Fast noisy long read alignment with multi-level parallelism.

Authors: Xia Z; College of Computer Science and Technology, National University of Defense Technology, 410073, Changsha, China., Yang C; College of Computer Science and Technology, National University of Defense Technology, 410073, Changsha, China.; National Supercomputer Center in Tianjin, 300457, Tianjin, China.; Haihe Lab of ITAI, 300457, Tianjin, China., Peng C; College of Computer Science and Technology, National University of Defense Technology, 410073, Changsha, China., Guo Y; College of Computer Science and Technology, National University of Defense Technology, 410073, Changsha, China., Guo Y; College of Computer Science and Technology, National University of Defense Technology, 410073, Changsha, China., Tang T; College of Computer Science and Technology, National University of Defense Technology, 410073, Changsha, China., Cui Y; College of Computer Science and Technology, National University of Defense Technology, 410073, Changsha, China. yingbocui@nudt.edu.cn.

Source: BMC bioinformatics [BMC Bioinformatics] 2025 May 02; Vol. 26 (1), pp. 118. Date of Electronic Publication: 2025 May 02.

Publication Type: Journal Article

Journal Info: Publisher: BioMed Central Country of Publication: England NLM ID: 100965194 Publication Model: Electronic Cited Medium: Internet ISSN: 1471-2105 (Electronic) Linking ISSN: 14712105 NLM ISO Abbreviation: BMC Bioinformatics Subsets: MEDLINE

MeSH Terms: Algorithms* , Sequence Alignment*/methods , High-Throughput Nucleotide Sequencing*/methods , Sequence Analysis, DNA*/methods, Software

High-performance protocol for ultra-short DNA sequencing using Oxford Nanopore Technology (ONT).

Authors: Žemaitis L; Department of DNA data storage, Genomika, Kaunas, Lithuania., Palepšienė R; Department of DNA data storage, Genomika, Kaunas, Lithuania.; Ultrasound Research Institute, Kaunas University of Technology, Kaunas, Lithuania., Juzėnas S; Department of DNA data storage, Genomika, Kaunas, Lithuania., Alzbutas G; Department of DNA data storage, Genomika, Kaunas, Lithuania.; Institute for Digestive Research, Academy of Medicine, Lithuanian University of Health Sciences, Kaunas, Lithuania., Burgi PY; Department of Information and Communication Systems and Technologies, University of Geneva, Geneva, Switzerland., Heinis T; Department of Computing, Imperial College London, London, United Kingdom., Charmet J; Western Switzerland, Neuchâtel, Switzerland., Angeloni Suter S; Western Switzerland, Neuchâtel, Switzerland., Jost M; MABEAL GmbH, Graz, Austria., Raišutis R; Ultrasound Research Institute, Kaunas University of Technology, Kaunas, Lithuania., Simmel F; Department of Bioscience, TU Munich, School of Natural Sciences, Garching, Germany., Galminas I; Department of DNA data storage, Genomika, Kaunas, Lithuania.; Faculty of Natural Sciences, Vytautas Magnus University, Kaunas, Lithuania.

Source: PloS one [PLoS One] 2025 Apr 29; Vol. 20 (4), pp. e0318040. Date of Electronic Publication: 2025 Apr 29 (Print Publication: 2025).

Publication Type: Journal Article

Journal Info: Publisher: Public Library of Science Country of Publication: United States NLM ID: 101285081 Publication Model: eCollection Cited Medium: Internet ISSN: 1932-6203 (Electronic) Linking ISSN: 19326203 NLM ISO Abbreviation: PLoS One Subsets: MEDLINE

MeSH Terms: Sequence Analysis, DNA*/methods , Nanopores* , High-Throughput Nucleotide Sequencing*/methods , DNA*/genetics , Nanopore Sequencing*/methods, Gene Library

PtWAVE: a high-sensitive deconvolution software of sequencing trace for the detection of large indels in genome editing.

