Michael Gribskov Publications

Journal

Suman M.,  Jannasch, A., Adamec, J., Gribskov, M., Thomas, N., Höök, T.O., Sepúlveda, M.S. “Metabolite Profiles in Starved Diporeia Spp. Using Liquid Chromatography-Mass Spectrometry (LC-MS) Based Metabolomics.” Journal of Crustacean Biology 32, 239-248, 2012.

Gupta, A., Rahman, R., Li, K., Gribskov, M., “Comprehensive Prediction of RNA Structure Including Pseudoknots”, RNA Biology, 9, 188-200, 2012.

Khadka, S., Vangeloff, A.D., Zhang, C., Siddavatam, P., Heaton, N.S., Wang, L., Sengupta, R., Sahasrabudhe, S., Randall, G., Gribskov, M., Kuhn, R.J., Perera, R., Lacount, D.J. “A physical interaction network of dengue virus and human proteins.” Molecular & Cellular Proteomics 10, M111.012187, 2011.

Curran, A., Chang, I.-F., Chang, C.-L., Garg, S., Miguel, R.M., Barron, Y.D., Li, Y., Romanowsky, S., Cushman, J., Gribskov, M., Harmon, A.C., Harper, J.F., “Calcium-Dependent  Protein Kinases from Arabidopsis show substrate specificity differences in an analysis of 103 substrates”, Frontiers in Plant Physiology 2, article 36, 2011.

Gupta, A., Gribskov, M., “The Role of RNA Sequence and Structure in RNA-Protein Interactions”, Journal of Molecular Biology 409, 574-587, 2011.

Banks, J.A., Nishiyama, T., Hasebe, M., Bowman, J.L., Gribskov, M., dePamphilis, C., Albert, V.A., Aono, N., Aoyama, T., Ambrose, B.A., Ashton, N.W., Axtell, M.J., Barker, E., Barker, M.S., Bennetzen, J.L., Bonawitz, N.D., Chapple, C., Cheng, C., Correa, L.G.G., Dacre, M., DeBarry, J., Dreyer, I., Durnford, D.G., Elias, M., Engstrom, E.M., Estelle, M., Feng, L., Finet, C., Floyd, S.K., Frommer, W.B., Fujita, T., Gramzow, L., Gutensohn, M., Harholt, J., Hattori, M., Heyl, A., Hirai, T., Hiwatashi, Y., Ishikawa, M., Iwata, M., Karol, K.G., Koehler, B., Kolukisaoglu, H.U., Kubo, M., Kurata, T., Lalonde, S., Li, K., Li, Y., Litt, A., Loqué, D., Lyons, E., Manning, G., Maruyama, T., Michael, T.P., Mikami, K., Miyazaki, S., Morinaga, S., Murata, T., Mueller-Roeber, B., Neilson, J.A.D., Nelson, D.R., Obara, M., Oguri, Y., Olmstead, R.G., Onodera, N., Petersen, B.L., Pils, B., Prigge, M., Rensing, S.A., Riaño-Pachón, D.M., Roberts, A.W., Sato, Y., Scheller, H.V., Schulz, B., Schulz, C., Shakirov, E.V., Shibagaki, N., Shinohara, N., Shippen, D.E., Sørensen, I., Sotooka, R., Sugimoto, N., Sugita, M., Sumikawa, N., Tanurdzic, M., Theissen, G., Ulvskov, P., Weng, J., Willats, W.W.G.T., Wipf, D., Wolf, P.G., Yang, L., Zimmer, A.D., Zhu, Q., Mitros, T., Helstein, U., Otillar, R., Salamov, A., Schmutz, J., Shapiro, H., Lindquist, E., Lucas, S., Rokhsar, D., Grigoriev, I.V., "The compact Selaginella genome identifies changes in gene content associated with the evolution of vascular plants.", Science 332, 960-963, 2011.

