Works matching DE "SHOTGUN sequencing"

Results: 1727

Characterization and ex vivo modelling of endodontic infections from the Arabian Gulf region.

Published in:

International Endodontic Journal, 2025, v. 58, n. 7, p. 1091, doi. 10.1111/iej.14227

By:

Nassar, Rania;
Nassar, Mohannad;
Mohamed, Lobna;
Senok, Abiola;
Williams, David

Publication type:

Article

Metagenomic analysis reveals the roles of Actinobacteria in plasticizer-contaminated landfills and aids in identifying key degraders.

Published in:

Scientific Reports, 2025, v. 15, n. 1, p. 1, doi. 10.1038/s41598-025-03316-w

By:

Rungsihiranrut, Adisan;
Muangchinda, Chanokporn;
Pinyakong, Onruthai

Publication type:

Article

Shotgun metagenomic composition, microbial interactions and functional insights into the uterine microbiome of postpartum dairy cows with clinical and subclinical endometritis.

Published in:

Scientific Reports, 2025, v. 15, n. 1, p. 1, doi. 10.1038/s41598-025-03265-4

By:

Rashid, Muhammad Hussnain;
Pascottini, Osvaldo Bogado;
Xie, Lei;
Niazi, Mehrnaz;
Lietaer, Leen;
Comlekcioglu, Ugur;
Opsomer, Geert

Publication type:

Article

Optimization of TaqMan-based quantitative PCR diagnosis for Entamoeba histolytica using droplet digital PCR.

Published in:

PLoS Neglected Tropical Diseases, 2025, v. 19, n. 6, p. 1, doi. 10.1371/journal.pntd.0012935

By:

Kawashima, Akira;
Yanagawa, Yasuaki;
Chikata, Takayuki;
Shimogawara, Rieko;
Mizushima, Daisuke;
Tsuchiya, Kiyoto;
Yagita, Kenji;
Gatanaga, Hiroyuki;
Watanabe, Koji

Publication type:

Article

Gut microbiota dysbiosis and metabolic shifts in pediatric norovirus infection: a metagenomic study in Northeast China.

Published in:

Frontiers in Cellular & Infection Microbiology, 2025, p. 1, doi. 10.3389/fcimb.2025.1600470

By:

Wang, Ziju;
Wei, Xinhong;
Piao, Lizhen;
Zhang, Xiaofei;
Wang, Hong

Publication type:

Article

Gut mycobiome maturation and its determinants during early childhood: a comparison of ITS2 amplicon and shotgun metagenomic sequencing approaches.

Published in:

Frontiers in Microbiology, 2025, p. 1, doi. 10.3389/fmicb.2025.1539750

By:

Heisel, Timothy;
Gonia, Sara;
Dillon, Abrielle;
Hoops, Susan L.;
Al-Ghalith, Gabriel A.;
Gohl, Daryl;
Mukhopadhyay, Sagori;
Puopolo, Karen;
Kennedy, Peter;
Sadowsky, Michael J.;
Knights, Dan;
Johnson, Abigail J.;
Gerber, Jeffrey S.;
Gale, Cheryl A.

Publication type:

Article

A One Health Approach Metagenomic Study on Antimicrobial Resistance Traits of Canine Saliva.

Published in:

Antibiotics (2079-6382), 2025, v. 14, n. 5, p. 433, doi. 10.3390/antibiotics14050433

By:

Tóth, Adrienn Gréta;
Tóth, Darinka Lilla;
Remport, Laura;
Tóth, Imre;
Németh, Tibor;
Dubecz, Attila;
Patai, Árpád V.;
Wagenhoffer, Zsombor;
Makrai, László;
Solymosi, Norbert

Publication type:

Article

Impact of SARS-CoV-2 P.1 Variant Infection on the Nasopharyngeal Commensal Bacterial Microbiome of Individuals from the Brazilian Amazon.

