Publications
For an updated list of the publications view:
orcid.org/0000-0001-9170-576734. Quigley S, Damas J, Larkin DM, Farré M. SyntenyPlotteR: a user friendly R package to visualize genome synteny, ideal for both experienced and novice bioinformaticians. Bioinformatics Advances Volume 3, Issue 1, 2023, vbad161, https://doi.org/10.1093/bioadv/vbad161
33. Arias-Sardá C, Quigley S, Farré M. 2023. Patterns of chromosome evolution in ruminants. Molecular Ecology, 00:1–11 https://doi.org/10.1111/mec.17197.
32. Burden F, Ellis PJI, Farré M. 2023. A shared ‘vulnerability code’ underpins varying sources of DNA damage throughout paternal germline transmission in mouse. Nucleic Acids Research, 51(5), 2319–2332. https://doi.org/10.1093/nar/gkad089.
31. Álvarez-González L, Arias-Sardá C, Montes-Espuña L, Marín-Gual L, Vara C, Lister NC, Cuartero Y, Garcia F, Deakin J, Renfree MB, ... Farré M, Ruiz-Herrera A. 2022. Principles of 3D chromosome folding and evolutionary genome reshuffling in mammals. Cell Rep 41: 111839. doi.org/10.1016/j.celrep.2022.111839
30. Alvarez-Gonzalez L*, Burden F*, Doddamani D*, Malinverni R, Leach E, Marin-Garcia C, Marin-Gual L, Gubern A, Vara C, Paytuvi-Gallart A, Buschbeck M, Ellis PJI^, Farré M^, Ruiz-Herrera A^. 2022. 3D chromatin remodelling in the germ line modulates genome evolutionary plasticiy. Nature Communications, May 11; 13(1). doi.org/10.1038/s41467-022-30296-6
29. Farré M, Johnstone C, Hopper J, Kitchener A, Roos C, King T. Novel mtDNA haplotypes represented in the European captive population of the Endangered François' langur. 2022. Int. Journ. Primat, 43. doi.org/10.1007/s10764-022-00295-x
33. Arias-Sardá C, Quigley S, Farré M. 2023. Patterns of chromosome evolution in ruminants. Molecular Ecology, 00:1–11 https://doi.org/10.1111/mec.17197.
32. Burden F, Ellis PJI, Farré M. 2023. A shared ‘vulnerability code’ underpins varying sources of DNA damage throughout paternal germline transmission in mouse. Nucleic Acids Research, 51(5), 2319–2332. https://doi.org/10.1093/nar/gkad089.
31. Álvarez-González L, Arias-Sardá C, Montes-Espuña L, Marín-Gual L, Vara C, Lister NC, Cuartero Y, Garcia F, Deakin J, Renfree MB, ... Farré M, Ruiz-Herrera A. 2022. Principles of 3D chromosome folding and evolutionary genome reshuffling in mammals. Cell Rep 41: 111839. doi.org/10.1016/j.celrep.2022.111839
30. Alvarez-Gonzalez L*, Burden F*, Doddamani D*, Malinverni R, Leach E, Marin-Garcia C, Marin-Gual L, Gubern A, Vara C, Paytuvi-Gallart A, Buschbeck M, Ellis PJI^, Farré M^, Ruiz-Herrera A^. 2022. 3D chromatin remodelling in the germ line modulates genome evolutionary plasticiy. Nature Communications, May 11; 13(1). doi.org/10.1038/s41467-022-30296-6
29. Farré M, Johnstone C, Hopper J, Kitchener A, Roos C, King T. Novel mtDNA haplotypes represented in the European captive population of the Endangered François' langur. 2022. Int. Journ. Primat, 43. doi.org/10.1007/s10764-022-00295-x
28. Silvestri G, Canedo-Ribeiro C, Serrano-Albal M, Labrecque R, Blondin P, Larmer SG, Marras G, Tutt DAR, Handyside AH, Farré M, et al. 2021. Preimplantation Genetic Testing for Aneuploidy Improves Live Birth Rates with In Vitro Produced Bovine Embryos: A Blind Retrospective Study. Cells 10: 2284. doi.org/10.3390/cells10092284
