Publications on MnM

• - S. Rajasekaran, J.C. Merlin, V. Kundeti, A. Oommen, T. Mi, A. Oommen, J. Vyas, I. Alaniz, K. Chung, F. Chowdhury, S. Deverasatty, T. M. Irvey, D. Lacambacal, D. Lara, S. Panchangam, V. Rathnayake, P. Watts, and M. R Schiller, A computational tool for identifying minimotifs in protein-protein interactions and improving the accuracy of minimotif predictions, Proteins: Structure, Function, and Bioinformatics, Vol. 79, No. 1, October 2010, pp. 153-164.


• - S. Rajasekaran, T. Mi, J.C. Merlin, A. Oommen, P. Gradie, and M.R. Schiller, Partitioning of minimotifs based on function with improved prediction accuracy, PLoS ONE 5(8): e12276, 2010.


• - S. Rajasekaran, S. Balla, P. Gradie, M.R. Gryk, K. Kadaveru, V. Kundeti, M.W. Maciejewski, T. Mi, N. Rubino, J. Vyas, and M.R. Schiller, Minimotif miner 2nd release: a database and web system for motif search, Nucleic Acids Research 37, 2009, D185-D190.


• - 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


• - Rajasekaran S, Balla S, Huang C, Thapar C, Gryk M, Maciejewski M, and Schiller M. (2005) "Exact Algorithms for Motif Search" J. Clin. Mon. Comp., 19, 319-328.


• - Jay Vyas, Ronald J Nowling, Mark W Maciejewski, Sanguthevar Rajasekaran, Michael R Gryk, Martin R Schiller (2009) "A proposed syntax for Minimotif Semantics, version 1" BMC Genomics 2009, 10:360

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., López, 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


• - Rajasekaran S, Balla S, Gradie P, Gryk M R, Kadaveru K, Kundeti V, Maciejewski M W, Mi T, Rubino N, Vyas J, and Schiller M R Minimotif miner 2nd release: a database and web system for motif search Nucl. Acids Res. (2009) 37(suppl 1): D185-D190 first published online October 31, 2008 doi:10.1093/nar/gkn865


• - Gould C M, Diella F, Via A, Puntervoll P, Gemünd C, Chabanis-Davidson S, Michael S, Sayadi A, Bryne J C, Chica C, Seiler M, Davey N E, Haslam N, Weatheritt R J, Budd A, Hughes T, Pas J, Rychlewski L, Travé G, Aasland R, Citterich M H, Linding R, and Gibson T J ELM: the status of the 2010 eukaryotic linear motif resource Nucl. Acids Res. (2010) 38(suppl 1): D167-D180 first published online November 17, 2009 doi:10.1093/nar/gkp1016


• - Via A , Gould C M, Gemünd C, Gibson T J and Citterich M H A structure filter for the Eukaryotic Linear Motif Resource BMC Bioinformatics 2009, 10:351doi:10.1186/1471-2105-10-351


• - Davey N E, Haslam N J, Shields D C, and Edwards R J, SLiMFinder: a web server to find novel, significantly over-represented, short protein motifs Nucl. Acids Res. (2010) 38(suppl 2): W534-W539 first published online May 23, 2010 doi:10.1093/nar/gkq440


• - Davey N E, Haslam N J, Shields D C, and Edwards R J SLiMSearch 2.0: biological context for short linear motifs in proteins Nucl. Acids Res. (2011) first published online May 26, 2011 doi:10.1093/nar/gkr402


• - Davey N E, Haslam N J, Shields D C, and Edwards R J, SLiMSearch: A Webserver for Finding Novel Occurrences of Short Linear Motifs in Proteins, Incorporating Sequence Context Lecture Notes in Computer Science, 2010, Volume 6282/2010, 50-61, DOI: 10.1007/978-3-642-16001-1_5


• - Rajasekaran S. Merlin J. C, Kundeti V, Mi T, Oommen A., Vyas J., Alaniz I., Chung K., Chowdhury F., Deverasatty S., Irvey T. M., Lacambacal D., Lara D., Panchangam S., Rathnayake V., Watts P. and Schiller M. R. (2011), A computational tool for identifying minimotifs in protein–protein interactions and improving the accuracy of minimotif predictions. Proteins: Structure, Function, and Bioinformatics, 79: 153–164. doi: 10.1002/prot.22868


