Publications
✻ co-first author, ◆ corresponding author
95 publications; h-index= 38, i10-index= 67
2025 (1)
Biegler, M.T., Belay, B. , Wei Wang, W. , Szi, C. et al. (2025) Pronounced early differentiation underlies zebra finch gonadal germ cell development. Dev. Bio, January 2025, 527:3-90 https://doi.org/10.1016/j.ydbio.2024.08.006
2024 (15)
Baker, N. , Abueg, L., Escalona, M. , Farquharson, K.A. et al. (2023) A chromosome-level genome assembly for the dugong (Dugong dugon). J. Hered. https://doi.org/10.1093/jhered/esae003
Larivière, D., Abueg , L., Brajuka, N., Gallardo-Alba, C., Grüning, B., Ko, B.J., Ostrovsky, A. et al. (2024) Scalable, accessible, and reproducible reference genome assembly and evaluation in Galaxy. Nat Biotechnol. https://doi.org/10.1038/s41587-023-02100-3
Bukhman, Y., Meyer, S., Chu, L-F., Abueg, L. , Antosiewicz-Bourget , J. et al. (2024) Chromosome-level genome assembly of the Etruscan shrew, Suncus etruscus. Sci Data. 11(1):176. https://doi.org/10.1038/s41597-024-03011-x
Bukhman, Y., Morin, P. A., Meyer, S., Li-Fang Chu, L-F et al. (2024) A high-quality blue whale genome, segmental duplications, and historical demography, Mol. Biol. Evol, Volume 41, Issue 3, March 2024, msae036, https://doi.org/10.1093/molbev/msae036
Mirahab, S., Rivas-Gonzalez, I., Feng, S., Stiller, J. et al. (2024) A region of suppressed recombination misleads neoavian phylogenomics. PNAS. 121 (15) e2319506121. https://doi.org/10.1073/pnas.2319506121
Joglekar, A., Hu, W., Zhang, B., Narykov, O. et al. Single-cell long-read mRNA isoform regulation is pervasive across mammalian brain regions, cell types, and development. Nat Neuro. Apr 9. https://doi.org/10.1038/s41593-024-01616-4
Merondun, J., Marques, C.I., Andrade, P., Meshcheryagin, S. et al. (2024) Genetic architecture and evolutionary maintenance of sex-limited polymorphism in cuckoos. Sci. Adv. In press Sci. Adv. 10 eadl5255. https://doi.org/10.1126/sciadv.adl5255
Sebastianelli, M., Lukhele, S.M., Secomandi, S. et al. (2024) A genomic basis of vocal rhythm in birds. Nat Commun. 15, 3095. https://doi.org/10.1038/s41467-024-47305-5
Cadena, D. , Pabon, L. , DoNascimiento, C. et al. (2024) A reference genome for the Andean cavefish Trichomycterus rosablanca (Siluriformes, Trichomycteridae): building genomic resources to study evolution in cave environments. Journal of Heredity. esae019, https://doi.org/10.1093/jhered/esae019
Canesin, L.E.C., Vilaça, S.T., Oliveira, R.R.M. et al. (2024) A reference genome for the Harpy Eagle reveals steady demographic decline and chromosomal rearrangements in the origin of Accipitriformes. Sci Rep 14, 19925 https://doi.org/10.1038/s41598-024-70305-w
Ishigohoka, J., Bascón-Cardozo, K., Bours, et al. (2024) Distinct patterns of genetic variation at low-recombining genomic regions represent haplotype structure. Evolution; qpae117 https://doi.org/10.1093/evolut/qpae117
Al-Ajli, F. O. , Formenti, G., 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
Laso-Jadart , R., Corrigan , S., Yang , L., Lee , A. et al. The checkered past of the world’s white shark populations. In revision
Velotta, J. P., Iqbal, A., Glenn, E. S., Franckowiak, R. P. et al. A complete assembly of the American shad genome and insights into the origins of diadromy. Draft
Lesturgie, P., Denton, J., Yang, L., Corrigan, S. et al. A size-determining supergene hampers a vulnerable population recovery. Draft
2023 (19)
Liao, W-W, Asri, M., Ebler, J. , Doerr, D. et al. (2023) A draft human pangenome reference. Nature. 17, 312–324. https://doi.org/10.1038/s41586-023-05896-x
Guarracino, A., Buonaiuto, S., de Lima, L.G. et al. (2023) Recombination between heterologous human acrocentric chromosomes. Nature. 617(7960):335-343. https://doi.org/10.1038/s41586-023-05976-y
Vollger ,M.R., Dishuck, P.C., Harvey, W.T., DeWitt, W.S. et al. (2023) Increased mutation and gene conversion within human segmental duplications. Nature. 617(7960):325-334. https://doi.org/10.1038/s41586-023-05895-y
