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M.N. Price and A.P. Arkin (2024) Interactive Tools for Functional Annotation of Bacterial Genomes. bioRxiv, doi: https://doi.org/10.1101/2024.04.15.589591.
M.N. Price and A.P. Arkin (2024) A fast comparative genome browser for diverse bacteria and archaea. PLoS ONE, doi: https://doi.org/10.1371/journal.pone.0301871.
Or try fast.genomics
J. Ramoneda, T. Jensen, M. Price, E. Casamayor, and N. Fierer. (2023) Taxonomic and environmental distribution of bacterial amino acid auxotrophies. Nature Communications, doi: https://doi.org/10.1038/s41467-023-43435-4
D.B. Bernstein, B. Akkas, M.N. Price, A.P. Arkin (2023). Evaluating E. coli genome-scale metabolic model accuracy with high-throughput mutant fitness data. Molecular Systems Biology 2023, doi: https://doi.org/10.1101/2023.01.05.522875.
Also see the preprint.
M.N. Price, A.M. Deutschbauer, and A.P. Arkin (2023) Many Families of Lids for TonB-dependent Transporters in Bacteroides. boiRxiv 2023, doi: https://doi.org/10.1101/2023.03.17.533168.
Valentine V. Trotter, Maxim Shatsky, Morgan N. Price, Thomas R. Juba, Grant M. Zane, Kara P. De Leon, Erica L. Majumder, Qin Gui, Rida Ali, Kelly M. Wetmore, Jennifer V. Kuehl, Adam P. Arkin, Judy D. Wall, Adam M. Deutschbauer, John-Marc Chandonia, Gareth P. Butland. Large-scale genetic characterization of the model sulfate-reducing bacterium, Desulfovibrio vulgaris Hildenborough. Frontiers in Microbiology 2023, doi: 10.3389/fmicb.2023.1095191
Also see preprint
M.N. Price. (2022) Erroneous predictions of auxotrophies by CarveMe. Nature Ecology & Evolution, https://doi.org/10.1038/s41559-022-01936-3. link
Y.Y. Huang, M.N. Price, A. Hung, O. Gal-Oz, D. Ho, H. Carion, A.M. Deutschbauer, A.P. Arkin. (2022) Functional screens of barcoded expression libraries uncover new gene functions in carbon utilization among gut Bacteroidales. bioRxiv, doi: https://doi.org/10.1101/2022.10.10.511384
Morgan N Price and Adam P Arkin (2022).
Interactive analysis of functional residues in protein families.
mSystems, doi: 10.1128/msystems.00705-22
Or try SitesBLAST or Sites on a Tree
or see the preprint
Morgan N Price, Adam M Deutschbauer, Adam P. Arkin. (2021)
Filling gaps in bacterial catabolic pathways with computation and high-throughput genetics.
PLoS Genetics, doi: 10.1371/journal.pgen.1010156.
Or try GapMind for carbon sources
or see the preprint
Hualan Liu, Anthony L Shiver, Morgan N Price, Hans K Carlson, Valentine V Trotter, Yan Chen, Veronica Escalante, Jayashree Ray, Kelsey E Hern, Christopher J Petzold, Peter J Turnbaugh, Kerwyn Casey Huang, Adam P Arkin, and Adam M Deutschbauer. (2021) Functional genetics of human gut commensal Bacteroides thetaiotaomicron reveals metabolic requirements for growth across environments. Cell Rep. 34(9):108789, doi: 10.1016/j.celrep.2021.108789.
Or browse genes' mutant phenotypes at the Fitness Browser, or see the preprint.
Sean Carim, Ashley L. Azadeh, Alexey E. Kazakov, Morgan N. Price, Peter J. Walian, Lauren M. Lui, Torben N. Nielsen, Romy Chakraborty, Adam M. Deutschbauer, Vivek K. Mutalik and Adam P. Arkin. (2021) Systematic discovery of pseudomonad genetic factors involved in sensitivity to tailocins. ISME J., doi: 10.1038/s41396-021-00921-1.
