Publications from the Center for the Study of Biological Complexity, Virginia Commonwealth University.

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Submissions from 2016

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Network Topology Analysis of Post-Mortem Brain Microarrays Identifies More Alzheimer’s Related Genes and MicroRNAs and Points to Novel Routes for Fighting with the Disease, Sreedevi Chandrasekaran and Danail Bonchev

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The interactome of Streptococcus pneumoniae and its bacteriophages show highly specific patterns of interactions among bacteria and their phages, Rachelle Mariano, Stefan Wuchty, Maria G. Vizoso-Pinto, Roman Häuser, and Peter Uetz

Submissions from 2015

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The truth about metagenomics: quantifying and counteracting bias in 16S rRNA studies, J. Paul Brooks, David J. Edwards, Michael D. Harwich, Maria C. Rivera, Jennifer M. Fettweis, Myrna G. Serrano, Robert Reris, Nihar U. Sheth, Bernice Huang, Phillipe Girerd, Vaginal Microbiome Consortium, Jerome F. Strauss III, Kimberly K. Jefferson, and Gregory A. Buck

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Protein Complexes in Bacteria, J. Harry Caufield, Marco A. Abreu, Christopher Wimble, and Peter Uetz

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Highly Iterated Palindromic Sequences (HIPs) and Their Relationship to DNA Methyltransferases, Jeff Elhai

Submissions from 2014

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Arabidopsis Transcriptome Analysis Reveals Key Roles of Melatonin in Plant Defense Systems, Sarah Weeda, Na Zhang, Xiaolei Zhao, Grace Ndip, Yangdong Guo, Gregory A. Buck, Conggui Fu, and Shuxin Ren

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AGROBEST: an efficient Agrobacterium-mediated transient expression method for versatile gene function analyses in Arabidopsis seedlings, Hang-Yi Wu, Kun-Hsiang Liu, Yi-Chieh Wang, Jing-Fen Wu, Wan-Ling Chiu, Chao-Ying Chen, Shu-Hsing Wu, Jen Sheen, and Erh-Min Lai

Submissions from 2013

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Endosymbiosis in trypanosomatids: the genomic cooperation between bacterium and host in the synthesis of essential amino acids is heavily influenced by multiple horizontal gene transfers, João M.P. Alves, Cecilia C. Klein, Flávia Maia da Silva, André G. Costa-Martins, Myrna G. Serrano, Gregory A. Buck, Ana Tereza R. Vasconcelos, Marie-France Sagot, Marta M.G. Teixeira, Maria Cristina M. Motta, and Erney P. Camargo

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Natural Plasmodium infection in monkeys in the state of Rondônia (Brazilian Western Amazon), Maisa S. Araújo, Mariluce R. Messias, Marivaldo R . Figueiró, Luiz Herman S. Gil, Christian M. Probst, Newton M. Vidal, Tony H. Katsuragawa, Luiz H. Pereira da Silva, and Luiz S. Ozaki

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The E. coli Effector Protein NleF Is a Caspase Inhibitor, Sonja Blasche, Mario Mortl, Holger Steuber, Gabriella Siszler, Shahista Nisa, Frank Schwarz, Inna Lavrik, Thomas M. A. Gronewold, Klaus Maskos, Michael S. Donnenberg, Dirk Ullmann, Peter Uetz, and Manfred Kogl

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Predicting Dyspnea Inducers by Molecular Topology, María Gálvez-Llompart,; Jorge Gálvez; Ramón García-Domenech; and Lemont B. Kier

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A core microbiome associated with the peritoneal tumors of pseudomyxoma peritonei, Jeremy J. Gilreath, Cristina Semino-Mora, Christopher J. Friedline, Hui Liu, Kip L. Bodi, Thomas J. McAvoy, Jennifer Francis, Carol Nieroda, Armando Sardi, Andre Dubois, David W. Lazinski, Andrew Camilli, Traci L. Testerman, and D Scott Merrell

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Biosynthesis of Vitamins and Cofactors in Bacterium-Harbouring Trypanosomatids Depends on the Symbiotic Association as Revealed by Genomic Analyses, Cecilia C. Klein, Joao M. P. Alves, Myrna G. Serrano, Gregory A. Buck, Ana T. R. Vasconcelos, Marie-France Sagot, Marta M. G. Teixeira, Emey P. Camargo, and Maria C. M. Motta

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Global Taxonomic Diversity of Living Reptiles, Daniel Pincheira-Donoso, Aaron M. Bauer, Shai Meiri, and Peter Uetz

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Whole Brain and Brain Regional Coexpression Network Interactions Associated with Predisposition to Alcohol Consumption, Lauren A. Vanderlinden, Laura M. Saba, Katerina Kechris, Michael F. Miles, Paula L. Hoffman, and Boris Tabakoff

Submissions from 2012

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Detection of horizontal transfer of individual genes by anomalous oligomer frequencies, Jeff Elhai, Hailan Liu, and Arnaud Taton

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RsfA (YbeB) Proteins Are Conserved Ribosomal Silencing Factors, Roman Hauser, Markus Pech, Jaroslaw Kijek, Hiroshi Yamamoto, Bjrn Titz, Florian Naeve, Andrey Tovchigrechko, Kaori Yamamoto, Witold Szaflarski, Nono Takeuchi, Thorsten Stellberger, Markus E. Diefenbacher, Knud H. Nierhaus, and Peter Uetz

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Optimizing Read Mapping to Reference Genomes to Determine Composition and Species Prevalence in Microbial Communities, John Martin, Sean Sykes, Sarah Young, Karthik Kota, Riva Sanka, Nihar U. Sheth, Joshua Orvis, Erica Sodergren, Zhengyuan Wang, George M. Weinstock, and Makedonka Mitreva

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A comparison of two distinct murine macrophage gene expression profiles in response to Leishmania amazonensis infection, Christian M. Probst, Rodrigo A. Silva, Juliana P.B. Menezes, Tais F. Almeida, Ivana N. Gomes, Andréia C. Dallabona, Luiz S. Ozaki, Gregory A. Buck, Daniel P. Pavoni, Marco A. Krieger, and Patrícia S.T. Veras

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Genome-Wide Association Study Heterogeneous Cohort Homogenization via Subject Weight Knock-Down, Andre X. C. N. Valente, Joseph Zischkau, Joo H. Shin, Yuan Gao, and Abhijit Sarkar

Submissions from 2011

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Water Chreodes and the Mechanisms of Ligand Diffusion, General Anesthesia, and Sleep, Lemont B. Kier

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Evolution combined with genomic study elucidates genetic bases of isobutanol tolerance in Escherichia coli, Jeremy J. Minty, Ann A. Lesnefsky, Fengming Lin, Yu Chen, Ted A. Zaroff, Artur B. Veloso, Bin Xie, Catie A. McConnell, Rebecca J. Ward, Donald R. Schwartz, Jean-Marie Rouillard, Yuan Gao, Erdogan Gulari, and Xiaoxia Nina Lin

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The protein interaction map of bacteriophage lambda, Seesandra V. Rajagopala, Sherwood Casjens, and Peter Uetz

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Marine Reptiles, Arne R. Rasmessen, John D. Murphy, Medy Ompi, J. Whitfield Gibbons, and Peter Uetz

Submissions from 2010

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A high-throughput cloning system for reverse genetics in Trypanosoma cruzi, Michel Batista, Fabricio K. Marchini, Paola A.F. Celedon, Stenio P. Fragoso, Christian M. Probst, Henrique Preti, Luiz S. Ozaki, Gregory A. Buck, Samuel Goldenberg, and Marco A. Krieger