Graduate Student Publications

Martincic K, Alkan SA, Cheatle A, Borghesi L, Milcarek C. Transcription Elongation Factor ELL2 Directs Immunoglobulin Secretion in Plasma Cells by Stimulating Altered RNA Processing. Nature Immunology, Published online: 13 September 2009.

Benedetti BL, Glazewski S, Barth AL. Reliable and Precise Neuronal Firing during Sensory Plasticity in Superficial Layers of Primary Somatosensory Cortex. Journal of Neuroscience 29 (38): 11817-11827, 2009.

Sheehan JJ, Benedetti BL, Barth AL. Anticonvulsant effects of the BK-channel antagonist paxilline. Epilepsia, 50 (4): 711-720, 2009.

Yadav S, Puri S, Linstedt AD. A Primary Role for Golgi Positioning in Directed Secretion, Cell Polarity, and Wound Healing. Molecular Biology of the Cell, 20(6): 1728-1736, 2009.

Mills PH, Wu YL, Ho C and Ahrens ET. Sensitive and automated detection of iron-oxide-labeled cells using phase image cross-correlation analysis. Magnetic Resonance Imaging, 26(5) 618-628, 2008.

Baughman C, Morin-Leisk J and Lee T. Nucleoside diphosphate kinase B (NDKB) scaffolds endoplasmic reticulum membranes in vitro. Exp Cell Res, 314(14):2702-14, 2008.

Morin-Leisk J and Lee T. Nucleotide-dependent self-assembly of Nucleoside Diphosphate Kinase (NDPK) in vitro. Biochim Biophys Acta 1782(12):2045-51, 2008.

Raghupathy N and Durand D. Gene cluster statistics with gene families, Molecular Biology and Evolution, Mol Biol Evol, 26(5):957-68, May 2009. Epub 2009 Jan 15.

Song N, Joseph JM, Davis GB, Durand D. Sequence Similarity Network Reveals Common Ancestry of Multidomain Proteins. PLoS Computational Biology 4(5): e1000063, 2008.

Puri M, Goyal A, Senutovich N, Dowd SR, Minden J. Building proteomic pathways using Drosophila ventral furrow formation as a model. Molecular Biosystems, 4 (11): 1126-35, 2008. 

Tang L, Sahasranaman A, Jakovljevic J, Schleifman E, Woolford JL Jr. Interactions Among Ytm1, Erb1 and Nop7 Required for Assembly of the Nop7-Subcomplex in Yeast Preribosomes. Molecular Biology of the Cell, 19(7):2844-2856, 2008.

Witzberger MM, Fitzpatrick JA, Crowley JC, Minden JS. End-on imaging: A new perspective on dorsoventral development in Drosophila embryos. Dev Dyn, 237(11):3252-9, Nov 2008.

Toppings M, Castro C, Mills PH, Reinhart B, Schatten G, Ahrens ET, Chaillet JR, Trasler JM. Profound phenotypic variation among mice deficient in the maintenance of genomic imprints. Human Reproduction, 23:807-818, 2008.

Shruti S, Clem RL, Barth AL. A seizure-induced gain-of-function in BK channels is associated with elevated firing activity in neocortical pyramidal neurons. Neurobiol Dis, 30(3):323-30, Jun 2008. Epub 2008 Feb 20.

Janjic J, Srinivas M, Kadayakkara D, Ahrens E. Self-delivering Nanoemulsions for Dual Fluorine-19 MRI and Fluorescence Detection. Journal of American Chemical Society, 130 (9): 2832 -2841, 2008.

Szent-Gyorgyi C, Schmidt B, Creeger Y, Fisher G, Zakel K, Adler S, Fitzpatrick J, Woolford C, Yan Q, Vasilev K, Berget P, Bruchez M, Jarvik J, Waggoner A. Fluorogen-Activating Single-Chain Antibodies for Imaging Cell Surface Proteins. Nature Biotechnology, 26 (2): 235-240, 2008.

