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Biological Sciences

2016 Publications

Woolford CA¥, Lagree K, Xu W, Aleynikov T, Adhikari H, Sanchez H, Cullen PJ, Lanni F*, Andes DR, Mitchell AP*. Bypass of Candida albicans Filamentation/Biofilm Regulators through Diminished Expression of Protein Kinase Cak1. PLoS Genet. 2016 Dec 9;12(12):e1006487

Gokhale A, Hartwig C, Freeman AH, Das R, Zlatic SA, Vistein R, Burch A, Carrot G, Lewis AF, Nelms S, Dickman DK, Puthenveedu MA*, Cox DN, Faundez V. The Proteome of BLOC-1 Genetic Defects Identifies the Arp2/3 Actin Polymerization Complex to Function Downstream of the Schizophrenia Susceptibility Factor Dysbindin at the Synapse. J Neurosci. 2016 Dec 7;36(49):12393-12411.

Ettensohn CA*, Dey D¥. KirrelL, a member of the Ig-domain superfamily of adhesion proteins, is essential for fusion of primary mesenchyme cells in the sea urchin embryo. Dev Biol. 2016 Nov 17. pii: S0012-1606(16)30650-9.

Cheatle Jarvela AM, Yankura KA, Hinman VF*. A gene regulatory network for apical organ neurogenesis and its spatial control in sea star embryos. Development. 2016 Nov 15;143(22):4214-4223.

Sinha K, Sangani SS, Kehr AD, Rule GS*, Jen-Jacobson L. Metal Ion Binding at the Catalytic Site Induces Widely Distributed Changes in a Sequence Specific Protein-DNA Complex. Biochemistry. 2016 Nov 8;55(44):6115-6132.

Wei G, Lo C, Walsh C, Hiller NL*, Marculescu R. In Silico Evaluation of the Impacts of Quorum Sensing Inhibition (QSI) on Strain Competition and Development of QSI Resistance. Sci Rep. 2016 Oct 13;6:35136

Wang H, McManus J*, Kingsford C*. Accurate Recovery of Ribosome Positions Reveals Slow Translation of Wobble-Pairing Codons in Yeast. J Comput Biol. 2016 Oct 11.

Bowman SL, Shiwarski DJ, Puthenveedu MA*. Distinct G protein-coupled receptor recycling pathways allow spatial control of downstream G protein signaling. J Cell Biol. 2016 Sep 19. pii: jcb.201512068.

Wu S, Tan D, Woolford JL Jr*, Dong MQ, Gao N. Atomic modelling of the ITS2 ribosome assembly subcomplex from Cryo-EM together with mass spectrometry-identified protein-protein crosslinks. Protein Sci. 2016 Sep 19. doi: 10.1002/pro.3045.

Foley LM, Clark RS, Vazquez AL, Hitchens TK, Alexander H, Ho C*, Kochanek PM, Manole MD. Enduring Disturbances in Regional Cerebral Blood Flow and Brain Oxygenation at 24 Hours after Asphyxial Cardiac Arrest in Developing Rats. Pediatr Res. 2016 Sep 16. doi: 10.1038/pr.2016.175.

Song L, Bachert C, Linstedt AD*. Activity Detection of GalNAc Transferases by Protein-Based Fluorescence Sensors In Vivo. Methods Mol Biol. 2016;1496:123-31.

Hackney DD*, McGoff MS. Nucleotide-free kinesin motor domains reversibly convert to an inactive conformation with characteristics of a molten globule. Arch Biochem Biophys. 2016 Oct 15;608:42-51.

Wang H*, Becuwe M, Housden BE, Chitraju C, Porras AJ, Graham MM, Liu XN, Thiam AR, Savage DB, Agarwal AK, Garg A, Olarte MJ, Lin Q, Fröhlich F, Hannibal-Bach HK, Upadhyayula S, Perrimon N, Kirchhausen T, Ejsing CS, Walther TC, Farese RV. Seipin is required for converting nascent to mature lipid droplets. Elife. 2016 Aug 26;5. pii: e16582. 

Tutuncuoglu B, Jakovljevic J, Wu S, Gao N, Woolford JL Jr*. The N-terminal extension of yeast ribosomal protein L8 is involved in two major remodeling events during late nuclear stages of 60S ribosomal subunit assembly. RNA. 2016 Sep;22(9):1386-99. doi: 10.1261/rna.055798.115 

Gertz EM, Chowdhury SA, Lee WJ, Wangsa D, Heselmeyer-Haddad K, Ried T, Schwartz R*, Schäffer AA. FISHtrees 3.0: Tumor Phylogenetics Using a Ploidy Probe. PLoS One. 2016 Jun 30;11(6):e0158569

Min K, Ichikawa Y, Woolford CA¥, Mitchell AP*. Candida albicans Gene Deletion with a Transient CRISPR-Cas9 System. mSphere. 2016 Jun 15;1(3). pii: e00130-16.

Li Y, Majarian TD, Naik AW, Johnson GR, Murphy RF*. Point process models for localization and interdependence of punctate cellular structures. Cytometry A. 2016 Jul;89(7):633-43.

Ramesh M, Woolford JL Jr*. Eukaryote-specific rRNA expansion segments function in ribosome biogenesis. RNA. 2016 Aug;22(8):1153-62. 

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. 534(7605):133-7.

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.

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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.

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

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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Lanni F*.  Fluorescence grating imager systems for optical-sectioning microscopy.  In: Imaging, A Laboratory Manual.  RM Yuste Ed., Cold Spring Harbor Laboratory Press. Chapter 47, pp735-744, 2011.

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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Makowski L, Bardhan J, Gore D, Lal J, Mandava S, Park S, Rodi DJ, Ho NT, Ho C*, Fischetti RF.  WAXS Studies of the Structural Diversity of Hemoglobin in Solution. Journal of Molecular Biology 2011; 408, 909-921.

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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.

Morel PA, Srinivas M, Turner MS, Fuschiotti P, Munshi R, Bahar I, Feili-Hariri M, Ahrens ET*. Gene expression analysis of dendritic cells that prevent diabetes in NOD mice: analysis of chemokines and costimulatory molecules. J Leukoc Biol. 2011 Sep;90(3):539-50. Epub 2011 May 31.

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

Mukhopadhyay S, Linstedt AD. Identification of a gain-of-function mutation in a Golgi P-type ATPase 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.

