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4. ChREBP is activated by reductive stress and mediates GCKR-associated metabolic traits

Author

Singh, Charandeep, Jin, Byungchang, Shrestha, Nirajan, Markhard, Andrew L., Panda, Apekshya, Calvo, Sarah E., Deik, Amy, Pan, Xingxiu, Zuckerman, Austin L., Ben Saad, Amel, Corey, Kathleen E., Sjoquist, Julia, Osganian, Stephanie, AminiTabrizi, Roya, Rhee, Eugene P., Shah, Hardik, Goldberger, Olga, Mullen, Alan C., Cracan, Valentin, Clish, Clary B., Mootha, Vamsi K., and Goodman, Russell P.

Published
2024
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7. Bayesian Hidden Markov Tree Models for Clustering Genes with Shared Evolutionary History

Author

Li, Yang, Ning, Shaoyang, Calvo, Sarah E., Mootha, Vamsi K., and Liu, Jun S.

Subjects
Statistics - Applications
Abstract

Determination of functions for poorly characterized genes is crucial for understanding biological processes and studying human diseases. Functionally associated genes are often gained and lost together through evolution. Therefore identifying co-evolution of genes can predict functional gene-gene associations. We describe here the full statistical model and computational strategies underlying the original algorithm, CLustering by Inferred Models of Evolution (CLIME 1.0) recently reported by us [Li et al., 2014]. CLIME 1.0 employs a mixture of tree-structured hidden Markov models for gene evolution process, and a Bayesian model-based clustering algorithm to detect gene modules with shared evolutionary histories (termed evolutionary conserved modules, or ECMs). A Dirichlet process prior was adopted for estimating the number of gene clusters and a Gibbs sampler was developed for posterior sampling. We further developed an extended version, CLIME 1.1, to incorporate the uncertainty on the evolutionary tree structure. By simulation studies and benchmarks on real data sets, we show that CLIME 1.0 and CLIME 1.1 outperform traditional methods that use simple metrics (e.g., the Hamming distance or Pearson correlation) to measure co-evolution between pairs of genes., Comment: 34 pages, 8 figures

Published
2018

8. Mitochondrial genome copy number variation across tissues in mice and humans.

Author

Rath, Sneha P., Gupta, Rahul, Todres, Ellen, Hong Wang, Jourdain, Alexis A., Ardlie, Kristin G., Calvo, Sarah E., and Mootha, Vamsi K.

Abstract

The mammalian mitochondrial genome (mtDNA) is multicopy and its copy number (mtCN) varies widely across tissues, in development and in disease. Here, we systematically catalog this variation by assaying mtCN in 52 human tissues across 952 donors (10,499 samples from the Genotype-Tissue Expression project) and 20 murine tissues using qPCR, capturing 50-and 200-fold variation, respectively. We also estimate per cell mtCN across 173 human cell lines from the Cancer Cell Line Encyclopedia using whole-genome sequencing data and observe >50-fold variation. We then leverage the vast amount of genomics data available for these repositories to credential our resource and uncover mtDNA-related biology. Using already existing proteomics data, we show that variation in mtCN can be predicted by variation in TFAM, histone, and mitochondrial ribosome protein abundance. We also integrate mtCN estimates with the CRISPR gene dependency measurements to find that cell lines with high mtCN are resistant to loss of GPX4, a glutathione phospholipid hydroperoxidase. Our resource captures variation in mtCN across mammalian tissues and should be broadly useful to the research community. [ABSTRACT FROM AUTHOR]

Published
2024
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9. Fatal Perinatal Mitochondrial Cardiac Failure Caused by Recurrent De Novo Duplications in the ATAD3 Locus

