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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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5. 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. 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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9. 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.

Subjects
MITOCHONDRIAL DNA, WHOLE genome sequencing, DATA libraries, MITOCHONDRIAL proteins, CELL lines
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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15. Widespread Chromosomal Losses and Mitochondrial DNA Alterations as Genetic Drivers in Hürthle Cell Carcinoma

Author

Gopal, Raj K., Kübler, Kirsten, Calvo, Sarah E., Polak, Paz, Livitz, Dimitri, Rosebrock, Daniel, Sadow, Peter M., Campbell, Braidie, Donovan, Samuel E., Amin, Salma, Gigliotti, Benjamin J., Grabarek, Zenon, Hess, Julian M., Stewart, Chip, Braunstein, Lior Z., Arndt, Peter F., Mordecai, Scott, Shih, Angela R., Chaves, Frances, Zhan, Tiannan, Lubitz, Carrie C., Kim, Jiwoong, Iafrate, A. John, Wirth, Lori, Parangi, Sareh, Leshchiner, Ignaty, Daniels, Gilbert H., Mootha, Vamsi K., Dias-Santagata, Dora, Getz, Gad, and McFadden, David G.

Published
2018
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17. 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

18. 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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19. 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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20. 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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21. 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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22. 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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23. 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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24. 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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25. 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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26. 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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27. 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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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 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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29. Biallelic C1QBP Mutations Cause Severe Neonatal-, Childhood-, or Later-Onset Cardiomyopathy Associated with Combined Respiratory-Chain Deficiencies

Author

Feichtinger, René G., Oláhová, Monika, Kishita, Yoshihito, Garone, Caterina, Kremer, Laura S., Yagi, Mikako, Uchiumi, Takeshi, Jourdain, Alexis A., Thompson, Kyle, D’Souza, Aaron R., Kopajtich, Robert, Alston, Charlotte L., Koch, Johannes, Sperl, Wolfgang, Mastantuono, Elisa, Strom, Tim M., Wortmann, Saskia B., Meitinger, Thomas, Pierre, Germaine, Chinnery, Patrick F., Chrzanowska-Lightowlers, Zofia M., Lightowlers, Robert N., DiMauro, Salvatore, Calvo, Sarah E., Mootha, Vamsi K., Moggio, Maurizio, Sciacco, Monica, Comi, Giacomo P., Ronchi, Dario, Murayama, Kei, Ohtake, Akira, Rebelo-Guiomar, Pedro, Kohda, Masakazu, Kang, Dongchon, Mayr, Johannes A., Taylor, Robert W., Okazaki, Yasushi, Minczuk, Michal, and Prokisch, Holger

Published
2017
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30. Biallelic Mutations in MRPS34 Lead to Instability of the Small Mitoribosomal Subunit and Leigh Syndrome

Author

Lake, Nicole J., Webb, Bryn D., Stroud, David A., Richman, Tara R., Ruzzenente, Benedetta, Compton, Alison G., Mountford, Hayley S., Pulman, Juliette, Zangarelli, Coralie, Rio, Marlene, Boddaert, Nathalie, Assouline, Zahra, Sherpa, Mingma D., Schadt, Eric E., Houten, Sander M., Byrnes, James, McCormick, Elizabeth M., Zolkipli-Cunningham, Zarazuela, Haude, Katrina, Zhang, Zhancheng, Retterer, Kyle, Bai, Renkui, Calvo, Sarah E., Mootha, Vamsi K., Christodoulou, John, Rötig, Agnes, Filipovska, Aleksandra, Cristian, Ingrid, Falk, Marni J., Metodiev, Metodi D., and Thorburn, David R.

Published
2017
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32. 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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33. 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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34. 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., Hock, Daniella H., Lake, Nicole J., Calvo, Sarah E., Grønborg, Sabine W., Krzesinski, Emma I., Amor, David J., Fahey, Michael C., Simons, Cas, Wibrand, Flemming, Mootha, Vamsi K., Lek, Monkol, Lunke, Sebastian, Stark, Zornitza, Østergaard, Elsebet, Christodoulou, John, Thorburn, David R., Stroud, David A., Compton, Alison G., Amarasekera, Sumudu S.C., Hock, Daniella H., Lake, Nicole J., Calvo, Sarah E., Grønborg, Sabine W., Krzesinski, Emma I., Amor, David J., Fahey, Michael C., Simons, Cas, Wibrand, Flemming, Mootha, Vamsi K., Lek, Monkol, Lunke, Sebastian, Stark, Zornitza, Østergaard, Elsebet, Christodoulou, John, Thorburn, David R., Stroud, David A., and Compton, Alison G.

