Graduate Student Publications-Department of Biological Sciences - Carnegie Mellon University

Graduate Student Publications


McCauley BS, Akyar E, Filliger L, Hinman VF. Expression of wnt and frizzled genes during early sea star development. Gene Expr Patterns. 2013 Jul 27. doi:pii: S1567-133X(13)00084-7. 10.1016/j.gep.2013.07.007. [Epub ahead of print]

Wen JA, Deblois MC, Barth AL. Initiation, labile, and stabilization phases of experience-dependent plasticity at neocortical synapses. J Neurosci. 2013 May 8;33(19):8483-93.

Yankura KA, Koechlein CS, Cryan AF, Cheatle A, Hinman VF. Gene regulatory network for neurogenesis in a sea star embryo connects broad neural specification and localized patterning. Proc Natl Acad Sci U S A. 2013 May 6.

Gamalinda M, Jakovljevic J, Babiano R, Talkish J, de la Cruz J, Woolford JL Jr. Yeast polypeptide exit tunnel ribosomal proteins L17, L35 and L37 are necessary to recruit late-assembling factors required for 27SB pre-rRNA processing. Nucleic Acids Res. 2013 Feb 1;41(3):1965-83. doi: 10.1093/nar/gks1272. Epub 2012 Dec 24.

Desai JV, Bruno VM, Ganguly S, Stamper RJ, Mitchell KF, Solis N, Hill EM, Xu W, Filler SG, Andes DR, Fanning S, Lanni F, Mitchell AP. Regulatory Role of Glycerol in Candida albicans Biofilm Formation. MBio. 2013 Apr 9;4(2). pii: e00637-12. doi: 10.1128/mBio.00637-12. (Full Text)

Soohoo AL, Puthenveedu MA. Divergent modes for cargo-mediated control of clathrin-coated pit dynamics. Mol Biol Cell. 2013 Mar 27.

Dykstra KM, Ulengin I, Delrose N and Lee TH. Identification of discrete sites in Yip1A necessary for regulation of endoplasmic reticulum structure. PloS One 8(1):e54413. Epub 2013 Jan 14.


Gamalinda M, Jakovljevic J, Babiano R, Talkish J, de la Cruz J, Woolford JL Jr. Yeast polypeptide exit tunnel ribosomal proteins L17, L35 and L37 are necessary to recruit late-assembling factors required for 27SB pre-rRNA processing. Nucleic Acids Res. 2012 Dec 24.

Yates BP, Peck MA, Berget PB. Directed Evolution of a Fluorogen-Activating Single Chain Antibody for Function and Enhanced Brightness in the Cytoplasm. Mol Biotechnol. 2012 Dec 14.

Jakovljevic J, Ohmayer U, Gamalinda M, Talkish J, Alexander L, Linnemann J, Milkereit P, Woolford JL Jr. Ribosomal proteins L7 and L8 function in concert with six A₃ assembly factors to propagate assembly of domains I and II of 25S rRNA in yeast 60S ribosomal subunits. RNA. 2012 Oct;18(10):1805-22.

Stolzer M, Lai H, Xu M, Sathaye D, Vernot B, Durand D. Inferring duplications, losses, transfers and incomplete lineage sorting with nonbinary species trees. Bioinformatics. 2012 Sep 15;28(18):i409-i415.

Benedetti BL, Takashima Y, Wen JA, Urban-Ciecko J, Barth AL. Differential Wiring of Layer 2/3 Neurons Drives Sparse and Reliable Firing During Neocortical Development. Cereb Cortex. 2012 Aug 23.

Jakovljevic J, Ohmayer U, Gamalinda M, Talkish J, Alexander L, Linnemann J, Milkereit P, Woolford JL Jr. Ribosomal proteins L7 and L8 function in concert with six A3 assembly factors to propagate assembly of domains I and II of 25S rRNA in yeast 60S ribosomal subunits. RNA. 2012 Aug 14.