Morgan N. Price, Adam M. Deutschbauer, and Adam P. Arkin. (2021) Four families of folate-independent methionine synthases. PLoS Genetics, doi: 10.1371/journal.pgen.1009342
Also see the preprint
Vivek K. Mutalik, Benjamin A. Adler, Harneet S. Rishi, Denish Piya, Crystal Zhong, Britt Koskella, Elizabeth M. Kutter, Richard Calendar, Pavel S. Novichkov, Morgan N. Price, Adam M. Deutschbauer, Adam P. Arkin. (2020) High-throughput mapping of the phage resistance landscape in E. coli. PLoS Biology, doi: 10.1371/journal.pbio.3000877.
Hans K. Carlson, Lauren M. Lui, Morgan N. Price, Alexey E. Kazakov, Alex V. Carr, Jennifer V. Kuehl, Trenton K. Owens, Torben Nielsen, Adam P. Arkin, Adam M. Deutschbauer. (2020) Selective carbon sources influence the end-products of microbial nitrate respiration. ISME J, doi: 10.1038/s41396-020-0666-7
Also see the preprint
Morgan N Price, Adam M Deutschbauer, and Adam P Arkin. (2019) GapMind: Automated annotation of amino acid biosynthesis. mSystems, doi: 10.1128/mSystems.00291-20.
Or try GapMind
or see preprint.
Michael Thorgersen, Xiaoxuan Ge, Farris Poole, Morgan Price, Adam Arkin, and Michael Adams. (2019) Nitrate-utilizing microorganisms resistant to multiple metals from the heavily contaminated oak ridge reservation. Applied and Environmental Microbiology, doi: 10.1128/AEM.00896-19
Morgan N. Price and Adam P. Arkin. (2019) Curated BLAST for Genomes. mSystems, 10.1128/mSystems.00072-19.
Or try Curated BLAST
or see the preprint.
Morgan N. Price, Jayashree Ray, Anthony T. Iavarone, Hans K. Carlson, Elizabeth M. Ryan, Rex R. Malmstrom, Adam P. Arkin, Adam M. Deutschbauer (2019) Oxidative pathways of deoxyribose and deoxyribonate catabolism. mSystems, doi: 10.1128/msystems.00297-18
Also see the preprint
Vivek K. Mutalik, Pavel S. Novichkov, Morgan N. Price, Trenton K. Owens, Mark Callaghan, Sean Carim, Adam M. Deutschbauer, and Adam P. Arkin (2019) Dual-barcoded shotgun expression library sequencing for high-throughput characterization of functional traits in bacteria. Nature Communications 10:308.
Also see data downloads or preprint.
Lara Rajeev, Megan E. Garber, Grant M. Zane, Morgan N. Price, Inna Dubchak, Judy D. Wall, Pavel S. Novichkov, Aindrila Mukhopadhyay, and Alexey E. Kazakov (2018). A new family of transcriptional regulators of tungstoenzymes and molybdate/tungstate transport. Environmental Microbiology, doi: 10.1111/1462-2920.14500.
Hans K. Carlson, Morgan N. Price, Mark Callaghan, Alex Aaring, Romy Chakraborty, Hualan Liu, Jennifer V. Kuehl, Adam P. Arkin, and Adam M. Deutschbauer. (2018) The selective pressures on the microbial community in a metal-contaminated aquifer. ISME Journal, doi: 10.1038/s41396-018-0328-1.
Also see the preprint.
Morgan Price, Grant M Zane, Jennifer V Kuehl, Ryan A Melnyk, Judy D Wall, Adam M Deutschbauer, Adam P Arkin (2018) Filling Gaps in Bacterial Amino Acid Biosynthesis Pathways with High-throughput Genetics. PLoS Genetics 14(1), doi: 10.1371/journal.pgen.1007147.
Also see data downloads or the preprint.
