Carnegie Mellon University


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.