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Submissions from 2014

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Growth factors and early mesoderm morphogenesis: insights from the sea urchin embryo., Ashrifia Adomako-Ankomah and Charles A. Ettensohn

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Identification of novel mutations by exome sequencing in African American colorectal cancer patients., Hassan Ashktorab, Mohammad Daremipouran, Joe Devaney, Sudhir Varma, Hamed Rahi, Edward Lee, Babak Shokrani, Russell Schwartz, Michael L Nickerson, and Hassan Brim

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A Study of the Different Phases of Refinement of an Inhibitory Circuit in the Mouse Auditory Brainstem, Jineta Banerjee

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Computational biology and bioinformatics., Serafim Batzoglou and Russell S. Schwartz

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Mutational analysis of essential septins reveals a role for septin-mediated signaling in filamentation., Jill R. Blankenship, Shaoji Cheng, Carol A. Woolford, Wenjie Xu, Tanner M. Johnson, P. David Rogers, Saranna Fanning, M. Hong Nguyen, Cornelius J. Clancy, and Aaron P. Mitchell

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Greater excitability and firing irregularity of tufted cells underlies distinct afferent-evoked activity of olfactory bulb mitral and tufted cells., Shawn D. Burton and Nathaniel N. Urban

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Modular Evolution of DNA-Binding Preference of a Tbrain Transcription Factor Provides a Mechanism for Modifying Gene Regulatory Networks., Alys M. Cheatle Jarvela, Lisa Brubaker, Anastasia Vedenko, Anisha Gupta, Bruce A. Armitage, Martha L. Bulyk, and Veronica F. Hinman

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Algorithms to model single gene, single chromosome, and whole genome copy number changes jointly in tumor phylogenetics., Salim A. Chowdhury, Stanley E. Shackney, Kerstin M. Heselmeyer-Haddad, Thomas Ried, Alejandro H. Schäffer, and Russell S. Schwartz

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Tempo and mode of regulatory evolution in Drosophila., Joseph D. Coolon, C. Joel McManus, Kraig R. Stevenson, Brenton R. Graveley, and Patricia J. Wittkopp

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Encoding and storage of spatial information in the retrosplenial cortex., Rafał Czajkowski, Balaji Jayaprakash, Brian Wiltgen, Thomas Rogerson, Mikael C. Guzman-Karlsson, Alison L. Barth, Joshua T. Trachtenberg, and Alcino J. Silva

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The Roles of Glycerol in Candida Albicans Biofilm Formation and Invasion, Jigarkumar V. Desai

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Fungal Biofilms, Drug Resistance, and Recurrent Infection., Jigar V Desai, Aaron P. Mitchell, and David R. Andes

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Horizontal transfer of the msp130 gene supported the evolution of metazoan biomineralization., Charles A. Ettensohn

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Multifunctional RNA Processing Protein SRm160 Induces Apoptosis and Regulates Eye and Genital Development in Drosophila., Yu-Jie Fan, Aryn H. Gittis, François Juge, Chen Qiu, Yong-Zhen Xu, and Leonard Rabinow

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Self-Checking Cell-Based Assays for GPCR Desensitization and Resensitization., Gregory W. Fisher, Margaret H. Fuhrman, Sally A. Adler, Christopher Szent-Gyorgyi, Alan S. Waggoner, and Jonathan Jarvik

Investigating the Role of Hsp27 in Drosophila : Genetic and Phospho - mutant Analysis, Emily Christine Furbee

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Fluorogen-activating scFv biosensors target surface markers on live cells via streptavidin or single-chain avidin., Eugenio Gallo and Jonathan Jarvik

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Fluorogen-activating-proteins as universal affinity biosensors for immunodetection., Eugenio Gallo, Kalin V. Vasilev, and Jonathan Jarvik

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A Single-Chain-Variable-Fragment Fluorescence Biosensor Activates Fluorogens from Dissimilar Chemical Families., Eugenio Gallo, Sophia Wienbar, Avin C. Snyder, Kalin V. Vasilev, Bruce A. Armitage, and Jonathan Jarvik

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Ribosomal Proteins Orchestrate the Biogenesis of Eukaryotic Large Ribosomal Subunits in a Sequential Fashion, Michael Gamalinda

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A hierarchical model for assembly of eukaryotic 60S ribosomal subunit domains., Michael Gamalinda, Uli Ohmayer, Jelena Jakovljevic, Beril Kumcuoglu, Joshua Woolford, Bertrade Mbom, Lawrence Lin, and John L. Woolford Jr.