Hualan Liu, Morgan Price, Robert Jordan Waters, Jayashree Ray, Hans K. Carlson, Jacob S. Lamson, Romy Chakraborty, Adam P. Arkin, Adam M. Deutschbauer (2018) Magic pools: parallel assessment of transposon delivery vectors in bacteria. mSystems, doi: 10.1128/mSystems.00143-17
Also see data downloads
or the preprint.
Jacqueline M. Rand, Tippapha Pisithkul, Ryan L. Clark, Joshua M. Thiede, Christopher R. Mehrer, Daniel E. Agnew, Candace E. Campbell, Andrew L. Markley, Morgan N. Price, Jayashree Ray, Kelly M. Wetmore, Yumi Suh, Adam P. Arkin, Adam M. Deutschbauer, Daniel Amador-Noguez, Brian F. Pfleger (2017) A metabolic pathway for catabolizing levulinic acid in bacteria. Nature Microbiology, doi:10.1038/s41564-017-0028-z.
M. N. Price and A. P. Arkin. (2017) PaperBLAST: Text-mining papers for information about homologs. mSystems, 10.1128/mSystems.00039-17.
Also see preprint or try PaperBLAST.
S. Sagawa, M. N. Price, A. M. Deutschbauer, A. P. Arkin. (2017) Validating Regulatory Predictions from Diverse Bacteria with Mutant Fitness Data. PLoS ONE, doi: 10.1371/journal.pone.0178258
Also see downloads or the preprint.
M. N. Price, K. M. Wetmore, R. J. Waters, M. Callaghan, J. Ray, J. V. Kuehl, R. A. Melnyk, J. S. Lamson, Y. Suh, Z. Esquivel, H. Sadeeshkumar, R. Chakraborty, B. E Rubin, J. Bristow, M. J. Blow, A. P. Arkin, A. M. Deutschbauer. (2016) Deep Annotation of Protein Function across Diverse Bacteria from Mutant Phenotypes. bioRxiv, doi: 10.1101/072470.
Also see Fitness Browser or the final version with data downloads.
M. N. Price and A. P. Arkin. (2016) A Theoretical Lower Bound for Selection on the Expression Levels of Proteins. Genome Biology and Evolution, doi: 10.1093/gbe/evw126.
M. N. Price, K. M. Wetmore, A. M. Deutschbauer, A. P. Arkin. (2016) A Comparison of the Costs and Benefits of Bacterial Gene Expression.
Freely available at PLoS ONE.
Also see data downloads
or earlier version at bioRxiv.
M. N. Price and A. P. Arkin. (2015) Weakly deleterious mutations and low rates of recombination limit the impact of natural selection on bacterial genomes. mBio, doi:10.1128/mBio.01302-15.
Also see simulations
B. Vaccaro, M. Thorgersen, W. Lancaster, M. Price, K. Wetmore, F. Poole, A. Deutschbauer, A. Arkin, and M. Adams. (2015) Determining Roles of Accessory Genes in Denitrification by Mutant Fitness Analyses. Applied and Environmental Microbiology, doi:10.1128/AEM.02602-15.
B. E. Rubin, K. M. Wetmore, M. N. Price, S. Diamond, R. K. Shultzaberger, L. C. Lowe, G. Curtin, A. P Arkin, A. Deutschbauer, S. S. Golden. (2015) The Essential Gene Set of a Photosynthetic Organism. PNAS, doi:10.1073/pnas.1519220112.
K. Wetmore, M. Price, R. Waters, J. Lamson, J. He, C. Hoover, M. Blow, J. Bristow, G. Butland, A. Arkin, and A. Deutschbauer. (2015) Rapid quantification of mutant fitness in diverse bacteria by sequencing randomly barcoded transposons (RB-TnSeq). mBio, doi: 10.1128/mBio.00306-15
Freely available at mBio, or see fitness data and code
R. A. Melnyk, I. C. Clark, H. K. Carlson, K. M. Wetmore, M. N. Price, A. T. Iavarone, A. M. Deutschbauer, A. P. Arkin, and John D. Coates. (2015) A novel mechanism for scavenging of hypochlorite involving a periplasmic methionine-rich peptide and methionine sulfoxide reductase. mBio, doi: 10.1128/mBio.00233-15.
