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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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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

Poly(a) selection introduces bias and undue noise in direct RNA-sequencing.

  • Authors : Viscardi MJ; Department of Molecular, Cellular and Developmental Biology, University of California at Santa Cruz, Santa Cruz, CA, USA.; Arribere JA

Subjects: Poly A*/Poly A*/Poly A*/genetics ; Poly A*/Poly A*/Poly A*/metabolism ; RNA*/RNA*/RNA*/metabolism

  • Source: BMC genomics [BMC Genomics] 2022 Jul 22; Vol. 23 (1), pp. 530. 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

A high-quality de novo genome assembly based on nanopore sequencing of a wild-caught coconut rhinoceros beetle (Oryctes rhinoceros).

  • Authors : Filipović I; School of Biological Sciences, The University of Queensland, St. Lucia, Australia. .; Mosquito Control Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia. .

Subjects: Coleoptera*/Coleoptera*/Coleoptera*/genetics ; Nanopore Sequencing* ; Nudiviridae*

  • Source: BMC genomics [BMC Genomics] 2022 Jun 07; Vol. 23 (1), pp. 426. Date of Electronic Publication: 2022 Jun 07.Publisher: BioMed Central Country of Publication: England NLM ID: 100965258 Publication Model: Electronic Cited Medium:

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Academic Journal

Harnessing changes in open chromatin determined by ATAC-seq to generate insulin-responsive reporter constructs.

  • Authors : Merrill CB; Department of Psychiatry, Huntsman Mental Health Institute, University of Utah, Salt Lake City, UT, 84108, USA. .; Montgomery AB

Subjects: Chromatin*/Chromatin*/Chromatin*/genetics ; Chromatin Immunoprecipitation Sequencing*; Animals

  • Source: BMC genomics [BMC Genomics] 2022 May 25; Vol. 23 (1), pp. 399. Date of Electronic Publication: 2022 May 25.Publisher: BioMed Central Country of Publication: England NLM ID: 100965258 Publication Model: Electronic Cited Medium:

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Academic Journal

SCSilicon: a tool for synthetic single-cell DNA sequencing data generation.

  • Authors : Feng X; School of Software, Northwestern Polytechnical University, Xi'an, Shaanxi, 710072, China. .; Chen L

Subjects: DNA Copy Number Variations* ; Silicon*; DNA

  • Source: BMC genomics [BMC Genomics] 2022 May 11; Vol. 23 (Suppl 4), pp. 359. 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

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

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

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

Comparison of SARS-CoV-2 sequencing using the ONT GridION and the Illumina MiSeq.

  • Authors : Tshiabuila D; KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal Durban 4001, KwaZulu-Natal, South Africa. .; Centre for Epidemic Response and Innovation (CERI), Stellenbosch University, Stellenbosch, South Africa. .

Subjects: COVID-19* ; SARS-CoV-2*/SARS-CoV-2*/SARS-CoV-2*/genetics; Genome, Viral

  • Source: BMC genomics [BMC Genomics] 2022 Apr 22; Vol. 23 (1), pp. 319. Date of Electronic Publication: 2022 Apr 22.Publisher: BioMed Central Country of Publication: England NLM ID: 100965258 Publication Model: Electronic Cited Medium:

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Academic Journal

Are we there yet? Benchmarking low-coverage nanopore long-read sequencing for the assembling of mitochondrial genomes using the vulnerable silky shark Carcharhinus falciformis.

  • Authors : Baeza JA; Department of Biological Sciences, 132 Long Hall, Clemson University, Clemson, SC, 29634, USA. .; Smithsonian Marine Station at Fort Pierce, 701 Seaway Drive, Fort Pierce, Florida, 34949, USA. .

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

  • Source: BMC genomics [BMC Genomics] 2022 Apr 22; Vol. 23 (1), pp. 320. Date of Electronic Publication: 2022 Apr 22.Publisher: BioMed Central Country of Publication: England NLM ID: 100965258 Publication Model: Electronic Cited Medium:

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Academic Journal

Oxford Nanopore and Bionano Genomics technologies evaluation for plant structural variation detection.

  • Authors : Canaguier A; Université Paris-Saclay, INRAE, Etude du Polymorphisme des Génomes Végétaux EPGV, 91000, Evry-Courcouronnes, France.; Guilbaud R

Subjects: Nanopores*; Genome ; Genomic Structural Variation

  • Source: BMC genomics [BMC Genomics] 2022 Apr 21; Vol. 23 (1), pp. 317. Date of Electronic Publication: 2022 Apr 21.Publisher: BioMed Central Country of Publication: England NLM ID: 100965258 Publication Model: Electronic Cited Medium:

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Academic Journal

Genomic and resistome analysis of Alcaligenes faecalis strain PGB1 by Nanopore MinION and Illumina Technologies.

  • Authors : Lang J; Geneis (Beijing) Co., Ltd, Beijing, 100102, China.; Qingdao Geneis Institute of Big Data Mining and Precision Medicine, Qingdao, People's Republic of China.

Subjects: Alcaligenes faecalis*/Alcaligenes faecalis*/Alcaligenes faecalis*/genetics ; Nanopores*; Anti-Bacterial Agents/Anti-Bacterial Agents/Anti-Bacterial Agents/pharmacology

  • Source: BMC genomics [BMC Genomics] 2022 Apr 20; Vol. 23 (Suppl 1), pp. 316. Date of Electronic Publication: 2022 Apr 20.Publisher: BioMed Central Country of Publication: England NLM ID: 100965258 Publication Model: Electronic Cited Medium:

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Academic Journal

A comparison of mRNA sequencing (RNA-Seq) library preparation methods for transcriptome analysis.

