Nanopore Analysis

Nanopore Analysis

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1-20 of 36 ARTICLES
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Featured Article
https://doi.org/10.12688/f1000research.15507.1
Brief Report metrics
Real time portable genome sequencing for global food security
[version 1; peer review: 1 approved, 1 approved with reservations]
Laura Boykin, Ammar Ghalab, Bruno Rossitto De Marchi, Anders Savill, James M. Wainaina, Tonny Kinene, Stephen Lamb, Myriam Rodrigues, Monica Kehoe, Joseph Ndunguru, Fred Tairo, Peter Sseruwagi, Charles Kayuki, Deogratius Mark, Joel Erasto, Hilda Bachwenkizi, Titus Alicai, Geoffrey Okao-Okuja, Phillip Abridrabo, Emmanuel Ogwok, John Francis Osingada, Jimmy Akono, Elijah Ateka, Brenda Muga, Samuel Kiarie
Peer Reviewers Invited
  • Funder
  • Crawford Fund
PUBLISHED 18 Jul 2018
https://doi.org/10.12688/f1000research.161731.2
Research Article metrics
Revised
Salivary microbiome and periodontopathogen/denitrifying bacteria associated with gingivitis and periodontitis in people with type 2-diabetes
[version 2; peer review: 2 not approved]
Endang Bachtiar, Boy M. Bachtiar, Dicky L Tahapary, Turmidzi Fath, Citra Fragrantia Theodora, Natalina Haerani, Selvi Nafisa Shahab, Yuniarti Soeroso, Ardy Wildan, Fergie Marie Joe Grizella Runtu, Fatimah Maria Tadjoedin, Dewi Ayuningtyas
Peer Reviewers Gaetano Isola; Sonia Nath
  • Funder
  • Direktorat Riset and Pengembangan, Universitas Indonesia
LATEST VERSION PUBLISHED 06 Oct 2025
https://doi.org/10.12688/f1000research.162894.1
Genome Note metrics
The genome sequence of the red-legged partridge, Alectoris rufa Linnaeus 1758
[version 1; peer review: 2 approved]
Abderrahmane Eleiwa, Pol Mestre, Ana Usie, Ester Vilaprinyo, Alberto Marin-Sanguino, Albert Sorribas, Cristobal Richart, Judit Salces-Ortiz, Rosa Fernández, Mar Biarnés, Noélia Antilles, Jesus Nadal, Rui Alves
Peer Reviewers Marc Palmada-Flores; Greta Bellinzona
  • Funders
  • Departament d'Innovació, Universitats i Empresa, Generalitat de Catalunya
  • Fundação para a Ciência e a Tecnologia
  • Fundacio Rovira i Virgili
  • European Research Council
  • Secretaria d’Universitats i Recerca del Departament d’Economia i Coneixement
PUBLISHED 02 Sep 2025
https://doi.org/10.12688/f1000research.164583.1
Software Tool Article metrics
Assembly and quantification of transcripts from noisy long reads with NIFFLR
[version 1; peer review: 1 approved with reservations, 2 not approved]
Alina Guo, Mihaela Pertea, Aleksey V Zimin
Peer Reviewers Colin Dewey; Fairlie Reese; Yuan Gao
  • Funders
  • Directorate for Biological Sciences
  • NIH
PUBLISHED 20 Jun 2025
https://doi.org/10.12688/f1000research.163516.1
Method Article metrics
NAD: Noise-augmented direct sequencing of target nucleic acids by augmenting with noise and selective sampling
[version 1; peer review: 1 approved, 1 approved with reservations]
Hyunjin Shim
Peer Reviewers Ruslan Kalendar; Runsheng Li
PUBLISHED 10 Apr 2025
https://doi.org/10.12688/f1000research.158856.1
Research Article metrics
Whole Genome Characterization of Potential Isolates for Next-Generation SARS-CoV-2 Vaccine Development Utilizing Structural Protein of Multiple Variants
[version 1; peer review: 1 approved with reservations]
Diyantoro Diyantoro, Fedik Abdul Rantam, Juniastuti Juniastuti, Andy Yasmin Wijaya, Helen Susilowati, Suryo Kuncorojakti, Ahmad Aswin, Firdausy Kurnia Maulana
Peer Reviewers Kanwal Khalid
  • Funder
  • Education Funding Institution (LPDP) and the Education Funding Service Center (BPPT)
PUBLISHED 21 Mar 2025
https://doi.org/10.12688/f1000research.150836.2
Genome Note metrics
Revised
The genomes of the aquarium sponges Tethya wilhelma and Tethya minuta (Porifera: Demospongiae)
[version 2; peer review: 2 approved]