Cuevas Tabarés J, MacLachlan RA, Ettensohn CA*, Riviere, CN. Cell micromanipulation with an active handheld micromanipulator. Conf. Proc. IEEE Eng. Med. Biol. Soc. 4363-4366, 2010.

DeStefino NR, Pilato AA, Dittrich M, Cherry SV, Cho S, Stiles JR*, Meriney SD. (R)-roscovitine prolongs the mean open time of unitary N-type calcium channel currents. Neuroscience. 2010 May 19;167(3):838-49. Epub 2010 Feb 24.

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.

Fanning S§, Mitchell AP*. The Fungal Pathogen Candida albicans. In KA Borkovich & DJ Ebbole (ed.), Cellular and Molecular Biology of Filamentous Fungi. ASM Press, Washington, DC, 2010.

Fisher GW, Adler SA, Fuhrman MH, Waggoner AS*, Bruchez MP*, Jarvik JW*. Detection and quantification of beta2AR internalization in living cells using FAP-based biosensor technology. J Biomol Screen. 15(6):703-9, 2010. Epub 2010 May 20.

Fishilevich E§, Fitzpatrick JAJ, Minden JS*. pHMA, a pH-sensitive GFP reporter for cell engulfment in Drosophila embryos, tissues and cells. Dev. Dyn. 238, 559-73, 2010.

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.

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

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.

Helfer BM, Nelson AD, Janjic JM, Gil RR, Kalinski P, de Vries J, Ahrens ET*, Mailliard RB. Functional assessment of human dendritic cells labeled for in vivo 19F magnetic resonance imaging cell tracking. Cytotherapy 12(2): 238-250, 2010.

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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Ho C*, Yuan Y, Simplaceanu V. NMR Provides a New Structural and Dynamic View of Hemoglobin Allostery in Solution, in Hemoglobin:  Recent Developments and Topics, edited by Masako Nagai, Research Signpost, Kerala, India, 17-36, 2010.

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

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.

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

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.

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

McManus CJ*, Coolon JD, Duff MO, Eipper-Mains J, Graveley BR, Wittkopp PJ. Regulatory Divergence in Drosophila revealed by mRNA-seq. Genome Res 20(6):816-825, 2010.

McManus CJ*, Duff MO, Eipper-Mains J, Graveley BR. Global analysis of trans-splicing in Drosophila. Proc Natl Acad Sci USA 107(29):12975-12979, 2010.

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.

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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.

Srinivas M, Heerschap A, Ahrens ET*, Figdor CG, de Vries IJ. 19)F MRI for quantitative in vivo cell tracking. Trends Biotechnol. 28(7):363-70, 2010 Jul. Epub 2010 Apr 26.

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.

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

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.

Zhang X, Badea CT, Hood G, Wetzel AW, Stiles JR*, Johnson GA. Free-space fluorescence tomography with adaptive sampling based on anatomical information from microCT. Proc Soc Photo Opt Instrum Eng. 7757(775706), 2010. pii: 755706 (2010).

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

Arbour M, Epp E, Hogues H, Sellam A, Lacroix C, Rauceo J, Mitchell A*, Whiteway M, Nantel A. Widespread occurrence of chromosomal aneuploidy following the routine production of Candida albicans mutants. FEMS Yeast Res 9, 1070-1077, 2009.

Ballou B, Ernst LA, Andreko S, Fitzpatrick JA, Lagerholm BC, Waggoner AS*, Bruchez MP*. Imaging vasculature and lymphatic flow in mice using quantum dots. Methods Mol Biol. 574:63-74, 2009.

Bencherif SA, Gao H, Srinivasan A, Siegwart DJ, Hollinger JO**, Washburn NR, Matyjaszewski K. Cell-adhesive star polymers prepared by ATRP. Biomacromolecules. 10(7):1795-803, 2009 Jul 13. Epub 2009 Jun 11.

Bencherif SA, Sheehan JA, Hollinger JO*, Walker LM, Matyjaszewski K, Washburn NR. Influence of cross-linker chemistry on release kinetics of PEG-co-PGA hydrogels. J Biomed Mater Res A. 90(1):142-53, 2009 Jul.

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.

Bencherif SA, Srinivasan A, Sheehan JA, Walker LM, Gayathri C, Gil R, Hollinger JO*, Matyjaszewski K, Washburn NR. End-group effects on the properties of PEG-co-PGA hydrogels. Acta Biomater. 5(6):1872-83, 2009 Jul. Epub 2009 Feb 28.

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.

Boysen JH, Fanning S§, Newberg J, Murphy RF*, Mitchell AP*. Detection of protein-protein interactions through vesicle targeting. Genetics 182:33-9, 2009.

Brinegar C, Wu YJL, Foley LM, Hitchens TK, Ye Q, Ho C*, Liang ZP. Real-Time Cardiac MRI Without Triggering, Gating, or Breath Holding. IEEE Eng Med Biol Soc 2008; pp. 3381-3384.

Buck TE, Rao A, Coelho LP, Fuhrman MH, Jarvik JW*, Berget PB*, Murphy RF*. Cell cycle dependence of protein subcellular location inferred from static, asynchronous images. Conf Proc IEEE Eng Med Biol Soc. 2009:1016-9, 2009.

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

Chamilos G, Nobile CJ, Bruno VM, Lewis RE, Mitchell AP*, Kontoyiannis DP. Candida albicans Cas5, a regulator of cell wall integrity, is required for virulence in murine and toll mutant fly models. J Infect Dis 200:152-7, 2009.

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.

Czech J, Dittrich M, Stiles JR*. Rapid creation, Monte Carlo simulation, and visualization of realistic 3D cell models. Methods Mol Biol. 500:237-87, 2009.

Emr S, Glick BS, Linstedt AD*, Lippincott-Schwartz J, Luini A, Malhotra V, Marsh BJ, Nakano A, Pfeffer SR, Rabouille C, Rothman JE, Warren G, Wieland FT. Journeys through the Golgi—taking stock in a new era. J. Cell Biol. 187: 449-53, 2009.

Ettensohn CA*. Lessons from a gene regulatory network: echinoderm skeletogenesis provides insights into evolution, plasticity, and morphogenesis. Development 136, 11-21, 2009.

Falco CF, Dykstra KM, Yates BP, Berget PB*. scFv-based Fluorogen Activating Proteins and Variable Domain Inhibitors as Fluorescent Biosensor Platforms. Biotechnol. J. 4 (9): 1328-1336, 2009.

