Publications

Dorothy Nevé Baker, Linelle Abueg, Merly Escalona, Katherine A Farquharson, Janet M Lanyon, Diana Le Duc, Torsten Schöneberg, Dominic Absolon, Ying Sims, Olivier Fedrigo, Erich D Jarvis, Katherine Belov, Carolyn J Hogg, Beth Shapiro, A chromosome-level genome assembly for the dugong (Dugong dugon), Journal of Heredity, Volume 115, Issue 2, March 2024, Pages 212–220, https://doi.org/10.1093/jhered/esae003  

Bukhman, Y.V., Meyer, S., Chu, LF. et al. Chromosome level genome assembly of the Etruscan shrew Suncus etruscus. Sci Data 11, 176 (2024). https://doi.org/10.1038/s41597-024-03011-x 

Siavash Mirarab, Iker Rivas-González, Shaohong Feng, Josefin Stiller, Qi Fang, Uyen Mai, Glenn Hickey, Guangji Chen, Nadolina Brajuka, Olivier Fedrigo, Giulio Formenti, Jochen B. W. Wolf, Kerstin Howe, Agostinho Antunes, Mikkel H. Schierup, Benedict Paten, Erich D. Jarvis, Guojie Zhang, and Edward L. Braun. Proceedings of the National Academy of SciencesVol. 121, No. 15. (2024). https://doi.org/10.1073/pnas.2319506121 

Volpe, E., Corda, L., Di Tommaso, E., Pelliccia, F., Ottalevi, R., Licastro, D., ... & Giunta, S. (2023). The complete human diploid reference genome of RPE-1 identifies the phased epigenetic landscapes from multi-omics data. bioRxiv, 2023- 11. https://doi.org/10.1101/2023.11.01.565049

Sendell-Price, A.T., Tulenko, F.J., Pettersson, M. et al. 2023 Low mutation rate in epaulette sharks is consistent with a slow rate of evolution in sharks. Nat Commun 14, 6628 . https://doi.org/10.1038/s41467-023-42238-x

Skorupski J, Brandes F, Seebass C, Festl W, Śmietana P, Balacco J, Jain N, Tilley T, Abueg L, Wood J, et al. Prioritizing Endangered Species in Genome Sequencing: Conservation Genomics in Action with the First Platinum-Standard Reference-Quality Genome of the Critically Endangered European Mink Mustela lutreola L., 1761. International Journal of Molecular Sciences. 2023; 24(19):14816. https://doi.org/10.3390/ijms241914816

Mc Cartney, A. M., Formenti, G., Mouton, A., De Panis, D., Marins, L. S., Leitão, H. G., ... & Pippel, M. (2023). The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics. bioRxiv, 2023-09. https://doi.org/10.1101/2023.09.25.559365

Sharaf, A., Ndiribe, C.C., Omotoriogun, T.C. et al. Bridging the gap in African biodiversity genomics and bioinformatics. Nat Biotechnol 41, 1348–1354 (2023). https://doi.org/10.1038/s41587-023-01933-2

Sozzoni, M., Ferrer Obiol, J., Formenti, G., Tigano, A., Paris, J. R., Balacco, J. R., ... & Rubolini, D. (2023). A chromosome-level reference genome for the black-legged kittiwake (Rissa tridactyla), a declining circumpolar seabird. Genome Biology and Evolution, 15(8), https://doi.org/10.1093/gbe/evad153

Rhie, A., Nurk, S., Cechova, M. et al. 2023 The complete sequence of a human Y chromosome. Nature 621, 344–354 https://doi.org/10.1038/s41586-023-06457-y

Lee, H., Greer, S. U., Pavlichin, D. S., Zhou, B., Urban, A. E., Weissman, T., ... & Paten, B. 2023. Pan-conserved segment tags identify ultra-conserved sequences across assemblies in the human pangenome. Cell Reports Methods,  DOI: 10.1016/j.crmeth.2023.100543