Hickey, G., Monlong, J., Ebler, J., Novak, A.M. et al. (2023) Pangenome graph construction from genome alignments with Minigraph-Cactus. Nat Biotechnol. https://doi.org/10.1038/s41587-023-01793-w
Porubsky, D., Vollger, M.R., Harvey, W.T., Rozanski, A.N. et al. (2023) Gaps and complex structurally variant loci in phased genome assemblies. Genome Res. 33: 496-510. https://www.genome.org/cgi/doi/10.1101/gr.277334.122
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
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
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
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
Theissinger, K., Fernandes. C., Formenti, G., Bista, I. et al. (2023) How genomics can help conservation. Trend in Genetics S0168-9525(23)00020-3. https://doi.org/10.1016/j.tig.2023.01.005
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
Timoshevskaya, N, Eşkut, K. I, Timoshevskiy, V.A. et al. (2023) An improved sea lamprey (Petromyzon marinus) germline genome assembly illuminates the evolution of germline-specific chromosomes. Cell Reports. 42(3):112263. https://doi.org/10.1016/j.celrep.2023.112263
Skorupski, J., Brandes, F., Seebass, C., Festl, W., Śmietana, P., Balacco, J., Jain, N.; Tilley, T., Abueg, L.; Wood, J.;, Sims, Y., Formenti, G., Fedrigo O., Jarvis, E.D. (2023) 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. Int. J. Mol. Sci. 2023, 24, 14816. https://doi.org/10.3390/ijms241914816
Lee, H., Greer, S.U., Oavlichin, D.S., Zhou, B., Urban, A.E., Weissman, T. and the Human Pangenome Reference Consortium. (2023) Pan-conserved segment tags identify ultra-conserved sequences across assemblies in the human pangenome, Cell Reports Methods, Volume 3, Issue 8, 2023, 100543, ISSN 2667-2375, https://doi.org/10.1016/j.crmeth.2023.100543
Bond, D.M., Ortega-Recalde, O., Laird, M.K. et al. (2023) The admixed brushtail possum genome reveals invasion history in New Zealand and novel imprinted genes. Nat Commun 14, 6364. https://doi.org/10.1038/s41467-023-41784-8
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
Rice, E.S., Alberdi, A., Alfieri, J. et al. (2023) A pangenome graph reference of 30 chicken genomes allows genotyping of large and complex structural variants. BMC Biol 21, 267. https://doi.org/10.1186/s12915-023-01758-0
Lee ,YH, Abueg L, Kim , JK, Kim ,YW, Fedrigo, O. et al. (2023) Chromosome-level genome assembly of chub mackerel (Scomber japonicus) from the Indo-Pacific Ocean. Sci Data Dec 8;10(1):880. https://doi.org/10.1038/s41597-023-02782-z
2022 (14)
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. (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
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
Jarvis, E.D., Formenti, G. , Rhie, A., Guarracino, A. , Yang, C. , Wood, J., Tracy, A., Thibaud-Nissen, F. , Vollger, M. R. , Porubsky, D., Cheng, H., Asri, M., Logsdon, G. A.. Carnevali, P. , Chaisson, M. J. P. , Chin, C.-S. , Cody, S., Collins, J., Ebert, P., Escalona, M., Fedrigo, O., Fulton, R. S. et al. (2022) Semi-automated assembly of high-quality diploid human reference genomes. Nature. 611, 519–531. https://doi.org/10.1038/s41586-022-05325-5
Webster, A.L., Sanders, M.A., Patel, K., Dietrich, R,. Noonan, R.J., Lach, F.P., White, R.R., Goldfarb, A., Hadi, K., Edwards, M.M., Donovan, F.X,. Jung, M., Sridhar, S., Fedrigo, O., Tian, H., et al. (2022). Fanconi Anemia Pathway Deficiency Drives Copy Number Variation in Squamous Cell Carcinomas. Nature. 612, 495–502 (2022). https://doi.org/10.1038/s41586-022-05253-4
Formenti, G, Abueg, L., Brajuka, A., Brajuka, N., Gallardo-Alba, C., Giani, A., Fedrigo, O., Jarvis E.D. (2022) 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., Al-Ajli, F.O., Ceballos, G., Crawford, A.J., Fedrigo, O., Finnegan, S., 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., and Fedrigo O.◆ (2022) Benchmarking ultra-high molecular weight DNA preservation methods for long-read and long-range sequencing. Gigascience Volume 11, 2022, giac068. https://doi.org/10.1093/gigascience/giac068