Rohila, J.S., Chen, M., Chen, S., Chen, J., Cerny, R.L., Dardick, C., Canlas, P., Fujii, H., Gribskov, M., Kanrar, S., Knoflicek, L., Stevenson, B., Xie, M., Xu, X., Zheng, X., Zhu, J.K., Ronald, P., Fromm, M.E. “Protein-protein interactions of tandem affinity purified protein kinases from rice”. PLoS One 4, e6685, 2009.

Coleman, J.J., Rounsley,S.D., Rodriguez-Carres,M., KuoA., Wasmann,C.C., Grimwood,J., Schmutz,J., Taga,M., White,G.J., Zhou,S., Schwartz,D.C., Freitag,M., Ma,L.-J., Danchin,E.GJ., Henrissat,B., Coutinho,P.M., Nelson,D.R., Straney,D., Napoli,C.A., Barker, B.M., Gribskov,M., Rep,M., Kroken,S., Molnár,I., Rensing,C., Kennell,J.C., Zamora, J., Farman,M.L., Selker,E.U., Salamov,A., Shapiro,H.,Pangilinan,J., Lindquist,E., Lamers,C., Grigoriev,I.V., Geiser,D.M., Covert,S.F., Temporini,E., VanEtten, H.D., "The genome of Nectria haematococca: contribution of supernumerary chromosomes to gene expansion", PLOS Genetics 5, e1000618.  doi: 10.1371/journal.pgen.1000618, 2009. PDF PubMed PMID: 19714214.

Ding, X., Richter, T., Chen, M., Fujii, H., Seo, Y.S., Xie, M., Zheng, X., Kanrar, S., Stevenson, R.A., Dardick, C., Li Y., Jiang, H., Zhang, Y., Yu, F., Bartley, L.E., Chern, M., Bart, R., Chen, X., Zhu, L., Farmerie, W.G., Gribskov, M., Zhu, J.K., Fromm, M.E., Ronald, P.C., Song, W.Y.. “A rice kinase-protein interaction map.”  Plant Physiology 149, 1478-1492, 2009. 

Li, K., Rahman, R., Gupta, A., Siddavatam, P., Gribskov, M., "Pattern Matching in RNA Structures", Proceedings of International Symposium on Bioinformatics Research and Applications, 2008.  Lecture Notes in Computer Science 4983, 317-330, 2008.

Ranganathan, S., Gribskov, M., Tan, T.W.  “Bioinformatics research in the Asia Pacific: a 2007 update.”  BMC Bioinformatics 9 Suppl 1, S1, 2008. PubMed PMID: 18315840.

Ryabov Y, Gribskov M.  “Spontaneous symmetry breaking in genome evolution.”  Nucleic Acids Research 36, 2756-2763, 2008. PubMed PMID: 18367477.

Hu, J.C., Aramayo, R., Bolser, D., Conway, T., Elsik, C.G., Gribskov, M., Kelder, T., Kihara, D., Knight, T.F. Jr, Pico, A.R., Siegele, D.A., Wanner, B.L., Welch, R.D.  “The emerging world of wikis.”  Science. 320, 1289-1290, 2008.

Gu, J., Gribskov, M., Bourne, P. E. "Wiggle - Predicting functionally flexible regions from primary sequence." Plos Computational Biology 2, 769-785, 2006. 

Niedner, R.H., Buzko, O.V., Haste, N.M., Taylor, A., Gribskov, M., Taylor, S.S. “Protein kinase resource: an integrated environment for phosphorylation research” Proteins 63, 78-86, 2006. PubMed PMID: 16435372.

Rohila, J. S., Chen, M., Chen, S., Chen, J., Cerny, R., Dardick, C., Canlas, P., Xu, X., Gribskov, M., Kanrar, S., Zhu, J. K., Ronald, P., Fromm, M. E. 2006. Protein-protein interactions of tandem affinity purification-tagged protein kinases in rice. Plant Journal 46: 1-13.