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Deletion of L4 domains reveals insights into the importance of ribosomal protein extensions in eukaryotic ribosome assembly., Michael Gamalinda and John L. Woolford Jr.

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Myristoylation restricts orientation of the GRASP domain on membranes and promotes membrane tethering., Frank Heinrich, Hirsh Nanda, Haw Zan Goh, Collin Bachert, Mathias Losche, and Adam D. Linstedt

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Single-Cell Genetic Analysis Reveals Insights into Clonal Development of Prostate Cancers and Indicates Loss of PTEN as a Marker of Poor Prognosis., Kerstin M. Heselmeyer-Haddad, Lissa Y. Berroa Garcia, Amanda Bradley, Leanora Hernandez, Yue Hu, Jens K. Habermann, Christoph Dumke, Christoph Thorns, Sven Perner, Ekaterina Pestova, Catherine Burke, Salim A. Chowdhury, Russell S. Schwartz, Alejandro H. Schäffer, Pamela L. Paris, and Thomas Ried

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Developmental gene regulatory network evolution: insights from comparative studies in echinoderms., Veronica F. Hinman and Alys M. Cheatle Jarvela

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Combining perfluorocarbon and superparamagnetic iron-oxide cell labeling for improved and expanded applications of cellular MRI., T. Kevin Hitchens, Li Liu, Lesley M. Foley, Virgil Simplaceanu, Eric T. Ahrens, and Chien Ho

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Genetic labeling of neurons in mouse brain., Z Josh Huang, Hiroki Taniguchi, Miao He, and Sandra J. Kuhlman

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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., Uzoma K. Iheagwara, Pamela L. Beatty, Phu T. Van, Ted M. Ross, Jonathan S. Minden, and Olivera J. Finn

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Evolution of DNA Recognition in a Tbrain Transcription Factor and Its Impact on Larval Neurogenesis in Echinoderms, Alys Cheatle Jarvela

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Isoform-specific tethering links the Golgi ribbon to maintain compartmentalization., Timothy S. Jarvela and Adam D. Linstedt

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The application of KillerRed for acute protein inactivation in living cells., Timothy S. Jarvela and Adam D. Linstedt

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Spatially restricted G protein-coupled receptor activity via divergent endocytic compartments., Frederic Jean-Alphonse, Shanna Bowersox, Stanford Chen, Gemma Beard, Manojkumar A. Puthenveedu, and Aylin C. Hanyaloglu

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Brain tumor specifies intermediate progenitor cell identity by attenuating β-catenin/Armadillo activity., Hideyuki Komori, Qi Xiao, Brooke M. McCartney, and Cheng-Yu Lee

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Structural plasticity within the barrel cortex during initial phases of whisker-dependent learning., Sandra J. Kuhlman, Daniel H. O'Connor, Kevin Fox, and Karel Svoboda

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Role of APC Proteins in Regulating Wnt Signaling and Cytoskeletal Organization in Drosophila, Ezgi Kunttas-Tatli

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Self-association of the APC tumor suppressor is required for the assembly, stability, and activity of the Wnt signaling destruction complex., Ezgi Kunttas-Tatli, David M. Roberts, and Brooke M. McCartney

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Grating imager systems for fluorescence optical-sectioning microscopy., Frederick Lanni

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Transgenic mouse lines subdivide external segment of the globus pallidus (GPe) neurons and reveal distinct GPe output pathways., Kevin J. Mastro, Rachel S. Bouchard, Hiromi A.K. Holt, and Aryn H. Gittis

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Evolution of splicing regulatory networks in Drosophila., C. Joel McManus, Joseph D. Coolon, Jodi Eipper-Mains, Patricia J. Wittkopp, and Brenton R. Graveley

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Ribosome profiling reveals post-transcriptional buffering of divergent gene expression in yeast., C. Joel McManus, Gemma E. May, Pieter Spealman, and Alan Shteyman

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A new era in bioimage informatics., Robert F. Murphy

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Disrupting information coding via block of 4-AP-sensitive potassium channels., Krishnan Padmanabhan and Nathaniel N. Urban

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Induction of HIV-blocking anti-CCR5 IgA in Peyers's patches without histopathological alterations., Claudia Pastori, Lorenzo Diomede, Assunta Venuti, Gregory W. Fisher, Jonathan Jarvik, Morgane Bomsel, Francesca Sanvito, and Lucia Lopalco

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Genome-wide analysis of the skeletogenic gene regulatory network of sea urchins., Kiran Rafiq, Tanvi Shashikant, C. Joel McManus, and Charles A. Ettensohn

