Publications
36. NeMu: a comprehensive pipeline for accurate reconstruction of neutral mutation spectra from evolutionary data
Efimenko B, Popadin K, Gunbin K, Nucleic Acids Res, 2024
35. Reanalysis of mtDNA mutations of human primordial germ cells (PGCs) reveals NUMT contamination and suggests that selection in PGCs may be positive
Fleischmann Z, Cote-L’Heureux A, Franco M, Oreshkov S, Annis S, Khrapko M, Aidlen D, Popadin K, Woods DC, Tilly JL, Khrapko K., Mitochondrion, 2024
34. Secondary structure of the human mitochondrial genome affects formation of deletions
Shamanskiy V, Mikhailova AA, Tretiakov EO, Ushakova K, Mikhailova AG, Oreshkov S, Knorre DA, Ree N, Overdevest JB, Lukowski SW, Gostimskaya I, Yurov V, Liou CW, Lin TK, Kunz WS, Reymond A, Mazunin I, Bazykin GA, Fellay J, Tanaka M, Khrapko K, Gunbin K, Popadin K., BMC Biol, 2023
33. Live Birth of a Healthy Child in a Couple with Identical mtDNA Carrying a Pathogenic c.471_477delTTTAAAAinsG Variant in the MOCS2 Gene
Tofilo M, Voronova N, Nigmatullina L, Kuznetsova E, Timonina V, Efimenko B, Turgunkhujaev O, Avdeichik S, Ansar M, Popadin K, Kirillova A, Mazunin I., Genes (Basel), 2023
32. Dynamics of the most common pathogenic mtDNA variant m.3243A > G demonstrate frequency-dependency in blood and positive selection in the germline
Franco M, Pickett SJ, Fleischmann Z, Khrapko M, Cote-L’Heureux A, Aidlen D, Stein D, Markuzon N, Popadin K, Braverman M, Woods DC, Tilly JL, Turnbull DM, Khrapko K., Hum Mol Genet, 2022
31. A mitochondria-specific mutational signature of aging: increased rate of A > G substitutions on the heavy strand
Mikhailova AG, Mikhailova AA, Ushakova K, Tretiakov EO, Iliushchenko D, Shamansky V, Lobanova V, Kozenkov I, Efimenko B, Yurchenko AA, Kozenkova E, Zdobnov EM, Makeev V, Yurov V, Tanaka M, Gostimskaya I, Fleischmann Z, Annis S, Franco M, Wasko K, Denisov S, Kunz WS, Knorre D, Mazunin I, Nikolaev S, Fellay J, Reymond A, Khrapko K, Gunbin K, Popadin K., Nucleic Acids Res, 2022
30. Mitochondrial Pseudogenes Suggest Repeated Inter-Species Hybridization among Direct Human Ancestors
Popadin K, Gunbin K, Peshkin L, Annis S, Fleischmann Z, Franco M, Kraytsberg Y, Markuzon N, Ackermann RR, Khrapko K., Genes (Basel), 2022
29. Increased prevalence of clonal hematopoiesis of indeterminate potential amongst people living with HIV
Bick AG, Popadin K, Thorball CW, Uddin MM, Zanni MV, Yu B, Cavassini M, Rauch A, Tarr P, Schmid P, Bernasconi E, Günthard HF, Libby P, Boerwinkle E, McLaren PJ, Ballantyne CM, Grinspoon S, Natarajan P, Fellay J; Swiss HIV Cohort Study., Sci Rep, 2022
28. Molecular design of hypothalamus development
Romanov RA, Tretiakov EO, Kastriti ME, Zupancic M, Häring M, Korchynska S, Popadin K, Benevento M, Rebernik P, Lallemend F, Nishimori K, Clotman F, Andrews WD, Parnavelas JG, Farlik M, Bock C, Adameyko I, Hökfelt T, Keimpema E, Harkany T., Nature, 2020
27. From Normal to Obesity and Back: The Associations between Mitochondrial DNA Copy Number, Gender, and Body Mass Index
Skuratovskaia D, Litvinova L, Vulf M, Zatolokin P, Popadin K, Mazunin I., Cells, 2019
26. ImtRDB: a database and software for mitochondrial imperfect interspersed repeats annotation
Shamanskiy VA, Timonina VN, Popadin KY, Gunbin KV., BMC Genomics, 2019
25. mtProtEvol: the resource presenting molecular evolution analysis of proteins involved in the function of Vertebrate mitochondria
Kuzminkova AA, Sokol AD, Ushakova KE, Popadin KY, Gunbin KV., BMC Evol Biol, 2019
