Publications by authors named "Alan M Durham"

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

Gigascience· January 2024

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Computational Analysis of Transposable Elements and CircRNAs in Plants.
Liliane Santana Oliveira, Andressa Caroline Patera, Douglas Silva Domingues, Danilo Sipoli Sanches, Fabricio Martins Lopes, Alan Mitchell Durham

Methods Mol Biol· January 2022

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TSSFinder-fast and accurate ab initio prediction of the core promoter in eukaryotic genomes.
Mauro de Medeiros Oliveira, Igor Bonadio, Alicia Lie de Melo, Glaucia Mendes Souza, Alan Mitchell Durham

Brief Bioinform· November 2021

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

Brief Bioinform· May 2021

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Assembly of the 373k gene space of the polyploid sugarcane genome reveals reservoirs of functional diversity in the world's leading biomass crop.
Glaucia Mendes Souza, Marie-Anne Van Sluys, Carolina Gimiliani Lembke, Hayan Lee, Gabriel Rodrigues Alves Margarido, Alan Mitchell Durham

Gigascience· December 2019

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Noncoding RNAs Databases: Current Status and Trends.
Vinicius Maracaja-Coutinho, Alexandre Rossi Paschoal, José Carlos Caris-Maldonado, Pedro Vinícius Borges, Almir José Ferreira, Alan Mitchell Durham

Methods Mol Biol· June 2019

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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.
João M P Alves, André L de Oliveira, Tatiana O M Sandberg, Jaime L Moreno-Gallego, Marcelo A F de Toledo, Alan M Durham

Front Microbiol· March 2016

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Small RNAs in metastatic and non-metastatic oral squamous cell carcinoma.
Patricia Severino, Liliane Santana Oliveira, Flávia Maziero Andreghetto, Natalia Torres, Otávio Curioni, Alan Mitchell Durham

BMC Med Genomics· June 2015

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ToPS: a framework to manipulate probabilistic models of sequence data.
André Yoshiaki Kashiwabara, Igor Bonadio, Vitor Onuchic, Felipe Amado, Rafael Mathias, Alan Mitchell Durham

PLoS Comput Biol· May 2014

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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.
Patricia Severino, Liliane Santana Oliveira, Natalia Torres, Flavia Maziero Andreghetto, Maria de Fatima Guarizo Klingbeil, Alan Mitchell Durham

BMC Genomics· October 2013

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

Database (Oxford)· June 2013

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Non-coding transcription characterization and annotation: a guide and web resource for non-coding RNA databases.
Alexandre Rossi Paschoal, Vinicius Maracaja-Coutinho, João Carlos Setubal, Zilá Luz Paulino Simões, Sergio Verjovski-Almeida, Alan Mitchell Durham

RNA Biol· March 2012

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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.
Jeniffer Novaes, Luiz Thibério L D Rangel, Milene Ferro, Ricardo Y Abe, Alessandra P S Manha, Alan M Durham

Int J Parasitol· January 2012

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

BMC Genomics· December 2010

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A transcriptome analysis of the Aedes aegypti vitellogenic fat body.
Fabiana M Feitosa, Eric Calvo, Emilio F Merino, Alan M Durham, Anthony A James

J Insect Sci· August 2009

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Sequence and structural analysis of the 5' noncoding region of hepatitis C virus in patients with chronic infection.
Flávio Marcos Gomes Araújo, Ariane Machado-Lima, Alan Mitchell Durham, Rosangela Teixeira, Guilherme Oliveira

J Med Virol· July 2009

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Molecular characterization of Mycobacterium massiliense and Mycobacterium bolletii in isolates collected from outbreaks of infections after laparoscopic surgeries and cosmetic procedures.
Cristina Viana-Niero, Karla Valéria Batista Lima, Maria Luiza Lopes, Michelle Christiane da Silva Rabello, Lourival Rodrigues Marsola, Alan Mitchel Durham

J Clin Microbiol· March 2008

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Reliable identification of mycobacterial species by PCR-restriction enzyme analysis (PRA)-hsp65 in a reference laboratory and elaboration of a sequence-based extended algorithm of PRA-hsp65 patterns.
Erica Chimara, Lucilaine Ferrazoli, Suely Yoko Misuka Ueky, Maria Conceição Martins, Alan Mitchel Durham

BMC Microbiol· March 2008

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Computational methods in noncoding RNA research.
Ariane Machado-Lima, Hernando A del Portillo, Alan Mitchell Durham

J Math Biol· January 2008

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Sequencing and analysis of chromosome 1 of Eimeria tenella reveals a unique segmental organization.
King-Hwa Ling, Marie-Adele Rajandream, Pierre Rivailler, Alasdair Ivens, Soon-Joo Yap, Alan M Durham

Genome Res· March 2007

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Extense variant gene family repertoire overlap in Western Amazon Plasmodium falciparum isolates.
Letusa Albrecht, Emilio Fernando Merino, Erika H E Hoffmann, Marcelo U Ferreira, Ricardo G de Mattos Ferreira, Alan M Durham

Mol Biochem Parasitol· December 2006

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Multi-character population study of the vir subtelomeric multigene superfamily of Plasmodium vivax, a major human malaria parasite.
Emilio F Merino, Carmen Fernandez-Becerra, Alan M Durham, João E Ferreira, Vanessa F Tumilasci

Mol Biochem Parasitol· September 2006

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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.
Erika H E Hoffmann, Rosely S Malafronte, Sandra L Moraes-Avila, Ana Lúcia Osakabe, Gerhard Wunderlich, Alan M Durham

Gene· July 2006

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

Bioinformatics· February 2006

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

Bioinformatics· June 2005

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