Theissinger, K., Fernandes. C., Formenti, G., Bista, I. et al. 2023. How genomics can help conservation. Trend in Genetics https://doi.org/10.1016/j.tig.2023.01.005

Marques, J. P., Alves, P. C., Amorim, I. R., Lopes, R. J., Moura, M., Meyers, G., ... & Sousa, V. C. (2023). Building a Portuguese Coalition for Biodiversity Genomics. https://doi.org/10.32942/X20W3Q

Uliano-Silva, M., Ferreira, J. G. R., Krasheninnikova, K., Formenti, G., Abueg, L., Torrance, J., ... & McCarthy, S. A. (2023). MitoHiFi: a python pipeline for mitochondrial genome assembly from PacBio high fidelity reads. BMC bioinformatics, 24(1), 288.doi: https://doi.org/10.1101/2022.12.23.521667

Smith, J., Alfieri, J. M., Anthony, N., Arensburger, P., Athrey, G. N., Balacco, J., ... & Zhou, H. (2023). Fourth report on chicken genes and chromosomes 2022. Cytogenetic and Genome Research, 162(8-9), 405-528. https://doi.org/10.1159/000529376

Larivière, D., Abueg, L., Brajuka, N., Gallardo-Alba, C., Grüning, B., Ko, B. J., ... & Formenti, G. (2023). Scalable, accessible, and reproducible reference genome assembly and evaluation in Galaxy. bioRxiv. https://www.biorxiv.org/content/10.1101/2023.06.28.546576v1

Liao, W. W., Asri, M., Ebler, J., Doerr, D., Haukness, M., Hickey, G., ... & Paten, B. (2023). A draft human pangenome reference. Nature, 617(7960), 312-324. In text

Porubsky, D., Vollger, M. R., Harvey, W. T., Rozanski, A. N., Ebert, P., Hickey, G., ... & Human Pangenome Reference Consortium. (2023). Gaps and complex structurally variant loci in phased genome assemblies. Genome Research, 33(4), 496-510. In text

PE, R. M., Squires, T. E., Formenti, G., Tracey, A., Abueg, L. A., Brajuka, N., ... & Magnusson, K. P. (2023). A Chromosome-Level Genome Assembly for the Rock Ptarmigan (Lagopus muta). https://doi.org/10.1101/2023.01.31.526508 

Sendell-Price, A.T., Tulenko, F.J., Pettersson, M. et al. Low mutation rate in epaulette sharks is consistent with a slow rate of evolution in sharks. Nat Commun 14, 6628 (2023). https://doi.org/10.1038/s41467-023-42238-x

Timoshevskaya, N, Eşkut, K. I, imoshevskiy, V.A. An improved sea lamprey (Petromyzon marinus) germline genome assembly illuminates the evolution of germline-specific chromosomes.  Cell Reports (in press)

Gabrielli, M.,  Benazzo, A., Biello, R., Ancona, L.,  Fuselli, S. et al. 2023. A high-quality reference genome for the critically endangered Aeolian wall lizard, Podarcis raffonei. Journal of Heredity, esad014, https://doi.org/10.1093/jhered/esad014

Al-Ajli, F. O. , Formenti, G., Olivier Fedrigo, O. et al. Genomic, genetic and phylogenetic evidence for a new falcon species using chromosome-level genome assembly of the gyrfalcon and population genomics. BioRxiv https://doi.org/10.1101/2023.02.12.525808

Bentley, B. P, Carrasco-Valenzuela, T., Ramos, E.K.S. et al. 2023.  Divergent sensory and immune gene evolution in sea turtles with contrasting demographic and life histories. PNAS. 120 (7) e2201076120. https://doi.org/10.1073/pnas.2201076120

Smith J, Alfieri JM, Anthony N, Arensburger P, Athrey GN, Balacco J, et al. 2023. Fourth Report on Chicken Genes and Chromosomes 2022. Cytogenet Genome Res. 2023 Jan 30.  https://doi.org/10.1159/000529376

