Publications

Trainee time of publication: postdoctoral fellow#, graduate student*, undergraduate student^

    1. Guzman-Torres, C.R.^, Trybulec, E.§ ^, LeVasseur*, H.§ ^, Akella, H., Amee, M., Strickland, E., Pauloski, N., Williams, M., Romero-Severson, J., Hoban, S., Woeste, K., Pike, C.C., Karl C. Fetter, K.C.**, Webster, C.N.**, Neitzey, M.L.** *, O’Neill, R.J.**, Wegrzyn, J.L.** 2024. Conserving a threatened North American walnut: a chromosome-scale reference genome for butternut (Juglans cinerea) G3 Genes|Genomes|Genetics, Volume 14, Issue 2, February 2024, doi: 10.1093/g3journal/jkad189 § co-first author, **co-senior author
    2. Escalona M., VanCampen J., Maurer N.W., Haukness M., Okhovat M., Harris R.S., Watwood A., Hartley G.A., O'Neill R.J., Medvedev P., Makova K.D., Vollmers C., Carbone L., Green R.E.. Whole-genome sequence and assembly of the Javan gibbon (Hylobates moloch). J Hered. 2023 Mar 16;114(1):35-43. doi: 10.1093/jhered/esac043. PMID: 36146896; PMCID: PMC10019027.
    3. Castellano, K.R.*, Batta-Lona, P., Bucklin, A., O’Neill, R.J. 2023. Salps in Bloom: Genomics of Salpa thompsoni and Salpa aspera reveal complex genomic features and true hermaphroditic life phases. Scientific Advances 13, 21056. DOI: 1038/s41598-023-47429-6
    4. McEvoy, S.L., Grady, P.G.S.*, Pauloski, N., O’Neill, R.J., Wegrzyn, J.L. Profiling genome-wide methylation in two maples: fine-scale approaches to detection with nanopore technology.bioRxiv 2022.08.02.502577; doi: https://doi.org/10.1101/2022.08.02.502577; Evolutionary Applications In press
    5. Koga, A., Nishihara, H., Tanabe, H., Tanaka, R., Kayano, R., Matsumoto, S., Endo, T., O’Neill, R.J. 2023Kangaroo endogenous retrovirus (KERV) forms megasatellite DNA with a simple repetition pattern in which the provirus structure is retained. Virology 586, 56-66. DOI: 10.1016/j.virol.2023.07.005
    6. Hosseini, M., Palmer, A., Manka, W., Patchigoll, V., Grady, P.G.S.*, Bi, J., O’Neill, R.J., Chi, Z., Aguiar, D. 2023. Deep statistical modelling of nanopore sequencing translocation times reveals latent non-B DNA structures. Bioinformatics 39, Issue Supplement_1, June 2023, i242–i251, DOI: 10.1093/bioinformatics/btad220
    7. Rhie, A., Nurk, S. §, Cechova, M. §, Hoyt, S.J.* §, Taylor, D.J., Altemose, N., Hook, P.W., Koren, S., Rautiainen, M., Alexandrov, I.A., Allen, J., Asri, M., Bzikadze, A.V., Chen, N-C., Chin, C-S., Diekhans, M., Flicek, P., Formenti, G., Fungtammasan, A., Giron, C.S., Garrison, E., Gershman, A., Gerton, J., Grady, P.G.S.*, Guarracino, A., Haggerty, L., Halabian, R., Hansen, N.F., Harris, R., Hartley, G.A.*, Harvey, W.T., Haukness, M., Heinz, J., Hourlier, T., Hubley, R.M., Hunt, S.E., Hwang, S., Jain, M., Kesharwani, R.K., Lewis, A.P., Li, H., Logsdon, G.A., Lucas, J.K., Makalowski, W., Markovic, C., Martin, F.J., Mc Cartney, A.M., McCoy, R.C., McDaniel, J., McNulty, B.M., Medvedev, P., Mikheenko, A., Munson, K.M., Murphy, T.D., Olsen, H.E., Olson, N.D., Paulin, L.F., Porubsky, D., Potapova, T.,  Ryabov, F.,.Salzberg, S.L., Sauria, M.E.G., Sedlazeck, F.J., Shafin, K., Shepelev, V.A., Shumate, A., Storer, J.M.,  Surapaneni, L., Taravella Oill, A.M., Thibaud-Nissen, F., Timp, W., Tomaszkiewicz, M., Vollger, M.R., Walenz, B.P., Watwood, A.C., Weissensteiner, M.H., Wenger, A.M., Wilson, M.A., Zarate, S., Zhu, Y., Zook, J.M., Eichler, E.E., O’Neill, R., Schatz, M.C., Miga, K.H., Makova, K.D., Phillippy, A.M. 2023 The complete sequence of a human Y chromosome Nature 621, 344–354. https://doi.org/10.1038/s41586-023-06457-y, § co-first author
    8. Hallast, P., Ebert, P., Loftus, M., Yilmaz, F., Audano, P.A., Logsdon, G.A., Bonder, M.J., Zhou, W., Hops, W., Kim, K., Li, C., Hoyt, S.J. *, Dishuck, P.C., Porubsky, D., Tsetsos, F., Kwon, J.Y., Zhu, Q., Munson, K.M., Hasenfeld, P., Garvey, W.T., Lewis, A.P., Kordosky, J., Hoekzema, K., Human Genome Structural Variation Consortium, O’Neill, R.J., Korbel, J.O., Tyler-Smith, C., Eichler, E.E., Shi, X., Beck, C.R., Marschall, T., Konkel, M.K., Lee, C. 2023. Assembly of 43 diverse human Y chromosomes reveals extensive complexity and variation. Nature 621, 355-364. DOI:1038/s41586-023-06425-6.