Abstract

MRPL39 encodes one of 52 proteins comprising the large subunit of the mitochondrial ribosome (mitoribosome). In conjunction with 30 proteins in the small subunit, the mitoribosome synthesizes the 13 subunits of the mitochondrial oxidative phosphorylation (OXPHOS) system encoded by mitochondrial Deoxyribonucleic acid (DNA). We used multi-omics and gene matching to identify three unrelated individuals with biallelic variants in MRPL39 presenting with multisystem diseases with severity ranging from lethal, infantile-onset (Leigh syndrome spectrum) to milder with survival into adulthood. Clinical exome sequencing of known disease genes failed to diagnose these patients; however quantitative proteomics identified a specific decrease in the abundance of large but not small mitoribosomal subunits in fibroblasts from the two patients with severe phenotype. Re-analysis of exome sequencing led to the identification of candidate single heterozygous variants in mitoribosomal genes MRPL39 (both patients) and MRPL15. Genome sequencing identified a shared deep intronic MRPL39 variant predicted to generate a cryptic exon, with transcriptomics and targeted studies providing further functional evidence for causation. The patient with the milder disease was homozygous for a missense variant identified through trio exome sequencing. Our study highlights the utility of quantitative proteomics in detecting protein signatures and in characterizing gene-disease associations in exome-unsolved patients. We describe Relative Complex Abundance analysis of proteomics data, a sensitive method that can identify defects in OXPHOS disorders to a similar or greater sensitivity to the traditional enzymology. Relative Complex Abundance has potential utility for functional validation or prioritization in many hundreds of inherited rare diseases where protein complex assembly is disrupted., MRPL39 encodes one of 52 proteins comprising the large subunit of the mitochondrial ribosome (mitoribosome). In conjunction with 30 proteins in the small subunit, the mitoribosome synthesizes the 13 subunits of the mitochondrial oxidative phosphorylation (OXPHOS) system encoded by mitochondrial Deoxyribonucleic acid (DNA). We used multi-omics and gene matching to identify three unrelated individuals with biallelic variants in MRPL39 presenting with multisystem diseases with severity ranging from lethal, infantile-onset (Leigh syndrome spectrum) to milder with survival into adulthood. Clinical exome sequencing of known disease genes failed to diagnose these patients; however quantitative proteomics identified a specific decrease in the abundance of large but not small mitoribosomal subunits in fibroblasts from the two patients with severe phenotype. Re-analysis of exome sequencing led to the identification of candidate single heterozygous variants in mitoribosomal genes MRPL39 (both patients) and MRPL15. Genome sequencing identified a shared deep intronic MRPL39 variant predicted to generate a cryptic exon, with transcriptomics and targeted studies providing further functional evidence for causation. The patient with the milder disease was homozygous for a missense variant identified through trio exome sequencing. Our study highlights the utility of quantitative proteomics in detecting protein signatures and in characterizing gene-disease associations in exome-unsolved patients. We describe Relative Complex Abundance analysis of proteomics data, a sensitive method that can identify defects in OXPHOS disorders to a similar or greater sensitivity to the traditional enzymology. Relative Complex Abundance has potential utility for functional validation or prioritization in many hundreds of inherited rare diseases where protein complex assembly is disrupted.

Published
2023

37. Mitochondrial Disease Sequence Data Resource (MSeqDR): A global grass-roots consortium to facilitate deposition, curation, annotation, and integrated analysis of genomic data for the mitochondrial disease clinical and research communities

Author

Bale, Sherri, Bedoyan, Jirair, Behar, Doron, Bonnen, Penelope, Brooks, Lisa, Calabrese, Claudia, Calvo, Sarah, Chinnery, Patrick, Christodoulou, John, Church, Deanna, Clima, Rosanna, Cohen, Bruce H., Cotton, Richard G., de Coo, I.F.M., Derbenevoa, Olga, den Dunnen, Johan T., Dimmock, David, Enns, Gregory, Gasparre, Giuseppe, Goldstein, Amy, Gonzalez, Iris, Gwinn, Katrina, Hahn, Sihoun, Haas, Richard H., Hakonarson, Hakon, Hirano, Michio, Kerr, Douglas, Li, Dong, Lvova, Maria, Macrae, Finley, Maglott, Donna, McCormick, Elizabeth, Mitchell, Grant, Mootha, Vamsi K., Okazaki, Yasushi, Pujol, Aurora, Parisi, Melissa, Perin, Juan Carlos, Pierce, Eric A., Procaccio, Vincent, Rahman, Shamima, Reddi, Honey, Rehm, Heidi, Riggs, Erin, Rodenburg, Richard, Rubinstein, Yaffa, Saneto, Russell, Santorsola, Mariangela, Scharfe, Curt, Sheldon, Claire, Shoubridge, Eric A., Simone, Domenico, Smeets, Bert, Smeitink, Jan A., Stanley, Christine, Suomalainen, Anu, Tarnopolsky, Mark, Thiffault, Isabelle, Thorburn, David R., Van Hove, Johan, Wolfe, Lynne, Wong, Lee-Jun, Falk, Marni J., Shen, Lishuang, Gonzalez, Michael, Leipzig, Jeremy, Lott, Marie T., Stassen, Alphons P.M., Diroma, Maria Angela, Navarro-Gomez, Daniel, Yeske, Philip, Bai, Renkui, Boles, Richard G., Brilhante, Virginia, Ralph, David, DaRe, Jeana T., Shelton, Robert, Terry, Sharon F., Zhang, Zhe, Copeland, William C., van Oven, Mannis, Prokisch, Holger, Wallace, Douglas C., Attimonelli, Marcella, Krotoski, Danuta, Zuchner, Stephan, and Gai, Xiaowu

Published
2015
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39. 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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45. 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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50. 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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