• - Vyas J, Nowling R J, Meusburger T, Sargeant D, Kadaveru K, Gryk MR, Kundeti V, Rajasekaran S and Schiller M R MimoSA: a system for minimotif annotation BMC Bioinformatics 2010, 11:328doi:10.1186/1471-2105-11-328


• - Sargeant D, Deverasetty S, Luo Y, Villahoz Baleta A, Zobrist S, Rathnayake V, Russo JC, Vyas J, Muesing MA, Schiller MR, HIVToolbox, an Integrated Web Application for Investigating HIV. 2011 PLoS ONE 6(5): e20122. doi:10.1371/journal.pone.0020122


• - Kowal1 A S, and Chisholm R L, Uncovering a Role for the Tail of the Dictyostelium discoideum SadA Protein in Cell-Substrate Adhesion, Eukaryotic Cell, May 2011, p. 662-671, Vol. 10, No. 5 1535-9778/11/$12.00+0 doi:10.1128/EC.00221-10


• - Costa-Junior H M & Vieira F S & Silv R C, C terminus of the P2X7 receptor: treasure hunting, 2011, PURINERGIC SIGNALLING Volume 7, Number 1, 7-19, DOI: 10.1007/s11302-011-9215-1


• - Xu, H., Schaniel, C., Lemischka, I. R. and Ma'ayan, A. (2010), Toward a complete in silico, multi-layered embryonic stem cell regulatory network. Wiley Interdisciplinary Reviews: Systems Biology and Medicine, 2: 708–733. doi: 10.1002/wsbm.93


• - Guo J, Wu X, Zhang D, and Lin K, Genome-wide inference of protein interaction sites: lessons from the yeast high-quality negative protein–protein interaction dataset Nucl. Acids Res. (2008) 36(6): 2002-2011 first published online February 14, 2008 doi:10.1093/nar/gkn016


• - Xue, Yu; Gao, Xinjiao; Cao, Jun; Liu, Zexian; Jin, Changjiang; Wen, Longping; Yao, Xuebiao; Ren, Jian, A Summary of Computational Resources for Protein Phosphorylation (2010) DOI: 10.2174/138920310791824138


• - Davey, Norman E., Edwards, Richard J. and Shields, Denis C. (2010) Computational identification and analysis of protein short linear motifs. Frontiers in Bioscience, 15, 801-825.


• - Davey1 N E, Travé G and Gibson T J How viruses hijack cell regulation, 2011, 1doi:10.1016/j.physletb.2003.10.071


• - Gould C M, Diella F, Via A, Puntervoll P, Gemünd C, Chabanis-Davidson S, Michael S, Sayadi A, Bryne J C, Chica C, Seiler M, Davey N E, Haslam N, Weatheritt R J, Budd A, Hughes T, Pas J, Rychlewski L, Travé G, Aasland R, Citterich M H, Linding R, and Gibson T J ELM: the status of the 2010 eukaryotic linear motif resource Nucl. Acids Res. (2010) 38(suppl 1): D167-D180 first published online November 17, 2009 doi:10.1093/nar/gkp1016


• - Diella F, Haslam N, Chica C, Budd A, Michael S, Brown N P, Travà G, Gibson T J, Understanding eukaryotic linear motifs and their role in cell signaling and regulation, 2008, [Frontiers in Bioscience 13, 6580-6603, May 1, 2008]


• - Dampier, William, Analysis of host-pathogen interactions: a bioinformatics approach, (2010) http://hdl.handle.net/1860/3249


• - Davidson N.J; Xueyi Wang; Non-Alignment Features Based Enzyme/Non-Enzyme Classification Using an Ensemble Method, Machine Learning and Applications (ICMLA), 2010, DOI 10.1109/ICMLA.2010.167


• - Kaminska, K. H., Milanowska, K. and Bujnicki, J. M. (2008) The Basics of Protein Sequence Analysis, in Prediction of Protein Structures, Functions, and Interactions (ed J. M. Bujnicki), John Wiley & Sons, Ltd, Chichester, UK. doi: 10.1002/9780470741894.ch1