    9. Velotta, J., O’Neill, R.J. and Schultz, E. Comparative genomics of alewife: insights into the genetic basis of diadromy. Geological Society of America Abstracts with Programs. Vol. 54, no. 5. DOI: 10.1130/abs/2022AM-381747.
    10. Fuller, E.P.*, M.P. Weiner, O’Neill, R.J. 2021. Derivation of Splice Junction-Specific Antibodies Using a Phosphoserine Targeting Strategy and Directed Evolution. New Biotechnology vol 71, pp 1-10. DOI: 10.1016/j.nbt.2022.06.003
    11. Hoyt S*, Hartley G*§, Grady P*§, Storer J§, Gershman A§, de Lima L, Limouse C, Halabian R, Wojenski L, Rodriguez M, Altemose N, Core L, Gerton J, Makalowski W, Olson D, Rosen J, Smit A, Straight A, Vollger M, Wheeler T, Schatz M, Eichler E, Phillippy A, Timp W, Miga K, O’Neill R.J. 2021. From telomere to telomere: the transcriptional and epigenetic state of human repeat elements. Science vol 376, issue 6588. DOI: 10.1101/2021.07.12.451456 (COVER); co-second author
    12. Nurk S, Koren S, Rhie A, Rautiainen M, Bzikadze A, Mikheenko A, Vollger M, Altemose N, Uralsky L, Gershman A, Aganezov S, Hoyt S*, Diekhans M, Logsdon G, Alonge M, Antonarakis S, Borchers M, Bouffard G, Brooks S, Caldas G, Cheng H, Chin C, Chow W, de Lima L, Dishuck P, Durbin R, Dvorkina T, Fiddes I, Formenti G, Fulton R, Fungtammasan A, Garrison E, Grady P*, Graves-Lindsay T, Hall I, Hansen N, Hartley G*, Haukness M, Howe K, Hunkapiller M, Jain C, Jain M, Jarvis E, Kerpedjiev P, Kirsche M, Kolmogorov M, Korlach J, Kremitzki M, Li H, Maduro V, Marschall T, McCartney A, McDaniel J, Miller D, Mullikin J, Myers E, Olson N, Paten B, Peluso P, Pevzner P, Porubsky D, Potapova T, Rogaev E, Rosenfeld J, Salzberg S, Schneider V, Sedlazeck F, Shafin K, Shew C, Shumate A, Sims Y, Smit A, Soto D, Sović I, Storer J, Streets A, Sullivan B, Thibaud-Nissen F, Torrance J, Wagner J, Walenz B, Wenger A, Wood J, Xiao C, Yan S, Young A, Zarate S, Surti U, McCoy R, Dennis M, Alexandrov I, Gerton J, O’Neill R.J., Timp W, Zook J, Schatz M, Eichler E, Miga K, Phillippy A.  The complete sequence of a human genome. Science vol 376, issue 6588. DOI: 10.1101/2021.05.26.445798 (COVER)
    13. Gershman A, Sauria M, Hook P, Hoyt S*, Razaghi R, Koren S, Altemose N, Caldas G, Vollger M, Logsdon G, Rhie A, Eichler E, Schatz M, O’Neill R.J., Phillippy A, Miga K, Timp W.  Epigenetic Patterns in a Complete Human Genome. Science vol 376, issue 6588. DOI: 10.1101/2021.05.26.443420 (COVER)
    14. Altemose N, Logsdon G, Bzikadze A, Sidhwani P, Langley S, Caldas G, Hoyt S,* Uralsky L, Ryabov F, Shew C, Sauria M, Borchers M, Gershman A, Mikheenko A, Shepelev V, Dvorkina T, Kunyavskaya O, Vollger M, Rhie A, McCartney A, Asri M, Lorig-Roach R, Shafin K, Aganezov S, Olson D, Gomes de Lima L, Potapova T, Hartley G*, Haukness M, Kerpedjiev P, Gusev F, Tigyi K, Brooks S, Young A, Nurk S, Koren S, Salama S, Paten B, Rogaev E, Streets A, Karpen G, Dernburg A, Sullivan B, Straight A, Wheeler T, Gerton J, Eichler E, Phillippy A, Timp W, Dennis M, O’Neill R.J., Zook J, Schatz M, Pevzner P, Diekhans M, Langley C, Alexandrov I, Miga K.  Complete genomic and epigenetic maps of human centromeres. Science vol 376, issue 6588. DOI: 10.1101/2021.07.12.452052 (COVER)
    15. Harris A. Lewin, Stephen Richards and The Earth Biogenome Project Working Group (alphabetical): Erez Lieberman Aiden, Miguel L. Allende, John M. Archibald, Miklós Bálint, Katharine B. Barker, Bridget Baumgartner, Katherine Belov, Giorgio Bertorelle, Mark L. Blaxter, Jing Cai, Nicolette D. Caperello, Keith Carlson, Juan Carlos Castilla‐Rubio, Shu‐Miaw Chaw, Lei Chen, Anna K. Childers, Jonathan A. Coddington, Dalia A. Conde, Montserrat Corominas, Keith A. Crandall, Andrew J. Crawford, Federica DiPalma, Richard Durbin, ThankGod E. Ebenezer, Scott V. Edwards, Olivier Federigo, Paul Flicek, Guilio Formenti, Richard A. Gibbs, M. Thomas P. Gilbert, Melissa M. Goldstein, Jennifer A.M. Graves, Henry T. Greely, Igor V. Grigoriev, Kevin J. Hackett, Neil Hall, David Haussler, Kristofer M. Helgen, Carolyn Hogg, Sachiko Isobe, Kjetill Sigurd Jakobsen, Axel Janke, Erich D. Jarvis, Warren E. Johnson, Steven