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  • Artigo de periodico

    Characterizing the regulatory logic of transcriptional control at the DNA sequence level by ensembles of thermodynamic models (2025)

    Sabino, Alan Utsuni ; Guerreiro, Drielly de Moraes ; Kim, Ah-Ram; Ramos, Alexandre Ferreira ; Reinitz, John

    Source: Bioinformatics. Unidades: EACH, FM

    Assunto: DNA

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      SABINO, Alan Utsuni et al. Characterizing the regulatory logic of transcriptional control at the DNA sequence level by ensembles of thermodynamic models. Bioinformatics, v. 41, n. 10, p. 01-11, 2025Tradução . . Disponível em: http://dx.doi.org/10.1093/bioinformatics/btaf534. Acesso em: 20 nov. 2025.

    • APA

      Sabino, A. U., Guerreiro, D. de M., Kim, A. -R., Ramos, A. F., & Reinitz, J. (2025). Characterizing the regulatory logic of transcriptional control at the DNA sequence level by ensembles of thermodynamic models. Bioinformatics, 41( 10), 01-11. doi:10.1093/bioinformatics/btaf534

    • NLM

      Sabino AU, Guerreiro D de M, Kim A-R, Ramos AF, Reinitz J. Characterizing the regulatory logic of transcriptional control at the DNA sequence level by ensembles of thermodynamic models [Internet]. Bioinformatics. 2025 ; 41( 10): 01-11.[citado 2025 nov. 20 ] Available from: http://dx.doi.org/10.1093/bioinformatics/btaf534

    • Vancouver

      Sabino AU, Guerreiro D de M, Kim A-R, Ramos AF, Reinitz J. Characterizing the regulatory logic of transcriptional control at the DNA sequence level by ensembles of thermodynamic models [Internet]. Bioinformatics. 2025 ; 41( 10): 01-11.[citado 2025 nov. 20 ] Available from: http://dx.doi.org/10.1093/bioinformatics/btaf534

  • Artigo de periodico

    A mixture model for determining SARS-Cov-2 variant composition in pooled samples (2022)

    Valieris, Renan; Drummond, Rodrigo D.; Defelicibus, Alexandre; Dias Neto, Emmanuel; Mitrowsky, Rafael Andres Rosales ; Silva, Israel Tojal da

    Source: Bioinformatics. Unidades: Interunidades em Bioinformática, ICMC, FFCLRP

    Subjects: VACINAS, COVID-19, PANDEMIAS, TRANSMISSÃO DE DOENÇAS, MODELOS MATEMÁTICOS, PROGRAMAS DE VACINAÇÃO

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      VALIERIS, Renan et al. A mixture model for determining SARS-Cov-2 variant composition in pooled samples. Bioinformatics, v. 38, n. 7, p. 1809-1815, 2022Tradução . . Disponível em: https://doi.org/10.1093/bioinformatics/btac047. Acesso em: 20 nov. 2025.

    • APA

      Valieris, R., Drummond, R. D., Defelicibus, A., Dias Neto, E., Mitrowsky, R. A. R., & Silva, I. T. da. (2022). A mixture model for determining SARS-Cov-2 variant composition in pooled samples. Bioinformatics, 38( 7), 1809-1815. doi:10.1093/bioinformatics/btac047

    • NLM

      Valieris R, Drummond RD, Defelicibus A, Dias Neto E, Mitrowsky RAR, Silva IT da. A mixture model for determining SARS-Cov-2 variant composition in pooled samples [Internet]. Bioinformatics. 2022 ; 38( 7): 1809-1815.[citado 2025 nov. 20 ] Available from: https://doi.org/10.1093/bioinformatics/btac047

    • Vancouver

      Valieris R, Drummond RD, Defelicibus A, Dias Neto E, Mitrowsky RAR, Silva IT da. A mixture model for determining SARS-Cov-2 variant composition in pooled samples [Internet]. Bioinformatics. 2022 ; 38( 7): 1809-1815.[citado 2025 nov. 20 ] Available from: https://doi.org/10.1093/bioinformatics/btac047

  • Artigo de periodico

    CNVRanger: association analysis of CNVs with gene expression and quantitative phenotypes (2020)