Author

Frazier, Ann E., Compton, Alison G., Kishita, Yoshihito, Hock, Daniella H., Welch, AnneMarie E., Amarasekera, Sumudu S.C., Rius, Rocio, Formosa, Luke E., Imai-Okazaki, Atsuko, Francis, David, Wang, Min, Lake, Nicole J., Tregoning, Simone, Jabbari, Jafar S., Lucattini, Alexis, Nitta, Kazuhiro R., Ohtake, Akira, Murayama, Kei, Amor, David J., McGillivray, George, Wong, Flora Y., van der Knaap, Marjo S., Vermeulen, R. Jeroen, Wiltshire, Esko J., Fletcher, Janice M., Lewis, Barry, Baynam, Gareth, Ellaway, Carolyn, Balasubramaniam, Shanti, Bhattacharya, Kaustuv, Freckmann, Mary-Louise, Arbuckle, Susan, Rodriguez, Michael, Taft, Ryan J., Sadedin, Simon, Cowley, Mark J., Minoche, André E., Calvo, Sarah E., Mootha, Vamsi K., Ryan, Michael T., Okazaki, Yasushi, Stroud, David A., Simons, Cas, Christodoulou, John, and Thorburn, David R.

Published
2021
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11. Figure 1 from Effectors Enabling Adaptation to Mitochondrial Complex I Loss in Hürthle Cell Carcinoma

Author

Gopal, Raj K., primary, Vantaku, Venkata R., primary, Panda, Apekshya, primary, Reimer, Bryn, primary, Rath, Sneha, primary, To, Tsz-Leung, primary, Fisch, Adam S., primary, Cetinbas, Murat, primary, Livneh, Maia, primary, Calcaterra, Michael J., primary, Gigliotti, Benjamin J., primary, Pierce, Kerry A., primary, Clish, Clary B., primary, Dias-Santagata, Dora, primary, Sadow, Peter M., primary, Wirth, Lori J., primary, Daniels, Gilbert H., primary, Sadreyev, Ruslan I., primary, Calvo, Sarah E., primary, Parangi, Sareh, primary, and Mootha, Vamsi K., primary

Published
2023
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12. Figure 2 from Effectors Enabling Adaptation to Mitochondrial Complex I Loss in Hürthle Cell Carcinoma

Author

Gopal, Raj K., primary, Vantaku, Venkata R., primary, Panda, Apekshya, primary, Reimer, Bryn, primary, Rath, Sneha, primary, To, Tsz-Leung, primary, Fisch, Adam S., primary, Cetinbas, Murat, primary, Livneh, Maia, primary, Calcaterra, Michael J., primary, Gigliotti, Benjamin J., primary, Pierce, Kerry A., primary, Clish, Clary B., primary, Dias-Santagata, Dora, primary, Sadow, Peter M., primary, Wirth, Lori J., primary, Daniels, Gilbert H., primary, Sadreyev, Ruslan I., primary, Calvo, Sarah E., primary, Parangi, Sareh, primary, and Mootha, Vamsi K., primary

Published
2023
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13. Supplementary_Table5 from Effectors Enabling Adaptation to Mitochondrial Complex I Loss in Hürthle Cell Carcinoma

Author

Gopal, Raj K., primary, Vantaku, Venkata R., primary, Panda, Apekshya, primary, Reimer, Bryn, primary, Rath, Sneha, primary, To, Tsz-Leung, primary, Fisch, Adam S., primary, Cetinbas, Murat, primary, Livneh, Maia, primary, Calcaterra, Michael J., primary, Gigliotti, Benjamin J., primary, Pierce, Kerry A., primary, Clish, Clary B., primary, Dias-Santagata, Dora, primary, Sadow, Peter M., primary, Wirth, Lori J., primary, Daniels, Gilbert H., primary, Sadreyev, Ruslan I., primary, Calvo, Sarah E., primary, Parangi, Sareh, primary, and Mootha, Vamsi K., primary

Published
2023
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14. Figure 7 from Effectors Enabling Adaptation to Mitochondrial Complex I Loss in Hürthle Cell Carcinoma

Author

Gopal, Raj K., primary, Vantaku, Venkata R., primary, Panda, Apekshya, primary, Reimer, Bryn, primary, Rath, Sneha, primary, To, Tsz-Leung, primary, Fisch, Adam S., primary, Cetinbas, Murat, primary, Livneh, Maia, primary, Calcaterra, Michael J., primary, Gigliotti, Benjamin J., primary, Pierce, Kerry A., primary, Clish, Clary B., primary, Dias-Santagata, Dora, primary, Sadow, Peter M., primary, Wirth, Lori J., primary, Daniels, Gilbert H., primary, Sadreyev, Ruslan I., primary, Calvo, Sarah E., primary, Parangi, Sareh, primary, and Mootha, Vamsi K., primary