Warren, W., Fedrigo, O., Tracey, A., Maso et al. 2023. Multiple chicken (Gallus gallus) genome references to advance genetic variation studies. Single haplotype chicken genome assemblies. Cytogenetic and Genome Research. https://doi.org/10.1159/000529376

Secomandi, S., Gallo, G.R., Sozzoni, M., Janucci, A. et al. 2023. A chromosome-level reference genome and pangenome for barn swallow population genomics. Cell Genomics. 2023 Jan 18;42(1):111992. https://doi.org/10.1016/j.celrep.2023.111992

Meyer, B., Moiron, M., Caswara, C., Chow, W. et al. 2023. Sex-specific changes in autosomal methylation rate in ageing common terns. Frontiers Ecology And Evolution. Volume 11 - 2023. https://doi.org/10.3389/fevo.2023.982443

Karawita, A.L.H., Cheng, Y., Keng Yih Chew, K.Y. et al. 2023. Swan genome and transcriptome; it is not all black and white.  Genome Biology 24, 13 (2023). https://doi.org/10.1186/s13059-022-02838-0

Cadena, D., Pabon, L., DoNascimiento, C., Abueg, L., Tiley, T., O-Toole, B., ... & Torres, M. (2023). A reference genome for the Andean cavefish Trichomycterus rosablanca (Siluriformes, Trichomycteridae): building genomic resources to study evolution in cave environments. bioRxiv, 2023-11. https://doi.org/10.1101/2023.11.11.566715

Mc Cartney AM, Shafin K, Alonge M, Bzikadze AV, Formenti G, Fungtammasan A, Howe K, Jain C, Koren S, Logsdon GA, Miga KH, Mikheenko A, Paten B, Shumate A, Soto DC, Sović I, Wood JMD, Zook JM, Phillippy AM, Rhie A.  2022. Chasing perfection: validation and polishing strategies for telomere-to-telomere genome assemblies. Nature Methods. 2022 Mar 31. https://www.nature.com/articles/s41592-022-01440-3

Nurk S, Koren S, Rhie A, Rautiainen M, Bzikadze AV, Mikheenko A, Vollger MR, Altemose N, Uralsky L, Gershman A, Aganezov S, Hoyt SJ, Diekhans M, Logsdon GA, Alonge M, Antonarakis SE, Borchers M, Bouffard GG, Brooks SY, Caldas GV, et al.  2022. The complete sequence of a human genome. Science. 2022 Apr;376(6588):44-53. https://www.science.org/doi/10.1126/science.abj6987

Formenti G, Rhie A, Walenz BP, Thibaud-Nissen F, Shafin K, Koren S, Myers EW, Jarvis ED, Phillippy AM. 2022.  Merfin: improved variant filtering, assembly evaluation and polishing via k-mer validation. Nature Methods. 2022 Mar 31.  https://doi.org/10.1038/s41592-022-01445-y

Lewin, H.A., Richards ,S., Aiden, E.L., Allende, M.L., Archibald, J.M., Bálint, M., Barker, K.B., Baumgartner, B., Belov, K., Bertorelle, G., Blaxter, M.L., Cai, J., Caperello, N.D., Carlson, K., Castilla‐Rubio, J.C., Chaw, S., Chen, L., Childers, A.K., Coddington, J.A., Conde, D.A., Corominas, M., Crandall, K.A., Crawford, A.J., DiPalma, F., Durbin, R., Ebenezer, T.E., Edwards, S.V., Fedrigo, O., Flicek, P., et al. 2022. The Earth BioGenome Project 2020: Starting the Clock. Proc Natl Acad Sci U S A. January 25, 2022 119 (4) e2115635118; https://doi.org/10.1073/pnas.2115635118

Formenti, G., Tehissinger, K., Fernandes, C., Bista, I., Bombarely, A., et al. 2022. The era of reference genomes in conservation genomics. Trends in Ecology & Evolution. Jan 24: https://doi.org/10.1016/j.tree.2021.11.008