Authors: Nakamae K; Genome Editing Innovation Center, Hiroshima University, 3-10-23 Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-0046, Japan. kazuki-nakamae@hiroshima-u.ac.jp.; PtBio Inc., Hiroshima, 739-0046, Japan. kazuki-nakamae@hiroshima-u.ac.jp., Ide S; Genome Editing Innovation Center, Hiroshima University, 3-10-23 Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-0046, Japan.; PtBio Inc., Hiroshima, 739-0046, Japan., Ohnuki N; Genome Editing Innovation Center, Hiroshima University, 3-10-23 Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-0046, Japan.; PtBio Inc., Hiroshima, 739-0046, Japan., Nakagawa Y; PtBio Inc., Hiroshima, 739-0046, Japan., Okuhara K; PtBio Inc., Hiroshima, 739-0046, Japan.; Graduate School of Integrated Sciences for Life, Hiroshima University, 3-10-23 Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-0046, Japan., Bono H; Genome Editing Innovation Center, Hiroshima University, 3-10-23 Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-0046, Japan. bonohu@hiroshima-u.ac.jp.; Graduate School of Integrated Sciences for Life, Hiroshima University, 3-10-23 Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-0046, Japan. bonohu@hiroshima-u.ac.jp.

Source: BMC bioinformatics [BMC Bioinformatics] 2025 Apr 29; Vol. 26 (1), pp. 114. Date of Electronic Publication: 2025 Apr 29.

Publication Type: Journal Article

Journal Info: Publisher: BioMed Central Country of Publication: England NLM ID: 100965194 Publication Model: Electronic Cited Medium: Internet ISSN: 1471-2105 (Electronic) Linking ISSN: 14712105 NLM ISO Abbreviation: BMC Bioinformatics Subsets: MEDLINE

MeSH Terms: INDEL Mutation* , Software* , Gene Editing*/methods , Sequence Analysis, DNA*/methods, Humans ; Algorithms

Kastor: a reference-based comparative approach for assessment and correction of gene-fragmenting errors in long-read assemblies of small genomes.

Authors: Lorv JSH; Department of Biology, University of Waterloo, Waterloo, ON, Canada., McConkey BJ; Department of Biology, University of Waterloo, Waterloo, ON, Canada. Brendan.mcconkey@uwaterloo.ca.

Source: BMC genomics [BMC Genomics] 2025 Apr 18; Vol. 26 (1), pp. 388. Date of Electronic Publication: 2025 Apr 18.

Publication Type: Journal Article; Comparative Study

Journal Info: Publisher: BioMed Central Country of Publication: England NLM ID: 100965258 Publication Model: Electronic Cited Medium: Internet ISSN: 1471-2164 (Electronic) Linking ISSN: 14712164 NLM ISO Abbreviation: BMC Genomics Subsets: MEDLINE

MeSH Terms: Software* , Genomics*/methods , Sequence Analysis, DNA*/methods , Genome*, Pseudogenes ; High-Throughput Nucleotide Sequencing/methods

Analysis of targeted and whole genome sequencing of PacBio HiFi reads for a comprehensive genotyping of gene-proximal and phenotype-associated Variable Number Tandem Repeats.

Authors: Javadzadeh S; Department of Computer Science and Engineering, University of California San Diego, La Jolla, California, United States of America., Adamson A; Department of Population Sciences, Beckman Research Institute of City of Hope, Duarte, California, United States of America., Park J; Department of Computer Science and Engineering, University of California San Diego, La Jolla, California, United States of America., Jo SY; Department of Computer Science and Engineering, University of California San Diego, La Jolla, California, United States of America.; Department of Biomedical Systems Informatics, Yonsei University College of Medicine, Seoul, South Korea., Ding YC; Department of Population Sciences, Beckman Research Institute of City of Hope, Duarte, California, United States of America., Bakhtiari M; Department of Computer Science and Engineering, University of California San Diego, La Jolla, California, United States of America., Bansal V; School of Medicine, University of California, San Diego La Jolla, California, United States of America., Neuhausen SL; Department of Population Sciences, Beckman Research Institute of City of Hope, Duarte, California, United States of America., Bafna V; Department of Computer Science and Engineering, University of California San Diego, La Jolla, California, United States of America.

Source: PLoS computational biology [PLoS Comput Biol] 2025 Apr 07; Vol. 21 (4), pp. e1012885. Date of Electronic Publication: 2025 Apr 07 (Print Publication: 2025).