Published in:

Microorganisms, 2025, v. 13, n. 5, p. 1088, doi. 10.3390/microorganisms13051088

By:

Mendes Silva Cruz, Amanda;
Cardoso, Jedson Ferreira;
Pinheiro, Kenny Costa;
Ferreira, Jessylene Almeida;
Barbagelata, Luana Soares;
Silva, Sandro Patroca;
Chagas Junior, Wanderley Dias;
Lobo, Patrícia Santos;
Teixeira, Dielle Monteiro;
André Junior, Walter;
Ordenes Silva, Inaiah;
Santos, Mirleide Cordeiro;
Soares Farias, Luana Silva;
Sousa, Maisa Silva;
Neto Tavares, Fernando

Publication type:

Article

The Impact of Probiotic Supplementation on the Development of the Infant Gut Microbiota: An Exploratory Follow-Up of a Randomised Controlled Trial.

Published in:

Microorganisms, 2025, v. 13, n. 5, p. 984, doi. 10.3390/microorganisms13050984

By:

Coates, Niall;
John, Daniel A.;
Jordan, Sue;
Storey, Melanie;
Thornton, Catherine A.;
Garaiova, Iveta;
Wang, Duolao;
Allen, Stephen J.;
Michael, Daryn R.;
Plummer, Susan F.;
Facey, Paul D.

Publication type:

Article

The first whole genome sequence and characterization of narcissus latent virus based on metagenomic analysis of iris in Iran; analyses of the genetic structure of the virus.

Published in:

European Journal of Plant Pathology, 2022, v. 164, n. 4, p. 601, doi. 10.1007/s10658-022-02574-y

By:

Moradi, Zohreh;
Mehrvar, Mohsen

Publication type:

Article

Occurrence of maize lethal necrosis in Ecuador: a disease without boundaries?

Published in:

European Journal of Plant Pathology, 2016, v. 146, n. 3, p. 705, doi. 10.1007/s10658-016-0943-5

By:

Quito-Avila, D.;
Alvarez, R.;
Mendoza, A.

Publication type:

Article

Bullseye: shotgun metagenomics taking aim at the microbial diversity associated with tubes of Ceriantharia.

Published in:

Aquatic Ecology, 2024, v. 58, n. 4, p. 1287, doi. 10.1007/s10452-024-10144-z

By:

Ceriello, Hellen;
Brito, Gustavo R.;
de Oliveira, Bruno Francesco Rodrigues;
Cunha, Marielton dos Passos;
Stampar, Sérgio N.

Publication type:

Article

Assessments of the impacts of chemical and hydrocarbon pollution on Ologe Lagoon water and its prokaryotic community structure.

Published in:

Aquatic Ecology, 2024, v. 58, n. 3, p. 741, doi. 10.1007/s10452-024-10102-9

By:

Ashade, Ahmeed Olalekan;
Obayori, Oluwafemi Sunday;
Salam, Lateef Babatunde;
Fashola, Muibat Omotola;
Nwaokorie, Francisca Obiageri

Publication type:

Article

Unlocking the jar: revealing gastric content in Ceriantharia (Cnidaria, Anthozoa) through whole-genome shotgun sequencing.

Published in:

Aquatic Ecology, 2024, v. 58, n. 2, p. 375, doi. 10.1007/s10452-023-10076-0

By:

Santos, Thaís Barbosa;
Poliseno, Angelo;
Bendia, Amanda G.;
Pellizari, Vivian H.;
Reimer, James D.;
Stampar, Sérgio N.

Publication type:

Article

Years After a Fire, Biocrust Microbial Communities are Similar to Unburned Communities in a Coastal Grassland.

Published in:

Microbial Ecology, 2023, v. 85, n. 3, p. 1028, doi. 10.1007/s00248-022-02137-y

By:

Palmer, Brianne;
Lawson, Dawn;
Lipson, David A.

Publication type:

Article

Metagenomics Analysis to Investigate the Microbial Communities and Their Functional Profile During Cyanobacterial Blooms in Lake Varese.