Published
2023
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15. Figure 6 from Effectors Enabling Adaptation to Mitochondrial Complex I Loss in Hürthle Cell Carcinoma

Author

Gopal, Raj K., primary, Vantaku, Venkata R., primary, Panda, Apekshya, primary, Reimer, Bryn, primary, Rath, Sneha, primary, To, Tsz-Leung, primary, Fisch, Adam S., primary, Cetinbas, Murat, primary, Livneh, Maia, primary, Calcaterra, Michael J., primary, Gigliotti, Benjamin J., primary, Pierce, Kerry A., primary, Clish, Clary B., primary, Dias-Santagata, Dora, primary, Sadow, Peter M., primary, Wirth, Lori J., primary, Daniels, Gilbert H., primary, Sadreyev, Ruslan I., primary, Calvo, Sarah E., primary, Parangi, Sareh, primary, and Mootha, Vamsi K., primary

Published
2023
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16. Supplementary Figures S1-S7 from Effectors Enabling Adaptation to Mitochondrial Complex I Loss in Hürthle Cell Carcinoma

Author

Gopal, Raj K., primary, Vantaku, Venkata R., primary, Panda, Apekshya, primary, Reimer, Bryn, primary, Rath, Sneha, primary, To, Tsz-Leung, primary, Fisch, Adam S., primary, Cetinbas, Murat, primary, Livneh, Maia, primary, Calcaterra, Michael J., primary, Gigliotti, Benjamin J., primary, Pierce, Kerry A., primary, Clish, Clary B., primary, Dias-Santagata, Dora, primary, Sadow, Peter M., primary, Wirth, Lori J., primary, Daniels, Gilbert H., primary, Sadreyev, Ruslan I., primary, Calvo, Sarah E., primary, Parangi, Sareh, primary, and Mootha, Vamsi K., primary

Published
2023
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17. Data from Effectors Enabling Adaptation to Mitochondrial Complex I Loss in Hürthle Cell Carcinoma

Author

Gopal, Raj K., primary, Vantaku, Venkata R., primary, Panda, Apekshya, primary, Reimer, Bryn, primary, Rath, Sneha, primary, To, Tsz-Leung, primary, Fisch, Adam S., primary, Cetinbas, Murat, primary, Livneh, Maia, primary, Calcaterra, Michael J., primary, Gigliotti, Benjamin J., primary, Pierce, Kerry A., primary, Clish, Clary B., primary, Dias-Santagata, Dora, primary, Sadow, Peter M., primary, Wirth, Lori J., primary, Daniels, Gilbert H., primary, Sadreyev, Ruslan I., primary, Calvo, Sarah E., primary, Parangi, Sareh, primary, and Mootha, Vamsi K., primary

Published
2023
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18. Figure 3 from Effectors Enabling Adaptation to Mitochondrial Complex I Loss in Hürthle Cell Carcinoma

Author

Gopal, Raj K., primary, Vantaku, Venkata R., primary, Panda, Apekshya, primary, Reimer, Bryn, primary, Rath, Sneha, primary, To, Tsz-Leung, primary, Fisch, Adam S., primary, Cetinbas, Murat, primary, Livneh, Maia, primary, Calcaterra, Michael J., primary, Gigliotti, Benjamin J., primary, Pierce, Kerry A., primary, Clish, Clary B., primary, Dias-Santagata, Dora, primary, Sadow, Peter M., primary, Wirth, Lori J., primary, Daniels, Gilbert H., primary, Sadreyev, Ruslan I., primary, Calvo, Sarah E., primary, Parangi, Sareh, primary, and Mootha, Vamsi K., primary

Published
2023
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19. Figure 5 from Effectors Enabling Adaptation to Mitochondrial Complex I Loss in Hürthle Cell Carcinoma

