Peer-Reviewed Publications

Takac T, Samajova O, Vadovic P, Pechan T, Kosutova P, Ovecka M, Husickova A, Komis G, Samaj J (2014) Proteomic and biochemical analyses show a functional network of proteins involved in antioxidant defense of the Arabidopsis anp2anp3 double mutant. Journal of Proteome Research 13(12): 5347-5361. DOI: 10.1021/pr500588c • SCOPUS ID: 2-s2.0-84915751026 • SCOPUS CITATION COUNT: 18

Edelmann MJ, Shack LA, Naske CD, Walters KB, Nanduri B (2014) SILAC-based quantitative proteomic analysis of human lung cell response to copper oxide nanoparticles. PLoS ONE 9(12): e114390. DOI: 10.1371/journal.pone.0114390 • SCOPUS ID: 2-s2.0-84898925931 • SCOPUS CITATION COUNT: 34

Suh A, Weber CC, Kehlmaier C, Braun EL, Green RE, Fritz U, Ray DA, Ellegren H (2014) Early mesozoic coexistence of amniotes and hepadnaviridae. PLoS Genetics 10(12): e1004559. DOI: 10.1371/journal.pgen.1004559 • SCOPUS ID: 2-s2.0-84919663851 • SCOPUS CITATION COUNT: 56

Villeneuve DL, Crump D, Garcia-Reyero N, Hecker M, Hutchinson TH, LaLone CA, Landesmann B, Lettieri T, Munn S, Nepelska M, Ottinger MA, Vergauwen L,Whelan M (2014) Adverse outcome pathway (AOP) development I: Strategies and principles. Toxicological Sciences 142(2): 312-20. DOI: 10.1093/toxsci/kfu199 • SCOPUS ID: 2-s2.0-84921451260 • SCOPUS CITATION COUNT: 579

Villeneuve DL, Crump D, Garcia-Reyero N, Hecker M, Hutchinson TH, LaLone CA, Landesmann B, Lettieri T, Munn S, Nepelska M, Ottinger MA, Vergauwen L,Whelan M (2014) Adverse outcome pathway development II: Best practices. Toxicological Sciences 142(2): 321-30. DOI: 10.1093/toxsci/kfu200 • SCOPUS ID: 2-s2.0-84922465985 • SCOPUS CITATION COUNT: 221

Narayanan LA, Edelmann MJ (2014) Ubiquitination as an efficient molecular strategy employed in salmonella infection. Frontiers in Immunology 5: 558. DOI: 10.3389/fimmu.2014.00558 • SCOPUS ID: 2-s2.0-84919457029 • SCOPUS CITATION COUNT: 26

Ricklefs RE, Outlaw DC, Svensson-Coelho M, Medeiros MC, Ellis VA, Latta S (2014) Species formation by host shifting in avian malaria parasites. Proceedings of the National Academy of Sciences of the United States of America 111(41): 14816-14821. DOI: 10.1073/pnas.1416356111 • SCOPUS ID: 2-s2.0-84907938532 • SCOPUS CITATION COUNT: 120

Wang XQ, Showmaker KC, Yu XQ, Bi T, Hsu CY, Baird SM, Peterson DG, Li XD, Lu SE (2014) Draft Genome Sequence of Burkholderia pyrrocinia Lyc2, a Biological Control Strain That Can Suppress Multiple Plant Microbial Pathogens. Genome Announcements 2(5): e00991-14. DOI: 10.1128/genomeA.00991-14 • SCOPUS ID: 2-s2.0-85004148111 • SCOPUS CITATION COUNT: 4

Tollefsen KE, Scholz S, Cronin MT, Edwards SW, de KJ, Crofton K, Garcia-Reyero N, Hartung T, Worth A, Patlewicz G (2014) Applying Adverse Outcome Pathways (AOPs) to support Integrated Approaches to Testing and Assessment (IATA). Regulatory Toxicology and Pharmacology 70(3): 629-640. DOI: 10.1016/j.yrtph.2014.09.009 • SCOPUS ID: 2-s2.0-84922433050 • SCOPUS CITATION COUNT: 309

Colosimo G, Knapp CR, Wallace LE, Welch ME (2014) Inferred vs Realized Patterns of Gene Flow: An Analysis of Population Structure in the Andros Island Rock Iguana. PLoS ONE 9(9): e106963. DOI: 10.1371/journal.pone.0106963 • SCOPUS ID: 2-s2.0-84900303812 • SCOPUS CITATION COUNT: 12

