Literature DB >> 28179406

Online Databases for Taxonomy and Identification of Pathogenic Fungi and Proposal for a Cloud-Based Dynamic Data Network Platform.

Peralam Yegneswaran Prakash1,2,3, Laszlo Irinyi2, Catriona Halliday3, Sharon Chen2,3, Vincent Robert4, Wieland Meyer5.   

Abstract

The increase in public online databases dedicated to fungal identification is noteworthy. This can be attributed to improved access to molecular approaches to characterize fungi, as well as to delineate species within specific fungal groups in the last 2 decades, leading to an ever-increasing complexity of taxonomic assortments and nomenclatural reassignments. Thus, well-curated fungal databases with substantial accurate sequence data play a pivotal role for further research and diagnostics in the field of mycology. This minireview aims to provide an overview of currently available online databases for the taxonomy and identification of human and animal-pathogenic fungi and calls for the establishment of a cloud-based dynamic data network platform.
Copyright © 2017 American Society for Microbiology.

Entities:  

Keywords:  databases; fungi; nomenclature; pathogenic; taxonomy

Mesh:

Year:  2017        PMID: 28179406      PMCID: PMC5377827          DOI: 10.1128/JCM.02084-16

Source DB:  PubMed          Journal:  J Clin Microbiol        ISSN: 0095-1137            Impact factor:   5.948


  49 in total

1.  Biological identifications through DNA barcodes.

Authors:  Paul D N Hebert; Alina Cywinska; Shelley L Ball; Jeremy R deWaard
Journal:  Proc Biol Sci       Date:  2003-02-07       Impact factor: 5.349

Review 2.  Assembling the Fungal Tree of Life: constructing the structural and biochemical database.

Authors:  G J Celio; M Padamsee; B T M Dentinger; R Bauer; D J McLaughlin
Journal:  Mycologia       Date:  2006 Nov-Dec       Impact factor: 2.696

3.  Identification and nomenclature of the genus Penicillium.

Authors:  C M Visagie; J Houbraken; J C Frisvad; S-B Hong; C H W Klaassen; G Perrone; K A Seifert; J Varga; T Yaguchi; R A Samson
Journal:  Stud Mycol       Date:  2014-06       Impact factor: 16.097

4.  Development of a Multilocus Sequence Typing System for Medically Relevant Bipolaris Species.

Authors:  Cau D Pham; Anne E Purfield; Robert Fader; Neil Pascoe; Shawn R Lockhart
Journal:  J Clin Microbiol       Date:  2015-07-22       Impact factor: 5.948

Review 5.  Consensus guidelines for the treatment of yeast infections in the haematology, oncology and intensive care setting, 2014.

Authors:  S C Chen; T C Sorrell; C C Chang; E K Paige; P A Bryant; M A Slavin
Journal:  Intern Med J       Date:  2014-12       Impact factor: 2.048

6.  MycoBank gearing up for new horizons.

Authors:  Vincent Robert; Duong Vu; Ammar Ben Hadj Amor; Nathalie van de Wiele; Carlo Brouwer; Bernard Jabas; Szaniszlo Szoke; Ahmed Dridi; Maher Triki; Samy Ben Daoud; Oussema Chouchen; Lea Vaas; Arthur de Cock; Joost A Stalpers; Dora Stalpers; Gerard J M Verkley; Marizeth Groenewald; Felipe Borges Dos Santos; Gerrit Stegehuis; Wei Li; Linhuan Wu; Run Zhang; Juncai Ma; Miaomiao Zhou; Sergio Pérez Gorjón; Lily Eurwilaichitr; Supawadee Ingsriswang; Karen Hansen; Conrad Schoch; Barbara Robbertse; Laszlo Irinyi; Wieland Meyer; Gianluigi Cardinali; David L Hawksworth; John W Taylor; Pedro W Crous
Journal:  IMA Fungus       Date:  2013-12-17       Impact factor: 3.515

7.  The International Nucleotide Sequence Database Collaboration.

Authors:  Yasukazu Nakamura; Guy Cochrane; Ilene Karsch-Mizrachi
Journal:  Nucleic Acids Res       Date:  2012-11-24       Impact factor: 16.971

8.  mlstdbNet - distributed multi-locus sequence typing (MLST) databases.

