List of Publications


Shtolz, N., Mishmar, D. The metazoan landscape of mitochondrial DNA gene order and content is shaped by selection and affects mitochondrial transcription. Commun Biol 6, 93 (2023). link


Papier, O., Minor, G., Medini, H., Mishmar, D. Coordination of mitochondrial and nuclear gene-expression regulation in health, evolution, and disease, Current Opinion in Physiology,Volume 27,2022,100554,ISSN 2468-8673, link

Meshnik, L., Bar-Yaacov, D., Kasztan, D. et al. Mutant C. elegans mitofusin leads to selective removal of mtDNA heteroplasmic deletions across generations to maintain fitness. BMC Biol 20, 40 (2022). link

Cohen, T., Medini, H., Mordechai, C. et al. Human mitochondrial RNA modifications associate with tissue-specific changes in gene expression, and are affected by sunlight and UV exposure. Eur J Hum Genet (2022). link


Medini, H. Zirman, A. and Mishmar, D. Immune system cells from COVID-19 patients display compromised mitochondrial-nuclear expression co-regulation and rewiring toward glycolysis. iScience (2021), link

Bershtein, S., Kleiner, D. & Mishmar, D. Predicting 3D protein structures in light of evolution. Nat Ecol Evol 5, 1195–1198 (2021). link

Medini, H., Cohen, T. & Mishmar, D. Mitochondrial gene expression in single cells shape pancreatic beta cells’ sub-populations and explain variation in insulin pathway. Sci Rep 11, 466 (2021). link


Levy T, Ventura T, De Leo G, Grinshpan N, Abu Abayed FA, Manor R, Savaya A, Sklarz MY, Chalifa-Caspi V, Mishmar D, Sagi A. Two Homogametic Genotypes – One Crayfish: On the Consequences of Intersexuality. iScience. 2020 Oct 6;23(11):101652. doi: 10.1016/j.isci.2020.101652. link

Medini H, Cohen T, Mishmar D. Mitochondria Are Fundamental for the Emergence of Metazoans: On Metabolism, Genomic Regulation, and the Birth of Complex Organisms [published online ahead of print, 2020 Aug 28]. Annu Rev Genet. 2020;10.1146/annurev-genet-021920-105545. doi:10.1146/annurev-genet-021920-105545. link 

Mishmar, D. mtDNA in the crossroads of evolution and disease. Nat Rev Mol Cell Biol (2020). link


Barshad, G., Zlotnikov-Poznianski, N., Gal, L. et al. Disease-causing mutations in subunits of OXPHOS complex I affect certain physical interactions. Sci Rep 9, 9987 (2019) doi:10.1038/s41598-019-46446-8. link

Mishmar D., Levin R., Naeem Mansur M., Sondheimer N., (2019). The Mitochondrial Genome–on Selective Constraints and Signatures at the Organism, Cell, and Single Mitochondrion Levels. Front. Genet., doi: 10.3389/fgene.2019.01285. link 

Shtolz N., Mishmar, D., (2019). The Mitochondrial Genome–on Selective Constraints and Signatures at the Organism, Cell, and Single Mitochondrion Levels. Front. Ecol. Evol., doi: 10.3389/fevo.2019.00342. link 

Marom, S., Blumberg, A., Kundaje, A., Mishmar, D., (2019). mtDNA Chromatin-like Organization Is Gradually Established during Mammalian Embryogenesis. iScience, doi: 10.1016/j.isci.2018.12.032. link


Chalkia, D., Chang, Y. C., Derbeneva, O., Lvova, M., Wang, P., Mishmar, D., … & Wallace, D. C. (2018). Mitochondrial DNA associations with East Asian metabolic syndrome. Biochimica et Biophysica Acta (BBA)-Bioenergetics, 1859(9), 878-892.‏ link

Barshad, G., Marom, S., Cohen, T., & Mishmar, D. (2018). Mitochondrial DNA transcription and its regulation: an evolutionary perspective. Trends in Genetics, doi:10.1016/j.tig.2018.05.009. link

Barshad, G., Blumberg, A., Cohen, T., & Mishmar, D. (2018). Human primitive brain displays negative mitochondrial-nuclear expression correlation of respiratory genes. Genome research, doi:10.1101/gr.226324.117. link

Blumberg, A., Danko, C. G., Kundaje, A., & Mishmar, D. (2018). A common pattern of DNase I footprinting throughout the human mtDNA unveils clues for a chromatin-like organization. Genome research, doi:10.1101/gr.230409.117.‏ link