J.M. Jones, Elinor K. Karlsson, Paul Kersey, Jin‐Hyoung Kim, W. John Kress, Shigehiro Kuraku, Mara K.N. Lawniczak, James Leebens‐Mack, Xueyan Li, Kerstin Lindblad‐Toh, Xin Liu, Jose Lopez, Tomas Marques‐Bonet, Sophie Mazard, Jonna A.K. Mazet, Camila J. Mazzoni, Gene Myers, Rachel J. O’Neill, Sadye Paez, Hyun Park, Gene E. Robinson, Cristina Roquet, Oliver A. Ryder, Jamal S.M. Sabir, H. Bradley, Shaffer, Timothy M. Shank, Jacob S. Sherkow, Pamela S. Soltis, Boping Tang, Leho Tedersoo, Marcela Uliano‐Silva, Kun Wang, Xiaofeng Wei, Regina Wetzer, Julia L. Wilson, Xun Xu, Huanming Yang, Anne D. Yoder, and Guojie Zhang. The Earth BioGenome Project 2020: Starting the Clock. Proceedings of the National Academy of Sciences Jan 2022, 119 (4) e2115635118; DOI:10.1073/pnas.2115635118. (COVER)
    16. Hartley, G.*, Ohkavat, M.#, Carbone, L., O’Neill, R. J.* (Co last authors). 2021. Comparative analyses of gibbon centromeres reveal dynamic species-specific shifts in repeat composition. Molecular Biology and Evolution msab148, DOI: 10.1093/mol-bev/msab148.
    17. Ahmad, S.F.*; Jehangir, M.; Cardoso, A.L.; Wolf, I.R.; Margarido, V.P.; Cabral-de-Mello, D.C.; O’Neill, R.; Valente, G.T.; Martins, C. B chromosomes of multiple species have intense evolutionary dynamics and accumulated genes related to important biological processes. BMC Genomics 2020, 21, 656, DOI:10.1186/s12864-020-07072-1.
    18. Mariam Okhovat#, M., Nevonen, K.A., Davis, B., Michener, P., Ward, S., Milhaven, M., Harshman, L., Sohota, A., O’Neill, R.J., Ahituv, N., Veeramah, K.R., and Carbone, L. Co-option of the lineage-specific LAVA retrotransposon in the gibbon genome. Proceedings of the National Academy of Sciences 117 (32) 19328-19338.
    19. Keiser, P., Kosisky, S., Marks, M., Reese, B., Maas, K., O'Neill, R.J., Hang, J.. 2020. Correlation of atmospheric mold with the upper airway mycobiomes of healthy volunteers. Journal of Allergy and Clinical Immunology. 145: 2.
    20. O’Neill, R.J., 2020. Seq’ing identity and function in a repeat-derived noncoding RNA world. Chromosome Research 28, 111–127.
    21. Deakin, J., and O’Neill, R.J. 2019. Evolution of Marsupial Genomes. Annual Review of Animal Biosciences vol 8.
    22. Deakin, J. , Potter,, O'Neill, R.J., Ruiz-Herrera, A., Cioffi, M., Eldridge, M., Fukui, K., Graves, J.M., Griffin, D., Grutzner, F., Kratochvíl, L., IMiura, I., Rovatsos, M., Srikulnath, K., Wapstra, E., Ezaz, T., 2019. Chromosomics: bridging the gap between genomes and chromosomes. Genes 10 (8), 627.
    23. Bellantoni,F. ,Hartnett-McCann, K., Conlogue, G.J., Ullinger, J.M., O’Neill, R.J., Reese, B., Hartley, G.*. 2019. A Possible “Ritual” Killing from Farmington Connecticut.
    24. Hartley, G.*, & O'Neill, R. J. 2019. Centromere Repeats: Hidden Gems of the Genome. Genes, (3 ed., vol. 10). 10.3390/genes10030223.
    25. Duan, J.*, Flock, K., Jue, N.#, Zhang, M., Jones, A., Seesi, S., Mandoiu, I. I., Pillai, S., Hoffman, M., O'Neill, R. J., Zinn, S., Govoni, K., Reed, S. A., Jiang, H., Jiang, Z., & Tian, X. 2019. Dosage Compensation and Gene Expression of the X Chromosome in Sheep. G3: GENES, GENOMES, GENETICS 9  1305-314; 10.1534/g3.118.200815 (COVER)
    26. Duan, J.*, Shi, , Jue, N.#, Jiang, Z., Kuo, L., O’Neill, R.J., Wolf, E., Dong, H., Zheng, X., Chen,J. and Tian, X.. 2019. Dosage Compensation of the X Chromosomes in Bovine Germline, Early Embryos and Somatic Tissues, G3: GENES, GENOMES, GENETICS 9 no. 1 pp305-314; doi.org/10.1534/g3.118.200815
    27. Smalec, B. M.^, Heider, T.N.*, Flynn, B.L.*, and O’Neill, R.J. A centromere satellite concomitant with extensive karyotypic diversity across the Peromyscus genus defies predictions of molecular drive. Chromosome Research. doi.org/10.1007/s10577-019-09605-1
    28. Cilhoroz, B*; Schifano, E; Ash, G; Panza, Gr; Lamberti, L; Chen, M-H; Deshpande, V; Zaleski, A; Farinatti, P ; Santos, Lu; Taylor, Beth; O'Neill, R; Thompson, P; Pescatello, L. 2018. Furin variant associations with postexercise hypotension are intensity and race dependent. Physiological Reports 274. 10.1249/01.mss.0000535988.19797.e9.