M. N. Price, J. Ray, K. M. Wetmore, J. V. Kuehl, S. Bauer, A. M. Deutschbauer, A. P. Arkin. (2014) The genetic basis of energy conservation in the sulfate-reducing bacterium Desulfovibrio alaskensis G20. Frontiers in Microbiology, doi: 10.3389/fmicb.2014.00577.
Freely available at Frontiers. An older version is available at bioRxiv.
H. Carlson, J. Kuehl, A. Hazra, N. Justice, M. Stoeva, A. Sczesnak, M. Mullan, A. Iavarone, A. Engelbrektson, M. Price, A. Deutschbauer, A. Arkin, and J. Coates. (2014) Mechanisms of direct inhibition of the respiratory sulfate-reduction pathway by (per)chlorate and nitrate. The ISME Journal, doi:10.1038/ismej.2014.216.
A. Deutschbauer, M. N. Price, K. M. Wetmore, D. R. Tarjan, Z. Xu, W. Shao, D. Leon, A. P. Arkin, J. M. Skerker. (2014) Towards an informative mutant phenotype for every bacterial gene. J. Bacteriology doi:10.1128/JB.01836-14.
Freely available at JB. Also see data downloads
W. Shao, M. N. Price, A. M. Deutschbauer, M. F. Romine, A. P. Arkin. (2014)
Conservation of transcription start sites within genes across a bacterial genus. mBio 5:e01398-14.
Freely available at mBio or see the data
J. Kuehl, M. Price, J. Ray, K. Wetmore, Z. Esquivel, A. Kazakov, M. Nguyen, R. Kuehn, R. Davis, T. Hazen, A. Arkin, and A. Deutschbauer. Functional genomics with a comprehensive library of transposon mutants for the sulfate-reducing bacterium Desulfovibrio alaskensis G20. mBio 2014, 5:e01041-14.
Freely available, also see fitness experiments, fitness heatmap for the choline regulator Dde_3291, or view transcript data in Artemis
H. L. Korte, S. R. Fels, G. A. Christensen, M. N. Price, J. V. Kuehl, G. M. Zane, A. M. Deutschbauer, A. P. Arkin, and J. D. Wall. Genetic basis for nitrate resistance in Desulfovibrio strains. Front Microbiol. 2014; 5: 153.
Freely available
P. S. Novichkov, X. Li, J. V. Kuehl, A. M. Deutschbauer, A. P. Arkin, M. N. Price, and D. A. Rodionov. Control of methionine metabolism by the SahR transcriptional regulator in Proteobacteria. Environmental Microbiology 2013, doi:10.1111/1462-2920.12273
See Env. Micro., the SahR regulon in Desulfovibrios, or see predicted regulons in other bacteria at RegPrecise.
J. M. Skerker, D. Leon, M. N. Price, J. S. Mar, D. R. Tarjan, K. M. Wetmore, A. M. Deutschbauer, J. Baumohl, S. Bauer, A. Ibanez, V. Mitchell, C. H. Wu, P. Hu, T. Hazen, A. P. Arkin. (2013) Dissecting a complex chemical stress: chemogenomic profiling of plant hydrolysates. Molecular Systems Biology 9:674, doi:10.1038/msb.2013.30.
Freely available; also see data downloads
M. N. Price, A. M. Deutschbauer, J. M. Skerker, K. M. Wetmore, T. Ruths, J. S. Mar, J. V. Kuehl, W. Shao, A. P. Arkin. (2013) Indirect and Suboptimal Control of Gene Expression is Widespread in Bacteria. Molecular Systems Biology 9:660.
Freely available; also see data downloads
B. Meyer, J. Kuehl, A. M. Deutschbauer, M. N. Price, A. P. Arkin, D. A. Stahl. (2013) Variation among Desulfovibrio species in electron transfer systems used for syntrophic growth. J. Bacteriology 195:990-1004.