Tuskan, G. A., DiFazio, S., Jansson, S., Bohlmann, J., Grigoriev, I., Hellsten, U., Putnam, N., Ralph, S., Rombauts, S., Salamov, A., Schein, J., Sterck, L., Aerts, A., Bhalerao, R. R., Bhalerao, R. P., Blaudez, D., Boerjan, W., Brun, A., Brunner, A., Busov, V., Campbell, M., Carlson, J., Chalot, M., Chapman, J., Chen, G. L., Cooper, D., Coutinho, P. M., Couturier, J., Covert, S., Cronk, Q., Cunningham, R., Davis, J., Degroeve, S., Dejardin, A., Depamphilis, C., Detter, J., Dirks, B., Dubchak, I., Duplessis, S., Ehlting, J., Ellis, B., Gendler, K., Goodstein, D., Gribskov, M., Grimwood, J., Groover, A., Gunter, L., Hamberger, B., Heinze, B., Helariutta, Y., Henrissat, B., Holligan, D., Holt, R., Huang, W., Islam-Faridi, N., Jones, S., Jones-Rhoades, M., Jorgensen, R., Joshi, C., Kangasjarvi, J., Karlsson, J., Kelleher, C., Kirkpatrick, R., Kirst, M., Kohler, A., Kalluri, U., Larimer, F., Leebens-Mack, J., Leple, J. C., Locascio, P., Lou, Y., Lucas, S., Martin, F., Montanini, B., Napoli, C., Nelson, D. R., Nelson, C., Nieminen, K., Nilsson, O., Pereda, V., Peter, G., Philippe, R., Pilate, G., Poliakov, A., Razumovskaya, J., Richardson, P., Rinaldi, C., Ritland, K., Rouze, P., Ryaboy, D., Schmutz, J., Schrader, J., Segerman, B., Shin, H., Siddiqui, A., Sterky, F., Terry, A., Tsai, C. J., Uberbacher, E., Unneberg, P. 2006. The genome of black cottonwood, Populus trichocarpa (Torr. & Gray). Science. 313: 1596-1604.

Eide, D.J., Clark, S., Nair, T.M., Gehl, M., Gribskov, M., Guerinot, M.L. and Harper, J.F. “Characterization of the yeast ionome: a genome-wide analysis of nutrient mineral and trace element homeostasis in Saccharomyces cerevisiae”. Genome Biology 6, R77, PMID: 16168084, 2005.

Gribskov, M. "The ISCB: Growing and Evolving in Step with Science." PLoS Comput Biol. 1: e51, 2005. 

Gribskov, M. "An open forum for computational biology." PLoS Computational Biology 1: e5, 2005. 

Wang, D. and Gribskov, M., “Examining the architecture of cellular computing through a comparative study with a computer”. Journal of the Royal Society Interface 2, 187–195, 2005.

Zheng, C.L., Fu, X.D. and Gribskov, M., “Characteristics and regulatory elements defining constitutive splicing and different modes of alternative splicing in human and mouse”. RNA 11, 1777-1787, PMID: 16251388, 2005.

Zheng, C.L., Kwon, Y.S., Li, H.R., Zhang, K., Coutinho-Mansfield, G., Yang, C., Nair, T.M., Gribskov, M. and Fu, X.D. “MAASE: An alternative splicing database designed for supporting splicing microarray applications”. RNA 11, 1767-1776, PMID: 16251387, 2005.

Podell, S., and Gribskov, M., “Predicting N-terminal myristoylation sites in plant proteins”. BMC Genomics 5, 37 (DOI:10.1186/1471-2164-5-37), 2004.

Baxter, I., Tchieu, J., Sussman, M.R., Boutry, M., Palmgren, M., Gribskov, M., Harper, J.F., and Axelsen, K.B., “Genomic comparison of P-Type ATPase ion pumps in Arabidopsis and Rice”. Plant Physiology 132, 618-628, 2003.

Fink, J.L., Drewes, S., Patel, H., Welsh, J.B., Masys, D.R., Corbeil, J., and Gribskov, M.R., “2HAPI: A web-based microarray data analysis system”. Bioinformatics 19, 1443-1445, 2003.