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Visual Statistical Learning in Monkey Inferotemporal Cortex, Suchitra Ramachandran

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Mechanistic Insights into Homotypic Fusion of ER Membranes by the Atlastin GTPase, Simran G. Saini

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Membrane tethering by the atlastin GTPase depends on GTP hydrolysis but not on forming the crossover configuration., Simran G Saini, Chuang Liu, Peijun Zhang, and Tina H. Lee

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A Bifunctional Converter: Fluorescein Quenching scFv/Fluorogen Activating Protein for Photostability and Improved Signal to Noise in Fluorescence Experiments., Matthew J Saunders, Ethan Block, Alexander Sorkin, Alan S. Waggoner, and Marcel P. Bruchez

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To "Grow" or "Go": TMEM16A Expression as a Switch between Tumor Growth and Metastasis in SCCHN., Daniel J. Shiwarski, Chunbo Shao, Anke Bill, Jean Kim, Dong Xiao, Carol A. Bertrand, Raja S. Seethala, Daisuke Sano, Jeffery N. Myers, Patrick Ha, Jennifer Grandis, L. Alex Gaither, Manojkumar A. Puthenveedu, and Umamaheswar Duvvuri

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Applying molecular crowding models to simulations of virus capsid assembly in vitro., Gregory R. Smith, Lu Xie, Byoungkoo Lee, and Russell S. Schwartz

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Development of isoform-specific sensors of polypeptide GalNAc-transferase activity., Lina Song, Collin Bachert, Katrine T. Schjoldager, Henrik Clausen, and Adam D. Linstedt

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Ribosome assembly factors Pwp1 and Nop12 are important for folding of 5.8S rRNA during ribosome biogenesis in Saccharomyces cerevisiae., Jason Talkish, Ian W. Campbell, Aarti Sahasranaman, Jelena Jakovljevic, and John L. Woolford Jr.

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Mod-seq: high-throughput sequencing for chemical probing of RNA structure., Jason Talkish, Gemma May, Yizhu Lin, John L. Woolford Jr., and C. Joel McManus

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Reply to 'Complexity of molecular crowding in cell-free enzymatic reaction networks'., Cheemeng Tan, Saumya Saurabh, Marcel P. Bruchez, Russell S. Schwartz, and Philip LeDuc

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Phenotypic signatures arising from unbalanced bacterial growth., Cheemeng Tan, Robert Phillip Smith, Ming-Chi Tsai, Russell S. Schwartz, and Lingchong You

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Computational and experimental characterization of a fluorescent dye for detection of potassium ion concentration., Matteus Tanha, Subhasish K Chakraborty, Beth Gabris, Alan S. Waggoner, Guy Salama, and David Yaron

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Manganese induces oligomerization to promote down-regulation of the intracellular trafficking receptor used by Shiga toxin., Ritika Tewari, Timothy S. Jarvela, and Adam D. Linstedt

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NeuroElectro: a window to the world's neuron electrophysiology data., Shreejoy J. Tripathy, Judith Savitskaya, Shawn D. Burton, Nathaniel N. Urban, and Richard C. Gerkin

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Improving 2D Gel Proteomics With The Structured Illumination Gel Imager, Phu T. Van

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High dynamic range proteome imaging with the structured illumination gel imager., Phu T. Van, Victor Bass, Dan Shiwarski, Frederick Lanni, and Jonathan S. Minden

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In-gel equilibration for improved protein retention in 2DE-based proteomic workflows., Phu T. Van, Vinitha Ganesan, Victor Bass, Amritha Parthasarathy, Danielle Schlesinger, and Jonathan S. Minden

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Disruption of the Transcriptional Regulator Cas5 Results in Enhanced Killing of Candida albicans by Fluconazole., Erin M. Vasicek, Elizabeth L. Berkow, Vincent M. Bruno, Aaron P. Mitchell, Nathan P. Wiederhold, Katherine S. Barker, and P. David Rogers

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GRASP65 controls the cis Golgi integrity in vivo., Tineke Veenendaal, Timothy S. Jarvela, Adam G. Grieve, Johan H. van Es, Adam D. Linstedt, and Catherine Rabouille

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Hierarchical Sorting And Trafficking Of β - 2 Adrenergic Receptors Via Endosomal Microdomains, Rachel Vistein

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Src Regulates Sequence-Dependent Beta-2 Adrenergic Receptor Recycling via Cortactin Phosphorylation., Rachel Vistein and Manojkumar A. Puthenveedu

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Bioinformatics curriculum guidelines: toward a definition of core competencies., Lonnie Welch, Fran Lewitter, Russell S. Schwartz, Cath Brooksbank, Predrag Radivojac, Bruno Gaeta, and Maria Victoria Schneider

