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Academic Journal

T-RHEX-RNAseq - a tagmentation-based, rRNA blocked, random hexamer primed RNAseq method for generating stranded RNAseq libraries directly from very low numbers of lysed cells.

  • Authors : Gustafsson C; Department of Laboratory Medicine, Division of Clinical Immunology, Karolinska Institutet, ANA Futura, Alfred Nobels Allé 8 floor 7, Huddinge, SE-141 52, Sweden.; Hauenstein J

Subjects: High-Throughput Nucleotide Sequencing*/High-Throughput Nucleotide Sequencing*/High-Throughput Nucleotide Sequencing*/methods ; RNA, Ribosomal*/RNA, Ribosomal*/RNA, Ribosomal*/genetics; Base Sequence

  • Source: BMC genomics [BMC Genomics] 2023 Apr 17; Vol. 24 (1), pp. 205. Date of Electronic Publication: 2023 Apr 17.Publisher: BioMed Central Country of Publication: England NLM ID: 100965258 Publication Model: Electronic Cited Medium:

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Academic Journal

Highly accurate long reads are crucial for realizing the potential of biodiversity genomics.

  • Authors : Hotaling S; Department of Watershed Sciences, Utah State University, Logan, UT, USA. .; Wilcox ER

Subjects: Genomics*/Genomics*/Genomics*/methods ; Genomics*/Genomics*/Genomics*/standards ; Genomics*/Genomics*/Genomics*/trends

  • Source: BMC genomics [BMC Genomics] 2023 Mar 16; Vol. 24 (1), pp. 117. Date of Electronic Publication: 2023 Mar 16.Publisher: BioMed Central Country of Publication: England NLM ID: 100965258 Publication Model: Electronic Cited Medium:

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Academic Journal

Benchmarking datasets for assembly-based variant calling using high-fidelity long reads.

  • Authors : Lee H; Institute of Molecular Biology and Genetics, Seoul National University, Seoul, 08826, Korea.; Department of Biological Sciences, Seoul National University, Seoul, 08826, Korea.

Subjects: Benchmarking* ; High-Throughput Nucleotide Sequencing*/High-Throughput Nucleotide Sequencing*/High-Throughput Nucleotide Sequencing*/methods; Humans

  • Source: BMC genomics [BMC Genomics] 2023 Mar 27; Vol. 24 (1), pp. 148. Date of Electronic Publication: 2023 Mar 27.Publisher: BioMed Central Country of Publication: England NLM ID: 100965258 Publication Model: Electronic Cited Medium:

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Academic Journal

Comparison of the Illumina NextSeq 2000 and GeneMind Genolab M sequencing platforms for spatial transcriptomics.

  • Authors : Pavel I; Laboratory of Cancer Progression Biology, Cancer Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, Tomsk, 634009, Russia.; Laboratory of Translational Cellular and Molecular Biomedicine, Tomsk State University, Tomsk, 634050, Russia.

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

  • Source: BMC genomics [BMC Genomics] 2023 Mar 07; Vol. 24 (1), pp. 102. Date of Electronic Publication: 2023 Mar 07.Publisher: BioMed Central Country of Publication: England NLM ID: 100965258 Publication Model: Electronic Cited Medium:

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Academic Journal

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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Academic Journal

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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Academic Journal

Using single-worm RNA sequencing to study C. elegans responses to pathogen infection.

  • Authors : Wang AJ; Genomics Core, Washington State University, Spokane, WA, USA.; Wibisono P

Subjects: Caenorhabditis elegans*/Caenorhabditis elegans*/Caenorhabditis elegans*/genetics ; High-Throughput Nucleotide Sequencing*/High-Throughput Nucleotide Sequencing*/High-Throughput Nucleotide Sequencing*/methods; Animals

  • Source: BMC genomics [BMC Genomics] 2022 Sep 14; Vol. 23 (1), pp. 653. Date of Electronic Publication: 2022 Sep 14.Publisher: BioMed Central Country of Publication: England NLM ID: 100965258 Publication Model: Electronic Cited Medium:

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Academic Journal

Performance comparison of Agilent new SureSelect All Exon v8 probes with v7 probes for exome sequencing.