Gribskov, M., “Challenges in data management for functional genomics”, Omics 7, 3-5, 2003.

Hrabak, E.M., Chan, C.W.M. , Harmon, A.C. ,  Harper, J.F., Choi, J.H., Halford, N., Kudla, J., Luan, S., Nimmo, H.G., Sussman, M.R., Thomas, M, Welker-Simmons, K., Zhu, J.-K., and Gribskov, M., “The CDPK-SnRK superfamily of protein kinases”. Plant Physiology 132, 666-680, 2003.

Nair, T.M., Zheng, C.L., Fink, J.L, Stuart, R.O., Gribskov, M., “Rival penalized competitive learning (RPCL): a topology determining algorithm for analyzing gene-expression data”. Computational Biology and Chemistry, 27, 563-574, 2003.

Tchieu J.H., Fana F., Fink J.L., Harper J., Nair T.M., Niedner R.H., Smith D.W., Steube K., Tam T.M., Veretnik S., Wang D., and Gribskov M., “The PlantsP and PlantsT Functional Genomics Databases”, Nucleic Acids Research 31, 342-344, 2003.

Wang, D., Harper,, J.F., and Gribskov,, M., “Systematic trans-genomic comparison of protein kinases between Arabidopsis thaliana and Saccharomyces cerevisiae”. Plant Physiology 132, 2152-2165, 2003.

  1. Zheng, C.L., Fana, F., Udupi, P.V., and Gribskov, M., “Modulewriter: A program for automatic generation of database interfaces”, Computational Biology and Chemistry 27, 135-139, 2003.

Bailey, T.L.; and Gribskov, M., “Estimating and evaluating the statistics of gapped local-alignment scores.”  Journal of Computational Biology 9, 575-593, 2002.

Chien, S., Reiter, L.T., Bier, E., and Gribskov, M., “Homophila: human disease genes in Drosophila”, Nucleic Acids Research 30, 149-151, 2002. 

Kerk, D., Bulgrien, J., Smith, D.W., Barsam, B., Veretnik, S., and Gribskov, M., “The complement of protein phosphatase catalytic subunits encoded in the genome of Arabidopsis.  Plant Physiology 129 908-925, 2002.

  1. Ghassemian, M., Waner, D., Tchieu, J., Gribskov, M., and Schroeder, J.I., “An integrated Arabidopsis annotation database for Affymetrix Genechip (R) data analysis, and tools for regulatory motif searches”, Trends In Plant Science 6, 448-449, 2001. 

Gribskov, M., Fana, F., Harper, J., Hope, D.A., Harmon, A.C., Smith, D.W., Tax, F.E., and Zhang, G.F.,  “PlantsP: a functional genomics database for plant phosphorylation”, Nucleic Acids Research 29, 111-113, 2001. 

  1. Maser, P., Thomine, S., Schroeder, J.I., Ward, J.M., Hirschi, K., Sze, H., Talke, I.N., Amtmann, A., Maathuis, F.J.M., Sanders, D., Harper, J.F., Tchieu, J., Gribskov, M., Persans, M.W., Salt, D.E., Kim, S.A., and Guerinot, M.L., “Phylogenetic relationships within cation transporter families of Arabidopsis”, Plant Physiology 126, 1646-1667, 2001. 

Masys, D.R., Welsh, J.B., Fink, J.L., Gribskov, M., Klacansky, I., and Corbeil, J., “Use of keyword hierarchies to interpret gene expression patterns”, Bioinformatics 17, 319-326, 2001.

  1. Reiter, L.T., Potocki, L., Chien, S., Gribskov, M., and Bier, E., “A systematic analysis of human disease-associated gene sequences in Drosophila melanogaster”, Genome Research 11, 1114-1125, 2001. 

Bailey, T.L., Gribskov, M., “Concerning the accuracy of MAST E-values”, Bioinformatics 16, 488-489, 2000. 