Published in:

Microbial Ecology, 2022, v. 83, n. 4, p. 850, doi. 10.1007/s00248-021-01914-5

By:

Sanseverino, Isabella;
Pretto, Patrizia;
António, Diana Conduto;
Lahm, Armin;
Facca, Chiara;
Loos, Robert;
Skejo, Helle;
Beghi, Andrea;
Pandolfi, Franca;
Genoni, Pietro;
Lettieri, Teresa

Publication type:

Article

Differences in Precipitation Regime Shape Microbial Community Composition and Functional Potential in Namib Desert Soils.

Published in:

Microbial Ecology, 2022, v. 83, n. 3, p. 689, doi. 10.1007/s00248-021-01785-w

By:

Naidoo, Yashini;
Valverde, Angel;
Pierneef, Rian E.;
Cowan, Don A.

Publication type:

Article

Relationship Between Peat Type and Microbial Ecology in Sphagnum-Containing Peatlands of the Adirondack Mountains, NY, USA.

Published in:

Microbial Ecology, 2021, v. 82, n. 2, p. 429, doi. 10.1007/s00248-020-01651-1

By:

St. James, Andrew R.;
Lin, Janni;
Richardson, Ruth E.

Publication type:

Article

Influence of Environmental Stressors on the Microbiota of Zebra Mussels (Dreissena polymorpha).

Published in:

Microbial Ecology, 2021, v. 81, n. 4, p. 1042, doi. 10.1007/s00248-020-01642-2

By:

Mathai, Prince P.;
Bertram, Jonathan H.;
Padhi, Soumesh K.;
Singh, Vikash;
Tolo, Isaiah E.;
Primus, Alexander;
Mor, Sunil K.;
Phelps, Nicholas B. D.;
Sadowsky, Michael J.

Publication type:

Article

Depicting Temporal, Functional, and Phylogenetic Patterns in Estuarine Diazotrophic Communities from Environmental DNA and RNA.

Published in:

Microbial Ecology, 2021, v. 81, n. 1, p. 36, doi. 10.1007/s00248-020-01562-1

By:

Zilius, Mindaugas;
Samuiloviene, Aurelija;
Stanislauskienė, Rūta;
Broman, Elias;
Bonaglia, Stefano;
Meškys, Rolandas;
Zaiko, Anastasija

Publication type:

Article

Microbial Assemblage Dynamics Within the American Alligator Nesting Ecosystem: a Comparative Approach Across Ecological Scales.

Published in:

Microbial Ecology, 2020, v. 80, n. 3, p. 603, doi. 10.1007/s00248-020-01522-9

By:

Grajal-Puche, Alejandro;
Murray, Christopher M.;
Kearley, Matthew;
Merchant, Mark;
Nix, Christopher;
Warner, Jonathan K.;
Walker, Donald M.

Publication type:

Article

Vaginal Microbiome of Pregnant Indian Women: Insights into the Genome of Dominant Lactobacillus Species.

Published in:

Microbial Ecology, 2020, v. 80, n. 2, p. 487, doi. 10.1007/s00248-020-01501-0

By:

Mehta, Ojasvi;
Ghosh, Tarini Shankar;
Kothidar, Akansha;
Gowtham, M. Rama;
Mitra, Ridhima;
Kshetrapal, Pallavi;
Wadhwa, Nitya;
Thiruvengadam, Ramachandran;
GARBH-Ini study group;
Bhatnagar, Shinjini;
Das, Bhabatosh;
Kshetrapal, Pallavi S.;
Balakrish Nair, Balakrish G.;
Natchu, Uma Chandra Mouli;
Rath, Satyajit;
Sachdeva, Kanika;
Sopory, Shailaja;
Misra, Sumit;
Singh, Amanpreet;
Sharma, Dharmendra

Publication type:

Article

Biological Soil Crusts from Different Soil Substrates Harbor Distinct Bacterial Groups with the Potential to Produce Exopolysaccharides and Lipopolysaccharides.