Author

Gopal, Raj K., primary, Vantaku, Venkata R., primary, Panda, Apekshya, primary, Reimer, Bryn, primary, Rath, Sneha, primary, To, Tsz-Leung, primary, Fisch, Adam S., primary, Cetinbas, Murat, primary, Livneh, Maia, primary, Calcaterra, Michael J., primary, Gigliotti, Benjamin J., primary, Pierce, Kerry A., primary, Clish, Clary B., primary, Dias-Santagata, Dora, primary, Sadow, Peter M., primary, Wirth, Lori J., primary, Daniels, Gilbert H., primary, Sadreyev, Ruslan I., primary, Calvo, Sarah E., primary, Parangi, Sareh, primary, and Mootha, Vamsi K., primary

Published
2023
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20. Figure 4 from Effectors Enabling Adaptation to Mitochondrial Complex I Loss in Hürthle Cell Carcinoma

Author

Gopal, Raj K., primary, Vantaku, Venkata R., primary, Panda, Apekshya, primary, Reimer, Bryn, primary, Rath, Sneha, primary, To, Tsz-Leung, primary, Fisch, Adam S., primary, Cetinbas, Murat, primary, Livneh, Maia, primary, Calcaterra, Michael J., primary, Gigliotti, Benjamin J., primary, Pierce, Kerry A., primary, Clish, Clary B., primary, Dias-Santagata, Dora, primary, Sadow, Peter M., primary, Wirth, Lori J., primary, Daniels, Gilbert H., primary, Sadreyev, Ruslan I., primary, Calvo, Sarah E., primary, Parangi, Sareh, primary, and Mootha, Vamsi K., primary

Published
2023
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21. Effectors Enabling Adaptation to Mitochondrial Complex I Loss in Hürthle Cell Carcinoma

Author

Gopal, Raj K., primary, Vantaku, Venkata R., additional, Panda, Apekshya, additional, Reimer, Bryn, additional, Rath, Sneha, additional, To, Tsz-Leung, additional, Fisch, Adam S., additional, Cetinbas, Murat, additional, Livneh, Maia, additional, Calcaterra, Michael J., additional, Gigliotti, Benjamin J., additional, Pierce, Kerry A., additional, Clish, Clary B., additional, Dias-Santagata, Dora, additional, Sadow, Peter M., additional, Wirth, Lori J., additional, Daniels, Gilbert H., additional, Sadreyev, Ruslan I., additional, Calvo, Sarah E., additional, Parangi, Sareh, additional, and Mootha, Vamsi K., additional

Published
2023
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23. Macrocytic Anemia and Mitochondriopathy Resulting from a Defect in Sideroflexin 4

Author

Hildick-Smith, Gordon J, Cooney, Jeffrey D, Garone, Caterina, Kremer, Laura S, Haack, Tobias B, Thon, Jonathan N, Miyata, Non, Lieber, Daniel S, Calvo, Sarah E, Akman, H Orhan, Yien, Yvette Y, Huston, Nicholas C, Branco, Diana S, Shah, Dhvanit I, Freedman, Matthew L, Koehler, Carla M, Italiano, Joseph E, Merkenschlager, Andreas, Beblo, Skadi, Strom, Tim M, Meitinger, Thomas, Freisinger, Peter, Donati, M Alice, Prokisch, Holger, Mootha, Vamsi K, DiMauro, Salvatore, and Paw, Barry H

Subjects
Hematology, Pediatric, Adolescent, Anemia, Macrocytic, Animals, Child, Erythropoiesis, Exome, Female, Gene Knockdown Techniques, Humans, Membrane Proteins, Mitochondrial Diseases, Mitochondrial Proteins, Mutation, Zebrafish, Biological Sciences, Medical and Health Sciences, Genetics & Heredity
Abstract

We used exome sequencing to identify mutations in sideroflexin 4 (SFXN4) in two children with mitochondrial disease (the more severe case also presented with macrocytic anemia). SFXN4 is an uncharacterized mitochondrial protein that localizes to the mitochondrial inner membrane. sfxn4 knockdown in zebrafish recapitulated the mitochondrial respiratory defect observed in both individuals and the macrocytic anemia with megaloblastic features of the more severe case. In vitro and in vivo complementation studies with fibroblasts from the affected individuals and zebrafish demonstrated the requirement of SFXN4 for mitochondrial respiratory homeostasis and erythropoiesis. Our findings establish mutations in SFXN4 as a cause of mitochondriopathy and macrocytic anemia.