Harmon, A.C., Gribskov, M., and Harper, J.F., “CDPKs – A kinase for every Ca2+”, Trends in Plant Science 5, 154-159, 2000. 

Bourne, P.E., and Gribskov, M. “ISMB-2000: Bioinformatics enters a new millennium”, Bioinformatics 16, 749, 2000. 

Gribskov, M., “The new biological literature”. Bioinformatics 15, 347, 1999. 

Veretnik, S., and Gribskov, M., “RNA binding domain of HDV is homologous to the HMG box of SRY”, Archives of Virology 144, 1-20, 1999.

Bailey, T.L. and Gribskov, M., "Methods and statistics for combining motif match scores", Journal of Computational Biology 5, 211-221, 1998.

Bailey, T.L. and Gribskov, M., "Combining evidence using p-values:  Application to sequence homology searches", Bioinformatics 14, 48-54, 1998. 

Bailey, T.L. and Gribskov, M., “Score distributions for simultaneous matching to multiple motifs”, Journal of Computational Biology 4, 45-59, 1997.

Miller, M., Geller, M., Gribskov, M., and Kent, S.B.H., “Analysis of the structure of chemically synthesized HIV-1 protease complexed with a hexapeptide inhibitor.  Part I: crystallographic refinement of 2 Å data”, Proteins 27, 184-194, 1997.

Smith, C.M., Shindyalov, I.N., Veretnik, S., Gribskov, M., Taylor, S.S., Ten Eyck, L.F., and Bourne, P.E., “The protein kinase resource”, Trends in Biochemical Sciences 22, 444-446, 1997.

Gribskov, M., and Robinson, N.L., “The use of receiver operating characteristic (ROC) analysis to evaluate sequence matching”, Computers and Chemistry 20, 25-34, 1996.

Gribskov, M. and Veretnik, S. “Identification of Sequence Patterns with Profile Analysis”, Methods in Enzymology 266, 198-212, 1996.

Gribskov, M. and Veretnik, S. “Identification of Sequence Patterns with Profile Analysis”, Methods in Enzymology 266, 198-212, 1996.

Gribskov, M. “Chapter 22: Profile analysis”, in Computer Analysis of Sequence Data, Part II, Methods in Molecular Biology Vol. 25, A.M. Griffin and H.G. Griffin Eds., pp 247-266, 1994.

Gribskov, M. “A mechanistic view of proteins and their sequences”, Computers and Chemistry 7, 113-116, 1993.

Miller, M., Rao, J.K.M. Wlodawer, A., and Gribskov, M.R. “A left-handed crossover involved in amidohydrolase catalysis: crystal structure of Erwinia chrysanthemi L-asparaginase with bound L-aspartate”, FEBS Letters 328, 275-279, 1993.

  1. Gribskov, M., “Translational initiation factors IF-1 and eIF-2α share an RNA-binding motif with prokaryotic ribosomal protein S1 and polynucleotide phosphorylase”, Gene 119, 107-111, 1993.

Lonetto, M, Gribskov, M, and Gross, C.A., “Minireview: The σ70 family: sequence conservation and evolutionary relationships” Journal of Bacteriology 174, 3843-3849, 1992.

  1. Gribskov, M., Lüthy, R., and Eisenberg, D., “Profile analysis”, in Methods in Enzymology, vol 183, R.F. Doolittle, ed., Academic Press, San Diego, pp 146-159, 1990.

Mullen, J.R., Kayne, P.S., Moerschell, R.P., Tsunasawa, S., Gribskov, M., Shepanski-Colavito, M., Grunstein, M., Sherman, F., and Sternglanz, R. “Identification and characterization of genes and mutants for an N-terminal acetyltransferase from yeast”, EMBO Journal 8, 2067-2075, 1989.

Gribskov, M., Homyak, M., Edenfield, J., and Eisenberg, D., “Profile scanning for three--dimensional structural patterns in protein sequences”, CABIOS 4, 61-66, 1988. 