Publication Type: Journal Article

Journal Info: Publisher: Public Library of Science Country of Publication: United States NLM ID: 101238922 Publication Model: eCollection Cited Medium: Internet ISSN: 1553-7358 (Electronic) Linking ISSN: 1553734X NLM ISO Abbreviation: PLoS Comput Biol Subsets: MEDLINE

MeSH Terms: Minisatellite Repeats*/genetics , Whole Genome Sequencing*/methods , Genotyping Techniques*/methods , Genome, Human*/genetics , High-Throughput Nucleotide Sequencing*/methods , Sequence Analysis, DNA*/methods, Humans ; Phenotype ; Genotype ; Computational Biology

A method for PCR-free library preparation for sequencing palaeogenomes.

Authors: Henneberger K; Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany., Barlow A; School of Environmental and Natural Sciences, Bangor University, Bangor, United Kingdom., Alberti F; Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany., Preick M; Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany., Constantin S; Department of Geospeleology and Paleontology, Emil Racovita Institute of Speleology, Bucharest, Romania.; Centro Nacional de Investigacion sobre la Evolucion Humana, CENIEH, Burgos, Spain., Döppes D; Reiss-Engelhorn-Museen, Mannheim, Germany., Rosendahl W; Reiss-Engelhorn-Museen, Mannheim, Germany.; Curt-Engelhorn-Centre for Archaeometry, Mannheim, Germany., Hofreiter M; Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany., Paijmans JLA; School of Environmental and Natural Sciences, Bangor University, Bangor, United Kingdom.; Department of Zoology, University of Cambridge, Cambridge, United Kingdom.

Source: PloS one [PLoS One] 2025 Mar 19; Vol. 20 (3), pp. e0319573. Date of Electronic Publication: 2025 Mar 19 (Print Publication: 2025).

Publication Type: Journal Article

Journal Info: Publisher: Public Library of Science Country of Publication: United States NLM ID: 101285081 Publication Model: eCollection Cited Medium: Internet ISSN: 1932-6203 (Electronic) Linking ISSN: 19326203 NLM ISO Abbreviation: PLoS One Subsets: MEDLINE

MeSH Terms: Gene Library* , Sequence Analysis, DNA*/methods , Ursidae*/genetics , DNA, Ancient*/analysis , Genomics*/methods, Animals ; Polymerase Chain Reaction ; Phylogeny ; Fossils ; DNA, Single-Stranded/genetics

Large indel detection in region-based phased diploid assemblies from linked-reads.

Authors: Luo C; Department of Biomedical Engineering, Vanderbilt University, Nashville, 37235, TN, USA., Peters BA; Advanced Genomics Technology Lab, Complete Genomics Inc, 2904 Orchard Parkway, San Jose, 95134, CA, USA., Zhou XM; Department of Biomedical Engineering, Vanderbilt University, Nashville, 37235, TN, USA. maizie.zhou@vanderbilt.edu.; Department of Computer Science, Vanderbilt University, Nashville, 37235, TN, USA. maizie.zhou@vanderbilt.edu.

Source: BMC genomics [BMC Genomics] 2025 Mar 18; Vol. 26 (Suppl 2), pp. 263. Date of Electronic Publication: 2025 Mar 18.

Publication Type: Journal Article

Journal Info: Publisher: BioMed Central Country of Publication: England NLM ID: 100965258 Publication Model: Electronic Cited Medium: Internet ISSN: 1471-2164 (Electronic) Linking ISSN: 14712164 NLM ISO Abbreviation: BMC Genomics Subsets: MEDLINE

MeSH Terms: Diploidy* , INDEL Mutation* , Sequence Analysis, DNA*/methods , Genomics*/methods, Haplotypes ; Humans ; Algorithms ; High-Throughput Nucleotide Sequencing ; Computational Biology/methods ; Software

FPGA-based accelerator for adaptive banded event alignment in nanopore sequencing data analysis.

