDF

• Marshall, C.C., Golovchinsky, G., and Price, M.N. Digital libraries and mobility. Communications of the ACM. 44(5) ACM Press. pp. 55-56.

• Marshall, C.C., Price, M.N., Golovchinsky, G., and Schilit, B.N. Designing e-Books for Legal Research. In Proc. JCDL 2001 (Roanoke, VA, June 23-27). ACM Press. pp. 41-48.
  Honorable Mention -- Vanevar Bush Best Paper Award
  See abstract or PDF from FXPAL

• Marshall, C.C., Price, M.N., Golovchinsky, G., and Schilit, B.N. Introducing a digital library reading appliance into a reading group. In Proceedings of ACM Digital Libraries 99, ACM Press, pp.77-84.
  See abstract or PDF from FXPAL

• Golovchinsky, G., Price, M.N., and Schilit, B.N. From Reading to Retrieval: Freeform Ink Annotations as Queries. In Proceedings of ACM SIGIR 99, ACM Press, pp. 19-25.
  See abstract or PDF from FXPAL

• Marshall, C.C., Price, M.N., Golovchinsky, G., and Schilit, B.N. Collaborating over portable reading appliances. In Personal Technologies, Vol. 3, No. 1, March 1999.
  See abstract or PDF from FXPAL

• Hong, J., Price, M.N., Schilit, B.N., and Golovchinsky, G. Printertainment: Printing With Interactive Cover Sheets. In CHI 99 Extended Abstracts, ACM Press, pp. 240-241.
  See abstract or PDF from FXPAL

• Davis, R.C., Landay, J.A., Chen, V., Huang, J., Lee, R.B., Li, F.C., Lin, J., Morrey, C.B. III, Schleimer, B., Price, M.N., and Schilit, B.N. NotePals: Lightweight Note Sharing by the Group, for the Group. In Proceedings of CHI 99, ACM Press, pp. 338-345.
  See abstract or PDF from FXPAL

• Schilit, B.N., Price, M.N., Golovchinsky, G., Tanaka, K., and Marshall, C.C. As We May Read: The Reading Appliance Revolution. IEEE Computer 32(1):65-73, January 1999.
  See abstract or PDF from FXPAL

• Davis, R.C., Lin, J., Brotherton, J.A., Landay, J.A., Price, M.N., and Schilit, B.N. A Framework for Sharing Handwritten Notes. In Proceedings of UIST 98, ACM Press, pp. 119-120.
  See abstract or PDF from FXPAL

• Schilit, B.N., Price, M.N., and Golovchinsky, G. Digital Library Information Appliances. In Digital Libraries '98 (June 23-26, 1998 Pittsburgh, PA), ACM Press, pp. 217-225.
  See abstract or PDF from FXPAL

• Price, M.N., Golovchinsky, G., and Schilit, B.N. Linking By Inking: Trailblazing in a Paper-like Hypertext. In Proceedings of Hypertext '98 (June 20-24, 1998 Pittsburgh, PA), ACM Press, pp. 30-39.
  See abstract or PDF from FXPAL

• Schilit, B.N., Golovchinsky, G., and Price, M.N. Beyond Paper: Supporting Active Reading with Free Form Digital Ink Annotations. In Proceedings of CHI 98 (April 18-23, 1998, Los Angeles, CA), ACM Press, pp. 249-256.
  See abstract or PDF from FXPAL

• Price, M.N., Schilit, B.N, and Golovchinsky, G. XLibris: The Active Reading Machine. In CHI 98 Summary (April 18-23, 1998, Los Angeles, CA), ACM Press, pp. 22-23.
  See abstract or PDF from FXPAL

• Satyanarayanan, M., Noble, B., Kumar, P., and Price. M.N. Application-Aware Adaptation for Mobile Computing. In Proceedings of the 6th ACM SIGOPS European Workshop, September 1995.
  See postscript or PDF.

• Noble, B., Price, M.N., and Satyanarayanan, M. A Programming Interface for Application-Aware Adaptation in Mobile Computing. In Proceedings of the 2nd USENIX Symposium on Mobile and Location-Independent Computing, April 1995.
  See postscript or PDF.

• Hagstrom, J. N., Hagstrom, R., Overbeek, R., Price, M.N., and Schrage, L. Maximum Likelihood Genetic Sequence Reconstruction from Oligo Content. Networks 24:297-302, June 1994.
  See abstract

• Michaels, G. S., Taylor, R., Munson, P., Hagstrom, R., Price, M.N., and Overbeek, R. Searching for Genomic Organizational Motifs: Explorations of the E. coli Chromosome. Computers in Chemistry 17: 209-217 (1993).

• Hagstrom, R., Michaels, G. S., Overbeek, R., Price, M.N., and Taylor, R. Overview of GRACE - A Database System for Analysis of Multiple Genomes. In Proceedings of the 23rd Hawaiian International Conference on System Science, 1993.