27. Johnson CA, McGreig JE, Jeanfavre ST, Walklate J, Vera CD, Farré M, Mulvihill DP, Baines AJ, Ridout M, Leinwand LA, et al. 2021. Identification of sequence changes in myosin II that adjust muscle contraction velocity. PLoS Biol 19: e3001248. doi.org/10.1371/journal.pbio.3001248
26. Kirkland C & Farré M. 2021. Mitochondrial genome evolution, genetic diversity and population structure in British Water Voles. Genes Volume 12, Issue 2, 21 January 2021. doi.org/10.3390/genes12020138
27. Johnson CA, McGreig JE, Jeanfavre ST, Walklate J, Vera CD, Farré M, Mulvihill DP, Baines AJ, Ridout M, Leinwand LA, et al. 2021. Identification of sequence changes in myosin II that adjust muscle contraction velocity. PLoS Biol 19: e3001248. doi.org/10.1371/journal.pbio.3001248
26. Kirkland C & Farré M. 2021. Mitochondrial genome evolution, genetic diversity and population structure in British Water Voles. Genes Volume 12, Issue 2, 21 January 2021. doi.org/10.3390/genes12020138
25. Farré M. & Ruiz-Herrera A. 2020 The plasticity of genome architecture. Genes Volume 11, Issue 12, 27 November 2020 doi.org/10.3390/genes11121413
30. Proskuryakova AA, Kulemzina AI, Perelman PL, Yudkin DV, Lemskaya NA, Okhlopkov IM, Kirillin EV, Farré M, Larkin DM, Roelke-Parker ME, et al. 2019. Comparative Chromosome Mapping of Musk Ox and the X Chromosome among Some Bovidae Species. Genes (Basel) 10: 857. doi.org/10.3390/genes10110857
29. Rando HM, Wadlington WH, Johnson JL, Stutchman JT, Trut LN, Farré M, Kukekova AV. 2019. The Red Fox Y-Chromosome in Comparative Context. Genes (Basel) 10: 409. doi.org/10.3390/genes10060409
28. Ruvinskii D, Larkin D, Farré M. 2019. A Near Chromosome Assembly of the Dromedary Camel Genome. Frontiers in genetics 10: 32. doi.org/10.3389/fgene.2019.00032
27. Darolti I, Wright AE, Sandkam BA, Morris J, Bloch NI, Farre M, Fuller RC, Bourne GR, Larkin DM, Breden F, et al. 2019. Extreme heterogeneity in sex chromosome differentiation and dosage compensation in livebearers. Proc Natl Acad Sci U S A 116: 19031–19036. doi.org/10.1073/pnas.1905298116
26. Farré M, Kim J, Proskuryakova AA, Zhang Y, Kulemzina AI, Li Q, Zhou Y, Xiong Y, Johnson JL, Perelman PL, et al. 2019a. Evolution of gene regulation in ruminants differs between evolutionary breakpoint regions and homologous synteny blocks. Genome Res 29: 576–589. doi.org/10.1101/gr.239863.118
25. Farre M, Li Q, Darolti I, Zhou Y, Damas J, Proskuryakova AA, Kulemzina AI, Chemnick LG, Kim J, Ryder OA, et al. 2019. An integrated chromosome-scale genome assembly of the Masai giraffe (Giraffa camelopardalis tippelskirchi). Gigascience 8 doi.org/10.1093/gigascience/giz090
24. Farré M. et al. 2019 A near-chromosome-scale genome assembly of the gemsbok (Oryx gazella): an iconic antelope of the Kalahari desert. GigaScience Volume 8, Issue 2, 1 February 2019 doi.org/10.1093/gigascience/giy162
29. Rando HM, Wadlington WH, Johnson JL, Stutchman JT, Trut LN, Farré M, Kukekova AV. 2019. The Red Fox Y-Chromosome in Comparative Context. Genes (Basel) 10: 409. doi.org/10.3390/genes10060409