Authors: Feng Y; Department of Computer Science and Engineering, The Pennsylvania State University, 201 Old Main, University Park, PA, 16802, USA. ypf5071@psu.edu., Li Z; Department of Computer Science and Engineering, The Pennsylvania State University, 201 Old Main, University Park, PA, 16802, USA., Gudukbay Akbulut G; Department of Computer Science and Engineering, The Pennsylvania State University, 201 Old Main, University Park, PA, 16802, USA., Narayanan V; Department of Computer Science and Engineering, The Pennsylvania State University, 201 Old Main, University Park, PA, 16802, USA., Kandemir MT; Department of Computer Science and Engineering, The Pennsylvania State University, 201 Old Main, University Park, PA, 16802, USA., Das CR; Department of Computer Science and Engineering, The Pennsylvania State University, 201 Old Main, University Park, PA, 16802, USA.

Source: BMC bioinformatics [BMC Bioinformatics] 2025 Mar 17; Vol. 26 (1), pp. 83. Date of Electronic Publication: 2025 Mar 17.

Publication Type: Journal Article

Journal Info: Publisher: BioMed Central Country of Publication: England NLM ID: 100965194 Publication Model: Electronic Cited Medium: Internet ISSN: 1471-2105 (Electronic) Linking ISSN: 14712105 NLM ISO Abbreviation: BMC Bioinformatics Subsets: MEDLINE

MeSH Terms: Nanopore Sequencing*/methods , Sequence Analysis, DNA*/methods , Sequence Alignment*/methods, Algorithms

GoldPolish-target: targeted long-read genome assembly polishing.

Authors: Zhang E; Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, V5Z 4S6, Canada. ezhang@bcgsc.ca., Coombe L; Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, V5Z 4S6, Canada., Wong J; Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, V5Z 4S6, Canada., Warren RL; Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, V5Z 4S6, Canada., Birol I; Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, V5Z 4S6, Canada. ibirol@bcgsc.ca.

Source: BMC bioinformatics [BMC Bioinformatics] 2025 Mar 07; Vol. 26 (1), pp. 78. Date of Electronic Publication: 2025 Mar 07.

Publication Type: Journal Article

Journal Info: Publisher: BioMed Central Country of Publication: England NLM ID: 100965194 Publication Model: Electronic Cited Medium: Internet ISSN: 1471-2105 (Electronic) Linking ISSN: 14712105 NLM ISO Abbreviation: BMC Bioinformatics Subsets: MEDLINE

MeSH Terms: Sequence Analysis, DNA*/methods , High-Throughput Nucleotide Sequencing*/methods , Software* , Genomics*/methods, Algorithms ; Drosophila melanogaster/genetics ; Humans ; Animals

TopoQual polishes circular consensus sequencing data and accurately predicts quality scores.

Authors: Weerakoon M; Auburn University, Auburn, AL, 36849, USA. wmw0016@auburn.edu., Lee S; Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK., Mitchell E; Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK.; Wellcome-MRC Cambridge Stem Cell Institute, Cambridge Biomedical Campus, Cambridge, UK.; Department of Haematology, University of Cambridge, Cambridge, UK., Heaton H; Auburn University, Auburn, AL, 36849, USA. haynesheaton@auburn.edu.

Source: BMC bioinformatics [BMC Bioinformatics] 2025 Jan 16; Vol. 26 (1), pp. 17. Date of Electronic Publication: 2025 Jan 16.

Publication Type: Journal Article

Journal Info: Publisher: BioMed Central Country of Publication: England NLM ID: 100965194 Publication Model: Electronic Cited Medium: Internet ISSN: 1471-2105 (Electronic) Linking ISSN: 14712105 NLM ISO Abbreviation: BMC Bioinformatics Subsets: MEDLINE

MeSH Terms: Sequence Analysis, DNA*/methods , High-Throughput Nucleotide Sequencing*/methods , Software* , Consensus Sequence*, Humans ; Algorithms ; Genomics/methods ; Deep Learning

CGRclust: Chaos Game Representation for twin contrastive clustering of unlabelled DNA sequences.

Authors: Alipour F; School of Computer Science, University of Waterloo, Waterloo, Canada. falipour@uwaterloo.ca., Hill KA; Department of Biology, University of Western Ontario, London, Canada., Kari L; School of Computer Science, University of Waterloo, Waterloo, Canada.

Source: BMC genomics [BMC Genomics] 2024 Dec 18; Vol. 25 (1), pp. 1214. Date of Electronic Publication: 2024 Dec 18.