Authors:  Keith A Jolley; Man-Suen Chan; Martin C J Maiden
Journal:  BMC Bioinformatics       Date:  2004-07-01       Impact factor: 3.169

9.  The Aspergillus Genome Database: multispecies curation and incorporation of RNA-Seq data to improve structural gene annotations.

Authors:  Gustavo C Cerqueira; Martha B Arnaud; Diane O Inglis; Marek S Skrzypek; Gail Binkley; Matt Simison; Stuart R Miyasato; Jonathan Binkley; Joshua Orvis; Prachi Shah; Farrell Wymore; Gavin Sherlock; Jennifer R Wortman
Journal:  Nucleic Acids Res       Date:  2013-11-04       Impact factor: 16.971

10.  GenBank.

Authors:  Dennis A Benson; Karen Clark; Ilene Karsch-Mizrachi; David J Lipman; James Ostell; Eric W Sayers
Journal:  Nucleic Acids Res       Date:  2013-11-11       Impact factor: 16.971

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  13 in total

Review 1.  DNA barcoding of phytopathogens for disease diagnostics and bio-surveillance.

Authors:  Prassan Choudhary; Bansh Narayan Singh; Hillol Chakdar; Anil Kumar Saxena
Journal:  World J Microbiol Biotechnol       Date:  2021-02-19       Impact factor: 3.312

Review 2.  Updates in Laboratory Diagnostics for Invasive Fungal Infections.

Authors:  David Terrero-Salcedo; Margaret V Powers-Fletcher
Journal:  J Clin Microbiol       Date:  2020-05-26       Impact factor: 5.948

Review 3.  Gut mycobiota under scrutiny: fungal symbionts or environmental transients?

Authors:  William D Fiers; Iris H Gao; Iliyan D Iliev
Journal:  Curr Opin Microbiol       Date:  2019-11-11       Impact factor: 7.934

4.  The Interaction between Rice Genotype and Magnaporthe oryzae Regulates the Assembly of Rice Root-Associated Microbiota.

Authors:  Dagang Tian; Zaijie Chen; Yan Lin; Tingmin Liang; Ziqiang Chen; Xinrui Guo; Feng Wang; Zonghua Wang
Journal:  Rice (N Y)       Date:  2021-05-11       Impact factor: 4.783

Review 5.  Molecular diagnostics in medical mycology.

Authors:  Brian L Wickes; Nathan P Wiederhold
Journal:  Nat Commun       Date:  2018-12-03       Impact factor: 14.919

6.  Rapid and real-time identification of fungi up to species level with long amplicon nanopore sequencing from clinical samples.

Authors:  Sara D'Andreano; Anna Cuscó; Olga Francino
Journal:  Biol Methods Protoc       Date:  2020-12-23

7.  Production, purification, characterization, antioxidant and antiproliferative activities of extracellular L-asparaginase produced by Fusarium equiseti AHMF4.

Authors:  Mervat Morsy Abbas Ahmed El-Gendy; Mohamed F Awad; Fareed Shawky El-Shenawy; Ahmed Mohamed Ahmed El-Bondkly
Journal:  Saudi J Biol Sci       Date:  2021-02-10       Impact factor: 4.219

8.  Fungal Genomic Resources for Strain Identification and Diversity Analysis of 1900 Fungal Species.

Authors:  Mir Asif Iquebal; Sarika Jaiswal; Vineet Kumar Mishra; Rahul Singh Jasrotia; Ulavappa B Angadi; Bhim Pratap Singh; Ajit Kumar Passari; Purbajyoti Deka; Ratna Prabha; Dhananjaya P Singh; Vijai Kumar Gupta; Rukam Singh Tomar; Harinder Singh Oberoi; Anil Rai; Dinesh Kumar
Journal:  J Fungi (Basel)       Date:  2021-04-12

Review 9.  Clinical Pathogen Genomics.

Authors:  Andrew Cameron; Jessica L Bohrhunter; Samantha Taffner; Adel Malek; Nicole D Pecora
Journal:  Clin Lab Med       Date:  2020-10-01       Impact factor: 1.935

Review 10.  Fun(gi)omics: Advanced and Diverse Technologies to Explore Emerging Fungal Pathogens and Define Mechanisms of Antifungal Resistance.

Authors:  B Ball; M Langille; J Geddes-McAlister
Journal:  mBio       Date:  2020-10-06       Impact factor: 7.867

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