Fitzpatrick JA, Andreko SK, Ernst LA, Waggoner AS*, Ballou B, Bruchez MP*. Long-term persistence and spectral blue shifting of quantum dots in vivo. Nano Lett. 9(7):2736-41, 2009.

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

Fitzpatrick JAJ, Andreko SK, Ernst LA, Waggoner AS*, Ballou B, Bruchez MP*. Long term persistence and spectral blue-shifting of quantum dots in vivo. Nano Letters 2009.

Guler SD, Ghosh DD, Pan J, Mathai JC, Zeidel ML, Nagle JF*, Tristram-Nagle S. Effects of Ether Linkage on Lipid Bilayer Structure and Water Permeability. Chem Phys Lipids. 160:33-44, 2009.

Hackney DD*, Baek N, Snyder AC. Half-site inhibition of dimeric kinesin head domains by monomeric tail domains, Biochemistry. 48, 3448-3456, 2009.

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

Huh S, Lee D, Murphy RF*. Efficient framework for automated classification of subcellular patterns in budding yeast. Cytometry A. 75(11):934-40, 2009 Nov.

Jackson C, Murphy RF*, Kovacević J. Intelligent acquisition and learning of fluorescence microscope data models. IEEE Trans Image Process. 18(9):2071-84, 2009 Sep. Epub 2009 Jun 5.

Janjic JM, Ahrens ET*. Fluorine-containing nanoemulsions for MRI cell tracking Wiley Interdiscip Rev Nanomed Nanobiotechnol. 1(5):492-501, 2009 Sep-Oct.

Joseph JM, Durand D*. Family classification without domain chaining. Bioinformatics 25(12):i45-i53, 2009.

Kaan HY, Ulaganathan V, Hackney DD*, Kozielski F. An Allosteric Transition Trapped in an Intermediate State of a New Kinesin-Inhibitor Complex. Biochem. J. 425, 55-60, 2009.

Kadri S, Hinman V*, Benos PV. HHMMiR: Efficient de novo prediction of microRNAs using hierarchical hidden Markov models. BMC Bioinformatics;10 Suppl 1:S35, 2009 Jan 30.

Kang DS, Kern RC, Puthenveedu MA*, von Zastrow M, Williams JC, Benovic JL. Structure of an arrestin2-clathrin complex reveals a novel clathrin binding domain that modulates receptor trafficking. J Biol Chem. 284(43):29860-72, 2009 Oct 23. Epub 2009 Aug 25.

Lee B, LeDuc PR*, Schwartz R*. Parameter effects on binding chemistry in crowded media using a two-dimensional stochastic off-lattice model. Physical Review E, 80:041918, 2009.

Lim JK, Tan DX, Lanni F*, Tilton RD, Majetich SA. Optical imaging and magnetophoresis of nanorods. J. Magnetism Mag. Mater. 321:1557-1562, 2009.

Manole MD, Foley LM, Hitchens TK, Kochanek PM, Hickey RW, Bayir H, Alexander H, Ho C*, Clark RSB. Magnetic Resonance Imaging Assessment of Regional Cerebral Blood Flow After Asphyxial Cardiac Arrest in Immature Rats. Journal of Cerebral Blood Flow & Metabolism. 29(1); 197-205, 2009.

Mills TT, Huang J, Feigenson GW, Nagle JF*. Effects of Cholesterol and Unsaturated DOPC Lipid on Chain Packing of Saturated Gel-Phase DPPC Bilayers. Gen. Physiol. Biophys. 28, 126-139, 2009.

Minden JS*, Dowd SR, Meyer HE, Stühler K. Difference Gel Electrophoresis. Electrophoresis 30, S156-S161, 2009.

Mittal R, Bruchez MP*. Calibration of Flow Cytometry for Quantitative Quantum Dot Measurements. Curr Protoc Cytom. Chapter 6:Unit6.26, 2009 Jul 1.

Näthke IS, McCartney BM*. APC proteins. Preface. Adv Exp Med Biol. 656:vii-x, 2009.

Newberg J, Hua J, Murphy RF*. Location proteomics: systematic determination of protein subcellular location. Methods Mol Biol. 500:313-32, 2009.

Newberg JY, Li J, Rao A, Pontén F, Uhlén M, Lundberg E, Murphy RF*. Automated Analysis of Human Protein Atlas Immunofluorescence Images. Proc IEEE Int Symp Biomed Imaging. 5193229:1023-1026, 2009.

Nobile CJ, Mitchell AP*. Large-scale gene disruption using the UAU1 cassette. Methods Mol Biol. 499:175-94, 2009.

Nobile CJ, Nett JE, Hernday AD, Homann OR, Deneault JS, Nantel A, Andes DR, Johnson AD, Mitchell AP*. Biofilm matrix regulation by Candida albicans Zap1. PLoS Biol 7:e1000133, 2009.

Pan J, Tieleman DP, Nagle JF*, Kucerka N, Tristram-Nagle S. Alamethicin in Lipid Bilayers: Combined Use of X-ray Scattering and MD Simulations. Biochim. Biophys. Acta 1788, 1387-1397, 2009.

Pan J, Tristram-Nagle S, Nagle JF*. Alamethicin aggregation in lipid membranes. J. Membrane Biol. 231, 11-27, 2009.

Pan J, Tristram-Nagle S, Nagle JF*. Effect of cholesterol on structural and mechanical properties of membranes depends on lipid chain saturation. Phys. Rev. E. 80, 021931(1-12), 2009.

Park H, Liu Y, Solis N, Spotkov J, Hamaker J, Blankenship JR§, Yeaman MR, Mitchell AP*, Liu H, Filler SG. Transcriptional responses of candida albicans to epithelial and endothelial cells. Eukaryot Cell 8:1498-510, 2009.

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

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.

Raghupathy N, Durand D*. Gene cluster statistics with gene families. Molecular Biology and Evolution, 26:957-968, 2009.

Rule GS*, Bajzek D. Building an Online Biochemistry Course with Assessment and Feedback Embedded Into All Online Instructional Activities. In Proceedings of World Conference on E-Learning in Corporate, Government, Healthcare, and Higher Education 2009. Chesapeake, VA: AACE.

Sengupta D, Truschel S§, Bachert C, Linstedt AD*. Organelle tethering by a homotypic PDZ interaction underlies formation of the Golgi membrane network.  J. Cell Biol. 186:51-55, 2009.

