Source: BMC bioinformatics [BMC Bioinformatics] 2023 Jan 31; Vol. 24 (1), pp. 33. Date of Electronic Publication: 2023 Jan 31.Publisher: BioMed Central Country of Publication: England NLM ID: 100965194 Publication Model: Electronic Cited Medium:

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Detecting genomic deletions from high-throughput sequence data with unsupervised learning.

Authors : Li X; Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, 20892, USA. .; Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc, Frederick, MD, 21702, USA. .

Subjects: Unsupervised Machine Learning* ; High-Throughput Nucleotide Sequencing*/High-Throughput Nucleotide Sequencing*/High-Throughput Nucleotide Sequencing*/methods; Humans

Source: BMC bioinformatics [BMC Bioinformatics] 2023 Jan 27; Vol. 23 (Suppl 8), pp. 568. Date of Electronic Publication: 2023 Jan 27.Publisher: BioMed Central Country of Publication: England NLM ID: 100965194 Publication Model: Electronic Cited Medium:

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peaksat: an R package for ChIP-seq peak saturation analysis.

Authors : Boyd JR; Department of Biomedical and Health Sciences, University of Vermont, 106 Carrigan Drive, 302 Rowell, VT, 04505, Burlington, USA.; Gao C

Subjects: Chromatin Immunoprecipitation Sequencing*/Chromatin Immunoprecipitation Sequencing*/Chromatin Immunoprecipitation Sequencing*/methods ; High-Throughput Nucleotide Sequencing*; Sequence Analysis, DNA/Sequence Analysis, DNA/Sequence Analysis, DNA/methods

Source: BMC genomics [BMC Genomics] 2023 Jan 25; Vol. 24 (1), pp. 43. Date of Electronic Publication: 2023 Jan 25.Publisher: BioMed Central Country of Publication: England NLM ID: 100965258 Publication Model: Electronic Cited Medium:

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XCVATR: detection and characterization of variant impact on the Embeddings of single -cell and bulk RNA-sequencing samples.

Authors : Harmanci A; University of Texas Health Science Center, School of Biomedical Informatics, Center for Secure Artificial intelligence For hEalthcare (SAFE), Center for Precision Health, Houston, USA. .; Harmanci AS

Subjects: Gene Expression Profiling*/Gene Expression Profiling*/Gene Expression Profiling*/methods ; High-Throughput Nucleotide Sequencing*/High-Throughput Nucleotide Sequencing*/High-Throughput Nucleotide Sequencing*/methods; Transcriptome

Source: BMC genomics [BMC Genomics] 2022 Dec 20; Vol. 23 (1), pp. 841. Date of Electronic Publication: 2022 Dec 20.Publisher: BioMed Central Country of Publication: England NLM ID: 100965258 Publication Model: Electronic Cited Medium:

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srnaMapper: an optimal mapping tool for sRNA-Seq reads.

Authors : Zytnicki M; Unité de Mathématiques et Informatique Appliquées, INRAE, Castanet-Tolosan, France. .; Gaspin C

Subjects: High-Throughput Nucleotide Sequencing*/High-Throughput Nucleotide Sequencing*/High-Throughput Nucleotide Sequencing*/methods ; MicroRNAs*; Sequence Analysis, RNA/Sequence Analysis, RNA/Sequence Analysis, RNA/methods

Source: BMC bioinformatics [BMC Bioinformatics] 2022 Nov 18; Vol. 23 (1), pp. 495. Date of Electronic Publication: 2022 Nov 18.Publisher: BioMed Central Country of Publication: England NLM ID: 100965194 Publication Model: Electronic Cited Medium:

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Modeling and cleaning RNA-seq data significantly improve detection of differentially expressed genes.

Authors : Deyneko IV; Laboratory of Functional Genomics, К.А. Timiryazev Institute of Plant Physiology RAS, Moscow, Russia, 127276. .; Mustafaev ON

Subjects: RNA* ; High-Throughput Nucleotide Sequencing*; RNA-Seq

Source: BMC bioinformatics [BMC Bioinformatics] 2022 Nov 16; Vol. 23 (1), pp. 488. Date of Electronic Publication: 2022 Nov 16.Publisher: BioMed Central Country of Publication: England NLM ID: 100965194 Publication Model: Electronic Cited Medium:

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Annotation of structural variants with reported allele frequencies and related metrics from multiple datasets using SVAFotate.

Authors : Nicholas TJ; Department of Human Genetics, Utah Center for Genetic Discovery, University of Utah, Salt Lake City, UT, 84112, USA. .; Cormier MJ

Subjects: Gene Frequency* ; High-Throughput Nucleotide Sequencing* ; Software*

Source: BMC bioinformatics [BMC Bioinformatics] 2022 Nov 16; Vol. 23 (1), pp. 490. Date of Electronic Publication: 2022 Nov 16.Publisher: BioMed Central Country of Publication: England NLM ID: 100965194 Publication Model: Electronic Cited Medium:

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SparkEC: speeding up alignment-based DNA error correction tools.

Authors : Expósito RR; Universidade da Coruña, CITIC, Computer Architecture Group, Campus de Elviña, 15071, A Coruña, Spain. .; Martínez-Sánchez M

Subjects: Software* ; High-Throughput Nucleotide Sequencing*/High-Throughput Nucleotide Sequencing*/High-Throughput Nucleotide Sequencing*/methods; Sequence Analysis, DNA/Sequence Analysis, DNA/Sequence Analysis, DNA/methods

Source: BMC bioinformatics [BMC Bioinformatics] 2022 Nov 07; Vol. 23 (1), pp. 464. Date of Electronic Publication: 2022 Nov 07.Publisher: BioMed Central Country of Publication: England NLM ID: 100965194 Publication Model: Electronic Cited Medium:

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Sketching and sampling approaches for fast and accurate long read classification.

Authors : Das A; Department of Computer Science, Johns Hopkins University, Baltimore, MD, 21218, USA. .; Schatz MC

Subjects: High-Throughput Nucleotide Sequencing*/High-Throughput Nucleotide Sequencing*/High-Throughput Nucleotide Sequencing*/methods ; Software*; Sequence Analysis, DNA/Sequence Analysis, DNA/Sequence Analysis, DNA/methods

Source: BMC bioinformatics [BMC Bioinformatics] 2022 Oct 31; Vol. 23 (1), pp. 452. Date of Electronic Publication: 2022 Oct 31.Publisher: BioMed Central Country of Publication: England NLM ID: 100965194 Publication Model: Electronic Cited Medium:

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Feasibility and outcome of reproducible clinical interpretation of high-dimensional molecular data: a comparison of two molecular tumor boards.

Authors : Rieke DT; Comprehensive Cancer Center, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Chariteplatz 1, 10117, Berlin, Germany. .; Department of Hematology, Oncology and Cancer Immunology, Campus Benjamin Franklin, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Hindenburgdamm 30, 12203, Berlin, Germany. .

Subjects: High-Throughput Nucleotide Sequencing*/High-Throughput Nucleotide Sequencing*/High-Throughput Nucleotide Sequencing*/methods ; Neoplasms*/Neoplasms*/Neoplasms*/diagnosis ; Neoplasms*/Neoplasms*/Neoplasms*/genetics

Source: BMC medicine [BMC Med] 2022 Oct 24; Vol. 20 (1), pp. 367. Date of Electronic Publication: 2022 Oct 24.Publisher: BioMed Central Country of Publication: England NLM ID: 101190723 Publication Model: Electronic Cited Medium:

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