• - Amort M, Wotzel B, Bakowska-Zywicka K, Erlacher M D, Micura R, and Polacek N An intact ribose moiety at A2602 of 23S rRNA is key to trigger peptidyl-tRNA hydrolysis during translation termination Nucl. Acids Res. (2007) 35(15): 5130-5140 first published online July 26, 2007 doi:10.1093/nar/gkm539


• - Castillo F J D, Cohen-Salmon M, Charollais A, Caille D, Lampe P D, Chavrier P, Meda P, and Petit C Consortin, a trans-Golgi network cargo receptor for the plasma membrane targeting and recycling of connexins Hum. Mol. Genet. (2010) 19(2): 262-275 first published online October 28, 2009 doi:10.1093/hmg/ddp490


• - Wacker1 S A, Alvarado C, Wichert G, Knippschild U, Wiedenmann J, Clauß K, Nienhaus G U, Hameister H, Baumann B, Borggrefe T, Knöche W and Oswald F, RITA, a novel modulator of Notch signalling, acts via nuclear export of RBP-J The EMBO Journal (2011) 30, 43 - 56 doi:10.1038/emboj.2010.289


• - Davey NE, Edwards RJ and Shields DC The SLiMDisc server: short, linear motif discovery in proteins (2007) Nucl. Acids Res. 35 (suppl 2): W455-W459. doi: 10.1093/nar/gkm400


• - Petsalakia E and Russell RB Peptide-mediated interactions in biological systems: new discoveries and applications (2008) Current Opinion in Biotechnology Volume 19, Issue 4, Pages 344-350


• - Diella F, Haslam N, Chica C, Budd A, Michael S, Brown NP, Trave G, Gibson TJ Understanding eukaryotic linear motifs and their role in cell signaling and regulation (2008) Frontiers in Bioscience 13, 6580-6603


• - Guo J, Xiaomei Wu X, Zhang DY and Lin K Genome-wide inference of protein interaction sites: lessons from the yeast high-quality negative protein–protein interaction dataset (2008) Nucl. Acids Res. 36 (6): 2002-2011. doi: 10.1093/nar/gkn016


• - Fox-Erlich S, Schiller MR, and Gryk MR Structural conservation of a short, functional, peptide-sequence motif (2009) Front Biosci.; 14: 1143–1151.


• - Chica C, Diella F, Gibson TJ Evidence for the Concerted Evolution between Short Linear Protein Motifs and Their Flanking Regions. (2009) PLoS ONE 4(7): e6052. doi:10.1371/journal.pone.0006052


• - Via A, Gould CM, Gemünd C, Gibson TJ, Helmer-Citterich M. A structure filter for the Eukaryotic Linear Motif Resource. 2009 BMC Bioinformatics;10:351.


• - Vyas J, Nowling1 RJ, Meusburger T, Sargeant D, Kadaveru K, Gryk MR, Kundeti V, Rajasekaran S and Schiller MR MimoSA: a system for minimotif annotation 2010 BMC Bioinformatics, 11:328 doi:10.1186/1471-2105-11-328


• - Sargeant D, Deverasetty S, Luo Y, Baleta AV, Zobrist S, Rathnayake V, Russo JC, Vyas J, Muesing MA, Schiller MR HIVToolbox, an Integrated Web Application for Investigating HIV (2011) PLoS ONE 6(5): e20122. doi:10.1371/journal.pone.0020122


• - Ren S, Yang G, He Y, Wang Y, Li Y and Chen Z The conservation pattern of short linear motifs is highly correlated with the function of interacting protein domains (2008) BMC Genomics, 9:452 doi:10.1186/1471-2164-9-452


• - Kowal AS and Chisholm RL Uncovering a Role for the Tail of the Dictyostelium discoideum SadA Protein in Cell-Substrate Adhesion (2011) Eukaryotic Cell, p. 662-671, Vol. 10, No. 5 1535-9778


• - Kredel S, Oswald F, Nienhaus K, Deuschle K, Röcker C, Wolff M, Heilker R, Nienhaus GU, and Wiedenmann J, mRuby, a Bright Monomeric Red Fluorescent Protein for Labeling of Subcellular Structures. (2009) PLoS ONE 4(2): e4391. doi:10.1371/journal.pone.0004391


• - Hugo W, Song F, Aung Z, Ng SK, Sung WK. SLiM on Diet: finding short linear motifs on domain interaction interfaces in Protein Data Bank (2010) Bioinformatics. Apr 15;26(8):1036-42. Epub 2010 Feb 18.


