Literature DB >> 18566966

MITOMASTER: a bioinformatics tool for the analysis of mitochondrial DNA sequences.

Marty C Brandon1, Eduardo Ruiz-Pesini, Dan Mishmar, Vincent Procaccio, Marie T Lott, Kevin Cuong Nguyen, Syawal Spolim, Upen Patil, Pierre Baldi, Douglas C Wallace.   

Abstract

We have developed a computer system, MITOMASTER, to make analysis of human mitochondrial DNA (mtDNA) sequences efficient, accurate, and easily available. From imported sequences, the system identifies nucleotide variants, determines the haplogroup, rules out possible pseudogene contamination, identifies novel DNA sequence variants, and evaluates the potential biological significance of each variant. This system should be beneficial for mtDNA analyses of biomedical physicians and investigators, population biologists and forensic scientists. MITOMASTER can be accessed at http://mammag.web.uci.edu/twiki/bin/view/Mitomaster. Copyright 2008 Wiley-Liss, Inc.

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Year:  2009        PMID： 18566966      PMCID： PMC4292933          DOI： 10.1002/humu.20801

Source DB:  PubMed          Journal:  Hum Mutat        ISSN： 1059-7794            Impact factor:   4.878


  43 in total

1.  Comprehensive scanning of the entire mitochondrial genome for mutations.

Authors:  Lee-Jun C Wong; Min-Hui Liang; Haeyoung Kwon; John Park; Ren-Kui Bai; Duan-Jun Tan
Journal:  Clin Chem       Date:  2002-11       Impact factor: 8.327

2.  Effects of purifying and adaptive selection on regional variation in human mtDNA.

Authors:  Eduardo Ruiz-Pesini; Dan Mishmar; Martin Brandon; Vincent Procaccio; Douglas C Wallace
Journal:  Science       Date:  2004-01-09       Impact factor: 47.728

3.  Sequence and organization of the human mitochondrial genome.

Authors:  S Anderson; A T Bankier; B G Barrell; M H de Bruijn; A R Coulson; J Drouin; I C Eperon; D P Nierlich; B A Roe; F Sanger; P H Schreier; A J Smith; R Staden; I G Young
Journal:  Nature       Date:  1981-04-09       Impact factor: 49.962

4.  Mitochondrial DNA and human evolution.

Authors:  R L Cann; M Stoneking; A C Wilson
Journal:  Nature       Date:  1987 Jan 1-7       Impact factor: 49.962

5.  Ancient mtDNA sequences in the human nuclear genome: a potential source of errors in identifying pathogenic mutations.

Authors:  D C Wallace; C Stugard; D Murdock; T Schurr; M D Brown
Journal:  Proc Natl Acad Sci U S A       Date:  1997-12-23       Impact factor: 11.205

6.  Mitochondrial DNA inherited variants are associated with successful aging and longevity in humans.

Authors:  G De Benedictis; G Rose; G Carrieri; M De Luca; E Falcone; G Passarino; M Bonafe; D Monti; G Baggio; S Bertolini; D Mari; R Mattace; C Franceschi
Journal:  FASEB J       Date:  1999-09       Impact factor: 5.191

7.  Strikingly higher frequency in centenarians and twins of mtDNA mutation causing remodeling of replication origin in leukocytes.

Authors:  Jin Zhang; Jordi Asin-Cayuela; Jennifer Fish; Yuichi Michikawa; Massimiliano Bonafe; Fabiola Olivieri; Giuseppe Passarino; Giovanna De Benedictis; Claudio Franceschi; Giuseppe Attardi
Journal:  Proc Natl Acad Sci U S A       Date:  2003-01-21       Impact factor: 11.205

8.  The Human MitoChip: a high-throughput sequencing microarray for mitochondrial mutation detection.

Authors:  Anirban Maitra; Yoram Cohen; Susannah E D Gillespie; Elizabeth Mambo; Noriyoshi Fukushima; Mohammad O Hoque; Nila Shah; Michael Goggins; Joseph Califano; David Sidransky; Aravinda Chakravarti
Journal:  Genome Res       Date:  2004-05       Impact factor: 9.043

9.  Radiation of human mitochondria DNA types analyzed by restriction endonuclease cleavage patterns.

Authors:  M J Johnson; D C Wallace; S D Ferris; M C Rattazzi; L L Cavalli-Sforza
Journal:  J Mol Evol       Date:  1983       Impact factor: 2.395

Review 10.  Why do we still have a maternally inherited mitochondrial DNA? Insights from evolutionary medicine.

