Publications

Jonathan P Velotta, Azwad R Iqbal, Emma S Glenn, Ryan P Franckowiak, Giulio Formenti, Jacquelyn Mountcastle, Jennifer Balacco, Alan Tracey, Ying Sims, Kerstin Howe, Olivier Fedrigo, Erich D Jarvis, Nina O Therkildsen, A Complete Assembly and Annotation of the American Shad Genome Yields Insights into the Origins of Diadromy, Genome Biology and Evolution, Volume 17, Issue 1, January 2025, evae276, https://doi.org/10.1093/gbe/evae276

Giulio Formenti, Bonhwang Koo, Marco Sollitto, Jennifer Balacco, Nadolina Brajuka, Richard Burhans, Erick Duarte, Alice M. Giani, Kirsty McCaffrey, Jack A. Medico, Eugene W. Myers, Patrik Smeds, Anton Nekrutenko, Erich D. Jarvis. Evaluation of sequencing reads at scale using rdeval. bioRxiv 2025.02.01.636073; doi: https://doi.org/10.1101/2025.02.01.636073

Secomandi, S., Gallo, G.R., Rossi, R. et al. Pangenome graphs and their applications in biodiversity genomics. Nat Genet 57, 13–26 (2025). https://doi.org/10.1038/s41588-024-02029-6

Halpern B, Vörös J, Mc Cartney AM et al. The genome sequence of the Hungarian meadow viper, Vipera ursinii rakosiensis (Méhely, 1893) [version 2; peer review: 6 approved]. Wellcome Open Res 2025, 9:404 (https://doi.org/10.12688/wellcomeopenres.22694.2)

Geslain E, Volckaert FAM, Mc Cartney AM et al. The genome sequence of the common sole, Solea solea (Linnaeus, 1758) [version 1; peer review: 2 approved]. Wellcome Open Res 2025, 10:25 (https://doi.org/10.12688/wellcomeopenres.23353.1)

Al-Ajli, F.O., Formenti, G., Fedrigo, O. et al. 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 (2025). https://doi.org/10.1038/s41598-025-88216-9

Oomen, Rebekah A., Alessia Cariani, Louise Chavarie, Agostino Leone, Adriana Vella, Noel Vella, Gustav Hellström, Tomas Brodin, Andreas Sundelöf, Mark Blaxter, Ann M. Mc Cartney, Giulio Formenti, Alice Mouton, Fausto Tinti, Fulvio Garibaldi, and Petter Lundberg. 2025. “The Genome Sequence of Atlantic Bluefin Tuna, Thunnus Thynnus (Linnaeus, 1758).” Wellcome Open Research 10:163. doi: 10.12688/wellcomeopenres.23971.1.

Simmons, Nancy B., Melissa R. Ingala, Brian P. O’Toole, Linelle Abueg, Kirsty McCaffrey, Bonhwang Koo, Giulio Formenti, Erich D. Jarvis, Myrtani Pieri, Meike Mai, Larry N. Singh, Philge Philip, Laramie L. Lindsey, Ning Zhang, Jonathan L. Gray, Emma C. Teeling, and Sonja C. Vernes. 2025. “The Genome Sequence of Glossophaga Mutica (Chiroptera, Phyllostomidae, Glossophaginae; Merriam, 1898).” Wellcome Open Research 10:174. doi: 10.12688/wellcomeopenres.23611.1.

Simmons, Nancy B., Melissa R. Ingala, Brian P. O’Toole, Giulio Formenti, Philip Philge, Nina Zhang, Erich D. Jarvis, Jonathan L. Gray, Kirsty McCaffrey, Nadolina Brajuka, Myrtani Pieri, Meike Mai, Emma C. Teeling, and Sonja C. Vernes. 2025. “The Genome Sequence of Artibeus Lituratus (Chiroptera, Phyllostomidae, Stenodermatinae; Olfers, 1818).” Wellcome Open Research 10:170. doi: 10.12688/wellcomeopenres.23088.1.

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 

Simmons NB, Ingala MR, Pieri M et al. The genome sequence of Molossus alvarezi González-Ruiz, Ramírez-Pulido and Arroyo-Cabrales, 2011 (Chiroptera, Molossidae) [version 1; peer review: 2 approved]. Wellcome Open Res 2024, 9:522 (https://doi.org/10.12688/wellcomeopenres.22726.1) 

Formenti, Giulio. "Transposable Elements, Structural Variation, Telomeres, and Vertebrate Chromosome Evolution." Plant and Animal Genome Conference/PAG 31 (January 12-17, 2024). PAG, 2024.