Marom, S., Friger, M., & Mishmar, D. (2017). MtDNA meta-analysis reveals both phenotype specificity and allele heterogeneity: a model for differential association. Scientific Reports, 7., 43449; doi: 10.1038/srep43449‏ link

Levin.L & Mishmar.D.(2017).The genomic landscape of evolutionary convergence in mammals, birds and reptiles. Nature Ecology & Evolution,10.1038/s41559-016-0041 link

Blumberg, A., Kundaje, A., Danko, C. G., & Mishmar, D. (2017). Initiation of mtDNA transcription is followed by pausing, and diverge across human cell types and during evolution. Genome Research, gr-209924.‏  link


Cohen T, Levin L, Mishmar D (2016) Ancient Out-of-Africa Mitochondrial DNA Variants Associate with Distinct Mitochondrial Gene Expression Patterns. PLoS Genet 12(11): e1006407. doi:10.1371/journal.pgen.1006407 link

Bar-Yaacov, D., I. Frumkin, Y. Yashiro, T. Chujo, Y. Ishigami, Y. Chemla, A. Blumberg, O. Schlesinger, P. Bieri, B. Greber, N. Ban, R. Zarivach, L. Alfonta, Y. Pilpel, T. Suzuki and D. Mishmar (2016). “Mitochondrial 16S rRNA Is Methylated by tRNA Methyltransferase TRMT61B in All Vertebrates.” PLoS Biol 14(9): e1002557. link


Bar-Yaacov D, Hadjivasiliou Z, Levin L, Barshad G, Zarivach R, Bouskila A, Mishmar D. Mitochondrial involvement in vertebrate speciation? The case of mito-nuclear genetic divergence in chameleons. Genome Biol Evol . 2015 Dec 1;7(12):3322-36. link 

Levin L, Bar-Yaacov D, Bouskila A, Chorev M, Carmel L, Mishmar D. LEMONS–A Tool for the Identification of Splice Junctions in Transcriptomes of Organisms Lacking Reference Genomes. PloS one. 2015;10(11). link

Levin L and Mishmar D. A Genetic View of the Mitochondrial Role in Ageing: Killing Us Softly. In: Atzmon G (ed).  Longevity Genes, 2015‏ (Springer). link  

Valenci I, Yonai L, Bar-Yaacov D, Mishmar D and Ben-Zvi A. “Parkin modulates heteroplasmy of truncated mtDNA in Caenorhabditis elegans”. Mitochondrion 2015; 20: 64-70. doi: 10.1016/j.mito.2014.11.001. link


Levin L, Blumberg A, Barshad G, Mishmar D. Mito-nuclear co-evolution: the positive and negative sides of functional ancient mutations.Frontiers in Genetics 2014;5:448. doi:10.3389/fgene.2014.00448.  link

Gershoni M, Levin L, Ovadia O, Toiw Y, Shani N, Dadon S, Barzilai N, Bergman A, Atzmon G, Wainstein J, Tsur A, Nijtmans L, Glaser B, Mishmar D. Disrupting mitochondrial-nuclear co-evolution affects OXPHOS complex I integrity and impacts human health. Genome Biol Evol published online October 9, 2014, 6: 2665-2680. link 

Blumberg A, Sailaja BS, Kundaje A, Levin L, Dadon S, Shmorak S, Shaulian E, Meshorer E, Mishmar D. Transcription Factors Bind Negatively Selected Sites within Human mtDNA Genes. Genome Biol Evol published online October 8, 2014, 6: 2634-2646. link


Bar-Yaacov D, Bouskila A, Mishmar D. The first chameleon transcriptome: Comparative genomic analysis of the OXPHOS system reveals loss of COX8 in iguanian lizards. Genome Biol Evol. published online September 4, 2013 link

Bar-Yaacov D, Avital G, Levin L, Richards A, Hachen N, Jaramillo BR, Nekrutenko A, Zarivach R, and Mishmar D. RNA-DNA differences in human mitochondria restore ancestral form of 16S ribosomal RNA. Genome Research. published online August 2, 2013 link

Levin L, Zhidkov I, Gurman Y, Hawlena H, and Mishmar D. Functional Recurrent Mutations in the Human Mitochondrial Phylogeny – Dual Roles in Evolution and Disease. Genome Biol Evol. published online April 5, 2013 link