Gert Wörheide, Warren R. Francis, Fabian Deister, Stefan Krebs, Dirk Erpenbeck, Sergio Vargas
Peer Reviewers Bernie Degnan; Eric Bautista-Guerrero
  • Funders
  • Deutsche Forschungsgemeinschaft
  • Villum Fonden
  • H2020 Marie Skłodowska-Curie Actions
  • LMUexcellent
LATEST VERSION PUBLISHED 01 Aug 2024
https://doi.org/10.12688/f1000research.145790.2
Genome Note metrics
Revised
Re-sequencing of the complete chloroplast genome of Cinnamomum burmanni (Nees & T.Nees) Blume (Lauraceae) from Indonesia using MinION Oxford Nanopore Technologies
[version 2; peer review: 2 approved with reservations, 1 not approved]
Richard Andreas Salindeho, Fifi Gus Dwiyanti, Rahadian Pratama, Deden Derajat Matra, Muhammad Majiidu, Iskandar Z. Siregar
Peer Reviewers Hoang Dang Khoa Do; Jakub Sawicki; Minh Trong Quang
  • Funder
  • National Competitive Basic Research 2022-2023
LATEST VERSION PUBLISHED 21 May 2024
https://doi.org/10.12688/f1000research.148511.1
Genome Note metrics
Two draft genomes of enigmatic Solenogastres (Mollusca, Aplacophora) Epimenia babai and Neomenia megatrapezata
[version 1; peer review: 1 approved, 1 approved with reservations]
Meghan K. Yap-Chiongco, Stacy Pirro, Rebecca M. Varney, Hiroshi Saito, Kenneth M. Halanych, Kevin M. Kocot
Peer Reviewers Gloria Arriagada; Alice Dennis
  • Funders
  • Iridian Genomes
  • National Science Foundation
PUBLISHED 23 Apr 2024
https://doi.org/10.12688/f1000research.144155.1
Genome Note metrics
Long-read datasets of Kayu Bawang (Azadirachta excelsa (Jack) Jacobs) from 3 different identified seed stands in Bengkulu (Sumatra), Indonesia and its phylogenetic relationships
[version 1; peer review: 2 approved with reservations]
Efratenta Katherina Depari, Nurheni Wijayanto, Lina Karlinasari, Mohamad Rafi, Iskandar Zulkarnaen Siregar
Peer Reviewers Hoang Dang Khoa Do; Maria Stefanie Dwiyanti
  • Funder
  • Beasiswa Pendidikan Pascasarjana Dalam Negeri (BPPDN) 2019
PUBLISHED 05 Apr 2024
https://doi.org/10.12688/f1000research.141307.1
Systematic Review metrics AWAITING PEER REVIEW
A systematic review on application of next-generation sequencing on microbes isolated from cultured species
[version 1; peer review: awaiting peer review]
Yap Sing Yee, Nur Diyana Mohamad Tahir, Mohamed Shariff Mohamed Din, Nurul Izzati Uda Zahli
Peer Reviewers Invited
  • Funder
  • Southeast Asian Regional Center for Graduate Study and Research in Agriculture
PUBLISHED 15 Nov 2023
https://doi.org/10.12688/f1000research.122019.2
Research Article metrics
Revised
Observation of SARS-CoV-2 genome characteristics and clinical manifestations within eight family clusters from GH and GK clades in Jakarta, Indonesia
[version 2; peer review: 2 approved with reservations, 2 not approved]
Fera Ibrahim, Augustine Natasha, Andi Yasmon, Fithriyah Fithriyah, Anis Karuniawati, Rivia Gina Rahmawaty, Yulia Saharman, Pratiwi Sudarmono
Peer Reviewers So Nakagawa; Serafeim C. Chaintoutis; Pakorn Aiewsakun; Gusti N Mahardika
  • Funder
  • Direktorat Riset and Pengembangan, Universitas Indonesia
LATEST VERSION PUBLISHED 16 Oct 2023
https://doi.org/10.12688/f1000research.131283.2
Genome Note metrics
Revised
The genome sequence of the Loggerhead sea turtle, Caretta caretta Linnaeus 1758
[version 2; peer review: 2 approved]
Glenn Chang, Samantha Jones, Sreeja Leelakumari, Jahanshah Ashkani, Luka Culibrk, Kieran O'Neill, Kane Tse, Dean Cheng, Eric Chuah, Helen McDonald, Heather Kirk, Pawan Pandoh, Sauro Pari, Valeria Angelini, Christopher Kyle, Giorgio Bertorelle, Yongjun Zhao, Andrew Mungall, Richard Moore, Sibelle Vilaça, Steven Jones
Peer Reviewers Richard Challis; Cinta Pegueroles
  • Funders
  • Canadian BioGenome Project
  • CanSeq150 program
  • European Union's Horizon 2020 Research and Innovation Programme (Marie Skłodowska-Curie grant agreement)
LATEST VERSION PUBLISHED 27 Jun 2023