Published in:

Microbial Ecology, 2020, v. 79, n. 2, p. 326, doi. 10.1007/s00248-019-01415-6

By:

Cania, Barbara;
Vestergaard, Gisle;
Kublik, Susanne;
Köhne, John Maximilian;
Fischer, Thomas;
Albert, Andreas;
Winkler, Barbro;
Schloter, Michael;
Schulz, Stefanie

Publication type:

Article

From the High Arctic to the Equator: Do Soil Metagenomes Differ According to Our Expectations?

Published in:

Microbial Ecology, 2019, v. 77, n. 1, p. 168, doi. 10.1007/s00248-018-1215-z

By:

Kerfahi, Dorsaf;
Tripathi, Binu M.;
Dong, Ke;
Kim, Mincheol;
Kim, Hyoki;
Ferry Slik, J. W.;
Go, Rusea;
Adams, Jonathan M.

Publication type:

Article

The Functional Potential of the Rhizospheric Microbiome of an Invasive Tree Species, Acacia dealbata.

Published in:

Microbial Ecology, 2019, v. 77, n. 1, p. 191, doi. 10.1007/s00248-018-1214-0

By:

Kamutando, Casper N.;
Vikram, Surendra;
Kamgan-Nkuekam, Gilbert;
Makhalanyane, Thulani P.;
Greve, Michelle;
Le Roux, Johannes J.;
Richardson, David M.;
Cowan, Don A.;
Valverde, Angel

Publication type:

Article

IncP-1β Plasmids Are Important Carriers of Fitness Traits for Variovorax Species in the Mycosphere-Two Novel Plasmids, pHB44 and pBS64, with Differential Effects Unveiled.

Published in:

Microbial Ecology, 2015, v. 70, n. 1, p. 141, doi. 10.1007/s00248-014-0550-y

By:

Zhang, Miaozhi;
Warmink, Jan;
Pereira e Silva, Michele;
Brons, Jolanda;
Smalla, Kornelia;
van Elsas, Jan

Publication type:

Article

Soil-Borne Microbiome: Linking Diversity to Function.

Published in:

Microbial Ecology, 2015, v. 70, n. 1, p. 255, doi. 10.1007/s00248-014-0559-2

By:

Mendes, Lucas;
Tsai, Siu;
Navarrete, Acácio;
Hollander, Mattias;
Veen, Johannes;
Kuramae, Eiko

Publication type:

Article

Exploring the role of the human microbiome in forensic identification: opportunities and challenges.

Published in:

International Journal of Legal Medicine, 2024, v. 138, n. 5, p. 1891, doi. 10.1007/s00414-024-03217-z

By:

Franceschetti, Lorenzo;
Lodetti, Giorgia;
Blandino, Alberto;
Amadasi, Alberto;
Bugelli, Valentina

Publication type:

Article

Comparison of whole mitochondrial genome variants between hair shafts and reference samples using massively parallel sequencing.

Published in:

International Journal of Legal Medicine, 2020, v. 134, n. 3, p. 853, doi. 10.1007/s00414-019-02205-y

By:

Kim, Bo Min;
Hong, Sae Rom;
Chun, Hein;
Kim, Sangwoo;
Shin, Kyoung-Jin

Publication type:

Article

MetaCache: context-aware classification of metagenomic reads using minhashing.

Published in:

Bioinformatics, 2017, v. 33, n. 23, p. 3740, doi. 10.1093/bioinformatics/btx520

By:

Müller, André;
Hundt, Christian;
Hildebrandt, Andreas;
Hankeln, Thomas;
Schmidt, Bertil

Publication type:

Article

PARTIE: a partition engine to separate metagenomic and amplicon projects in the Sequence Read Archive.

Published in:

Bioinformatics, 2017, v. 33, n. 15, p. 2389, doi. 10.1093/bioinformatics/btx184

By:

Torres, Pedro J.;
Edwards, Robert A.;
Mcnair, Katelyn A.

Publication type:

Article

MetaShot: an accurate workflow for taxon classification of host-associated microbiome from shotgun metagenomic data.