Gribskov, M., McLachlan, A.D., and Eisenberg, D., “Profile analysis: detection of distantly related proteins”, Proceedings of the National Academy of Sciences 84, 4355-4358, 1987. 

Gribskov, M., and Burgess, R.R., “Sigma factors from E. coli, B. subtilis, phage SPO1, and phage T4 are homologous proteins.”, Nucleic Acids Research 14, 6745-6763, 1986.

Gribskov, M., Burgess, R.R., and Devereux, J., “PEPPLOT, a protein secondary structure analysis program for the UWGCG sequence analysis software package.” Nucleic Acids Research 14, 327-334, 1986. 

Gribskov, M., Devereux, J., and Burgess, R.R., “The codon preference plot:  graphic analysis of protein coding sequences and prediction of gene expression”, Nucleic Acids Research 12, 359-549, 1984. 

Gribskov, M. and Burgess, R.R., “Overexpression and purification of the sigma subunit of E. coli RNA polymerase”. Gene 26, 109-118, 1983. 

Hengenius, J.B., Gribskov, M., Rundell, A.E., Fowlkes, C.C., Umulis, D.M. ”Analysis of Gap Gene Regulation in an Organism-Scale Model of the Drosophila melanogaster Embryo.” PLoS One 6, e26797, 2011

Gribskov, M, Wu, Q. "Textpresso with Stemming." Bioinformatics, submitted, 2012.

Hu, J. C., Aramayo, R., Bolser, D., Conway, T., Elsik, C. G., Gribskov, M., Kelder, T., Kihara, D., Knight, T. F., Pico, A. R., Siegele, D. A., Wanner, B. L., Welch, R. D. 2008. The emerging world of wikis. Science. 320: 1289-1290.

Kerk, D., Bulgrien, J., Smith, D.W., and Gribskov, M., “Arabidopsis proteins containing similarity to the universal stress protein domain of bacteria”, Plant Physiology 131, 1209–1219, 2003.

Harmon, A.C., Gribskov, M., Gubrium, E., and Harper, J.F., “The CDPK superfamily of protein kinases”, New Phytologist 151, 175-183, 2001. 

Bourne, P. E., Gribskov, M. 2000. ISMB-2000: bioinformatics enters a new millennium. Bioinformatics. 16: 749.

Gribskov, M. 1992. The Language Metaphor in Sequence-Analysis. Computers & Chemistry. 16: 85-88.

Conference Proceedings

Zheng, C.L., Nair, T.M., Gribskov, M., Kwon, Y.S., Li, H.R., and Fu, X-.D., “A Database Designed to Computationally Aid An Experimental Approach to Alternative Splicing”, Pacific Symposium on Biocomputing 2004, Altman, R.B., Dunker, A.K., Hunter, L., Jung, T.A., and Klein T.E., Eds, World Scientific, New Jersey, pp 78-88, 2004.

Buzko, O., Niedner, H., Haste, N., Taylor, A., Gribskov, M., and Taylor, S.S. “The Protein Kinase Resource”, 12th International Conference on Second Messengers and Phosphoproteins. MedimondS.r.l. E803C0263:87-92, 2004.

Zheng, C.L., de Sa, V.R., Gribskov, M., Nair, T.M., “On selecting features from splice junctions: An analysis using information theoretic and machine learning approaches”. Genome Informatics 14, 73-83, 2003.

Bourne, P.E., Gribskov, M., Johnson, G., Moreland, J., and Weissig, H., “A Prototype Molecular Interactive Collaborative Environment (MICE)”,in Proceedings of the  Pacific Symposium on Biocomputing, R Altman, R., Dunker, K., Hunter, L., and Klein T., eds., pp.118-129, 1998.

Bailey, T.L., and Gribskov, M., “The megaprior heuristic for discovering protein sequence patterns”, in Proceedings of the Fourth International Conference on Intelligent Systems for Molecular Biology, pp 15-24, 1996.