Kunttas-Tatli E, Zhou MN, Zimmerman S, Molinar O, Zhouzheng F, Carter K, Kapur M, Cheatle A, Decal R, McCartney BM. Destruction complex function in the Wnt signaling pathway of Drosophila requires multiple interactions between Adenomatous polyposis coli 2 and Armadillo. Genetics. 2012 Mar;190(3):1059-75. Epub 2011 Dec 14.

Remus ML, Thiels E. Stimulus-specific and differential distribution of activated extracellular signal-regulated kinase in the nucleus accumbens core and shell during Pavlovian-instrumental transfer. Brain Struct Funct. 2012 Jul 5.

Talkish J, Zhang J, Jakovljevic J, Horsey EW, Woolford JL Jr. Hierarchical recruitment into nascent ribosomes of assembly factors required for 27SB pre-rRNA processing in Saccharomyces cerevisiae. Nucleic Acids Res. 2012 Jun 26.

Babiano R, Gamalinda M, Woolford JL Jr, de la Cruz J. Saccharomyces cerevisiae ribosomal protein L26 is not essential for ribosome assembly and function. Mol Cell Biol. 2012 Jun 11.

Truschel ST, Zhang M, Bachert C, Macbeth MR, Linstedt AD. Allosteric regulation of GRASP protein-dependent Golgi membrane tethering by mitotic phosphorylation. J Biol Chem. 2012 Jun 8;287(24):19870-5. Epub 2012 Apr 20.

Grover A, Schmidt BF, Salter RD, Watkins SC, Waggoner AS, Bruchez MP. Genetically Encoded pH Sensor for Tracking Surface Proteins through Endocytosis. Angew Chem Int Ed Engl. 2012 Mar 29. doi: 10.1002/anie.201108107. [Epub ahead of print]

Shruti S, Urban-Ciecko J, Fitzpatrick JA, Brenner R, Bruchez MP, Barth AL. The Brain-Specific Beta4 Subunit Downregulates BK Channel Cell Surface Expression. PLoS One. 2012;7(3):e33429. Epub 2012 Mar 16.

Senutovitch N, Stanfield RL, Bhattacharyya S, Rule GS, Wilson IA, Armitage BA, Waggoner AS, Berget PB. A Variable Light Domain Fluorogen Activating Protein Homodimerizes To Activate Dimethylindole Red. Biochemistry. 2012 Mar 14. [Epub ahead of print]

Rafiq K, Cheers MS, Ettensohn CA. The genomic regulatory control of skeletal morphogenesis in the sea urchin. Development. 2012 Feb;139(3):579-90. Epub 2011 Dec 21.

Wen JA, Barth AL. Synaptic lability after experience-dependent plasticity is not mediated by calcium-permeable AMPARs. Front. Mol. Neurosci. 5:15, 2012. doi: 10.3389/fnmol.2012.00015

Ganguly S, Mitchell AP. Mini-blaster-Mediated Targeted Gene Disruption and Marker Complementation in Candida albicans. Methods Mol Biol. 2012;845:19-39.

Shimoji K, Jakovljevic J, Tsuchihashi K, Umeki Y, Wan K, Kawasaki S, Talkish J, Woolford JL Jr, Mizuta K. Ebp2 and Brx1 function cooperatively in 60S ribosomal subunit assembly in Saccharomyces cerevisiae. Nucleic Acids Res. 2012 Feb 8.


Adomako-Ankomah A, Ettensohn CA. P58-A and P58-B: novel proteins that mediate skeletogenesis in the sea urchin embryo. Dev. Biol. 353:81-93, 2011 May 1. Epub 2011 Feb 26. PMID: 21362416.

Alcala MA, Kwan SY, Shade CM, Lang M, Uh H, Wang M, Weber SG, Bartlett DL, Petoud S, Lee YJ. Luminescence targeting and imaging using a nanoscale generation 3 dendrimer in an in vivo colorectal metastatic rat model.

