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Biological Sciences

2016 Publications

Urban-Ciecko, J.¥ and Barth A.L.* Somatostatin neurons in cortical networks (2016) Nature Reviews Neuroscience 17:401-409.

Ye, L., Allen, W.F., Thompson, K.R., Tian, Q., Hsueh, B.,  Ramakrishnan, C., Wang A.-C., Jennings, J., Adhikari, A., Witten, I.B., Barth, A.L.*, Luo, L. Halpern C.H., McNab, J., and  Deisseroth, K. Wiring and Molecular Features of Prefrontal Ensembles Representing Distinct Experiences. (2016) Cell Jun 16;165(7):1776-88.

Blundon MA, Schlesinger DR, Parthasarathy A, Smith SL, Kolev HM, Vinson DA, Kunttas-Tatli E, McCartney BM*, Minden JS*. Proteomic analysis reveals APC-dependent post translational modifications and identifies a novel regulator of β-catenin. 
Development. 2016 Jun 10.

Min K, Ichikawa Y, Woolford CD¥, Mitchell AP*. Candida albicans Gene Deletion with a Transient CRISPR-Cas9 System. mSphere Jun 2016, 1 (3) e00130-16.
Shan Wu, Beril Tutuncuoglu, Kaige Yan, Hailey Brown, Yixiao Zhang, Dan Tan, Michael Gamalinda, Yi Yuan, Zhifei Li, Jelena Jakovljevic, Chengying Ma, Jianlin Lei, Meng-Qiu Dong, John L. Woolford Jr & Ning Gao. Diverse roles of assembly factors revealed by structures of late nuclear pre-60S ribosomes. Nature. In press.

Ichikawa Y, Morohashi N, Tomita N, Mitchell AP*, Kurumizaka H, Shimizu M. Sequence-directed nucleosome-depletion is sufficient to activate transcription from a yeast core promoter in vivo. Biochem Biophys Res Commun. 2016 May 18.

Ganesan V, Ascherman DP, Minden JS*. Immunoproteomics technologies in the discovery of autoantigens in autoimmune diseases. Biomol Concepts. 2016 May 1;7(2):133-43.

Talkish J§, Biedka S, Jakovljevic J, Zhang J, Tang L, Strahler JR, Andrews PC, Maddock JR, Woolford JL Jr*. Disruption of ribosome assembly in yeast blocks cotranscriptional pre-rRNA processing and affects the global hierarchy of ribosome biogenesis. RNA. 2016 Jun;22(6):852-66.

Mitchell AP*. Microbiology: Fungus produces a toxic surprise. Nature (2016). 2016 Mar 30.

Kormuth KA, Woolford JL Jr*, Armitage BA*. Homologous PNA Hybridization to Noncanonical DNA G-Quadruplexes. Biochemistry. 2016 Mar 29;55(12):1749-57.

Pafundo DE§, Nicholas MA, Zhang R, Kuhlman SJ*. Top-Down-Mediated Facilitation in the Visual Cortex Is Gated by Subcortical Neuromodulation. J Neurosci. 2016 Mar 9;36(10):2904-14

Xu W§, Solis NV, Filler SG, Mitchell AP*. Gene Expression Profiling of Infecting Microbes Using a Digital Bar-coding Platform. J Vis Exp. 2016 Jan 13;(107).

Yu Y, Lee HC, Chen KC, Suhan J*, Qiu M, Ba Q, Yang G. Inner membrane fusion mediates spatial distribution of axonal mitochondria. Sci Rep. 2016 Jan 8;6:18981

Spealman P†, Wang H, May G, Kingsford C, McManus CJ*. Exploring Ribosome Positioning on Translating Transcripts with Ribosome Profiling. Methods Mol Biol. 2016;1358:71-97.

Xu W§, Solis NV, Filler SG, Mitchell AP*. Pathogen Gene Expression Profiling During Infection Using a Nanostring nCounter Platform. Methods Mol Biol. 2016;1361:57-65.

Past Publications

Mitchell AP*. The New Shape of EC. Eukaryot Cell. 2015 Dec;14(12):1151-2.

Wong EV, Cao W, Vörös J, Merchant M, Modis Y, Hackney DD*, Montpetit B, De La Cruz EM. Pi release limits the intrinsic and RNA-stimulated ATPase cycles of DEAD-box protein 5 (Dbp5). J Mol Biol. 2015 Dec 27. pii: S0022-2836(15)00709-3.

Snyder JC, Pack TF, Rochelle LK, Chakraborty SK, Zhang M, Eaton AW, Bai Y, Ernst LA, Barak LS, Waggoner AS*, Caron MG. A rapid and affordable screening platform for membrane protein trafficking. BMC Biol. 2015 Dec 17;13(1):107.

Chandrasekaran S, Navlakha S, Audette NJ, McCreary DD, Suhan J*, Bar-Joseph Z, Barth AL*. Unbiased, High-Throughput Electron Microscopy Analysis of Experience-Dependent Synaptic Changes in the Neocortex. J Neurosci. 2015 Dec 16;35(50):16450-62.

Mustapha MM, Marsh JW, Krauland MG, Fernandez JO, de Lemos AP, Dunning Hotopp JC, Wang X, Mayer LW, Lawrence JG, Hiller NL*, Harrison LH. Genomic Epidemiology of Hypervirulent Serogroup W, ST-11 Neisseria meningitidis. EBioMedicine. 2015 Sep 8;2(10):1447-55.

Johnson GR, Li J, Shariff A, Rohde GK, Murphy RF*. Automated Learning of Subcellular Variation among Punctate Protein Patterns and a Generative Model of Their Relation to Microtubules. PLoS Comput Biol. 2015 Dec 1;11(12):e1004614.

Cheetham CE*, Grier BD, Belluscio L. Bulk regional viral injection in neonatal mice enables structural and functional interrogation of defined neuronal populations throughout targeted brain areas. Front Neural Circuits. 2015 Nov 5;9:72.

Kang J, Schwartz R*, Flickinger J, Beriwal S. Machine Learning Approaches for Predicting Radiation Therapy Outcomes: A Clinician's Perspective. Int J Radiat Oncol Biol Phys. 2015 Dec 1;93(5):1127-35.

Murphy RF*. Building cell models and simulations from microscope images. Methods. 2015 Oct 17. pii: S1046-2023(15)30129-8.

Spealman P, Wang H, May G, Kingsford C, McManus CJ*. Exploring Ribosome Positioning on Translating Transcripts with Ribosome Profiling. Methods Mol Biol. 2016;1358:71-97.

M. Stolzer§, K. Siewert, H. Lai, M. Xu, D. Durand*, 2015. Event inference in multidomain families with phylogenetic reconciliation. BMC Bioinformatics, Oct 2;16 Suppl 14:S8

Willard AM, Gittis AH*. Mapping neural circuits with CLARITY. Elife. 2015 Oct 9;4:e11409.

Xu W§, Solis NV, Filler SG, Mitchell AP*. Pathogen Gene Expression Profiling During Infection Using a Nanostring nCounter Platform. Methods Mol Biol. 2016;1361:57-65.

Ganesan V, Schmidt B, Avula R, Cooke D, Maggiacomo T, Tellin L, Ascherman DP, Bruchez MP*, Minden J*. Immuno-proteomics: Development of a novel reagent for separating antibodies from their target proteins. Biochim Biophys Acta. 2015 Jun;1854(6):592-600.

Tewari R, Bachert C¥, Linstedt AD*. Induced-oligomerization targets Golgi proteins for degradation in lysosomes. Mol Biol Cell. 2015 Oct 7. pii: mbc.E15-04-0207.

Kunttas-Tatli E, Von Kleeck RA, Greaves BD, Vinson D, Roberts DM, McCartney BM*. The two SAMP repeats and their phosphorylation state in Drosophila Adenomatous polyposis coli-2 play mechanistically distinct roles to negatively regulate Wnt signaling. Mol Biol Cell. 2015 Oct 7. pii: mbc.E15-07-0515.

Wu Y, Stauffer SR, Stanfield RL, Tapia PH, Ursu O, Fisher GW, Szent-Gyorgyi C, Evangelisti A, Waller A, Strouse JJ, Carter MB, Bologa C, Gouveia K, Poslusney M, Waggoner AS*, Lindsley CW, Jarvik JW*, Sklar LA. Discovery of Small-Molecule Nonfluorescent Inhibitors of Fluorogen-Fluorogen Activating Protein Binding Pair. J Biomol Screen. 2015 Oct 6. pii: 1087057115609145.

Cary GA§, Vinh DB, May P, Kuestner R, Dudley AM. Proteomic Analysis of Dhh1 Complexes Reveals a Role for Hsp40 Chaperone Ydj1 in Yeast P-Body Assembly. G3 (Bethesda). 2015 Sep 21. pii: g3.115.021444.

Grimsey NJ, Aguilar B, Smith TH, Le P, Soohoo AL, Puthenveedu MA*, Nizet V, Trejo J. Ubiquitin plays an atypical role in GPCR-induced p38 MAP kinase activation on endosomes. J Cell Biol. 2015 Sep 28;210(7):1117-31.

Bowman SL, Soohoo AL, Puthenveedu MA*. Visualizing and quantitating sequence-dependent GPCR recycling. Methods Cell Biol. 2015;130:333-45.

Johnson GR, Buck TE, Sullivan DP, Rohde GK, Murphy RF*. Joint Modeling of Cell and Nuclear Shape Variation. Mol Biol Cell. 2015 Sep 9. pii: mbc.E15-06-0370.

Hiller NL*, Chauhan A, Palmer M, Jain S, Sotereanos NG, Altman GT, Nistico L, Kreft R, Post JC, Demeo PJ. Presence of bacteria in failed anterior cruciate ligament reconstructions. Springerplus. 2015 Aug 28;4:460.

Saurabh S, Zhang M, Mann VR, Costello AM, Bruchez MP*. Kinetically Tunable Photostability of Fluorogen-Activating Peptide-Fluorogen Complexes. Chemphyschem. 2015 Oct 5;16(14):2974-80.

Pratt CP, He J, Wang Y, Barth AL*, Bruchez MP*. Fluorogenic Green-Inside Red-Outside (GIRO) Labeling Approach Reveals Adenylyl Cyclase-Dependent Control of BKα Surface Expression. Bioconjug Chem. 2015 Sep 16;26(9):1963-71.

Gittis AH*, Brasier DJ*. NEUROSCIENCE. Astrocytes tell neurons when to listen up. Science. 2015 Aug 14;349(6249):690-1.

Roman T, Nayyeri A, Fasy BT, Schwartz R*. A simplicial complex-based approach to unmixing tumor progression data. BMC Bioinformatics. 2015 Aug 12;16:254.

McManus J*, Cheng Z, Vogel C. Next-generation analysis of gene expression regulation - comparing the roles of synthesis and degradation. Mol Biosyst. 2015 Sep 15;11(10):2680-9.

Canady TD, Telmer CA¥, Oyaghire SN, Armitage BA, Bruchez MP*. In Vitro Reversible Translation Control Using γPNA Probes. J Am Chem Soc. 2015 Aug 19;137(32):10268-75.

Navlakha, S., Barth, A.L.*, and Bar-Joseph, Z. Synapse pruning rates optimize construction of efficient and robust networks. (2015) PLoS Computational Biology July 28; 11(7): e1004347.

Desai JV, Cheng S, Ying T, Nguyen MH, Clancy CJ, Lanni F*, Mitchell AP*.Coordination of Candida albicans Invasion and Infection Functions by Phosphoglycerol Phosphatase Rhr2. Pathogens. 2015 Jul 24;4(3):573-589.

Magenau AJ, Saurabh S, Andreko SK, Telmer CA¥, Schmidt BF, Waggoner AS*, Bruchez MP*. Genetically targeted fluorogenic macromolecules for subcellular imaging and cellular perturbation. Biomaterials. 2015 Jul 2;66:1-8.

Temerinac-Ott M, Naik AW, Murphy RF*. Deciding when to stop: efficient experimentation to learn to predict drug-target interactions. BMC Bioinformatics. 2015 Jul 9;16:213

Desai JV, Mitchell AP*. Candida albicans Biofilm Development and Its Genetic Control. Microbiol Spectr. 2015 Jun;3(3).

Huppler AR, Whibley N, Woolford CA, Childs EE, He J, Biswas PS, McGeachy MJ, Mitchell AP*, Gaffen SL. A Candida albicans strain expressing mammalian IL-17A results in early control of fungal growth during disseminated infection. Infect Immun. 2015 Jul 6. pii: IAI.03057-14.

