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	Martin R. Schiller Lab Website
Home Affiliations Alumni Bibliography Collaborators Employment Frontiers in Bioscience *Funding* Minimotif Miner Marty's web tool page News People Projects Videos Contact	Publications on MnM Balla S, Thapar V, Verma S, Luong T, Faghri T, Huang C-H, Rajasekaran S, del Campo JJ, Shinn JH, Mohler WA, Maciejewski MW, Gryk MR, Piccirillo B, Schiller SR, and Schiller MR* (2006) Minimotif Miner, a tool for investigating protein function. Nat. Methods 3:175-177 PMID: 16489333 Krishna Kadaveru K, Vyas J, and Schiller MR* (2008) "Viral infection and human disease - insights from minimotifs" Front. Biosci. 13:6455-71. PMID: 18508672 Schiller MR* (2007) "Minimotif Miner, a computational tool to investigate protein function, disease, and genetic diversity" Current Protocols in Protein Science, Eds. Coligan JE, Dunn BM, Speicher DW, Winkler H., Unit 2.12.1 - 2.12.14 John Wiley & Sons, Inc. PMID: 16489333 Publications citing MnM Schiller, M.R., Chakrabarti, K., King, G.F., Schiller, N.I., Eipper, B.A., Maciejewski, M.W. Regulation of RhoGEF activity by intramolecular and intermolecular SH3 domain interactions (2006) Journal of Biological Chemistry, 281 (27), pp. 18774-18786. Chica, C., Labarga, A., Gould, C.M., Lo?pez, R., Gibson, T.J. A tree-based conservation scoring method for short linear motifs in multiple alignments of protein sequences (2008) BMC Bioinformatics, 9, art. no. 229. Edwards, R.J., Davey, N.E., Shields, D.C. CompariMotif: Quick and easy comparisons of sequence motifs (2008) Bioinformatics, 24 (10), pp. 1307-1309. Perrodou, E., Chica, C., Poch, O., Gibson, T.J., Thompson, J.D. A new protein linear motif benchmark for multiple sequence alignment software (2008) BMC Bioinformatics, 9, art. no. 213. Guo, J., Wu, X., Zhang, D.-Y., Lin, K. Genome-wide inference of protein interaction sites: Lessons from the yeast high-quality negative protein - Protein interaction dataset (2008) Nucleic Acids Research, 36 (6), pp. 2002-2011. Plewczynski, D., Tkacz, A., Wyrwicz, L.S., Rychlewski, L., Ginalski, K. AutoMotif Server for prediction of phosphorylation sites in proteins using support vector machine: 2007 update (2008) Journal of Molecular Modeling, 14 (1), pp. 69-76. Dinkel, H., Sticht, H. A computational strategy for the prediction of functional linear peptide motifs in proteins (2007) Bioinformatics, 23 (24), pp. 3297-3303. Glassmann, A., Molly, S., Surchev, L., Nazwar, T.A., Holst, M., Hartmann, W., Baader, S.L., Oberdick, J., Pietsch, T., Schilling, K. Developmental expression and differentiation-related neuron-specific splicing of metastasis suppressor 1 (Mtss1) in normal and transformed cerebellar cells (2007) BMC Developmental Biology, 7, art. no. 111. Edwards, R.J., Davey, N.E., Shields, D.C. SLiMFinder: A probabilistic method for identifying over-represented, convergently evolved, short linear motifs in proteins (2007) PLoS ONE, 2 (10), art. no. e967. Kuravsky, M.L., Muronetz, V.I. Somatic and sperm-specific isoenzymes of glyceraldehyde-3-phosphate dehydrogenase: Comparative analysis of primary structures and functional features (2007) Biochemistry (Moscow), 72 (7), pp. 744-749. Van Der Westhuizen, E.T., Werry, T.D., Sexton, P.M., Summers, R.J. The relaxin family peptide receptor 3 activates extracellular signal-regulated kinase 1/2 through a protein kinase C-dependent mechanism (2007) Molecular Pharmacology, 71 (6), pp. 1618-1629. Peng, J., Dong, W., Chen, Y., Mo, R., Cheng, J.-F., Hui, C.-c., Mohandas, N., Huang, C.-H. Dusty protein kinases: Primary structure, gene evolution, tissue specific expression and unique features of the catalytic domain (2006) Biochimica et Biophysica Acta - Gene Structure and Expression, 1759 (11-12), pp. 562-572. Cao L, Yu K, Banh C, Nguyen V, Ritz A, Raphael BJ, Kawakami Y, Kawakami T, Salomon AR. Quantitative time-resolved phosphoproteomic analysis of mast cell signaling. (2007) J. Immunol. 179(9):5864-76 Ghosh M, Loper R, Gelb MH, Leslie CC. Identification of the expressed form of human cytosolic phospholipase A2beta (cPLA2beta): cPLA2beta3 is a novel variant localized to mitochondria and early endosomes. (2006) J. Biol. Chem. 281(24):16615-24. PMID: 16617059 Brandenburg J, Schimanski B, Nogoceke E, Nguyen TN, Padovan JC, Chait BT, Cross GA, Günzl A. Multifunctional class I transcription in Trypanosoma brucei depends on a novel protein complex. (2007) EMBO J. 2007 26(23):4856-66. PMID: 17972917 Related Publications from MnM team. Rajasekaran S, Balla S, Huang C-H, Thapar V, Gryk M, Maciejewski M, Schiller M, High-performance Exact Algorithms for Motif Search, Journal of Clinical Monitoring and Computing (Springer) (October 2005, Vol. 19, No. 4-5), pp 319-328. S. Rajasekaran, S. Balla, C.-H. Huang, V. Thapar, M. Gryk, M. Maciejewski, M. Schiller, Exact Algorithms for Motif Search, Proc. of the Third Asia-Pacific Bioinformatics Conference, 2005, (APBC 2005), pp 239-248. Jaime Davila, Sudha Balla and Sanguthevar Rajasekaran, Space and Time Efficient Algorithms For Planted Motif Search, Proc. 6th International Conference on Computational Science (ICCS 2006)/ 2nd International Workshop on Bioinformatics Research and Applications (IWBRA 2006), (accepted, to appear). S. Rajasekaran, S. Balla and C.-H. Huang, Exact Algorithms for Planted Motif Problems, Journal of Computational Biology (October 2005, Vol. 12, No. 8), pp 1117-1128. Sanguthevar Rajasekaran, Sudha Balla, Chun-Hsi Huang, Exact Algorithms for Planted Motif Challenge Problems, Proc. of the Third Asia-Pacific Bioinformatics Conference, 2005, (APBC 2005), pp 249-260. Fox-Erlich S, Schiller MR, Gryk MR (2008) "Structural Conservation of a short, functional, peptide sequence motif. Front. Biosci. In press. Machida K, Thompson CM, Dierck K, Jablonowski , K Karkkainen S, Liu B, Zhang H, Nash PD, Newman DK, Nollau P, Pawson T, Renkema, GH, Saksela K, Schiller MR, Shin DG, and Mayer BJ (2007) "High-Throughput Phosphotyrosine Profiling Using SH2 Domains" Mol. Cell 26:899-915. PMID: 17588523 Schiller MR, Chakrabarti K, King GF, Schiller NI, Eipper BA, and Maciejewski MW (2006) "Regulation of RhoGEF activity by intramolecular and intermolecular SH3 interactions" J. Biol. Chem. 281:17774-17786 PMID: 16644733 Related Activities* Martin R. Schiller is serving as managing editor for a special issue in Frontiers in Biociences. We are still accepting Reviews for this issue (see below) Special Issue: "Short Functional Peptide Motifs"

