Literature DB >> 28453676

fastMitoCalc: an ultra-fast program to estimate mitochondrial DNA copy number from whole-genome sequences.

Yong Qian1, Thomas J Butler1, Krista Opsahl-Ong1, Nicholas S Giroux1, Carlo Sidore2, Ramaiah Nagaraja1, Francesco Cucca2, Luigi Ferrucci3, Gonçalo R Abecasis4, David Schlessinger1, Jun Ding1.   

Abstract

Availability and Implementation: fastMitoCalc is available at https://lgsun.irp.nia.nih.gov/hsgu/software/mitoAnalyzer/index.html. Contact: jun.ding@nih.gov. Supplementary information: Supplementary data are available at Bioinformatics online. Published by Oxford University Press 2017. This work is written by US Government employees and is in the public domain in the US.

Mesh：

Year:  2017        PMID： 28453676      PMCID： PMC5860513          DOI： 10.1093/bioinformatics/btw835

Source DB:  PubMed          Journal:  Bioinformatics        ISSN： 1367-4803            Impact factor:   6.937


  8 in total

1.  The Sequence Alignment/Map format and SAMtools.

Authors:  Heng Li; Bob Handsaker; Alec Wysoker; Tim Fennell; Jue Ruan; Nils Homer; Gabor Marth; Goncalo Abecasis; Richard Durbin
Journal:  Bioinformatics       Date:  2009-06-08       Impact factor: 6.937

2.  A prospective study of mitochondrial DNA copy number and risk of non-Hodgkin lymphoma.

Authors:  Qing Lan; Unhee Lim; Chin-San Liu; Stephanie J Weinstein; Stephen Chanock; Matthew R Bonner; Jarmo Virtamo; Demetrius Albanes; Nathaniel Rothman
Journal:  Blood       Date:  2008-08-18       Impact factor: 22.113

3.  Assessing Mitochondrial DNA Variation and Copy Number in Lymphocytes of ~2,000 Sardinians Using Tailored Sequencing Analysis Tools.

Authors:  Jun Ding; Carlo Sidore; Thomas J Butler; Mary Kate Wing; Yong Qian; Osorio Meirelles; Fabio Busonero; Lam C Tsoi; Andrea Maschio; Andrea Angius; Hyun Min Kang; Ramaiah Nagaraja; Francesco Cucca; Gonçalo R Abecasis; David Schlessinger
Journal:  PLoS Genet       Date:  2015-07-14       Impact factor: 5.917

4.  Genetic Control over mtDNA and Its Relationship to Major Depressive Disorder.

Authors:  Na Cai; Yihan Li; Simon Chang; Jieqin Liang; Chongyun Lin; Xiufei Zhang; Lu Liang; Jingchu Hu; Wharton Chan; Kenneth S Kendler; Tomas Malinauskas; Guo-Jen Huang; Qibin Li; Richard Mott; Jonathan Flint
Journal:  Curr Biol       Date:  2015-12-10       Impact factor: 10.834

5.  Quantitative assessment of mitochondrial DNA copies from whole genome sequencing.

Authors:  Hsueh-Ting Chu; William W L Hsiao; Theresa T H Tsao; Ching-Mao Chang; Yen-Wenn Liu; Chen-Chieh Fan; Han Lin; Hen-Hong Chang; Tze-Jung Yeh; Jen-Chih Chen; Dun-Ming Huang; Chaur-Chin Chen; Cheng-Yan Kao
Journal:  BMC Genomics       Date:  2012-12-13       Impact factor: 3.969

6.  Mitochondrial DNA copy number is associated with breast cancer risk.

Authors:  Bharat Thyagarajan; Renwei Wang; Heather Nelson; Helene Barcelo; Woon-Puay Koh; Jian-Min Yuan
Journal:  PLoS One       Date:  2013-06-12       Impact factor: 3.240

7.  Molecular signatures of major depression.

Authors:  Na Cai; Simon Chang; Yihan Li; Qibin Li; Jingchu Hu; Jieqin Liang; Li Song; Warren Kretzschmar; Xiangchao Gan; Jerome Nicod; Margarita Rivera; Hong Deng; Bo Du; Keqing Li; Wenhu Sang; Jingfang Gao; Shugui Gao; Baowei Ha; Hung-Yao Ho; Chunmei Hu; Jian Hu; Zhenfei Hu; Guoping Huang; Guoqing Jiang; Tao Jiang; Wei Jin; Gongying Li; Kan Li; Yi Li; Yingrui Li; Youhui Li; Yu-Ting Lin; Lanfen Liu; Tiebang Liu; Ying Liu; Yuan Liu; Yao Lu; Luxian Lv; Huaqing Meng; Puyi Qian; Hong Sang; Jianhua Shen; Jianguo Shi; Jing Sun; Ming Tao; Gang Wang; Guangbiao Wang; Jian Wang; Linmao Wang; Xueyi Wang; Xumei Wang; Huanming Yang; Lijun Yang; Ye Yin; Jinbei Zhang; Kerang Zhang; Ning Sun; Wei Zhang; Xiuqing Zhang; Zhen Zhang; Hui Zhong; Gerome Breen; Jun Wang; Jonathan Marchini; Yiping Chen; Qi Xu; Xun Xu; Richard Mott; Guo-Jen Huang; Kenneth Kendler; Jonathan Flint
Journal:  Curr Biol       Date:  2015-04-23       Impact factor: 10.834

8.  Age-Related and Heteroplasmy-Related Variation in Human mtDNA Copy Number.

Authors:  Manja Wachsmuth; Alexander Hübner; Mingkun Li; Burkhard Madea; Mark Stoneking
Journal:  PLoS Genet       Date:  2016-03-15       Impact factor: 5.917
  8 in total
  12 in total

1.  A bioinformatics pipeline for estimating mitochondrial DNA copy number and heteroplasmy levels from whole genome sequencing data.