Publication Type: Journal Article

Journal Info: Publisher: BioMed Central Country of Publication: England NLM ID: 100965258 Publication Model: Electronic Cited Medium: Internet ISSN: 1471-2164 (Electronic) Linking ISSN: 14712164 NLM ISO Abbreviation: BMC Genomics Subsets: MEDLINE

MeSH Terms: Sequence Analysis, DNA*/methods, Cluster Analysis ; Neural Networks, Computer ; Unsupervised Machine Learning ; Genome, Viral ; Animals ; Computational Biology/methods ; Algorithms ; Genome, Mitochondrial

Impact of DNA extraction, PCR amplification, sequencing, and bioinformatic analysis on food-associated mock communities using PacBio long-read amplicon sequencing.

Authors: Baer M; Institute of Nutritional and Food Sciences, Food Microbiology and Hygiene, University of Bonn, Friedrich-Hirzebruch-Allee 7, 53115, Bonn, Germany. mabaer@uni-bonn.de., Höppe L; Institute of Nutritional and Food Sciences, Food Microbiology and Hygiene, University of Bonn, Friedrich-Hirzebruch-Allee 7, 53115, Bonn, Germany., Seel W; Institute of Nutritional and Food Sciences, Nutrition and Microbiota, University of Bonn, Katzenburgweg 7, 53115, Bonn, Germany., Lipski A; Institute of Nutritional and Food Sciences, Food Microbiology and Hygiene, University of Bonn, Friedrich-Hirzebruch-Allee 7, 53115, Bonn, Germany.

Source: BMC microbiology [BMC Microbiol] 2024 Dec 06; Vol. 24 (1), pp. 521. Date of Electronic Publication: 2024 Dec 06.

Publication Type: Journal Article

Journal Info: Publisher: BioMed Central Country of Publication: England NLM ID: 100966981 Publication Model: Electronic Cited Medium: Internet ISSN: 1471-2180 (Electronic) Linking ISSN: 14712180 NLM ISO Abbreviation: BMC Microbiol Subsets: MEDLINE

MeSH Terms: RNA, Ribosomal, 16S*/genetics , DNA, Bacterial*/genetics , Polymerase Chain Reaction*/methods , Computational Biology*/methods , Bacteria*/genetics , Bacteria*/classification , Bacteria*/isolation & purification , Sequence Analysis, DNA*/methods , Food Microbiology*, Microbiota/genetics ; Phylogeny ; Meat/microbiology ; Biofilms/growth & development ; High-Throughput Nucleotide Sequencing/methods

A regression based approach to phylogenetic reconstruction from multi-sample bulk DNA sequencing of tumors.

Authors: Schmidt H; Department of Computer Science, Princeton University, New Jersey, United States of America., Raphael BJ; Department of Computer Science, Princeton University, New Jersey, United States of America.

Source: PLoS computational biology [PLoS Comput Biol] 2024 Dec 04; Vol. 20 (12), pp. e1012631. Date of Electronic Publication: 2024 Dec 04 (Print Publication: 2024).

Publication Type: Journal Article

Journal Info: Publisher: Public Library of Science Country of Publication: United States NLM ID: 101238922 Publication Model: eCollection Cited Medium: Internet ISSN: 1553-7358 (Electronic) Linking ISSN: 1553734X NLM ISO Abbreviation: PLoS Comput Biol Subsets: MEDLINE

MeSH Terms: Phylogeny* , Algorithms* , Neoplasms*/genetics , Neoplasms*/classification , Sequence Analysis, DNA*/methods , Computational Biology*/methods, Humans ; Regression Analysis

Pseudomegasporoporia margallensis sp. nov. and Microporellus subadustus (Polyporaceae, Basidiomycota) newly described and recorded from Pakistan.