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 Volume 11, 2022, giac026. https://doi.org/10.1093/gigascience/giac026
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. 2, 4369. https://doi.org/10.1038/s41598-022-07434-7
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. https://doi.org/10.1038/s41587-022-01261-x
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 https://doi.org/10.1038/s41587-022-01231-3
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) Host genome analysis of structural variations by Optical Genome Mapping provides clinically valuable insights into genes implicated in critical immune, viral infection, and viral replication pathways in patients with severe COVID-19. iScience 18; 25(2): 103760. https://dx.doi.org/10.1016%2Fj.isci.2022.103760
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 January 24. https://doi.org/10.1016/j.tree.2021.11.008
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. PNAS January 25, 2022 119 (4) e2115635118. https://doi.org/10.1073/pnas.2115635118
2021 (13)
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 Research 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. Molecular Ecology Resources 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. Nature Communications 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. American Journal of Primatology 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. The Journal of Comparative Neurology Volume529, Issue12 August 202 pp. 3222-3246 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. Molecular Ecology Resources 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. Nature Communications 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
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 Biology 22, 120. https://doi.org/10.1186/s13059-021-02336-9
2020 (5)
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
Ray, T.A., Cochran, K., Kozlowski, C., Wang, J., Alexander, G., Cady, M.A., Spencer, W.J., Ruzycki, P.A., Clark, B.S., Laeremans, A., He, M.-X., Wang, X., Park, E., Hao, Y., Iannaccone, A., Hu, G., Fedrigo, O., Skiba, N.P., Arshavsky, V.Y., Kay, J.N. (2020) Comprehensive identification of mRNA isoforms reveals the diversity of neural cell-surface molecules with roles in retinal development and disease. Nature Communications 11, 3328. https://doi.org/10.1038/s41467-020-17009-7
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. Marine Mammal Science 36, 1356–1366. https://doi.org/10.1111/mms.12721
da Fonseca, R.R., Couto, A., Machado, A.M., Brejova, B., Albertin, C.B., Silva, F., Gardner, P., Baril, T., Hayward, A., Campos, A., Ribeiro, Â.M., Barrio-Hernandez, I., Hoving, H.-J., Tafur-Jimenez, R., Chu, C., Frazão, B., Petersen, B., Peñaloza, F., Musacchia, F., Alexander, G.C., Osório, H., Winkelmann, I., Simakov, O., Rasmussen, S., Rahman, M.Z., Pisani, D., Vinther, J., Jarvis, E., Zhang, G., Strugnell, J.M., Castro, L.F.C., Fedrigo, O., Patricio, M., Li, Q., Rocha, S., Antunes, A., Wu, Y., Ma, B., Sanges, R., Vinar, T., Blagoev, B., Sicheritz-Ponten, T., Nielsen, R., Gilbert, M.T.P. (2020) A draft genome sequence of the elusive giant squid, Architeuthis dux. Gigascience 9. https://doi.org/10.1093/gigascience/giz152
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 Research 5, 18. https://doi.org/10.12688/wellcomeopenres.15679.1
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Jung, K.M., Kim, Y.M., Keyte, A.L., Biegler, M.T., Rengaraj, D., Lee, H.J., Mello, C.V., Velho, T.A.F., Fedrigo, O., Haase, B., Jarvis, E.D., Han, J.Y. (2019) Identification and characterization of primordial germ cells in a vocal learning Neoaves species, the zebra finch. FASEB J 33, 13825–13836. https://doi.org/10.1096/fj.201900760RR