Delphine Lariviere, Alex Ostrovsky, Cristóbal Gallardo, Anna Syme, Linelle Abueg, Brandon Pickett, Giulio Formenti, Marcella Sozzoni, Anton Nekrutenko, Vertebrate genome assembly using HiFi, Bionano and Hi-C data - Step by Step (Galaxy Training Materials). https://training.galaxyproject.org/training-material/topics/assembly/tutorials/vgp_genome_assembly/tutorial.html Online; accessed Thu Feb 27 2025

Yury V Bukhman, Phillip A Morin, Susanne Meyer, Li-Fang Chu, Jeff K Jacobsen, Jessica Antosiewicz-Bourget, Daniel Mamott, Maylie Gonzales, Cara Argus, Jennifer Bolin, Mark E Berres, Olivier Fedrigo, John Steill, Scott A Swanson, Peng Jiang, Arang Rhie, Giulio Formenti, Adam M Phillippy, Robert S Harris, Jonathan M D Wood, Kerstin Howe, Bogdan M Kirilenko, Chetan Munegowda, Michael Hiller, Aashish Jain, Daisuke Kihara, J Spencer Johnston, Alexander Ionkov, Kalpana Raja, Huishi Toh, Aimee Lang, Magnus Wolf, Erich D Jarvis, James A Thomson, Mark J P Chaisson, Ron Stewart, A High-Quality Blue Whale Genome, Segmental Duplications, and Historical Demography, Molecular Biology and Evolution, Volume 41, Issue 3, March 2024, msae036, https://doi.org/10.1093/molbev/msae036

Larivière, D., Abueg, L., Brajuka, N. et al. Scalable, accessible and reproducible reference genome assembly and evaluation in Galaxy. Nat Biotechnol 42, 367–370 (2024). https://doi.org/10.1038/s41587-023-02100-3

Aurélien De Jode, Rui Faria, Giulio Formenti, Ying Sims, Timothy P Smith, Alan Tracey, Jonathan M D Wood, Zuzanna B Zagrodzka, Kerstin Johannesson, Roger K Butlin, Erica H Leder, Chromosome-scale Genome Assembly of the Rough Periwinkle Littorina saxatilis, Genome Biology and Evolution, Volume 16, Issue 4, April 2024, evae076, https://doi.org/10.1093/gbe/evae076

S. Mirarab, I. Rivas-González, S. Feng, J. Stiller, Q. Fang, U. Mai, G. Hickey, G. Chen, N. Brajuka, O. Fedrigo, G. Formenti, J.B.W. Wolf, K. Howe, A. Antunes, M.H. Schierup, B. Paten, E.D. Jarvis, G. Zhang, & E.L. Braun, A region of suppressed recombination misleads neoavian phylogenomics, Proc. Natl. Acad. Sci. U.S.A. 121 (15) e2319506121, https://doi.org/10.1073/pnas.2319506121 (2024).

Justin Merondun et al. ,Evolution and genetic architecture of sex-limited polymorphism in cuckoos.Sci. Adv.10,eadl5255(2024).DOI:10.1126/sciadv.adl5255

Carlos Daniel Cadena, Laura Pabón, Carlos DoNascimiento, Linelle Abueg, Tatiana Tilley, Brian O-Toole, Dominic Absolon, Ying Sims, Giulio Formenti, Olivier Fedrigo, Erich D Jarvis, Mauricio Torres, A reference genome for the Andean cavefish Trichomycterus rosablanca (Siluriformes, Trichomycteridae): Building genomic resources to study evolution in cave environments, Journal of Heredity, Volume 115, Issue 3, May 2024, Pages 311–316, https://doi.org/10.1093/jhered/esae019

Alvarez van Tussenbroek I, Knörnschild M, Nagy M et al. The genome sequence of Rhynchonycteris naso, Peters, 1867 (Chiroptera, Emballonuridae, Rhynchonycteris) [version 1; peer review: 3 approved]. Wellcome Open Res 2024, 9:361 (https://doi.org/10.12688/wellcomeopenres.19959.1)

Canesin, L.E.C., Vilaça, S.T., Oliveira, R.R.M. et al. A reference genome for the Harpy Eagle reveals steady demographic decline and chromosomal rearrangements in the origin of Accipitriformes. Sci Rep 14, 19925 (2024). https://doi.org/10.1038/s41598-024-70305-w