  • Authors : Belova V; Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Ostrovityanova str. 1, Moscow, 117997, Russian Federation. .; Shmitko A

Subjects: Exome* ; High-Throughput Nucleotide Sequencing*/High-Throughput Nucleotide Sequencing*/High-Throughput Nucleotide Sequencing*/methods; Exons

  • Source: BMC genomics [BMC Genomics] 2022 Aug 12; Vol. 23 (1), pp. 582. Date of Electronic Publication: 2022 Aug 12.Publisher: BioMed Central Country of Publication: England NLM ID: 100965258 Publication Model: Electronic Cited Medium:

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Academic Journal

Accuracy benchmark of the GeneMind GenoLab M sequencing platform for WGS and WES analysis.

  • Authors : Li C; GeneMind Biosciences Company Limited, Shenzhen, China.; Fan X

Subjects: Benchmarking* ; High-Throughput Nucleotide Sequencing*; INDEL Mutation

  • Source: BMC genomics [BMC Genomics] 2022 Jul 22; Vol. 23 (1), pp. 533. Date of Electronic Publication: 2022 Jul 22.Publisher: BioMed Central Country of Publication: England NLM ID: 100965258 Publication Model: Electronic Cited Medium:

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Academic Journal

Evaluation of nine statistics to identify QTLs in bulk segregant analysis using next generation sequencing approaches.

Subjects: High-Throughput Nucleotide Sequencing* ; Quantitative Trait Loci*; Benchmarking

  • Source: BMC genomics [BMC Genomics] 2022 Jul 06; Vol. 23 (1), pp. 490. Date of Electronic Publication: 2022 Jul 06.Publisher: BioMed Central Country of Publication: England NLM ID: 100965258 Publication Model: Electronic Cited Medium:

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Academic Journal

SUsPECT: a pipeline for variant effect prediction based on custom long-read transcriptomes for improved clinical variant annotation.

  • Authors : Salz R; Department of Medical BioSciences, Radboud University Medical Center, Nijmegen, 6525 GA, the Netherlands.; Saraiva-Agostinho N

Subjects: Transcriptome* ; Software*; Humans

  • Source: BMC genomics [BMC Genomics] 2023 Jun 06; Vol. 24 (1), pp. 305. Date of Electronic Publication: 2023 Jun 06.Publisher: BioMed Central Country of Publication: England NLM ID: 100965258 Publication Model: Electronic Cited Medium:

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Academic Journal

Integration of ATAC-Seq and RNA-Seq reveals FOSL2 drives human liver progenitor-like cell aging by regulating inflammatory factors.

  • Authors : Ding M; Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China.; Department of Interventional Oncology, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200127, China.

Subjects: Cellular Senescence*/Cellular Senescence*/Cellular Senescence*/genetics ; Chromatin*/Chromatin*/Chromatin*/genetics ; Chromatin Immunoprecipitation Sequencing*

  • Source: BMC genomics [BMC Genomics] 2023 May 13; Vol. 24 (1), pp. 260. Date of Electronic Publication: 2023 May 13.Publisher: BioMed Central Country of Publication: England NLM ID: 100965258 Publication Model: Electronic Cited Medium:

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Academic Journal

Comparison of Illumina and Oxford Nanopore Technology for genome analysis of Francisella tularensis, Bacillus anthracis, and Brucella suis.

  • Authors : Linde J; Institute of Bacterial Infections and Zoonoses, Federal Research Institute for Animal Health, Friedrich-Loeffler-Institute, Jena, Germany. .; Brangsch H

Subjects: Francisella tularensis*/Francisella tularensis*/Francisella tularensis*/genetics ; Brucella suis*/Brucella suis*/Brucella suis*/genetics ; Bacillus anthracis*/Bacillus anthracis*/Bacillus anthracis*/genetics

  • Source: BMC genomics [BMC Genomics] 2023 May 12; Vol. 24 (1), pp. 258. Date of Electronic Publication: 2023 May 12.Publisher: BioMed Central Country of Publication: England NLM ID: 100965258 Publication Model: Electronic Cited Medium:

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Academic Journal

Benchmark of tools for in silico prediction of MHC class I and class II genotypes from NGS data.

  • Authors : Claeys A; Department of Human Structure and Repair, Ghent University, Ghent, Belgium.; Cancer Research Institute Ghent, Ghent, Belgium.