Gupta, I., Collier, P.G., Haase, B., Mahfouz, A., Joglekar, A., Floyd, T., Koopmans, F., Barres, B., Smit, A.B., Sloan, S.A., Luo, W., Fedrigo, O., Ross, M.E., Tilgner, H.U. (2018) Single-cell isoform RNA sequencing characterizes isoforms in thousands of cerebellar cells. Nature Biotechnology https://doi.org/10.1038/nbt.4259
Ganapathy, G., Howard, J.T., Ward, J.M., Li, J., Li, B., Li, Y., Xiong, Y., Zhang, Y., Zhou, S., Schwartz, D.C., Schatz, M., Aboukhalil, R., Fedrigo, O., Bukovnik, L., Wang, T., Wray, G., Rasolonjatovo, I., Winer, R., Knight, J.R., Koren, S., Warren, W.C., Zhang, G., Phillippy, A.M., Jarvis, E.D. (2014) High-coverage sequencing and annotated assemblies of the budgerigar genome. Gigascience 3, 11. https://doi.org/10.1186/2047-217X-3-11
Horvath, J.E., Ramachandran, G.L., Fedrigo, O., Nielsen, W.J., Babbitt, C.C., St Clair, E.M., Pfefferle, L.W., Jernvall, J., Wray, G.A., Wall, C.E. (2014) Genetic comparisons yield insight into the evolution of enamel thickness during human evolution. Journal of Human Evolution 73, 75–87. https://doi.org/10.1016/j.jhevol.2014.01.005
Guo, X., Zheng, S., Dang, H., Pace, R.G., Stonebraker, J.R., Jones, C.D., Boellmann, F., Yuan, G., Haridass, P., Fedrigo, O., Corcoran, D.L., Seibold, M.A., Ranade, S.S., Knowles, M.R., O’Neal, W.K., Voynow, J.A. (2014) Genome reference and sequence variation in the large repetitive central exon of human MUC5AC. American Journal of Respiratory Cell and Molecular Biology 50, 223–232. https://doi.org/10.1165/rcmb.2013-0235OC
Ousterout, D.G., Perez-Pinera, P., Thakore, P.I., Kabadi, A.M., Brown, M.T., Qin, X., Fedrigo, O., Mouly, V., Tremblay, J.P., Gersbach, C.A. (2013) Reading frame correction by targeted genome editing restores dystrophin expression in cells from Duchenne muscular dystrophy patients. Molecular Therapy 21, 1718–1726. https://doi.org/10.1038/mt.2013.111
Shibata, Y., Sheffield, N.C., Fedrigo, O., Babbitt, C.C., Wortham, M., Tewari, A.K., London, D., Song, L., Lee, B.-K., Iyer, V.R., Parker, S.C.J., Margulies, E.H., Wray, G.A., Furey, T.S., Crawford, G.E., 2012. Extensive evolutionary changes in regulatory element activity during human origins are associated with altered gene expression and positive selection. PLOS Genetics 8, e1002789. https://doi.org/10.1371/journal.pgen.1002789
Fedrigo, O., Pfefferle, A.D., Babbitt, C.C., Haygood, R., Wall, C.E., Wray, G.A. (2011) A potential role for glucose transporters in the evolution of human brain size. Brain, Behavior and Evolution 78, 315–326. https://doi.org/10.1159/000329852
Pfefferle, A.D., Warner, L.R., Wang, C.W., Nielsen, W.J., Babbitt, C.C., Fedrigo, O., Wray, G.A. (2011) Comparative expression analysis of the phosphocreatine circuit in extant primates: Implications for human brain evolution. Journal of Human Evolution 60, 205–212. https://doi.org/10.1016/j.jhevol.2010.10.004
Babbitt, C.C., Warner, L.R., Fedrigo, O., Wall, C.E., Wray, G.A. (2011) Genomic signatures of diet-related shifts during human origins. Proceedings of the Royal Society B - Biological Sciences 278, 961–969. https://doi.org/10.1098/rspb.2010.2433
Cruz-Gordillo, P., Fedrigo, O., Wray, G.A., Babbitt, C.C. (2010) Extensive changes in the expression of the opioid genes between humans and chimpanzees. Brain, Behavior and Evolution 76, 154–162. https://doi.org/10.1159/000320968
Fedrigo, O., Warner, L.R., Pfefferle, A.D., Babbitt, C.C., Cruz-Gordillo, P., Wray, G.A. (2010) A pipeline to determine RT-QPCR control genes for evolutionary studies: application to primate gene expression across multiple tissues. PLOS One 5. https://doi.org/10.1371/journal.pone.0012545
Haygood, R., Babbitt, C.C., Fedrigo, O., Wray, G.A. (2010) Contrasts between adaptive coding and noncoding changes during human evolution. PNAS 107, 7853–7857. https://doi.org/10.1073/pnas.0911249107
Babbitt, C.C., Fedrigo, O., Pfefferle, A.D., Boyle, A.P., Horvath, J.E., Furey, T.S., Wray, G.A. (2010) Both noncoding and protein-coding RNAs contribute to gene expression evolution in the primate brain. Genome Biology and Evolution 2, 67–79.