Shank NI, Zanotti KJ, Lanni F*, Berget PB*, Armitage BA*. Enhanced photostability of genetically encodable fluoromodules based on fluorogenic cyanine dyes and a promiscuous protein partner. J Am Chem Soc. 131(36):12960-9, 2009 Sep 16.

Sheehan JS, Benedetti BL, Barth AL*. Anticonvulsant effects of the BK channel antagonist paxilline. Epilepsia Apr; 50(4):711-20, 2009.

Siegwart DJ, Srinivasan A, Bencherif SA, Karunanidhi A, Oh JK, Vaidya S, Jin R, Hollinger JO*, Matyjaszewski K. Cellular uptake of functional nanogels prepared by inverse miniemulsion ATRP with encapsulated proteins, carbohydrates, and gold nanoparticles. Biomacromolecules. 10(8):2300-9, 2009 Aug 10.

Srinivas M, Turner MS, Janjic JM, Morel PA, Laidlaw DH, Ahrens ET*. In vivo cytometry of antigen specific T-cells using 19F MRI. Magn. Reson. Med. 62: 747-753, 2009.

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

Staley J, Woolford Jr JL*. Assembly of ribosomes and spliceosomes:complex ribonucleoprotein machines.Current Opinion in Cell Biology 21:109-118, 2009.

Talkish J†,Woolford Jr JL*. The Rea1 tadpole loses its tail. Cell 138: 832-834, 2009.

Urban NN*, Arevian AC. Computing with dendrodendritic synapses in the olfactory bulb. Ann N Y Acad Sci. 1170:264-9, 2009 Jul. Review.

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

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

Yadav S, Puri S, Linstedt AD*. A Primary Role for Golgi Positioning in Directed Secretion, Cell Polarity and Wound Healing. Mol. Biol. of the Cell 20:1728-1736, 2009.

Yudowski GA, Puthenveedu MA*, Henry AG, von Zastrow M. Cargo-mediated regulation of a rapid Rab4-dependent recycling pathway. Mol Biol Cell. 20(11):2774-84, 2009 Jun.

Arevian AC, Kapoor V, Urban NN*. Dynamic Gating of Lateral inhibition in the Olfactory Bulb. Nature Neuroscience. 11(1):80-7, 2008.

Armitage BA*, Berget PB*. An Enlightening Structure-Function Relationship. Science, 319: 1195-1196, 2008.

Bajzek D, Brooks J, Jerome W, Lovett M, Rinderle J, Rule GS*, Thille C. Assessment and Instruction: Two Sides of the Same Coin. In Proceedings of World Conference on E-Learning in Corporate, Government, Healthcare, and Higher Education 2008. 2008.

Barth AL*, Wheeler ME. The barista on the bus: cellular and synaptic mechanisms for visual recognition memory. Neuron 24, 58(2):159-61, 2008.

Baughman C, Morin-Leisk J, Lee TH*. Nucleoside Diphosphate Kinase B (NDPKB) scaffolds endoplasmic reticulum membranes in vitro. Exp Cell Res, 314(14):2702-2714, 2008. Faculty of 1000 Recommended.

Bencherif SA, Srinivasan A, Horkay F, Hollinger JO*, Matyjaszewski K, Washburn NR. Influence of the degree of methacrylation on hyaluronic acid hydrogels properties. Biomaterials. 29(12):1739-49, 2008 Apr. Epub 2008 Jan 30.

Boyce M, Py BF, Ryazanov AG, Minden JS*, Long K, Ma D, Yuan J. A pharmacoproteomic approach implicates eukaryotic elongation factor 2 kinase in ER stress-induced cell death. Cell Death and Diff. 15, 589-99, 2008.

Chen S-C, Gordon GJ, Murphy RF*. Graphical Models for Structured Classification, with an Application to Interpreting Images of Protein Subcellular Location Patterns. J. Machine Learning Res. 9:651-682, 2008.

Clem RL, Celikel T, Barth AL*. Ongoing in vivo experience triggers synaptic metaplasticity in the neocortex. Science. 2008 Jan 4;319(5859):101-4.

Constantin TP, Silva GL, Robertson KL, Hamilton TP, Fague K, Waggoner AS*, Armitage BA*. Synthesis of new fluorogenic cyanine dyes and incorporation into RNA fluoromodules. Org Lett. 10(8):1561-4, 2008. Epub 2008 Mar 14.

Daneshvar H, Nelms J, Muhammad O, Jackson H, Tkach J, Davros W, Peterson T, Vogelbaum MA, Bruchez MP*, Toms SA. Imaging characteristics of zinc sulfide shell, cadmium telluride core quantum dots. Nanomedicine (Lond). 3(1):21-9, 2008 Feb.

Ermentrout GB, Galán RF, Urban NN*. Reliability, synchrony and noise. Trends Neurosci. 31(8):428-34, 2008 Aug.

Feinstein NT, Linstedt AD*. GRASP55 regulates Golgi ribbon formation. Mol. Biol. of the Cell, 19:2696–2707, 2008.

Foley LM, Hitchens TK, Melick JA, Bayir H, Ho C*, Kochanek PM. Effect of inducible nitric oxide synthase on cerebral blood flow after experimental traumatic brain injury in mice. J Neurotrauma. 25(4):299-310, 2008 Apr.

Galán RF, Ermentrout GB, Urban NN*. Optimal time scale for spike-time reliability: theory, simulations, and experiments. J Neurophysiol. 2008 Jan;99(1):277-83. Epub 2007 Oct 10.

Gibson FL, Anderson et al. Guidelines for reporting the use of gel electrophoresis in proteomics. Nat Biotech 26, 863-864, 2008.

Glory E, Newberg J, Murphy RF. Automated Comparison of Protein Subcellular Location Patterns Between Images of Normal and Cancerous Tissues. Proc IEEE Int Symp Biomed Imaging. 4540993:304-307, 2008.

Gong H, Sengupta D, Linstedt AD*, Schwartz R*. Simulated de novo assembly of Golgi compartments by selective cargo capture during vesicle budding and targeted vesicle fusion. Biophys. J., 95:1674–1688, 2008.

Greenwood AI, Pan J, Mills TT, Nagle JF*, Epand RM, Tristram-Nagle S. CRAC motif peptide of the HIV-1 gp41 protein thins SOPC membranes and interacts with cholesterol. Biochim Biophys Acta, 1778(4):1120-30, 2008 Apr. Epub 2008 Jan 16.