Subjects: Benchmarking* ; HLA Antigens*; Humans

  • Source: BMC genomics [BMC Genomics] 2023 May 09; Vol. 24 (1), pp. 247. Date of Electronic Publication: 2023 May 09.Publisher: BioMed Central Country of Publication: England NLM ID: 100965258 Publication Model: Electronic Cited Medium:

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Academic Journal

Highly-multiplexed and efficient long-amplicon PacBio and Nanopore sequencing of hundreds of full mitochondrial genomes.

  • Authors : Karin BR; Department of Integrative Biology, Valley Life Sciences Building, University of California, Berkeley, CA, 94708, USA. .; Museum of Vertebrate Zoology, University of California, Berkeley, CA, USA. .

Subjects: Genome, Mitochondrial* ; Nanopore Sequencing* ; Nanopores*

  • Source: BMC genomics [BMC Genomics] 2023 May 02; Vol. 24 (1), pp. 229. Date of Electronic Publication: 2023 May 02.Publisher: BioMed Central Country of Publication: England NLM ID: 100965258 Publication Model: Electronic Cited Medium:

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Academic Journal

Manipulating base quality scores enables variant calling from bisulfite sequencing alignments using conventional bayesian approaches.

  • Authors : Nunn A; ecSeq Bioinformatics GmbH, Sternwartenstraße 29, Leipzig, 04103, Germany.; Department of Computer Science, University of Leipzig, Härtelstraße 16-18, Leipzig, 04107, Germany.

Subjects: High-Throughput Nucleotide Sequencing*/High-Throughput Nucleotide Sequencing*/High-Throughput Nucleotide Sequencing*/methods; Bayes Theorem ; Humans

  • Source: BMC genomics [BMC Genomics] 2022 Jun 28; Vol. 23 (1), pp. 477. Date of Electronic Publication: 2022 Jun 28.Publisher: BioMed Central Country of Publication: England NLM ID: 100965258 Publication Model: Electronic Cited Medium:

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Academic Journal

B-assembler: a circular bacterial genome assembler.

  • Authors : Huang F; Informatics Institute, Heersink School of Medicine, the University of Alabama at Birmingham, AL, 35294, Birmingham, USA.; Department of Genetics, Heersink School of Medicine, the University of Alabama at Birmingham, AL, 35294, Birmingham, USA.

Subjects: Genome, Bacterial* ; High-Throughput Nucleotide Sequencing*/High-Throughput Nucleotide Sequencing*/High-Throughput Nucleotide Sequencing*/methods; Bacteria/Bacteria/Bacteria/genetics

  • Source: BMC genomics [BMC Genomics] 2022 May 11; Vol. 23 (Suppl 4), pp. 361. Date of Electronic Publication: 2022 May 11.Publisher: BioMed Central Country of Publication: England NLM ID: 100965258 Publication Model: Electronic Cited Medium:

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Academic Journal

Comprehensive evaluation of structural variant genotyping methods based on long-read sequencing data.

  • Authors : Duan X; State Key Laboratory of Genetic Engineering, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Fudan University, Shanghai, 200438, China.; MOE Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai, 200433, China.

Subjects: Genomics*/Genomics*/Genomics*/methods ; High-Throughput Nucleotide Sequencing*; Genomic Structural Variation

  • Source: BMC genomics [BMC Genomics] 2022 Apr 23; Vol. 23 (1), pp. 324. Date of Electronic Publication: 2022 Apr 23.Publisher: BioMed Central Country of Publication: England NLM ID: 100965258 Publication Model: Electronic Cited Medium:

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Academic Journal

Protocol variations in run-on transcription dataset preparation produce detectable signatures in sequencing libraries.

  • Authors : Hunter S; BioFrontiers Institute, University of Colorado, Boulder, 80309, USA.; Sigauke RF

Subjects: Genomic Library* ; High-Throughput Nucleotide Sequencing*/High-Throughput Nucleotide Sequencing*/High-Throughput Nucleotide Sequencing*/methods; Databases, Genetic

  • Source: BMC genomics [BMC Genomics] 2022 Mar 07; Vol. 23 (1), pp. 187. Date of Electronic Publication: 2022 Mar 07.Publisher: BioMed Central Country of Publication: England NLM ID: 100965258 Publication Model: Electronic Cited Medium:

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Academic Journal

HiFiAdapterFilt, a memory efficient read processing pipeline, prevents occurrence of adapter sequence in PacBio HiFi reads and their negative impacts on genome assembly.

