2021

Zhou Y, Shearwin-Whyatt L, Li J, Song Z, Hayakawa T, Stevens D, Fenelon JC, Peel E, Cheng Y, Pajpach F, Bradley N, Suzuki H, Nikaido M, Damas J, Daish T, Perry T, Zhu Z, Geng Y, Rhie A, Sims Y, Wood J, Haase B, Mountcastle J, Fedrigo O, Li Q, Yang H, Wang J, Johnston SD, Phillippy AM, Howe K, Jarvis ED, Ryder OA, Kaessmann H, Donnelly P, Korlach J, Lewin HA, Graves J, Belov K, Renfree MB, Grutzner F, Zhou Q, Zhang G. Platypus and echidna genomes reveal mammalian biology and evolution. Nature. 2021. doi:10.1038/s41586-020-03039-0.

Damas J, Corbo M, Lewin HA. Vertebrate Chromosome Evolution. Annual Review of Animal Biosciences. 2021. doi:10.1146/annurev-animal-020518-114924.

2020

Rhie A, McCarthy SA, Fedrigo O, Damas J, Formenti G, Koren S, Uliano-Silva M, Chow W, Fungtammasan A, Gedman GL, Cantin LJ, Thibaud-Nissen F, Haggerty L, Lee C, Ko BJ, Kim J, Bista I, Smith M, Haase B, Mountcastle J, Winkler S, Paez S, Howard J, Vernes SC, Lama TM, Grutzner FC, Warren WC, Balakrishnan C, Burt D, George JM, Biegler M, Iorns D, Digby A, Eason D, Edwards T, Wilkinson M, Turner GF, Meyer A, Kautt AF, Franchini P, Detrich III HW, Svardal H, Wagner M, Naylor GJP, Pippel M, Malinsky M, Mooney M, Simbirsky M, Hannigan BT, Pesout T, Houck M, Misuraca A, Kingan SB, Hall R, Kronenberg Z, Korlach J, Sović I, Dunn C, Ning Z, Hastie A, Lee J, Selvaraj S, Green RE, Putnam NH, Ghurye J, Garrison E, Sims Y, Collins J, Pelan S, Torrance J, Tracey A, Wood J, Guan D, London SE, Clayton DF, Mello CV, Friedrich SR, Lovell PV, Osipova E, Al-Ajli FO, Secomandi S, Kim H, Theofanopoulou C, Zhou Y, Harris RS, Makova KD, Medvedev P, Hoffman J, Masterson P, Clark K, Martin F, Howe K, Flicek P, Walenz BP, Kwak W, Clawson H, Diekhans M, Nassar L, Paten B, Kraus RHS, Lewin HA, Crawford AJ, Gilbert MTP, Zhang G, Venkatesh B, Murphy RW, Koepfli KP, Shapiro B, Johnson WE, Di Palma F, Marques-Bonet T, Teeling EC, Warnow T, Marshall Graves J, Ryder OA, Haussler D, O'Brien SJ, Howe K, Myers EW, Durbin R, Phillippy AM, Jarvis ED. Towards complete and error-free genome assemblies of all vertebrate species. doi:10.1101/2020.05.22.110833. (submitted)

Damas J, Hughes GM, Keough KC, Painter CA, Persky NS, Corbo M, Hiller M, Koepfli K-P, Pfenning AR, Zhao H, Genereux DP, Swofford R, Pollard KS, Ryder OA, Nweeia MT, Lindblad-Toh K, Teeling EC, Karlsson EK, Lewin HA. Broad Host Range of SARS-CoV-2 Predicted by Comparative and Structural Analysis of ACE2 in Vertebrates. PNAS. 2020. doi:10.1073/pnas.2010146117.

Genereux DP, Serres A, Armstrong J, Johnson J, Marinescu VD, Muren E, Juan D, Bejerano G, Casewell NR, Chemnick LG, Damas J, Di Palma F, Diekhans M, Fiddes IT, Garber M, Goodman L, Haerty W, Houck ML, Hubley R, Kivioja T, Kuderna LFK, Lander ES, Meadows JRS, Murphy WJ, Nash W, Noh HJ, Nweeia M, Pfenning AR, Pollard KS, Ray D, Shapiro B, Smit A, Springer M, Steiner CC, Swofford R, Taipale J, Teeling EC, Turner-Maier J, Alfoldi J, Birren B, Ryder OA, Lewin HA, Paten B, Marques-Bonet T, Lindblad-Toh K, Karlsson EK. A comparative genomics multitool for scientific discovery and conservation. Nature. 2020. doi:10.1038/s41586-020-2876-6.

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2019

Damas J, O' Connor RE, Griffin DK, Larkin DM. Avian Chromosomal Evolution in Avian Genomics in Ecology and Evolution: From the Lab into the Wild. 2019. doi:10.1007/978-3-030-16477-5_4. (book chapter)

Farré M, Li Q, Darolti I, Zhou Y, Damas J, Proskuryakova AA, Kulemzina AI, Chemnick LG, Kim J, Ryder OA, Ma J, Graphodatsky AS, Zhang G, Larkin DM, Lewin HA. An integrated chromosome-scale genome assembly of the Masai giraffe (Giraffa camelopardalis tippelskirchi). GigaScience. 2019. doi:10.1093/giga-science/giz090.

