Carnegie Mellon SURP Publications and Presentations

Full Publications: 2003 2002, 2001, 2000, 1999, 1998, 1997,1996, 1994, 1993, 1992, 1991

Presentations and Published Abstracts:, 2003, 2002, 2001, 1999, 1997, 1996, 1995, 1994, 1993, 1992, 1991

I. Full Publications

2003
Murphy, R.F., Velliste, M., and Porreca, G. (2003). Robust Numerical Features for Description and Classification of Subcellular Location Patterns in Fluorescence Microscope Images. J. VLSI Sig. Proc. 35: 311-321.

Puri, S., Telfer, H., Velliste, M., Murphy, R.F., and Linstedt, A.D. (2003). Dispersal of Golgi matrix proteins during mitotic Golgi disassembly. J. Cell Sci. 116, in press.

2002
Csink, A.K., A. Bounoutas, M.L. Griffith, J.F. Sabl, B.T. Sage (2002). Differential gene silencing by trans-heterochromatin in Drosophila melanogaster.Genetics 160: 257-69.

Gupta, S.S., M. Stadler, C.A. Noser, A. Ghosh, B. Steinhoff, D. Lenoir, C.P. Horwitz, K.W. Schramm, and T.J. Collins (2002). Rapid total destruction of chlorophenols by activated hydrogen peroxide. Science 296: 326-328.

Huang, K., J. Lin, J.A. Gajnak, and R.F. Murphy (2002). Image Content-based Retrieval and Automated Interpretation of Fluorescence Microscope Images via the Protein Subcellular Location Image Database. Proceedings of the 2002 IEEE International Symposium on Biomedical Imaging (ISBI 2002), pp. 325-328.

Murphy, R.F., M. Velliste, and G. Porreca (2002). Robust Classification of Subcellular Location Patterns in Fluorescence Microscope Images.Proceedings of the 2002 IEEE International Workshop on Neural Networks for Signal Processing (NNSP 12), pp. 67-76.

2001
Murphy, R.F., M. Velliste, J. Yao, and G. Porreca (2001). Searching Online Journals for Fluorescence Microscope Images Depicting Protein Subcellular Location Patterns. Proceedings of the 2nd IEEE International Symposium on Bio-Informatics and Biomedical Engineering (BIBE 2001), pp. 119-128.

2000
McCallum, S.A., T.K. Hitchens, C. Torborg, and G.S. Rule (2000). Ligand-induced changes in the structure and dynamics of a human class Mu glutathione S-transferase. Biochemistry 39:7343-56.

1999
Markey, M. K., M.V. Boland, and R.F. Murphy (1999). Towards Objective Selection of Representative Microscope Images. Biophys. J. 76: 2230-2237.

1998
Boland, M.V., M.K. Markey, and R.F. Murphy (1998). Automated recognition of patterns characteristic of subcellular structures in fluorescence microscopy images. Cytometry 33: 366-375.

Horwitz, C.P., D.R. Fooksman, and T.J. Collins (1998). Ligand Design Approach for Securing Robust Oxidation Catalysts. J. Am. Chem. Soc. 120: 4867.

Sreenivas, A., J.L. Patton-Vogt, V. Bruno, P. Griac, and S.A. Henry (1998). A role for phospholipase D (Pld1p) in growth, secretion, and regulation of membrane lipid synthesis in yeast. J. Biol. Chem. 273: 16635-16638.

Tristram-Nagle, S., T. Moore, H. Petrache, and J. Nagle (1998). DMSO produces a new subgel phase in DPPC: DSC and X-ray diffraction study.Biochim. Biophys. Acta 1369: 19-33.

Woolford, C., G. Bounoutas, S. Frew, and E. Jones (1998). Genetic interaction with vps8-200 allows partial suppression of the vestigial vacuole phenotype caused by a pep5 mutation in Saccharomyces cerevisiae. Genetics 148: 85-98.