Authors: Razzaq F; Fungal Biology and Systematics Research Laboratory, Institute of Botany, University of the Punjab, Quaid-e-Azam Campus, Lahore, 54590, Pakistan. razzaqfauzia8@gmail.com., Murtaza R; Fungal Biology and Systematics Research Laboratory, Institute of Botany, University of the Punjab, Quaid-e-Azam Campus, Lahore, 54590, Pakistan., Usman M; Fungal Biology and Systematics Research Laboratory, Institute of Botany, University of the Punjab, Quaid-e-Azam Campus, Lahore, 54590, Pakistan., Khalid AN; Fungal Biology and Systematics Research Laboratory, Institute of Botany, University of the Punjab, Quaid-e-Azam Campus, Lahore, 54590, Pakistan., Ashraf S; Fungal Biology and Systematics Research Laboratory, Institute of Botany, University of the Punjab, Quaid-e-Azam Campus, Lahore, 54590, Pakistan., Li Q; State Key Laboratory of Functions and Applications of Medicinal Plants & Engineering and Research Center for Southwest Bio-Pharmaceutical Resources of National Ministry of China, Guizhou Medical University, Guiyang, China.

Source: BMC microbiology [BMC Microbiol] 2024 Nov 19; Vol. 24 (1), pp. 484. Date of Electronic Publication: 2024 Nov 19.

Publication Type: Journal Article

Journal Info: Publisher: BioMed Central Country of Publication: England NLM ID: 100966981 Publication Model: Electronic Cited Medium: Internet ISSN: 1471-2180 (Electronic) Linking ISSN: 14712180 NLM ISO Abbreviation: BMC Microbiol Subsets: MEDLINE

MeSH Terms: Phylogeny* , DNA, Fungal*/genetics , Sequence Analysis, DNA*, Pakistan ; Polyporaceae/genetics ; Polyporaceae/classification ; Hyphae/genetics ; DNA, Ribosomal Spacer/genetics ; DNA, Ribosomal/genetics

Single nucleus DNA sequencing of flow sorted archived frozen and formalin fixed paraffin embedded solid tumors.

Authors: Zhou Y; Department of Research, Mayo Clinic in Arizona, Scottsdale, AZ, USA., Chen X; Department of Research, Mayo Clinic in Arizona, Scottsdale, AZ, USA., Chapman JS; Division of Gynecologic Oncology, Department of Obstetrics, Gynecology & Reproductive Sciences, University of California, San Francisco, CA, USA., Barrett MT; Department of Research, Mayo Clinic in Arizona, Scottsdale, AZ, USA. barrett.michael@mayo.edu.; Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic in Arizona, Scottsdale, AZ, USA. barrett.michael@mayo.edu.

Source: BMC genomics [BMC Genomics] 2024 Oct 08; Vol. 25 (1), pp. 943. Date of Electronic Publication: 2024 Oct 08.

Publication Type: Journal Article

Journal Info: Publisher: BioMed Central Country of Publication: England NLM ID: 100965258 Publication Model: Electronic Cited Medium: Internet ISSN: 1471-2164 (Electronic) Linking ISSN: 14712164 NLM ISO Abbreviation: BMC Genomics Subsets: MEDLINE

MeSH Terms: Paraffin Embedding* , Formaldehyde* , Single-Cell Analysis*/methods , Sequence Analysis, DNA*/methods , Tissue Fixation*, Humans ; Neoplasms/genetics ; Neoplasms/pathology ; Flow Cytometry/methods ; High-Throughput Nucleotide Sequencing/methods ; Cell Nucleus/genetics ; Female

Validated DNA isolation method ensuring successful long-read sequencing of cattle semen genome.

Authors: Denis E; INRAE, Castanet-Tolosan, France., Grohs C; INRAE, AgroParisTech, GABI, Université Paris-Saclay, Jouy-en-Josas, France., Donnadieu C; INRAE, Castanet-Tolosan, France., Iampietro C; INRAE, Castanet-Tolosan, France.

Source: PloS one [PLoS One] 2024 Aug 07; Vol. 19 (8), pp. e0308011. Date of Electronic Publication: 2024 Aug 07 (Print Publication: 2024).

Publication Type: Journal Article

Journal Info: Publisher: Public Library of Science Country of Publication: United States NLM ID: 101285081 Publication Model: eCollection Cited Medium: Internet ISSN: 1932-6203 (Electronic) Linking ISSN: 19326203 NLM ISO Abbreviation: PLoS One Subsets: MEDLINE

MeSH Terms: Semen* , DNA*/isolation & purification , DNA*/genetics , Sequence Analysis, DNA*/methods , Genome*, Animals ; Cattle ; Male ; Spermatozoa ; High-Throughput Nucleotide Sequencing/methods

Quantifying variation across 16S rRNA gene sequencing runs in human microbiome studies.