Sahajpal, N.S., Lai, C.-Y.J., Hastie, A., Mondal, A.K., Dehkordi, S.R., van der Made, C., Fedrigo, O., Al-Ajli, F., Jalnapurkar, S., Kanagal-Shamanna, R., 2022. Optical genome mapping identifies rare structural variations as predisposition factors associated with severe COVID-19. iScience. 18; 25(2): 103760. https://dx.doi.org/10.1016%2Fj.isci.2022.103760

Hardwick, S.A., Hu, W.,  Joglekar, A., Fan, L., Collier, P.G. , Foord, C., Balacco, J., Lanjewar, S., McGuirk, M., Koopmans, F., Prjibelski ,A., Mikheenko, A., Belchikov, N., Jarroux, J., Palkovits, M., Luo, W., Milner, T.A., Ndhlovu, L.C., Smit, A.B., Trojanowski ,J.Q., Lee, V.M.Y., Fedrigo, O., Sloan, S.A., et al. 2022. Single-nuclei isoform RNA sequencing reveals combination patterns of transcript elements across human brain cell types. Nature Biotechnology. 2022 Mar 7.  https://doi.org/10.1038/s41587-022-01231-3

Cheng, H., Jarvis, E.D., Fedrigo, O., Koepfli, K.-P., Urban, L., Gemmell, N.J., Li, H., 2022. Robust haplotype-resolved assembly of diploid individuals without parental data.  Nature Biotechnology.  2022 Mar 24.  https://doi.org/10.1038/s41587-022-01261-x

Biegler, M.T., Fedrigo, O., Collier, P., Mountcastle, J., Haase, B., Tilgner, H.U., Jarvis, E.D., 2022. Induction of an immortalized songbird cell line allows for gene characterization and knockout by CRISPR-Cas9. Scientific reports. 2002, 2, 4369. https://doi.org/10.1038/s41598-022-07434-7

Palmada-Flores, M., Orkin, J. D., Haase, B., Mountcastle, J., Frost-Bertelsen, M., Fedrigo, O., Kuderna, L., Jarvis, E.D., Marques-Bonet, T. 2022. A high-quality, long-read genome assembly of the endangered ring-tailed lemur (Lemur catta). Gigascience. 2022, Volume 11. https://doi.org/10.1093/gigascience/giac026

Formenti, G., Abueg, L., Brajuka, A., Brajuka, N., Gallardo-Alba, C., Giani, A., Fedrigo, O. Jarvis, E.D. 2002. Gfastats: conversion, evaluation and manipulation of genome sequences using assembly graphs. Bioinformatics. btac460. https://doi.org/10.1093/bioinformatics/btac460

Paez, S., Kraus, R.H.S., Shapiro, B., Gilbert, M.T.P. , et al. 2022. Reference genomes for conservation. Science.  21 Jul 2022 Vol 377, Issue 6604 pp. 364-366. https://doi.org/10.1126/science.abm8127

Dahn, H.A., Mountcastle, J., Balacco, J., Winkler, S., Bista, I., Schmitt ,A.D., Pettersson ,O.V., Formenti ,G., Oliver, K., Smith, M., Tan W., Kraus, A., Mac S., Komoroske, L.M., Lama T., Crawford, A.J., Murphy, R.W., Brown, S., Scott, A.F., Morin, P.A., Jarvis, E.D., Fedrigo O. 2022. Benchmarking ultra-high molecular weight DNA preservation methods for long-read and long-range sequencing. Gigascience. Aug 10;11:giac068. https://doi.org/10.1093/gigascience/giac068

Kim, J., Lee, C., Ko, B.J., Yoo, D., Won, S., Phillippy, A., Fedrigo, O., Zhang, G., Howe, K., Wood, J., Durbin, R., Formenti, G., Brown, S., Cantin, L., Mello, C.V., Cho, S., Rhie, A., Kim, H., Jarvis, E.D. 2022. False gene and chromosome losses in genome assemblies caused by GC content variation and repeats. Genome Biology. Sep 27;23(1):204.  https://doi.org/10.1186/s13059-022-02765-0

