HIVtoolbox2 updates for investigating HIV released
Research Papers
SchillerLab Web Publications
Sharma S, Toledo O, Hedden M, Lyon KF, Brooks S, David RP, Limtong J, Newsome J, Rajasekaran S, Thapar V, Williams S, and Schiller MR . (2016). The Human C-terminome. PLOS One, 11, e0152731. PMID: 27050421 PDF
Benjamin R, Berges BK, Solis-Leal A, Igbinedion O, Strong CL, and Schiller MR. (2016). TALEN gene editing takes aim on HIV . Human Genetics , 135(9), 1059-1070, 1059-1070. PMID: 27170155 PDF
Schiller MR. (2016). The Minimotif Synthesis Hypothesis for the Origin of Life. J. of Translational Sci., 2, 289-296. PMID: 28083146 PMCID: PMC5223774 PDF
Strong CL , Guerra HP , Mathew KR, Roy N, Simpson LR, and Schiller MR . (2015). Damaging the Integrated HIV Proviral DNA with TALENs. PLOS ONE, 10, e0125652. PMID: 25946221 PDF
Lyon K, Strong CL, Schooler S, Young R, Roy N, Ozar B, Bachmeier M, Rajasekaran S, Schiller M,. (2015). Natural variability of minimotifs in 1,092 people indicates that minimotifs are targets of evolution. Nucleic Acids Res., pii, gkv580. PMID: 26068475 PDF
Sargeant DP, Hedden MW, Deverasetty S, Strong CL, Alaniz IJ, Bartlett AB, Brandon NR, Brooks SB, Brown FA, Bufi F, Charkarova M, David RP, Dobritch KM, Guerra HP, Levit KS, Mathew KR, Matti R, Maza DQ, Mistry S, Novakovic N, Pomerantz A, Rafalski T, Rathna. (2014). The Geogenomic Mutational Atlas of Pathogens (GoMAP) Web System. PLoS ONE, 9, e92877. PMID: 24675726 PDF
Sargeant DP, Deverasetty S, Strong CL, Alaniz IJ, Bartlett A, Brandon NR, Brooks SB, Brown FA, Bufi F, Charkarova M, David RP, Dobritch KM, Guerra HP, Hedden MP, et al.. (2014). The HIVToobox 2 web system integrates sequence, structure, function and mutation analysis. PLoS One, 9, e98810. PMID: 24886930 PDF
Pathak S, Kundeti VK, Schiller MR, and Rajasekaran S. (2013). A Structure Based Algorithm for Improving Motifs Prediction. Pattern Recognition in Bioinformatics, 7986, 242-252. PDF
Li L, Tibiche C., Fu C, Kaneko T, Moran MF, Schiller MR, Li SS, Wang E. (2012). The human phosphotyrosine signaling network: Evolution and hotspots of hijacking in cancer.. Genome Res., 22, 1222-30. PMID: 22194470 PDF
Mi T, Merlin JC, Deverasetty S, Gryk MR, Bill TJ, Brooks AW, Lee LY, Rathnayake V, Ross CA, Sargeant DP, Strong CL, Watts P, Rajasekaran S, Schiller MR. (2012). Minimotif Miner 3.0: database expansion and significantly improved reduction of false-positive predictions from consensus sequences.. Nucleic Acids Res., 40 (Database issue), D252-60. PMID: 22146221 PDF
Gorbatyuk VY, Schiller MR, Gorbatyuk OI, Barwinski M, Hoch JC. (2012). N-terminal Dbl domain of the RhoGEF, Kalirin. J Biomol NMR., 52, :269-76. PMID: 22314704 PMCID: PMC3362688 PDF
Merlin JC, Rajasekaran S, Mi T, and Schiller MR. (2012). Reducing false-positive prediction of minimotifs with a genetic interaction filter. PLoS One, 7, e32630. PMID: 22403687 PMCID: PMC3293834 PDF
Mi T, Rajasekaran S, Merlin JC, Gryk M, Schiller MR.. (2012). Achieving High Accuracy Prediction of Minimotifs.. PLoS One. , 7, e45589. PMID: 23029121 PDF
Fenwick M, Sesanker C, Schiller M, Ellis HJC, Hinman ML, Vyas J, Gryk M . (2012). RudolF: An Open-Source Sandbox for increasing the accessibility of Functional Programming to the Bioinformatics and Scientific Communities. Int. J. Software Eng. , Article number 6209130, 89-94. PDF