Published
2013

24. Multi-omics identifies large mitoribosomal subunit instability caused by pathogenic MRPL39 variants as a cause of pediatric onset mitochondrial disease

Author

Amarasekera, Sumudu S C, primary, Hock, Daniella H, additional, Lake, Nicole J, additional, Calvo, Sarah E, additional, Grønborg, Sabine W, additional, Krzesinski, Emma I, additional, Amor, David J, additional, Fahey, Michael C, additional, Simons, Cas, additional, Wibrand, Flemming, additional, Mootha, Vamsi K, additional, Lek, Monkol, additional, Lunke, Sebastian, additional, Stark, Zornitza, additional, Østergaard, Elsebet, additional, Christodoulou, John, additional, Thorburn, David R, additional, Stroud, David A, additional, and Compton, Alison G, additional

Published
2023
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26. GeNets: a unified web platform for network-based genomic analyses

Author

Li, Taibo, Kim, April, Rosenbluh, Joseph, Horn, Heiko, Greenfeld, Liraz, An, David, Zimmer, Andrew, Liberzon, Arthur, Bistline, Jon, Natoli, Ted, Li, Yang, Tsherniak, Aviad, Narayan, Rajiv, Subramanian, Aravind, Liefeld, Ted, Wong, Bang, Thompson, Dawn, Calvo, Sarah, Carr, Steve, Boehm, Jesse, Jaffe, Jake, Mesirov, Jill, Hacohen, Nir, Regev, Aviv, and Lage, Kasper

Published
2018
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28. Effectors enabling adaptation to mitochondrial complex I loss in Hürthle cell carcinoma

Author

Gopal, Raj K., primary, Vantaku, Venkata R., additional, Panda, Apekshya, additional, Reimer, Bryn, additional, Rath, Sneha, additional, To, Tsz-Leung, additional, Fisch, Adam S., additional, Cetinbas, Murat, additional, Livneh, Maia, additional, Calcaterra, Michael J., additional, Gigliotti, Benjamin J., additional, Pierce, Kerry, additional, Clish, Clary B., additional, Dias-Santagata, Dora, additional, Sadow, Peter M., additional, Wirth, Lori J., additional, Daniels, Gilbert H., additional, Sadreyev, Ruslan I., additional, Calvo, Sarah E., additional, Parangi, Sareh, additional, and Mootha, Vamsi K., additional

Published
2022
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35. The Fusarium graminearum Genome Reveals a Link between Localized Polymorphism and Pathogen Specialization

Author

Cuomo, Christina A., Güldener, Ulrich, Xu, Jin-Rong, Trail, Frances, Turgeon, B. Gillian, Di Pietro, Antonio, Walton, Jonathan D., Ma, Li-Jun, Baker, Scott E., Rep, Martijn, Adam, Gerhard, Antoniw, John, Baldwin, Thomas, Calvo, Sarah, Chang, Yueh-Long, DeCaprio, David, Gale, Liane R., Gnerre, Sante, Goswami, Rubella S., Hammond-Kosack, Kim, Harris, Linda J., Hilburn, Karen, Kennell, John C., Kroken, Scott, Magnuson, Jon K., Mannhaupt, Gertrud, Mauceli, Evan, Mewes, Hans-Werner, Mitterbauer, Rudolf, Muehlbauer, Gary, Münsterkötter, Martin, Nelson, David, O'Donnell, Kerry, Ouellet, Thérèse, Qi, Weihong, Quesneville, Hadi, Roncero, M. Isabel G., Seong, Kye-Yong, Tetko, Igor V., Urban, Martin, Waalwijk, Cees, Ward, Todd J., Yao, Jiqiang, Birren, Bruce W., and Kistler, H. Corby

Published
2007
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40. Mutation of C20orf7 disrupts complex I assembly and causes lethal neonatal mitochondrial diseasedd

Author

Sugiana, Canny, Pagliarini, David J., Mckenzie, Matthew, Kirby, Denise M., Salemi, Renato, Abu-Amero, Khaled K., Dahl, Hans-Henrik M., Hutchison, Wendy M., Vascotto, Katherine A., Smith, Stacey M., Newbold, Robert F., Christodoulou, John, Calvo, Sarah, Mootha, Vamsi K., Ryan, Michael T., and Thorburn, David R.