    Silva, Vinicius da ; Ramos, Marcel; Groenen, Martien; Crooijmans, Richard; Johansson, Anna; Regitano, Luciana; Coutinho, Luiz Lehmann ; Zimmer, Ralf; Waldron, Levi ; Geistlinger, Ludwig

    Source: Bioinformatics. Unidade: ESALQ

    Subjects: DNA, EXPRESSÃO GÊNICA, FENÓTIPOS, GENÔMICA, MARCADOR MOLECULAR, SEQUENCIAMENTO GENÉTICO, SOFTWARES, VARIAÇÃO GENÉTICA

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      SILVA, Vinicius da et al. CNVRanger: association analysis of CNVs with gene expression and quantitative phenotypes. Bioinformatics, v. 36, n. 3, 2020Tradução . . Disponível em: https://doi.org/10.1093/bioinformatics/btz632. Acesso em: 20 nov. 2025.

    • APA

      Silva, V. da, Ramos, M., Groenen, M., Crooijmans, R., Johansson, A., Regitano, L., et al. (2020). CNVRanger: association analysis of CNVs with gene expression and quantitative phenotypes. Bioinformatics, 36( 3). doi:10.1093/bioinformatics/btz632

    • NLM

      Silva V da, Ramos M, Groenen M, Crooijmans R, Johansson A, Regitano L, Coutinho LL, Zimmer R, Waldron L, Geistlinger L. CNVRanger: association analysis of CNVs with gene expression and quantitative phenotypes [Internet]. Bioinformatics. 2020 ; 36( 3):[citado 2025 nov. 20 ] Available from: https://doi.org/10.1093/bioinformatics/btz632

    • Vancouver

      Silva V da, Ramos M, Groenen M, Crooijmans R, Johansson A, Regitano L, Coutinho LL, Zimmer R, Waldron L, Geistlinger L. CNVRanger: association analysis of CNVs with gene expression and quantitative phenotypes [Internet]. Bioinformatics. 2020 ; 36( 3):[citado 2025 nov. 20 ] Available from: https://doi.org/10.1093/bioinformatics/btz632

  • Artigo de periodico

    ELMER v.2: an R/Bioconductor package to reconstruct gene regulatory networks from DNA methylation and transcriptome profiles (2019)

    Silva, Tiago Chedraoui ; Coetzee, Simon G.; Gull, Nicole; Yao, Lijing; Hazelett, Dennis J.; Noushmehr, Houtan ; Lin, De-Chen; Berman, Benjamin P.

    Source: Bioinformatics. Unidade: FMRP

    Subjects: DNA, METILAÇÃO, EXPRESSÃO GÊNICA

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      SILVA, Tiago Chedraoui et al. ELMER v.2: an R/Bioconductor package to reconstruct gene regulatory networks from DNA methylation and transcriptome profiles. Bioinformatics, v. 35, n. 11, p. 1974-1977, 2019Tradução . . Disponível em: https://doi.org/10.1093/bioinformatics/bty902. Acesso em: 20 nov. 2025.

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      Silva, T. C., Coetzee, S. G., Gull, N., Yao, L., Hazelett, D. J., Noushmehr, H., et al. (2019). ELMER v.2: an R/Bioconductor package to reconstruct gene regulatory networks from DNA methylation and transcriptome profiles. Bioinformatics, 35( 11), 1974-1977. doi:10.1093/bioinformatics/bty902

    • NLM

      Silva TC, Coetzee SG, Gull N, Yao L, Hazelett DJ, Noushmehr H, Lin D-C, Berman BP. ELMER v.2: an R/Bioconductor package to reconstruct gene regulatory networks from DNA methylation and transcriptome profiles [Internet]. Bioinformatics. 2019 ; 35( 11): 1974-1977.[citado 2025 nov. 20 ] Available from: https://doi.org/10.1093/bioinformatics/bty902

    • Vancouver

      Silva TC, Coetzee SG, Gull N, Yao L, Hazelett DJ, Noushmehr H, Lin D-C, Berman BP. ELMER v.2: an R/Bioconductor package to reconstruct gene regulatory networks from DNA methylation and transcriptome profiles [Internet]. Bioinformatics. 2019 ; 35( 11): 1974-1977.[citado 2025 nov. 20 ] Available from: https://doi.org/10.1093/bioinformatics/bty902