    29. Brown, J. D., Crivello, J.*, and O'Neill, R. J. 2018. An Updated Genetic Map of Peromyscus with Chromosomal Assignment of Linkage Groups. Mammalian Genome 29:5–6, pp344–352 (COVER)
    30. Lazar, H.#, Nevonen, K.A., O’Connell, B., McCann, C., O’Neill, R.J., Green, R.E., Meyer, T.J., Okhovat, M.#, and L. Carbone 2018. Epigenetic maintenance of topological domains in the highly rearranged gibbon genome. Genome Research. 28(7):983-997, doi:10.1101/gr.233874.117
    31. Johnson, R. ,O’Meally, D., Chen, Z., Etherington, G.J., Ho, S.Y.W., Nash, W.J., Grueber, C.E., Yuanyuan Cheng, Y., Whittington, C.M., Dennison, S., Peel, E., Haerty, W., O’Neill, R.J., Colgan, D.C., Russell, T.L., Alquezar-Planas, D.A., Attenbrow, V., Bragg, J.G., Brandies, P.A., Chong, A.Y., Deakin, J.E., Di Palma, F., Duda, Z.*, Eldridge, M.D.B., Ewart, K.M., Hogg, C.J., Frankham, G.J., Georges, A., Gillett, A.K., Govendir, M., Greenwood, A.D., Hayakawa, T., Helgen, K.M., Hobbs, M., Holleley, C.E., Heider, T.N.*, Jones, E.A., King, A., Madden, D., Graves, J.A.M., Morris, K.M., Neaves, L.E., Patel, H.R., Polkinghorne, Renfree, M.B., Robin, C., Salinas, R., Tsangaras, K., Waters, P.D., Waters, S.A., Wright, B., Wilkins, M.R., Timms, P., Belov, K. 2018. Adaptation and conservation insights from the koala genome. Nature Genetics 50, 1102–1111 h (COVER) https://doi.org/10.1038/s41588-018-0153-5.
    32. Jue, N.#, Foley, R.*, Reznick, D., O’Neill, R.J. and O’Neill, M.J. 2018. Tissue-specific transcriptome for Poeciliopsis prolifica reveals evidence for genetic adaptation related to the evolution of a placental fish. G3: Genes|Genomes|Genetics 8(7):2181-2192; 10.1534/g3.118.200270.
    33. Yang Y.*, Gu, , Sasaki, T., Crivello, J.*, O’Neill, R.J., Gilbert, D. and J. Ma. 2018. Continuous-trait probabilistic model for comparing multi-species functional genomic data. Cell Systems 7(2): 208-218.e11. doi: 10.1016/j.cels.2018.05.022.
    34. O’Neill, M.J. and O’Neill, R.J. 2018. Sex chromosome repeats tip the balance towards speciation. Molecular Ecology Apr 6. doi: 10.1111/mec.14577.
    35. O’Neill, R.J. and O’Neill, M.J. 2018 Replication timing kept in LINE. Journal of Cell Biology. Jan 2018, jcb.201712173; DOI:1083/jcb.201712173.
    36. Klein, S.J.* and O’Neill, R. J. 2018. Transposable elements: genome innovation, chromosome diversity, and centromere conflict. Chromosome Research. Volume 26, Issue1–2, pp 5–23 https://doi.org/10.1007/s10577-017-9569-5 (COVER)
    37. Bucklin, , Questel, J.M.*, DiVito, K.*, Smolina, I., Choquet, M.#, Hoarau, G. and O’Neill, R.J. 2018. Population Genomics of Marine Zooplankton; Chapter 19 in: Population Genomics: Marine Organisms, Editors: Om P. Rajora and Marjorie Oleksiak
    38. Feigin, C.*, Axel, Y.*, Newton, H., Schmitz, J., Doronina, L., Hipsley, C.A., Mitchell, K.J., Gower, G., Llamas, B., Soubrier, J., Heider, T.N.*, Menzies, B.R.#, Cooper, A., O’Neill, R.J. and Pask, A.J. 2018. Genome of the Tasmanian Tiger Provides Insights into the Evolution and Demography of an Extinct Marsupial. Nature Ecology and Evolution 2:182–192; DOI:10.1038/s41559-017-0417-y
    39. Pescatello, L., Schifano, E., Ash, G., Panza, G., Lamberti, L., Chen, M., Deshpande, V., Zaleski, A., Cilhoroz, , Farinatti, P., Taylor, B., O'Neill, R., Thompson, P. 2017. Deep-Targeted Sequencing of Endothelial Nitric Oxide Synthase Gene Exons Uncover Exercise Intensity and Ethnicity Dependent Associations with Postexercise Hypotension. Physiological Reports Vol. 5 no. e13510 DOI: 10.14814/phy2.13510.
    40. Johnson, W.*, Yewdell, W.T., Bell, J.C., McNutty, S.M.*, Duda, Z.*, O’Neill, R.J., Sullivan, B.A., and Straight, A. 2017. RNA-dependent stabilization of SUV39H1 at constitutive heterochromatin. eLife. 6:e25299 DOI: 10.7554/eLife.25299
    41. Duda, Z.*, Trusiak, S.* and J. O’Neill. 2017. Centromere Transcription: means and motive. in Centromere and Kinetochores, ed B. Black, Springer publishing.
