Abstract Background While keyword based queries of databases such as Pubmed are frequently of great utility, the ability to use regular expressions in place of a keyword can often improve the results output by such databases. Regular expressions can allow for the identification of element types that cannot be readily specified by a single keyword and can allow for different words with similar character sequences to be distinguished. Results A Perl based utility was developed to allow the use of regular expressions in Pubmed searches, thereby improving the accuracy of the searches. Conclusion This utility was then utilized to create a comprehensive listing of all DFN deafness mutations discussed in Pubmed records containing the keywords "human ear".</p

AK Lalwani

Christopher M Frenz

CM Frenz

D Rebholz-Schuhmann

D Zou

DL Wheeler

E van Wijk

E Verpy

EM De Leenheer

ER Wilcox

F Donaudy

F Horn

H Bolz

H Morishita

H Odeh

H Shahin

I Zwaenepoel

JE Leonard

K Fukushima

K Verhoeven

KI Cho

KR Johnson

L Van Laer

LL Parker

M Ansar

M Guipponi

M Palmada

M Rodriguez-Ballesteros

M Yoshida

MA Andrade

MI Shabbir

NG Robertson

R Hertzano

RK McHugh

S Albert

S Delmaghani

S Ernest

S Kanzaki

S Masmoudi

S Xiao

T Kharkovets

T Walsh

VV Pilipenko

W Marcotti

ZM Ahmed

City University of New York

Crossref

Springer - Publisher Connector

Directory of Open Access Journals

PubMed Central

English

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Avraham KB, Gasparini P: Multiple mutations of MYO1A, a cochlear-expressed gene, in sensorineural hearing loss.

Avraham KB: From flies' eyes to our ears: mutations in a human class III myosin cause progressive nonsyndromic hearing loss DFNB30. Proc Natl Acad Sci USA

Avraham KB: Transcription profiling of inner ears from

Ayadi H: Refined mapping of the autosomal recessive non-syndromic deafness locus DFNB13 using eight novel microsatellite markers. Clin Genet

Blin N: Loss of function mutations of the GJB2 gene detected in patients with DFNB1-associated hearing impairment. Neurobiol Dis

Camp G: Mice lacking Dfna5 show a diverging number of cochlear fourth row outer hair cells. Neurobiol Dis

Camp G: Mutations in the human alpha-tectorin gene cause autosomal dominant non-syndromic hearing impairment. Nat Genet

CC: Cochlin immunostaining of inner ear pathologic deposits and proteomic analysis in DFNA9 deafness and vestibular dysfunction. Hum Mol Genet

Cremers CW: Audiological characteristics of some affected members of a Dutch DFNA13/COL11A2 family. Ann Otol Rhinol Laryngol

DC: Characterization of two transgene insertional mutations at pirouette, a mouse deafness locus. Audiol Neurootol

Del Castillo I: Auditory neuropathy in patients carrying mutations in the otoferlin gene (OTOF). Hum Mutat

Denoyelle F: SLC26A4 gene is frequently involved in nonsyndromic hearing impairment with enlarged vestibular aqueduct in Caucasian populations.

FE: Automated extraction of mutation data from the literature: application of MuteXt to G proteincoupled receptors and nuclear hormone receptors. Bioinformatics

Friedman TB: Mutations in the gene encoding tight junction claudin-14 cause autosomal recessive deafness DFNB29. Cell

Genetics of hearing loss: Allelism and modifier genes produce a phenotypic continuum. Anat Rec A Discov Mol Cell Evol Biol

Greinwald JH: Genomic organization and expression analysis of the murine Fam3c gene. Gene

H: A mutation in the gamma actin 1 (ACTG1) gene causes autosomal dominant hearing loss (DFNA20/26).

H: Automatic extraction of mutations from Medline and cross-validation with OMIM. Nucleic Acids Res

JL: Finding relevant references to genes and proteins in Medline using a Bayesian approach. Bioinformatics

KI: Deafness due to degeneration of cochlear neurons in casAdditional file 1 The PREP.pl Perl script. Click here for file [http://www.biomedcentral.com/content/supplementary/1472-6947-7-32-S1.pl]BMC Medical Informatics and Decision Making

Kong X: Dentinogenesis imperfecta 1 with or without progressive hearing loss is associated with distinct mutations in DSPP. Nat Genet

Kros CJ: Tmc1 is necessary for normal functional maturation and survival of inner and outer hair cells in the mouse cochlea.

Leal SM: A novel autosomal recessive non-syndromic deafness locus (DFNB35) maps to 14q24.1–14q24.3 in large consanguineous kindred from Pakistan. Eur J Hum Genet

Mariner is defective in myosin VIIA: a zebrafish model for human hereditary deafness. Hum Mol Genet

Mutations in a novel isoform of TRIOBP that encodes a filamentous-actin binding protein are responsible for DFNB28 recessive nonsyndromic hearing loss.

Mutations in the gene encoding pejvakin, a newly identified protein of the afferent auditory pathway, cause DFNB59 auditory neuropathy. Nat Genet

Nishizaki K: Deletion mapping of split hand/split foot malformation with hearing impairment: a case report.

Otoancorin, an inner ear protein restricted to the interface between the apical surface of sensory epithelia and their overlying acellular gels, is defective in autosomal recessive deafness DFNB22. Proc Natl Acad Sci USA

PE: Further characterization of the DFNA1 audiovestibular phenotype. Arch Otolaryngol Head Neck Surg

Petit C: Mutations in a new gene encoding a protein of the hair bundle cause non-syndromic deafness at the DFNB16 locus. Nat Genet

Pro Perl Parsing

PX: Eya1 regulates the growth of otic epithelium and interacts with Pax2 during the development of all sensory areas in the inner ear. Dev Biol

Riazuddin S: Mutations of human TMHS cause recessively inherited non-syndromic hearing loss.

Rossier BC: The transmembrane serine protease (TMPRSS3) mutated in deafness DFNB8/10 activates the epithelial sodium channel (ENaC) in vitro. Hum Mol Genet

Ryoo ZY: Fine mapping of the circling (cir) gene on the distal portion of mouse chromosome 9. Comp Med

Savoia A: Nonmuscle myosin heavy-chain gene MYH14 is expressed in cochlea and mutated in patients affected by autosomal dominant hearing impairment (DFNA4).

Takagi T: PNAD-CSS: a workbench for constructing a protein name abbreviation dictionary. Bioinformatics

TB: The tip-link antigen, a protein associated with the transduction complex of sensory hair cells, is protocadherin-15.

TJ: Mice with altered KCNQ4 K+ channels implicate sensory outer hair cells in human progressive deafness.

Transgene correction maintains normal cochlear structure and function in 6-month-old Myo15a mutant mice. Hear Res

Yaschenko E: Database resources of the National Center for Biotechnology Information. Nucleic Acids Res

Zheng QY: Mouse models of USH1C and DFNB18: phenotypic and molecular analyses of two new spontaneous mutations of the Ush1c gene. Hum Mol Genet

Deafness mutation mining using regular expression based pattern matching

Background: While keyword based queries of databases such as Pubmed are frequently of great utility, the ability to use regular expressions in place of a keyword can often improve the results output by such databases. Regular expressions can allow for the identification of element types that cannot be readily specified by a single keyword and can allow for different words with similar character sequences to be distinguished.
Results: A Perl based utility was developed to allow the use of regular expressions in Pubmed searches, thereby improving the accuracy of the searches.
Conclusion: This utility was then utilized to create a comprehensive listing of all DFN deafness mutations discussed in Pubmed records containing the keywords  human ear 

Frenz, Christopher M