Hjelm BE, Rollins B, Morgan L, Sequeira A, Mamdani F, Pereira F, Damas J, Webb MG, Weber MD, Schatzberg AF, Barchas JD, Lee FS, Akil H, Watson SJ, Myers RM, Chao EC, Kimonis V, Thompson PM, Bunney WE, Vawter MP. Splice-Break: exploiting and RNA-seq splice junction algorithm to discover mitochondrial DNA deletion breakpoints and analyses of psychiatric disorders. Nucleic Acids Research. 2019. doi:10.1093/nar/gkz164.

Farré M, Li Q, Zhou Y, Damas J, Chemnick LG, Kim J, Ryder OA, Ma J, Zhang G, Larkin DM, Lewin HA. A near-chromosome-scale genome assembly of the gemsbok (Oryx gazella): an iconic antelope of the Kalahari desert. GigaScience. 2019. doi:10.1093/giga-science/giy162.

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2018

Damas J, Kim J, Farré M, Griffin DK, Larkin DM. Reconstruction of avian ancestral karyotypes reveals differences in the evolutionary history of macro- and microchromosomes. Genome biology. 2018. doi:10.1186/s13059-018-1544-8.

O'Connor R, Farré M, Joseph S, Damas J, Kiazim L, Jennings R, Bennett S, Slack EA, Allanson E, Larkin DM, Griffin DK. Chromosome-level assembly reveals extensive rearrangement in saker falcon and budgerigar, but not ostrich, genomes. Genome Biology. 2018. doi:10.1186/s13059-018-1550-x.

O'Connor R, Romanov MN, Kiazim LG, Barrett PM, Farré M, Damas J, Ferguson-Smith M, Valenzuela N, Larkin DM, Griffin DK. Reconstruction of the diapsid ancestral genome permits chromosome evolution tracing in avian and non-avian dinosaurs. Nature Communications. 2018. doi:10.1038/s41467-018-04267-9.

Drpic D, Almeida AC, Aguiar P, Renda F, Damas J, Lewin HA, Larkin DM, Khodjakov A, Maiato H. Chromosome segregation is biased by kinetochore size. Current Biology. 2018. doi:10.1016/j.cub.2018.03.023.

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2017

Damas J, O'Connor R, Farré M, Lenis VPE, Martell HJ, Mandawala A, Fowler K, Joseph S, Swain MT, Griffin DK, Larkin DM. Upgrading short read animal genomes to chromosome level using comparative genomics and a universal probe set. Genome Research. 2017. doi:10.1101/gr.213660.116.

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2016

Farré M, Narayan J, Slavov GT, Damas J, Auvil L, Li C, Jarvis ED, Burt DW, Griffin DK, Larkin DM. Novel insights into chromosome evolution in birds, archosaurs, and reptiles. Genome Biology and Evolution. 2016. doi:10.1093/gbe/evw166.

Belmonte FR, Martin JL, Frescura K, Damas J, Pereira F, Tarnopolsky MA, Kaufman BA. Digital PCR methods improve detection sensitivity and measurement precision of low abundance mtDNA deletions. Scientific Reports. 2016. doi:10.1038/srep25186.

O'Connor R, Damas J, Farre M, Romanov MN, Martell H, Fonseka G, Jennings R, Kiazam L, Bennett S, Ward J, Mandawala A, Joseph S, Frodsham R, Lawrie M, Archibald AL, Walling GA, Fowler KE, Larkin DM, Griffin DK. Upgrading molecular cytogenetics to study reproduction and reproductive isolation in mammals, birds, and dinosaurs. Cytogenetic and Genome Research. 2016. 148(2):151-152. (conference proceedings)

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2015

Larkin DM, Farre M, Damas J. Comparative genomics in Third report on chicken genes and chromosomes 2015. Cytogenetic and Genome Research. 2015. 145 (2): 78-179 doi:10.1159/000430927. (book chapter)

Damas J, Farre M, Lithgow P, Romanov MN, Li C, Griffin DK, Larkin DM. Towards the construction of avian chromosome assemblies. Chromosome Research. 2015. 23(2):378-379. doi:10.1007/s10577-014-9447-3. (conference proceedings)

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2014

Damas J, Carneiro J, Amorim A, Pereira F. MitoBreak: The mitochondrial DNA breakpoints database. Nucleic Acids Research. 2014. 42 (D1): D1261-D1268 doi:10.1093/nar/gkt982.

 Damas J, Samuels DC, Carneiro J, Amorim A, Pereira F. Mitochondrial DNA rearrangements in health and disease - a comprehensive study. Human mutation. 2014. 35(1):1-14. doi: 10.1002/humu.22452.

Dong DW, Pereira F, Barrett SP, Kolesar JE, Cao K, Damas J, Yatsunyk LA, Johnson FB, Kaufman BA. Association of G-quadruplex forming sequences with human mtDNA deletion breakpoints. BMC Genomics. 2014. 15:677. doi:10.1186/1471-2164-15-677.

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2012

Damas J, Carneiro J, Gonçalves J, Stewart JB, Samuels DC, Amorim A, Pereira F. Mitochondrial DNA deletions are associated with non-B DNA conformations. Nucleic Acids Research. 2012. 40 (16): 7606-7621. doi:10.1093/nar/gks500.

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2011

Damas J, Amorim A, Gusmao L. InDels in Y chromosome haplogroup definition. Forensic Sci Int: Gen Supp Series. 2011. 3(1): e178-e179. doi:10.1016/j.fsigss.2011.08.089. (conference proceedings)