  • Authors : Sim SB; USDA-ARS Daniel K. Inouye US Pacific Basin Agricultural Research Center, 64 Nowelo Street, Hilo, HI, 96720, USA. .; Corpuz RL

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

  • Source: BMC genomics [BMC Genomics] 2022 Feb 22; Vol. 23 (1), pp. 157. Date of Electronic Publication: 2022 Feb 22.Publisher: BioMed Central Country of Publication: England NLM ID: 100965258 Publication Model: Electronic Cited Medium:

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Academic Journal

TC-hunter: identification of the insertion site of a transgenic gene within the host genome.

Subjects: Genome* ; High-Throughput Nucleotide Sequencing*/High-Throughput Nucleotide Sequencing*/High-Throughput Nucleotide Sequencing*/methods; Animals

  • Source: BMC genomics [BMC Genomics] 2022 Feb 20; Vol. 23 (1), pp. 149. Date of Electronic Publication: 2022 Feb 20.Publisher: BioMed Central Country of Publication: England NLM ID: 100965258 Publication Model: Electronic Cited Medium:

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Academic Journal

Optimization of enzymatic fragmentation is crucial to maximize genome coverage: a comparison of library preparation methods for Illumina sequencing.

  • Authors : Ribarska T; Department Medical Genetics, Oslo University Hospital and University of Oslo, Kirkeveien 166, 0450, Oslo, Norway.; Bjørnstad PM

Subjects: Genome* ; High-Throughput Nucleotide Sequencing*; Gene Library

  • Source: BMC genomics [BMC Genomics] 2022 Feb 01; Vol. 23 (1), pp. 92. Date of Electronic Publication: 2022 Feb 01.Publisher: BioMed Central Country of Publication: England NLM ID: 100965258 Publication Model: Electronic Cited Medium:

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Academic Journal

Long range PCR-based deep sequencing for haplotype determination in mixed HCMV infections.

  • Authors : Brait N; Center for Virology, Medical University of Vienna, Vienna, Austria.; Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, Netherlands.

Subjects: Cytomegalovirus*/Cytomegalovirus*/Cytomegalovirus*/genetics ; High-Throughput Nucleotide Sequencing*; Haplotypes

  • Source: BMC genomics [BMC Genomics] 2022 Jan 06; Vol. 23 (1), pp. 31. Date of Electronic Publication: 2022 Jan 06.Publisher: BioMed Central Country of Publication: England NLM ID: 100965258 Publication Model: Electronic Cited Medium:

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Academic Journal

High-quality single amplicon sequencing method for illumina MiSeq platform using pool of 'N' (0-10) spacer-linked target specific primers without PhiX spike-in.

  • Authors : Naik T; National Centre for Biological Science, Tata Institute of Fundamental Research, Bengaluru, Karnataka, 560065, India.; Sharda M

Subjects: Bacteria*/Bacteria*/Bacteria*/genetics ; Microbiota*/Microbiota*/Microbiota*/genetics; Sequence Analysis, DNA/Sequence Analysis, DNA/Sequence Analysis, DNA/methods

  • Source: BMC genomics [BMC Genomics] 2023 Mar 23; Vol. 24 (1), pp. 141. Date of Electronic Publication: 2023 Mar 23.Publisher: BioMed Central Country of Publication: England NLM ID: 100965258 Publication Model: Electronic Cited Medium:

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Academic Journal

Long read isoform sequencing reveals hidden transcriptional complexity between cattle subspecies.

  • Authors : Ren Y; The Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, Adelaide, SA, 5371, Australia.; Tseng E

Subjects: Transcriptome* ; Genome*; Cattle/Cattle/Cattle/genetics

  • Source: BMC genomics [BMC Genomics] 2023 Mar 13; Vol. 24 (1), pp. 108. Date of Electronic Publication: 2023 Mar 13.Publisher: BioMed Central Country of Publication: England NLM ID: 100965258 Publication Model: Electronic Cited Medium:

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Academic Journal

Identification and analysis of miRNAs differentially expressed in male and female Trichosanthes kirilowii maxim.