Sargeant DP, Gryk MR, Maciejewski MW, Thapar V, Kundeti V, Rajasekaran S, Romero P, Dunker K, Li S-C, Kaneka T, and Schiller MR. (2012). Secondary Structure, a Missing Component of Sequence-Based Minimotif Definitions. PLoS One, 7, e49957. PMID: 23236358 PDF
Borck G, Rehman AU, Lee K, Pogoda HM, Kakar N, von Ameln S, Grillet N, Hildebrand MS, Ahmed ZM, N├╝rnberg G, Ansar M, Basit S, Javed Q, Morell RJ, Nasreen N, Shearer AE, Ahmad A, Kahrizi K, Shaikh RS, Ali RA, Khan SN, Goebel I, Meyer NC, Kimberling WJ, Web. (2011). Loss-of-Function Mutations of ILDR1 Cause Autosomal-Recessive Hearing Impairment DFNB42. Am J Hum Genet, 88, 127-137. PMID: 21255762 PMCID: PMC3035704 PDF
Gradie PR, Litster M, Thomas R, Vyas J, Schiller MR. (2011). SciReader enables reading of medical content with instantaneous definitions. BMC Med Inform Decis Mak, 11, 4. PMID: 21266060 PDF
Sargeant D, Deverasetty S, Luo Y, Baleta AV, Zobrist S, Rathnayake V, Russo JC, Vyas J, Muesing MA, and Schiller MR. (2011). HIVToolbox, an integrated web application for investigating HIV. PLoS One, 6, e20122. PMID: 21647445 PDF
Kundeti V, Rajasekaran S, and Schiller MR. (2010). Algorithms for local structural alignment and structural motif identification. Algorithms in Computational Molecular Biology: Techniques, Approaches and Applications, Wiley Series in Bioinformatics, Summary PDF
Kaneko T, Huang H, Zhao B, Li L, Liu H, Voss CK, Wu C, Schiller MR, Li SS.. (2010). Loops govern SH2 domain specificity by controlling access to binding pockets.. Science Signaling, 3, RA34. PMID: 20442417 PDF
Jay Vyas, Ronald J.Nowling, Thomas Meusberger, David Sargeant, Krishna Kadaveru. Michael R. Gryk, Vamsi Kundeti Sanguthevar Rajasekaran and Martin R. Schiller. (2010). MimoSA: a system for minimotif annotation. BMC Bioinformatics, 11, 328. PMID: 19656955 PDF
Rajasekaran S, Mi T, Camilus J, Vyas J, Schiller MR. (2010). Partitioning of Minimotifs Based on Function with Improved Prediction Accuracy. Plos One, 19, pii: e12276. 20808856 PDF
Rajasekaran S, Merlin JC, Kundeti V, Mi T, Oommen A, Vyas J, Alaniz I, Chung K, Chowdhury F, Deverasatty S, Irvey TM, Lacambacal D, Lara D, Panchangam S, Rathnayake V, Watts P, Schiller MR. (2010). A computational tool for identifying minimotifs in protein-protein interactions and improving the accuracy of minimotif predictions. Proteins, 79, 153-164. PMID: 20938975 PDF
Vyas J, Nowling RJ, Maciejewski MW, Rajasekaran S, Gryk MR, and Schiller MR. (2009). A Proposed Syntax for Minimotif Semantics, Version 1. BMC Genomics., 10, 360. PMID: 19656396 PDF
Rajasekaran S, Balla S, Gradie P, Gryk MR, Kadaveru K, Kundeti V, Maciejewski MW, Mi T, Rubino N, Vyas J, Schiller MR. (2009). Minimotif Miner 2nd release: a database and web system for motif search. Nucleic. Acids Res., 37, D185-190. PMID: 18978024 PDF
Fox-Erlich S, Schiller MR, Gryk MR. (2009). Structural Conservation of a short, functional, peptide sequence motif. Front. Biosci., 14, 1143-1151. PMID: 19273121 PDF
Schiller MR*, Ferraro F, Wang Y, McPherson CE, Sobota J, Schiller NI and Eipper BA. (2008). Autonomous functions for the Sec14p and spectrin-repeat regions of Kalirin. Exp. Cell Res., 314, 2674-2691. PMID: 18585704 PDF
Krishna Kadaveru K, Vyas J, and Schiller MR. (2008). Viral infection and human disease - insights from minimotifs. Front. Biosci., 6455-6471. PMID: 18508672 PDF
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 PDF