28. Ruvinskii D, Larkin D, Farré M. 2019. A Near Chromosome Assembly of the Dromedary Camel Genome. Frontiers in genetics 10: 32. doi.org/10.3389/fgene.2019.00032
27. Darolti I, Wright AE, Sandkam BA, Morris J, Bloch NI, Farre M, Fuller RC, Bourne GR, Larkin DM, Breden F, et al. 2019. Extreme heterogeneity in sex chromosome differentiation and dosage compensation in livebearers. Proc Natl Acad Sci U S A 116: 19031–19036. doi.org/10.1073/pnas.1905298116
26. Farré M, Kim J, Proskuryakova AA, Zhang Y, Kulemzina AI, Li Q, Zhou Y, Xiong Y, Johnson JL, Perelman PL, et al. 2019a. Evolution of gene regulation in ruminants differs between evolutionary breakpoint regions and homologous synteny blocks. Genome Res 29: 576–589. doi.org/10.1101/gr.239863.118
25. Farre M, Li Q, Darolti I, Zhou Y, Damas J, Proskuryakova AA, Kulemzina AI, Chemnick LG, Kim J, Ryder OA, et al. 2019. An integrated chromosome-scale genome assembly of the Masai giraffe (Giraffa camelopardalis tippelskirchi). Gigascience 8 doi.org/10.1093/gigascience/giz090
24. Farré M. et al. 2019 A near-chromosome-scale genome assembly of the gemsbok (Oryx gazella): an iconic antelope of the Kalahari desert. GigaScience Volume 8, Issue 2, 1 February 2019 doi.org/10.1093/gigascience/giy162
23. Damas J., Kim J., Farré M., Griffin D.K., Larkin D.M. Reconstruction of avian ancestral karyotypes reveals differences in the evolutionary history of macro- and microchromosomes. Genome Biology. 2018 Oct 5. doi.org/10.1186/s13059-018-1544-8
22. Rando H.M., Farré M., et al. Construction of Red Fox Chromosomal Fragments from the Short-Read Genome Assembly. Genes. 2018 June 9:6. doi.org/10.3390/genes9060308
21. O’Connor R. E., Romanov M. N., Kiazim L.G., Barret P.M, Farré M., Damas J., Ferguson-Smith M., Valenzuela N., Larkin D.M., Griffin D.K. Reconstruction of the diapsid ancestral genome permits chromosome evolution tracing in avian and non-avian dinosaurs. Nature Communications. 2018 May 9:1883. doi.org/10.1038/s41467-018-04267-9
22. Rando H.M., Farré M., et al. Construction of Red Fox Chromosomal Fragments from the Short-Read Genome Assembly. Genes. 2018 June 9:6. doi.org/10.3390/genes9060308
21. O’Connor R. E., Romanov M. N., Kiazim L.G., Barret P.M, Farré M., Damas J., Ferguson-Smith M., Valenzuela N., Larkin D.M., Griffin D.K. Reconstruction of the diapsid ancestral genome permits chromosome evolution tracing in avian and non-avian dinosaurs. Nature Communications. 2018 May 9:1883. doi.org/10.1038/s41467-018-04267-9
20. Proskuryakova AA., Kulemzina AI., Perelman PL., Makunin AI., Larkin DM., Farré M., et al. X Chromosome evolution in Cetartiodactyla. Genes. 2017 Aug 31:8.
19. Kim J.*, Farré M.*, Auvril L., Capitanu B., Larkin D.M., Ma J’, Lewin H.A. Reconstruction and evolutionary history of eutherian chromosomes. PNAS. 2017 July 114:27.
19. Kim J.*, Farré M.*, Auvril L., Capitanu B., Larkin D.M., Ma J’, Lewin H.A. Reconstruction and evolutionary history of eutherian chromosomes. PNAS. 2017 July 114:27.
18. Damas J., O’Connor R., Farré M., et al. Upgrading short read animal genome assemblies to chromosome level using comparative genomics and a universal probe set. Genome Res. 2016 Nov 30.