Alcala MA, Shade CM, Uh H, Kwan SY, Bischof M, Thompson ZP, Gogick KA, Meier AR, Strein TG, Bartlett DL, Modzelewski RA, Lee YJ, Petoud S, Brown CK. Preferential accumulation within tumors and in vivo imaging by functionalized luminescent dendrimer lanthanide complexes. Biomaterials. 32(35):9343-52, 2011 Dec. Epub 2011 Sep 16.

Dwivedi P, Thompson A, Xie Z, Kashleva H, Ganguly S, Mitchell AP, Dongari-Bagtzoglou A. Role of Bcr1-activated genes Hwp1 and Hyr1 in Candida albicans oral mucosal biofilms and neutrophil evasion. PLoS One. 2011 Jan 25;6(1):e16218.

Flynn CJ, Sharma T, Ruffins SW, Guerra SL, Crowley JC, Ettensohn CA. High- resolution, three-dimensional mapping of gene expression using GeneExpressMap (GEM). Dev. Biol.,357, 532-540, 2011. PMID: 21741377.

Ganguly S, Bishop AC, Xu W, Ghosh S, Nickerson KW, Lanni F, Patton-Vogt J, Mitchell AP. Zap1 control of cell-cell signaling in Candida albicans biofilms. Eukaryot Cell. 2011 Sep 2.

Ganguly S, Mitchell AP. Mucosal biofilms of Candida albicans. Curr Opin Microbiol. 2011 Jul 7.

Jarvela T, Linstedt AD. Irradiation-induced protein inactivation reveals Golgi enzyme cycling to cell periphery, J. Cell Sci., 2011, in press.

Ker DF, Weiss LE, Junkers SN, Chen M, Yin Z, Sandbothe MF, Huh SI, Eom S, Bise R, Osuna-Highley E, Kanade T, Campbell PG. An engineered approach to stem cell culture: automating the decision process for real-time adaptive subculture of stem cells. PLoS One. 2011;6(11):e27672. Epub 2011 Nov 16.

Ker ED, Chu B, Phillippi JA, Gharaibeh B, Huard J, Weiss LE, Campbell PG. Engineering spatial control of multiple differentiation fates within a stem cell population. Biomaterials. 32(13):3413-22, 2011 May. Epub 2011 Feb 12. 532-540. PMID: 21741377.

Ker ED, Nain AS, Weiss LE, Wang J, Suhan J, Amon CH, Campbell PG. Bioprinting of growth factors onto aligned sub-micron fibrous scaffolds for simultaneous control of cell differentiation and alignment. Biomaterials. 2011 Aug 4.

Mills PH, Hitchens TK, Foley LM, Link T, Ye Q, Weiss CR, Thompson JD, Gilson WD, Arepally A, Melick JA, Kochanek PM, Ho C, Bulte JW, Ahrens ET. Automated detection and characterization of SPIO-labeled cells and capsules using magnetic field perturbations. Magn Reson Med. 2011 Jun 7.

Morin-Leisk J, Saini SG, Meng X, Makhov AM, Zhang P and Lee TH. An intramolecular salt bridge drives the soluble domain of GTP-bound atlastin into the postfusion conformation. The Journal of Cell Biology, 195(4): 605-615, 2011.

Mukhopadhyay S, Linstedt AD. Identification of a gain of function mutation in a Golgi P-type ATPase: implications for Mn2+ homeostasis and detoxification, Proc. Natl. Acad. Sci. USA, 108(2):858-63, 2011. PMID: 21187401

Rafiq K, Cheers M, Ettensohn CA. The genomic regulatory control of skeletal morphogenesis in the sea urchin. Development, 2011, in press.

Roy S, Zanotti KJ, Murphy CT, Tanious FA, Wilson WD, Ly DH, Armitage BA. Kinetic discrimination in recognition of DNA quadruplex targets by guanine-rich heteroquadruplex-forming PNA probes. Chem Commun (Camb). 2011 Aug 14;47(30):8524-6. Epub 2011 Jun 30.