1997
Boland, M.V. M.K. Markey and R.F. Murphy (1997). Automated Classification of Cellular Protein Localization Patterns Obtained via Fluorescence Microscopy. Proceedings of the 19th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, pp. 594-597.

Namba, R., T.M. Pazdera, R. Cerrone, and J.S. Minden (1997). Drosophila embryonic pattern repair: How embryos respond to bicoid mRNA dosage alteration. Development 124: 1393-1403.

Patton-Vogt, J. L., P. Griac, A. Sreenivas, V. Bruno, S. Dowd, M.J. Swede, and S.A. Henry (1997). Role of the yeast phosphatidylinositol/phosphatidylcholine transfer protein (Sec14p) in phosphatidylcholine turnover and INO1 regulation. J. Biol. Chem. 272: 20873-20883.

Pollock, J. A., B. Maneckshana,., and T.E. Leonardo (1997). Three-Dimensional Time-Lapse Digital Movie Analysis Of The Developing Fruit Fly Eye In Organ Culture. Microscopy and Microanalysis 3: 1129-1130.

Taylor, D. L., K. Burton, R.L. DeBiasio, K.A. Giuliano, A.H. Gough, T. Leonardo,, J.A. Pollock, and D.L. Farkas (1997). Automated light microscopy for the study of the brain: cellular and molecular dynamics, development, and tumorigenesis. Ann N Y Acad Sci 820: 208-228.

Webb, G., M. Hoedt,, L. Poole,, and E. Jones (1997). Genetic interactions between a pep7 mutation and the PEP12 and VPS45 genes; evidence for a novel SNARE component in transport between the S. cerevisiae Golgi complex and endosome. Genetics 147: 467-478.

1996
Batterham, P., J.R. Crew, A.M. Sokac, J.R. Andrews, G.M.F. Pasquini, A.G. Davies, R.F. Stocker, and J.A. Pollock (1996). Genetic analysis of the lozenge gene complex in Drosophila melanogaster: adult visual system phenotypes. J. Neurogenet. 10: 193-220.

1994
Mastick G., R. McKay, T. Oligino, K. Donovan,, and J. Lopez (1994). Identification of target genes regulated by homeotic proteins in Drosophila melanogaster through genetic selection of Ultrabithorax protein-binding sites in yeast. Genetics 139: 349-363.

1993
Bachhawat, A.K., M.F. Manolson, D.G. Murdock, J.D. Garman, and E.W. Jones (1993). The VPH2 gene encodes a 25kDa protein required for activity of the yeast vacuolar ATPase. Yeast 9: 175-184.

Brosnan, M.J., S.P. Raman (S. Pattabhiraman), L. Chen, and A.P. Koretsky (1993). Altering creatine kinase enzymes in transgenic mouse muscle by over-expression of the B subunit. Am. J. Physiol. 264: C151-C160.

Lopes, J.M., K.L. Schulze, J.W. Yates, J.P. Hirsch, and S.A. Henry. (1993). The INO1 promoter of Saccharomyces cerevisiae includes an upstream repressor sequence (URS1) common to a diverse set of yeast genes. J. Bacteriol. 175: 4235-4238.

Ripmaster, T., G. Vaughn, and J.L. Woolford Jr. (1993). DRS1 to DRS7, Novel genes required for ribosome assembly and function in Saccharomyces cerevisiae. Mol. Cell. Biol. 13: 7901-7912.

Sun, Z.-Y., H.-T.N. Truong, E.A. Pratt, D.C. Sutherland, C.E. Kulig, R.J. Homer, S.M. Groetsch, P.Y. Hsue, and C. Ho (1993). 19F-NMR Investigation of Membrane-Binding Domain of D-Lactate Dehydrogenase of E. coli. Protein Science 2: 1938-1947.