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. PMID: 18429315 PDF
Zhang G, Hirai H, Cai T, Miura J, Yu P, Huang H, Schiller MR, Swaim WD, Leapman RD, and Notkins AL. (2007). RESP18, a homolog of the luminal domain IA-2, is found in dense core vesicles in pancreatic islet cells and is induced by high glucose. J. Endocrinol., 195, 313-321. PMID: 17951542 PDF
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 PDF
Schiller MR*. (2006). Coupling Receptor Tyrosine Kinases to Rho GTPases - GEFs what's the link. Cell. Signal., 18, 1834-1843. PMID: 16725310 PDF
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 PDF
Rajasekaran S, Balla S, Huang C, Thapar C, Gryk M, Maciejewski M, and Schiller M.. (2005). High Performance Algorithms for Motif Search. J. Clin. Mon. Comp., 19, 319-328. PMID: 16328946 PDF
Chakrabarti K, Lin R, Schiller NI, Wang Y, Fan Y-X, Koubi D, Rudkin BB, Johnson GR, Schiller MR. (2005). A critical role for Kalirin in NGF signaling through TrkA. Mol. Cell. Biol., 25, 5106-5118. PMID: 15923627 PDF
Schiller MR*, Blangy A, Huang J, Mains RE, Eipper BA. (2005). Induction of lamellipodia by Kalirin does not require its guanine nucleotide exchange factor activity. Exp. Cell Res., 307, 402-417. PMID: 15950621 PDF
Penzes P, Besser A, Chernoff J, Schiller MR, Eipper BA, Mains RE, and Huganir RL. (2003). Rapid induction of spine morphogenesis by trans-synaptic ephirin B- EphB receptor activation of the Rho-GEF Kalirin. Neuron, 29, 229-242. PMID: 12546821 PDF
May V, Schiller MR, Eipper BA, and Mains RE. (2001). Kalirin Dbl-homology GEF1 domain initiates new axon outgrowth through RhoG-mediated mechanisms. J. Neurosci., 22, 6980-6990. PMID: 12177196 PDF
Xu X, Joh H-D, Pin S, Schiller NI, Prange C., Burger PC, Schiller MR. (2001). Expression of multiple larger-sized transcripts for several genes in oligodendrogliomas; potential markers for glioma subtypes. Cancer Lett., 171, 67-77. PMID: 11485829 PDF
Monnito C, Pin S, Palmer D, Lee K, Breslow M, Berkowitz D, Schiller M. (2001). Ferritin, IGFBP4, and retroviral genes are overexpressed in a murine cachexia model. Am. J. Physiol. Endocrinol. Metab., 281, E289-97. PMID: 11440905 PDF
Schiller MR*. (2000). Genes expressed in the mouse pituitary corticotrope AtT-20 cell line. Pituitary, 3, 143-54. PMID: 11383478 PDF
Park YS, Kawasaki E, Kelemen L, Yu L, Schiller MR, Rewers M, Eisenbarth GS, and Hutton JC. (2000). Humoral autoreactivity to an alternatively spliced variant of ICA512/IA-2 in Type 1 diabetes. Diabetolgia, 43, 1293-1301. PMID: 11079748 PDF
Brat DJ, James CD, Jedlicka AE, Connolly DC, Chang, E, Castellani RJ, Schid M, Schiller MR, Carson DA, Burger PC. (1999). Molecular genetic alterations in radiation-induced astrocytomas. Am. J. Pathol., 154, 1431-1438. PMID: 10329596 PDF
Ciccotosto GD, Schiller MR, Eipper BA, and Mains RE. (1999). Induction of integral membrane PAM expression in AtT 20 cells alters the storage and trafficking of POMC and PC1. J. Cell Biol., 144, 459-471. PMID: 9971741 PDF
Hook VYH, Kang YH, Schiller MR, Tezapsidis N, Johnston JM, Azaryan A. (1998). Prohormone thiol protease' (PTP) a novel cysteine protein for proenkephalin and prohormone processing" in Proteolytic and cellular mechanisms in prohormone and proprotein processing. RG Landes Co, Georgetown, 89-104. PDF
Darlington N, Schiller MR, Mains RE, and Eipper BA. (1997). Expression of RESP18 in peptidergic and catecholaminergic neurons. J. Histochem. Cytochem., 45, 1265-1277. PMID: 9283614 PDF