Authors:  Douglas C Wallace
Journal:  Annu Rev Biochem       Date:  2007       Impact factor: 23.643
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  29 in total

1.  The diversity present in 5140 human mitochondrial genomes.

Authors:  Luísa Pereira; Fernando Freitas; Verónica Fernandes; Joana B Pereira; Marta D Costa; Stephanie Costa; Valdemar Máximo; Vincent Macaulay; Ricardo Rocha; David C Samuels
Journal:  Am J Hum Genet       Date:  2009-05-07       Impact factor: 11.025

2.  Data structures and compression algorithms for genomic sequence data.

Authors:  Marty C Brandon; Douglas C Wallace; Pierre Baldi
Journal:  Bioinformatics       Date:  2009-05-15       Impact factor: 6.937

3.  Analysis of human mitochondrial DNA sequences from fecally polluted environmental waters as a tool to study population diversity.

Authors:  Vikram Kapoor; Michael Elk; Carlos Toledo-Hernandez; Jorge W Santo Domingo
Journal:  AIMS Environ Sci       Date:  2017

4.  Multiplex analysis of mitochondrial DNA pathogenic and polymorphic sequence variants.

Authors:  Jason C Poole; Vincent Procaccio; Martin C Brandon; Greg Merrick; Douglas C Wallace
Journal:  Biol Chem       Date:  2010-10       Impact factor: 3.915

5.  Neolithic phylogenetic continuity inferred from complete mitochondrial DNA sequences in a tribal population of Southern India.

Authors:  Charles Sylvester; Mysore Siddaiah Krishna; Jaya Sankar Rao; Adimoolam Chandrasekar
Journal:  Genetica       Date:  2018-07-21       Impact factor: 1.082

6.  MtDNA mutation pattern in tumors and human evolution are shaped by similar selective constraints.

Authors:  Ilia Zhidkov; Erez A Livneh; Eitan Rubin; Dan Mishmar
Journal:  Genome Res       Date:  2009-02-10       Impact factor: 9.043

7.  Mitochondrial DNA variant discovery and evaluation in human Cardiomyopathies through next-generation sequencing.

Authors:  Michael V Zaragoza; Joseph Fass; Marta Diegoli; Dawei Lin; Eloisa Arbustini
Journal:  PLoS One       Date:  2010-08-20       Impact factor: 3.240

8.  Common Mitochondrial Haplogroups and Cutaneous Squamous Cell Carcinoma Risk.

Authors:  Eric Jorgenson; Hélène Choquet; Jie Yin; Maryam M Asgari
Journal:  Cancer Epidemiol Biomarkers Prev       Date:  2018-04-25       Impact factor: 4.254

9.  Warburg and Crabtree effects in premalignant Barrett's esophagus cell lines with active mitochondria.

Authors:  Martin T Suchorolski; Thomas G Paulson; Carissa A Sanchez; David Hockenbery; Brian J Reid
Journal:  PLoS One       Date:  2013-02-27       Impact factor: 3.240

10.  Genomic Patterns of De Novo Mutation in Simplex Autism.

Authors:  Tychele N Turner; Bradley P Coe; Diane E Dickel; Kendra Hoekzema; Bradley J Nelson; Michael C Zody; Zev N Kronenberg; Fereydoun Hormozdiari; Archana Raja; Len A Pennacchio; Robert B Darnell; Evan E Eichler
Journal:  Cell       Date:  2017-09-28       Impact factor: 66.850
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