Yang J, Zhang T, Wan XF (2014) Sequence-based antigenic change prediction by a sparse learning method incorporating co-evolutionary information. PLoS ONE 9(9): e106660. DOI: 10.1371/journal.pone.0106660 • SCOPUS ID: 2-s2.0-84884223718 • SCOPUS CITATION COUNT: 22

Magbanua ZV, Arick M, Buza T, Hsu CY, Showmaker KC, Chouvarine P, Deng P, Peterson DG, Lu S (2014) Transcriptomic dissection of the rice - Burkholderia glumae interaction. BMC Genomics 15: 755. DOI: 10.1186/1471-2164-15-755 • SCOPUS ID: 2-s2.0-84907021084 • SCOPUS CITATION COUNT: 21

Li S, Tighe SW, Nicolet CM, Grove D, Levy S, Farmerie W, Viale A, Wright C, Schweitzer PA, Gao Y, Kim D, Boland J, Hicks B, Kim R, Chhangawala S, Jafari N, Raghavachari N, Gandara J, Garcia-Reyero N, Hendrickson C, Roberson D, Rosenfeld J, Smith T, Underwood JG, Wang M, Zumbo P, Baldwin DA, Grills GS, Mason CE (2015) Multi-platform assessment of transcriptome profiling using RNA-seq in the ABRF next-generation sequencing study. Nature Biotechnology 32(9): 915-925. DOI: 10.1038/nbt.2972 • SCOPUS ID: 2-s2.0-84922578455 • SCOPUS CITATION COUNT: 180

Smekalova V, Luptovciak I, Komis G, Samajova O, Ovecka M, Doskocilova A, Takac T, Vadovic P, Novak O, Pechan T, Ziemann A, Kosutova P, Samaj J (2014) Involvement of YODA and mitogen activated protein kinase 6 in Arabidopsis post-embryogenic root development through auxin up-regulation and cell division plane orientation. New Phytologist 203(4): 1175-1193. DOI: 10.1111/nph.12880 • SCOPUS ID: 2-s2.0-84905121389 • SCOPUS CITATION COUNT: 87

Nadeau NJ, Ruiz M, Salazar P, Counterman B, Medina JA, Ortiz-Zuazaga H, Morrison A, McMillan WO, Jiggins CD, Papa R (2014) Population genomics of parallel hybrid zones in the mimetic butterflies, H. melpomene and H. erato. Genome Research 24(8): 1316-1333. DOI: 10.1101/gr.169292.113 • SCOPUS ID: 2-s2.0-84905666210 • SCOPUS CITATION COUNT: 91

Eme L, Sharpe SC, Brown MW, Roger AJ (2014) On the Age of Eukaryotes: Evaluating Evidence from Fossils and Molecular Clocks. Cold Spring Harbor Perspectives in Biology 6(8): a016139. DOI: 10.1101/cshperspect.a016139 • SCOPUS ID: 2-s2.0-84894381498 • SCOPUS CITATION COUNT: 201

Pramod S, Perkins AD, Welch ME (2014) Patterns of microsatellite evolution inferred from the Helianthus annuus (Asteraceae) transcriptome. Journal of Genetics 93(2): 431-442. SCOPUS CITATION COUNT:

Takac T, Pechan T, Samajova O, Samaj J (2014) Integrative chemical proteomics and cell biology methods to study endocytosis and vesicular trafficking in Arabidopsis. Methods in Molecular Biology 1209: 265-283. DOI: 10.1007/978-1-4939-1420-3_20 • SCOPUS ID: 2-s2.0-84934436136 • SCOPUS CITATION COUNT: 4

Watson PM, Sorrell SC, Brown MW (2014) Ptolemeba n. gen., a Novel Genus of Hartmannellid Amoebae (Tubulinea, Amoebozoa); with an Emphasis on the Taxonomy of Saccamoeba. Journal of Eukaryotic Microbiology 61(6): 611-619. DOI: 10.1111/jeu.12139 • SCOPUS ID: 2-s2.0-84933521421 • SCOPUS CITATION COUNT: 6

Lee N, Horstemeyer MF, Rhee H, Nabors B, Liao J, Williams LN (2014) Hierarchical multiscale structure-property relationships of the red-bellied woodpecker (Melanerpes carolinus) beak. Journal of the Royal Society Interface 11(96): 20140274. DOI: 10.1098/rsif.2014.0274 • SCOPUS ID: 2-s2.0-84901388383 • SCOPUS CITATION COUNT: 142