Ko BJ, Lee C, Kim J, Rhie A, Yoo DA, Howe K, Wood J, Cho S, Brown S, Formenti G, Jarvis ED, Kim H. 2022. Widespread false gene gains caused by duplication errors in genome assemblies. Genome Biology. Sep 27;23(1):205. https://doi.org/10.1186/s13059-022-02764-1

Jarvis, E.D., Formenti, G., Rhie, A. et al. Semi-automated assembly of high-quality diploid human reference genomes. Nature 611, 519–531 (2022). https://doi.org/10.1038/s41586-022-05325-5

Toh, H., Yang C., Formenti G., Raja K., Yan L., Tracey A., Chow W., Howe, K., Bergeron, L.A., Zhang, G., Haase, B., Mountcastle, J., Fedrigo, O., Fogg, J., Kirilenko, B., Munegowda, C., Hiller, M., Jain, A. , DKihara, D., Rhie, A.,  Phillippy, A.M. , Swanson, S., P. Jiang, Clegg, D.O., Jarvis, E.D., Thomson, J.A., Stewart, R. , Chaisson, M.J.P., Bukhman, Y.V. 2022. A haplotype-resolved genome assembly of the Nile rat facilitates exploration of the genetic basis of diabetes. BMC Biology. 20: 245. https://doi.org/10.1186/s12915-022-01427-8

Webster, A.L.H., Sanders, M.A., Patel, K., Dietrch, R., Noonan, R.J. et al. 2022 Genomic signature of Fanconi anemia DNA repair pathway deficiency in cancer. Nature. https://doi.org/10.1038/s41586-022-05253-4

Mueller, R.C., Ellström, P., Howe, K., Uliano-Silva, M., Kuo, R.I., Miedzinska, K., Warr, A., Fedrigo, O., Haase, B., Mountcastle, J., Chow, W., Torrance, J., Wood, J., Järhult, J.D., Naguib, M.M., Olsen, B., Jarvis, E.D., Smith, J., Eöry, L., Kraus, R.H., 2021. A high-quality Genome and Comparison of Short versus Long Read Transcriptome of the Palaearctic duck Aythya fuligula (Tufted Duck).Gigascience 12. https://doi.org/10.1093/gigascience/giab081

Dussex, N., Van Der Valk, T., Morales, H.E., Wheat, C.W., Díez-del-Molino, D., Von Seth, J., Foster, Y., Kutschera, V.E., Guschanski, K., Rhie, A., Phillippy, A.M., JKorlach, J., Howe, K., Chow, W., Pelan, S., Mendes Damas, J.D., H.A., Hastie, A.R., Formenti .G., Fedrigo, O., Guhlin, J., et al. 2021. Population genomics of the critically endangered kākāpō. Cell Genomics 1, 100002. https://doi.org/10.1016/j.xgen.2021.100002

Hansen, T., Fjelldal, P.G., Lien, S., Smith, M., Corton, C., Oliver, K., Skelton, J., Betteridge, E., Doulcan, J., Fedrigo, O., Mountcastle, J., Jarvis, E.D., McCarthy, S.A., Chow, W., Howe, K., Torrance, J., Wood, J., et al. 2021. The genome sequence of the brown trout, Salmo trutta Linnaeus 1758. Wellcome Open Res 6, 108. https://doi.org/10.12688/wellcomeopenres.16838.1

Peart, C.R., Williams, C., Pophaly, S.D., Neely, B.A., Gulland, F.M., Adams, D.J., Ng, B.L., Cheng, W., Goebel, M.E., Fedrigo, O., et al.  2021. Hi‐C scaffolded short‐and long‐read genome assemblies of the California sea lion are broadly consistent for syntenic inference across 45 million years of evolution. Mol Ecol Resour 21, 2455-2470. https://doi.org/10.1111/1755-0998.13443