Eutsey RA, Powell E, Dordel J, Salter SJ, Clark TA, Korlach J, Ehrlich GD, Hiller NL*. Genetic Stabilization of the Drug-Resistant PMEN1 Pneumococcus Lineage by Its Distinctive DpnIII Restriction-Modification System. MBio. 2015 Jun 16;6(3). pii: e00173-15.

Wang W, Tripathy SJ, Padmanabhan K, Urban NN*, Kass RE. An Empirical Model for Reliable Spiking Activity. Neural Comput. 2015 Jun 16:1-15.

Chowdhury SA, Gertz EM, Wangsa D, Heselmeyer-Haddad K, Ried T, Schäffer AA, Schwartz R*. Inferring models of multiscale copy number evolution for single-tumor phylogenetics. Bioinformatics. 2015 Jun 15;31(12):i258-i267.

Lin Y, May GE¥, Joel McManus C*. Mod-seq: A High-Throughput Method for Probing RNA Secondary Structure. Methods Enzymol. 2015;558:125-52.

Willard AM, Bouchard RS¥, Gittis AH*. Differential degradation of motor deficits during gradual dopamine depletion with 6-hydroxydopamine in mice. Neuroscience. 2015 Jun 9. pii: S0306-4522(15)00519-9.

Bruchez MP*. Dark dyes-bright complexes: fluorogenic protein labeling. Curr Opin Chem Biol. 2015 Jun 5;27:18-23.

Bowman SL, Puthenveedu MA*. Postendocytic Sorting of Adrenergic and Opioid Receptors: New Mechanisms and Functions. Prog Mol Biol Transl Sci. 2015;132:189-206.

Coolon JD, Stevenson KR, McManus CJ*, Yang B, Graveley BR, Wittkopp PJ. Molecular mechanisms and evolutionary processes contributing to accelerated divergence of gene expression on the Drosophila X chromosome. Mol Biol Evol. 2015 Jun 2.

Liu L§, Ye Q¥, Lu M, Lo YC, Hsu YH, Wei MC, Chen YH, Lo SC, Wang SJ, Bain DJ, Ho C*. A new approach to reduce toxicities and to improve bioavailabilities of platinum-containing anti-cancer nanodrugs. Sci Rep. 2015 Jun 3;5:10881

Figge MT, Murphy RF*. Image-based systems biology. Cytometry A. 2015 Jun;87(6):459-61.

Liu Y, Shetty AC, Schwartz JA, Bradford LL, Xu W¥, Phan QT, Kumari P, Mahurkar A, Mitchell AP*, Ravel J, Fraser CM, Filler SG, Bruno VM. New signaling pathways govern the host response to C. albicans infection in various niches. Genome Res. 2015 Apr 9.

Gallo E, Snyder AC, Jarvik JW*. Engineering tandem single-chain Fv as cell surface reporters with enhanced properties of fluorescence detection. Protein Eng Des Sel. 2015 Apr 5.

Woolford J*. Assembly of ribosomes in eukaryotes. RNA. 2015 Apr;21(4):766-8.

de la Cruz J, Karbstein K, Woolford JL Jr*. Functions of ribosomal proteins in assembly of eukaryotic ribosomes in vivo. Annu Rev Biochem. 2015;84:93-129.

Bowman SL, Soohoo AL, Shiwarski DJ, Schulz S, Pradhan AA, Puthenveedu MA*. Cell-Autonomous Regulation of Mu-Opioid Receptor Recycling by Substance P. Cell Rep. 2015 Mar 17

Mitchell KF, Zarnowski R, Sanchez H, Edward JA, Reinicke E1, Nett JE, Mitchell AP*, Andes DR. Community participation in biofilm matrix assembly and function. Proc Natl Acad Sci U S A. 2015 Mar 13.

Ulengin I, Park JJ, Lee TH*. ER network formation and membrane fusion by atlastin1/SPG3A disease variants. Mol Biol Cell. 2015 Mar 11.

Yan Q, Bruchez MP*. Advances in chemical labeling of proteins in living cells. Cell Tissue Res. 2015 Mar 7.

Urban-Ciecko J¥, Fanselow EE¥, Barth AL*. Neocortical Somatostatin Neurons Reversibly Silence Excitatory Transmission via GABAb Receptors. Curr Biol. 2015 Feb 25. pii: S0960-9822(15)00067-6.

Telmer CA¥, Verma R, Teng H¥, Andreko S, Law L‡, Bruchez MP*. Rapid, Specific, No-wash, Far-red Fluorogen Activation in Subcellular Compartments by Targeted Fluorogen Activating Proteins. ACS Chem Biol. 2015 Feb 16.

Yan Q, Schmidt BF¥, Perkins LA, Naganbabu M, Saurabh S, Andreko SK, Bruchez MP*. Near-instant surface-selective fluorogenic protein quantification using sulfonated triarylmethane dyes and fluorogen activating proteins. Org Biomol Chem. 2015 Feb 21;13(7):2078-86.

González LM, Ruder WC, Mitchell AP*, Messner WC, LeDuc PR. Sudden motility reversal indicates sensing of magnetic field gradients in Magnetospirillum magneticum AMB-1 strain. ISME J. 2014 Dec 5.

Xu W¥, Solis NV, Ehrlich RL, Woolford CA, Filler SG, Mitchell AP*. Activation and Alliance of Regulatory Pathways in C. albicans during Mammalian Infection. PLoS Biol. 2015 Feb 18;13(2):e1002076.

Gamalinda M, Woolford JL Jr*. Paradigms of ribosome synthesis: Lessons learned from ribosomal proteins. Translation, DOI: 10.4161/21690731.2014.975018

Kadam A, Janto B, Eutsey R¥, Earl JP, Powell E, Dahlgren ME, Hu FZ, Ehrlich GD, Hiller NL*. Streptococcus pneumoniae Supragenome Hybridization Arrays for Profiling of Genetic Content and Gene Expression. Curr Protoc Microbiol. 2015 Feb 2;36:9D.4.1-9D.4.20.

Cheatle Jarvela AM§, Hinman VF*. Evolution of transcription factor function as a mechanism for changing metazoan developmental gene regulatory networks. Evodevo. 2015 Jan 29;6(1):3

Wang Y, Telmer CA¥, Schmidt BF, Franke JD, Ort S, Arndt-Jovin DJ, Bruchez MP*. Fluorogen activating protein-affibody probes: modular, no-wash measurement of epidermal growth factor receptors. Bioconjug Chem. 2015 Jan 21;26(1):137-44.

Schwartz SL, Yan Q, Telmer CA¥, Lidke KA, Bruchez MP*, Lidke DS. ACS Chem Biol. 2015 Feb 20;10(2):539-46. ACS Chem Biol. 2015 Feb 20;10(2):539-46.

Mastro KJ, Gittis AH*. Striking the right balance: cortical modulation of the subthalamic nucleus-globus pallidus circuit. Neuron. 2015 Jan 21;85(2):233-5.

Yuan Y, Tam MF¥, Simplaceanu V, Ho C*. New Look at Hemoglobin Allostery. Chem Rev. 2015 Jan 21.

Faust JE, Desai T, Verma A, Ulengin I, Sun TL, Moss TJ, Betancourt MA, Huang HW, Lee T*, McNew JA.  The Atlastin C-terminal tail is an amphipathic helix that perturbs bilayer structure during endoplasmic reticulum homotypic fusion. J Biol Chem. 2015 Jan 2.

Glazewski S¥, Barth AL*. Stimulus intensity determines experience-dependent modifications in neocortical neuron firing rates. Eur J Neurosci. 2014 Dec 26. doi: 10.1111/ejn.12805.

Pongpom M, Liu H, Xu W¥, Snarr BD, Sheppard DC, Mitchell AP*, Filler SG. Divergent Targets of Aspergillus fumigatus AcuK and AcuM Transcription Factors during Growth in vitro versus Invasive Disease. Infect Immun. 2014 Dec 22. pii: IAI.02685-14.

Casadevall A, Mitchell, AP*, Berman J,Kwon-Chung KJ, Perfect, Heitman J. Human Fungal Pathogens. Book Series: A Cold Spring Harbor Perspectives in Medicine Collection. 2014.

Saurabh S, Beck LE, Maji S, Baty CJ, Wang Y, Yan Q, Watkins SC, Bruchez MP*. Multiplexed modular genetic targeting of quantum dots. ACS Nano. 2014 Nov 25;8(11):11138-46.

Gittis AH*, Berke JD, Bevan MD, Chan CS, Mallet N, Morrow MM, Schmidt R. New roles for the external globus pallidus in Basal Ganglia circuits and behavior. J Neurosci. 2014 Nov 12;34(46):15178-83.

Shackney SE, Chowdhury SA, Schwartz R*. A Novel Subset of Human Tumors That Simultaneously Overexpress Multiple E2F-responsive Genes Found in Breast, Ovarian, and Prostate Cancers. Cancer Inform. 2014 Nov 3;13(Suppl 5):89-100.

Chung D, Barker BM, Carey CC, Merriman B, Werner ER, Lechner BE, Dhingra S, Cheng C, Xu W§, Blosser SJ, Morohashi K, Mazurie A, Mitchell TK, Haas H, Mitchell AP*, Cramer RA. ChIP-seq and In Vivo Transcriptome Analyses of the Aspergillus fumigatus SREBP SrbA Reveals a New Regulator of the Fungal Hypoxia Response and Virulence. PLoS Pathog. 2014 Nov 6;10(11):e1004487.

Song L, Bachert C¥, Schjoldager KT, Clausen H, Linstedt AD*. Development of Isoform-specific Sensors of Polypeptide GalNAc-transferase Activity. J Biol Chem. 2014 Oct 31

Soohoo AL, Bowersox SL, Puthenveedu MA*. Visualizing Clathrin-mediated Endocytosis of G Protein-coupled Receptors at Single-event Resolution via TIRF Microscopy. J Vis Exp. 2014 Oct 20

Stolzer M§, Wasserman L, Durand D*. Robustness of birth-death and gain models for inferring evolutionary events. BMC Genomics 2014, 15(Suppl 6):S9

Liu T, Sae-Ueng U, Li D, Lander GC, Zuo X, Jönsson B, Rau D, Shefer I, Evilevitch A. Solid-to-fluid-like DNA transition in viruses facilitates infection. Proc Natl Acad Sci U S A. 2014 Oct 14;111(41):14675-80.

Desai JV, Mitchell AP*, Andes DR. Fungal Biofilms, Drug Resistance, and Recurrent Infection. Cold Spring Harb Perspect Med. 2014 Oct 1;4(10).

Saini SG, Liu C, Zhang P, Lee TH*. Membrane tethering by the atlastin GTPase depends on GTP hydrolysis but not on forming the crossover configuration. Mol Biol Cell. 2014 Sep 24.

Gamalinda M, Woolford JL Jr*. Deletion of L4 domains reveals insights into the importance of ribosomal protein extensions in eukaryotic ribosome assembly. RNA. 2014 Sep 22.

Blankenship JR§, Cheng S, Woolford CA¥ , Xu W¥, Johnson TM, Rogers PD, Fanning S§, Nguyen MH, Clancy CJ, Mitchell AP*. Mutational analysis of essential septins reveals a role for septin-mediated signaling in filamentation. Eukaryot Cell. 2014 Sep 12.

Kunttas-Tatli E, Roberts DM, McCartney BM*. Self-association of the APC tumor suppressor is required for the assembly, stability, and activity of the Wnt signaling destruction complex. Mol Biol Cell. 2014 Sep 10.

Vasicek EM, Berkow EL, Bruno VM, Mitchell AP*, Wiederhold NP, Barker KS, Rogers PD. Disruption of the Transcriptional Regulator Cas5 Results in Enhanced Killing of Candida albicans by Fluconazole. Antimicrob Agents Chemother. 2014 Sep 2.

Cheatle Jarvela AM, Hinman V*. A Method for Microinjection of Patiria minata Zygotes. J Vis Exp. 2014 Sep 1;(91).

Sae-Ueng U, Liu T, Catalano CE, Huffman JB, Homa FL, Evilevitch A. Major capsid reinforcement by a minor protein in herpesviruses and phage. Nucleic Acids Res. 2014 Aug;42(14):9096-107.