Sahasranaman A, Dembowski J, Strahler J, Andrews P, Maddock J, Woolford JL Jr. Assembly of Saccharomyces cerevisiae 60S ribosomal subunits: role of factors required for 27S pre-rRNA processing. EMBO J. 2011 Sep 16.

Sengupta D, Linstedt AD. Control of Organelle Size: The Golgi Complex. Annu Rev Cell Dev Biol. 2011 May 31.

Sharma T, Ettensohn CA. Regulative deployment of the skeletogenic gene regulatory network during sea urchin development. Development 138:2581-2590, 2011. PMID: 21610034.

Stadler AL, Delos Santos JO, Stensrud ES, Dembska A, Silva GL, Liu S, Shank NI, Kunttas-Tatli E, Sobers CJ, Gramlich PM, Carell T, Peteanu LA, McCartney BM, Armitage BA. Fluorescent DNA Nanotags Featuring Covalently Attached Intercalating Dyes: Synthesis, Antibody Conjugation and Intracellular Imaging. Bioconjugate Chemistry 22(8):1491-1502, 2011 Aug 17.

Subramanian A, Shackney S, Schwartz R. Inference of tumor phylogenies from genomic assays on heterogeneous samples. Proceedings of the ACM Conference on Bioinformatics and Computational Biology, 2011.

Truschel ST, Sengupta D, Foote A, Heroux A, Macbeth M, Linstedt AD. Structure of the membrane tethering GRASP domain reveals a unique PDZ ligand interaction that mediates Golgi biogenesis, J Biol Chem. 2011. Epub PMID: 21515684

Wen JA and Barth AL. Input-Specific Critical Periods for Experience-Dependent Plasticity in Layer 2/3 Pyramidal Neurons. J Neurosci. 31(12):4456-65, 2011 March 23.

Yadav S and Linstedt AD. Golgi Positioning. Cold Spring Harb Perspect Biol. pii: cshperspect.a005322v1, 2011 Apr 6.

Zhou MN, Kunttas-Tatli E, Zimmerman S, Zhouzheng F, McCartney BM. Cortical localization of APC2 plays a role in actin organization but not in Wnt signaling in Drosophila. Journal of Cell Science, 124(Pt 9):1589-600, 2011 May 1.


Castro CA, Ben-Yehudah A, Ozolek JA, Mills PH, Redinger CJ, Mich-Basso JD, McFarland DA, Oliver SL, Ahrens ET, Schatten G. Semiquantitative histopathology and 3D magnetic resonance microscopy as collaborative platforms for tissue identification and comparison within teratomas derived from pedigreed primate embryonic stem cells. Stem Cell Res. 2010 Nov;5(3):201-11. Epub 2010 Aug 6.

Gerkin RC, Clem RL, Shruti S, Kass RE, Barth AL. Cortical up state activity is enhanced after seizures: a quantitative analysis. J Clin Neurophysiol. 27(6): 425-32, 2010 Dec.

Iordanova B, Robison CS, Goins WF, Ahrens ET. Single chain ferritin chimera as an improved MRI gene reporter. Prilozi. 31(2):151-5, 2010 Dec.

Sengupta D, Linstedt AD. Mitotic inhibition of GRASP65 organelle tethering involves Polo-like kinase 1 (PLK1) phosphorylation proximate to an internal PDZ ligand. J Biol Chem. 285: 39994-40003, 2010. PMID: 20937827.

Stamateris RE, Rafiq K, Ettensohn CA. The expression and distribution of Wnt and Wnt receptor mRNAs during early sea urchin development. Gene Expr. Patterns 10: 60-64, 2010.

