Publications

2022

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. 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

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. 2022, 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

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.,False gene and chromosome losses in genome assemblies caused by GC content variation and repeats. Genome Biology. In press.

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. Benchmarking ultra-high molecular weight DNA preservation methods for long-read and long-range sequencing. Gigascience. In press.

Webster, A.L.H., Sanders, M.A., Patel, K., Dietrch, R., Noonan, R.J. et al. Genomic signature of Fanconi anemia DNA repair pathway deficiency in cancer. Nature. In press.

Jarvis, E.D., Formenti, G., Rhie. A., Guarracino, A., et al. Semi-automated assembly of high-quality diploid human reference genomes. Nature. In review.

2021

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

2020

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

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

Ray TA, Cochran KN, Kozlowski C, et al. Comprehensive identification of mRNA isoforms reveals massive diversity of neural cell-surface molecules with roles in retinal development and disease. Nat Commun 2020; 11(3328). https://doi.org/10.1038/s41467-020-17009-7

2019

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

2018

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. Nat Biotechnol. https://doi.org/10.1038/nbt.4259