17. Capilla L., Sanchez-Guillen RA., Farré M., Paytuvi-Gallart A., Maliverni R., Ventura J., Larkin DM., Ruiz-Herrera A. Mammalian comparative genomics reveals epigenetic features associated with genome reshuffling in rodentia. Genome Biol Evol. 2016 8(12):3703–3717.
16. Farré M., Narayan J., Slavov G.T., Auvil L., Li C., Jarvis E.D., Burt D.W., Griffin D.K., Larkin D.M. Novel insights into chromosome evolution in birds, archosaurs, and reptiles. Genome Biol Evol. 2016 Aug 25: 2442-51.
15. Bryan C., Guterman G., Ma KL., Lewin HA., Larkin DM., Kim J., Ma J., Farré M. Synteny Explorer: An interactive visualization application for teaching genome evolution. IEEE Trans Vis Comput Graph. 2016 Aug 5.
17. Capilla L., Sanchez-Guillen RA., Farré M., Paytuvi-Gallart A., Maliverni R., Ventura J., Larkin DM., Ruiz-Herrera A. Mammalian comparative genomics reveals epigenetic features associated with genome reshuffling in rodentia. Genome Biol Evol. 2016 8(12):3703–3717.
16. Farré M., Narayan J., Slavov G.T., Auvil L., Li C., Jarvis E.D., Burt D.W., Griffin D.K., Larkin D.M. Novel insights into chromosome evolution in birds, archosaurs, and reptiles. Genome Biol Evol. 2016 Aug 25: 2442-51.
15. Bryan C., Guterman G., Ma KL., Lewin HA., Larkin DM., Kim J., Ma J., Farré M. Synteny Explorer: An interactive visualization application for teaching genome evolution. IEEE Trans Vis Comput Graph. 2016 Aug 5.
14. Beynon S., Slavov G.T., Farré M., Sunduimijid B., Waddams K., Davies B., Haresign W., Kijas J., MacLeod I.M., Newbold J., Davies L., Larkin D.M. Population structure and history of the Welsh sheep breeds determined by whole genome genotyping. BMC Genetics 2015 Jun20;16(1):65.
13. Schimd M., Smith J., Burt DW., … Farré M., Fasold M. et al. Third report on chicken genes and chromosomes 2015. Cytogenet Genome Res. 2015; 145:78-179.
12. Farré M., Robinson T.J., Ruiz-Herrera A. An integrative breakage model of genome architecture, reshuffling and evolution. BioEssays 2015 Mar 4.
13. Schimd M., Smith J., Burt DW., … Farré M., Fasold M. et al. Third report on chicken genes and chromosomes 2015. Cytogenet Genome Res. 2015; 145:78-179.
12. Farré M., Robinson T.J., Ruiz-Herrera A. An integrative breakage model of genome architecture, reshuffling and evolution. BioEssays 2015 Mar 4.
11. Zhang G., Li C., Li Q., Li B., Larkin D.M., ...Farré M., Narayan J., et al. Comparative genomics across modern bird species reveal insights into pan-avian genome evolution and trait biodiversity. Science 2014 Dec 12:1311-20.
10. Romanov M.N.*, Farré M.*, Lithgow P.E., Fowler K.E., Skinner B.M., O’Connor R., Fonseka G., Backström N., Matsuda Y., Nishida C., Houde P., Jarvis E.D., Ellegren H., Burt D.W., Larkin D.M. and Griffin D.K. Reconstruction of the avian genome organization and evolution from a chromosomal perspective suggests that the chicken lineage most closely resembles the dinosaur avian ancestor. BMC Genomics 2014 Dec 11:1060.
9. Fang X., Nevo E., Han L., Levanon E.Y., Zhao J., Avivi A., Larkin D.M., … Farré M., Kim J., et al. Genome-wide adaptive complexes to underground stresses in blind mole rats, Spalax. Nature communications 2014 Jun3; 5:3966.
8. Ullastres A., Farré M., Capilla L., Ruiz-Herrera A. Unravelling the effect of genomic structural changes on genetic recombination in the rhesus macaque - implications for the adaptive role of inversions. BMC Genomics 2014 Jun 26;15(1):530.