Guo Y, Punj V, Sengupta D, Linstedt AD*. Coat-tether interaction in Golgi organization. Mol. Biol. of the Cell, 19:2830–2843, 2008.

Hackney DD*, Stock MF. Kinesin tail domains and Mg2+ directly inhibit release of ADP from head domains in the absence of microtubules, Biochemistry. 47, 7770-7778, 2008.

Henn A, Cao W, Hackney DD*, De La Cruz EM. The ATPase cycle mechanism of the DEAD-box rRNA helicase, DbpA, J.Mol.Biol. 377, 193-205.2, 2008.

Hinkovska-Galcheva VA, Clark S, VanWay M, Hiraoka, Abe A, Borofsky M, Kunkel RG, Huang JB, Shanley T, Shayman JA, Lanni F*, Petty HR, Boxer LA. Ceramide kinase promotes Ca+2 signaling near IgG-opsonized targets and enhances phagolysosomal fusion in COS-1 cells.  J. Lipid Res. 49: 531-542, 2008.

Hodor PG, Ettensohn CA*. Mesenchymal cell fusion in the sea urchin embryo. Meth. Mol. Biol., 475, 315-334, 2008.

Hollinger JO*, Onikepe AO, MacKrell J, Einhorn T, Bradica G, Lynch S, Hart CE. Accelerated fracture healing in the geriatric, osteoporotic rat with recombinant human platelet-derived growth factor-BB and an injectable beta-tricalcium phosphate/collagen matrix. J Orthop Res. 26(1):83-90, 2008 Jan.

Janjic JM, Srinivas M, Kadayakkara DK, Ahrens ET*. Self-delivering nanoemulsions for dual fluorine-19 MRI and fluorescence detection. J Am Chem Soc., 130(9):2832-2841, 2008 Mar 5.

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Kerr RA, Bartol TM, Kaminsky B, Dittrich M, Chang JC, Baden SB, Sejnowski TJ, Stiles JR*. Fast Monte Carlo Simulation Methods for Biological Reaction-Diffusion Systems in Solution and on Surfaces. SIAM J Sci Comput. 30(6):3126, 2008 Oct 13.

Kucerka N, Nagle JF*, Sachs JN, Feller SE, Pencer J, Jackson A, Katsaras J. Lipid bilayer structure determined by the simultaneous analysis of neutron and X-ray scattering data. Biophys J, 95(5):2356-67, 2008 Sep. Epub 2008 May 23.

Lee B, LeDuc PR*, Schwartz R*. Stochastic off-lattice modeling of molecular self-assembly in crowded environments by Greens function reaction dynamics. Physical Review E, 78:031911, 2008.

Lim JK, Eggeman A, Lanni F*, Tilton RD, Majetich SA. Synthesis and single-particle optical detection of low-polydispersity plasmonic-superparamagnetic nanoparticles. Adv. Mater. 20: 1721-1726, 2008.

Maillett DH§, Simplaceanu V, Shen T-J, Ho NT, Olson JS, Ho C*. Interfacial and Distal Pocket Mutations Exhibit Additive Effects on the Structure and Function of Hemoglobin. Biochemistry 47, 10551-10563, 2008. PMC2692483

Mathai JC, Tristram-Nagle S, Nagle JF*, Zeidel ML. Structural Determinants of Water Permeability through the Lipid Membrane. J. Gen. Physiol,131:59-68, 2008.

McCartney BM*, Näthke IS. Cell regulation by the Apc protein Apc as master regulator of epithelia. Curr Opin Cell Biol. 20(2):186-93, 2008 Apr, Epub 2008 Mar 24.

McManus CJ*, Graveley BR. Getting the message out. Mol Cell. 31(1):4-6, 2008.

Mills PH§, Wu YJ, Ho C*, Ahrens ET*. Sensitive and automated detection of iron-oxide-labeled cells using phase image cross-correlation analysis. Magn Reson Imaging. 26(5):618-28, 2008 Jun. Epub 2008 May 2.

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.

Mills TT, Tristram-Nagle S, Heberle FA, Morales NF, Zhao J, Wu J, Toombes GE, Nagle JF*, Feigenson GW. Liquid-liquid domains in bilayers detected by wide angle X-ray scattering. Biophys J, 95(2):682-90, 2008 Jul. Epub 2008 Apr 4.

Minden J*. Dissection of the embryonic brain using photoactivated gene expression. Adv Exp Med Biol 628, 57-68, 2008.

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

Misra N, Schwartz R*. Efficient stochastic sampling of first-passage times with applications to self-assembly simulations. Journal of Chemical Physics, 129:204109, 2008.

Mitchell AP*. A VAST staging area for regulatory proteins. Proc Natl Acad Sci U S A. 2008 May 20;105(20):7111-2. Epub 2008 May 12.

Morin-Leisk J, Lee TH*. Nucleotide dependent self-assembly of Nucleoside Diphosphate Kinase (NDPK) in vitro. Biochimica et Biophysica Acta, 1784(12):2045-2051, 2008.

Murphy RF*. Automated Proteome-Wide Determination of Subcellular Location Using High Throughput Microscopy. Proc IEEE Int Symp Biomed Imaging. 2008 May 14;2008:308-311.

N'Diaye EN, Hanyaloglu AC, Kajihara KK, Puthenveedu MA*, Wu P, von Zastrow M, Brown EJ. The ubiquitin-like protein PLIC-2 is a negative regulator of G protein-coupled receptor endocytosis. Mol Biol Cell. 19(3):1252-60, 2008 Mar.

Nagle JF*, Mathai JC, Zeidel ML, Tristram-Nagle S. Theory of passive permeability through lipid bilayers. J Gen Physiol. 131(1):77-85, 2008 Jan.

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.

Ozhalici-Unal H, Pow CL, Marks SA, Jesper LD, Silva GL, Shank NI, Jones EW*, Burnette JM 3rd*, Berget PB*, Armitage BA*. A rainbow of fluoromodules: a promiscuous scFv protein binds to and activates a diverse set of fluorogenic cyanine dyes. J Am Chem Soc. 130(38):12620-1, 2008 Sep 24. Epub 2008 Aug 30.

Pan J, Mills TT, Tristram-Nagle S, Nagle JF*. Cholesterol perturbs lipid bilayers nonuniversally. Phys Rev Lett, 100(19):198103, 2008 May 16. Epub 2008 May 15.