Simmons NB, Ingala MR, Pieri M et al. The genome sequence of Molossus alvarezi González-Ruiz, Ramírez-Pulido and Arroyo-Cabrales, 2011 (Chiroptera, Molossidae) [version 1; peer review: 2 approved]. Wellcome Open Res 2024, 9:522 (https://doi.org/10.12688/wellcomeopenres.22726.1)

Marques, J.P., Alves, P.C., Amorim, I.R. et al. Building a Portuguese coalition for biodiversity genomics. npj biodivers 3, 27 (2024). https://doi.org/10.1038/s44185-024-00061-7

Mc Cartney, A.M., Formenti, G., Mouton, A. et al. The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics. npj biodivers 3, 28 (2024). https://doi.org/10.1038/s44185-024-00054-6

DongAhn Yoo, Arang Rhie, Prajna Hebbar, Francesca Antonacci, Glennis A. Logsdon, Steven J. Solar, Dmitry Antipov, Brandon D. Pickett, Yana Safonova, Francesco Montinaro, Yanting Luo, Joanna Malukiewicz, Jessica M. Storer, Jiadong Lin, Abigail N. Sequeira, Riley J. Mangan, Glenn Hickey, Graciela Monfort Anez, Parithi Balachandran, Anton Bankevich, Christine R. Beck, Arjun Biddanda, Matthew Borchers, Gerard G. Bouffard, Emry Brannan, Shelise Y. Brooks, Lucia Carbone, Laura Carrel, Agnes P. Chan, Juyun Crawford, Mark Diekhans, Eric Engelbrecht, Cedric Feschotte, Giulio Formenti, Gage H. Garcia, Luciana de Gennaro, David Gilbert, Richard E. Green, Andrea Guarracino, Ishaan Gupta, Diana Haddad, Junmin Han, Robert S. Harris, Gabrielle A. Hartley, William T. Harvey, Michael Hiller, Kendra Hoekzema, Marlys L. Houck, Hyeonsoo Jeong, Kaivan Kamali, Manolis Kellis, Bryce Kille, Chul Lee, Youngho Lee, William Lees, Alexandra P. Lewis, Qiuhui Li, Mark Loftus, Yong Hwee Eddie Loh, Hailey Loucks, Jian Ma, Yafei Mao, Juan F. I. Martinez, Patrick Masterson, Rajiv C. McCoy, Barbara McGrath, Sean McKinney, Britta S. Meyer, Karen H. Miga, Saswat K. Mohanty, Katherine M. Munson, Karol Pal, Matt Pennell, Pavel A. Pevzner, David Porubsky, Tamara Potapova, Francisca R. Ringeling, Joana L. Rocha, Oliver A. Ryder, Samuel Sacco, Swati Saha, Takayo Sasaki, Michael C. Schatz, Nicholas J. Schork, Cole Shanks, Linnéa Smeds, Dongmin R. Son, Cynthia Steiner, Alexander P. Sweeten, Michael G. Tassia, Françoise Thibaud-Nissen, Edmundo Torres-González, Mihir Trivedi, Wenjie Wei, Julie Wertz, Muyu Yang, Panpan Zhang, Shilong Zhang, Yang Zhang, Zhenmiao Zhang, Sarah A. Zhao, Yixin Zhu, Erich D. Jarvis, Jennifer L. Gerton, Iker Rivas-González, Benedict Paten, Zachary A. Szpiech, Christian D. Huber, Tobias L. Lenz, Miriam K. Konkel, Soojin V. Yi, Stefan Canzar, Corey T. Watson, Peter H. Sudmant, Erin Molloy, Erik Garrison, Craig B. Lowe, Mario Ventura, Rachel J. O’Neill, Sergey Koren, Kateryna D. Makova, Adam M. Phillippy, Evan E. Eichler, bioRxiv 2024.07.31.605654; doi: https://doi.org/10.1101/2024.07.31.605654

Rincon-Sandoval, M., De-Kayne, R., Shank, S.D. et al. Ecological diversification of sea catfishes is accompanied by genome-wide signatures of positive selection. Nat Commun 15, 10040 (2024). https://doi.org/10.1038/s41467-024-54184-3

Nash, W.J., Man, A., McTaggart, S. et al. The genome sequence of the Violet Carpenter Bee, Xylocopa violacea (Linnaeus, 1785): a hymenopteran species undergoing range expansion. Heredity 133, 381–387 (2024). https://doi.org/10.1038/s41437-024-00720-2

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

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