24. Slightly deleterious genomic variants and transcriptome perturbations in Down syndrome embryonic selection
Popadin K, Peischl S, Garieri M, Sailani MR, Letourneau A, Santoni F, Lukowski SW, Bazykin GA, Nikolaev S, Meyer D, Excoffier L, Reymond A, Antonarakis SE., Genome Res, 2018
23. The Immune Signaling Adaptor LAT Contributes to the Neuroanatomical Phenotype of 16p11.2 BP2-BP3 CNVs
Loviglio MN, Arbogast T, Jønch AE, Collins SC, Popadin K, Bonnet CS, Giannuzzi G, Maillard AM, Jacquemont S; 16p11.2 Consortium; Yalcin B, Katsanis N, Golzio C, Reymond A., Am J Hum Genet, 2017
22. The genomic landscape of human cellular circadian variation points to a novel role for the signalosome
Gaspar L, Howald C, Popadin K, Maier B, Mauvoisin D, Moriggi E, Gutierrez-Arcelus M, Falconnet E, Borel C, Kunz D, Kramer A, Gachon F, Dermitzakis ET, Antonarakis SE, Brown SA., Elife, 2017
21. Data on the time of integration of the human mitochondrial pseudogenes (NUMTs) into the nuclear genome
Gunbin K, Peshkin L, Popadin K, Annis S, Ackermann RR, Khrapko K., Data Brief, 2017
20. Integration of mtDNA pseudogenes into the nuclear genome coincides with speciation of the human genus. A hypothesis
Gunbin K, Peshkin L, Popadin K, Annis S, Ackermann RR, Khrapko K., Mitochondrion, 2017
19. Amelioration of premature aging in mtDNA mutator mouse by exercise: the interplay of oxidative stress, PGC-1α, p53, and DNA damage. A hypothesis
Safdar A, Annis S, Kraytsberg Y, Laverack C, Saleem A, Popadin K, Woods DC, Tilly JL, Khrapko K., Curr Opin Genet Dev, 2016
18. Genomic analysis identifies new drivers and progression pathways in skin basal cell carcinoma
Bonilla X, Parmentier L, King B, Bezrukov F, Kaya G, Zoete V, Seplyarskiy VB, Sharpe HJ, McKee T, Letourneau A, Ribaux PG, Popadin K, Basset-Seguin N, Ben Chaabene R, Santoni FA, Andrianova MA, Guipponi M, Garieri M, Verdan C, Grosdemange K, Sumara O, Eilers M, Aifantis I, Michielin O, de Sauvage FJ, Antonarakis SE, Nikolaev SI., Nat Genet, 2016
17. Corrigendum: Domains of genome-wide gene expression dysregulation in Down’s syndrome
Letourneau A, Santoni FA, Bonilla X, Sailani MR, Gonzalez D, Kind J, Chevalier C, Thurman R, Sandstrom RS, Hibaoui Y, Garieri M, Popadin K, Falconnet E, Gagnebin M, Gehrig C, Vannier A, Guipponi M, Farinelli L, Robyr D, Migliavacca E, Borel C, Deutsch S, Feki A, Stamatoyannopoulos JA, Herault Y, van Steensel B, Guigo R, Antonarakis SE., Nature, 2016
16. APOBEC-induced mutations in human cancers are strongly enriched on the lagging DNA strand during replication
Seplyarskiy VB, Soldatov RA, Popadin KY, Antonarakis SE, Bazykin GA, Nikolaev SI., Genome Res, 2016
15. DNA-Methylation Patterns in Trisomy 21 Using Cells from Monozygotic Twins
Sailani MR, Santoni FA, Letourneau A, Borel C, Makrythanasis P, Hibaoui Y, Popadin K, Bonilla X, Guipponi M, Gehrig C, Vannier A, Carre-Pigeon F, Feki A, Nizetic D, Antonarakis SE., PLoS One, 2015
14. Biased allelic expression in human primary fibroblast single cells
Borel C, Ferreira PG, Santoni F, Delaneau O, Fort A, Popadin KY, Garieri M, Falconnet E, Ribaux P, Guipponi M, Padioleau I, Carninci P, Dermitzakis ET, Antonarakis SE., Am J Hum Genet, 2015
13. Gene age predicts the strength of purifying selection acting on gene expression variation in humans
Popadin KY, Gutierrez-Arcelus M, Lappalainen T, Buil A, Steinberg J, Nikolaev SI, Lukowski SW, Bazykin GA, Seplyarskiy VB, Ioannidis P, Zdobnov EM, Dermitzakis ET, Antonarakis SE., Am J Hum Genet, 2014