Pan J, Tristram-Nagle S, Kucerka N, Nagle JF*. Temperature dependence of structure, bending rigidity, and bilayer interactions of dioleoylphosphatidylcholine bilayers. Biophys J. 94(1):117-24, 2008 Jan 1. Epub 2007 Sep 7.

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.

Song N, Joseph JM, Davis GB, Durand D*. Sequence similarity network reveals common ancestry of multidomain proteins. PLOS Computational Biology, 4(5): e1000063, 2008.

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.

Sridhar S, Lam F, Blelloch GE, Ravi R, Schwartz R*. Mixed integer linear programming for maximum-parsimony phylogeny inference. IEEE/ACM Trans Comput Biol Bioinform. 5(3):323-31, 2008 Jul-Sep.

Sridhar S, Schwartz R*. A human genome-wide library of local phylogeny predictions for whole-genome inference problems. BMC Genomics. 2008 Aug 18;9:389.

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

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

Szent-Gyorgyi C, Schmidt BA, Creeger Y, Fisher GW, Zakel KL, Adler S, Fitzpatrick JA, Woolford CA, Yan Q, Vasilev KV, Berget PB*, Bruchez MP*, Jarvik JW*, Waggoner A*. Fluorogen-activating single-chain antibodies for imaging cell surface proteins. Nature biotechnology, 26: 235-240, 2008.

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

Toppings M, Castro C, Mills PH†, Reinhart B, Schatten G, Ahrens ET*, Chaillet JR, Trasler JM. Profound phenotypic variation among mice deficient in the maintenance of genomic imprints. Hum Reprod. 23(4):807-18, 2008 Apr. Epub 2008 Feb 13.

Vernot B, Stolzer M, Goldman A, Durand D*. Reconciliation with non-binary species trees. Journal of Computational Biology, 15(8): 981-1006, 2008.

Weinstein S, Pane D, Ernst LA, Warren-Rhodes K, Dohm JM, Hock AN, Piatek JL, Emani S, Lanni F*, Wagner M, Fisher GW, Minkley E, Dansey LE, Smith T, Grin EA, Stubbs K, Thomas G, Cockell CS, Marinangeli L, Ori GG, Heys S, Teza JP, Moersch JE, Coppin P, Chong Diaz G, Wettergreen DS, Cabrol NA, Waggoner AS*.  Application of pulsed-excitation fluorescence imager for daylight detection of sparse life in tests in the Atacama Desert.  J. Geophys. Res. 113, 2008.

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

Ye Q, Wu Y-JL, Foley LM, Hitchens TK, Eytan DF, Shirwan H, Ho C*. Longitudinal Tracking of Recipient Macrophages in a Rat Chronic Cardiac Allograft Rejection Model with Noninvasive Magnetic Resonance Imaging Using Micrometer-Sized Paramagnetic Iron Oxide Particles. Circulation 118:149-156, 2008.

Bachert C, Fimmel CJ, Linstedt AD*. Furin cleavage of cis-Golgi protein GP73 produces marker for liver disease. Traffic 8:1415-23, 2007.

Bagley J, LaRocca G, Jimenez DA, Urban NN*. Adult neurogenesis and specific replacement of interneuron subtypes in the mouse main olfactory bulb. BMC Neuroscience; 8(1):92, 2007.

Ballou B, Ernst LA, Andreko S, Harper TF, Fitzpatrick JAJ, Waggoner AS*, Bruchez MP*. Sentinel Lymph Node Imaging using Quantum Dots in Mouse Tumor Models, Bioconjug Chem 2007, 18(2):389-396.

Barth AL*. Visualizing circuits and systems using transgenic reporters of neural activity. Current Opinion in Neurobiology, 2007. (epub Nov 23 2007)

Benvin AL, Creeger Y, Fisher GW, Ballou B, Waggoner AS*, Armitage BA*. Fluorescent DNA nanotags: supramolecular fluorescent labels based on intercalating dye arrays assembled on nanostructured DNA templates. J Am Chem Soc. 129(7):2025-34, 2007. Epub 2007 Jan 26.

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

Cannon RC, Gewaltig MO, Gleeson P, Bhalla US, Cornelis H, Hines ML, Howell FW, Muller E, Stiles JR*, Wils S, De Schutter E. Interoperability of neuroscience modeling software: current status and future directions. Neuroinformatics. 5(2):127-38, 2007 Summer.

Castro JB, Hovis KR, Urban NN*. Recurrent dendrodendritic inhibition of accessory olfactory bulb mitral cells requires activation of group I metabotropic glutamate receptors. J. Neurosci. 27(21):5664-71, 2007.

Chakraborty SK, Fitzpatrick JAJ, Phillippi JA, Andreko S, Waggoner AS*, Bruchez MP*, Ballou, B. Cholera Toxin B Conjugated Quantum Dots for Live Cell Labeling, Nano Letters 2007, 7(9),2618-2626.

Chebira A, Barbotin Y, Jackson C, Merryman T, Srinivasa G, Murphy RF*, Kovacević J. A multiresolution approach to automated classification of protein subcellular location images. BMC Bioinformatics. 8:210, 2007 Jun 19.

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.

Eagleson KL, Schlueter McFadyen-Ketchum LJ, Ahrens ET*, Mills PH, Does MD, Nickols J, Levitt P. Disruption of Foxg1 expression by knock-in of cre recombinase: effects on the development of the mouse telencephalon. Neuroscience. 148(2):385-99, 2007 Aug 24. Epub 2007 Jul 19.

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.

Ettensohn CA*, Kitazawa C, Cheers MS, Leonard JD and Sharma T. Gene regulatory networks and developmental plasticity in the early sea urchin embryo: alternative deployment of the skeletogenic gene regulatory network. Development, 134:3077-3087, 2007.

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

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.

Giuliano KA, Taylor DL, Waggoner AS*. Reagents to measure and manipulate cell functions. Methods Mol Biol. 356:141-63, 2007.

Glazewski S, Benedetti BL, Barth AL*. Ipsilateral sensory deprivation enhances cortical plasticity. Journal of Neuroscience, 27 (14): 3910-20, 2007.

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

Hackney DD*. Jump-starting kinesin, J.Cell Biol. 176, 7-9, 2007.

Hackney DD*. Processive motor movement, Science. 316, 58-59, 2007.

Hinman VF*, Davidson EH. Evolutionary plasticity of developmental gene regulatory network architecture. Proceedings National Academy of Sciences (USA); 104(49):19404-9, 2007.