    42. Velotta, J.P.*, Wegrzyn, J.L., Ginzburg, S.^, Kang, L.^, Czesny, S., O’Neill, R.J., McCormick, S.D., Michalak, P., and Schultz, E.T. 2017. Transcriptomic imprints of adaptation to fresh water: parallel evolution of osmoregulatory gene expression in the Alewife. Molecular Ecology 26 (3): 831-848. doi: 10.1111/mec.13983
    43. Batta-Lona PG*, Maas AE*, O'Neill RJ, Wiebe PH, Bucklin A. 2016. Transcriptomic profiles of spring and summer populations of the Southern Ocean salp, Salpa thompsoni, in the Western Antarctic Peninsula region. Polar biology. December pp1-16. doi:10.1007/s00300-016-2051-6
    44. Jue N.K.# Batta-Lona, P.G.*, Trusiak S*, Obergfell C, Bucklin A, O'Neill MJ, O'Neill R.J. 2016. Rapid Evolutionary Rates and Unique Genomic Signatures Discovered in the First Reference Genome for the Southern Ocean Salp, Salpa thompsoni (Urochordata, Thaliacea). Genome Biol Evol. Oct 30;8(10):3171-3186. PubMed PMID: 27624472; PubMed Central PMCID: PMC5174732. (COVER)
    45. Ramos, E^, Cardoso, L*., Brown, J., Marques, D.F.*, Fantinatti, B.E.A.*, Cabral-de-Mello, D.C.*, Oliveira, R.A.*, O’Neill, R.J., and Martins, C. 2016. The repetitive DNA element BncDNA, enriched in the B chromosome of the cichlid fish Astatotilapia latifasciata, transcribes a potentially noncoding RNA. Chromosoma,  2016 May 12. [Epub ahead of print] PubMed PMID: 27169573.
    46. Goossens, B.,* Sharma, R*; Othman. N.*; Kun-Rodrigues, C. ;Sakong, R.; Ancrenaz, M.; Ambu, L.N.; Jue, N.K.#, O'Neill, R.J. ; Bruford,l W ; Chikhi, L. 2016. Habitat fragmentation and genetic diversity in natural populations of the Bornean elephant: implications for conservation. Biological Conservation; 196:80-92.
    47. Tork, B.*, Nenastyeva, E.*, Artyomenko, A.*, Mancuso, N.*, Khan, M.I., O’Neill, R., Mandoiu, I.I., Zelikovsky, A. 2016. Reconstruction of Infectious Bronchitis Virus Quasispecies from NGS Data. In Computational Methods for Next Generation Sequencing Data Analysis (eds I. Măndoiu and A. Zelikovsky). doi:10.1002/9781119272182.ch17.
    48. Chen, *, S. Bowers, S. ,# Lipinszki,, Z., Palladino, J. *, Trusiak,S.*, Bettini, E.*, Rosin, L.*, Przewloka, M.R., Glover, D.M., R. J. O’Neill, and B. G. Mellone. 2015. Sequence-independent transcription is required for CENP-A deposition by its assembly factor. Dev Cell 34(1): 73-84.
    49. Brown, J., Longo, M.*, M. J. O’Neill and J. O’Neill. 2015. Identification of a recently active mammalian SINE derived from ribosomal RNA, Genome Biology and Evolution 7(3):775-88.
    50. Itoh, Y., R. Mackie, K. Kampf, S. Domadia, J. D. Brown, J. O'Neill and A. P. Arnold. 2015. Four Core Genotypes Mouse Model: Localization of the Sry Transgene and Bioassay for Testicular Hormone Levels. BMC Research Notes Mar 7;8:69.
    51. Harris, S.E.*, J. O’Neill, J. Munshi-South, 2015. Transcriptome resources for the white-footed deermouse (Peromyscus leucopus): new genomic tools for investigating ecologically divergent urban and rural populations. Molecular Ecology doi: 10.1111/1755-0998.12301.
    52. O’Neill, M.J. and J. O’Neill. 2014. Something to Swing About. Nature 513: 174–175.
    53. Brown, J.D. and J. O’Neill. 2014. The Evolution of Centromeric DNA Sequences eLS Wiley and Sons, DOI: 10.1002/9780470015902.a0020827.pub2.
    54. Jiang, A.*, J. Sun, H. Dong, O. Luo, X. Zheng, C. Obergfell, Y. Tang, J. Bi, J. O’Neill, Y. Ruan, J. Chen, Z. Tian. 2014.Complete Transcriptional Profiles of Bovine In Vivo Pre-implantation Development. BMC Genomics 15:756.
    55. O’Neill, R.J., Vrana, C.S. Rosenfeld. 2014. Maternal Methyl Supplemented Diets and Effects on Offspring Health. Frontiers in Genetics 5:289. doi: 10.3389/fgene.2014.00289.
    56. Velotta, J.O.*, E.T. Schultz, S.D. McCormick, and J. O’Neill. 2014. Relaxed selection causes microevolution of seawater osmoregulation and gene expression in landlocked Alewives. Oecologia 175(4):1081-92.