  • Artigo de periodico

    ProbMetab: an R package for Bayesian probabilistic annotation of LC–MS-based metabolomics (2014)

    Silva, Ricardo S; Jourdan, Fabien; Salvanha, Diego M; Letisse, Fabien; Jamin, Emilien L; Guidetti Gonzalez, Simone; Labate, Carlos Alberto; Vêncio, Ricardo Zorzetto Nicoliello

    Source: Bioinformatics. Unidades: ESALQ, FFCLRP

    Subjects: INFERÊNCIA BAYESIANA, PROBABILIDADE, R (SOFTWARE ESTATÍSTICO)

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      SILVA, Ricardo S et al. ProbMetab: an R package for Bayesian probabilistic annotation of LC–MS-based metabolomics. Bioinformatics, v. 30, n. 9, p. 1336-1337, 2014Tradução . . Disponível em: https://doi.org/10.1093/bioinformatics/btu019. Acesso em: 20 nov. 2025.

    • APA

      Silva, R. S., Jourdan, F., Salvanha, D. M., Letisse, F., Jamin, E. L., Guidetti Gonzalez, S., et al. (2014). ProbMetab: an R package for Bayesian probabilistic annotation of LC–MS-based metabolomics. Bioinformatics, 30( 9), 1336-1337. doi:10.1093/bioinformatics/btu019

    • NLM

      Silva RS, Jourdan F, Salvanha DM, Letisse F, Jamin EL, Guidetti Gonzalez S, Labate CA, Vêncio RZN. ProbMetab: an R package for Bayesian probabilistic annotation of LC–MS-based metabolomics [Internet]. Bioinformatics. 2014 ; 30( 9): 1336-1337.[citado 2025 nov. 20 ] Available from: https://doi.org/10.1093/bioinformatics/btu019

    • Vancouver

      Silva RS, Jourdan F, Salvanha DM, Letisse F, Jamin EL, Guidetti Gonzalez S, Labate CA, Vêncio RZN. ProbMetab: an R package for Bayesian probabilistic annotation of LC–MS-based metabolomics [Internet]. Bioinformatics. 2014 ; 30( 9): 1336-1337.[citado 2025 nov. 20 ] Available from: https://doi.org/10.1093/bioinformatics/btu019

  • Artigo de periodico

    XiP: a computational environment to create, extend and share workflows (2013)

    Nagasaki, Masao ; Fujita, André ; Sekiya, Yayoi; Saito, Ayumu ; Ikeda, Emi; Li, Chen; Miyano, Satoru

    Source: Bioinformatics. Unidade: IME

    Assunto: PROGRAMAÇÃO INTEIRA E FLUXOS EM REDE

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      NAGASAKI, Masao et al. XiP: a computational environment to create, extend and share workflows. Bioinformatics, v. 29, n. 1, p. 137-139, 2013Tradução . . Disponível em: https://doi.org/10.1093/bioinformatics/bts630. Acesso em: 20 nov. 2025.

    • APA

      Nagasaki, M., Fujita, A., Sekiya, Y., Saito, A., Ikeda, E., Li, C., & Miyano, S. (2013). XiP: a computational environment to create, extend and share workflows. Bioinformatics, 29( 1), 137-139. doi:10.1093/bioinformatics/bts630

    • NLM

      Nagasaki M, Fujita A, Sekiya Y, Saito A, Ikeda E, Li C, Miyano S. XiP: a computational environment to create, extend and share workflows [Internet]. Bioinformatics. 2013 ; 29( 1): 137-139.[citado 2025 nov. 20 ] Available from: https://doi.org/10.1093/bioinformatics/bts630

    • Vancouver

      Nagasaki M, Fujita A, Sekiya Y, Saito A, Ikeda E, Li C, Miyano S. XiP: a computational environment to create, extend and share workflows [Internet]. Bioinformatics. 2013 ; 29( 1): 137-139.[citado 2025 nov. 20 ] Available from: https://doi.org/10.1093/bioinformatics/bts630

  • Artigo de periodico

    Modeling associations between genetic markers using Bayesian networks (2010)

    Villanueva, Edwin; Maciel, Carlos Dias

    Source: Bioinformatics. Unidade: EESC

    Assunto: GEOMETRIA E MODELAGEM COMPUTACIONAL

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      VILLANUEVA, Edwin e MACIEL, Carlos Dias. Modeling associations between genetic markers using Bayesian networks. Bioinformatics, v. 26, n. 18, p. i632-i637, 2010Tradução . . Disponível em: https://doi.org/10.1093/bioinformatics/btq392. Acesso em: 20 nov. 2025.