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.

Jackson H, Muhammad O, Daneshvar H, Nelms J, Popescu A, Vogelbaum MA, Bruchez M*, Toms SA. Quantum dots are phagocytized by macrophages and co-localize with experimental glioma, Neurosurgery 2007, 60(3):524-529.

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

Kou Z, Cohen WW, Murphy RF*. A stacked graphical model for associating sub-images with sub-captions. Pac Symp Biocomput. 257-68, 2007.

Lanni F*, Pane DA, Weinstein SJ, Waggoner AS*. Compact flashlamp-based fluorescence imager for use under ambient-light conditions. Rev Sci Instrum. 78(3):033702, 2007 Mar.

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.

Levitan ES, Lanni F*, Shakiryanova D. In vivo imaging of vesicle motion and release at the Drosophila neuromuscular junction. Nature Protocols 2: 1117-1125, 2007.

Li D, Manjula BN, Ho NT, Simplaceanu V, Ho C*, Acharya AS. Molecular Aspects of the High Oxygen Affinity of Non-Hypertensive Hexa Pegylated Hemoglobin, [(SP-PEG5K)6-Hb].Artificial Cells, Blood Substitutes, and Biotechnology. 35,19-29, 2007.

Macbeth MR*, Bass BL. Large-scale overexpression and purification of ADARs from Saccharomyces cerevisiae for biophysical and biochemical studies. In Methods in Enzymology, (ed. J.M. Gott) Elsevier Inc., 424:319-331, 2007.

McManus CJ*, Schwartz M, Brow DA. A dynamic bulge in the U6 RNA internal stem-loop functions in spliceosome assembly and activation. RNA. 2007 Dec;13(12):2252-65, 2007. Epub 2007 Oct 9.

Mills PH†, Ahrens ET*. Theoretical MRI contrast model for exogenous T2 agents. Magn Reson Med. 57(2):442-7, 2007 Feb.

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

Morohashi N, Nakajima K, Kurihara D, Mukai Y, Mitchell AP*, Shimizu M. A nucleosome positioned by alpha2/Mcm1 prevents Hap1 activator binding in vivo. Biochem Biophys Res Commun 364, 583-588, 2007.

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.

Pagliano O, Brown W, Rule G*, Bajzek D. Improving Animation Tutorials by Integrating Simulation, Assessment, and Feedback to Promote Active Learning. In G. Richards (Ed.), Proceedings of World Conference on E-Learning in Corporate, Government, Healthcare, and Higher Education 2007 (pp. 144-150). Chesapeake, VA: AACE, 2007.

Patrick MJ, Ernst LA, Waggoner AS*, Thai D, Tai D, Salama G. Enhanced Aqueous Solubility of Long Wavelength Voltage-Sensitive Dyes by Covalent Attachment of Polyethylene Glycol Org. Biomol. Chem., 5, 3347-3353, 2007.

Pennington G, Smith CA, Shackney S, Schwartz R*. Reconstructing tumor phylogenies from heterogeneous single-cell data. J Bioinform Comput Biol. 5(2a):407-27, 2007 Apr.

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

Puthenveedu MA*, Yudowski GA, von Zastrow M. Endocytosis of neurotransmitter receptors: location matters. Cell. 130(6):988-9, 2007.

Sahu SC§, Simplaceanu V, Gong Q§, Ho NT, Tian F, Prestegard JH, Ho C*. Insights into the Solution Structure of Human Deoxyhemoglobin in Absence and Presence of an Allostertic Effector. Biochemistry 46, 9973-9980, 2007.

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

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.

Smith JD, Melhem ME, Magge KT, Waggoner AS*, Campbell PG*. Improved growth factor directed vascularization into fibrin constructs through inclusion of additional extracellular molecules. Microvasc Res. 73(2):84-94, 2007 Mar. Epub 2007 Jan 16.

Song N, Sedgewick RD, Durand D*. Domain architecture comparison for multidomain homology identification. Journal of Computational Biology, 14(4): 496-516, 2007.

Song XJ§, Yuan Y, Simplaceanu V, Sahu SC§, Ho NT, Ho C*. A comparative NMR study of the polypeptide backbone dynamics of hemoglobin in the deoxy and carbonmonoxy forms. Biochemistry. 46(23):6795-803, 2007 Jun 12. Epub 2007 May 12.

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.

Tristram-Nagle S, Nagle JF*. HIV-1 fusion peptide decreases bending energy and promotes curved fusion intermediates. Biophys J. 93(6):2048-55, 2007 Sep 15. Epub 2007 May 25.

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.

Wilt FH, Ettensohn CA*. Morphogenesis of biomineralized structures. In: "Handbook of Biomineralization" (E. Bauerlein, Ed.), Wiley-VCH Press, pp. 183-210, 2007.

Yudowski GA, Puthenveedu MA*, Leonoudakis D, Panicker S, Thorn KS, Beattie EC, von Zastrow M. Real-time imaging of discrete exocytic events mediating surface delivery of AMPA receptors. J Neurosci. 2007 Oct 10;27(41):11112-21.

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.

Ahrens ET*, Srinivas M, Capuano S, Simhan HN, Schatten GP. Magnetic resonance imaging of embryonic and fetal development in model systems. Methods Mol Med. 124:87-101, 2006.

Bajzek DM, Burnette JM*, Rule GS*. Constructing computer models to provide accurate visualizations and authentic online laboratory experiences in an introductory biochemistry course. In Proceedings of World Conference on E-Learning in Corporate, Government, Healthcare, and Higher Education 2006. Chesapeake, VA: AACE.

Banerjee D, Markley AL, Yano T, Ghosh A, Berget PB*, Minkley EG Jr, Khetan SK, Collins TJ. "Green" oxidation catalysis for rapid deactivation of bacterial spores. Angew Chem Int Ed Engl. 45(24):3974-7, 2006 Jun 12.

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.

Castellana N, Dhamdhere K, Sridhar S, Schwartz R*. Relaxing haplotype block models for association testing. Pac Symp Biocomput. 454-66, 2006.

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.

Chattopadhyay PK, Price DA, Harper TF, Betts MR, Yu J, Gostick E, Perfetto SP, Goepfert P, Koup RA, De Rosa SC, Bruchez MP*, Roederer M. Quantum dot semiconductor nanocrystals for immunophenotyping by polychromatic flow cytometry. Nature Medicine 2006, 12:972-977.