Joglekar, A., Prjibelski, A., Mahfouz, A., Collier, P., Lin, S., Schlusche, A.K., Marrocco, J., Williams, S.R., Haase, B., Hayes, A., Chew, J.G., Weisenfeld, N.I., Wong, M.Y., Stein, A.N., Hardwick, S.A., Hunt, T., Wang, Q., Dieterich, C., Bent, Z., Fedrigo, O., Sloan, S.A., Risso, D., Jarvis, E.D., Flicek, P., Luo, W., Pitt, G.S., Frankish, A., Smit, A.B., Ross, M.E., Tilgner, H.U., 2021. A spatially resolved brain region- and cell type-specific isoform atlas of the postnatal mouse brain. Nat Commun 12, 463. https://doi.org/10.1038/s41467-020-20343-5

Melin, A.D., Orkin, J.D., Janiak, M.C., Valenzuela, A., Kuderna, L., Marrone, F., Ramangason, H., Horvath, J.E., Roos, C., Kitchener, A.C., Khor, C.C., Lim, W.K., Lee, J.G.H., Tan, P., Umapathy, G., Raveendran, M., Alan Harris, R., Gut, I., Gut, M., Lizano, E., Nadler, T., Zinner, D., Le, M.D., Manu, S., Rabarivola, C.J., Zaramody, A., Andriaholinirina, N., Johnson, S.E., Jarvis, E.D., Fedrigo, O., Wu, D., Zhang, G., Farh, K.K.-H., Rogers, J., Marques-Bonet, T., Navarro, A., Juan, D., Arora, P.S., Higham, J.P., 2021. Variation in predicted COVID-19 risk among lemurs and lorises. Am J Primatol e23255. https://doi.org/10.1002/ajp.23255

Gedman, G., Haase, B., Durieux, G., Biegler, M.T., Fedrigo, O., Jarvis, E.D., 2021. As above, so below: Whole transcriptome profiling demonstrates strong molecular similarities between avian dorsal and ventral pallial subdivisions. J Comp Neurol. https://doi.org/10.1002/cne.25159

Rhie, A., McCarthy, S.A., Fedrigo, O., Joana Damas, Giulio Formenti, Sergey Koren, et al. 2021. Towards complete and error-free genome assemblies of all vertebrate species. Nature 592, 737–746. https://doi.org/10.1038/s41586-021-03451-0

Morin, P.A., Archer, F.I., Avila, C.D., Balacco, J.R., Bukhman, Y.V., Chow, W., Fedrigo, O., Formenti, G., Fronczek, J.A., Fungtammasan, A., Gulland, F.M.D., Haase, B., Peter Heide-Jorgensen, M., Houck, M.L., Howe, K., Misuraca, A.C., Mountcastle, J., Musser, W., Paez, S., Pelan, S., Phillippy, A., Rhie, A., Robinson, J., Rojas-Bracho, L., Rowles, T.K., Ryder, O.A., Smith, C.R., Stevenson, S., Taylor, B.L., Teilmann, J., Torrance, J., Wells, R.S., Westgate, A.J., Jarvis, E.D., 2021. Reference genome and demographic history of the most endangered marine mammal, the vaquita. Mol Ecol Resour 21, 1008–1020. https://doi.org/10.1111/1755-0998.13284

Yang, C., Zhou, Y., Marcus, S., Formenti, G., Bergeron, L.A., Song, Z., Bi, X., Bergman, J., Rousselle, M.M.C., Zhou, C., Zhou, L., Deng, Y., Fang, M., Xie, D., Zhu, Y., Tan, S., Mountcastle, J., Haase, B., Balacco, J., Wood, J., Chow, W., Rhie, A., Pippel, M., Fabiszak, M.M., Koren, S., Fedrigo, O., Freiwald, W.A., Howe, K., Yang, H., Phillippy, A.M., Schierup, M.H., Jarvis, E.D., Zhang, G., 2021. Evolutionary and biomedical insights from a marmoset diploid genome assembly. Nature https://doi.org/10.1038/s41586-021-03535-x

