Publications -Department of Biological Sciences - Carnegie Mellon University

Publications

Selected publications from all members of the department.

* Faculty

† Graduate Student
‡ Undergraduate Student
§ Postdoctoral Fellow
¥ Research Scientist
€ Research Staff/Technician


2014 Publications

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

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).

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Yeh FC, Ye Q, Hitchens TK¥, Wu YL, Parwani AV, Ho C*. Mapping stain distribution in pathology slides using whole slide imaging. J Pathol Inform. 2014 Jan 31;5:1

Hitchens TK¥, Liu L, Foley LM, Simplaceanu V, Ahrens ET*, Ho C*. Combining perfluorocarbon and superparamagnetic iron-oxide cell labeling for improved and expanded applications of cellular MRI. Magn Reson Med. 2014 Jan 29.

Tan X, Dey SK, Telmer C¥, Zhang X, Armitage BA*, Bruchez MP*. Aptamers act as activators for the thrombin mediated-hydrolysis of peptide substrates. Chembiochem. 2014 Jan 24;15(2):205-8.

Gamalinda M, Ohmayer U, Jakovljevic J, Kumcuoglu B, Mbom B, Lin L, Woolford JL Jr*. A hierarchical model for assembly of eukaryotic 60S ribosomal subunit domains. Genes Dev. 2014 Jan 15;28(2):198-210.

Smith GR, Xie L, Lee B, Schwartz R*. Applying molecular crowding models to simulations of virus capsid assembly in vitro. Biophys J. 2014 Jan 7;106(1):310-20.

Komori H, Xiao Q, McCartney BM*, Lee CY. Brain tumor specifies intermediate progenitor cell identity by attenuating β-catenin/Armadillo activity. Development. 2014 Jan;141(1):51-62

Wu Y, Tapia PH, Jarvik J*, Waggoner AS*, Sklar LA. Real-time detection of protein trafficking with high-throughput flow cytometry (HTFC) and fluorogen-activating protein (FAP) base biosensor. Curr Protoc Cytom. 2014 Jan 2;67:Unit 9.43.

Capra JA, Stolzer M§, Durand D*, Pollard KS. How old is my gene? Trends in Genetics. Volume 29, Issue 11.

 

Past Publications

2013

2012

2011

2010

2009

2008

2007

2006

2005