  • Authors : Hu XQ; Medical College, Linyi University, Lin'yi, 276000, China.; School of Pharmacy, Shandong University of Traditional Chinese Medicine, Ji'nan, 250355, China.

Subjects: Trichosanthes*/Trichosanthes*/Trichosanthes*/genetics ; MicroRNAs*/MicroRNAs*/MicroRNAs*/genetics ; Cucurbitaceae*/Cucurbitaceae*/Cucurbitaceae*/genetics

  • Source: BMC genomics [BMC Genomics] 2023 Feb 21; Vol. 24 (1), pp. 81. Date of Electronic Publication: 2023 Feb 21.Publisher: BioMed Central Country of Publication: England NLM ID: 100965258 Publication Model: Electronic Cited Medium:

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Academic Journal

Baiting out a full length sequence from unmapped RNA-seq data.

  • Authors : Li D; Animal Functional Genomics Group, Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China.; Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, 510642, China.

Subjects: High-Throughput Nucleotide Sequencing*; DNA, Complementary ; RNA-Seq

  • Source: BMC genomics [BMC Genomics] 2021 Nov 27; Vol. 22 (1), pp. 857. Date of Electronic Publication: 2021 Nov 27.Publisher: BioMed Central Country of Publication: England NLM ID: 100965258 Publication Model: Electronic Cited Medium:

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Academic Journal

Optimization of library preparation based on SMART for ultralow RNA-seq in mice brain tissues.

  • Authors : Jia E; State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University, Nanjing, 210096, China.; Shi H

Subjects: High-Throughput Nucleotide Sequencing* ; Transcriptome*; Animals

  • Source: BMC genomics [BMC Genomics] 2021 Nov 10; Vol. 22 (1), pp. 809. Date of Electronic Publication: 2021 Nov 10.Publisher: BioMed Central Country of Publication: England NLM ID: 100965258 Publication Model: Electronic Cited Medium:

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Academic Journal

Breed-specific reference sequence optimized mapping accuracy of NGS analyses for pigs.

  • Authors : Wang D; National Engineering Laboratory for Animal Breeding, Ministry of Agricultural Key Laboratory of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, China Agricultural University, Beijing, China.; College of Animal Science and Technology, Shandong Agricultural University, Tai'an, China.

Subjects: High-Throughput Nucleotide Sequencing* ; Polymorphism, Single Nucleotide*; Animals

  • Source: BMC genomics [BMC Genomics] 2021 Oct 12; Vol. 22 (1), pp. 736. Date of Electronic Publication: 2021 Oct 12.Publisher: BioMed Central Country of Publication: England NLM ID: 100965258 Publication Model: Electronic Cited Medium:

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Academic Journal

Impact of human gene annotations on RNA-seq differential expression analysis.

  • Authors : Hamaguchi Y; Faculty of Science and Engineering, Waseda University, 55N-06-10, 3-4-1 Okubo Shinjuku-ku, Tokyo, 169-8555, Japan. .; Zeng C

Subjects: Genome, Human* ; High-Throughput Nucleotide Sequencing*; Humans

  • Source: BMC genomics [BMC Genomics] 2021 Oct 08; Vol. 22 (1), pp. 730. Date of Electronic Publication: 2021 Oct 08.Publisher: BioMed Central Country of Publication: England NLM ID: 100965258 Publication Model: Electronic Cited Medium:

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Academic Journal

CAMPAREE: a robust and configurable RNA expression simulator.

  • Authors : Lahens NF; The Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.; Brooks TG

Subjects: High-Throughput Nucleotide Sequencing* ; Software*; Algorithms

  • Source: BMC genomics [BMC Genomics] 2021 Sep 25; Vol. 22 (1), pp. 692. Date of Electronic Publication: 2021 Sep 25.Publisher: BioMed Central Country of Publication: England NLM ID: 100965258 Publication Model: Electronic Cited Medium:

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Academic Journal

High contiguity de novo genome assembly and DNA modification analyses for the fungus fly, Sciara coprophila, using single-molecule sequencing.