• - Wong RW and Blobel G Cohesin subunit SMC1 associates with mitotic microtubules at the spindle pole (2008) PNAS doi: 10.1073/pnas.0807660105


• - Costa-Junior HM, Vieira FS and Coutinho-Silva R C terminus of the P2X7 receptor: treasure hunting (2011) Purinergic Signalling Volume 7, Number 1, 7-19, DOI: 10.1007/s11302-011-9215-1


• - Davey NE, Edwards RJ and Shields DC Estimation and efficient computation of the true probability of recurrence of short linear protein sequence motifs in unrelated proteins (2010) BMC Bioinformatics, 11:14doi:10.1186/1471-2105-11-14


• - Schulte, G. (2010) Molecular Pharmacology of Frizzleds—with Implications for Possible Therapy, in GPCR Molecular Pharmacology and Drug Targeting: Shifting Paradigms and New Directions (ed A. Gilchrist), John Wiley & Sons, Inc., Hoboken, NJ, USA. doi: 10.1002/9780470627327.ch5


• - Lin TH, Murphy RF, Joseph ZB Discriminative Motif Finding for Predicting Protein Subcellular Localization (2011) IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB) Volume 8 Issue 2


• - Park C and Zhang J Genome-wide evolutionary conservation of N-glycosylation sites (2011) Mol Biol Evol doi: 10.1093/molbev/msr055


• - Xue, B., Hsu, W.-L., Lee, J.-H., Lu, H., Dunker, A. K. and Uversky, V. N. SPA: Short peptide analyzer of intrinsic disorder status of short peptides (2010). Genes to Cells, 15: 635–646. doi: 10.1111/j.1365-2443.2010.01407.


• - Xu1 L,Kanda1 V A, Choi1 E, Panaghie1 F, Roepke1 T.K, Gaeta1 S.A, Christini1 D.J, Lerner D.J and Abbott1 G.W, MinK-dependent internalization of the IKs potassium channel (2009) Cardiovasc Res 82 (3): 430-438. doi: 10.1093/cvr/cvp047


• - Lieber DS, Elemento O, Tavazoie S, 2010 Large-Scale Discovery and Characterization of Protein Regulatory Motifs in Eukaryotes. PLoS ONE 5(12): e14444. doi:10.1371/journal.pone.0014444


• - Glassmann1 A, Molly1 S, Surchev1 L, Nazwar1 T A, Holst1 M, Hartmann W, Baader S L, Oberdick J, Pietsch T and Schilling K, Developmental expression and differentiation-related neuron-specific splicing of metastasis suppressor 1 (Mtss1) in normal and transformed cerebellar cells BMC Developmental Biology 2007, 7:111doi:10.1186/1471-213X-7-111


• - Ritz A, Shakhnarovich G, Salomon A R, and Raphael B.J, Discovery of phosphorylation motif mixtures in phosphoproteomics data Bioinformatics (2009) 25(1): 14-21 first published online November 7, 2008 doi:10.1093/bioinformatics/btn569


• - Li M, Rollins J.A, The development-specific protein (Ssp1) from Sclerotinia sclerotiorum is encoded by a novel gene expressed exclusively in sclerotium tissues (2009) DOI: 10.3852/08-114 Mycologia, 101(1), 2009, pp. 34-43.by The Mycological Society of America


• - Nguyen Ba A N and Moses A M, Evolution of Characterized Phosphorylation Sites in Budding Yeast Mol Biol Evol (2010) 27(9): 2027-2037 first published online April 5, 2010 doi:10.1093/molbev/msq090


• - Herring M, Davenport N, Stephan K, Campbell S, White R, Kark J, and Tom D. Wolkow Fission yeast Rad26ATRIP delays spindle-pole-body separation following interphase microtubule damage J Cell Sci 2010 123:1537-1545; Advance Online Publication April 7, 2010, doi:10.1242/jcs.049478