Publications on MnM

Balla S, Thapar V, Verma S, Luong T, Faghri T, Huang C-H, Rajasekaran S, del Campo JJ, Shinn JH, Mohler WA, Maciejewski MW, Gryk MR, Piccirillo B, Schiller SR, and Schiller MR* (2006) Minimotif Miner, a tool for investigating protein function. Nat. Methods 3:175-177 PMID: 16489333

Krishna Kadaveru K, Vyas J, and Schiller MR* (2008) "Viral infection and human disease - insights from minimotifs" Front. Biosci. 13:6455-71. PMID: 18508672

Schiller MR* (2007) "Minimotif Miner, a computational tool to investigate protein function, disease, and genetic diversity" Current Protocols in Protein Science, Eds. Coligan JE, Dunn BM, Speicher DW, Winkler H., Unit 2.12.1 - 2.12.14 John Wiley & Sons, Inc. PMID: 16489333

Publications citing MnM

Schiller, M.R., Chakrabarti, K., King, G.F., Schiller, N.I., Eipper, B.A., Maciejewski, M.W. Regulation of RhoGEF activity by intramolecular and intermolecular SH3 domain interactions (2006) Journal of Biological Chemistry, 281 (27), pp. 18774-18786.

Chica, C., Labarga, A., Gould, C.M., Lo?pez, R., Gibson, T.J. A tree-based conservation scoring method for short linear motifs in multiple alignments of protein sequences (2008) BMC Bioinformatics, 9, art. no. 229.

Edwards, R.J., Davey, N.E., Shields, D.C. CompariMotif: Quick and easy comparisons of sequence motifs (2008) Bioinformatics, 24 (10), pp. 1307-1309.

Perrodou, E., Chica, C., Poch, O., Gibson, T.J., Thompson, J.D. A new protein linear motif benchmark for multiple sequence alignment software (2008) BMC Bioinformatics, 9, art. no. 213.

Guo, J., Wu, X., Zhang, D.-Y., Lin, K. Genome-wide inference of protein interaction sites: Lessons from the yeast high-quality negative protein - Protein interaction dataset (2008) Nucleic Acids Research, 36 (6), pp. 2002-2011.

Plewczynski, D., Tkacz, A., Wyrwicz, L.S., Rychlewski, L., Ginalski, K. AutoMotif Server for prediction of phosphorylation sites in proteins using support vector machine: 2007 update (2008) Journal of Molecular Modeling, 14 (1), pp. 69-76.