  • Authors : Urban JM; Department of Molecular Biology, Cell Biology and Biochemistry, Brown University Division of Biology and Medicine, Sidney Frank Hall for Life Sciences, 185 Meeting Street, Providence, RI, 02912, USA. .; Department of Embryology, Carnegie Institution for Science, Howard Hughes Medical Institute Research Laboratories, 3520 San Martin Drive, Baltimore, MD, 21218, USA. .

Subjects: High-Throughput Nucleotide Sequencing* ; X Chromosome*; DNA

  • Source: BMC genomics [BMC Genomics] 2021 Sep 06; Vol. 22 (1), pp. 643. Date of Electronic Publication: 2021 Sep 06.Publisher: BioMed Central Country of Publication: England NLM ID: 100965258 Publication Model: Electronic Cited Medium:

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Academic Journal

Benchmarking full-length transcript single cell mRNA sequencing protocols.

  • Authors : Probst V; Genomic Medicine, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark.; Simonyan A

Subjects: Benchmarking* ; Transcriptome*; Sequence Analysis, RNA/Sequence Analysis, RNA/Sequence Analysis, RNA/methods

  • Source: BMC genomics [BMC Genomics] 2022 Dec 29; Vol. 23 (1), pp. 860. Date of Electronic Publication: 2022 Dec 29.Publisher: BioMed Central Country of Publication: England NLM ID: 100965258 Publication Model: Electronic Cited Medium:

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Academic Journal

Comparison of structural variants detected by PacBio-CLR and ONT sequencing in pear.

  • Authors : Liu Y; State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China.; Zhang M

Subjects: Pyrus*/Pyrus*/Pyrus*/genetics ; Nanopores*; Sequence Analysis

  • Source: BMC genomics [BMC Genomics] 2022 Dec 14; Vol. 23 (1), pp. 830. Date of Electronic Publication: 2022 Dec 14.Publisher: BioMed Central Country of Publication: England NLM ID: 100965258 Publication Model: Electronic Cited Medium:

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Academic Journal

kataegis: an R package for identification and visualization of the genomic localized hypermutation regions using high-throughput sequencing.

  • Authors : Lin X; Department of Bioinformatics, School of Biomedical Engineering and Informatics, Nanjing Medical University, 211166, Nanjing, People's Republic of China. .; Hua Y

Subjects: Genomics* ; High-Throughput Nucleotide Sequencing*; Mutation

  • Source: BMC genomics [BMC Genomics] 2021 Jun 12; Vol. 22 (1), pp. 440. Date of Electronic Publication: 2021 Jun 12.Publisher: BioMed Central Country of Publication: England NLM ID: 100965258 Publication Model: Electronic Cited Medium:

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Academic Journal

Cruxome: a powerful tool for annotating, interpreting and reporting genetic variants.

  • Authors : Han Q; Berry Genomics Company Limited, Building 5, Courtyard 4, Shengmingyuan Road, ZGC Life Science Park, Changping District, 102200, Beijing, China.; Yang Y

Subjects: Genomics* ; High-Throughput Nucleotide Sequencing*; Algorithms

  • Source: BMC genomics [BMC Genomics] 2021 Jun 03; Vol. 22 (1), pp. 407. Date of Electronic Publication: 2021 Jun 03.Publisher: BioMed Central Country of Publication: England NLM ID: 100965258 Publication Model: Electronic Cited Medium:

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Academic Journal

Evaluation of tools for identifying large copy number variations from ultra-low-coverage whole-genome sequencing data.

  • Authors : Smolander J; Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520, Turku, Finland.; Khan S

Subjects: DNA Copy Number Variations* ; High-Throughput Nucleotide Sequencing*; Algorithms

  • Source: BMC genomics [BMC Genomics] 2021 May 17; Vol. 22 (1), pp. 357. Date of Electronic Publication: 2021 May 17.Publisher: BioMed Central Country of Publication: England NLM ID: 100965258 Publication Model: Electronic Cited Medium:

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Academic Journal

Hybrid genome de novo assembly with methylome analysis of the anaerobic thermophilic subsurface bacterium Thermanaerosceptrum fracticalcis strain DRI-13 T .