• - Willy H, Song F, Aung Z, Ng S-K and Sung W-K, SLiM on DIet: Finding Short Linear Motifs on Domain Interaction Interfaces in PDB Bioinformatics (2010) doi: 10.1093/bioinformatics/btq065


• - Kaminska, K. H., Milanowska, K. and Bujnicki, J. M. (2008) The Basics of Protein Sequence Analysis, in Prediction of Protein Structures, Functions, and Interactions (ed J. M. Bujnicki), John Wiley & Sons, Ltd, Chichester, UK. doi: 10.1002/9780470741894.ch1


• - Xue, Yu; Gao, Xinjiao; Cao, Jun; Liu, Zexian; Jin, Changjiang; Wen, Longping; Yao, Xuebiao; Ren, Jian, A Summary of Computational Resources for Protein Phosphorylation (2010) DOI: 10.2174/138920310791824138


• - Dienia C A and Storeyb K B, Creatine kinase regulation by reversible phosphorylation in frog muscle, doi:10.1016/j.physletb.2003.10.071


• - Chen Y-C, Aguan K, Yang C-W, Wang Y-T, Pal NR, Chuang I-F, Discovery of Protein Phosphorylation Motifs through Exploratory Data Analysis (2011). PLoS ONE 6(5): e20025. doi:10.1371/journal.pone.0020025


• - Emma T. Westhuizen V D, Werry T D, Sexton P M and Summers R J, The Relaxin Family Peptide Receptor 3 (RXFP3) activates ERK1/2 through a PKC dependent mechanism. Molecular Pharmacology Fast Forward. Published on March 9, 2007 as doi:10.1124/mol.106.032763 MOL #32763


• - Gould C M, Diella F, Via A, Puntervoll P, Gemünd C, Chabanis-Davidson S, Michael S, Sayadi A, Bryne J C, Chica C, Seiler M, Davey N E, Haslam N, Weatheritt R J, Budd A, Hughes T, Pas J, Rychlewski L, Travà G, Aasland R, Citterich M H, Linding R, and Gibson T J ELM: the status of the 2010 eukaryotic linear motif resource Nucl. Acids Res. (2010) 38(suppl 1): D167-D180 first published online November 17, 2009 doi:10.1093/nar/gkp1016


• - Geng X, Lou H, Wang J, Li L, Swanson A L, Sun M, Beers-Stolz D, Watkins S, Perez R G, and Drain P a-Synuclein binds the KATP channel at insulin-secretory granules and inhibits insulin secretion Am J Physiol Endocrinol Metab February 2011 300:E276-E286; published ahead of print September 21, 2010, doi:10.1152/ajpendo.00262.2010


• - Wacker1 S A, Alvarado C, Wichert G, Knippschild U, Wiedenmann J, Clauß K, Nienhaus G U, Hameister H, Baumann B, Borggrefe T, Knöche W and Oswald F, RITA, a novel modulator of Notch signalling, acts via nuclear export of RBP-J The EMBO Journal (2011) 30, 43 - 56 doi:10.1038/emboj.2010.289


• - Dampier, William, Analysis of host-pathogen interactions: a bioinformatics approach, (2010)


• - Oren-Suissa, M. and Podbilewicz, B. (2010), Evolution of programmed cell fusion: Common mechanisms and distinct functions. Developmental Dynamics, 239: 1515–1528. doi: 10.1002/dvdy.22284


• - Chang D T, Chien T Y, and Chen C Y seeMotif: exploring and visualizing sequence motifs in 3D structures Nucl. Acids Res. (2009) 37(suppl 2): W552-W558 first published online May 28, 2009 doi:10.1093/nar/gkp439


• - Pasikowski P, Cydzik M, Kluczyk A, Stefanowicz P and Szewczuk Z, Ubiquitin fragments: their known biological activities and putative roles BioMolecular Concepts 2010 1:1 , 67-83


• - Castillo F J D, Cohen-Salmon M, Charollais A, Caille D, Lampe P D, Chavrier P, Meda P, and Petit C Consortin, a trans-Golgi network cargo receptor for the plasma membrane targeting and recycling of connexins Hum. Mol. Genet. (2010) 19(2): 262-275 first published online October 28, 2009 doi:10.1093/hmg/ddp490