A. E. Kazakov and D. A. Rodionov and M. N. Price and A. P. Arkin and I. Dubchak and P. S. Novichkov. (2012) Transcription factor family-based reconstruction of singleton regulons: study of the Crp/Fnr, ArsR and GntR families in Desulfovibrionales genomes. J. Bacteriology.
R. Baran and B. P. Bowen and M. N. Price and A. P. Arkin and A. M. Deutschbauer and T. R. Northen. (2012) Metabolic footprinting of mutant libraries to map metabolite utilization to genotype. ACS Chemical Biology 8:189-199.
A. M. Deutschbauer, M. N. Price, K. Wetmore, W. Shao, J. K. Baumohl, Z. Xu, M. Nguyen, R. Tamse, R. W. Davis, A. P. Arkin. (2011) Evidence-based annotation of gene function in Shewanella oneidensis MR-1 using genome-wide fitness profiling across 121 conditions. PLoS Genetics 7(11):e1002385.
Freely available at PLoS Genetics
See fitness downloads or search by SO_ number at MicrobesOnline and navigate to Fitness pages
D. McDonald, M. N. Price, J. Goodrich, E. P. Nawrocki, T. Z. DeSantis, A. Probst, G. L. Andersen, R. Knight and P. Hugenholtz. (2011) An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea. ISME J., doi:10.1038/ismej.2011.139.
Lara Rajeev, Eric G Luning, Paramvir S Dehal, Morgan N Price, Adam P Arkin and Aindrila Mukhopadhyay. (2011) Systematic Mapping of Two component Response Regulators to Gene Targets in a Model Sulfate Reducing Bacterium. Genome Biology 12:R99.
Freely available at Genome Biology
Swapnil Chhabra, Gareth Butland, Dwayne Elias, John-Marc Chandonia, Veronica Fok, Thomas Juba, Amita Gorur, Simon Allen, Chin Man Leung, Kimberley Keller, Sonia Reveco, Grant Zane, Elizabeth Semkiw, Ramadevi Prathapam, Barbara Gold, Mary Singer, Mario Ouellet, Evelin Szakal, Daniel Jorgens, Morgan Price, Ewa Witkowska, Harry Beller, Terry Hazen, Mark Biggin, Manfred Auer, Judy Wall, and Jay Keasling. (2011) Generalized Schemes for High Throughput Manipulation of the Desulfovibrio vulgaris Hildenborough Genome. Applied and Environmental Microbiology.
Price, M.N., Deutschbauer, A.M., Kuehl, J.V., Liu, H., Witkowska, H. E., and Arkin, A. P. (2011) Evidence-based annotation of transcripts and proteins in the sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough. J. Bacteriology 193:5716-27.
Freely available at J. Bacteriology or see data downloads
Hauser, L.J., Land, ML, Brown, S.D., Larimer, F., Keller, K.L., Rapp-Giles, B.J., Price, M.N., Lin, M., Bruce, D.C., Detter, J.C., Tapia, R., Han, C.S., Goodwin, L.A., Cheng, J.F., Pitluck, S., Copeland, A., Lucas, S., Nolan, M., Lapidus, A.L., Palumbo, A.V., and Wall, J.D. (2011) The Complete Genome Sequence and Updated Annotation of Desulfovibrio alaskensis G20. J. Bacteriology, 193:4268-9.
See PubMed
Chhabra SR, Joachimiak MP, Petzold CJ, Zane GM, Price MN, Reveco SA, Fok V, Johanson AR, Batth TS, Singer M, Chandonia JM, Joyner D, Hazen TC, Arkin AP, Wall JD, Singh AK, Keasling JD. (2011)Towards a Rigorous Network of Protein-Protein Interactions of the Model Sulfate Reducer Desulfovibrio vulgaris Hildenborough. PLoS One 6(6):e21470.
Freely available at PubMed
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 or download a sqlite3 database
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.
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.
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)
