CodAn: predictive models for precise identification of coding regions in eukaryotic transcripts von Nachtigall, Pedro G, Kashiwabara, Andre Y, Durham, Alan M

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TRAP: automated classification, quantification and annotation of tandemly repeated sequences von Sobreira, Tiago José P., Durham, Alan M., Gruber, Arthur

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ToxCodAn-Genome: an automated pipeline for toxin-gene annotation in genome assembly of venomous lineages von Nachtigall, Pedro G, Durham, Alan M, Rokyta, Darin R, Junqueira-de-Azevedo, Inácio L M

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DNA Microarray-Based Genome Comparison of a Pathogenic and a Nonpathogenic Strain of Xylella fastidiosa Delineates Genes Important for Bacterial Virulence von KOIDE, Tie, ZAINI, Paulo A, VERJOVSKI-ALMEIDA, Sergio, DA SILVA, Aline M, GOMES, Suely L, MOREIRA, Leandro M, VENCIO, Ricardo Z. N, MATSUKUMA, Adriana Y, DURHAM, Alan M, TEIXEIRA, Diva C, EL-DORRY, Hamza, MONTEIRO, Patricia B, DA SILVA, Ana Claudia R

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Characterization of SCAR markers of Eimeria spp. of domestic fowl and construction of a public relational database (The Eimeria SCARdb) von Fernandez, Sandra, Katsuyama, Ângela M., Kashiwabara, André Y., Madeira, Alda Maria B.N., Durham, Alan M., Gruber, Arthur

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GenSeed-HMM: A Tool for Progressive Assembly Using Profile HMMs as Seeds and its Application in Alpavirinae Viral Discovery from Metagenomic Data von Alves, João M P, de Oliveira, André L, Sandberg, Tatiana O M, Moreno-Gallego, Jaime L, de Toledo, Marcelo A F, de Moura, Elisabeth M M, Oliveira, Liliane S, Durham, Alan M, Mehnert, Dolores U, Zanotto, Paolo M de A, Reyes, Alejandro, Gruber, Arthur

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A comparative transcriptome analysis reveals expression profiles conserved across three Eimeria spp. of domestic fowl and associated with multiple developmental stages von Novaes, Jeniffer, Rangel, Luiz Thibério L.D., Ferro, Milene, Abe, Ricardo Y., Manha, Alessandra P.S., de Mello, Joana C.M., Varuzza, Leonardo, Durham, Alan M., Madeira, Alda Maria B.N., Gruber, Arthur

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Sequencing and analysis of chromosome 1 of Eimeria tenella reveals a unique segmental organization von Ling, King-Hwa, Rajandream, Marie-Adele, Rivailler, Pierre, Ivens, Alasdair, Yap, Soon-Joo, Madeira, Alda M B N, Mungall, Karen, Billington, Karen, Yee, Wai-Yan, Bankier, Alan T, Carroll, Fionnadh, Durham, Alan M, Peters, Nicholas, Loo, Shu-San, Isa, Mohd Noor Mat, Novaes, Jeniffer, Quail, Michael, Rosli, Rozita, Nor Shamsudin, Mariana, Sobreira, Tiago J P, Tivey, Adrian R, Wai, Siew-Fun, White, Sarah, Wu, Xikun, Kerhornou, Arnaud, Blake, Damer, Mohamed, Rahmah, Shirley, Martin, Gruber, Arthur, Berriman, Matthew, Tomley, Fiona, Dear, Paul H, Wan, Kiew-Lian

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The Eimeria transcript DB: an integrated resource for annotated transcripts of protozoan parasites of the genus Eimeria von Rangel, Luiz Thibério, Novaes, Jeniffer, Durham, Alan M, Madeira, Alda Maria B N, Gruber, Arthur

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High-throughput sequencing of small RNA transcriptomes reveals critical biological features targeted by microRNAs in cell models used for squamous cell cancer research von Severino, Patricia, Oliveira, Liliane Santana, Torres, Natalia, Andreghetto, Flavia Maziero, Klingbeil, Maria de Fatima Guarizo, Moyses, Raquel, Wünsch-Filho, Victor, Nunes, Fabio Daumas, Mathor, Monica Beatriz, Paschoal, Alexandre Rossi, Durham, Alan Mitchell

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EGene: a configurable pipeline generation system for automated sequence analysis von Durham, Alan M., Kashiwabara, André Y., Matsunaga, Fernando T. G., Ahagon, Paulo H., Rainone, Flávia, Varuzza, Leonardo, Gruber, Arthur

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Extense variant gene family repertoire overlap in Western Amazon Plasmodium falciparum isolates von Albrecht, Letusa, Merino, Emilio Fernando, Hoffmann, Erika H.E., Ferreira, Marcelo U., de Mattos Ferreira, Ricardo G., Osakabe, Ana Lucia, Dalla Martha, Rosimeire C., Ramharter, Michael, Durham, Alan M., Ferreira, João Eduardo, del Portillo, Hernando A., Wunderlich, Gerhard

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Multi-character population study of the vir subtelomeric multigene superfamily of Plasmodium vivax, a major human malaria parasite von Merino, Emilio F., Fernandez-Becerra, Carmen, Durham, Alan M., Ferreira, João E., Tumilasci, Vanessa F., d’Arc-Neves, Joana, da Silva-Nunes, Monica, Ferreira, Marcelo U., Wickramarachchi, Thilan, Udagama-Randeniya, Preethi, Handunnetti, Shiroma M., del Portillo, Hernando A.

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Origins of sequence diversity in the malaria vaccine candidate merozoite surface protein-2 (MSP-2) in Amazonian isolates of Plasmodium falciparum von Hoffmann, Erika H.E., Malafronte, Rosely S., Moraes-Ávila, Sandra L., Osakabe, Ana Lúcia, Wunderlich, Gerhard, Durham, Alan M., Ribolla, Paulo Eduardo M., del Portillo, Hernando A., Ferreira, Marcelo U.

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A transcriptome analysis of the Aedes aegypti vitellogenic fat body von Feitosa, Fabiana M., Calvo, Eric, Merino, Emilio F., Durham, Alan M., James, Anthony A., de Bianchi, Antonio G., Marinotti, Osvaldo, Capurro, Margareth L.

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Characterization of SCAR markers of Eimeria spp. of domestic fowl and construction of a public relational database (The Eimeria SCARdb) von Fernandez, Sandra, Katsuyama, Ângela M., Kashiwabara, André Y., Madeira, Alda Maria B.N., Durham, Alan M., Gruber, Arthur

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Combined Learning of Neural Network Weights for Privacy in Collaborative Tasks von Ioste, Aline R, Durham, Alan M, Finger, Marcelo

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Decreasing the number of false positives in sequence classification von Machado-Lima, Ariane, Kashiwabara, André Yoshiaki, Durham, Alan Mitchell

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Does ecosystem sensitivity to precipitation at the site-level conform to regional-scale predictions? von Wilcox, Kevin R, Blair, John M, Smith, Melinda D, Knapp, Alan K

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A framework for run-time systems and its visual programming language von Durham, Alan M., Johnson, Ralph E.

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