Tewari R, Jarvela T§, Linstedt AD*. Manganese induces oligomerization to promote down-regulation of the intracellular trafficking receptor used by Shiga toxin. Mol Biol Cell. 2014 Jul 30. pii: mbc.E14-05-1003.

Chowdhury SA, Shackney SE, Heselmeyer-Haddad K, Ried T, Schäffer AA, Schwartz R*. Algorithms to Model Single Gene, Single Chromosome, and Whole Genome Copy Number Changes Jointly in Tumor Phylogenetics. PLoS Comput Biol. 2014 Jul 31;10(7):e1003740.

Vistein R, Puthenveedu MA*. Src regulates sequence-dependent beta-2 adrenergic receptor recycling via cortactin phosphorylation. Traffic. 2014 Jul 31. doi: 10.1111/tra.12202.

Van PT, Ganesan V, Bass V, Parthasarathy A, Schlesinger D, Minden JS*. In-gel equilibration for improved protein retention in 2DE-based proteomic workflows. Electrophoresis. 2014 Jul 17

Cheatle Jarvela AM, Brubaker L, Vedenko A, Gupta A, Armitage BA*, Bulyk ML, Hinman VF*. Modular Evolution of DNA-Binding Preference of a Tbrain Transcription Factor Provides a Mechanism for Modifying Gene Regulatory Networks. Mol Biol Evol. 2014 Jul 12

Meyer T, Ramachandran S, Olson CR. Statistical learning of serial visual transitions by neurons in monkey inferotemporal cortex. J Neurosci. 2014 Jul 9;34(28):9332-7.

Jarvela TS§, Linstedt AD*. The Application of KillerRed for Acute Protein Inactivation in Living Cells. Curr Protoc Cytom. 2014 Jul 1;69:12.35.1-12.35.10

Van PT†, Bass V, Shiwarski D, Lanni F*, Minden J*. High dynamic range proteome imaging with the Structured Illumination Gel Imager. Electrophoresis. 2014 Jun 17.

Gallo E, Wienbar S, Snyder AC§, Vasilev KV, Armitage BA*, Jarvik JW*. A Single-Chain-Variable-Fragment Fluorescence Biosensor Activates Fluorogens from Dissimilar Chemical Families. Protein Pept Lett. 2014 Jun 16.

Shiwarski DJ, Shao C, Bill A, Kim J, Xiao D, Bertrand C, Seethala RR, Sano D, Myers JN, Ha PK, Grandis JR, Gaither LA, Puthenveedu MA*, Duvvuri U. To "Grow" or "Go": TMEM16A Expression as a Switch between Tumor Growth and Metastasis in SCCHN. Clin Cancer Res. 2014 Jun 11. pii: clincanres.0363.2014.

Gonzalez-Burgos G, Miyamae T, Pafundo DE§, Yoshino H, Rotaru DC, Hoftman G, Datta D, Zhang Y, Hammond M, Sampson AR, Fish KN, Bard Ermentrout G, Lewis DA. Functional Maturation of GABA Synapses During Postnatal Development of the Monkey Dorsolateral Prefrontal Cortex. Cereb Cortex. 2014 Jun 5. pii: bhu122.

Padmanabhan K§, Urban NN*. Disrupting information coding via block of 4-AP sensitive potassium channels. J Neurophysiol. 2014 Jun 3. pii: jn.00823.2013.

Czajkowski R, Jayaprakash B, Wiltgen B, Rogerson T, Guzman-Karlsson MC, Barth AL*, Trachtenberg JT, Silva AJ. Encoding and storage of spatial information in the retrosplenial cortex. Proc Natl Acad Sci U S A. 2014 May 27. pii: 201313222.

Fisher GW, Fuhrman MH*, Adler SA, Szent-Gyorgyi C, Waggoner AS*, Jarvik JW*. Self-Checking Cell-Based Assays for GPCR Desensitization and Resensitization. J Biomol Screen. 2014 May 12.

Veenendaal T, Jarvela T§, Grieve AG, van Es JH, Linstedt AD*, Rabouille C. GRASP65 controls the cis Golgi integrity in vivo. Biol Open. 2014 May 2;3(6):431-43.

Kadayakkara DK, Damodaran K, Hitchens TK¥, Bulte JW, Ahrens ET*. (19)F spin-lattice relaxation of perfluoropolyethers: Dependence on temperature and magnetic field strength (7.0-14.1T). J Magn Reson. 2014 May;242:18-22.

Murphy RF*. A new era in bioimage informatics. Bioinformatics. 2014 May 15;30(10):1353

Ettensohn CA*. Horizontal transfer of the msp130 gene supported the evolution of metazoan biomineralization. Evol Dev. 2014 May;16(3):139-48.

Kuhlman SJ*, O'Connor DH, Fox K, Svoboda K. Structural plasticity within the barrel cortex during initial phases of whisker-dependent learning. J Neurosci. 2014 Apr 23; 34(17):6078-83.

Talkish J, Campbell IW, Sahasranaman A, Jakovljevic J¥, Woolford JL Jr*. Ribosome assembly factors Pwp1 and Nop12 are important for folding of 5.8S rRNA during ribosome biogenesis in Saccharomyces cerevisiae. Mol Cell Biol. 2014 May;34(10):1863-77.

Burton SD, Urban NN*. Greater excitability and firing irregularity of tufted cells underlies distinct afferent-evoked activity of olfactory bulb mitral and tufted cells. J Physiol. 2014 May 15;592(Pt 10):2097-118.

Tripathy SJ, Savitskaya J, Burton SD, Urban NN*, Gerkin RC§. NeuroElectro: a window to the world's neuron electrophysiology data. Front Neuroinform. 2014 Apr 29;8:40.

Wahab AA, Taj-Aldeen SJ, Kolecka A, Elgindi M, Finkel JS*, Boekhout T. High prevalence of Candida dubliniensis in lower respiratory tract secretions from cystic fibrosis patients may be related to increased adherence properties. Int J Infect Dis. 2014 Apr 26. pii: S1201-9712(14)01473-8.

Yan Q, Schwartz SL, Maji S, Huang F, Szent-Gyorgyi C, Lidke DS, Lidke KA, Bruchez MP*. Localization microscopy using noncovalent fluorogen activation by genetically encoded fluorogen-activating proteins. Chemphyschem. 2014 Mar 17;15(4):687-95.

Willard AM, Brasier DJ*. Controversies in Neuroscience: A Literature-Based Course for First Year Undergraduates that Improves Scientific Confidence While Teaching Concepts. J Undergrad Neurosci Educ. 2014 Mar 15;12(2):A159-66.

Welch L, Lewitter F, Schwartz R*, Brooksbank C, Radivojac P, Gaeta B, Schneider MV. Bioinformatics curriculum guidelines: toward a definition of core competencies. PLoS Comput Biol. 2014 Mar 6;10(3):e1003496.

Hinman VF*, Cheatle Jarvela AM. Developmental gene regulatory network evolution: insights from comparative studies in echinoderms. Genesis. 2014 Mar;52(3):193-207.

Adomako-Ankomah A, Ettensohn CA*. Growth factors and early mesoderm morphogenesis: insights from the sea urchin embryo. Genesis. 2014 Mar;52(3):158-72.

Iheagwara UK, Beatty PL, Van PT, Ross TM, Minden JS*, Finn OJ. Influenza virus infection elicits protective antibodies and T cells specific for host cell antigens also expressed as tumor-associated antigens: a new view of cancer immunosurveillance. Cancer Immunol Res. 2014 Mar;2(3):263-73.

Gallo E, Jarvik J*. Fluorogen-Activating scFv Biosensors Target Surface Markers on Live Cells Via Streptavidin or Single-Chain Avidin. Mol Biotechnol. 2014 Feb 23.

McManus CJ*, May GE, Spealman P, Shteyman A. Ribosome profiling reveals post-transcriptional buffering of divergent gene expression in yeast. Genome Res. 2014 Mar;24(3):422-30.

Mastro KJ*, Bouchard RS, Holt HA, Gittis AH*. Transgenic mouse lines subdivide external segment of the globus pallidus (GPe) neurons and reveal distinct GPe output pathways. J Neurosci. 2014 Feb 5;34(6):2087-99.

Rafiq K, Shashikant T, McManus CJ*, Ettensohn CA*. Genome-wide analysis of the skeletogenic gene regulatory network of sea urchins. Development. 2014 Feb;141(4):950-61.

Jean-Alphonse F, Bowersox S, Chen S, Beard G, Puthenveedu MA*, Hanyaloglu AC. Spatially restricted G protein-coupled receptor activity via divergent endocytic compartments. J Biol Chem. 2014 Feb 14;289(7):3960-77

Lan L, Nakajima S, Wei L, Sun L, Hsieh CL, Sobol RW, Bruchez M*, Van Houten B, Yasui A, Levine AS. Novel method for site-specific induction of oxidative DNA damage reveals differences in recruitment of repair proteins to heterochromatin and euchromatin. Nucleic Acids Res. 2014 Feb;42(4):2330-45.

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Iordanova B, Hitchens TK¥, Robison CS, Ahrens ET*. Engineered mitochondrial ferritin as a magnetic resonance imaging reporter in mouse olfactory epithelium. PLoS One. 2013 Aug 30;8(8):e72720. doi: 10.1371/journal.pone.0072720.

Barth AL*, Kuhlman SJ*. The many layers of specification and plasticity in the neocortex. Neuron. 2013 Sep 4;79(5):829-31. doi: 10.1016/j.neuron.2013.08.021.

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Chowdhury SA, Shackney SE, Heselmeyer-Haddad K, Ried T, Schäffer AA, Schwartz R*. Phylogenetic analysis of multiprobe fluorescence in situ hybridization data from tumor cell populations. Bioinformatics. 2013 Jul 1;29(13):i189-i198. doi: 10.1093/bioinformatics/btt205.

Sinha K§, Jen-Jacobson L, Rule GS*. Divide and conquer is always best: sensitivity of methyl correlation experiments. J Biomol NMR. 2013 Jun 15.

Raman SB, Nguyen MH, Cheng S, Badrane H, Iczkowski KA, Wegener M, Gaffen SL, Mitchell AP*, Clancy CJ. A competitive infection model of hematogenously disseminated candidiasis in mice redefines the role of Candida albicans IRS4 in pathogenesis. Infect Immun. 2013 May;81(5):1430-8. doi: 10.1128/IAI.00743-12. Epub 2013 Feb 19.

Mukhopadhyay S§, Redler B, Linstedt AD*. Shiga toxin binding site for host cell receptor GPP130 reveals unexpected divergence in toxin trafficking mechanisms. Mol Biol Cell. 2013 Jun 12.

Ryder PV, Vistein R, Gokhale A, Seaman MN, Puthenveedu M*, Faundez V. The WASH Complex, an Endosomal Arp2/3 Activator, Interacts with the Hermansky-Pudlak Syndrome Complex BLOC-1 and its Cargo Phosphatidylinositol-4-kinase Type II Alpha. Mol Biol Cell. 2013 May 15. [Epub ahead of print].

Zhong J, Sakaki M, Okada H, Ahrens ET*. In vivo intracellular oxygen dynamics in murine brain glioma and immunotherapeutic response of cytotoxic T cells observed by fluorine-19 magnetic resonance imaging. PLoS One. 2013 May 8;8(5):e59479. doi: 10.1371/journal.pone.0059479. Print 2013.

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.

Youker RT, Bruns JR, Costa SA, Rbaibi Y, Lanni F*, Kashlan OB, Teng H, Weisz OA. Multiple motifs regulate apical sorting of p75 via a mechanism that involves dimerization and higher-order oligomerization. Mol Biol Cell. 2013 May 1.

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Ahrens ET*, Zhong J. In vivo MRI cell tracking using perfluorocarbon probes and fluorine-19 detection. NMR Biomed. 2013 Apr 22.

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)

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Sahasranaman A. and Woolford J.L. Ribosome Assembly. In: Lennarz W.J. and Lane M.D. (eds.) The Encyclopedia of Biological Chemistry. 4:116-121. Waltham, MA: Academic Press. 2013.

Ettensohn CA. Encoding anatomy: Developmental gene regulatory networks and morphogenesis. Genesis. 2013 Feb 21.

Raman SB, Nguyen MH, Cheng S, Badrane H, Iczkowski KA, Wegener M, Gaffen SL, Mitchell AP*, Clancy CJ. A competitive infection model of hematogenously disseminated candidiasis in mice redefines the role of Candida albicans IRS4 in pathogenesis. Infect Immun. 2013 Feb 19.