• Michaels, G. S., Taylor, R., Hagstrom, R., Price, M., and Overbeek, R. Comparative Analysis of Genomic Data: a global look at structural and regulatory features. In Proceedings of the Second (June 1992) International Conference on Bioinformatics, Supercomputing, and Complex Genome Analysis, ed. Hua A. Lim, World Scientific Publishing Co., River Edge, NJ (1992).

• R. Butler, T. Butler, I. Foster, N. Karonis, R. Olson, R. Overbeek, N. Pfluger, M. Price, and S. Tuecke. Aligning genetic sequences. In "Strand: New Concepts in Parallel Programming," I. Foster and S. Taylor eds., Prentice Hall, 1989, pp.253-271.

Patent Applications

• Golovchinsky, G., Marshall, C.C., Price, M.N., and Schilit, W.N. Detection and Processing of Annotated Anchors. U.S. Patent Application No. 09/944,817 (granted 2007).

• Golovchinsky, G., Price, M.N., Schilit, W.N. A method and system for browsing through free-form digital ink annotations made on a "back of the book" index. JP2000227915

• Golovchinsky, G., Schilit, W.N., Price, M.N. A method and apparatus for annotating components of graphical user interfaces. EP1016956.

• Schilit, W.N., Price, M.N., Golovchinsky, G. A method and system for maintaining free form ink annotations on changing views. EP1016983.

• Schilit, W.N., Golovchinsky, G., Price, M.N. Free-form ink reminders. EP1074930.

• Price, M.N., Schilit, W.N., Golovchinsky, G., O'Hara, K.P.A., Sellen, A.J., Mont-Reynaud, B.M. Method and system for creating ad-hoc links from free-form ink. US09094730, 06/15/98.

• Price, M.N., Golovchinsky, G., Schilit, W.N. A method and system for free-form digital ink annotation of data traces. JP2000187541, 11/03/98.

• Golovchinsky, G., Schilit, W.N., Weiser, M.D., Price, M.N. A method and system for suggesting related documents. EP0902380, 1999-03-17.

• Golovchinsky, G., Schilit, W.N., Wilcox, L., Price, M.N. A method and system for organizing documents based upon annotations in context. EP0902379, 1999-03-17.

• Schilit, W.N., Price, M.N., Golovchinsky, G. Method and system for document storage management based on document content. EP0950965.

• Golovchinsky, G., Schilit, W.N., Price, M.N. Method and apparatus for facilitating skimming of text. US6128634.

• Golovchinsky, G., Price, M.N., Schilit, W.N. Method and apparatus for displaying references to a user's document browsing history within the context of a new document. EP0950964.

Position Papers & Technical Reports

• Price, M.N. Ancient origins of flagellar operons.

• Price, M.N. mRNA Degradation and the Fitness of Unicellular Organisms.
  See Word

• Price, M.N. Information Exploration: More than Just Gathering Information. CHI98 workshop on information exploration interfaces.
  Available on the web.

• Davis, R., Brotherton, J., Price, M., Landay, J. and Schilit, B. NotePals: Lightweight Note Taking by the Group, for the Group. University of California at Berkeley, Computer Science Division, Technical Report CSD-98-997, February 24, 1998.
  See abstract or PDF.

• Price, M.N. What's wrong with systems research in mobile computing. CHI '97 workshop on ubiquitous computing.
  Available on the web.

• Price, M. and Nettles, S. Transactions in a Flash. Technical Report MS-CIS-96-53, CIS Dept. University of Pennsylvania, 1996.
  See abstract. Also see slides from a talk at CMU:  postscript, PDF, or PowerPoint.

• Price, M.N., Raju, M., and Taylor, R. A Summary of Genomic Data Relating to E. coli Organized by Metabolic Pathways: An Initial Version. Argonne technical report MCS-TM-174, Math and Computer Science Division, Argonne National Laboratory, Argonne, Ill. (January 1993)

• Ross Overbeek and Morgan Price. Accessing Integrated Genomic Data Using GRACE: a Tutorial, Part 1. Argonne technical report MCS-TM-173, Math and Computer Science Division, Argonne National Laboratory, Argonne, Ill. (January 1993).

• Ray Hagstrom, Ross Overbeek, and Morgan Price. Users Guide and Tutorial for PC-GenoGraphics Version I. Argonne technical report ANL-92/45, Math and Computer Science Division, Argonne National Laboratory, Argonne, Ill. (December 1992)
  See text.

• Hagstrom, R., Michaels, G., Overbeek, R., Price, M., and Taylor, R. Overview of the Integrated Genomic Data System (IGD). Argonne technical report MCS-P325-0992, Math and Computer Science Division, Argonne National Laboratory, Argonne, Ill. (October 1992)

• Hagstrom, R., Michaels, G. S., Overbeek, R., Price, M., Taylor, R., Yoshida, K., and Zawada, D. GenoGraphics for OpenWindows. Argonne technical report ANL-92/11, Math and Computer Science Division, Argonne National Laboratory, Argonne, Ill. (April 1992)

MorganNPrice@yahoo.com