Avital G, Buchshtav M, Zhidkov I, Tuval Feder J, Dadon S, Rubin E, Glass D, Spector TD and Mishmar D. Mitochondrial DNA heteroplasmy in diabetes and normal adults: role of acquired and inherited mutational patterns in twins. Hum Mol Genet. 2012 Jul

Bar Yaacov D, Arbel-Thau K, Zilka Y, Ovadia O, Bouskila and Mishmar, D. (2012) Mitochondrial DNA Variation, but Not Nuclear DNA, Sharply Divides Morphologically Identical Chameleons along an Ancient Geographic Barrier. PloS one 7(3):e31372.doi:10.1371/journal.pone.0031372. link

Zhidkov, I., Nagar, T., Mishmar, D. & Rubin, E. MitoBamAnnotator: A web-based tool for detecting and annotating heteroplasmy in human mitochondrial DNA sequences. Mitochondrion (2011).link

Bar-Yaacov, D., Blumberg, A. & Mishmar, D. Mitochondrial-nuclear co-evolution and its effects on OXPHOS activity and regulation.Biochimica et Biophysica Acta (BBA)-Gene Regulatory Mechanisms (2011). link

Zhidkov, I., Cohen, R., Geifman, N., Mishmar, D. & Rubin, E. CHILD: a new tool for detecting low-abundance insertions and deletions in standard sequence traces. Nucleic Acids Research 39, e47 (2011).link

Mishmar D. and Zhidkov, I. (2010). Evolution and disease converge in the mitochondrion, BBA-Bioenergetics, 1797: 1099-104. . link

Gershoni, M. Fuchs, A., Shani, N., Fridman, Y., Corral-Debrinski, M., Aharoni, A., Frishman, D. and Mishmar, D. (2010). Co-evolution predicts direct interactions between mtDNA and nuclear DNA-encoded subunits of oxidative phosphorylation complex I, Journal of Molecular biology, 404: 158–171. link

Amar, S., Ovadia, O., Maier, W., Ebstein, R., Belmaker RH, Mishmar, D. and Agam, G. (2010). Copy number variation of the SELENBP1 gene in schizophrenia, Behavioral and Brain Functions, 6: 40. link

o   In this Behavioral and Brain Functions paper Prof. Agam and I are co-corresponding authors.

Garbian, Y., Ovadia, O., Dadon, S. and Mishmar, D. (2010). Gene expression patterns of oxidative phosphorylation complex I subunits are organized in modules PloS one, 5(4): e9983 . link


Feder, J. Ovadia, O., Blech, I., Cohen, J., Wainstein, J., Harman-Boehm, I., Glaser, B., and Mishmar, D. (2009). Parental diabetes status reveals association of Mitochondrial DNA Haplogroup J1 with Type 2 Diabetes , BMC Med Genet, 10(1):60. link

Suissa, S., Wang, Z., Poole, J., Wittkopp, S., Feder, J., Shutt, TE, Wallace, DC, Shadel, GS and Mishmar, D. (2009). Ancient mtDNA genetic variants modulate mtDNA transcription and replication, PLoS Genetics, 5 (5): e1000474.  link

Gershoni, M., Templeton, AR and Mishmar, D. (2009). Mitochondrial biogenesis as a major motive force of speciation, BioEssays, 31(6):642-650.  link

o   This BioEssays paper was thoroughly discussed in: Lane, N. (2009). Nature, 462: 272-74.

Zhidkov, I., Livneh, EA, Rubin, E. and Mishmar, D. (2009). mtDNA mutation pattern in tumors and human evolution are shaped by similar selective constraints, Genome Research, 19:576-580. (Cover article).  link

o   This Genome Research paper was selected to present the cover page of the April issue of the Journal, 2009.

Potluri, P., Davila, A., Ruiz-Pesini, E., Mishmar, D., O’Hearn, S., Hancock, S., Simon, M., Scheffler, I.E., Wallace, D.C., and Procaccio, V.F. (2009). Progressive Complex I-Specific Neurodegenerative Disease Caused by Faulty Nuclear-Cytoplasmic Interaction, Molecular Genetics and Metabolism, 96(4):189-95.  link 


Kozminsky-Atias, A., Bar-Shalom, A., Mishmar, D., and Zilberberg N. (2008) Assembling an arsenal, the scorpion way. BMC Evolutionary Biology 8(1):333. link