Talkowski ME, McCann KL, Chen, M Y-M, McClain L, Bamne M, Wood J, Chowdari KV, Kirov G, Georgieva L, Toncheva D, Mansour H, Lewis DA, Owen M, O’Donovan M, Papasaikas P, Sullivan P, Sklar P, Ruderfer D and ISC consortium, Yao JK, Leonard S, Thomas P, Miyajima F, Quinn J, Lopez AJ, Nimgaonkar VL. Fine mapping reveals novel alternative splicing of the dopamine transporter. Am J Med Genet B Neuropsychiatr Genet. 153B(8):1434-1447, 2010.

Yankura KA, Martik ML, Jennings CK, Hinman VF. Uncoupling of complex regulatory patterning during evolution of larval development in echinoderms. BMC Biol. 8:143, 2010 Nov 30.

Yassin L, Benedetti BL, Jouhanneau JS, Wen JA, Poulet JF, Barth AL. An embedded subnetwork of highly active neurons in the neocortex. Neuron. 68(6):1043-50, 2010 Dec 22.

Zimmerman SG, Thorpe LM, Medrano VR, Mallozzi CA, McCartney BM. Apical constriction and invagination downstream of the canonical Wnt signaling pathway requires Rho1 and Myosin II. Developmental Biology 340:54-66, 2010.

Puthenveedu MA, Lauffer B, Temkin P, Vistein R, Carlton P, Thorn K, Taunton J, Weiner OD, Parton RG, von Zastrow M. Sequence-dependent sorting of recycling proteins by actin-stabilized endosomal microdomains. Cell. 2010 Nov 24; 143(5):761-73.

Holleran J, Brown D, Fuhrman MH, Adler SA, Fisher GW, Jarvik JW. Fluorogen-activating proteins as biosensors of cell-surface proteins in living cells. Cytometry A, 77(8):776-82, 2010 Aug.

Tolliver D, Tsourakakis C, Subramanian A, Shackney S, Schwartz R. Robust unmixing of tumor states in array comparative genomic hybridization data. Bioinformatics (Proceedings Issue for Intelligent Systems for Molecular Biology (ISMB 2010)), 26(12):i106-i114, 2010..

Hovis KR, Padmanabhan K, Urban NN. A simple method of in vitro electroporation allows visualization, recording, and calcium imaging of local neuronal circuits. J Neurosci Methods;191(1):1-10, 2010 Aug 15.

Kadayakkara DK, Janjic JM, Pusateri LK, Young WB, Ahrens ET. In vivo observation of intracellular oximetry in perfluorocarbon-labeled glioma cells and chemotherapeutic response in the CNS using fluorine-19 MRI. Magnetic Resonance in Medicine 64(5): 1252-1259, 2010.

Dykstra KM, Pokusa JE, Suhan J, Lee TH. Yip1A structures the mammalian endoplasmic reticulum. Mol Biol Cell, 21(9):1556-68, May 2010. Epub 2010 Mar 17.

Kadayakkara DK, Beatty PL, Turner MS, Janjic JM, Ahrens ET, Finn OJ. Inflammation driven by overexpression of the hypoglycosylated abnormal mucin 1 (MUC1) links inflammatory bowel disease and pancreatitis. Pancreas, 39(4):510-5, May 2010.

Kaur A, Van P, Busch C, Robinson C, Pan M, Pang, WL, Reiss D, DiRuggiero J, Baliga NS. Coordination of frontline defense mechanisms under severe oxidative stress. Molecular Systems Biology, 6:393, 2010.

Holleran J, Brown D, Fuhrman MH, Adler SA, Fisher GW, Jarvik JW. Fluorogen-activating proteins as biosensors of cell-surface proteins in living cells. Cytometry A, 77(8):776-82, Aug 2010.

Iordanova B, Robison CS, Ahrens ET. Design and characterization of a chimeric ferritin with enhanced iron loading and transverse NMR relaxation rate. J Biol Inorg Chem, 17 Apr 2010.

Sharma T and Ettensohn CA. Activation of the skeletogenic gene regulatory network in the early sea urchin embryo. Development,137(7):1149-57, Apr 2010. Epub 2010 Feb 24.