• - Gunnar Schulte International Union of Basic and Clinical Pharmacology. LXXX. The Class Frizzled Receptors Pharmacol Rev December 2010 62:632-667; doi:10.1124/pr.110.002931


• - Filatova, A., Leyerer, M., Gorboulev, V., Chintalapati, C., Reinders, Y., Müller, T. D., Srinivasan, A., Hübner, S. and Koepsell, H. (2009), Novel Shuttling Domain in a Regulator (RSC1A1) of Transporter SGLT1 Steers Cell Cycle-Dependent Nuclear Location. Traffic, 10: 1599–1618. doi: 10.1111/j.1600-0854.2009.00982.


• - Anna Ritz, A Minimum Description Length Approach to the Multiple Motif Problem Research Comps Defense, 2008


• - Andrii Domanskyi, ANDROGEN RECEPTOR-DEPENDENT AND INDEPENDENT FUNCTIONS OF ARIP4 2007


• - Beno Hendrik Kuns, Detection and sorting of micro-beads and bacteriophages in a microfluidic biochip, 2006


• - Wu X, Shen Q T, Daniel S. Oristian, Catherine P. Lu, Zheng Q, Wang H W, Fuchs E Cell Skin Stem Cells Orchestrate Directional Migration by Regulating Microtubule-ACF7 Connections through GSK3ß - 4 February 2011 (Vol. 144, Issue 3, pp. 341-352)


• - Gould, C. M., Diella, F., Via, A., Puntervoll, P., Gemuend, C., Chabanis-Davidson, S., Michael, S., Sayadi, A., Bryne, J. C., Chica, C., Seiler, M., Davey, N. E., Haslam, N., Weatheritt, R. J., Budd, A., Hughes, T., Pas, J., Rychlewski, L., Trave, G., Aasland, R., Helmer-Citterich, M., Linding, R., Gibson, T. J. (2010) ELM: the status of the 2010 eukaryotic linear motif resource. NUCLEIC ACIDS RESEARCH, 38 (Suppl. 1). D167-D180. ISSN 0305-1048


• - Zur Erlangung de Identification and Characterisation of the Domains of RS1 (RSC1A1) Inhibiting the Monosaccharide ependent Exocytotic Pathway of Na-D-Glucose Cotransporter SGLT1 with High Affinit 2007


• - GProtein-COUPLED RECEPTORS http://www.monash.edu.au/cemo/molecular/Program.pdf


• - Xu, H., Schaniel, C., Lemischka, I. R. and Ma'ayan, A. (2010), Toward a complete in silico, multi-layered embryonic stem cell regulatory network. Wiley Interdisciplinary Reviews: Systems Biology and Medicine, 2: 708–733. doi: 10.1002/wsbm.93

Related Publications from MnM team.

• - J. Davila, S. Balla, and S. Rajasekaran, Fast and practical algorithms for planted (l, d) motif search, IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB), 2007, pp. 544-552.


• - S. Rajasekaran and H. Dinh, A speedup technique for (l, d)-motif finding algorithms, BMC Research Notes, 4:54, 8 March 2011


• - S. Rajasekaran, Computational techniques for motif search, Frontiers in Bioscience 14, June 1, 2009, pp. 5052-5065.


• - J. Vyas, R.J. Nowling, T. Meusburger, D. Sargeant, K. Kadaveru, M.R. Gryk, V. Kundeti, S. Rajasekaran, and M.R. Schiller, MimoSA: a system for minimotif annotation, BMC Bioinformatics, 2010, 11:328.


• - D. Sharma and S. Rajasekaran, A simple algorithm for (l, d) motif search, Proc. IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, Nashville, TN, March 30-April 2, 2009.


• - S. Rajasekaran, Efficient algorithms and system for motif search, Proc. National Symposium on Biocomputing, Annamalai University, India, February 23, 2009, pp. 1-12.


• - 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

- Frontiers in Bioscience special issue on short Functional motifs – Martin Schiller, managing editor (http://schiller.sols.unlv.edu:8080/SchillerUNLV/private/FBS.htm)