  • Authors : Murphy TR; Department of Microbiology, Southern Illinois University Carbondale, Carbondale, IL, USA.; Xiao R

Subjects: Epigenome* ; High-Throughput Nucleotide Sequencing*; Anaerobiosis

  • Source: BMC genomics [BMC Genomics] 2021 Mar 23; Vol. 22 (1), pp. 209. Date of Electronic Publication: 2021 Mar 23.Publisher: BioMed Central Country of Publication: England NLM ID: 100965258 Publication Model: Electronic Cited Medium:

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Academic Journal

Impact of short-read sequencing on the misassembly of a plant genome.

  • Authors : Wang P; Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA.; DOE Great Lake Bioenergy Research Center, Michigan State University, East Lansing, MI, 48824, USA.

Subjects: Genome, Plant* ; High-Throughput Nucleotide Sequencing*; DNA Transposable Elements/DNA Transposable Elements/DNA Transposable Elements/genetics

  • Source: BMC genomics [BMC Genomics] 2021 Feb 02; Vol. 22 (1), pp. 99. Date of Electronic Publication: 2021 Feb 02.Publisher: BioMed Central Country of Publication: England NLM ID: 100965258 Publication Model: Electronic Cited Medium:

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Academic Journal

Reliability of genomic variants across different next-generation sequencing platforms and bioinformatic processing pipelines.

  • Authors : Weißbach S; Institute of Human Genetics, University Medical Center of the Johannes Gutenberg-University Mainz, Mainz, Germany.; Institute of Developmental Biology and Neurobiology, Johannes Gutenberg-University Mainz, Mainz, Germany.

Subjects: Computational Biology* ; High-Throughput Nucleotide Sequencing*; Cross-Sectional Studies

  • Source: BMC genomics [BMC Genomics] 2021 Jan 19; Vol. 22 (1), pp. 62. Date of Electronic Publication: 2021 Jan 19.Publisher: BioMed Central Country of Publication: England NLM ID: 100965258 Publication Model: Electronic Cited Medium:

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Academic Journal

intePareto: an R package for integrative analyses of RNA-Seq and ChIP-Seq data.

  • Authors : Cao Y; Bioinformatics and Computational Biophysics, Faculty of Biology and Center for Medical Biotechnology (ZMB), University of Duisburg-Essen, Universitätsstr.2, Essen, 45141, Germany. .; Kitanovski S

Subjects: Chromatin Immunoprecipitation Sequencing* ; High-Throughput Nucleotide Sequencing*; Chromatin Immunoprecipitation

  • Source: BMC genomics [BMC Genomics] 2020 Dec 29; Vol. 21 (Suppl 11), pp. 802. Date of Electronic Publication: 2020 Dec 29.Publisher: BioMed Central Country of Publication: England NLM ID: 100965258 Publication Model: Electronic Cited Medium:

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Academic Journal

A comprehensive evaluation of long read error correction methods.

  • Authors : Zhang H; School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, 30332, GA, USA.; Jain C

Subjects: Algorithms* ; High-Throughput Nucleotide Sequencing*; Genomics

  • Source: BMC genomics [BMC Genomics] 2020 Dec 21; Vol. 21 (Suppl 6), pp. 889. Date of Electronic Publication: 2020 Dec 21.Publisher: BioMed Central Country of Publication: England NLM ID: 100965258 Publication Model: Electronic Cited Medium:

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Academic Journal

NGS-Integrator: An efficient tool for combining multiple NGS data tracks using minimum Bayes' factors.

  • Authors : Wen B; Epithelial Systems Biology Laboratory, Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA.; Jung HJ

Subjects: High-Throughput Nucleotide Sequencing* ; Software*; Animals

  • Source: BMC genomics [BMC Genomics] 2020 Nov 19; Vol. 21 (1), pp. 806. Date of Electronic Publication: 2020 Nov 19.Publisher: BioMed Central Country of Publication: England NLM ID: 100965258 Publication Model: Electronic Cited Medium:

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Academic Journal

Optimizing performance of GATK workflows using Apache Arrow In-Memory data framework.

  • Authors : Ahmad T; Accelerated Big Data Systems Group, Quantum & Computer Engineering Department, Delft University of Technology, Delft, The Netherlands. .; Ahmed N

Subjects: High-Throughput Nucleotide Sequencing* ; Software*; Genomics

  • Source: BMC genomics [BMC Genomics] 2020 Nov 18; Vol. 21 (Suppl 10), pp. 683. Date of Electronic Publication: 2020 Nov 18.Publisher: BioMed Central Country of Publication: England NLM ID: 100965258 Publication Model: Electronic Cited Medium:

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Academic Journal

A hybrid correcting method considering heterozygous variations by a comprehensive probabilistic model.