Authors:  Stephanie L Battle; Daniela Puiu; Joost Verlouw; Linda Broer; Eric Boerwinkle; Kent D Taylor; Jerome I Rotter; Stephan S Rich; Megan L Grove; Nathan Pankratz; Jessica L Fetterman; Chunyu Liu; Dan E Arking
Journal:  NAR Genom Bioinform       Date:  2022-05-17

2.  Neither cardiac mitochondrial DNA variation nor copy number contribute to congenital heart disease risk.

Authors:  Jon A L Willcox; Joshua T Geiger; Sarah U Morton; David McKean; Daniel Quiat; Joshua M Gorham; Angela C Tai; Steven DePalma; Daniel Bernstein; Martina Brueckner; Wendy K Chung; Alessandro Giardini; Elizabeth Goldmuntz; Jonathan R Kaltman; Richard Kim; Jane W Newburger; Yufeng Shen; Deepak Srivastava; Martin Tristani-Firouzi; Bruce Gelb; George A Porter; J G Seidman; Christine E Seidman
Journal:  Am J Hum Genet       Date:  2022-04-08       Impact factor: 11.043

Review 3.  Thinking outside the nucleus: Mitochondrial DNA copy number in health and disease.

Authors:  Christina A Castellani; Ryan J Longchamps; Jing Sun; Eliseo Guallar; Dan E Arking
Journal:  Mitochondrion       Date:  2020-06-13       Impact factor: 4.160

Review 4.  Mitochondrial DNA copy number in human disease: the more the better?

Authors:  Roberta Filograna; Mara Mennuni; David Alsina; Nils-Göran Larsson
Journal:  FEBS Lett       Date:  2020-12-25       Impact factor: 4.124

5.  Influence of cell distribution and diabetes status on the association between mitochondrial DNA copy number and aging phenotypes in the InCHIANTI study.

Authors:  Ann Zenobia Moore; Jun Ding; Marcus A Tuke; Andrew R Wood; Stefania Bandinelli; Timothy M Frayling; Luigi Ferrucci
Journal:  Aging Cell       Date:  2017-10-19       Impact factor: 9.304

6.  Investigating Human Mitochondrial Genomes in Single Cells.

Authors:  Maria Angela Diroma; Angelo Sante Varvara; Marcella Attimonelli; Graziano Pesole; Ernesto Picardi
Journal:  Genes (Basel)       Date:  2020-05-11       Impact factor: 4.096

7.  Quantitative mitochondrial DNA copy number determination using droplet digital PCR with single-cell resolution.

Authors:  Ryan O'Hara; Enzo Tedone; Andrew Ludlow; Ejun Huang; Beatrice Arosio; Daniela Mari; Jerry W Shay
Journal:  Genome Res       Date:  2019-09-23       Impact factor: 9.043

8.  Evaluation of mitochondrial DNA copy number estimation techniques.

Authors:  Ryan J Longchamps; Christina A Castellani; Stephanie Y Yang; Charles E Newcomb; Jason A Sumpter; John Lane; Megan L Grove; Eliseo Guallar; Nathan Pankratz; Kent D Taylor; Jerome I Rotter; Eric Boerwinkle; Dan E Arking
Journal:  PLoS One       Date:  2020-01-31       Impact factor: 3.240

Review 9.  Measuring biological aging in humans: A quest.

Authors:  Luigi Ferrucci; Marta Gonzalez-Freire; Elisa Fabbri; Eleanor Simonsick; Toshiko Tanaka; Zenobia Moore; Shabnam Salimi; Felipe Sierra; Rafael de Cabo
Journal:  Aging Cell       Date:  2019-12-12       Impact factor: 9.304

10.  Asthma and its relationship to mitochondrial copy number: Results from the Asthma Translational Genomics Collaborative (ATGC) of the Trans-Omics for Precision Medicine (TOPMed) program.

Authors:  Maxwell P Cocco; Evan White; Shujie Xiao; Donglei Hu; Angel Mak; Patrick Sleiman; Mao Yang; Kevin R Bobbitt; Hongsheng Gui; Albert M Levin; Samantha Hochstadt; Kyle Whitehouse; Dean Rynkowski; Andrea J Barczak; Gonçalo Abecasis; Thomas W Blackwell; Hyun Min Kang; Deborah A Nickerson; Soren Germer; Jun Ding; David E Lanfear; Frank Gilliland; W James Gauderman; Rajesh Kumar; David J Erle; Fernando Martinez; Hakon Hakonarson; Esteban G Burchard; L Keoki Williams
Journal:  PLoS One       Date:  2020-11-25       Impact factor: 3.240
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