Clem RL, Celikel T, Barth AL. Ongoing in vivo experience triggers synaptic metaplasticity in the neocortex. Science, 318(5859): 101-104, 2008.

Glazewski S, Benedetti B, Barth A. Ipsilateral Whiskers Suppress Experience-dependent Plasticity in the Barrel Cortex. Journal of Neuroscience, 27 (14):3910-20, 2007.

Eagleson KL, McFadyen-Ketchum LJ S, Ahrens ET, Mills PH, Does MD, Nickols J, Levitt P. Direct and Adaptive Disruption of Forebrain Development in Foxg1 Haploinsufficient Mice. Neuroscience, 148:385-399, 2007.

Feinstein T and Linstedt AD. Mitogen-activated Protein Kinase Kinase-dependent Golgi Unlinking Occurs in G2 phase and Promotes the G2/M Cell Cycle Transition. Molecular Biology of the Cell, 18:594-604, 2007.

Capaldi E, Flynn CJ, and Wcislo WT. Sex Ratio and Nest Observations of Euglossa hyacinthina (Hymenoptera, Apidae, Euglossini). Journal of the Kansas Entomological Society, 80(4): 295-399, 2007.

Castro J, Hovis K, Urban N. Recurrent Dendrodendritic Inhibition of Accessory Olfactory Bulb Mitral Cells Requires Activation if Group I Metabotropic Glutamate Receptors. Journal of Neuroscience, 27 (21):5664-71, 2007.

Mills PH, Ahrens ET. Theoretical MRI Contrast Model for Exogenous T2 Agents. Magnetic Resonance Medicine 57:442-447, 2007.

Raghupathy N, Hoberman R, Durand D. Two Plus Two Does Not Equal Three: Statistical Tests for Multiple Genome Comparison. In Proceedings of the 5th Asia-Pacific Bioinformatics Conference. D, Wang L and Chin F, eds. Advances in Bioinformatics and Computational Biology, Vol.5, Imperial College Press, 215-225, 2007.

Sankoff D, Wang L and Chin F, eds. Advances in Bioinformatics and Computational Biology, Vol.5, Imperial College Press, 215-225, 2007.

Song N, Sedgewick RD, Durand D. Domain Architecture Comparison for Multidomain Homology Identification. Journal of Computational Biology, 14(4): 496-516, 2007.

Vernot B, Stolzer M, Goldman A, Durand D. Reconciliation with Non-Binary Species Trees. Journal of Computational Biology, 15(8):981-1006, 2008.

Zhang J, Harnpicharnchai P, Jakovljevic J, Tang L, Guo Y, Oeffinger M, Rout MP, Hiley SL, Hughes T, and Woolford, Jr JL. Assembly Factors Rpf2 and Rrs1 Recruit 5S rRNA and Ribosomal Proteins rpL5 and rpL11 into Nascent Ribosomes. Genes and Development, 21: 2580-2592, 2007.

Arun K and Langmead CJ. Structure Based Chemical Shift Prediction Using Random Forests Non-linear Regression. Proceedings of The Forth Asia-Pacific Bioinformatics Conference, (APBC) 317-326; Taipei, Taiwan, 2006.

Clem RL and Barth A. 2006. Pathway-specific trafficking of native AMPARs by in vivo experience. Neuron 49: 663-70, 2006.

Guo Y, Linstedt AD.COPII-Golgi Protein Interactions Regulate COPII Coat Assembly and Golgi Size. Journal of Cell Biology. 174(1):53-63, 2006.

Mills PH, Ahrens ET. Enhanced Detection of Paramagnetic Contrast Agents in Magnetic Resonance Images via Phase Image Cross-correlation Analysis. Proceedings IEEE International Symposium of Biomedical Imaging; 1:21-25, 2006.

Natarajan R and Linstedt AD. A Cycling cis Golgi Protein Mediates Endosome-to-Golgi Traffic. Molecular Biology of the Cell. 15: 4798-4806, 2006.

