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Academic Journal

Beware to ignore the rare: how imputing zero-values can improve the quality of 16S rRNA gene studies results.

  • Authors : Baruzzo G; Department of Information Engineering, University of Padova, Padua, Italy.; Patuzzi I

Subjects: Bacteria*/Bacteria*/Bacteria*/genetics ; Data Analysis*; Genes, rRNA

  • Source: BMC bioinformatics [BMC Bioinformatics] 2022 Feb 07; Vol. 22 (Suppl 15), pp. 618. Date of Electronic Publication: 2022 Feb 07.Publisher: BioMed Central Country of Publication: England NLM ID: 100965194 Publication Model: Electronic Cited Medium:

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Academic Journal

LuxRep: a technical replicate-aware method for bisulfite sequencing data analysis.

  • Authors : Malonzo MH; Department of Computer Science, Aalto University, 00076, Espoo, Finland. .; Halla-Aho V

Subjects: Data Analysis* ; Sulfites*; DNA Methylation

  • Source: BMC bioinformatics [BMC Bioinformatics] 2022 Jan 14; Vol. 23 (1), pp. 41. Date of Electronic Publication: 2022 Jan 14.Publisher: BioMed Central Country of Publication: England NLM ID: 100965194 Publication Model: Electronic Cited Medium:

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Academic Journal

HOME-BIO (sHOtgun MEtagenomic analysis of BIOlogical entities): a specific and comprehensive pipeline for metagenomic shotgun sequencing data analysis.

  • Authors : Ferravante C; Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, Via S. Allende, 1, 84081, Baronissi, SA, Italy.; Department of Veterinary Medicine and Animal Production, University of Naples Federico II, Via Delpino 1, 80137, Naples, Italy.

Subjects: Data Analysis* ; Metagenomics*; Computational Biology

  • Source: BMC bioinformatics [BMC Bioinformatics] 2021 Jul 05; Vol. 22 (Suppl 7), pp. 106. Date of Electronic Publication: 2021 Jul 05.Publisher: BioMed Central Country of Publication: England NLM ID: 100965194 Publication Model: Electronic Cited Medium:

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Academic Journal

RNAdetector: a free user-friendly stand-alone and cloud-based system for RNA-Seq data analysis.

  • Authors : La Ferlita A; Department of Clinical and Experimental Medicine, Bioinformatics Unit, University of Catania, Catania, Italy.; Department of Cancer Biology and Genetics, The Ohio State University, Columbus, OH, USA.

Subjects: Cloud Computing* ; Data Analysis*; Computational Biology

  • Source: BMC bioinformatics [BMC Bioinformatics] 2021 Jun 03; Vol. 22 (1), pp. 298. Date of Electronic Publication: 2021 Jun 03.Publisher: BioMed Central Country of Publication: England NLM ID: 100965194 Publication Model: Electronic Cited Medium:

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Academic Journal

Paired-end small RNA sequencing reveals a possible overestimation in the isomiR sequence repertoire previously reported from conventional single read data analysis.

Subjects: Data Analysis* ; MicroRNAs*/MicroRNAs*/MicroRNAs*/genetics; High-Throughput Nucleotide Sequencing

  • Source: BMC bioinformatics [BMC Bioinformatics] 2021 Apr 26; Vol. 22 (1), pp. 215. Date of Electronic Publication: 2021 Apr 26.Publisher: BioMed Central Country of Publication: England NLM ID: 100965194 Publication Model: Electronic Cited Medium:

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Academic Journal

uap: reproducible and robust HTS data analysis.

  • Authors : Kämpf C; Young Investigators Group Bioinformatics and Transcriptomics, Department Molecular Systems Biology, Helmholtz Center for Environmental Research - UFZ, Permoserstraße 15, Leipzig, 04318, Germany.; Bioinformatics Department, Universität Leipzig, Härtelstraße 16-18, Leipzig, 04107, Germany.

Subjects: Data Analysis* ; High-Throughput Nucleotide Sequencing* ; Software*

  • Source: BMC bioinformatics [BMC Bioinformatics] 2019 Dec 12; Vol. 20 (1), pp. 664. Date of Electronic Publication: 2019 Dec 12.Publisher: BioMed Central Country of Publication: England NLM ID: 100965194 Publication Model: Electronic Cited Medium:

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Academic Journal

Improving CLIP-seq data analysis by incorporating transcript information.

  • Authors : Uhl M; Bioinformatics Group, Department of Computer Science, University of Freiburg, Georges-Köhler-Allee 106, Freiburg, 79110, Germany.; Tran VD

Subjects: Chromatin Immunoprecipitation Sequencing* ; Data Analysis*; Binding Sites

  • Source: BMC genomics [BMC Genomics] 2020 Dec 17; Vol. 21 (1), pp. 894. Date of Electronic Publication: 2020 Dec 17.Publisher: BioMed Central Country of Publication: England NLM ID: 100965258 Publication Model: Electronic Cited Medium:

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Academic Journal

Exact association test for small size sequencing data.

  • Authors : Lee J; Department of Statistics, Seoul National University, Seoul, South Korea.; Lee S

Subjects: Data Analysis* ; High-Throughput Nucleotide Sequencing*; Aged

  • Source: BMC medical genomics [BMC Med Genomics] 2018 Apr 20; Vol. 11 (Suppl 2), pp. 30. Date of Electronic Publication: 2018 Apr 20.Publisher: BioMed Central Country of Publication: England NLM ID: 101319628 Publication Model: Electronic Cited Medium:

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Academic Journal

Signal enrichment with strain-level resolution in metagenomes using topological data analysis.

  • Authors : Guzmán-Sáenz A; Computational Biology Center, IBM T. J. Watson Research Center, Yorktown Heights, NY, USA.; Haiminen N

Subjects: Algorithms* ; Data Analysis* ; Metagenome*

  • Source: BMC genomics [BMC Genomics] 2019 Apr 04; Vol. 20 (Suppl 2), pp. 194. Date of Electronic Publication: 2019 Apr 04.Publisher: BioMed Central Country of Publication: England NLM ID: 100965258 Publication Model: Electronic Cited Medium:

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