  • Authors : Ura H; Center for Clinical Genomics, Kanazawa Medical University Hospital, 1-1 Daigaku, Uchinada, Kahoku, Ishikawa, 920-0923, Japan. .; Division of Genomic Medicine, Department of Advanced Medicine, Medical Research Institute, Kanazawa Medical University, 1-1 Daigaku, Uchinada, Kahoku, Ishikawa, 920-0923, Japan. .

Subjects: Gene Expression Profiling*/Gene Expression Profiling*/Gene Expression Profiling*/methods ; Transcriptome*; Alternative Splicing

  • Source: BMC genomics [BMC Genomics] 2022 Apr 13; Vol. 23 (1), pp. 303. Date of Electronic Publication: 2022 Apr 13.Publisher: BioMed Central Country of Publication: England NLM ID: 100965258 Publication Model: Electronic Cited Medium:

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Academic Journal

High-quality chromosome-scale de novo assembly of the Paspalum notatum 'Flugge' genome.

  • Authors : Yan Z; College of Grassland Science, Qingdao Agricultural University, Qingdao, 266109, China.; Key Laboratory of National Forestry and Grassland Administration on Grassland Resources and Ecology in the Yellow River Delta, Qingdao Agricultural University, Qingdao, 266109, China.

Subjects: Paspalum*/Paspalum*/Paspalum*/genetics; Chromosomes ; Genome Size

  • Source: BMC genomics [BMC Genomics] 2022 Apr 11; Vol. 23 (1), pp. 293. Date of Electronic Publication: 2022 Apr 11.Publisher: BioMed Central Country of Publication: England NLM ID: 100965258 Publication Model: Electronic Cited Medium:

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Academic Journal

FindIT2: an R/Bioconductor package to identify influential transcription factor and targets based on multi-omics data.

  • Authors : Shang GD; National Key Laboratory of Plant Molecular Genetics (NKLPMG), CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology (SIPPE), Chinese Academy of Sciences (CAS), Shanghai, 200032, China.; University of Chinese Academy of Sciences (UCAS), Shanghai, 200032, P. R. China.

Subjects: Software* ; Transcription Factors*/Transcription Factors*/Transcription Factors*/genetics; Chromatin Immunoprecipitation Sequencing

  • Source: BMC genomics [BMC Genomics] 2022 Apr 07; Vol. 23 (Suppl 1), pp. 272. Date of Electronic Publication: 2022 Apr 07.Publisher: BioMed Central Country of Publication: England NLM ID: 100965258 Publication Model: Electronic Cited Medium:

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Academic Journal

Development of a versatile resource for post-genomic research through consolidating and characterizing 1500 diverse wild and cultivated soybean genomes.

  • Authors : Zhang H; Donald Danforth Plant Science Center, St Louis, MO 63132, USA.; Jiang H

Subjects: Genomics* ; Soybeans*/Soybeans*/Soybeans*/genetics; Chromosome Mapping

  • Source: BMC genomics [BMC Genomics] 2022 Mar 31; Vol. 23 (1), pp. 250. Date of Electronic Publication: 2022 Mar 31.Publisher: BioMed Central Country of Publication: England NLM ID: 100965258 Publication Model: Electronic Cited Medium:

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Academic Journal

Identification and characterization of heat-responsive lncRNAs in maize inbred line CM1.

  • Authors : Hu X; The National Engineering Laboratory of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei, 203036, China.; Wei Q

Subjects: MicroRNAs*/MicroRNAs*/MicroRNAs*/genetics ; RNA, Long Noncoding*/RNA, Long Noncoding*/RNA, Long Noncoding*/genetics ; RNA, Long Noncoding*/RNA, Long Noncoding*/RNA, Long Noncoding*/metabolism

  • Source: BMC genomics [BMC Genomics] 2022 Mar 16; Vol. 23 (1), pp. 208. Date of Electronic Publication: 2022 Mar 16.Publisher: BioMed Central Country of Publication: England NLM ID: 100965258 Publication Model: Electronic Cited Medium:

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Academic Journal

High-throughput sequencing data revealed genotype-specific changes evoked by heat stress in crown tissue of barley sdw1 near-isogenic lines.

Subjects: Hordeum*/Hordeum*/Hordeum*/genetics; Gene Expression Regulation, Plant ; Genotype

  • Source: BMC genomics [BMC Genomics] 2022 Mar 04; Vol. 23 (1), pp. 177. Date of Electronic Publication: 2022 Mar 04.Publisher: BioMed Central Country of Publication: England NLM ID: 100965258 Publication Model: Electronic Cited Medium:

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Academic Journal

Systematic benchmark of state-of-the-art variant calling pipelines identifies major factors affecting accuracy of coding sequence variant discovery.

  • Authors : Barbitoff YA; Bioinformatics Institute, St. Petersburg, Russia. .; Department of Genomic Medicine, D.O. Ott Research Institute of Obstetrics, Gynaecology and Reproductology, St. Petersburg, Russia. .

Subjects: Benchmarking* ; Polymorphism, Single Nucleotide*; Exome

  • Source: BMC genomics [BMC Genomics] 2022 Feb 22; Vol. 23 (1), pp. 155. 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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