Subjects
Electron transport -- Analysis, Gene mutations -- Analysis, Mitochondrial DNA -- Research, Mitochondrial diseases -- Genetic aspects, Biological sciences
Abstract

The article presents the symptoms and effects of the complex I deficiency that is caused by the mutation of the putative complex I assembly factor C20orf7, which is known to cause the lethal neonatal mitochondrial disease. C20orf7 is shown to be extremely crucial for the assembly of complex I.

Published
2008

41. Insights from the genome of the biotrophic fungal plant pathogen Ustilago maydis

Author

Kamper, Jorg, Kahmann, Regine, Bolker, Michael, Ma, Li-Jun, Brefort, Thomas, Saville, Barry J., Banuett, Flora, Kronstad, James W., Gold, Scott E., Muller, Olaf, Perlin, Michael H., Wosten, Han A. B., de Vries, Ronald, Ruiz-Herrera, Jose, Reynaga-Pena, Cristina G., Snetselaar, Karen, McCann, Michael, Perez-Martin, Jose, Feldbrugge, Michael, Basse, Christoph W., Steinberg, Gero, Ibeas, Jose I., Holloman, William, Guzman, Plinio, Farman, Mark, Stajich, Jason E., Sentandreu, Rafael, Gonzalez-Prieto, Juan M., Kennell, John C., Molina, Lazaro, Schirawski, Jan, Mendoza-Mendoza, Artemio, Greilinger, Doris, Munch, Karin, Rossel, Nicole, Scherer, Mario, Vraneš, Miroslav, Ladendorf, Oliver, Vincon, Volker, Fuchs, Uta, Sandrock, Bjorn, Meng, Shaowu, Ho, Eric C. H., Cahill, Matt J., Boyce, Kylie J., Klose, Jana, Klosterman, Steven J., Deelstra, Heine J., Ortiz-Castellanos, Lucila, Li, Weixi, Sanchez-Alonso, Patricia, Schreier, Peter H., Hauser-Hahn, Isolde, Vaupel, Martin, Koopmann, Edda, Friedrich, Gabi, Voss, Hartmut, Schluter, Thomas, Margolis, Jonathan, Platt, Darren, Swimmer, Candace, Gnirke, Andreas, Chen, Feng, Vysotskaia, Valentina, Mannhaupt, Gertrud, Guldener, Ulrich, Munsterkotter, Martin, Haase, Dirk, Oesterheld, Matthias, Mewes, Hans-Werner, Mauceli, Evan W., DeCaprio, David, Wade, Claire M., Butler, Jonathan, Young, Sarah, Jaffe, David B., Calvo, Sarah, Nusbaum, Chad, Galagan, James, and Birren, Bruce W.

Abstract

Author(s): Jörg Kämper (corresponding author) [1]; Regine Kahmann (corresponding author) [1]; Michael Bölker (corresponding author) [2]; Li-Jun Ma [3]; Thomas Brefort [1]; Barry J. Saville [4, 27]; Flora Banuett [5]; [...]

