Carnegie Mellon University


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.