Woolford, C.A., J.A. Noble, J.D. Garman, M.F. Tam, M.A. Innis and E.W. Jones (1993). Phenotypic analysis of proteinase A mutants: Implications for autoactivation and maturation pathway of the vacuolar hydrolases of Saccharomyces cerevisiae. J. Biol. Chem. 268: 8990-8998.

1992
Henry, S.A., S.D. Kohlwein, J.M. Lopes, M.J. White, T.L. Gill, D.M. Nikoloff, J.A. Ambroziak, K.A. Hudak, M.J. Swede and D. Allen (1992). Biosynthesis of membrane phospholipids in yeast - Genetic and molecular studies. NATO ASI Series, Vol. H63, In Dynamics of Membrane Assembly, (J.A.F. Op den Kamp, ed.) pp. 33-48, Springer-Verlag, Berlin-Heidelberg.

Ripmaster, T., G. Vaughn, and J.L. Woolford Jr. (1992). A putative ATP-Dependent RNA helicase involved in Saccharomyces cerevisiae ribosome assembly. Proc. Natl. Acad. Sci. U.S.A. 89: 11131-11135.

1991
Busch, M.R., J.E. Mace, N.T. Ho, and C. Ho (1991). Roles of b146 histidyl residues in the molecular basis of the Bohr effect of hemoglobin: a Proton nuclear magnetic resonance study. Biochemistry 30: 1865-1877.

Lopes, J.M., J.P. Hirsch, P.A. Chorgo, K.L. Schulze, and S.A. Henry (1991). Analysis of sequences in the INO1 promoter that are involved in its regulation by phospholipid precursors. Nucl. Acids Res. 19: 1687-1693.

Moritz, M., B.A. Pulaski, and J.L. Woolford, Jr. (1991). Assembly of 60S ribosomal subunits is perturbed in temperature-sensitive mutants defective in yeast ribosomal protein L16. Mol. Cell. Biol. 11: 5681-5692.

Preston, R.A., J.D. Garman, L.B. Daniels, and E.W. Jones (1991). Map positions of pet9, pep1, and pdr4 with respect to CEN2. Yeast 7: 857-858.

Truong, H.-T N., E.A. Pratt, G.S. Rule, P.Y. Hsue, and C. Ho (1991). Inactive and temperature-sensitive folding mutants generated by tryptophan substitutions in the membrane-bound D-lactate dehydrogenase of E. coli. Biochemistry 30: 10722-10729.

II. Abstracts, Posters and Presentations

2003
J. Conde Adorno. 2003. Temporal texture features for location proteomics. Proceedings of the XIV Undergraduate Research Symposium, Universidad Metropolitana, San Juan, Puerto Rico, October 24-25, p. 35.

Y. Rivera Sierra. 2003. Computational methods for detecting alternative splicing involved in neural plasticity. Proceedings of the XIV Undergraduate Research Symposium, Universidad Metropolitana, San Juan, Puerto Rico, October 24-25, p. 75.

S. Soto. 2003. Segmenting polarized cell images for location proteomics. Proceedings of the XIV Undergraduate Research Symposium, Universidad Metropolitana, San Juan, Puerto Rico, October 24-25, p. 78.

2002
B. Joseph, K. Robertson and J. Minden. 2002. Triggered apoptosis in mutant Drosophila embryos: Determining the sequence of cell death. Sixth Annual Undergraduate Research Symposium, University of Maryland, Baltimore County, October 19, 2002.

M. Velliste, G. Porreca, and R. F. Murphy. 2002. Numerical Features for a Systematics of Protein Subcellular Location. Cytometry Supp. 11, 41.

S. Soto, M. Velliste, R. F. Murphy. 2002. Computational Modeling of Drug Effects on Protein Subcellular Location. Mol. Biol. Cell 13, in press.

2001
G. Porreca, M. Velliste, R. F. Murphy. 2001. Improved Classification of Subcellular Location Patterns in Fluorescence Microscope Images using Image Resampling and Support Vector Machines. Mol. Biol. Cell 12:259a.

