2013

Naik AW, Kangas JD, Langmead CJ*, Murphy RF*. Efficient modeling and active learning discovery of biological responses. PLoS One. 2013 Dec 17;8(12):e83996.

Yuan Y, Byrd C, Shen TJ, Simplaceanu V€, Tam TC, Ho C*. Role of β/δ101Gln in regulating the effect of temperature and allosteric effectors on oxygen affinity in woolly mammoth hemoglobin. Biochemistry. 2013 Dec 10;52(49):8888-97.

Ohmayer U, Gamalinda M†, Sauert M, Ossowski J, Pöll G, Linnemann J, Hierlmeier T, Perez-Fernandez J, Kumcuoglu B†, Leger-Silvestre I, Faubladier M, Griesenbeck J, Woolford JL Jr.*, Tschochner H, and Milkereit P (2013) Studies on the Assembly Characteristics of Large Subunit Ribosomal Proteins in S. cerevisae. PLoS ONE 8(7): e68412. Doi:10.1371/journal.pone. 0068412.

Curtis RE, Kim S, Woolford JL Jr.*, Xu W§, Xing EP* (2013) Structured association analysis leads to insight into Saccharomyces cerevisiae gene regulation by finding multiple contributing eQTL hotspots associated with functional gene modules. BMC Genomics. 14:196. doi: 10.1186/1471-2164-14-196.

O'Meara TR, Xu W§, Selvig KM, O'Meara MJ, Mitchell AP*, Alspaugh JA. The Cryptococcus neoformans Rim101 transcription factor directly regulates genes required for adaptation to the host. Mol Cell Biol. 2013 Dec 9.

Woolford, J.L., Jr.* and Baserga, S. (2013) Ribosome biogenesis in the yeast Saccharomyces cerevisiae. Genetics 195: 643-681.

Dembowski J.A.§, Ramesh M†, McManus C. J.*, and Woolford J.L. Jr.* (2013) Identification of the binding site of Rlp7 on assembling 60S ribosomal subunits in Saccharomyces cerevisiae. RNA 19:1639-1647.

Jarvela T† and Linstedt A.D.* (2013). “Isoform-specific tethering links the Golgi ribbon to maintain compartmentalization”, Mol Biol Cell, in press.

Mukhopadhyay S§, Redle  B†, and Linstedt A.D.* (2013). “Shiga toxin binding site for host cell receptor GPP130 reveals unexpected divergence in toxin trafficking mechanisms”, Mol Biol Cell, 24:2311-8 PMID 23761068.

Mukhopadhyay S§ and Linstedt A.D.* (2013). Retrograde trafficking of AB5 toxins: mechanisms to therapeutics, J Mol Med, 91:1131-1141. PMID: 23665994.

Bachert, C€ and Linstedt, A.D.* (2013). “A Sensor of Protein O-Glycosylation Based on Sequential Processing in the Golgi apparatus”, Traffic 14(1):47-56. PMID: 23046148

Bishop AC, Ganguly S†, Solis NV, Cooley BM, Jensen-Seaman MI, Filler SG, Mitchell AP*, Patton-Vogt J.  Glycerophosphocholine utilization by Candida albicans: Role of the Git3 transporter in virulence. J Biol Chem. 2013 Oct 10.

Kuhlman SJ*, Olivas ND, Tring E, Ikrar T, Xu X, Trachtenberg JT. A disinhibitory microcircuit initiates critical-period plasticity in the visual cortex. Nature. 2013 Sep 26;501(7468):543-6. doi: 10.1038/nature12485.

Gerkin RC§, Tripathy SJ, Urban NN*. Origins of correlated spiking in the mammalian olfactory bulb. Proc Natl Acad Sci U S A. 2013 Sep 30.

Cheng S, Clancy CJ, Xu W§, Schneider F, Hao B, Mitchell AP*, Nguyen MH. Profiling of Candida albicans Gene Expression During Intra-abdominal Candidiasis Identifies Biologic Processes Involved in Pathogenesis. J Infect Dis. 2013 Sep 4.

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

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

Vistein R†, Puthenveedu MA*. Reprogramming of G protein-coupled receptor recycling and signaling by a kinase switch. Proc Natl Acad Sci U S A. 2013 Sep 3. [Epub ahead of print]

Nagle JF*. Introductory lecture: basic quantities in model biomembranes. Faraday Discuss. 2013;161:11-29; discussion 113-50.

Kuhlman SJ*, Olivas ND, Tring E, Ikrar T, Xu X, Trachtenberg JT. A disinhibitory microcircuit initiates critical-period plasticity in the visual cortex. Nature. 2013 Aug 25. doi: 10.1038/nature12485. [Epub ahead of print]

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

Navlakha S, Suhan J, Barth AL*, Bar-Joseph Z*. A high-throughput framework to detect synapses in electron microscopy images. Bioinformatics. 2013 Jul 1;29(13):i9-i17. doi: 10.1093/bioinformatics/btt222.

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

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

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

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

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

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

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

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

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

Tripathy SJ, Padmanabhan K, Gerkin RC§, Urban NN*. Intermediate intrinsic diversity enhances neural population coding. Proc Natl Acad Sci U S A. 2013 Apr 29.

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

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

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

Le HS, Schulz MH, McCauley BM§, Hinman VF*, Bar-Joseph Z. Probabilistic error correction for RNA sequencing. Nucleic Acids Res. 2013 Apr 4. [Epub ahead of print]

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

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

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

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

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

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

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