    57. Kenney-Hunt, J.*, Lewandowski, A., Glenn, T.C., Glenn, J., Tsyusko, O.V., O’Neill, R.J. Brown, J.D., Ramsdell, C., Nguyen, Q., Phan, T., Shorter, K.S., Dewey, M.J., Szalai, G., Vrana, P.B., Felder, M.R. 2014. A Genetic Map of Peromyscus with Chromosomal Assignment of Linkage Groups. Mammalian Genome 25(3-4):160-79 (COVER)
    58. Harris, S.E.*, Munshi-South, J., Obergfell, C., O’Neill, R.J. 2013. Signatures of Rapid Evolution in Urban and Rural Transcriptomes of White-Footed Mice (Peromyscus leucopus) in the New York Metropolitan Area. PLoS ONE 8(8): e74938. doi:10.1371/journal.pone.0074938.
    59. Earnshaw WC, Allshire RC, Black BE, Bloom K, Brinkley BR, Brown W, Cheeseman IM, Choo KH, Copenhaver GP, Deluca JG, Desai A, Diekmann S, Erhardt S, Fitzgerald-Hayes M, Foltz D, Fukagawa T, Gassmann R, Gerlich DW, Glover DM, Gorbsky GJ, Harrison SC, Heun P, Hirota T, Jansen LE, Karpen G, Kops GJ, Lampson MA, Lens SM, Losada A, Luger K, Maiato H, Maddox PS, Margolis RL, Masumoto H, McAinsh AD, Mellone BG, Meraldi P, Musacchio A, Oegema K, O'Neill R.J., Salmon ED, Scott KC, Straight AF, Stukenberg PT, Sullivan BA, Sullivan KF, Sunkel CE, Swedlow JR, Walczak CE, Warburton PE, Westermann S, Willard HF, Wordeman L, Yanagida M, Yen TJ, Yoda K, Cleveland DW. 2013 Esperanto for histones: CENP-A, not CenH3, is the centromeric histone H3 variant. Chromosome Res. 21(2):101-6. doi: 10.1007/s10577-013-9347-y.
    60. Jue, N. K.#, Murphy, M. B., Kasowitz, S. D.*, Qureshi, S. M.*, Obergfell, C. J., Elsisi, S.*, Foley, R. J.*, O'Neill, R. J., O'Neill, M. J. 2013. Determination of dosage compensation of the mammalian X chromosome by RNA-seq is dependent on analytical approach. BMC Genomics 14, 150.
    61. Carone, D.M.* , Zhang, C.#, Hall, L.E.*, C. Obergfell, B.R. Carone*, M.J. O’Neill, J. O’Neill. 2013. Hypermorphic expression of centromeric retroelement-encoded small RNAs impairs CENP-A loading. Chromosome Research 21(1):49-62.DOI 10.1007/s10577-013-9337-0
    62. Tork, B.*, Nenastyeva, E.,Artyomenko, A., Mancuso, N., Khan, M., O’Neill, R.J., Mandoiu, I., Zelikovsky, A. 2013. Reconstruction of Infectious Bronchitis Virus Quasispecies from NGS Data. 9th International Symposium on Bioinformatics Research and Applications (ISBRA)
    63. Hall, L. E.*, Mitchell, S.E*, and J. O’Neill. 2012. Pericentric and centromeric transcription: a perfect balance required. Chromosome Res 20(5):535-546.
    64. O'Neill R. J. and Sullivan B. A. 2012. Foreword: the centromere and kinetochore in creatures great and small. Chromosome Res 20(5):461-463. (COVER)
    65. Lindsay, J.*, Carone, D.M.*, J. Brown, L. Hall*, S. Qureshi,* S. Mitchell*, N. Jannetty^, G. Hannon, A. Pask, M. Renfree, M. O’Neill and O’Neill. 2012. Unique small RNA signatures uncovered in the tammar wallaby genome. BMC Genomics 13: 559: 10.1186/1471-2164-13-559.
    66. Sharma, R.*, Goossens,B.*, Kun-Rodrigues, C., Teixeira, T., Othman, N.B., Bruford, M.W., Jue, N.K.#, Obergfell, C., O'Neill, R.J.,  Chikhi, L. 2012. Two different high throughput sequencing approaches identify thousands of de novo genomic markers for the genetically depleted Bornean elephant. PLoS One 7(11): e49533.
    67. Yu H,# Lindsay J*, Feng ZP, Frankenberg S#, Hu Y, Carone D*, Shaw G, Pask AJ, O'Neill R.J., Papenfuss AT, Renfree MB. 2012. Evolution of coding and non-coding genes in HOX clusters of a marsupial. BMC 2012 Jun 18;13(1):251.
    68. Brown, J.B.#, S. Mitchell*, and J. O’Neill. 2012. Making a long story short: noncoding RNAs and chromosome change. Heredity 108:42-49.
    69. Brown, J.D.*, V. Piccuillo^, and J. O’Neill. 2012. Retroelement Demethylation Associated with Abnormal Placentation in Mus musculus × Mus caroli Hybrids. Biology of Reproduction 86 (3) 88: 1-10.
    70. Renfree et al, (…..) Linday, J.*, Heider, T.*, (…..) J. O’Neill co-senior author.2011. Genome sequence of an Australian kangaroo, Macropus eugenii, provides insight into the evolution of mammalian reproduction and development. Genome Biology 12: R81.
    71. O'Neill, R.J., Mandoiu, I., Khan, M., Obergfell, C., Wang, H., Bligh, A. ,Tork, B.*, Mancuso, N.*, Zelikovsky, A. 2012. Workshop: Bioinformatics methods for reconstruction of Infectious Bronchitis Virus quasispecies from next generation sequencing data. Computational Advances in Bio and Medical Sciences (ICCABS), 2012 IEEE 2nd International Conference1 DOI: 0.1109/ICCABS.2012.6182674
    72. Ferreri, G.*, J. Brown, *N. Jue#, C. Obergfell, C. Finn^, M.J. O’Neill and J. O’Neill. 2011. Recent amplification of an endogenous retrovirus limited to the centromere. Journal of Virology 85(10): 4761-71.