Liu L, Hitchens TK, Ye Q, Wu Y, Barbe B, Prior DE, Li WF, Yeh FC, Foley LM, Bain DJ, Ho C*. Decreased reticuloendothelial system clearance and increased blood half-life and immune cell labeling for nano- and micron-sized superparamagnetic iron-oxide particles upon pre-treatment with Intralipid. Biochim Biophys Acta. 2013 Jun;1830(6):3447-53. doi: 10.1016/j.bbagen.2013.01.021. Epub 2013 Feb 8..

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.

Jung SI, Finkel JS, Solis NV, Chaili S, Mitchell AP*, Yeaman MR, Filler SG. Bcr1 Functions Downstream of Ssd1 to Mediate Antimicrobial Peptide Resistance in Candida albicans. Eukaryot Cell. 2013 Jan 11.

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.

Buck TE, Li J, Rohde GK, Murphy RF*. Toward the virtual cell: automated approaches to building models of subcellular organization "learned" from microscopy images. Bioessays. 2012 Sep;34(9):791-9.

Burton SD, Ermentrout GB, Urban NN*. Intrinsic heterogeneity in oscillatory dynamics limits correlation-induced neural synchronization. J Neurophysiol. 2012 Oct;108(8):2115-33.

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.

Hackney DD*. Oxygen isotopic exchange probes of ATP hydrolysis by RNA helicases. Methods Enzymol. 2012;511:65-74.

Bachert C, Linstedt A*. A Sensor of Protein O-Glycosylation Based on Sequential Processing in the Golgi apparatus. Traffic. 2012 Oct 9.

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Kim J, McBride S, Tellis B, Alvarez-Urena P, Song YH, Dean DD, Sylvia VL, Elgendy H, Ong J, Hollinger JO*. Rapid-prototyped PLGA/β-TCP/hydroxyapatite nanocomposite scaffolds in a rabbit femoral defect model. Biofabrication. 2012 Jun;4(2):025003. Epub 2012 Mar 19.

Iordanova B§, Goins WF, Clawson DS, Hitchens TK, Ahrens ET*. Quantification of HSV-1-mediated expression of the ferritin MRI reporter in the mouse brain. Gene Ther. 2012 Sep 20.

Krajcovic MM§, Minden JS*. Assessing the critical period for Rho kinase activity during Drosophila ventral furrow formation. Dev Dyn. 2012 Sep 12.

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.

Fanning S§, Xu W§, Beaurepaire C, Suhan J, Nantel A, Mitchell A*. Functional control of the Candida albicans cell wall by catalytic protein kinase A subunit Tpk1. Mol Microbiol. 2012 Aug 9. doi: 10.1111/j.1365-2958.2012.08193.x.

Subramanian S, Woolford CA, Desai JV, Lanni F, Mitchell AP*. Cis- and trans-acting localization determinants of pH-response regulator Rim13 in Saccharomyces cerevisiae. Eukaryot Cell. 2012 Aug 3. [Epub ahead of print]

Taff HT, Nett JE, Zarnowski R, Ross KM, Sanchez H, Cain MT, Hamaker J, Mitchell AP*, Andes DR. A Candida Biofilm-Induced Pathway for Matrix Glucan Delivery: Implications for Drug Resistance. PLoS Pathog 8(8): e1002848, 2012. doi:10.1371/journal.ppat.1002848

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.

Zhong J, Mills PH, Hitchens TK, Ahrens ET*. Accelerated fluorine-19 MRI cell tracking using compressed sensing. Magn Reson Med. 2012 Jul 26.

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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.

Yadav S§, Puthenveedu MA*, Linstedt AD*. Golgin160 recruits the Dynein motor to position the Golgi apparatus. Dev Cell. 2012 Jul 17;23(1):153-65.

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.

Li J, Xiong L, Schneider J, Murphy RF*. Protein subcellular location pattern classification in cellular images using latent discriminative models. Bioinformatics. 2012 Jun 15;28(12):i32-i39.

Badrane H, Nguyen MH, Blankenship JR§, Cheng S, Hao B, Mitchell AP*, Clancy CJ. Rapid redistribution of phosphatidylinositol-(4,5)-bisphosphate and septins during the Candida albicans response to caspofungin. Antimicrob Agents Chemother. 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.

Hovis KR§, Ramnath R, Dahlen JE, Romanova AL, Larocca G, Bier ME, Urban NN*. Activity regulates functional connectivity from the vomeronasal organ to the accessory olfactory bulb. J Neurosci. 2012 Jun 6;32(23):7907-16.

Subramanian A, Shackney S, Schwartz R*. Inference of tumor phylogenies from genomic assays on heterogeneous samples. J Biomed Biotechnol. 2012;2012:797812. Epub 2012 May 13.

Kim J, Hollinger JO*. Recombinant human bone morphogenetic protein-2 released from polyurethane-based scaffolds promotes early osteogenic differentiation of human mesenchymal stem cells. Biomed Mater. 2012 Jun 1;7(4):045008.

Barth AL*, Poulet JF. Experimental evidence for sparse firing in the neocortex. Trends Neurosci. 2012 May 12.

Oswald AM, Urban NN*. Interactions between Behaviorally Relevant Rhythms and Synaptic Plasticity Alter Coding in the Piriform Cortex. J Neurosci. 2012 May 2;32(18):6092-104.

Fanning S§, Xu W§, Solis N, Woolford CA, Filler SG, Mitchell AP*. Divergent targets of Candida albicans biofilm regulator Bcr1 in vitro and in vivo. Eukaryot Cell. 2012 Apr 27.

Ventura V, Gerkin RC§. Accurately estimating neuronal correlation requires a new spike-sorting paradigm. Proc Natl Acad Sci U S A. 2012 Apr 23.

Iordanova B§, Ahrens ET*. In vivo magnetic resonance imaging of ferritin-based reporter visualizes native neuroblast migration. Neuroimage. 2012 Jan 16;59(2):1004-12. Epub 2011 Sep 13.

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. 2012 Jan;67(1):278-89. doi: 10.1002/mrm.22998. Epub 2011 Jun 7.

Xu W, Mitchell AP*. Fungal morphogenesis: in hot pursuit. Curr Biol. 22(7):R225-7, 2012 Apr 10.

Fanning S§, Mitchell AP*. Fungal biofilms. PLoS Pathog. 8(4):e1002585, 2012 Apr. Epub 2012 Apr 5. No abstract available.

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]

Liu L, Ye Q, Wu Y, Hsieh WY, Chen CL, Shen HH, Wang SJ, Zhang H, Hitchens TK, Ho C*. Tracking T-cells in vivo with a new nano-sized MRI contrast agent. Nanomedicine. 2012 Nov;8(8):1345-54. doi: 10.1016/j.nano.2012.02.017. Epub 2012 Mar 7.

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.

Thevissen K, de Mello Tavares P, Xu D, Blankenship J§, Vandenbosch D, Idkowiak-Baldys J, Govaert G, Bink A, Rozental S, de Groot PW, Davis TR, Kumamoto CA, Vargas G, Nimrichter L, Coenye T, Mitchell A*, Roemer T, Hannun YA, Cammue BP. The plant defensin RsAFP2 induces cell wall stress, septin mislocalization and accumulation of ceramides in Candida albicans. Mol Microbiol. 2012 Mar 5. doi: 10.1111/j.1365-2958.2012.08017.x. [Epub ahead of print].

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

Alvarez P, Hee CK, Solchaga L, Snel L, Kestler HK, Lynch SE, Hollinger JO*. Growth factors and craniofacial surgery. J Craniofac Surg. 2012 Jan;23(1):20-9.

Jarvela T, Linstedt AD*. Irradiation-induced protein inactivation reveals Golgi enzyme cycling to cell periphery. J Cell Sci. 2012 Feb 15;125(Pt 4):973-80. doi: 10.1242/jcs.094441. Epub 2012 Mar 15..

Kadayakkara DK, Ranganathan S, Young WB, Ahrens ET*. Assaying macrophage activity in a murine model of inflammatory bowel disease using fluorine-19 MRI. Lab Invest. 2012 Feb 13. doi: 10.1038/labinvest.2012.7. [Epub ahead of print]

Finkel JS§, Xu W, Huang D, Hill EM, Desai JV, et al. (2012) Portrait of Candida albicans Adherence Regulators. PLoS Pathog 8(2): e1002525. doi:10.1371/journal.ppat.1002525

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

Minden JS*. DIGE: Past and Future. Methods Mol Biol. 2012;854:3-8.

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.

Lee B, Leduc PR, Schwartz R*. Three-dimensional stochastic off-lattice model of binding chemistry in crowded environments. PLoS One. 7(1):e30131, 2012. Epub 2012 Jan 17.

Mukhopadhyay S§, Linstedt AD*. Manganese Blocks Intracellular Trafficking of Shiga Toxin and Protects Against Shiga Toxicosis. Science. 335(6066): 332-335, 20 January 2012.

Barth AL*. AC-1 and synaptic development. J Physiol. 2012 Jan 1;590(Pt 1):3.

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

Ahrens ET*, Young WB, Xu H, Pusateri LK. Rapid quantification of inflammation in tissue samples using perfluorocarbon emulsion and fluorine-19 nuclear magnetic resonance. Biotechniques. 50(4):229-34, 2011 Apr.

Argimon S, Fanning S§ , Blankenship JR§, Mitchell AP*. Interaction between the Candida albicans High-Osmolarity Glycerol (HOG) Pathway and the Response to Human {beta}-defensins 2 and 3. Eukaryot Cell. 10(2):272-5, 2011 Feb. Epub 2010 Dec 3.

Bartoli KM, Jakovljevic J, Woolford JL Jr*, Saunders WS. Kinesin Molecular Motor Eg5 Functions during Polypeptide Synthesis. Mol Biol Cell. 2011 Jul 27. [Epub ahead of print]

Baudin-Creuza V, Ho C*, Marden MC. Hb Octamers by Introduction of Surface Cysteines, in Chemistry and Biochemistry of Oxygen Therapeutics:  From Transfusion to Artificial Blood  edited by Stefano Bettati and Andrea Mozzarelli, First Edition, John Wiley & Sons, Ltd., pp. 371-380, 2011.

Blankenship JR§, Mitchell AP*. Candida albicans Adds More Weight to Iron Regulation. Cell Host Microbe. 2011 Aug 18;10(2):93-4.

Bonetto F, Srinivas M, Heerschap A, Mailliard R, Ahrens ET*, Figdor CG, de Vries IJ. A novel (19)F agent for detection and quantification of human dendritic cells using magnetic resonance imaging. Int J Cancer. 2011 Jul 15;129(2):365-73. doi: 10.1002/ijc.25672. Epub 2010 Nov 3.

Brillet T, Baudin-Creuza V, Kettering R, Yeh JI, Shen, TJ, Ho NT,  Vasseur C, Domingues E, Ho C*, Marden MC. Interaction of Haptoglobin with Hemoglobin Octamers Based on the Mutation αAsn78Cys or βGly83Cys. American Journal of Molecular Biology, in press (2011).

Bruchez MP*. Quantum Dots Find Their Stride in Single Molecule Tracking. Current Opinion in Chemical Biology 2011. In press.

Cao W, Coman MM, Ding S, Henn A, Middleton ER, Bradley MJ, Rhoades E, Hackney DD*, Pyle AM, De La Cruz EM. Mechanism of Mss116 ATPase Reveals Functional Diversity of DEAD-Box Proteins. J. Mol. Biol. 409, 399-414, 2011.

Chen C-L, Zhang H, Ye Q, Hsieh W-Y, Hitchens TK, Shen H-H, Liu L, Wu Y-J, Foley LM, Wang S-J, Ho C*. A New Nano-Sized Iron Oxide Particle with High Sensitivity for Cellular Magnetic Resonance Imaging. Molecular Imaging & Biology 2011; 13, 825-839.

Cho HY, Srinivasan A, Hong J, Hsu E, Liu S, Shrivats A, Kwak D, Bohaty AK, Paik HJ, Hollinger JO*, Matyjaszewski K. Synthesis of Biocompatible PEG-Based Star Polymers with Cationic and Degradable Core for siRNA Delivery. Biomacromolecules. 2011 Oct 10;12(10):3478-86. Epub 2011 Sep 6.