    • APA

      Villanueva, E., & Maciel, C. D. (2010). Modeling associations between genetic markers using Bayesian networks. Bioinformatics, 26( 18), i632-i637. doi:10.1093/bioinformatics/btq392

    • NLM

      Villanueva E, Maciel CD. Modeling associations between genetic markers using Bayesian networks [Internet]. Bioinformatics. 2010 ; 26( 18): i632-i637.[citado 2025 nov. 20 ] Available from: https://doi.org/10.1093/bioinformatics/btq392

    • Vancouver

      Villanueva E, Maciel CD. Modeling associations between genetic markers using Bayesian networks [Internet]. Bioinformatics. 2010 ; 26( 18): i632-i637.[citado 2025 nov. 20 ] Available from: https://doi.org/10.1093/bioinformatics/btq392

  • Artigo de periodico

    PK/DB: database for pharmacokinetic properties and predictive in silico ADME models (2008)

    Moda, Tiago L.; Torres, Leonardo G.; Carrara, Alexandre E.; Andricopulo, Adriano Defini

    Source: Bioinformatics. Unidade: IFSC

    Subjects: BASES DE DADOS (FARMACOLOGIA), WORLD WIDE WEB, FÁRMACOS, FARMACOCINÉTICA (PROPRIEDADES), RELAÇÕES QUANTITATIVAS ENTRE ESTRUTURA QUÍMICA E ATIVIDADE BIOLÓGICA

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      MODA, Tiago L. et al. PK/DB: database for pharmacokinetic properties and predictive in silico ADME models. Bioinformatics, v. 24, n. 19, p. 2270-2271, 2008Tradução . . Disponível em: https://doi.org/10.1093/bioinformatics/btn415. Acesso em: 20 nov. 2025.

    • APA

      Moda, T. L., Torres, L. G., Carrara, A. E., & Andricopulo, A. D. (2008). PK/DB: database for pharmacokinetic properties and predictive in silico ADME models. Bioinformatics, 24( 19), 2270-2271. doi:10.1093/bioinformatics/btn415

    • NLM

      Moda TL, Torres LG, Carrara AE, Andricopulo AD. PK/DB: database for pharmacokinetic properties and predictive in silico ADME models [Internet]. Bioinformatics. 2008 ; 24( 19): 2270-2271.[citado 2025 nov. 20 ] Available from: https://doi.org/10.1093/bioinformatics/btn415

    • Vancouver

      Moda TL, Torres LG, Carrara AE, Andricopulo AD. PK/DB: database for pharmacokinetic properties and predictive in silico ADME models [Internet]. Bioinformatics. 2008 ; 24( 19): 2270-2271.[citado 2025 nov. 20 ] Available from: https://doi.org/10.1093/bioinformatics/btn415

  • Artigo de periodico

    Time-varying modeling of gene expression regulatory networks using the wavelet dynamic vector autoregressive method (2007)

    Fujita, André ; Sato, João Ricardo ; Garay-Malpartida, Humberto Miguel ; Morettin, Pedro Alberto ; Sogayar, Mari Cleide ; Ferreira, Carlos Eduardo

    Source: Bioinformatics. Unidades: IME, IQ, Interunidades em Bioinformática

    Subjects: EXPRESSÃO GÊNICA, BIOQUÍMICA

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      FUJITA, André et al. Time-varying modeling of gene expression regulatory networks using the wavelet dynamic vector autoregressive method. Bioinformatics, v. 23, n. 13, p. 1623-1630, 2007Tradução . . Disponível em: https://doi.org/10.1093/bioinformatics/btm151. Acesso em: 20 nov. 2025.