Published in:

Bioinformatics, 2017, v. 33, n. 11, p. 1730, doi. 10.1093/bioinformatics/btx036

By:

Fosso, B.;
Santamaria, M.;
D’Antonio, M.;
Lovero, D.;
Corrado, G.;
Vizza, E.;
Passaro, N.;
Garbuglia, A. R.;
Capobianchi, M. R.;
Crescenzi, M.;
Valiente, G.;
Pesole, G.

Publication type:

Article

PALADIN: protein alignment for functional profiling whole metagenome shotgun data.

Published in:

Bioinformatics, 2017, v. 33, n. 10, p. 1473, doi. 10.1093/bioinformatics/btx021

By:

Westbrook, Anthony;
Ramsdell, Jordan;
Schuelke, Taruna;
Normington, Louisa;
Bergeron, R. Daniel;
Thomas, W. Kelley;
MacManes, Matthew D.

Publication type:

Article

Large-scale 16S gene assembly using metagenomics shotgun sequences.

Published in:

Bioinformatics, 2017, v. 33, n. 10, p. 1447, doi. 10.1093/bioinformatics/btx018

By:

Feng Zeng;
Zicheng Wang;
Ying Wang;
Jizhong Zhou;
Ting Chen

Publication type:

Article

KAT: a K-mer analysis toolkit to quality control NGS datasets and genome assemblies.

Published in:

Bioinformatics, 2017, v. 33, n. 4, p. 574, doi. 10.1093/bioinformatics/btw663

By:

Mapleson, Daniel;
Accinelli, Gonzalo Garcia;
Kettleborough, George;
Wright, Jonathan;
Clavijo, Bernardo J.

Publication type:

Article

Uncertainty estimation of predictions of peptides' chromatographic retention times in shotgun proteomics.

Published in:

Bioinformatics, 2017, v. 33, n. 4, p. 508, doi. 10.1093/bioinformatics/btw619

By:

Afkham, Heydar Maboudi;
Xuanbin Qiu;
The, Matthew;
Käll, Lukas

Publication type:

Article

Gene-set association tests for next-generation sequencing data.

Published in:

Bioinformatics, 2016, v. 32, n. 17, p. i611, doi. 10.1093/bioinformatics/btw429

By:

Jaehoon Lee;
Young Jin Kim;
Juyoung Lee;
Bong-Jo Kim;
Seungyeoun Lee;
Taesung Park

Publication type:

Article

CoLoRMap: Correcting Long Reads by Mapping short reads.

Published in:

Bioinformatics, 2016, v. 32, n. 17, p. i545, doi. 10.1093/bioinformatics/btw463

By:

Haghshenas, Ehsan;
Hach, Faraz;
Sahinalp, S. Cenk;
Chauve, Cedric

Publication type:

Article

SUPER-FOCUS: a tool for agile functional analysis of shotgun metagenomic data.

Published in:

Bioinformatics, 2016, v. 32, n. 3, p. 354, doi. 10.1093/bioinformatics/btv584

By:

Silva, Genivaldo Gueiros Z.;
Green, Kevin T.;
Dutilh, Bas E.;
Edwards, Robert A.

Publication type:

Article

sapFinder: an R/Bioconductor package for detection of variant peptides in shotgun proteomics experiments.

Published in:

Bioinformatics, 2014, v. 30, n. 21, p. 3136, doi. 10.1093/bioinformatics/btu397

By:

Wen, Bo;
Xu, Shaohang;
Sheynkman, Gloria M.;
Feng, Qiang;
Lin, Liang;
Wang, Quanhui;
Xu, Xun;
Wang, Jun;
Liu, Siqi

Publication type:

Article

Exploration and retrieval of whole-metagenome sequencing samples.

Published in:

Bioinformatics, 2014, v. 30, n. 17, p. 2471, doi. 10.1093/bioinformatics/btu340

By:

Seth, Sohan;
Välimäki, Niko;
Kaski, Samuel;
Honkela, Antti

Publication type:

Article

An in silico Investigation of Anticancer Peptide Candidates in Fermented Food Microbiomes.