1999
J.-A. Kwon, S. Pacocha, L. Jorgensen, and R.F. Murphy 1999. Na+,K+-ATPase b2 Isoform Expression and Endosomal pH Regulation. Mol. Biol. Cell 10:113a.

J.-A. Kwon, C. De-Juan Ruffin, and R.F. Murphy. 1999. Chinese Hamster Ovary Cells Express mRNA for both Rab4a and Rab4b. Mol. Biol. Cell10:221a.

1997
Boland, M. V., Markey, M. K., and Murphy, R. F. 1997. Automated classification of cellular protein localization patterns obtained via fluorescence microscopy. 19th Annual International Conference of the IEEE Engineering in Medicine and Biology Society. Chicago, IL, October 30-November 2, 1997.

Collins, T. J., Horwitz, C. P., Gordon-Wylie, S. W., Woomer, C. G., Vuocolo, L. D., Bartos, M. J., Fooksman, D., Strazisar, S. A., Peraino, D. K., Clark, G. R., and Weintraub, S. T. 1997. Extended Abstract of Plenary Lecture "The Development of Green Oxidants". 1997 Green Chemistry and Engineering Conference, Implementing Vision 2020 for the Environment. Washington, DC, June 23-25, 1997.

Davis, K., O'Malley, J., Paik, H.-J., and Matyjaszewski, K. 1997. Effect of the Counteranion in Atom Transfer Radical Polymerization using Alkyl (Pseudo)halide Initiators. ACS Polym. Preprints 38:687.

M. Fattah, A. Deutschbauer, R. McKay, and A. J. Lopez. 1997. Role of BX-C target genes in regional differentiation and morphogenesis within the Drosophila heart and associated organs. Presented at: the 13th International Congress of Developmental Biology. July 5-10, 1997, Snowbird, UT.

Fox, S. J., McKay, J. P., and Pollock, J. A. 1997. The Identification of Homologues of N63, a Gene Expressed in the Developing Visual System of Drosophila Melanogaster. National Conference of Undergraduate Research (NCUR). Austin, TX, April 23-25, 1997.

Markey, M. K., Boland, M. V., and Murphy, R. F. 1997. Towards objective selection of representative microscope images. Mol. Biol. Cell 8:346a.

McKay, J. P., Fox*, S. J., Bianchi, N., Proekt, A., and Pollock, J. A. 1997. N63 is a novel gene involved in the formation of the adult visual system in Drosophila melanogaster. 38th Annual Drosophila Research Conference. Chicago, April 1997.

Murphy, R. F., Wilder, J. A., and Meharra, E. J. 1997. Overexpression of rab4b partially suppresses the receptor recycling defect, but not the lysosomal traffic defect, of the End6 mutant of Chinese hamster ovary cells. Mol. Biol. Cell 8:89a.

C.D. Nichols, J.R. Crew, T. Hoening, F. Cunningham, P. Batterham, J.A. Pollock. 1997. Physical mapping of mutant alleles and identification of alternative products from the lozenge locus. Presented at the 38th Annual Drosophila Research Conference, April 16-20, 1997, Chicago IL.

Pollock, J. A., Fox, S. J., Proekt, A., and McKay, J. P. 1997. helmsman Encodes A Complement-like Protein Involved in Cell Elongation in Tracheal and Neuronal Development. 39th Annual Drosophila Research Conference. Chicago, April 1997.

G. C. Webb, M. Hoedt, L. J. Poole and E. W. Jones. 1997. Pep7p, a novel SNARE component of Saccharomyces cerevisiae that functions in transport from the Golgi complex to the endosome. Presented at the Mid-Atlantic Yeast Meeting, June 19-21, 1997, Pittsburgh, PA.