    • APA

      Fujita, A., Sato, J. R., Garay-Malpartida, H. M., Morettin, P. A., Sogayar, M. C., & Ferreira, C. E. (2007). Time-varying modeling of gene expression regulatory networks using the wavelet dynamic vector autoregressive method. Bioinformatics, 23( 13), 1623-1630. doi:10.1093/bioinformatics/btm151

    • NLM

      Fujita A, Sato JR, Garay-Malpartida HM, Morettin PA, Sogayar MC, Ferreira CE. Time-varying modeling of gene expression regulatory networks using the wavelet dynamic vector autoregressive method [Internet]. Bioinformatics. 2007 ; 23( 13): 1623-1630.[citado 2025 nov. 20 ] Available from: https://doi.org/10.1093/bioinformatics/btm151

    • Vancouver

      Fujita A, Sato JR, Garay-Malpartida HM, Morettin PA, Sogayar MC, Ferreira CE. Time-varying modeling of gene expression regulatory networks using the wavelet dynamic vector autoregressive method [Internet]. Bioinformatics. 2007 ; 23( 13): 1623-1630.[citado 2025 nov. 20 ] Available from: https://doi.org/10.1093/bioinformatics/btm151

  • Artigo de periodico

    OBO to OWL: a protégé OWL tab to read/save OBO ontologies (2007)

    Moreira, Dilvan de Abreu ; Musen, Mark A.

    Source: Bioinformatics. Unidade: ICMC

    Subjects: HIPERMÍDIA, SISTEMAS DISTRIBUÍDOS

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      MOREIRA, Dilvan de Abreu e MUSEN, Mark A. OBO to OWL: a protégé OWL tab to read/save OBO ontologies. Bioinformatics, v. 23, n. 14, p. 1868-1870, 2007Tradução . . Disponível em: http://bioinformatics.oxfordjournals.org/cgi/content/full/23/14/1868?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&fulltext=obo+to+owl&searchid=1&FIRSTINDEX=0&volume=23&issue=14&resourcetype=HWCIT. Acesso em: 20 nov. 2025.

    • APA

      Moreira, D. de A., & Musen, M. A. (2007). OBO to OWL: a protégé OWL tab to read/save OBO ontologies. Bioinformatics, 23( 14), 1868-1870. Recuperado de http://bioinformatics.oxfordjournals.org/cgi/content/full/23/14/1868?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&fulltext=obo+to+owl&searchid=1&FIRSTINDEX=0&volume=23&issue=14&resourcetype=HWCIT

    • NLM

      Moreira D de A, Musen MA. OBO to OWL: a protégé OWL tab to read/save OBO ontologies [Internet]. Bioinformatics. 2007 ; 23( 14): 1868-1870.[citado 2025 nov. 20 ] Available from: http://bioinformatics.oxfordjournals.org/cgi/content/full/23/14/1868?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&fulltext=obo+to+owl&searchid=1&FIRSTINDEX=0&volume=23&issue=14&resourcetype=HWCIT

    • Vancouver

      Moreira D de A, Musen MA. OBO to OWL: a protégé OWL tab to read/save OBO ontologies [Internet]. Bioinformatics. 2007 ; 23( 14): 1868-1870.[citado 2025 nov. 20 ] Available from: http://bioinformatics.oxfordjournals.org/cgi/content/full/23/14/1868?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&fulltext=obo+to+owl&searchid=1&FIRSTINDEX=0&volume=23&issue=14&resourcetype=HWCIT

  • Artigo de periodico

    TRAP: automated classification, quantification and annotation of tandemly repeated sequences (2006)

    Sobreira, Tiago J. Paschoal; Durham, Alan Mitchell ; Gruber, Arthur

    Source: Bioinformatics. Unidades: IME, ICB

    Assunto: DESENVOLVIMENTO DE SOFTWARE

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      SOBREIRA, Tiago J. Paschoal e DURHAM, Alan Mitchell e GRUBER, Arthur. TRAP: automated classification, quantification and annotation of tandemly repeated sequences. Bioinformatics, v. 22, n. 3, p. 361-362, 2006Tradução . . Disponível em: https://doi.org/10.1093/bioinformatics/bti809. Acesso em: 20 nov. 2025.