Dagley MJ, Gentle IE, Beilharz TH, Pettolino FA, Djordjevic JT, Lo TL, Uwamahoro N, Rupasinghe T, Tull DL, McConville M, Beaurepaire C, Nantel A, Lithgow T, Mitchell AP, Traven A. Cell wall integrity is linked to mitochondria and phospholipid homeostasis in Candida albicans through the activity of the post-transcriptional regulator Ccr4-Pop2. Mol Microbiol. 79(4):968-989, 2011 Feb. Epub 2010 Dec 30.

Dahlen JE, Jimenez DA, Gerkin RC, Urban NN. Morphological analysis of activity-reduced adult-born neurons in the mouse olfactory bulb. Front Neurosci. 5:66, 2011. Epub 2011 May 9.

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 6, e16218, 2011.

Ettensohn CA. Linking developmental gene regulatory networks to morphogenesis. Genesis, 2011, in press.

Finkel JS, Mitchell AP. Genetic control of Candida albicans biofilm development. Nat Rev Microbiol. 9(2):109-18, 2011 Feb. Epub 2010 Dec 29.

Finkel JS§, Yudanin N, Nett JE, Andes DR, Mitchell AP*. Application of the systematic "DAmP" approach to create a partially defective C. albicans mutant. Fungal Genet Biol. 48, 1056-1061, 2011 Jul 27.

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 Jun 29. [Epub ahead of print].

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, 14, 380-385. 2011 Jul 7.

Giridhar S, Doiron B, Urban NN*. Timescale-dependent shaping of correlation by olfactory bulb lateral inhibition. Proc Natl Acad Sci USA.;108(14):5843-8, 2011 Apr 5. Epub 2011 Mar 21.

Hitchens TK, Ye Q, Eytan DF, Janjic JM, Ahrens ET, Ho C. (19) F MRI detection of acute allograft rejection with in vivo perfluorocarbon labeling of immune cells. Magn Reson Med. 2011 Feb 8, 65, 11-45-1154.

Iordanova B§, Ahrens ET*. In vivo magnetic resonance imaging of ferritin-based reporter visualizes native neuroblast migration. Neuroimage. 2011 Sep 13.

Jackson C, Glory E, Murphy RF*, Kovacevic J. Model building and intelligent acquisition with application to protein subcellular location classification. Bioinformatics 27:1854-1859, 2011.

Kaan HY, Hackney DD*, Kozielski F. The structure of the kinesin-1 motor-tail complex reveals the mechanism of autoinhibition. Science. 333(6044):883-5, 2011 Aug 12.

Kadri S, Hinman V*, Benos PV. RNA Deep sequencing reveals differential microRNA expression during development of the sea urchin and sea star. PLOS ONE, in press.

Kang J, Steward R, Schwartz R*, Leduc PR*, Puskar K. Controlled response of actin filament networks under cyclic stress through a coarse grained Monte Carlo model. Journal of Theoretical Biology, 274:109-119, 2011.

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.

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Kim J, Magno MH, Alvarez P, Darr A, Kohn J, Hollinger JO*. Osteogenic differentiation of pre-osteoblasts on biomimetic tyrosine-derived polycarbonate scaffolds .Biomacromolecules. 2011 Oct 10;12(10):3520-7. Epub 2011 Sep 12.

Kim J, Sharma A, Runge B, Waters H, Doll B, McBride S, Alvarez P, Dadsetan M, Yaszemski MJ, Hollinger JO*. Osteoblast growth and bone-healing response to three-dimensional poly(ε-caprolactone fumarate) scaffolds. J Tissue Eng Regen Med. 2011 Jul 11.

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Lee B§, LeDuc PR*, Schwartz R*. Unified regression model of binding equilibria in crowded environments. Scientific Reports, 1:97, 2011.

Lim JK, Lanni C, Evarts ER, Lanni F*, Tilton RD, Majetich SA.  Magnetophoresis of nanoparticles. ACS Nano 5: 217-226, 2011.

Lin T, Bar-Joseph Z*, Murphy RF*. Learning Cellular Sorting Pathways Using Protein Interactions and Sequence Motifs. Journal of Computational Biology, 2011, in press.

Lin TH, Murphy RF, Bar-Joseph Z. Discriminative motif finding for predicting protein subcellular localization. IEEE/ACM Trans Comput Biol Bioinform. 8(2):441-51, 2011 Mar-Apr.

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Micheva KD, Bruchez MP*. The gain in brain: novel imaging techniques and multiplexed proteomic imaging of brain tissue ultrastructure. Current Opinion in Neurobiology, 2011.

Miller GL, Peng R, Schwartz R*, Tsourakakis C. Approximate dynamic programming using halfspace queries and multiscale Monge decomposition. ACM Symposium on Discrete Algorithms (SODA2011), 1675-1682, 2011.

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.

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Misra N, Blelloch G, Ravi R, Schwartz R*. An optimization-based sampling scheme for phylogenetic trees. Journal of Computational Biology, in press, 2011. (extended version of RECOMB 2011 conference paper)

Misra N, Blelloch G, Ravi R, Schwartz R. Generalized buneman pruning for inferring the most parsimonious multi-state phylogeny. J Comput Biol. 18(3):445-57, 2011 Mar.

Mittal R, Bruchez MP*. Biotin-4-Fluorescein Based Fluorescence Quenching Assay for Determination of Biotin Binding Capacity of Streptavidin Conjugated Quantum Dots. Bioconjugate Chemistry 2011.

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Mukhopadhyay S, Linstedt AD. Identification of a gain-of-function mutation in a Golgi P-type ATPase that enhances Mn2+ efflux and protects against toxicity. Proc Natl Acad Sci U S A. 2011 Jan 11;108(2):858-63. Epub 2010 Dec 27.

Murphy RF*. An active role for machine learning in drug development. Nat Chem Biol. 7(6):327-30, 2011 Jun.

Murphy RF* CellOrganizer: Image-derived Models of Subcellular Organization and Protein Distribution. Methods in Cell Biology, 2011, in press.

Nimgaonkar VL, Chowdari KV, Prasad KM, Watson A, Mansour H, Wood JA, Lopez AJ*. What can be learned from nominally significant/discrepant associations? An illustration using dopamine gene variants and schizophrenia. in “Schizophrenia: The Final Frontier”. Edited by A.S. David, S. Kapur and P. McGuffin. Taylor and Francis Ltd., 2011. ISBN-13: 978-1848720770.

Peng T, Murphy RF*. Image-derived, Three-dimensional Generative Models of Cellular Organization. Cytometry Part A 79A:383-391, 2011.

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

Rao A and Murphy RF*. Determination of Protein Location Diversity Via Analysis of Immunohistochemical Images from the Human Protein Atlas. Proceedings of the 2011 IEEE International Symposium on Biomedical Imaging  (ISBI 2011), 1727-1729, 2011.

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.

Shariff A, Murphy RF*, Rohde GK. Automated Estimation of Microtubule Model Parameters from 3-D Live Cell Microscopy Images. Proc IEEE Int Symp Biomed Imaging. 2011 Jun 9;2011(March 30 2011-April 2 2011):1330-1333.

Sharma T, Ettensohn CA. Regulative deployment of the skeletogenic gene regulatory network during sea urchin development. Development. 138(12):2581-90, 2011 Jun.

Sinha K, Jen-Jacobson L, Rule G*. Site-Specific Labeling of Threonine Methyl Groups for NMR Studies of Protein-Nucleic Acid Complexes. Biochemistry, 2011, in press.

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.

Tiso M, Tejero J, Basu S, Azarov I, Wang X, Simplaceanu V, Frizzell S, Jayaraman T, Geary L, Shapiro C, Ho C*, Shiva S, Kim-Shapiro DB, Gladwin MT. Human Neuroglobin Functions as a Redox-regulated Nitrite Reductase. Journal of Biological Chemistry 2011; 286, 18277-18289.

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 Jun 10;286(23):20125-9. Epub 2011 Apr 22.

Tsai MC, Blelloch G, Ravi R, Schwartz R*. A consensus tree approach for reconstructing human evolutionary history and detecting population substructure. IEEE/ACM Trans Comput Biol Bioinform. 8(4):918-28, 2011 Jul-Aug.

Tsourakakis CE, Peng R, Tsiarli MA, Miller GL, Schwartz R*. Approximation algorithms for speeding up dynamic programming and denoising aCGH data. Journal of Experimental Algorithmics, accepted for publication, 2011.

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.

Wren NS, Schwartz R*, Dahl KN*. Modeling nuclear blebs in a nucleoskeleton of independent filament networks. Cellular and Molecular Bioengineering, accepted for publication, 2011.

Wu YJL, Ye Q, Zhang H, Hitchens TK, Ho C*. Other Non-Stem Cell Therapies for Cellular Tracking – Inflammatory Cell Tracking in Stem Cell Labeling for Delivery and Tracking Using Non-Invasive Imaging, edited by Dara L. Kraitchman and Joseph C. Wu, Taylor & Francis Group, in press, 2011.

Wu YL, Ye Q, Ho C. Cellular and Functional Imaging of Cardiac Transplant Rejection. Curr Cardiovasc Imaging Rep. 4(1):50-62, 2011 Feb 1.

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

Yuan Y, Shen T-J, Gupta P, Ho NT, Simplaceanu V, Tam TCS, Hofreiter M, Cooper A, Campbell KL, Ho C*. A Biochemical-Biophysical Study of Hemoglobins from Woolly Mammoth, Asian Elephant, and Humans. Biochemistry. 2011 Aug 2.

Zanotti KJ, Silva GL, Creeger Y, Robertson KL, Waggoner AS*, Berget PB*, Armitage BA*. Blue fluorescent dye-protein complexes based on fluorogenic cyanine dyes and single chain antibody fragments. Org Biomol Chem. 2011 Feb 21;9(4):1012-20. Epub 2010 Dec 22.

Zhou M-N, 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.

Bachert C, Linstedt AD*. Dual anchoring of the GRASP membrane tether promotes trans pairing. J Biol Chem. 285: 16294-16301, 2010.

Bermejo GA, Strub MP, Ho C*. Ligand-free Open-closed Transitions of Periplasmic Binding Proteins:  The Case of Glutamine-binding Protein.  Biochemistry 2010; 49, 1893-1902.

Blankenship JR§, Fanning S§, Hamaker JJ, Mitchell AP*. An extensive circuitry for cell wall regulation in Candida albicans. PLoS Pathog 6:e1000752, 2010.

Boysen JH, Subramanian S§, Mitchell AP*. Intervention of Bro1 in pH-responsive Rim20 localization in Saccharomyces cerevisiae. Eukaryot Cell 9:532-8, 2010.

Campbell KL, Roberts JEE, Watson LN, Stetefeld J, Sloan AM, Signore AV, Howatt JW, Tame JRH, Rohland N, Shen T-J, Austin JJ, Hofreiter M, Ho C*, Weber RE, Copper A. Substitutions in Woolly Mammoth Hemoglobin Confer Biochemical Properties Adaptive for Cold Tolerance. Nature Genetics 42, 536-540, 2010.

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.

Cho HY, Gao H, Srinivasan A, Hong J, Bencherif SA, Siegwart DJ, Paik HJ, Hollinger JO*, Matyjaszewski K. Rapid cellular internalization of multifunctional star polymers prepared by atom transfer radical polymerization. Biomacromolecules. 2010 Sep 13;11(9):2199-203.

Coelho LP, Ahmed A, Arnold A, Kangas J, Sheikh AS, Xing EP, Cohen WW, Murphy RF*. Structured Literature Image Finder: Extracting Information from Text and Images in Biomedical Literature. Lect Notes Comput Sci. 2010;6004:23-32.

Coelho LP, Peng T, Murphy RF*. Quantifying the distribution of probes between subcellular locations using unsupervised pattern unmixing. Bioinformatics 26:i7-i12, 2010.

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Dykstra KM, Pokusa JE, Suhan J, Lee TH*. Yip1A structures the mammalian endoplasmic reticulum. Mol Biol Cell. 2010 May 1;21(9):1556-68. Epub 2010 Mar 17.

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Foley LM, Hitchens TK, Barbe B, Zhang F, Ho C*, Rao GR, Nemoto EM. Quantitative Temporal Profiles of Penumbra and Infarction During Permanent Middle Cerebral Artery Occlusion in Rats. Transl Stroke Res. 1(3):220-229, 2010 Sep 1.