1996
M. V. Boland, M. Markey, and R. F. Murphy. Automated Classification of Protein Localization Patterns. Presented at the 6th International Congress on Cell Biology, December 7-11, 1996, San Francisco, CA (abstract published in Mol. Biol. Cell 7,157a., 1996).

Leonardo, T., and Pollock, J. A. 1996. Eye development in Drosophila melanogaster: a study with video microscopy. 37th Annual Drosophila Research Conference. San Diego, April 1996.

McKay, J. P., Kinchington, K., Vergnes, J. P., Fox, S. J., Babyak, L. M., and Pollock, J. A. 1996. Characterization of N63, a novel gene expressed in the visual system of Drosophila. 37th Annual Drosophila Research Conference. San Diego, April 1996.

Pollock, J. A., Leonardo, T., LaRocca, G., DeBiasio, R., and Mantarro, M. 1996. Three-Dimensional Time-Lapse Digital Movie Analysis of the Developing Fruit Fly Eye in Organ Culture. The Second Annual Symposium on Integrated Microscopy. Wisconsin Center, September 1996.

G. Webb, A. Srivastava, M. Hoedt, L. Poole, and E. Jones. Pep7p, a novel protein component, and Pth1p, a new syntaxin homologue, new members of SNARE complexes required for Golgi to vacuole transport in yeast. Presented at the Yeast Genetics and Human Disease Meeting, November, 1996, Baltimore, MD.

G. Webb, M. Hoedt, L. Poole, and E. Jones. Pep7p is a nw functional component of the yeast Golgi to Endosome SNARE Complex. Presented at the 6th International Congress on Cell Biology, December 7-11, 1996, San Francisco, CA (abstract published in Mol. Biol. Cell 7,134a., 1996).

1995
Schwartz*, J. A., Wightman, J. L., and Murphy, R. F. 1995. Recycling of lysosomal hydrolases and lysosomal membrane glycoproteins from lysosomes to endosomes in the End6 mutant of CHO cells. Mol. Biol. Cell 6:215a.

1994
Crew, J.R., C.D. Nichols, A.M. Sokac, P. Batterham and J.A. Pollock (1994). Mutations in the lozenge locus affect the development of several cell types in the adult compound eye of Drosophila melanogaster. 35th Annual National Drosophila Research Conference.

Crew, J.R., A.M. Sokac, C.D. Nichols, P. Batterham and J.A. Pollock (1994). Mutations in the lozenge locus of Drosophila melanogaster affect the normal interactions between cells of the developing compound eye and brain. 53rd Annual Meeting of the Society for Developmental Biology, Develop. Biol. 163: 548.

Hiller M.A., A. Heinzer, K.J. Dolinski, N. Fortin and E.W. Jones, (1994). Vacuolar Function and Ion Homeostasis in Saccharomyces cerevisiae.Mid-Atlantic Yeast Meeting, abstract.

Keen J.D., T.G. Kinzy and J.L. Woolford (1994). Characterization of SRL161, a Suppressor of a Mutation in the Yeast Ribosomal Protein L16 Gene. Sigma Xi Research Symposium, Carnegie Mellon University.

Kinzy T.G., J.D. Keen and J.L. Woolford (1994). Isolation of Suppressors of Mutant Alleles of Yeast Ribosomal Protein L16. Cold Spring Harbor Meeting on Translational Control.

McKay R., K. Donovan and J. Lopez (1994). Putative homeotic target genes specific to trunk, head, or tail. 35th Annual Drosophia Research Conference, poster.

Murdock, D.G., L.A. Komenda and E.W. Jones (1994). Translocation of Proteinase B Across the Endoplasmic Reticulum. Mid-Atlantic Yeast Meetings, abstract.

Pollock, J.A., P. Batterham, P. Maurides, C. Nichols, A.M. Sokac and J.R. Crew (1994). Mutations in lozenge affect the selection of cell type in the developing Drosophila eye. Keystone Symposia on Transmembrane Signal Transduction. J. Cellular Biochem. supp. 18B: 300.

