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For: Oliva M, Milicchio F, King K, Benson G, Boucher C, Prosperi M. Portable nanopore analytics: are we there yet? Bioinformatics 2021;36:4399-4405. [PMID: 32277811 DOI: 10.1093/bioinformatics/btaa237] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 02/07/2020] [Accepted: 04/06/2020] [Indexed: 01/23/2023]  Open
Number Cited by Other Article(s)
1
Marini S, Barquero A, Wadhwani AA, Bian J, Ruiz J, Boucher C, Prosperi M. OCTOPUS: Disk-based, Multiplatform, Mobile-friendly Metagenomics Classifier. AMIA ... ANNUAL SYMPOSIUM PROCEEDINGS. AMIA SYMPOSIUM 2025;2024:798-807. [PMID: 40417475 PMCID: PMC12099329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 05/27/2025]
2
Alsharksi AN, Sirekbasan S, Gürkök-Tan T, Mustapha A. From Tradition to Innovation: Diverse Molecular Techniques in the Fight Against Infectious Diseases. Diagnostics (Basel) 2024;14:2876. [PMID: 39767237 PMCID: PMC11674978 DOI: 10.3390/diagnostics14242876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2024] [Revised: 11/15/2024] [Accepted: 12/17/2024] [Indexed: 01/02/2025]  Open
3
Marini S, Barquero A, Wadhwani AA, Bian J, Ruiz J, Boucher C, Prosperi M. OCTOPUS: Disk-based, Multiplatform, Mobile-friendly Metagenomics Classifier. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.15.585215. [PMID: 38559026 PMCID: PMC10979967 DOI: 10.1101/2024.03.15.585215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
4
Kuzdraliński A, Miśkiewicz M, Szczerba H, Mazurczyk W, Nivala J, Księżopolski B. Unlocking the potential of DNA-based tagging: current market solutions and expanding horizons. Nat Commun 2023;14:6052. [PMID: 37770439 PMCID: PMC10539344 DOI: 10.1038/s41467-023-41728-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 09/18/2023] [Indexed: 09/30/2023]  Open
5
Yu R, Abdullah SMU, Sun Y. HMMPolish: a coding region polishing tool for TGS-sequenced RNA viruses. Brief Bioinform 2023;24:bbad264. [PMID: 37478372 PMCID: PMC10516367 DOI: 10.1093/bib/bbad264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Revised: 06/05/2023] [Accepted: 06/29/2023] [Indexed: 07/23/2023]  Open
6
Mikalsen AJ, Zola J. Coriolis: enabling metagenomic classification on lightweight mobile devices. Bioinformatics 2023;39:i66-i75. [PMID: 37387129 DOI: 10.1093/bioinformatics/btad243] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/01/2023]  Open
7
Marini S, Boucher C, Noyes N, Prosperi M. The K-mer antibiotic resistance gene variant analyzer (KARGVA). Front Microbiol 2023;14:1060891. [PMID: 36960290 PMCID: PMC10027697 DOI: 10.3389/fmicb.2023.1060891] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 02/08/2023] [Indexed: 03/09/2023]  Open
8
Barquero A, Marini S, Boucher C, Ruiz J, Prosperi M. KARGAMobile: Android app for portable, real-time, easily interpretable analysis of antibiotic resistance genes via nanopore sequencing. Front Bioeng Biotechnol 2022;10:1016408. [PMID: 36324897 PMCID: PMC9618647 DOI: 10.3389/fbioe.2022.1016408] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 09/27/2022] [Indexed: 02/03/2023]  Open
9
Rodríguez-Pérez H, Ciuffreda L, Flores C. NanoRTax, a real-time pipeline for taxonomic and diversity analysis of nanopore 16S rRNA amplicon sequencing data. Comput Struct Biotechnol J 2022;20:5350-5354. [PMID: 36212537 PMCID: PMC9522874 DOI: 10.1016/j.csbj.2022.09.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 09/16/2022] [Accepted: 09/16/2022] [Indexed: 11/05/2022]  Open
10
Comparing the significance of the utilization of next generation and third generation sequencing technologies in microbial metagenomics. Microbiol Res 2022;264:127154. [DOI: 10.1016/j.micres.2022.127154] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 07/05/2022] [Accepted: 07/29/2022] [Indexed: 01/07/2023]
11
Marini S, Oliva M, Slizovskiy IB, Das RA, Noyes NR, Kahveci T, Boucher C, Prosperi M. AMR-meta: a k-mer and metafeature approach to classify antimicrobial resistance from high-throughput short-read metagenomics data. Gigascience 2022;11:giac029. [PMID: 35583675 PMCID: PMC9116207 DOI: 10.1093/gigascience/giac029] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 01/27/2022] [Indexed: 12/15/2022]  Open
12
Serretti A. Precision medicine in mood disorders. PCN REPORTS : PSYCHIATRY AND CLINICAL NEUROSCIENCES 2022;1:e1. [PMID: 38868801 PMCID: PMC11114272 DOI: 10.1002/pcn5.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 11/09/2021] [Accepted: 12/05/2021] [Indexed: 06/14/2024]
13
Pucker B, Irisarri I, de Vries J, Xu B. Plant genome sequence assembly in the era of long reads: Progress, challenges and future directions. QUANTITATIVE PLANT BIOLOGY 2022;3:e5. [PMID: 37077982 PMCID: PMC10095996 DOI: 10.1017/qpb.2021.18] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 11/24/2021] [Accepted: 12/21/2021] [Indexed: 05/03/2023]
14
Prosperi M, Marini S. KARGA: Multi-platform Toolkit for k-mer-based Antibiotic Resistance Gene Analysis of High-throughput Sequencing Data. ... IEEE-EMBS INTERNATIONAL CONFERENCE ON BIOMEDICAL AND HEALTH INFORMATICS. IEEE-EMBS INTERNATIONAL CONFERENCE ON BIOMEDICAL AND HEALTH INFORMATICS 2021;2021:10.1109/bhi50953.2021.9508479. [PMID: 34447942 PMCID: PMC8383893 DOI: 10.1109/bhi50953.2021.9508479] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
15
Boucher C, Gagie T, Tomohiro I, Köppl D, Langmead B, Manzini G, Navarro G, Pacheco A, Rossi M. PHONI: Streamed Matching Statistics with Multi-Genome References. PROCEEDINGS. DATA COMPRESSION CONFERENCE 2021;2021:193-202. [PMID: 34778549 PMCID: PMC8583545 DOI: 10.1109/dcc50243.2021.00027] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
16
Huo W, Ling W, Wang Z, Li Y, Zhou M, Ren M, Li X, Li J, Xia Z, Liu X, Huang X. Miniaturized DNA Sequencers for Personal Use: Unreachable Dreams or Achievable Goals. FRONTIERS IN NANOTECHNOLOGY 2021. [DOI: 10.3389/fnano.2021.628861] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]  Open
17
Prendergast SC, Strobl A, Cross W, Pillay N, Strauss SJ, Ye H, Lindsay D, Tirabosco R, Chalker J, Mahamdallie SS, Sosinsky A, RNOH Pathology Laboratory and Biobank Team, Genomics England Research Consortium, Flanagan AM, Amary F. Sarcoma and the 100,000 Genomes Project: our experience and changes to practice. J Pathol Clin Res 2020;6:297-307. [PMID: 32573957 PMCID: PMC7578291 DOI: 10.1002/cjp2.174] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 05/21/2020] [Accepted: 05/27/2020] [Indexed: 11/06/2022]
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