Puthenveedu MA, Bachert C, Puri S, Lanni F and Linstedt AD. GM130 and GRASP65-dependent Lateral Cisternal Fusion Confers Uniform Golgi Enzyme Distribution. Nature Cell Biology. 8:238-248, 2006 .

Przytycka T, Davis GB, Song N, Durand D. Graph Theoretical Insights into Evolution of Multidomain Proteins. Journal of Computational Biology, 13 (2): 351-363, 2006.

Ahrens ET, Srinivas M, Capuano S, Simhan HN, Schatten GP. Magnetic Resonance Imaging of Embryonic and Fetal Development in Model Systems. Methods in Molecular Medicine,124:87-101, 2006.

McCartney BM, Price MH, Webb RL, Hayden MA, Holot LM, Zhou M, Bejsovec A, Peifer M. Testing Hypotheses for the Functions of APC Family Proteins Using Null and Truncation Alleles in Drosophila. Development.133(12):2407-18, 2006.

Zhang T and Schwartz R. Simulation Study of the Contribution of Oligomer/Oligomer Binding to Capsid Assembly Kinetics. Biophysical Journal. 90:57-64, 2006.

Kumar S and Lopez AJ. Negative Feedback Regulation among SR Splicing Factors encoded by Rbp1 and Rbp1-like in Drosophila. The EMBO Journal. 24(14):2646-2655, 2005.

Miles TD, Jakovljevic J, Horsey EW, Harnpicharnchai P, Tang L, and Woolford, JL, Jr. Ytm1,Nop7,and Erb1 Form a Complex Necessary for Maturation of 66S Preribosomes. Molecular and Cellular Biology. 25:10419-10432, 2005.

Puthenveedu MA and Linstedt AD. Subcompartmentalizing the Golgi Apparatus. Current Opinion in Cell Biology. 17:369-375, 2005.

Raghupathy N, Durand D. Individual Gene Cluster Statistics in Noisy Maps. RECOMB Workshop on Comparative Genomics, McLysaght and Huson, Eds., Lecture Notes in Bioinformatics vol. 3678, Springer-Verlag, 106-120, 2005.

Horsey EW, Jakovljevic J, Miles TD, Harnpicharnchai P, Woolford JL Jr. Role of the Yeast Rrp1 Protein in the Dynamics of Pre-ribosome Maturation. RNA. 10:813-827, 2004.

Jakovljevic J, Antunez de Mayolo P, Miles TD, Nguyen TM-L, Leger-Silvestre I, Gas N, Woolford JL Jr. The Carboxyl-terminal Extension of Yeast Ribosomal Protein S14 is Necessary for Maturation of 43S Preribosomes. Molecular Cell. 14: 331-342, 2004.

Puri S, Telfer H, Velliste M, Murphy R and Linstedt AD. Dispersal of Golgi Matrix Proteins during Mitotic Golgi Disassembly. Journal of Cell Science. 117:451-456, 2004.

Gong L, Puri M, Ünlü M, Young M, Robertson K, Viswanathan S, Krishnaswamy A, Dowd SR and Minden JS. Drosophila Ventral Furrow Morphogenesis: A Proteomic Analysis. Development. 131:643-656, 2004.

Puthenveedu MA and Linstedt AD. Gene Replacement Reveals that p115/SNARE Interactions are Essential for Golgi Biogenesis. Proceedings of the National Academy of Sciences USA. 101: 1253-1256, 2004.

Puri S and Linstedt AD. Capacity of the Golgi Apparatus for Biogenesis from the Endoplasmic Reticulum. Molecular Biology of the Cell. 14:5011-5018, 2003.

Vanni S, Lagerholm BC, Otey C, Taylor DL, Lanni F. Internet-based Image Analysis Quantifies Contractile Behavior of Individual Fibroblasts Inside Model Tissue. Biophysical Journal. 84: 2715-2727, 2003.