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      Sobreira, T. J. P., Durham, A. M., & Gruber, A. (2006). TRAP: automated classification, quantification and annotation of tandemly repeated sequences. Bioinformatics, 22( 3), 361-362. doi:10.1093/bioinformatics/bti809

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      Sobreira TJP, Durham AM, Gruber A. TRAP: automated classification, quantification and annotation of tandemly repeated sequences [Internet]. Bioinformatics. 2006 ; 22( 3): 361-362.[citado 2025 nov. 20 ] Available from: https://doi.org/10.1093/bioinformatics/bti809

    • Vancouver

      Sobreira TJP, Durham AM, Gruber A. TRAP: automated classification, quantification and annotation of tandemly repeated sequences [Internet]. Bioinformatics. 2006 ; 22( 3): 361-362.[citado 2025 nov. 20 ] Available from: https://doi.org/10.1093/bioinformatics/bti809

  • Artigo de periodico

    CaSPredictor: a new computer-based tool for caspase substrate prediction (2005)

    Garay-Malpartida, Humberto Miguel; Occhiucci, J. M.; Alves, J.; Belizário, José Ernesto

    Source: Bioinformatics. Unidade: ICB

    Assunto: FARMACOLOGIA

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      GARAY-MALPARTIDA, Humberto Miguel et al. CaSPredictor: a new computer-based tool for caspase substrate prediction. Bioinformatics, v. 21, p. i169-i176, 2005Tradução . . Disponível em: https://doi.org/10.1093/bioinformatics/bti1034. Acesso em: 20 nov. 2025.

    • APA

      Garay-Malpartida, H. M., Occhiucci, J. M., Alves, J., & Belizário, J. E. (2005). CaSPredictor: a new computer-based tool for caspase substrate prediction. Bioinformatics, 21, i169-i176. doi:10.1093/bioinformatics/bti1034

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      Garay-Malpartida HM, Occhiucci JM, Alves J, Belizário JE. CaSPredictor: a new computer-based tool for caspase substrate prediction [Internet]. Bioinformatics. 2005 ; 21 i169-i176.[citado 2025 nov. 20 ] Available from: https://doi.org/10.1093/bioinformatics/bti1034

    • Vancouver

      Garay-Malpartida HM, Occhiucci JM, Alves J, Belizário JE. CaSPredictor: a new computer-based tool for caspase substrate prediction [Internet]. Bioinformatics. 2005 ; 21 i169-i176.[citado 2025 nov. 20 ] Available from: https://doi.org/10.1093/bioinformatics/bti1034

  • Artigo de periodico

    Using credibility intervals instead of hypothesis tests in SAGE analysis (2003)

    Vêncio, Ricardo Zorzetto Nicoliello; Brentani, Helena; Pereira, Carlos Alberto de Bragança

    Source: Bioinformatics. Unidade: IME

    Subjects: INFERÊNCIA BAYESIANA, EXPRESSÃO GÊNICA

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      VÊNCIO, Ricardo Zorzetto Nicoliello e BRENTANI, Helena e PEREIRA, Carlos Alberto de Bragança. Using credibility intervals instead of hypothesis tests in SAGE analysis. Bioinformatics, v. 19, n. 18, p. 2461-2464, 2003Tradução . . Disponível em: https://doi.org/10.1093/bioinformatics/btg357. Acesso em: 20 nov. 2025.

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      Vêncio, R. Z. N., Brentani, H., & Pereira, C. A. de B. (2003). Using credibility intervals instead of hypothesis tests in SAGE analysis. Bioinformatics, 19( 18), 2461-2464. doi:10.1093/bioinformatics/btg357

    • NLM

      Vêncio RZN, Brentani H, Pereira CA de B. Using credibility intervals instead of hypothesis tests in SAGE analysis [Internet]. Bioinformatics. 2003 ; 19( 18): 2461-2464.[citado 2025 nov. 20 ] Available from: https://doi.org/10.1093/bioinformatics/btg357

    • Vancouver

      Vêncio RZN, Brentani H, Pereira CA de B. Using credibility intervals instead of hypothesis tests in SAGE analysis [Internet]. Bioinformatics. 2003 ; 19( 18): 2461-2464.[citado 2025 nov. 20 ] Available from: https://doi.org/10.1093/bioinformatics/btg357
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