12. Mitochondrial DNA mutations and cancer: lessons from the parathyroid
Popadin K, Gunbin KV, Khrapko K., Am J Pathol, 2014
11. When man got his mtDNA deletions?
Popadin K, Safdar A, Kraytsberg Y, Khrapko K., Aging Cell, 2014
10. Domains of genome-wide gene expression dysregulation in Down’s syndrome
Letourneau A, Santoni FA, Bonilla X, Sailani MR, Gonzalez D, Kind J, Chevalier C, Thurman R, Sandstrom RS, Hibaoui Y, Garieri M, Popadin K, Falconnet E, Gagnebin M, Gehrig C, Vannier A, Guipponi M, Farinelli L, Robyr D, Migliavacca E, Borel C, Deutsch S, Feki A, Stamatoyannopoulos JA, Herault Y, van Steensel B, Guigo R, Antonarakis SE., Nature, 2014
9. Genetic and epigenetic regulation of human lincRNA gene expression
Popadin K, Gutierrez-Arcelus M, Dermitzakis ET, Antonarakis SE., Am J Hum Genet, 2013
8. The complex SNP and CNV genetic architecture of the increased risk of congenital heart defects in Down syndrome
Sailani MR, Makrythanasis P, Valsesia A, Santoni FA, Deutsch S, Popadin K, Borel C, Migliavacca E, Sharp AJ, Duriaux Sail G, Falconnet E, Rabionet K, Serra-Juhé C, Vicari S, Laux D, Grattau Y, Dembour G, Megarbane A, Touraine R, Stora S, Kitsiou S, Fryssira H, Chatzisevastou-Loukidou C, Kanavakis E, Merla G, Bonnet D, Pérez-Jurado LA, Estivill X, Delabar JM, Antonarakis SE., Genome Res, 2013
7. Purifying selection in mammalian mitochondrial protein-coding genes is highly effective and congruent with evolution of nuclear genes
Popadin KY, Nikolaev SI, Junier T, Baranova M, Antonarakis SE., Mol Biol Evol, 2013
6. Roles of mitochondrial dynamics under stressful and normal conditions in yeast cells
Knorre DA, Popadin KY, Sokolov SS, Severin FF., Oxid Med Cell Longev, 2013
5. Repeats, longevity and the sources of mtDNA deletions: evidence from ‘deletional spectra’
Guo X, Popadin KY, Markuzon N, Orlov YL, Kraytsberg Y, Krishnan KJ, Zsurka G, Turnbull DM, Kunz WS, Khrapko K., Trends Genet, 2010
4. Life-history traits drive the evolutionary rates of mammalian coding and noncoding genomic elements
Nikolaev SI, Montoya-Burgos JI, Popadin K, Parand L, Margulies EH; National Institutes of Health Intramural Sequencing Center Comparative Sequencing Program; Antonarakis SE., Proc Natl Acad Sci U S A, 2007
3. A manually curated database of tetrapod mitochondrially encoded tRNA sequences and secondary structures
Popadin KY, Mamirova LA, Kondrashov FA., BMC Bioinformatics, 2007
2. Accumulation of slightly deleterious mutations in mitochondrial protein-coding genes of large versus small mammals
Popadin K, Polishchuk LV, Mamirova L, Knorre D, Gunbin K., Proc Natl Acad Sci U S A, 2007
1. Purifying selection in mitochondria, free-living and obligate intracellular proteobacteria
Mamirova L, Popadin K, Gelfand MS., BMC Evol Biol, 2007