Published in:

Experimed, 2023, v. 13, n. 1, p. 64, doi. 10.26650/experimed.1262138

By:

Arikan, Muzaffer

Publication type:

Article

Bovine host genome acts on rumen microbiome function linked to methane emissions.

Published in:

Communications Biology, 2022, v. 5, n. 1, p. 1, doi. 10.1038/s42003-022-03293-0

By:

Martínez-Álvaro, Marina;
Auffret, Marc D.;
Duthie, Carol-Anne;
Dewhurst, Richard J.;
Cleveland, Matthew A.;
Watson, Mick;
Roehe, Rainer

Publication type:

Article

Metagenome-assembled genomes and gene catalog from the chicken gut microbiome aid in deciphering antibiotic resistomes.

Published in:

Communications Biology, 2021, v. 4, n. 1, p. 1, doi. 10.1038/s42003-021-02827-2

By:

Feng, Yuqing;
Wang, Yanan;
Zhu, Baoli;
Gao, George Fu;
Guo, Yuming;
Hu, Yongfei

Publication type:

Article

Shotgun Metagenomic Sequencing of Extremophilic Community from Soda Lake, Ga’ar Lake, in Wadi Al-Natrun, Egypt.

Published in:

Egyptian Journal of Experimental Biology (Botany), 2021, v. 17, n. 1, p. 21, doi. 10.5455/egyjebb.20210309063625

By:

Hagagy, Nashwa I.;
Elshafi, Naglaa F.;
Selim, Samy A.;
Hamedo, Hend A.

Publication type:

Article

Genetic classification of two Vibrio species isolated from Florida Gulf Coast using multi-locus sequence analysis.

Published in:

Fine Focus, 2020, v. 6, n. 1, p. 34, doi. 10.33043/ff.6.1.34-53

By:

Warrick, Eric C.;
Thomas, Matthew J.;
Barlow, Travis;
Dean, Alexis;
Ramo, Ambar;
Slivonik, Brian;
Gasper, Brittany J.

Publication type:

Article

Probiotics and postoperative infections in colorectal surgery – what New Zealand and Australian surgeons need to know about this emerging field.

Published in:

ANZ Journal of Surgery, 2024, v. 94, n. 4, p. 506, doi. 10.1111/ans.18946

By:

Paterson, Claudia;
Hill, Andrew

Publication type:

Article

A pilot study: intraoperative 16S rRNA sequencing versus culture in predicting colorectal incisional surgical site infection.

Published in:

ANZ Journal of Surgery, 2023, v. 93, n. 10, p. 2464, doi. 10.1111/ans.18455

By:

Vishnoi, Veral;
Hoedt, Emily C.;
Gould, Tiffany;
Carroll, Georgia;
Carroll, Rosemary;
Lott, Natalie;
Pockney, Peter;
Smith, Stephen R.;
Keely, Simon

Publication type:

Article

Phytoplasma DNA Enrichment from Sugarcane White Leaves for Shotgun Sequencing Improvement.

Published in:

Plants (2223-7747), 2024, v. 13, n. 21, p. 3006, doi. 10.3390/plants13213006

By:

Lohmaneeratana, Karan;
Gutiérrez, Gabriel;
Thamchaipenet, Arinthip;
Wellinger, Ralf Erik

Publication type:

Article

Targeted Whole Genome Sequencing (TWG-Seq) of Cucumber Green Mottle Mosaic Virus Using Tiled Amplicon Multiplex PCR and Nanopore Sequencing.

Published in:

Plants (2223-7747), 2022, v. 11, n. 20, p. 2716, doi. 10.3390/plants11202716

By:

Mackie, Joanne;
Kinoti, Wycliff M.;
Chahal, Sumit I.;
Lovelock, David A.;
Campbell, Paul R.;
Tran-Nguyen, Lucy T. T.;
Rodoni, Brendan C.;
Constable, Fiona E.

Publication type:

Article