Kronenberg, Z.N., Rhie, A., Koren, S., Concepcion, G.T., Peluso, P., Munson, K.M., Porubsky, D., Kuhn, K., Mueller, K.A., Low, W.Y., Hiendleder, S., Fedrigo, O., Liachko, I., Hall, R.J., Phillippy, A.M., Eichler, E.E., Williams, J.L., Smith, T.P.L., Jarvis, E.D., Sullivan, S.T., Kingan, S.B., 2021. Extended haplotype-phasing of long-read de novo genome assemblies using Hi-C. Nat Commun 12, 1935. https://doi.org/10.1038/s41467-020-20536-y

Zhou, Y., Shearwin-Whyatt, L., Li, J., Song, Z., Hayakawa, T., Stevens, D., Fenelon, J.C., 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, S.D., Phillippy, A.M., Howe, K., Jarvis, E.D., Ryder, O.A., Kaessmann, H., Donnelly, P., Korlach, J., Lewin, H.A., Graves, J., Belov, K., Renfree, M.B., Grutzner, F., Zhou, Q., Zhang, G., 2021. Platypus and echidna genomes reveal mammalian biology and evolution. Nature 592, 756–762. https://doi.org/10.1038/s41586-020-03039-0

Jebb, D., Huang, Z., Pippel, M., Hughes, G.M., Lavrichenko, K., Devanna, P., Winkler, S., Jermiin, L.S., Skirmuntt, E.C., Katzourakis, A., Burkitt-Gray, L., Ray, D.A., Sullivan, K.A.M., Roscito, J.G., Kirilenko, B.M., Dávalos, L.M., Corthals, A.P., Power, M.L., Jones, G., Ransome, R.D., Dechmann, D.K.N., Locatelli, A.G., Puechmaille, S.J., Fedrigo, O., Jarvis, E.D., Hiller, M., Vernes, S.C., Myers, E.W., Teeling, E.C., 2020. Six reference-quality genomes reveal evolution of bat adaptations. Nature 583, 578–584. https://doi.org/10.1038/s41586-020-2486-3

Formenti, G., Rhie, A., Balacco, J., Haase, B., Mountcastle, J., Fedrigo, O., Brown, S., Capodiferro, M.R., Al-Ajli, F.O., Ambrosini, R., Houde, P., Koren, S., Oliver, K., Smith, M., Skelton, J., Betteridge, E., Dolucan, J., Corton, C., Bista, I., Torrance, J., Tracey, A., Wood, J., Uliano-Silva, M., Howe, K., McCarthy, S., Winkler, S., Kwak, W., Korlach, J., Fungtammasan, A., Fordham, D., Costa, V., Mayes, S., Chiara, M., Horner, D.S., Myers, E., Durbin, R., Achilli, A., Braun, E.L., Phillippy, A.M., Jarvis, E.D., 2021. Complete vertebrate mitogenomes reveal widespread repeats and gene duplications. Genome Biol 22, 120. https://doi.org/10.1186/s13059-021-02336-9

Morin, P.A., Alexander, A., Blaxter, M., Caballero, S., Fedrigo, O., Fontaine, M.C., Foote, A.D., Kuraku, S., Maloney, B., McCarthy, M.L., McGowen, M.R., Mountcastle, J., Nery, M.F., Olsen, M.T., Rosel, P.E., Jarvis, E.D., 2020. Building genomic infrastructure: Sequencing platinum‐standard reference‐quality genomes of all cetacean species. Mar Mam Sci 36, 1356–1366. https://doi.org/10.1111/mms.12721

Mead, D., Fingland, K., Cripps, R., Portela Miguez, R., Smith, M., Corton, C., Oliver, K., Skelton, J., Betteridge, E., Dolucan, J., Dudchenko, O., Omer, A.D., Weisz, D., Lieberman Aiden, E., Fedrigo, O., Mountcastle, J., Jarvis, E., McCarthy, S.A., Sims, Y., Torrance, J., Tracey, A., Howe, K., Challis, R., Durbin, R., Blaxter, M., 2020. The genome sequence of the Eurasian red squirrel, Sciurus vulgaris Linnaeus 1758. Wellcome Open Res 5, 18. https://doi.org/10.12688/wellcomeopenres.15679.1

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