Authors: Hoisington AJ; Veterans Health Administration, Rocky Mountain Mental Illness Research Education and Clinical Center (MIRECC) for Veteran Suicide Prevention, Rocky Mountain Regional Veterans Affairs Medical Center (RMRVAMC), Aurora, CO, USA. andrew.hoisington@va.gov.; Department of Physical Medicine and Rehabilitation, University of Colorado Anschutz Medical Campus, Aurora, CO, USA. andrew.hoisington@va.gov.; Military and Veteran Microbiome: Consortium for Research and Education (MVM-CoRE), Aurora, CO, USA. andrew.hoisington@va.gov.; Department of Systems Engineering and Management, Air Force Institute of Technology, Wright-Patterson Air Force Base, Dayton, OH, USA. andrew.hoisington@va.gov., Stamper CE; Veterans Health Administration, Rocky Mountain Mental Illness Research Education and Clinical Center (MIRECC) for Veteran Suicide Prevention, Rocky Mountain Regional Veterans Affairs Medical Center (RMRVAMC), Aurora, CO, USA.; Department of Physical Medicine and Rehabilitation, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.; Military and Veteran Microbiome: Consortium for Research and Education (MVM-CoRE), Aurora, CO, USA., Ellis JC; Netellis LLC, Knoxville, TN, USA., Lowry CA; Veterans Health Administration, Rocky Mountain Mental Illness Research Education and Clinical Center (MIRECC) for Veteran Suicide Prevention, Rocky Mountain Regional Veterans Affairs Medical Center (RMRVAMC), Aurora, CO, USA.; Department of Physical Medicine and Rehabilitation, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.; Military and Veteran Microbiome: Consortium for Research and Education (MVM-CoRE), Aurora, CO, USA.; Department of Integrative Physiology, Center for Neuroscience, and Center for Microbial Exploration, University of Colorado Boulder, Boulder, CO, USA., Brenner LA; Veterans Health Administration, Rocky Mountain Mental Illness Research Education and Clinical Center (MIRECC) for Veteran Suicide Prevention, Rocky Mountain Regional Veterans Affairs Medical Center (RMRVAMC), Aurora, CO, USA.; Department of Physical Medicine and Rehabilitation, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.; Military and Veteran Microbiome: Consortium for Research and Education (MVM-CoRE), Aurora, CO, USA.; Department of Psychiatry, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.; Department of Neurology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.

Source: Applied microbiology and biotechnology [Appl Microbiol Biotechnol] 2024 Jun 08; Vol. 108 (1), pp. 367. Date of Electronic Publication: 2024 Jun 08.

Publication Type: Journal Article

Journal Info: Publisher: Springer International Country of Publication: Germany NLM ID: 8406612 Publication Model: Electronic Cited Medium: Internet ISSN: 1432-0614 (Electronic) Linking ISSN: 01757598 NLM ISO Abbreviation: Appl Microbiol Biotechnol Subsets: MEDLINE

MeSH Terms: RNA, Ribosomal, 16S*/genetics , Feces*/microbiology , Microbiota*/genetics , Sequence Analysis, DNA*/methods , DNA, Bacterial*/genetics, Humans ; Bacteria/genetics ; Bacteria/classification ; Bacteria/isolation & purification ; Reproducibility of Results ; Mouth/microbiology ; High-Throughput Nucleotide Sequencing/methods

bsgenova: an accurate, robust, and fast genotype caller for bisulfite-sequencing data.

Authors: Feng Y; Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China. yance_feng@163.com., Gao F; Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China. flys828@gmail.com.; HIM-BGI Omics Center, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences (CAS), Hangzhou, China. flys828@gmail.com.

Source: BMC bioinformatics [BMC Bioinformatics] 2024 Jun 05; Vol. 25 (1), pp. 206. Date of Electronic Publication: 2024 Jun 05.