Jorgenson, J., Buskirk, S.F., Gribskov, M., and Smith D.W. “SEARCH: locating and identifying genes and intron-exon junctions in large genomic sequences using parallel computers”, in Proceedings of the Third International Conference on Bioinformatics and Genome Research, Lim, H. A., and Cantor, C. R., Eds, World Scientific Publishing Co., Ltd., Singapore.  pp. 143-158, 1995

Burgess, R.R., Erickson, B., Gentry, D., Gribskov, M., Hager, D., Lesley, S., Strickland, M., Thompson, N., “Bacterial RNA polymerase subunits and genes”, in Steenbock Symposium, University of Wisconsin, Madison, WI, 1986.

Book Section

Schaller,G.E., Mathews,D.E., Gribskov,M., Walker,J.C. “Two-Component Signaling Elements and Histidyl-Aspartyl Phosphorelays”, The Arabidopsis Book, eds. C.R. Somerville and E.M. Meyerowitz, American Society of Plant Biologists, Rockville, MD, doi:10.1199/tab.0086, 2003.

Gribskov, M., “Bioinformatic tools for functional Genomics”, in Biology of Plant Microbe Interactions, Leong, S.A., Allen, C., and Triplett, E.W., eds.  International Society for Plant Microbe Interactions, St. Paul  MI, pp 320-324, 2002.

Gribskov, M., “Sequence comparison”, in Genetics Databases, M. Bishop, ed., Academic Press, 105-120, 1999.

Gribskov, M., Bourne, P., and Smith, C.M., “Integrated data resource for protein kinases”, in Genetics Databases, M. Bishop, ed., Academic Press, pp 241-246, 1999.

Rao, J.K.M., Gribskov, M., Lubkowski, J., Miller, M., Swain, A.L., and Wlodawer, A., “A comparison of the crystal structures of bacterial L-asparaginases”, in Techniques in Protein Chemistry VII, Marshak, D.R., ed., Academic Press, San Diego CA, pp 373-381, 1996.

Ginsburg, S., Gribskov, M. and Wang, X., “Querying Secondary Structures in Nucleic-Acid Sequences via Patterns-with-Ties,” USC Technical Report. October 1995. 

Gribskov, M., “Sequence matching in homology modeling”, in Protein Folds, A Distance-Based Approach, H. Bohr and S. Brunak, eds., CRC Press, Boca Raton, pp 71-79, 1995.

Rice, P.M., Elliston, K., and Gribskov, M., “DNA”, Chapter 1, in Sequence Analysis Primer, Gribskov, M., and Devereux, J., eds., Stockton Press, New York, pp 1-59, 1991.

Gribskov, M., and Eisenberg D. “Detection of protein structural features with profile analysis”, in Techniques in Protein Chemistry, T.E. Hugli, ed., Academic Press, San Diego, pp 108-117, 1989.

Eisenberg, D., Wesson, M., Goodsell, D, Wilcox, W., Gribskov, M., Altschuh, D., Richmond, T.J., and Rees, D.C.  “Binding energies estimated from atomic solvation parameters”. in Protein Structure, Folding, and Design, Oxender, D.L., ed., Alan R. Liss, New York, pp 203-214, 1987.

Burgess, R.R., Burton, Z., Gross, C., Taylor, W., and Gribskov, M., “Structure and regulatory features of a complex operon encoding E. coli ribosomal protein S21, DNA primase, and the RNA polymerase sigma subunit”, in Gene Expression, New York, Alan R. Liss, pp 387-401, 1983.

Gross, C., Burton, Z., Gribskov, M., Grossman, A., Liebke, H., Taylor, W., Walter, W., and Burgess, R.R., “Genetic, functional and structural analysis of E. coli RNA polymerase sigma subunit: A heat shock protein”, in Promoters - Structure and Function, Rodriguez, R.L., and Chamberlin, M.J. eds., New York, Praeger, 1983.

Edited Book

Gribskov, M., and Devereux, J., eds., Sequence Analysis Primer, Stockton Press, New York, 279 pages, 1991.

 



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