Fedrigo, O., Wray, G.A. (2010) Developmental evolution: how beetles evolved their shields. Current Biology 20, R64-66. https://doi.org/10.1016/j.cub.2009.12.012
Tung, J., Fedrigo, O., Haygood, R., Mukherjee, S., Wray, G.A. (2009) Genomic Features That Predict Allelic Imbalance in Humans Suggest Patterns of Constraint on Gene Expression Variation. Molecular Biology and Evolution 26, 2047–2059. https://doi.org/10.1093/molbev/msp113
Haygood, R., Fedrigo, O., Wray, G.A. (2008) Reply to “Rapidly evolving human promoter regions.” Nature Genetics 40, 1263–1264. https://doi.org/10.1038/ng1108-1263
Haygood, R.✻, Fedrigo, O.✻, Hanson, B., Yokoyama, K.-D., Wray, G.A. (2007) Promoter regions of many neural- and nutrition-related genes have experienced positive selection during human evolution. Nature Genetics 39, 1140–1144. https://doi.org/10.1038/ng2104
Sodergren, E., Weinstock, G.M., Davidson, E.H., et al. (2006) The genome of the sea urchin Strongylocentrotus purpuratus. Science 314, 941–952. https://doi.org/10.1126/science.1133609
López, J.A., Ryburn, J.A., Fedrigo, O., Naylor, G.J.P. (2006) Phylogeny of sharks of the family Triakidae (Carcharhiniformes) and its implications for the evolution of carcharhiniform placental viviparity. Molecular Phylogenetic and Evolution 40, 50–60. https://doi.org/10.1016/j.ympev.2006.02.011
Fedrigo, O., Adams, D.C., Naylor, G.J.P. (2005) DRUIDS--detection of regions with unexpected internal deviation from stationarity. Journal of Experimental Zoology part B: Molecular and Developmental Evolution 304, 119–128. https://doi.org/10.1002/jez.b.21032
Naylor, G.J.P. , JRyburn, J.A., Fedrigo, O., Lopez, A. (2005) Phylogenetic Relationships among the major lineages of modern Elasmobranchs, in: Reproductive Biology and Phylogeny of Chondrichthyans (Sharks, Skates, Stingrays and Chimaeras). Univ. Queensland Press, pp. 1–25.
Collins, T.M., Fedrigo, O., Naylor, G.J.P. (2005) Choosing the Best Genes for the Job: The Case for Stationary Genes in Genome-Scale Phylogenetics. Systematic Biology 54, 493–500. https://doi.org/10.1080/10635150590947339
Fedrigo, O., Naylor, G. (2004) A gene-specific DNA sequencing chip for exploring molecular evolutionary change. Nucleic Acids Research 32, 1208–1213. https://doi.org/10.1093/nar/gkh210
Savolainen, V., Chase, M.W., Salamin, N., Soltis, D.E., Soltis, P.S., López, A.J., Fedrigo, O., Naylor, G.J.P., (2002) Phylogeny Reconstruction and Functional Constraints in Organellar Genomes: Plastid atpB and rbcL Sequences Versus Animal Mitochondrion. Systematic Biology 51, 638–647. https://doi.org/10.1080/10635150290102348
Baccam, P., Thompson, R.J., Fedrigo, O., Carpenter, S., Cornette, J.L. (2001) PAQ: Partition Analysis of Quasispecies. Bioinformatics 17, 16–22. https://doi.org/10.1093/bioinformatics/17.1.16
Tavaré, S., Adams, D.C., Fedrigo, O., Naylor, G.J. (2001) A model for phylogenetic inference using structural and chemical covariates. Pacific Symposium Biocomputing 215–225. https://doi.org/10.1142/9789814447362_0022
Fedrigo, O., Meunier, F.J., Duhamel, G., Sire, J.-Y. (1996) Morphological and histological study of scutes in Macroramphosidae (Teleostei, Gasterostéiformes). Cahiers de biologie marine 37, 189–204.