Published
2006
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42. Sequencing of Aspergillus nidulans and comparative analysis with A. fumigatus and A. oryzae

Author

Galagan, James E., Calvo, Sarah E., Cuomo, Christina, Ma, Li-Jun, Wortman, Jennifer R., Batzoglou, Serafim, Lee, Su-In, Başturkmen, Meray, Spevak, Christina C., Clutterbuck, John, Kapitonov, Vladimir, Jurka, Jerzy, Scazzocchio, Claudio, Farman, Mark, Butler, Jonathan, Purcell, Seth, Harris, Steve, Braus, Gerhard H., Draht, Oliver, Busch, Silke, D'Enfert, Christophe, Bouchier, Christiane, Goldman, Gustavo H., Bell-Pedersen, Deborah, Griffiths-Jones, Sam, Doonan, John H., Yu, Jaehyuk, Vienken, Kay, Pain, Arnab, Freitag, Michael, Selker, Eric U., Archer, David B., Penalva, Miguel A., Oakley, Berl R., Momany, Michelle, Tanaka, Toshihiro, Kumagai, Toshitaka, Asai, Kiyoshi, Machida, Masayuki, Nierman, William C., Denning, David W., Caddick, Mark, Hynes, Michael, Paoletti, Mathieu, Fischer, Reinhard, Miller, Bruce, Dyer, Paul, Sachs, Matthew S., Osmani, Stephen A., and Birren, Bruce W.

Subjects
Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Author(s): James E. Galagan (corresponding author) [1]; Sarah E. Calvo [1]; Christina Cuomo [1]; Li-Jun Ma [1]; Jennifer R. Wortman [2]; Serafim Batzoglou [3]; Su-In Lee [3]; Meray Baştürkmen [4]; [...]

Published
2005
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43. MitoCarta3.0: an updated mitochondrial proteome now with sub-organelle localization and pathway annotations

Author

Rath, Sneha, primary, Sharma, Rohit, additional, Gupta, Rahul, additional, Ast, Tslil, additional, Chan, Connie, additional, Durham, Timothy J, additional, Goodman, Russell P, additional, Grabarek, Zenon, additional, Haas, Mary E, additional, Hung, Wendy H W, additional, Joshi, Pallavi R, additional, Jourdain, Alexis A, additional, Kim, Sharon H, additional, Kotrys, Anna V, additional, Lam, Stephanie S, additional, McCoy, Jason G, additional, Meisel, Joshua D, additional, Miranda, Maria, additional, Panda, Apekshya, additional, Patgiri, Anupam, additional, Rogers, Robert, additional, Sadre, Shayan, additional, Shah, Hardik, additional, Skinner, Owen S, additional, To, Tsz-Leung, additional, Walker, Melissa A, additional, Wang, Hong, additional, Ward, Patrick S, additional, Wengrod, Jordan, additional, Yuan, Chen-Ching, additional, Calvo, Sarah E, additional, and Mootha, Vamsi K, additional

Published
2020
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44. The genome sequence of the rice blast fungus Magnaporthe grisea

Author

Dean, Ralph A., Talbot, Nicholas J., Ebbole, Daniel J., Farman, Mark L., Mitchell, Thomas K., Orbach, Marc J., Thon, Michael, Kulkarni, Resham, Xu, Jin-Rong, Pan, Huaqin, Read, Nick D., Lee, Yong-Hwan, Carbone, Ignazio, Brown, Doug, Oh, Yeon Yee, Donofrio, Nicole, Jeong, Jun Seop, Soanes, Darren M., Djonovic, Slavica, Kolomiets, Elena, Rehmeyer, Cathryn, Li, Weixi, Harding, Michael, Kim, Soonok, Lebrun, Marc-Henri, Bohnert, Heidi, Coughlan, Sean, Butler, Jonathan, Calvo, Sarah, Ma, Li-Jun, Nicol, Robert, Purcell, Seth, Nusbaum, Chad, Galagan, James E., and Birren, Bruce W.

Subjects
Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Author(s): Ralph A. Dean (corresponding author) [1]; Nicholas J. Talbot [2]; Daniel J. Ebbole [3]; Mark L. Farman [4]; Thomas K. Mitchell [1]; Marc J. Orbach [5]; Michael Thon [3]; [...]