Publication Type: Journal Article

Journal Info: Publisher: BioMed Central Country of Publication: England NLM ID: 100965194 Publication Model: Electronic Cited Medium: Internet ISSN: 1471-2105 (Electronic) Linking ISSN: 14712105 NLM ISO Abbreviation: BMC Bioinformatics Subsets: MEDLINE

MeSH Terms: Polymorphism, Single Nucleotide* , DNA Methylation*/genetics , Sulfites*/chemistry , Sequence Analysis, DNA*/methods, Humans ; Genotype ; Software ; Whole Genome Sequencing/methods ; Bayes Theorem

A full-length S1 gene sequencing of a novel emerged GI-19 and GI-23 lineages of Infectious bronchitis virus currently circulating in chicken flocks in upper Egypt reveals marked genetic diversity and recombination events.

Authors: Shosha E; Virology department, Faculty of Veterinary Medicine, New Valley University, El-Kharga, Egypt. Emanshosha25@gmail.com., Abdelnaser S; Virology department, Faculty of Veterinary Medicine, New Valley University, El-Kharga, Egypt., Zanaty AM; Gene Analysis Unit, Reference Laboratory for Quality Control on Poultry, Agriculture Research Center (ARC), Animal Health Institute, Giza, Egypt.

Source: Virology journal [Virol J] 2025 May 07; Vol. 22 (1), pp. 135. Date of Electronic Publication: 2025 May 07.

Publication Type: Journal Article

Journal Info: Publisher: BioMed Central Country of Publication: England NLM ID: 101231645 Publication Model: Electronic Cited Medium: Internet ISSN: 1743-422X (Electronic) Linking ISSN: 1743422X NLM ISO Abbreviation: Virol J Subsets: MEDLINE

MeSH Terms: Infectious bronchitis virus*/genetics , Infectious bronchitis virus*/classification , Infectious bronchitis virus*/isolation & purification , Poultry Diseases*/virology , Poultry Diseases*/epidemiology , Coronavirus Infections*/veterinary , Coronavirus Infections*/virology , Coronavirus Infections*/epidemiology , Genetic Variation* , Recombination, Genetic* , Spike Glycoprotein, Coronavirus*/genetics, Animals ; Egypt/epidemiology ; Chickens/virology ; Phylogeny ; Genotype ; Sequence Analysis, DNA ; Specific Pathogen-Free Organisms

The altitudinal patterns of global human gut microbial diversity.

Authors: Peng LL; Institute of Eastern-Himalaya Biodiversity Research, Dali University, Dali, 671003, Yunnan, China.; School of Basic Medicine, Dali University, Dali, Yunnan, 671000, China., Qi FL; Institute of Eastern-Himalaya Biodiversity Research, Dali University, Dali, 671003, Yunnan, China.; Institute of Natural Antioxidants and Anti-inflammation, Dali University, Dali, 671003, Yunnan, China., Tan K; Institute of Eastern-Himalaya Biodiversity Research, Dali University, Dali, 671003, Yunnan, China. tank@eastern-himalaya.cn.; Collaborative Innovation Center for Biodiversity and Conservation in the Three Parallel Rivers Region of China, Dali, 671003, Yunnan, China. tank@eastern-himalaya.cn., Xiao W; Institute of Eastern-Himalaya Biodiversity Research, Dali University, Dali, 671003, Yunnan, China.; Collaborative Innovation Center for Biodiversity and Conservation in the Three Parallel Rivers Region of China, Dali, 671003, Yunnan, China.; International Centre of Biodiversity and Primates Conservation, Dali University, Dali, 671003, Yunnan, China.

Source: BMC microbiology [BMC Microbiol] 2025 May 05; Vol. 25 (1), pp. 267. Date of Electronic Publication: 2025 May 05.

Publication Type: Journal Article

Journal Info: Publisher: BioMed Central Country of Publication: England NLM ID: 100966981 Publication Model: Electronic Cited Medium: Internet ISSN: 1471-2180 (Electronic) Linking ISSN: 14712180 NLM ISO Abbreviation: BMC Microbiol Subsets: MEDLINE

MeSH Terms: Altitude* , Gastrointestinal Microbiome*/genetics , Bacteria*/classification , Bacteria*/genetics , Bacteria*/isolation & purification , Biodiversity*, Humans ; RNA, Ribosomal, 16S/genetics ; DNA, Bacterial/genetics ; Phylogeny ; Feces/microbiology ; Sequence Analysis, DNA