Franke JD§. Approaches for using animal models to identify loci that genetically interact with human disease-causing point mutations. Methods Mol Biol. 634:203-13, 2010.

Fuchs BB, Eby J, Nobile CJ, El Khoury JB, Mitchell AP*, Mylonakis E. Role of filamentation in Galleria mellonella killing by Candida albicans. Microbes Infect 12, 488-496, 2010.

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Glory-Afshar E, Osuna-Highley E, Granger B, Murphy RF*. A Graphical Model to Determine the Subcellular Protein Location in Artificial Tissues. Proc IEEE Int Symp Biomed Imaging. 2010:1037-1040, 2010 Apr.

Gong H, Guo Y, Linstedt AD*, Schwartz R*. Discrete, continuous, and stochastic models of protein sorting in the Golgi. Physical Review E, 81(1):011914, 2010.

Goodman A, Bajzek D, Rule G*. Advantages and Challenges in Adopting Open Learning Initiative (OLI) materials to Supplement a Lecture Course in Biochemistry: Instructor’s Perspective. In Proceedings of World Conference on Educational Multimedia, Hypermedia and Telecommunications 2010 (pp. 1705-1708), 2010. Chesapeake, VA: AACE.

Goodman A, Bajzek D, Rule G*. Using Online Materials to Supplement a Lecture Course in Biochemistry: Student Attitudes and Student Success. In Proceedings of World Conference on Educational Multimedia, Hypermedia and Telecommunications 2010 (pp. 1709-1712), 2010. Chesapeake, VA: AACE.

Hackney DD*. When is weaker better? Design of an ADP sensor with weak ADP affinity, but still selective against ATP. ACS Chem Biol. 5(4):353-4, 2010 Apr 16.

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Henn A, Cao W, Licciardello N, Heitkamp SE, Hackney DD*, De La Cruz EM. Pathway of ATP Utilization and Duplex RRNA Unwinding by the DEAD-Box Helicase, DbpA. Proc. Natl. Acad. Sci. U. S. A. 107, 4046-4050, 2010.

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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.

Hu Y, Garcia Osuna E, Hua J, Nowicki TS, Stolz R, McKayle C, Murphy RF*. Automated Analysis of Protein Subcellular Locations in Time Series Images. Bioinformatics 26:1630-1636, 2010.

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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. 15(6): 957-965, 2010.

Kadayakkara DK, Beatty PL, Turner M, 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): 510-515, 2010.

Kadayakkara DKK, Janjic JM, Pusateri LB, 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. Magn. Reson. Med. 64(5): 1252-1259, 2010.

Kucerka N, Katsaras J, Nagle JF*. Comparing Membrane Simulations to Scattering Experiment: Introducing SIMtoEXP Software. J. Memb. Biol. 235, 43-50, 2010.

Kumar MS, Schwartz R*. A parameter estimation technique for stochastic self-assembly systems and its application to human papillomavirus self-assembly. Phys Biol. 2010 Dec 9;7(4):045005.

Lancia G, Rizzi R, Schwartz R*. Tiling Binary Matrices in Haplotyping: Complexity, Models and Algorithms. Proceedings of the Prague Stringology Conference (PSC 2010), pp. 89-102, 2010.

Lin T, Murphy RF*, Bar-Joseph Z*. Discriminative Motif Finding for Predicting Protein Subcellular Localization. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2010, in press.

Luo G, Ibrahim AS, Spellberg B, Nobile CJ, Mitchell AP*, Fu Y. Candida albicans Hyr1p confers resistance to neutrophil killing and is a potential vaccine target. J Infect Dis 201:1718-28, 2010.

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Monzo K, Dowd SR, Minden JS*, Sisson JS. Proteomic analysis reveals CCT is a target of Fragile X mental retardation protein regulation in Drosophila. Dev. Biol. 16, 2891-902, 2010.

Mukhopadhyay S§, Bachert C, Smith D, Linstedt AD*. Manganese-induced trafficking and turnover of the cis Golgi glycoprotein GPP130. Mol. Biol. of the Cell, 21: 1282-1292, 2010.

Murphy RF*. Communicating Subcellular Distributions. Cytometry Part A 77A:686-692, 2010.

Padmanabhan K§, Eddy WF*, Crowley JC*. A novel algorithm for optimal image thresholding of biological data. J Neurosci Methods. 2010 Nov 30;193(2):380-4. Epub 2010 Sep 15.

Padmanabhan K§, Urban NN*. Intrinsic biophysical diversity decorrelates neuronal firing while increasing information content. Nat Neurosci. 13(10):1276-82, 2010 Oct. Epub 2010 Aug 29.

Park S, Cho HY, Yoon JA, Kwak Y, Srinivasan A, Hollinger JO*, Paik HJ, Matyjaszewski K. Photo-cross-linkable thermoresponsive star polymers designed for control of cell-surface interactions. Biomacromolecules. 11(10):2647-52, 2010 Oct 11.

Peng T, Bonamy GMC, Glory-Afshar E, Rines DR, Chanda SK, Murphy RF*. Determining the distribution of probes between different subcellular locations through automated unmixing of subcellular patterns. Proc. Natl. Acad. Sci. U.S.A. 107:2944-2949, 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. 143(5):761-73, 2010 Nov 24.

Ribeiro AS, Dahl KN. The nucleus as a central structure in defining the mechanical properties of stem cells. Conf Proc IEEE Eng Med Biol Soc. 2010;1:831-4.

Rule GS*, Kessler A, Bajzek D. Molecular Visualization in STEM Education: Leveraging Jmol in an Integrated Assessment Platform. In Proceedings of World Conference on E-Learning in Corporate, Government, Healthcare, and Higher Education 2010. Chesapeake, VA: AACE.

Schwartz R*, Shackney S. Applying unmixing to gene expression data for tumor phylogeny inference. BMC Bioinformatics, 11:42, 2010.

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.

Shariff A, Kangas J, Coelho LP, Quinn S, Murphy RF*. Automated image analysis for high-content screening and analysis. J Biomol Screen. 726-34, 2010 Aug;15(7). Epub 2010 May 20.

Shariff A, Murphy RF*, Rohde GK. A generative model of microtubule distributions, and indirect estimation of its parameters from fluorescence microscopy images. Cytometry A. 77(5):457-66, 2010 May.

Shariff A, Rohde GK, Murphy RF*. A Generative Model of Microtubule Distributions, and Indirect Estimation of its Parameters from Fluorescence Microscopy Images. Cytometry 77A:457-466, 2010.

Sharma T, Ettensohn CA*. Activation of the skeletogenic gene regulatory network in the early sea urchin embryo. Development 137, 1149-1157, 2010.

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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.

Szent-Gyorgyi C, Schmidt BF, Fitzpatrick JAJ, Bruchez MP*. Fluorogenic Dyedrons with Multiple Donor Chromophores as Bright Genetically Targeted and Activated Probes. Journal of the American Chemical Society, 2010.

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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.

Tristram-Nagle S, Chan R, Kooijman E, Uppamoochikkal P, Qiang W, Weliky DP, Nagle JF*. HIV fusion peptide penetrates, disorders, and softens T-cell membrane mimics. J Mol Biol. 402(1):139-53, 2010 Sep 10. Epub 2010 Jul 22.

Tristram-Nagle S, Kim DJ, Akhunzada N, Kucerka N, Mathai JC, Katsaras J, Zeidel M, Nagle JF*. Structure and water permeability of fully hydrated diphytanoylPC. Chem. Phys. Lipids 163, 630-637, 2010.

Uppamoochikkal P, Tristram-Nagle S, Nagle JF*. Orientation of tie-lines in the phase diagram of DOPC/DPPC/cholesterol model biomembranes. Langmuir. 26(22):17363-8, 2010 Nov 16. Epub 2010 Oct 22.

Urban NN*, Castro JB. Functional polarity in neurons: what can we learn from studying an exception? Curr Opin Neurobiol. 20(5):538-42, 2010 Oct. Epub 2010 Aug 17.

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.

Yuan Y, Simplaceanu V, Ho NT, Ho C*. An Investigation of the Distal Histidyl H-bonds in Oxyhemoglobin: Effects of Temperature, pH, and Organic Phosphate. Biochemistry 49, 10606-10615, 2010. Selected by the Library of Faculty of 1000

Zanotti KJ, Silva GL, Creeger Y, Robertson KL, Waggoner AS*, Berget PB*, Armitage BA*. Blue fluorescent dye-protein complexes based on fluorogenic cyanine dyes and single chain antibody fragments. Org Biomol Chem. 9(4):1012-20, 2011. Epub 2010 Dec 22.

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Bencherif SA, Siegwart DJ, Srinivasan A, Horkay F, Hollinger JO*, Washburn NR, Matyjaszewski K. Nanostructured hybrid hydrogels prepared by a combination of atom transfer radical polymerization and free radical polymerization. Biomaterials. 30(29):5270-8, 2009 Oct. Epub 2009 Jul 9.

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Benedetti BL, Glazewski S, Barth AL*. Sensory plasticity improves spike timing precision and reliability in the neocortex. Journal of Neuroscience 29(38):11817-27, 2009.

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Castro JB, Urban NN*. Subthreshold Glutamate Release from Mitral Cell Dendrites. J. Neurosci. 29(21):7023-30, 2009 May 27.

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Chang HH, Moura JM, Wu YL, Ho C*.  Automatic Detection of Regional Heart Rejection in USPIO-Enhanced MRI. IEEE Transactions on Medical Imaging 2008; 27,1095-1106.

Coelho LP, Shariff A, Murphy RF*. Nuclear Segmentation in Microscope Cell Images: A hand-segmented Dataset and Comparison of Algorithms. Proc IEEE Int Symp Biomed Imaging. 5193098:518-521, 2009.

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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.

Peng T, Wang W, Rohde GK, Murphy RF*. Instance-Based Generative Biological Shape Modeling. Proc IEEE Int Symp Biomed Imaging. 2009;5193141:690-693.

Poll G, Braun T, Jakovljevic J, Neueder A, Jakob S, Woolford Jr JL*, Tschochner H, Milkereit P. rRNA maturation in yeast cells depleted of large ribosomal subunit proteins. PLOS One 4: e8249, 2009.

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Mills TT, Toombes GE, Tristram-Nagle S, Smilgies DM, Feigenson GW, Nagle JF*. Order parameters and areas in fluid-phase oriented lipid membranes using wide angle X-ray scattering. Biophys J, 95(2):669-81, 2008 Jul. Epub 2008 Apr 4.

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Newberg J, Murphy RF*. A Framework for the Automated Analysis of Subcellular Patterns in Human Protein Atlas Images. J. Proteome Res. 7: 2300-2308, 2008.

Nobile CJ, Schneider HA, Nett JE, Sheppard DC, Filler SG, Andes DR, Mitchell AP*. Complementary adhesin function in C. albicans biofilm formation. Curr Biol 18:1017-24, 2008.

Nobile CJ, Solis N, Myers CL, Fay AJ, Deneault JS, Nantel A, Mitchell AP*, Filler SG. Candida albicans transcription factor Rim101 mediates pathogenic interactions through cell wall functions. Cell Microbiol 10:2180-96, 2008.

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Phillippi JA, Miller E, Weiss L, Huard J, Waggoner A*, Campbell P*. Microenvironments engineered by inkjet bioprinting spatially direct adult stem cells toward muscle- and bone-like subpopulations. Stem Cells 26(1):127-34, 2008.

Puri M, Goyal A, Senutovich N, Dowd SR, Minden JS*. Building proteomic pathways using Drosophila ventral furrow formation as a model. Mol. Biosystems 4, 1126-35, 2008.

Qian Y, Murphy RF*. Improved recognition of figures containing fluorescence microscope images in online journal articles using graphical models. Bioinformatics. 24(4):569-76, 2008 Feb 15. Epub 2007 Nov 22.

Qui H, Eifert J, Wacheul L, Thiry M, Berger A, Jakovljevic J, Woolford Jr JL*, Corbett A, Lafontaine DLJ, Terns RM, Terns MP. Identification of Genes That Function In the Biogenesis and Localization of Small Nucleolar RNAs in Saccharomyces cerevisiae. Molecular and Cellular Biology, 28:3686-3699, 2008.

Raghupathy N, Hoberman R, Durand D*. Two plus two does not equal three: Statistical tests for multiple genome comparison. Journal of Bioinformatics and Computational Biology, 6(1): 1-22, 2008.