Published
2005
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45. The genome sequence of the filamentous fungus Neurospora crassa

Author

Galagan, James E., Calvo, Sarah E., Borkovich, Katherine A., Selker, Eric U., Read, Nick D., Jaffe, David, FitzHugh, William, Ma, Li-Jun, Smirnov, Serge, Purcell, Seth, Rehman, Bushra, Elkins, Timothy, Engels, Reinhard, Wang, Shunguang, Nielsen, Cydney B., Butler, Jonathan, Endrizzi, Matthew, Qui, Dayong, Ianakiev, Peter, Bell-Pedersen, Deborah, Nelson, Mary Anne, Werner-Washburne, Margaret, Selitrennikoff, Claude P., Kinsey, John A., Braun, Edward L., Zelter, Alex, Schulte, Ulrich, Kothe, Gregory O., Jedd, Gregory, Mewes, Werner, Staben, Chuck, Marcotte, Edward, Greenberg, David, Roy, Alice, Foley, Karen, Naylor, Jerome, Stange-Thomann, Nicole, Barrett, Robert, Gnerre, Sante, Kamal, Michael, Kamvysselis, Manolis, Mauceli, Evan, Bielke, Cord, Rudd, Stephen, Frishman, Dmitrij, Krystofova, Svetlana, Rasmussen, Carolyn, Metzenberg, Robert L., Perkins, David D., Kroken, Scott, Cogoni, Carlo, Macino, Giuseppe, Catcheside, David, Li, Weixi, Pratt, Robert J., Osmani, Stephen A., DeSouza, Colin P. C., Glass, Louise, Orbach, Marc J., Berglund, J. Andrew, Voelker, Rodger, Yarden, Oded, Plamann, Michael, Seiler, Stephan, Dunlap, Jay, Radford, Alan, Aramayo, Rodolfo, Natvig, Donald O., Alex, Lisa A., Mannhaupt, Gertrud, Ebbole, Daniel J., Freitag, Michael, Paulsen, Ian, Sachs, Matthew S., Lander, Eric S., Nusbaum, Chad, and Birren, Bruce

Subjects
Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Author(s): James E. Galagan (corresponding author) [1]; Sarah E. Calvo [1]; Katherine A. Borkovich [2]; Eric U. Selker [3]; Nick D. Read [4]; David Jaffe [1]; William FitzHugh [5]; Li-Jun [...]

Published
2003
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50. Mitochondrial DNA variation across 56,434 individuals in gnomAD

Author

Laricchia, Kristen M., Lake, Nicole J., Watts, Nicholas A., Shand, Megan, Haessly, Andrea, Gauthier, Laura, Benjamin, David, Banks, Eric, Soto, Jose, Garimella, Kiran, Emery, James, Rehm, Heidi L., MacArthur, Daniel G., Tiao, Grace, Lek, Monkol, Mootha, Vamsi K., and Calvo, Sarah E.

Abstract

Genomic databases of allele frequency are extremely helpful for evaluating clinical variants of unknown significance; however, until now, databases such as the Genome Aggregation Database (gnomAD) have focused on nuclear DNA and have ignored the mitochondrial genome (mtDNA). Here, we present a pipeline to call mtDNA variants that addresses three technical challenges: (1) detecting homoplasmic and heteroplasmic variants, present, respectively, in all or a fraction of mtDNA molecules; (2) circular mtDNA genome; and (3) misalignment of nuclear sequences of mitochondrial origin (NUMTs). We observed that mtDNA copy number per cell varied across gnomAD cohorts and influenced the fraction of NUMT-derived false-positive variant calls, which can account for the majority of putative heteroplasmies. To avoid false positives, we excluded contaminated samples, cell lines, and samples prone to NUMT misalignment due to few mtDNA copies. Furthermore, we report variants with heteroplasmy ≥10%. We applied this pipeline to 56,434 whole-genome sequences in the gnomAD v3.1 database that includes individuals of European (58%), African (25%), Latino (10%), and Asian (5%) ancestry. Our gnomAD v3.1 release contains population frequencies for 10,850 unique mtDNA variants at more than half of all mtDNA bases. Importantly, we report frequencies within each nuclear ancestral population and mitochondrial haplogroup. Homoplasmic variants account for most variant calls (98%) and unique variants (85%). We observed that 1/250 individuals carry a pathogenic mtDNA variant with heteroplasmy above 10%. These mtDNA population allele frequencies are freely accessible and will aid in diagnostic interpretation and research studies.

Published
2022
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