1993
Bucci, M., C.M. Brown, T.W. Moyer, R.B. Wilson and R.F. Murphy (1993). The receptor-recycling and lysosome biogenesis mutant TfT1.11 belongs to a new complementation group, End6. Molec. Bio. Cell 4: 325a.

Crew, J., P. Batterham, A. Sokac, and J.A. Pollock (1993). An analysis of the cellular defects elicited by mutations in thelozenge locus of Drosophila. 52nd Annual Meeting of the Society for Developmental Biology.

Crew, J., P. Batterham, A. Sokac, and J.A. Pollock (1993). Mutations in the lozenge locus affect the developing compound eye by perturbing the normal dynamics of cell recruitment and differentiation. Meeting on Neurobiology of Drosophila, Cold Spring Harbor Press, p. 98.

Keen J.D., T.G. Kinzy and J.L. Woolford (1993). Isolation of Suppressors of Mutant Alleles of Yeast Ribosomal Protein Gene RPL16. Yeast Genetics and Molecular Biology Meeting.

McKay, R., G. Mastick, A. Thompson and J. Lopez (1993). Genetic selection of Drosophila genomic fragments that mediate transcriptional activation by Ultrabithorax proteins. 34th Annual Drosophila Research Conference.

Melia, S., C.H. Claude and J.A. Pollock (1993).A molecular characterization of an eye specific gene; a work in progress. 34th Drosophila Research Conference.

Sun, Z.-Y., E.A. Pratt, H.-T.N. Truong, D.C. Sutherland, C.E. Kulig, R.J. Homer, and C. Ho (1993). 19F-NMR Investigation of Membrane-Binding Domain of D-Lactate Dehydrogenase of E. coli. Biological Society Meeting.

Weidenhammer, E., M. Singh, and J. Woolford (1993). A Novel Gene Necessary for pre-mRNA Processing in Yeast Saccharomyces cerevisiae. Cold Spring Harbor Meeting on RNA Processing.

1992
Adeyeye, O., J. Burkman, E. Chartoff, E. Leers, P. Maurides and J.A. Pollock (1992). Analysis of two genes expressed in the visual system. Genetics Society of America and 33rd Annual Drosophila Research Conference.

1991
Adeyeye, O., R. Brendza, J. Crew, P. Maurides and J. Pollock (1991). Gene expression in the developing visual system. 32nd Annual Drosophia Research Conference.

Brendza, R. and J. Pollock (1991). Molecular characterization of eye-specific genomic clones in Drosophila. The EUREKA Symposium, National Conference on Undergraduate Research (published in Proceedings of the Fifth National Conference on Undergraduate Research, p. 118-122).

Davis, A. and J. Jarvik (1991). Centrin levels in Chlamydommas vfl-2 mutants and revertants. NIH-MBRS-MARC Symposium, poster.

Halow, J.M., J. Roman, M.J. Brosnan, L. Chen and A.P. Koretsky (1991). The Effects of Creatine on Phosphates in Prefused Transgenic Mouse Livers that express Creatine Kinase. Society of Magnetic Resonance in Medicine, poster.

Roy, J. , S. Sparks, and J. Woolford (1991). Identification and characterization of new gene products involved in splicing. Yeast Genetics and Molecular Biology national Meeting, platform presentation.

Roy, J., S. Sparks and J. Woolford (1991). Identification and characterization of new gene products involved in yeast pre-mRNA splicing. Cold Spring Harbor Meeting on RNA Processing, (poster).

Roy, J., S. Sparks and J. Woolford (1991). Identification and characterization of new gene products involved in yeast pre-mRNA splicing. Cold Spring Harbor Meeting on Yeast Cell Biology, poster.

Woolford, C.A., J.D. Garman, and E.W. Jones (1991). Autoactivation of protease A and its internal cleavage site. Yeast Genetics and Molecular Biology Meeting, abstract.