    73. Brown, J.D.*,Carone, D.M.*, C. Finn^, and J. O’Neill. 2011. Centromere conversion and retention in somatic cell hybrids. Cytogenetics and Genome Research 134: 182-90.
    74. Heider, T.*, Lindsay, J.*, Wang, C.*, O'Neill, R. J. & Pask, A. 2011. Enhancing genome assemblies by integrating non-sequence data. BMC Proc 5 supp 2, S7.
    75. Longo, M. S.*, O'Neill, M. J. & O'Neill, R. J. 2011. Abundant human DNA contamination identified in non-primate genome databases. PLoS One 6(2): e16410.
    76. Lindsay, J.*, Zhang, J.*, Farnham, , Wu, Y., Mandoiu, I. O'Neill, R.J., Salooti, H., Bullwinkel, E., Zelikovsky, A. 2011. Scaffolding draft genomes using paired sequencing data. Computational Advances in Bio and Medical Sciences (ICCABS), 2011 IEEE 1st International Conference
    77. O’Neill, R.J. and J. Brown*. 2010. Chromosomes, Conflict and Epigenetics: chromosomal speciation revisited. Annual Reviews in Genomics and Human Genetics 11: 291-316.
    78. Carone, D.M.* and J.O’Neill. 2010. Marsupial Centomeres and Telomeres: Dynamic Chromosome Domains in Marsupial Genetics and Genomics.
    79. Mlynarski, E.E.*, C.J. Obergfell, M.J. O’Neill, J. O’Neill. 2010. Divergent patterns of breakpoint reuse in Muroid rodents. Mammalian Genome 21(1-2):77-87. Epub 2009 Dec 22.
    80. Mlynarski, E.E.*, C.J. Obergfell, M.J. O’Neill, J. O’Neill. 2010. A unique late-replicating XY to autosome translocation in Peromyscus melanophrys. Chromosome Research 18: 179-189.
    81. Brown, J.D.* and O’Neill, R. J. 2009.The mysteries of chromosome evolution in gibbons: methylation is a prime suspect. PLoS Genet June; 5(6).
    82. Longo, M.S.,* Carone, D.M.*, Marzelli, M.*, M.J. O’Neill, E. Green, NISC Sequencing Consortium, J. O’Neill. 2009. Distinct retroelement classes define evolutionary breakpoints demarcating sites of evolutionary novelty. BMC Genomics 10:334.
    83. Carone, D.M.*, M.S. Longo*, G.C. Ferreri*, L.Hall*, Kira V. Bulazel*, M.J. O’Neill and J. O’Neill. 2009. A novel class of retroviral and satellite encoded small RNAs emanate from mammalian centromeres. Chromosoma 118: 113-125.
    84. O’Neill, R.J. and D.M. Carone*. 2009. Chapter 4: The role of ncRNA in centromeres: lessons from marsupials. in: Centromere structure and evolution ed: D. Ugarkovic, Springer Press.
    85. Lawton, B.R*. B. R Carone*, C. Obergfell, G. Ferreri*, C. Gondolphi, J. L. VandeBerg, I. Imumorin, J. O’Neill, and M. J. O’Neill. 2008. Genomic Imprinting of IGF2 in Marsupials is Methylation Dependent. BMC Genomics 9: 205.
    86. Mlynarski, E.E*., C. Ramsdell, C*. Obergfell, W. Rens, M. J. O’Neill and J. O’Neill. 2008. Peromyscus maniculatus and Mus musculus Synteny Map Established by Reciprocal Chromosome Painting. Cytogenetics and Genome Research 121: 288-292.
    87. Ramsdell, C.*, Glenn, J.W., J. O’Neill and M. Dewey. 2008. Peromyscus linkage map closely resembles Rattus BMC Evolutionary Biology 26(8): 65.
    88. Brown, J.D., D. Golden*, J.O’Neill. 2008. Methylation perturbations in retroelements within the genome of a Mus interspecific hybrid correlate with double minute chromosome formation. Genomics 91 (3): 267-273.
    89. Metcalfe, C.J.#, K.V. Bulazel*, G. C. Ferreri,* W. Rens, E. Schroeder-Reiter, G. Wanner, M. D. B. Eldridge, and J. O'Neill. 2007. Genomic instability within centromeres of interspecific marsupial hybrids. Genetics 177 (4): 2507-17
    90. O’Neill, M.J., B. R. Lawton*, M. Mateos*, D. M. Liscinsky*, G. C. Ferreri*, T. Hrbek, D. N. Reznick and J. O’Neill. 2007. Ancient and Continuing Darwinian Selection on IGF2 in Placental Fishes. PNAS (COVER) 104: 12404-9.
    91. Bulazel, K.V.*, G. C. Ferreri,* M. D. B. Eldridge and J. O’Neill. 2007. Species-specific shifts in centromere sequence composition are coincident with break point reuse in karyotypically divergent lineages. Genome Biology 8(8):R170.
    92. Duselis, A. R. * C. Obergfell, J.A. Mack*, M. J. O’Neill, Q. K. Nguyen*, J. O’Neill and P. B. Vrana. 2007. Cell-Cycle and extra-cellular matrix gene expression changes during deer mouse (Peromyscus) hybrid placental development. Reproduction Fertility and Development 19: 1-14.