Rauceo JM, Blankenship JR§, Fanning S§, Hamaker JJ, Deneault JS, Smith FJ, Nantel A, Mitchell AP*. Regulation of the Candida albicans cell wall damage response by transcription factor Sko1 and PAS kinase Psk1. Mol Biol Cell 19:2741-51, 2008.

Rohde GK, Ribeiro A, Dahl KN*, Murphy RF*. Deformation-based nuclear morphometry: capturing nuclear shape variation in HeLa Cells. Cytometry, 73A:341-350, 2008.

Shruti S, Clem RL, Barth AL*. A seizure-induced gain-of-function in BK channel is associated with elevated firing activity in neocortical pyramidal neurons. Neurobiology of Disease, 30(3):323-30, 2008.

Siegwart DJ, Bencherif SA, Srinivasan A, Hollinger JO*, Matyjaszewski K. Synthesis, characterization, and in vitro cell culture viability of degradable poly(N-isopropylacrylamide-co-5,6-benzo-2-methylene-1,3-dioxepane)-based polymers and crosslinked gels. J Biomed Mater Res A. 87(2):345-58, 2008 Nov.

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Song XJ§, Simplaceanu V, Ho NT, Ho C*. Effector-Induced Structure Fluctuation Regulates the Ligand Affinity of an Allosteric Protein: Binding of Inositol Hexaphosphate Has Distinct Dynamic Consequences for the T and R States of Hemoglobin. Biochemistry 47:4907-4915, 2008.

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Blankenship JR§, Mitchell AP*. The fungal frontier. Genome Biol. 8(5):305, 2007.

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Chen SC, Zhao T, Gordon GJ, Murphy RF*. Automated image analysis of protein localization in budding yeast. Bioinformatics. 23(13):i66-71, 2007 Jul 1.

Chiang LY, Sheppard DC, Bruno VM, Mitchell AP*, Edwards JE Jr, Filler SG. Candida albicans protein kinase CK2 governs virulence during oropharyngeal candidiasis. Cell Microbiol 9, 233-245, 2007.

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Ermentrout GB, Galán RF, Urban NN*. Relating neural dynamics to neural coding. Physical Review Letters. Physical Review Letters. 99. 248103, 2007. Faculty of 1000 Must Read.

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Fu H, Doll B, McNelis T, Hollinger JO*. Osteoblast differentiation in vitro and in vivo promoted by Osterix. J Biomed Mater Res A. 83(3):770-8, 2007 Dec 1.

Galán RF, Ermentrout GB, Urban NN*. Reliability and stochastic synchronization in type I vs. type II neural oscillators. Neurocomputing, 70: 2102-2106, 2007.

Galán RF, Ermentrout GB, Urban NN*. Stochastic dynamics of uncoupled neural oscillators: Fokker Planck studies with the finite element method. Physical Review E. 76(5 Pt 2):056110, 2007.

García Osuna E, Hua J, Bateman NW, Zhao T, Berget PB*, Murphy RF*. Large-scale automated analysis of location patterns in randomly tagged 3T3 cells. Ann Biomed Eng. 35(6):1081-7, 2007 Jun. Epub 2007 Feb 7.

García Osuna E, Murphy RF*. Automated, systematic determination of protein subcellular location using fluorescence microscopy. Subcell Biochem. 2007;43:263-76.

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Glory E, Murphy RF*. Automated subcellular location determination and high-throughput microscopy. Dev Cell. 12(1):7-16, 2007 Jan. Review. No abstract available.

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Hinman VF*, Nguyen A, Davidson EH. Caught in the evolutionary act: precise cis-regulatory basis of difference in organization of gene networks of sea stars and sea urchins. Developmental Biology; 312(2):584-95, 2007.

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LeDuc P, Schwartz R*. Computational models of molecular self-organization in cellular environments. Cell Biochem Biophys. 48(1):16-31, 2007.

Leonard J, Ettensohn CA*. Analysis of dishevelled localization and function in the early sea urchin embryo. Dev. Biol., 306, 50-65, 2007.

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Minden JS*. Comparative Proteomics and Difference Gel Electrophoresis. BioTechniques 43, 739-745, 2007.

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Nauman JV, Campbell PG, Lanni F*, Anderson JL. Diffusion of insulin-like growth factor-I and ribonuclease through fibrin gels. Biophys. J. 92:4444-4450, 2007.

Nobile CJ, Mitchell AP*. Microbial biofilms: e pluribus unum. Curr Biol. 17(10):R349-53, 2007 May 15.

Norice CT, Smith FJ Jr, Solis N, Filler SG, Mitchell AP*. Requirement for Candida albicans Sun41 in biofilm formation and virulence. Eukaryot Cell. 6(11):2046-55, 2007 Nov. Epub 2007 Sep 14.

Oh JK, Siegwart DJ, Lee HI, Sherwood G, Peteanu L, Hollinger JO*, Kataoka K, Matyjaszewski K. Biodegradable nanogels prepared by atom transfer radical polymerization as potential drug delivery carriers: synthesis, biodegradation, in vitro release, and bioconjugation. J Am Chem Soc. 129(18):5939-45, 2007 May 9. Epub 2007 Apr 18.

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Pfenning AR, Schwartz R*, Barth AL*. A comparative genomics approach to identifying the plasticity transcriptome. BMC Neurosci. 8:20, 2007 Mar 13.

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Shaw RM, Fay AJ, Puthenveedu MA*, von Zastrow M, Jan YN, Jan LY. Microtubule plus-end-tracking proteins target gap junctions directly from the cell interior to adherens junctions. Cell. 128(3):547-60, 2007 Feb 9.

Shen T-J, Rogers H, Yu X, Lin F, Noguchi CT, Ho C*. Modification of Globin Gene Expression by RNA Targeting Strategies. Experimental Hematology 35, 1209-1218, 2007.

Smith JD, Chen A, Ernst LA, Waggoner AS*, Campbell PG*. Immobilization of aprotinin to fibrinogen as a novel method for controlling degradation of fibrin gels. Bioconjug Chem. 18(3):695-701, 2007 May-Jun. Epub 2007 Apr 14.

Smith JD, Fisher GW, Waggoner AS*, Campbell PG*. The use of quantum dots for analysis of chick CAM vasculature. Microvasc Res. 73(2):75-83, 2007 Mar. Epub 2006 Oct 27.

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Sridhar S, Dhamdhere K, Blelloch G, Halperin E, Ravi R, Schwartz R*. Algorithms for efficient near-perfect phylogenetic tree reconstruction in theory and practice. IEEE/ACM Trans Comput Biol Bioinform. 4(4):561-71, 2007 Oct-Dec.

Sridhar S, Lam F, Blelloch GE, Ravi R, Schwartz R*. Direct maximum parsimony phylogeny reconstruction from genotype data. BMC Bioinformatics. 8:472, 2007 Dec 5.

Srinivas M, Morel PA, Ernst LA, Laidlaw DH, Ahrens ET*. Fluorine-19 MRI for visualization and quantification of cell migration in a diabetes model. Magn Reson Med, 58(4):725-734, 2007 Oct.

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Villar CC, Kashleva H, Nobile CJ, Mitchell AP*, Dongari-Bagtzoglou, A. Mucosal tissue invasion by Candida albicans is associated with E-cadherin degradation, mediated by transcription factor Rim101p and protease Sap5p. Infect Immun 75, 2126-2135, 2007.

Williams JB§, Ye Q, Hitchens TK, Kaufman CL, Ho C*. MRI detection of macrophages labeled using micrometer-sized iron oxide particles. J Magn Reson Imaging. 25(6):1210-8, 2007 Jun.

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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.

Zhang J, Harnpicharnchai P, Jakovljevic J, Tang L, Guo Y, Oeffinger M, Rout MP, Hiley SL, Hughes T, Woolford JL Jr*. Assembly factors Rpf2 and Rrs1 recruit 5S rRNA and ribosomal proteins rpL5 and rpL11 into nascent ribosomes. Genes Dev. 21(20):2580-92, 2007 Oct 15.

Zhao T, Murphy RF*. Automated Learning of Generative Models for Subcellular Location: Building Blocks for Systems Biology. Cytometry 71A:978-990, 2007.

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Blankenship JR, Mitchell AP*. How to build a biofilm: a fungal perspective. Current opinion in microbiology 9, 588-594, 2006.

Boysen JH, Mitchell AP*. Control of Bro1-domain protein Rim20 localization by external pH, ESCRT machinery, and the Saccharomyces cerevisiae Rim101 pathway. Mol Biol Cell. 17(3):1344-53, 2006 Mar. Epub 2006 Jan 11.

Bruno VM, Kalachikov S, Subaran R, Nobile CJ, Kyratsous C, Mitchell AP*. Control of the C. albicans cell wall damage response by transcriptional regulator Cas5. PLoS Pathog. 2(3):e21, 2006 Mar. Epub 2006 Mar 17.

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Chang HH, Moura JM, Wu YL, Ho C*. Immune cells detection of the in vivo rejecting heart in USPIO-enhanced magnetic resonance imaging. IEEE Eng Med Biol Soc. 1:942-5, 2006.

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Chen X, Velliste M, Murphy RF*. Automated interpretation of subcellular patterns in fluorescence microscope images for location proteomics. Cytometry A. 69(7):631-40, 2006 Jul.

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Morohashi N, Yamamoto Y, Kuwana S, Morita W, Shindo H, Mitchell AP*, Shimizu M. Effect of sequence-directed nucleosome disruption on cell-type-specific repression by alpha2/Mcm1 in the yeast genome. Eukaryot Cell 5, 1925-1933, 2006.

Mukherjee PK, Mohamed S, Chandra J, Kuhn D, Liu S, Antar OS, Munyon R, Mitchell AP*, Andes D, Chance MR, et al. Alcohol dehydrogenase restricts the ability of the pathogen Candida albicans to form a biofilm on catheter surfaces through an ethanol-based mechanism. Infect Immun 74, 3804-3816, 2006.

Munshi R, Coalson RD, Ermentrout GB, Madura JD, Meirovitch H, Stiles JR*, Bahar I. An introduction to simulation and visualization of biological systems at multiple scales: a summer training program for interdisciplinary research. Biotechnol Prog. 22(1):179-85, 2006 Jan-Feb.

Nobile CJ, Andes DR, Nett JE, Smith FJ, Yue F, Phan QT, Edwards JE, Filler SG, Mitchell AP*. Critical role of Bcr1-dependent adhesins in C. albicans biofilm formation in vitro and in vivo. PLoS Pathog. 2(7):e63, 2006 Jul.

Nobile CJ, Mitchell AP*. Genetics and genomics of Candida albicans biofilm formation. Cell Microbiol. 8(9):1382-91, 2006 Sep. Epub 2006 Jul 11.

Nobile CJ, Nett JE, Andes DR, Mitchell AP*. Function of Candida albicans adhesin Hwp1 in biofilm formation. Eukaryot Cell. 5(10):1604-10, 2006 Oct.

Olivares AO, Chang W, Mooseker MS, Hackney DD*, De La Cruz EM. The tail domain of myosin Va modulates actin binding to one head, J.Biol.Chem. 281, 31326-31336, 2006.

Pennington G, Smith CA, Shackney S, Schwartz R*. Expectation-maximization method for reconstructing tumor phylogenies from single-cell data. Comput Syst Bioinformatics Conf. 2006:371-80.

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.

Puskar K, Ta 'asan S, Schwartz R*, LeDuc PR*. Evaluating spatial constraints in cellular assembly processes using a monte carlo approach. Cell Biochem Biophys. 45(2):195-201, 2006.

Puthenveedu MA*, von Zastrow M. Cargo regulates clathrin-coated pit dynamics. Cell. 127(1):113-24, 2006.

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Sahu SC§, Simplaceanu V, Ho NT, Giovannelli JL, Ho C*. Backbone resonance assignment of human adult hemoglobin in the deoxy form. J Biomol NMR. 36 Suppl 1:1, 2006.

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Sridhar S, Blelloch GE, Ravi R, Schwartz R*. Optimal imperfect phylogeny reconstruction and haplotyping (IPPH). Comput Syst Bioinformatics Conf. 199-210, 2006.

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Wu YL, Ye Q, Foley LM, Hitchens TK, Sato K, Williams JB§, Ho C*. In Situ Labeling of Immune Cells with Iron Oxide Particles: An Approach to Detect Organ Rejection by Cellular MRI. Proceedings of National Academy Sciences USA 103:1852-1857, 2006.