Chen SC, Murphy RF*. A graphical model approach to automated classification of protein subcellular location patterns in multi-cell images. BMC Bioinformatics. 7:90, 2006 Feb 23.

Chen X, Murphy RF*. Automated interpretation of protein subcellular location patterns. Int Rev Cytol. 249:193-227, 2006.

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.

Clem RL, Barth A*.  Pathway-specific trafficking of native AMPARs by in vivo experience. Neuron, 2;49 (5): 663-70, 2006.

Crawford JH, Isbell TS, Huang Z, Shiva S, Chacko BK, Schechter AN, Darley-Usmar VM,  Kerby JD, Lang JD, Kraus D, Ho C*, Gladwin MT, Patel R. Hypoxia, Red Blood Cells, and Nitrite Regulate NO-dependent Hypoxic Vasodilatation. Blood 2006; 107,566-574.

Durand D*, Hoberman R. Diagnosing duplications: can it be done? Trends in Genetics, 22(3):156-64, 2006 Mar.

Durand D*, Halldorsson BV, Vernot B. Hybrid micro-macroevolutionary approach to gene tree reconstruction. Journal of Computational Biology, 13 (2): 320-335, 2006.

Egger V, Urban NN*. Dynamic connectivity in the mitral cell-granule cell microcircuit. Semin Cell Dev Biol. 17(4):424-32, 2006 Aug. Epub 2006 May 5. Review.

Ettensohn, CA*. The emergence of pattern in embryogenesis: Regulation of beta-catenin localization during early sea urchin development. STKE Perspective, Science, 361:2006 Nov 14.

Galán RF, Fourcaud-Trocmé N, Ermentrout GB, Urban NN*. Correlation-induced synchronization of oscillations in olfactory bulb neurons. J Neurosci. 26(14):3646-55, 2006 Apr 5.

Galán RF,  Ermentrout GB, Urban NN*. Predicting synchronized neural assemblies from experimentally estimated phase-resetting curves. Neurocomputing, 69(10-12), p.1112-1115, 2006.

Gong Q§, Simplaceanu V, Lukin JA, Giovannelli JL, Ho NT, Ho C*. Quaternary Structure of Carbonmonoxyhemoglobins in Solution: Structural Changes Induced by the Allosteric Effector, Inositol Hexaphosphate. Biochemistry 45, 5140-5148, 2006.

Greenwood AI, Tristram-Nagle S, Nagle JF*. Partial molecular volumes of lipids and cholesterol. Chem Phys Lipids. 143(1-2):1-10, 2006 Sep. Epub 2006 Apr 28.

Gu C, Zhou W, Puthenveedu MA*, Xu M, Jan YN, Jan LY. The microtubule plus-end tracking protein EB1 is required for Kv1 voltage-gated K+ channel axonal targeting. Neuron. 52(5):803-16, 2006 Dec 7.

Guo Y, Linstedt AD*. COPII-Golgi protein interactions regulate COPII coat assembly and Golgi size. J Cell Biol. 174(1):53-63, 2006 Jul 3.

Hitchens TK, Zhan Y, Richardson LV, Richardson JP, Rule GS*. Sequence-specific interactions in the RNA-binding domain of Escherichia coli transcription termination factor Rho.J Biol Chem., 281:33697-703, 2006.

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

Kneipp J, Balakrishnan G, Chen R, Shen TJ, Sahu SC§, Ho NT, Giovannelli JL,  Simplaceanu V, Ho C*, Spiro TG. Dynamics of Allostery in Hemoglobin:  Roles of the Penultimate Tyrosine H-Bonds. Journal of Molecular Biology. 356,335-353, 2006.

Kucerka N, Tristram-Nagle S, Nagle JF*. Closer look at structure of fully hydrated fluid phase DPPC bilayers. Biophys J. 90(11):L83-5, 2006 Jun 1. Epub 2006 Apr 14.

Livingston BT, Killian CE, Wilt F, Cameron A, Landrum MJ, Ermolaeva O, Sapojnikov V, Maglott DR, Buchanan AM, Ettensohn CA*. A genome-wide analysis of biomineralization-related proteins in the sea urchin, Strongylocentrotus purpuratus. Dev. Biol., 300, 335-348, 2006.

Larroux C, Fahey B, Liubicich D, Hinman VF*, Gauthier M, Gongora M, Green K, Wörheide G, Leys SP, Degnan BM. Developmental expression of transcription factor genes in a demosponge: insights into the origin of metazoan multicellularity.  Evol Dev. 8(2):150-73, 2006 Mar-Apr.

Lozier RH, Nagle JF*. Comment on "An apparent general solution for the kinetic models of the bacteriorhodopsin photocycles". J Phys Chem B. 110(30):15041-2; discussion 15043-4, 2006 Aug 3.

McCartney BM*, Price MH, Webb RL, Hayden MA, Holot LM, Zhou M, Bejsovec A, Peifer M. Testing hypotheses for the functions of APC family proteins using null and truncation alleles in Drosophila. Development; 133(12):2407-18, 2006 Jun.

Mitchell AP*. Cryptococcal virulence: beyond the usual suspects. J Clin Invest. 116(6):1481-3, 2006 Jun.

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.

Puthenveedu MA, Bachert C, Puri S, Lanni F*, Linstedt AD*. GM130 and GRASP65-dependent lateral cisternal fusion allows uniform Golgi-enzyme distribution. Nat Cell Biol. 8(3):238-48, 2006 Mar. Epub 2006 Feb 19.

Robertson KL, Yu L, Armitage BA*, Lopez AJ*, Peteanu LA. Fluorescent PNA probes as hybridization labels for biological RNA. Biochemistry, 45(19):6066-6074, 2006.

Roux MM, Townley IK, Raisch M, Reade A, Bradham C, Humphreys G, Gunaratne HJ, Killian CE, Moy G, Su YH, Ettensohn CA*, Wilt F, Vacquier VD, Burke RD, Wessel G, Foltz KR. A functional genomic and proteomic perspective of sea urchin calcium signaling and egg activation. Dev. Biol. 300, 416-33, 2006.

Sahu SC§, Simplaceanu V, Gong Q§, Ho NT, Glushka JG, Prestegard JH, Ho C*. Orientation of deoxyhemoglobin at high magnetic fields: structural insights from RDCs in solution. J Am Chem Soc. 128(19):6290-1, 2006 May 17.

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