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Real-time detection of protein trafficking with high-throughput flow cytometry (HTFC) and fluorogen-activating protein (FAP) base biosensor., Yang Wu, Phillip H. Tapia, Jonathan Jarvik, Alan S. Waggoner, and Larry A. Sklar

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Automated grading of renal cell carcinoma using whole slide imaging., Fang-Cheng Yeh, Anil V. Parwani, Liron Pantanowitz, and Chien Ho

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Mapping stain distribution in pathology slides using whole slide imaging., Fang-Cheng Yeh, Qing Ye, T. Kevin Hitchens, Yi-jen L. Wu, Anil V. Parwani, and Chien Ho

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Novel entries in a fungal biofilm matrix encyclopedia., Robert Zarnowski, William M Westler, Ghislain Ade Lacmbouh, Jane M. Marita, Jameson R. Bothe, Jörg Bernhardt, Anissa Lounes-Hadj Sahraoui, Joël Fontaine, Hiram Sanchez, Ronald D. Hatfield, James M. Ntambi, Jeniel E. Nett, Aaron P. Mitchell, and David R. Andes

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Improve myocardial T1 measurement in rats with a new regression model: Application to myocardial infarction and beyond., Haosen Zhang, Qing Ye, Jie Zheng, Erik B. Schelbert, T. Kevin Hitchens, and Chien Ho

Submissions from 2013

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Cerebral blood flow changes after brain injury in human amyloid-beta knock-in mice., Eric E. Abrahamson, Lesley M. Foley, Steven T. Dekosky, T. Kevin Hitchens, Chien Ho, Patrick M. Kochanek, and Milos D. Ikonomovic

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A Molecular Analysis of Skeletal Morphogenesis in the Sea Urchin Embryo, Ashrifia Adomako-Ankomah

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Growth factor-mediated mesodermal cell guidance and skeletogenesis during sea urchin gastrulation., Ashrifia Adomako-Ankomah and Charles A. Ettensohn

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A sensor of protein O-glycosylation based on sequential processing in the Golgi apparatus., Collin Bachert and Adam D. Linstedt

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The many layers of specification and plasticity in the neocortex., Alison L. Barth and Sandra J. Kuhlman

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Differential wiring of layer 2/3 neurons drives sparse and reliable firing during neocortical development., Brett L. Benedetti, Yoshio Takashima, Jing Wen, Joanna Urban-Ciecko, and Alison L. Barth

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How old is my gene?, John A. Capra, Maureen Stolzer, Dannie Durand, and Katherine S. Pollard

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A mixed integer linear programming model to reconstruct phylogenies from single nucleotide polymorphism haplotypes under the maximum parsimony criterion., Daniele Catanzaro, R. Ravi, and Russell S. Schwartz

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Phylogenetic analysis of multiprobe fluorescence in situ hybridization data from tumor cell populations., Salim A. Chowdhury, Stanley E. Shackney, Kerstin M. Heselmeyer-Haddad, Thomas Ried, Alejandro H. Schäffer, and Russell S. Schwartz

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Determining the subcellular location of new proteins from microscope images using local features., Luis Pedro Coelho, Joshua D. Kangas, Armaghan W. Naik, Elvira Osuna-Highley, Estelle Glory-Afshar, Margaret H. Fuhrman, Ramanuja Simha, Peter B. Berget, Jonathan Jarvik, and Robert F. Murphy

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Structured association analysis leads to insight into Saccharomyces cerevisiae gene regulation by finding multiple contributing eQTL hotspots associated with functional gene modules., Ross E. Curtis, Seyoung Kim, John L. Woolford Jr., Wenjie Xu, and Eric P. Xing

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Has1 regulates consecutive maturation and processing steps for assembly of 60S ribosomal subunits., Jill A. Dembowski, Benjamin Kuo, and John L. Woolford Jr.

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Identification of the binding site of Rlp7 on assembling 60S ribosomal subunits in Saccharomyces cerevisiae., Jill A. Dembowski, Madhumitha Ramesh, C. Joel McManus, and John L. Woolford Jr.

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Regulatory role of glycerol in Candida albicans biofilm formation., Jigar V Desai, Vincent M. Bruno, Shantanu Ganguly, Ronald J. Stamper, Kaitlin F. Mitchell, Norma Solis, Elizabeth M. Hill, Wenjie Xu, Scott G. Filler, David R. Andes, Saranna Fanning, Frederick Lanni, and Aaron P. Mitchell