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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

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

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

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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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

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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