Publications

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

Zhou, Y, Jin, J., Xuemei Li, Gedman, G., Pelan, S., et al. Arang Rhie (2025) Chromosome-level echidna genome illuminates evolution of multiple sex chromosome system in monotremes, GigaScience, Volume 14, 2025, giae112, https://doi.org/10.1093/gigascience/giae112

Lesturgie, P., Denton, J., Yang, L., Corrigan, S. et al. Short-term evolutionary implications of an introgressed size-determining supergene in a vulnerable population. Nat. Commun. 16, 1096 (2025). https://doi.org/10.1038/s41467-025-56126-z

Velotta, J. P., Iqbal, A., Glenn, E. S., Franckowiak, R. P. et al. (2025) A complete assembly and annotation of the American shad genome yields insights into the origins of diadromy. GBE, Volume 17, Issue 1, January 2025, evae276, https://doi.org/10.1093/gbe/evae276

Al-Ajli, F.O., Formenti, G., Fedrigo, O. et al. (2025) Chromosome-level reference genome assembly of the gyrfalcon (Falco rusticolus) and population genomics offer insights into the falcon population in Mongolia. Sci Rep 15, 4154 . https://doi.org/10.1038/s41598-025-88216-9

Fontsere, C., Samuel A. Speak, S. A., Caven, A. J., et al. Persistent genomic erosion in whooping cranes despite demographic recovery. bioRxiv https://www.biorxiv.org/content/10.1101/2024.12.12.628160v1

Lee, S-H.,  Fedrigo, O., Soler-Clavel, L. et al. Insights into the Evolution of Ancient Shark and Ray Sex Chromosomes.  bioRxiv https://doi.org/10.1101/2025.02.26.637739

Laso-Jadart , R.,  Corrigan , S., Yang , L.,  Lee , A. et al. The checkered past of the world’s white shark populations. (In revision)

Kosch, T.A., Berger, L., Crawford, A.J., Gilbert, D.. et al. A chromosome-level reference genome for the critically endangered southern corroboree frog (Pseudophryne corroboree).  (In revision)

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

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

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 

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 

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.