Brandon MC, Ruiz-Pesini E, Mishmar D, Procaccio V, Lott MT, Nguyen KC, Spolim S, Patil U, Baldi P, Wallace DC. (2009). MITOMASTER: a bioinformatics tool for the analysis of mitochondrial DNA sequences. Hum Mutat. 30(1):1-6. link

Feder, J., Blech, I., Ovadia, O., Wainstein, J., Raz, I., Dadon, S., Arking DE, Glaser, B. and Mishmar D. (2008). Mitochondrial DNA Haplogroups Alter Susceptibility to Complications of Type 2 Diabetes Mellitus in three Jewish populations, BMC Genomics, 9: 198. link

Amar, S., Shamir A., Ovadia, O., Blanaru, M., Reshef, A., Kremer, I., Rietschel, M., Schulze, TG, Maier, W., Belmaker, RH, Ebstein, RE, Agam, G. and Mishmar D. (2007). Mitochondrial DNA HV lineage increases the susceptibility to schizophrenia among Israeli Arabs,Schizophrenia Research, 94(1-3): 354-8. link

Mishmar, D. and Gershoni, M. (2007). Treating speciation processes as complex traits, Nature Reviews Genetics, 8: doi:10.1038/nrg1968-c1. link

Feder, J., Ovadia, O., Glaser, B. and Mishmar, D. (2007). Ashkenazi Jewish mtDNA haplogroup distribution varies among distinct subpopulations: lessons of population sub-structure in a closed group, European Journal of Human genetics, 15(4):498-500.  link

Ruiz-Pesini, E., Lott, M, Procaccio, V, Poole, J., Brandon, M., Mishmar, D., Yi, C., Kreuziger, J., Baldi, P., Wallace, D. (2007). An Enhanced MITOMAP with a Global mtDNA Mutational Phylogeny, Nucleic Acid Research 35(Database issue):D823-8. link


 Mishmar, D., Ruiz-Pesini, E., Mondragon-Palomino, M., Procaccio, V., Gaut, B., and Wallace, D.C (2006). Adaptive Selection of Mitochondrial Complex I Subunits during Primate Radiation, Gene, 378: 11-18.  link

Ruiz-Pesini, E., Mishmar, D., Brandon, M., and Wallace, D.C. (2004). Effects of purifying and adaptive selection on regional variation in human mtDNA, Science, 303(5655): 223-6.  link

Mishmar, D., Ruiz-Pesini, E., Brandon, M., and Wallace, D.C. (2004). Mitochondrial DNA-like sequences in the Nucleus (NUMTs): Insights into our African origins and the mechanism of foreign DNA integration. Human Mutation, 23(2): 125-33.  link

Until 2003:

Wallace, D.C., Ruiz-Pesini, E., and Mishmar, D. (2003). MtDNA Variation, Climatic Adaptation, Degenerative Diseases and Longevity, Cold Spring Harb Symp Quant Biol, 68:479-86 link

Mishmar, D., Ruiz-Pesini, E., Golik, P., Macaulay, V., Clark A.G., Hosseini, S., Brandon, M., Easley, K., Chen, E., Brown, M.D., Sukernik, R.I., Olckers, A. and Wallace, D.C. (2003). Natural selection shaped Regional Mitochondrial DNA variation in humans, Proc.Natl.Acad.Sci., 100(1):171-176.  link

Mishmar, D., Mandel-Gutfreund, Y., Margalit, H., Rahat, A., and Kerem, B. (1999). Common fragile sites: G-band characteristics within an R-band, The American Journal of Human Genetics, 64: 908-910. link

Mishmar, D., Rahat, A., Scherer, S.W., Nyakatura, G., Hinzmann, B., Kohwi, Y., Mandel-Gutfroind, Y., Lee, J.R., Drescher, B., Sas, D.E., Margalit, H., Platzer, M., Kohwi-Shigematsu, T., Weiss,A., Tsui, L-C., Rosenthal, A. and Kerem, B. (1998). Molecular characterization of a common fragile site (FRA7H) on human chromosome 7 by the cloning of an SV40 integration site. Proc.Natl.Acad.Sci., 95(14):8141-8146.  link

Mishmar, D. (1997). Is He Our Ancestor? Galilleo, 24: 56-59 (Hebrew)

Reshef, D. (1994). Human origins: prehistory in the biology class, Journal for Biology Teachers, 137b: 65-68 (Hebrew)

Reshef, D. and Smith,P. (1993). Two Skeletal Remains from Hiam El Sagha, Revue Biblique, 101: 260-269