10. Romanov M.N.*, Farré M.*, Lithgow P.E., Fowler K.E., Skinner B.M., O’Connor R., Fonseka G., Backström N., Matsuda Y., Nishida C., Houde P., Jarvis E.D., Ellegren H., Burt D.W., Larkin D.M. and Griffin D.K. Reconstruction of the avian genome organization and evolution from a chromosomal perspective suggests that the chicken lineage most closely resembles the dinosaur avian ancestor. BMC Genomics 2014 Dec 11:1060.
9. Fang X., Nevo E., Han L., Levanon E.Y., Zhao J., Avivi A., Larkin D.M., … Farré M., Kim J., et al. Genome-wide adaptive complexes to underground stresses in blind mole rats, Spalax. Nature communications 2014 Jun3; 5:3966.
8. Ullastres A., Farré M., Capilla L., Ruiz-Herrera A. Unravelling the effect of genomic structural changes on genetic recombination in the rhesus macaque - implications for the adaptive role of inversions. BMC Genomics 2014 Jun 26;15(1):530.
7. Wang W., Lopez-Giraldez F., Farré M., Lehr N., Townsed JF. Global gene expression and knockout analysis reveals genes associated with fungal fruiting body development in Neurospora crassa. Eukaryot Cell. 2013 Nov 15.
6. Segura J., Capilla L., Ferreti L., Ramos-Onsins S., Farré M., Reis F., Garcia F., Garcia-Caldes M., Robinson TJ., Ruiz‐Herrera A., New insights into mechanisms that are shaping meiotic recombination rates and crossover interference in eutherian mammals. Proc. R. Soc. B. 2013 Jan 1; 48-218-28.
5. Farré M., Michelleti D., Ruiz‐Herrera A. Recombination rates and genomic shuffling in human and chimpanzee – a new twist in the chromosomal speciation theory. Mol Biol Evol. 2013 Apr(4): 853-864.
6. Segura J., Capilla L., Ferreti L., Ramos-Onsins S., Farré M., Reis F., Garcia F., Garcia-Caldes M., Robinson TJ., Ruiz‐Herrera A., New insights into mechanisms that are shaping meiotic recombination rates and crossover interference in eutherian mammals. Proc. R. Soc. B. 2013 Jan 1; 48-218-28.
5. Farré M., Michelleti D., Ruiz‐Herrera A. Recombination rates and genomic shuffling in human and chimpanzee – a new twist in the chromosomal speciation theory. Mol Biol Evol. 2013 Apr(4): 853-864.
4. Ruiz‐Herrera A., Farré M., Robinson TJ. Molecular cytogenetic and genomic insights to chromosomal evolution. Heredity 2012; 108(1):28‐36.
3. Farré M, Bosch M, López‐Giraldez F, Ponsà M, Ruiz‐Herrera A. Assessing the role of tandem repeats in shaping genomic architecture of Great Apes. PLoS One 2011; 6(11).
2. Ruiz‐Herrera A., Farré M., Ponsà M., Robinson TJ. Selection against Robertsonian fusions involving housekeeping genes in the house mouse: integrating data from gene expression arrays and chromosome evolution. Chromosome Res 2010; 18:801‐808.
1. Farré M, Ponsà M, Bosch M. Interstitial telomeric sequences (ITS) are not located at the exact evolutionary breakpoints in primates. Cytogenet Genome Res. 2009; 124(2): 128‐31.
3. Farré M, Bosch M, López‐Giraldez F, Ponsà M, Ruiz‐Herrera A. Assessing the role of tandem repeats in shaping genomic architecture of Great Apes. PLoS One 2011; 6(11).
2. Ruiz‐Herrera A., Farré M., Ponsà M., Robinson TJ. Selection against Robertsonian fusions involving housekeeping genes in the house mouse: integrating data from gene expression arrays and chromosome evolution. Chromosome Res 2010; 18:801‐808.
1. Farré M, Ponsà M, Bosch M. Interstitial telomeric sequences (ITS) are not located at the exact evolutionary breakpoints in primates. Cytogenet Genome Res. 2009; 124(2): 128‐31.