McCauley BS, Weideman EP, Hinman VF. A conserved gene regulatory network subcircuit drives different developmental fates in the vegetal pole of highly divergent echinoderm embryos. Dev. Biol. 340(2):200-8, 2010 Apr 15. Epub 2009 Nov 23.

Dykstra KM, Pokusa JE, Suhan J, Lee TH. Yip1A structures the mammalian endoplasmic reticulum. Molecular Biology of the Cell, 21(9):1556-68, 2010.

Stamateris RE, Rafiq K, Ettensohn CA. The expression and distribution of Wnt and Wnt receptor mRNAs during early sea urchin development. Gene Expr Patterns, 10(1):60-4, Jan 2010. Epub 2009 Oct 22.


Berdyyeva TK, Olson CR. Monkey supplementary eye field neurons signal the ordinal position of both actions and objects. J Neurosci. 29(3):591-9, 2009 Jan 21.

Fitzpatrick JA, Yan Q, Sieber JJ, Dyba M, Schwarz U, Szent-Gyorgyi C, Woolford CA, Berget PB, Waggoner AS, Bruchez MP. STED nanoscopy in living cells using Fluorogen Activating Proteins. Bioconjug Chem. 20(10):1843-1847, 2009.

Park Y, Shackney S, Schwartz R. Network-based inference of cancer progression from microarray data .IEEE/ACM Trans Comput Biol Bioinform. 6(2):200-12, 2009 Apr-Jun.

Srinivasa G, Fickus MC, Guo Y, Linstedt AD, Kovačević J. Active mask segmentation of fluorescence microscope images. IEEE Trans Image Process. 18(8):1817-29, 2009.

Webb RL, Rozov O, Watkins S, McCartney BM. Using Total Internal Reflection Fluorescence (TIRF) microscopy to visualize cortical actin and microtubules in the Drosophila syncytial embryo. Developmental Dynamics; 238:2622-2632, 2009.

Lusvarghi S, Murphy C, Roy S, Tanious F, Sacui I, Wilson W.D., Ly D, Armitage B. Loop and Backbone Modifications of Peptide Nucleic Acid Improve G-Quadruplex Binding Selectivity. Journal of the American Chemical Society, 131 (51): 18415–18424, 30 November, 2009.

Talkish J and Woolford JL. The Rea1 tadpole loses its tail. Cell, 138(5): 832-4, 2009.

Mills PH and Ahrens ET. Enhanced positive-contrast visualization of paramagnetic contrast agents using phase images. Magnetic Resonance in Medicine, 62(5): 1349-55, 2009.

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.

Falco CN, Dykstra KM, Yates BP, Berget PB. scFv-based fluorogen activating proteins and variable domain inhibitors as fluorescent biosensor platforms. Biotechnol J, 4(9):1328-36, Sept 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.

Sengupta D, Truschel S, Bachert C, Linstedt AD. Organelle tethering by a homotypic PDZ interaction underlies formation of the Golgi membrane network. J Cell Biol, 186(1):41-55, 13 Jul 2009. Epub 2009 Jul 6.

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.

Webb RL, Zhou MN, McCartney BM. A novel role for an APC2-Diaphanous complex in regulating actin organization in Drosophila. Development, 136(8):1283-93, Apr 2009. Epub 2009 Mar 11.

Hinman VF, Yankura KA, McCauley BS. Evolution of gene regulatory network architectures: examples of subcircuit conservation and plasticity between classes of echinoderms. Biochim Biophys Acta, 1789(4):326-32, Apr 2009. Epub 2009 Jan 22.

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.


Sweeney B, Zhang T, Schwartz R. Exploring the parameter space of complex self-assembly through virus capsid models. Biophysical Journal, 94:772-783 2008.

Srinivasa G, Fickus M, Gonzalez-Rivero, Hsieh S, Guo Y, Linstedt AD, Kovacevic J. Active-mask segmentation for the cell-volume computation and Golgi-body segmentation of HeLa cell images. Proc. IEEE Intl. Symp. Biomed. Imaging, Paris, France, pp. 348-351, 2008.