Dinkel, H., Sticht, H. A computational strategy for the prediction of functional linear peptide motifs in proteins (2007) Bioinformatics, 23 (24), pp. 3297-3303.

Glassmann, A., Molly, S., Surchev, L., Nazwar, T.A., Holst, M., Hartmann, W., Baader, S.L., Oberdick, J., Pietsch, T., Schilling, K. Developmental expression and differentiation-related neuron-specific splicing of metastasis suppressor 1 (Mtss1) in normal and transformed cerebellar cells (2007) BMC Developmental Biology, 7, art. no. 111.

Edwards, R.J., Davey, N.E., Shields, D.C. SLiMFinder: A probabilistic method for identifying over-represented, convergently evolved, short linear motifs in proteins (2007) PLoS ONE, 2 (10), art. no. e967.

Kuravsky, M.L., Muronetz, V.I. Somatic and sperm-specific isoenzymes of glyceraldehyde-3-phosphate dehydrogenase: Comparative analysis of primary structures and functional features (2007) Biochemistry (Moscow), 72 (7), pp. 744-749.

Van Der Westhuizen, E.T., Werry, T.D., Sexton, P.M., Summers, R.J. The relaxin family peptide receptor 3 activates extracellular signal-regulated kinase 1/2 through a protein kinase C-dependent mechanism (2007) Molecular Pharmacology, 71 (6), pp. 1618-1629.

Peng, J., Dong, W., Chen, Y., Mo, R., Cheng, J.-F., Hui, C.-c., Mohandas, N., Huang, C.-H. Dusty protein kinases: Primary structure, gene evolution, tissue specific expression and unique features of the catalytic domain (2006) Biochimica et Biophysica Acta - Gene Structure and Expression, 1759 (11-12), pp. 562-572.

Cao L, Yu K, Banh C, Nguyen V, Ritz A, Raphael BJ, Kawakami Y, Kawakami T, Salomon AR. Quantitative time-resolved phosphoproteomic analysis of mast cell signaling. (2007) J. Immunol. 179(9):5864-76 Ghosh M, Loper R, Gelb MH, Leslie CC. Identification of the expressed form of human cytosolic phospholipase A2beta (cPLA2beta): cPLA2beta3 is a novel variant localized to mitochondria and early endosomes. (2006) J. Biol. Chem. 281(24):16615-24. PMID: 16617059

Brandenburg J, Schimanski B, Nogoceke E, Nguyen TN, Padovan JC, Chait BT, Cross GA, Günzl A. Multifunctional class I transcription in Trypanosoma brucei depends on a novel protein complex. (2007) EMBO J. 2007 26(23):4856-66. PMID: 17972917

Related Publications from MnM team.

Rajasekaran S, Balla S, Huang C-H, Thapar V, Gryk M, Maciejewski M, Schiller M, High-performance Exact Algorithms for Motif Search, Journal of Clinical Monitoring and Computing (Springer) (October 2005, Vol. 19, No. 4-5), pp 319-328.

S. Rajasekaran, S. Balla, C.-H. Huang, V. Thapar, M. Gryk, M. Maciejewski, M. Schiller, Exact Algorithms for Motif Search, Proc. of the Third Asia-Pacific Bioinformatics Conference, 2005, (APBC 2005), pp 239-248.

Jaime Davila, Sudha Balla and Sanguthevar Rajasekaran, Space and Time Efficient Algorithms For Planted Motif Search, Proc. 6th International Conference on Computational Science (ICCS 2006)/ 2nd International Workshop on Bioinformatics Research and Applications (IWBRA 2006), (accepted, to appear).

S. Rajasekaran, S. Balla and C.-H. Huang, Exact Algorithms for Planted Motif Problems, Journal of Computational Biology (October 2005, Vol. 12, No. 8), pp 1117-1128.

Sanguthevar Rajasekaran, Sudha Balla, Chun-Hsi Huang, Exact Algorithms for Planted Motif Challenge Problems, Proc. of the Third Asia-Pacific Bioinformatics Conference, 2005, (APBC 2005), pp 249-260.

Fox-Erlich S, Schiller MR, Gryk MR (2008) "Structural Conservation of a short, functional, peptide sequence motif. Front. Biosci. In press.

Machida K, Thompson CM, Dierck K, Jablonowski , K Karkkainen S, Liu B, Zhang H, Nash PD, Newman DK, Nollau P, Pawson T, Renkema, GH, Saksela K, Schiller MR, Shin DG, and Mayer BJ (2007) "High-Throughput Phosphotyrosine Profiling Using SH2 Domains" Mol. Cell 26:899-915. PMID: 17588523

Schiller MR*, Chakrabarti K, King GF, Schiller NI, Eipper BA, and Maciejewski MW (2006) "Regulation of RhoGEF activity by intramolecular and intermolecular SH3 interactions" J. Biol. Chem. 281:17774-17786 PMID: 16644733

Related Activities

Martin R. Schiller is serving as managing editor for a special issue in Frontiers in Biociences. We are still accepting Reviews for this issue (see below)

Special Issue: "Short Functional Peptide Motifs"