Darlington N, Schiller MR, Mains RE, and Eipper BA. (1997). The expression of regulated endocrine-specific protein of 18 kDa in peptidergic cells of rat peripheral endocrine tissues and in blood. J. Endocrinol., 155, 329 341. PMID: 9415067 PDF
Hook VYH, Moran K, Kannan R, Kohn A, Lively MO, Azaryan AV, Schiller MR, Miller K. (1997). High level expression of the prohormones proenkephalin, pro- neuropeptide Y, proopiomelanocortin, and protachykinin in E. Coli for in vitro prohormone processing. Protein Expression Purif., 10, 80-88. PDF
Holmes LD and Schiller MR. (1997). Immobilized iron(III) metal affinity chromatography for the separation of phosphorylated macromolecules: ligands and applications. Liq. Chrom. Rel.Technol., 20, 123-142. PDF
Schiller MR, Mains, RE, Eipper BA. (1997). A Novel Neuroendocrine Intracellular Signaling Pathway. Mol. Endocrinol., 11, 1846-1857. PMID: 9369452 PDF
Schiller MR and Darlington DN. (1996). Stage-specific expression of RESP18 in the testes. J. Histochem. Cytochem., 44, 1489-1496. PMID: 8985141 PDF
Hook VYH, Schiller MR, Nguyen C, Yasothornsrikul S. (1996). Production of radiolabeled neuropeptide precursors by in vitro transcription and translation. Peptide Res., 9, 183-87. PMID: 8914165
Hook VYH, Schiller MR, and Azaryan AV. (1996). The processing proteases 'prohormone thiol protease' (PTP), PC1/3 and PC2, and 70 kDa aspartic proteinase show preferences among proenkephalin, pro-neuropeptide Y, and proopiomelanocortin substrates. Arch. Biochem. Biophys., 328, 107-114. PMID: 8638918 PDF
Hook VYH, Schiller MR, Azaryan AV, and Tezapsidis N.. (1996). Proenkephalin processing enzymes in chromaffin granules: a model for neuropeptide biosynthesis. Ann. N.Y. Acad. Sci., 780, 1221-133. PMID: 8602725 PDF
Schiller MR, Kohn AB, Mende-Mueller LM, Miller K, and Hook VYH. (1996). Expression of recombinant pro-neuropeptide Y, proopiomelanocortin, and proenkephalin: relative processing by 'prohormone thiol protease' (PTP). FEBS Lett., 382, 10-Jun. PMID: 8612764 PDF
Schiller MR*, Holmes LD, and Boeker EA. (1996). Analysis of wild-type and mutant aspartate aminotransferases using integrated rate equations. Biochim. Biophys. Acta, 1297, 17-27. PMID: 8841376 PDF
Schiller MR, Mains RE, and Eipper BA. (1995). A neuroendocrine specific protein localized to the endoplasmic reticulum by distal degradation. J. Biol. Chem, 270, 26129-26138. PMID: 7592816 PDF
Azaryan AV, Schiller MR, Mende-Mueller L, and Hook VYH. (1995). Characteristics of the chromaffin granule aspartic proteinase involved in proenkephalin processing". J. Neurochem, 65, 1771-1779. PMID: 7561875 PDF
Azaryan AV, Schiller MR, and Hook VYH. (1995). Chromaffin granule aspartic proteinase processes recombinant proopiomelanocortin. Biochem. Biophys. Res. Commun., 215, 937-944. PMID: 7488064 PDF
Schiller MR, Mende-Mueller L, Morona K, Meng M, Miller, KW, and Hook VYH. (1995). Prohormone thiol protease (PTP) processing of recombinant proenkephalin. Biochemistry, 34, 7988-7995. PMID: 7794912 PDF
Holmes LD, Schiller MR, and Boeker EA. (1993). Kinetic analysis of the lactate dehydrogenase reaction using integrated rate equations. Experientia, 49, 893-901. PMID: 8224107 PDF
Schiller MR and Busch J. (1993). Reinheitsgebot and the Fifth Ingredient. Brewing Techniques, 1, 30-33. PDF