https://doi.org/10.12688/f1000research.127990.2
Genome Note metrics
Revised
Draft genome sequences of three emerging beta-lactamase-producing Escherichia coli in the camel production system in Northern Kenya
[version 2; peer review: 2 approved]
Rachael Gachogo, Irene Karegi, Brian Ogoti, Victor Musyoki, Dino Martins, Frank Onyambu, Joseph Kamau
Peer Reviewers Meenakshi S. Iyer; Janet Midega
LATEST VERSION PUBLISHED 16 May 2023
https://doi.org/10.12688/f1000research.127935.1
Genome Note metrics
Draft genome of a clinical Pseudomonas qingdaonensis isolate from a hospitalized patient at Kenyatta National Hospital, Kenya
[version 1; peer review: 2 approved]
Brian Ogoti, Racheal Gachogo, Frank Onyambu
Peer Reviewers Gerald Mboowa; Aquillah Kanzi
  • Funder
  • Center of Molecular Biosciences
PUBLISHED 21 Dec 2022
https://doi.org/10.12688/f1000research.129212.1
Genome Note metrics
An updated version of the Madagascar periwinkle genome
[version 1; peer review: 2 approved]
Clément Cuello, Emily Amor Stander, Hans J. Jansen, Thomas Dugé De Bernonville, Audrey Oudin, Caroline Birer Williams, Arnaud Lanoue, Nathalie Giglioli Guivarc'h, Nicolas Papon, Ron P. Dirks, Michael Krogh Jensen, Sarah Ellen O'Connor, Sébastien Besseau, Vincent Courdavault
Peer Reviewers Evangelos Tatsis; Amit Rai
  • Funders
  • ARD CVL Biopharmaceutical program of the Région Centre-Val de Loire
  • Agence Nationale de la Recherche
  • Horizon 2020
PUBLISHED 21 Dec 2022
https://doi.org/10.12688/f1000research.110351.1
Brief Report metrics
High-quality genome assembly of a Pestalotiopsis fungus using DIY-friendly methods
[version 1; peer review: 3 approved with reservations]
Joshua L. McGinnis, Daniel J. Giguere
Peer Reviewers Paula Maria Moolhuijzen; Huzefa A Raja; Sinem Beyhan
  • Funder
  • Mitacs
PUBLISHED 20 Apr 2022
https://doi.org/10.12688/f1000research.109251.1
Brief Report metrics
Automated phenol-chloroform extraction of high molecular weight genomic DNA for use in long-read single-molecule sequencing
[version 1; peer review: 2 approved]
Andrew W. Liu, Alejandro Villar-Briones, Nicholas M. Luscombe, Charles Plessy
Peer Reviewers Genki N. Kanda; Shan Wei
  • Funder
  • Japan Society for the Promotion of Science
PUBLISHED 28 Feb 2022
https://doi.org/10.12688/f1000research.72845.1
Method Article metrics
Methods to measure calcitonin receptor activity, up-regulated in cell stress, apoptosis and autophagy
[version 1; peer review: 2 approved]
Peter Wookey, Pragya Gupta, Lucas Bittencourt, Shane Cheung, David Hare, Sebastian Furness
Peer Reviewers Virender Singh; Eshan Ghosh
  • Funder
  • Australian Research Council
PUBLISHED 07 Oct 2021
https://doi.org/10.12688/f1000research.52178.1
Brief Report metrics
Multi-modality detection of SARS-CoV-2 in faecal donor samples for transplantation and in asymptomatic emergency surgical admissions
[version 1; peer review: 2 approved]
Susan E. Manzoor, Shafquat Zaman, Celina Whalley, David Inglis, Andrew Bosworth, Michael Kidd, Sahida Shabir, Nabil Quraishi, Christopher A. Green, Tariq Iqbal, Andrew D. Beggs
Peer Reviewers Jonathan Landy; James Kinross
  • Funders
  • Cancer Research UK
  • Birmingham Experimental Cancer Medicine Centre
  • CRUK Centre Birmingham
PUBLISHED 11 May 2021
https://doi.org/10.12688/f1000research.25693.1
Research Article metrics
High-throughput multiplexed tandem repeat genotyping using targeted long-read sequencing
[version 1; peer review: 1 approved with reservations, 1 not approved]
Devika Ganesamoorthy, Mengjia Yan, Valentine Murigneux, Chenxi Zhou, Minh Duc Cao, Tania P. S. Duarte, Lachlan J. M. Coin
Peer Reviewers Rick M. Tankard; Mark T. W. Ebbert
  • Funder
  • National Health and Medical Research Council
PUBLISHED 02 Sep 2020
1-20 of 36 ARTICLES
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