  • Authors : Liu J; School of Computer Science and Technology, Xi'an Jiaotong University, Xi'an, 710048, China.; Shaanxi Engineering Research Center of Medical and Health Big Data, School of Computer Science and Technology, Xi'an Jiaotong University, Xi'an, 710048, China.

Subjects: High-Throughput Nucleotide Sequencing* ; Models, Statistical*; Algorithms

  • Source: BMC genomics [BMC Genomics] 2020 Nov 18; Vol. 21 (Suppl 10), pp. 753. Date of Electronic Publication: 2020 Nov 18.Publisher: BioMed Central Country of Publication: England NLM ID: 100965258 Publication Model: Electronic Cited Medium:

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Academic Journal

Differential venom gland gene expression analysis of juvenile and adult scorpions Androctonus crassicauda.

  • Authors : Salabi F; Department of Venomous Animals and Anti-Venom Production, Agricultural Research, Education and Extension Organization (AREEO), Razi Vaccine and Serum Research Institute, Ahvaz, Iran. .; Jafari H

Subjects: Scorpion Venoms*/Scorpion Venoms*/Scorpion Venoms*/genetics ; Scorpion Venoms*/Scorpion Venoms*/Scorpion Venoms*/metabolism ; Scorpions*/Scorpions*/Scorpions*/genetics

  • Source: BMC genomics [BMC Genomics] 2022 Sep 08; Vol. 23 (1), pp. 636. Date of Electronic Publication: 2022 Sep 08.Publisher: BioMed Central Country of Publication: England NLM ID: 100965258 Publication Model: Electronic Cited Medium:

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Academic Journal

Reducing costs for DNA and RNA sequencing by sample pooling using a metagenomic approach.

  • Authors : Teufel M; Philipps Universität Marburg, Synthetic Microbiology Center Marburg (SYNMIKRO), Marburg, 35043, Germany.; Sobetzko P

Subjects: Metagenome* ; Metagenomics*; DNA/DNA/DNA/genetics

  • Source: BMC genomics [BMC Genomics] 2022 Aug 24; Vol. 23 (1), pp. 613. Date of Electronic Publication: 2022 Aug 24.Publisher: BioMed Central Country of Publication: England NLM ID: 100965258 Publication Model: Electronic Cited Medium:

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Academic Journal

Low-cost and clinically applicable copy number profiling using repeat DNA.

  • Authors : Abujudeh S; Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK. .; Zeki SS

Subjects: DNA Copy Number Variations* ; Neoplasms*/Neoplasms*/Neoplasms*/genetics; Base Sequence

  • Source: BMC genomics [BMC Genomics] 2022 Aug 17; Vol. 23 (1), pp. 599. Date of Electronic Publication: 2022 Aug 17.Publisher: BioMed Central Country of Publication: England NLM ID: 100965258 Publication Model: Electronic Cited Medium:

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Academic Journal

High-throughput transcriptome sequencing reveals the key stages of cardiovascular development in zebrafish embryos.

  • Authors : Zhou C; College of Life Science, Henan Normal University, Xinxiang, 453007, Henan, China.; Zhao W

Subjects: Biological Phenomena* ; Transcriptome*; Animals

  • Source: BMC genomics [BMC Genomics] 2022 Aug 13; Vol. 23 (1), pp. 587. Date of Electronic Publication: 2022 Aug 13.Publisher: BioMed Central Country of Publication: England NLM ID: 100965258 Publication Model: Electronic Cited Medium:

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Academic Journal

Towards reliable whole genome sequencing for outbreak preparedness and response.

Subjects: Nanopore Sequencing* ; Zika Virus*/Zika Virus*/Zika Virus*/genetics ; Zika Virus Infection*

  • Source: BMC genomics [BMC Genomics] 2022 Aug 09; Vol. 23 (1), pp. 569. Date of Electronic Publication: 2022 Aug 09.Publisher: BioMed Central Country of Publication: England NLM ID: 100965258 Publication Model: Electronic Cited Medium:

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