Misra N, Lees D, Zhang T, Schwartz R. Pathway complexity of model virus capsid assembly systems. Computational and Mathematical Methods in Medicine, 9(3):277-293, 2008.

Mills PH, Wu YL, Ho C, 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, 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.

Gong H, Sengupta D, Linstedt AD, Schwartz R. Simulated de novo assembly of golgi compartments by selective cargo capture during vesicle budding and targeted vesicle fusion. Biophys J, 95(4):1674-88, Aug 2008. Epub 2008 May 9.

Guo Y, Punj V, Sengupta D, Linstedt AD. Coat-tether interaction in Golgi organization. Mol Biol Cell, 19(7):2830-43, Jul 2008. Epub 2008 Apr 23.

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 Apr. Epub 2008 Feb 13.

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.

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


Kellogg RA, Chebira A, Goyal A, Cuadra PA, Zappe SF, Minden JS, Kovacevic J. Towards an image analysis toolbox for high-throughput Drosophila embryo RNAi screens, Proc. IEEE Intl. Symp. Biomed. Imaging, Arlington, VA, Apr. 2007, 288-291.

Sellers KF, Miecznikowski J, Viswanathan S, Minden JS, Eddy WF. Lights, Camera, Action! Systematic variation in 2-D difference gel electrophoresis images. Electrophoresis 28, 3324-3332, 2007.

Zhang T, Kim WT, Schwartz R. Investigating scaling effects on virus capsid-like self-assembly using discrete event simulations. IEEE Trans Nanobioscience. 6(3):235-41, 2007 Sep.

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, 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.

Ettensohn CA, Kitazawa C, Cheers MS, Leonard JD, Sharma T. Gene regulatory networks and developmental plasticity in the early sea urchin embryo: alternative deployment of the skeletogenic gene regulatory network. Development, 134(17):3077-87, Sept 2007. Epub 2007 Aug 1.

Mills PH and 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.

Zhang J, Harnpicharnchai P, Jakovljevic J, Tang L, Guo Y, Oeffinger M, Rout MP, Hiley SL, Hughes T, 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.


Viswanathan S, Ünlü M, Minden JS. Two-dimensional difference gel electrophoresis. Nature Protocols, 1, 1351-1358, 2006.

Subramanian S, Woolford CA, Drill E, Lu M, Jones EW. Pbn1p: an essential endoplasmic reticulum membrane protein required for protein processing in the endoplasmic reticulum of budding yeast. Proc Natl Acad Sci U S A. 103(4):939-44, 2006 Jan 24. Epub 2006 Jan 17.

McCartney BM, Price MH, Webb RL, Hayden MA, Holot LM, Zhou MN, 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 Jun.

Kapoor V, Urban NN. Glomerulus-specific, long latency activity in the olfactory bulb granule-cell network. J. Neuroscience; 26(45):11709-19, 2006. Faculty of 1,00 Recommended.

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

Mills PH and 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, 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, 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 and 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.


Subramanian S, Woolford CA, Jones EW. The Sec1/Munc18 protein, Vps33p, functions at the endosome and the vacuole of Saccharomyces cerevisiae. Mol Biol Cell. 15(6):2593-605, 2004 Jun. Epub 2004 Mar 26.

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, 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, 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.


Antúnez de Mayolo P, Woolford JL Jr. Interactions of yeast ribosomal protein rpS14 with RNA. J Mol Biol. 333(4):697-709, 2003 Oct 31.

Lagerholm BC, Vanni S, Taylor DL, Lanni F. Cytomechanics applications of optical sectioning microscopy. Methods Enzymol. 361:175-97, 2003.

Puthenveedu MA, Bruns JR, Weisz OA, Linstedt AD. Basolateral cycling mediated by a lumenal domain targeting determinant. Mol Biol Cell. 14(5):1801-7, 2003 May. Epub 2003 Feb 6.

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.