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Bruno VM, Mitchell AP*. Regulation of azole drug susceptibility by Candida albicans protein kinase CK2. Mol Microbiol. 56(2):559-73, 2005 Apr.

Burnette JM, Miyamoto-Sato E, Schaub MA, Conklin J, Lopez AJ*. Subdivision of large introns in Drosophila by recursive splicing at nonexonic elements. Genetics, 170(2):661-674, 2005.

Celil AB, Hollinger JO*, Campbell PG*. Osx transcriptional regulation is mediated by additional pathways to BMP2/Smad signaling. J Cell Biochem. 95(3):518-28, 2005 Jun 1.

Cheers MS, Ettensohn CA*. P16 is an essential regulator of skeletogenesis in the sea urchin embryo. Dev. Biol. 283, 384-396, 2005.

Chen X, Murphy RF*. Objective clustering of proteins based on subcellular location patterns. J Biomed Biotechnol. 2005(2):87-95, 2005 Jun 30.

Chu N, Kucerka N, Liu Y, Tristram-Nagle S, Nagle JF*. Anomalous swelling of lipid bilayer stacks is caused by softening of the bending modulus. Phys Rev E Stat Nonlin Soft Matter Phys. 71(4 Pt 1):041904, 2005 Apr. Epub 2005 Apr 7.

Coggan JS, Bartol TM, Esquenazi E, Stiles JR*, Lamont S, Martone ME, Berg DK, Ellisman MH, Sejnowski TJ. Evidence for ectopic neurotransmission at a neuronal synapse. Science. 309(5733):446-51, 2005 Jul 15.

Conklin JF, Goldman A, Lopez AJ*. Stabilization and analysis of intron lariats in vivo. Methods, 37(4):368-375, 2005.

Fischer AJ, Rockwell NC, Jang AY, Ernst LA, Waggoner AS*, Duan Y, Lei H, Lagarias JC. Multiple roles of a conserved GAF domain tyrosine residue in cyanobacterial and plant phytochromes. Biochemistry. 44(46):15203-15, 2005 Nov 22.

Foley LM, Hitchens TK, Kochanek PM, Melick JA, Jackson EK, Ho C*. Murine orthostatic response during prolonged vertical studies: effect on cerebral blood flow measured by arterial spin-labeled MRI. Magn Reson Med. 54(4):798-806, 2005 Oct.

Fu H, Hu Y, McNelis T, Hollinger JO*. A calcium phosphate-based gene delivery system. J Biomed Mater Res A. 74(1):40-8, 2005 Jul 1.

Galan RF, Ermentrout GB, Urban NN*. Efficient estimation of phase-resetting curves in real neurons and its significance for neural-network modeling. Phys Rev Lett 94: 158101, 2005.

Genove G, DeMarco U, Xu H, Goins WF, Ahrens ET*. A novel transgene reporter for in vivo magnetic resonance imaging. Nat. Med. 11: 450-454, 2005.

Genové G, Glick BS, Barth AL*. Brighter reporter genes from multimerized fluorescent proteins. Biotechniques. 39(6):814, 816, 818 passim, 2005.

Granger BL, Flenniken ML, Davis DA, Mitchell AP*, Cutler JE. Yeast wall protein 1 of Candida albicans. Microbiology 151, 1631-1644, 2005.

Guelcher SA, Gallagher KM, Didier JE, Klinedinst DB, Doctor JS, Goldstein AS, Wilkes GL, Beckman EJ, Hollinger JO*. Synthesis of biocompatible segmented polyurethanes from aliphatic diisocyanates and diurea diol chain extenders. Acta Biomater. 1(4):471-84, 2005 Jul. Epub 2005 Mar 31.

Hackney DD*. The tethered motor domain of a kinesin-microtubule complex catalyzes reversible synthesis of bound ATP, Proc.Natl.Acad.Sci.U.S.A 102, 18338-18343, 2005.

Hoberman R, Sankoff D, Durand D*. The statistical analysis of spatially clustered genes under the maximum gap criterion. Journal of Computational Biology, 12(8): 1081-1100, 2005.

Huang Z,  Shiva S, Kim-Shapiro DB, Patel R, Ringwood LA, Irby CE, Huang KT, Ho C*, Hogg A, Schechter AN, Gladwin MT. Enzymatic Function of Hemoglobin as a Nitrite Reductase that Produces Nitric Oxide Under Allosteric Control. Journal of Clinical Investigation 2005; 115, 2099-2107.

Kapetanovich L, Baughman C, Lee TH*. Nm23H2 Facilitates Coat Protein Complex II Assembly and Endoplasmic Reticulum Export in Mammalian Cells. Molecular Biology of the Cell, 16(2):835-48, 2005.

Kaufman JA, Ahrens ET*, Laidlaw DH, Zhang S, Allman JM. Anatomical analysis of an aye-aye brain (Daubentonia madagascariensis, primates: Prosimii) combining histology, structural magnetic resonance imaging, and diffusion-tensor imaging. Anat Rec A Discov Mol Cell Evol Biol. 287(1):1026-37, 2005 Nov.

Kochanek PM, Hendrich,KS, Jackson E, Wisniewski SR, Melick JA, Shore PM, Janesko KL, Zacharia L, Ho C*. Characterization of the Effects of Adenosine Receptor Agonists on Cerebral Blood Flow in Uninjured and Traumatically Injured Rat Brain Using Continuous Arterial Spin-Labeled Magnetic Resonance Imaging. Journal of Cerebral Blood Flow and Metabolism 2005; 25, 1596-1612.

Koshibu K, Ahrens ET*, Levitt P. Postpubertal sex differentiation of forebrain structures and functions depend on transforming growth factor-alpha. J Neurosci. 25(15):3870-80, 2005 Apr 13.

Kou Z, Cohen WW, Murphy RF*. High-recall protein entity recognition using a dictionary. Bioinformatics. 21 Suppl 1:i266-73, 2005 Jun.

Kucerka N, Liu Y, Chu N, Petrache HI, Tristram-Nagle S, Nagle JF*. Structure of fully hydrated fluid phase DMPC and DLPC lipid bilayers using X-ray scattering from oriented multilamellar arrays and from unilamellar vesicles. Biophys J. 88(4):2626-37, 2005 Apr. Epub 2005 Jan 21.

Kucerka N, Tristram-Nagle S, Nagle JF*. Structure of fully hydrated fluid phase lipid bilayers with monounsaturated chains. J Membr Biol. 208(3):193-202, 2005 Dec. Epub 2006 Apr 8.

Kumar S, Lopez AJ*. Negative feedback regulation among SR splicing factors encoded by Rbp1 and Rbp1-like in Drosophila. EMBO J, 24(14):2646-2655, 2005.

Lanni F*. Fluorescence grating imager systems for optical-sectioning microscopy. In: Imaging in Neuroscience and Development. R.M. Yuste and A. Konnerth, eds. Cold Spring Harbor Laboratory Press, 2005. pp805-813 (Chapter 101), 2005.

Macbeth MR*, Schubert HL, VanDemark AP, Lingam AT, Hill CP, Bass BL. Inositol hexakisphosphate is bound in the ADAR2 core and required for RNA editing. Science, 309:1534-1539, 2005.

Manjula BN, A. Tsai G, Intaglietta M, Tsai CH, Ho C*, Smith PK, Perumalsamy K, Kanika ND, Friedman JM, Acharya SA. Conjugation of Multiple Copies of Polyethylene Glycol to Hemoglobin Facilitated Through Thiolation:  Influence on Hemoglobin Structure and Function. Protein Journal 2005; 24:133-145.

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

Mitchell AP*. Fungal CO2 sensing: a breath of fresh air. Curr Biol. 15(22):R934-6, 2005 Nov 22.
Morohashi N, Mitchell AP, Shimizu M. Effect of histone methyltransferase gene mutations on sporulation in S. cerevisiae. Nucleic Acids Symp Ser (Oxf), 325-326, 2005.

Murphy RF*. Cytomics and location proteomics: automated interpretation of subcellular patterns in fluorescence microscope images. Cytometry A. 67(1):1-3, 2005 Sep.

Murphy RF*. Location proteomics: a systems approach to subcellular location. Biochem Soc Trans. 33(Pt 3):535-8, 2005 Jun.

Nakahara K, Kim KK, Sciulli CC, Dowd SR, Minden JS*, Carthew RW. Targets of microRNA regulation in the Drosophila oocyte proteome. PNAS, 102, 12023-12028, 2005.

Nakao A, Murase N,  Ho C*,  Toyokawa H,  Billiar TB, Kanno S. Biliverdin Administration Prevents the Formation of Intimal Hyperplasia Induced by Vascular Injury. Circulation 2005; 112, 587-591.

Nobile CJ, Mitchell AP*. Regulation of cell-surface genes and biofilm formation by the C. albicans transcription factor Bcr1p. Curr Biol. 15(12):1150-5, 2005 Jun 21.

Otim O, Hinman VF*, Davidson EH. Expression of AmHNF6, a sea star orthologue of a transcription factor with multiple distinct roles in sea urchin development. Gene Expr Patterns. 5(3):381-6, 2005 Feb.

Pluempitiwiriyawej C,  Moura JMF, Wu YJL,  Ho C*. STACS:  New Active Contour Scheme for Cardiac MR Image segmentation. IEEE Transactions on Medical Imaging 2005; 24, 593-603.

Puthenveedu MA, Linstedt AD*. Subcompartmentalizing the Golgi apparatus. Curr Opin Cell Biol. 17(4):369-75, 2005 Aug.

Richard ML, Nobile CJ, Bruno VM, Mitchell AP*. Candida albicans biofilm-defective mutants. Eukaryot Cell. 4(8):1493-502, 2005 Aug.

Salama G, Choi BR, Azour G, Lavasani M, Tumbev V, Salzberg BM, Patrick MJ, Ernst LA, Waggoner AS*. Properties of new, long-wavelength, voltage-sensitive dyes in the heart. J Membr Biol. 208(2):125-40, 2005 Nov.

Sui X, Xu Y, Giovannelli JL, Ho NT, Ho C*, Yang D. Mapping Protein-Protein Interface on the Basis of Proton Density Difference. Angewandte Chemie International Edition 2005; 44, 5141- 5144.

Tam MF, Chen J§, Tam TCS, Tsai CH, Shen TJ, Simplaceanu V, Feinstein TN,  Barrick D, Ho C*. Enhanced Inhibition of Polymerization of Sickle Cell Hemoglobin the Presence of Recombinant Mutants of Human Fetal Hemoglobin With Substitutions at Position 43 in the γ-Chain. Biochemistry 2005; 44, 12188-12195.

Tristram-Nagle S, Lewis RN, Blickenstaff JW, Diprima M, Marques BF, McElhaney RN, Nagle JF*, Schneider JW. Thermodynamic and structural characterization of amino acid-linked dialkyl lipids. Chem Phys Lipids. 134(1):29-39, 2005 Mar. Epub 2004 Dec 9.

Urban NN*, Castro JB. Tuft calcium spikes in accessory olfactory bulb mitral cells. J Neurosci 25: 5024-5028, 2005.

Villar CC, Kashleva H, Mitchell AP*, Dongari-Bagtzoglou A. Invasive phenotype of Candida albicans affects the host proinflammatory response to infection. Infect Immun 73, 4588-4595, 2005.

Wiltrout ME, Giovannelli JL, Simplaceanu V, Lukin JA, Ho NT, Ho C*. A biophysical investigation of recombinant hemoglobins with aromatic B10 mutations in the distal heme pockets. Biochemistry. 44(19):7207-17, 2005 May 17.

Xu D, Liang Z-P, Wu YL, Hitchens TK, Ho C*. High-Resolution Dynamic Imaging of Contrast Agent Uptake in a Beating Heart. IEEE Engineering in Medicine and Biology 2005, pp. 7397-7400.

Xu Y, Lin Z, Ho C*, Yang D. A General Strategy for the Assignment of Aliphatic Side-Chain Resonances of Uniformly 13C, 15N-Labeled Large Proteins. Journal of the American Chemical Society 2005; 127, 11920-11921.

Zhan Y, Rule GS*. Stable triplet of uracil-uracil basepairs in a small antisense RNA.J Am Chem Soc., 127:15714-5, 2005.

Zhao T, Velliste M, Boland MV, Murphy RF*. Object type recognition for automated analysis of protein subcellular location. IEEE Trans Image Process. 14(9):1351-9, 2005 Sep.