    93. O’Neill, R.J., Szalai, G., Gibbs, R., Weinstock, G., Vrana, P., Glenn, J., Dewey, M., and M. Felder. 2007. White paper proposal for sequencing the genome of Peromyscus. National Human Genome Research Institute, http://www. genome. gov/pages/research/sequencing/seqproposals/peromyscus. pdf
    94. Smilowitz, H.M. J. Weissenberger, J. Weis, J. O’Neill, J. Brown* and J.A. Laissue. 2007. A Transplantable Mouse Tumor Model for Malignant Gliomas. J. Neurosurgery 106(4):652-9.
    95. Ambrosi, D.J.*, B. Tanasijevic, A*. Kaur, C. Obergfell, J. O’Neill, W. Krueger, and T.P. Rasmussen. 2007. Genome-wide Reprogramming in Hybrids of Somatic Cells and Embryonic Stem Cells. Stem Cells 25: 1104-1113.
    96. Kronforst, M.R.*, L.G.Yound, C. McNeely, J. O’Neill, and L.E. Gilbert. 2006. Linkage of butterfly mate preference and wing color preference cue at the genomic location of wingless. PNAS 103: 6575-6580.
    97. Bulazel, K*., Metcalfe, #, Ferreri, G.C.*, Yu, J.*, Eldridge, M.D.B. and R.J. O’Neill. 2006. Cytogenetic and molecular evaluation of centromere-associated DNA sequences from a marsupial (Macropodidae: Macropus rufogriseus) X chromosome. Genetics 172: 1129-1137.
    98. Lawton, B.R.*, C. Obergfell, J. O’Neill, and M. J. O’Neill. 2006.  Physical mapping of the IGF2 locus in the South American Opossum Monodelphis domestica. Cytogenetics and Genome Research 116: 130-1.
    99. Ford, K.K.*, J.A. Mack* and J. O’Neill. 2005. Multiple independent pseudogene derivations indicate increased instability of the mdm2 locus in Mus caroli. Molecular Biology Reports 32:95-101.
    100. Lawton, B.R.*, L. Sevigny*, C. Obergfell, D. Reznick, and J. O’Neill, O'Neill, M.J. 2005. Allelic Expression Profile of IGF2 in Live-bearing, Matrotrophic Fishes. Development, Genes and Evolution 215(4):207-12.
    101. Liscinsky, D,* Ferreri, G. C*.,Mack, J*.  D.B. Eldridge and R.J. O’Neill. 2005. Retention of latent centromeres in the mammalian genome. Journal of Heredity 96: 217-224.
    102. Ferreri, G. C*, M. Marzelli*, W. Rens, and J. O’Neill. 2004. Centromere specific retroviral element associated with breaks of synteny in macropodine marsupials. Cytogenetic and Genome Research 107: 115-118.
    103. Carvalho-Silva, D.R.*, J. O'Neill, J. D. Brown*, K. Huynh, P. D. Waters*, A. J. Pask, M. L. Delbridge and J. A. M. Graves. 2004. Molecular characterization and evolution of X and Y-borne ATRX homologues in American marsupials. Chromosome Research 12: 795-804.
    104. O’Neill, R.J., G.C. Ferreri*, and M.J. O’Neill. 2004. Elements and mechanisms of genome change. In Mammalian Genomics A. Ruvinsky and J. Graves. CABI: Oxford
    105. O’Neill, R.J., M.D.B. Eldridge, C.J. Metcalfe#. 2004. Centromere dynamics and chromosome evolution in marsupials. J. Heredity 95: 375-381. (COVER)
    106. Qu, H.*, J. Waugh O’Neill, and M. Wei. 2004. The effect of cell behavior on apatites with different fluorine contents. Key Engineering Materials 284-286: 577-580.
    107. Wilder J.A., E.G. Dyreson, J. O'Neill, M.L. Spangler, R. Gupta,^ A.S. Wilder*, and H. Hollocher 2004. Contrasting modes of natural selection acting on pigmentation genes in the Drosophila dunni subgroup.J Exp Zoolog B Mol Dev Evol. 15;302(5):469-82.
    108. Brown, J.D.*, M. Strbuncelj^, C. Giardina and J.W. O'Neill. 2003. Interspecific hybridization induced amplification of mdm2 on double minutes in a Mus hybrid. Cytogenet Genome Res 98:184-88.
    109. Pask, A.J., J.L. Harry, J.A.M. Graves, J. Waugh O’Neill, S.L.Layfield*, G. Shaw and M.B. Renfree. 2002. SOX9 has both conserved and novel roles in marsupial sexual differentiation. Genesis 33: 131-9.
    110. Wilder, J.A.*, T. Diaz^, J. O’Neill, J. Kenney*, and H. Hollocher. 2002. Characterization and isolation of novel microsatellites from the Drosophila dunni subgroup. Genet Res 80:177-85.
    111. O'Neill, R. J., M. D. B. Eldridge, and J.A.M Graves. 2001. Chromosome heterozygosity and de novo chromosome rearrangements in mammalian interspecific hybrids. Mammalian Genome 12: 256-259.
    112. Hollocher, H., K. Agopian*, J. Waterbury^, W. ONeill, A. W. Davis. 2000. Characterization of defects in adult germline development and oogenesis of sterile and rescued female hybrids in crosses between Drosophila simulans and Drosophila melanogaster. J. Exp Zoology (Mol and Dev Evol) 228: 205-218.
    113. O’Neill, M.J. and J. O’Neill. 1999. Whatever happened to SRY? Cellular and Molecular Life Sciences. 56: 883-893.
    114. O’Neill, R.J.Waugh, M.J. O’Neill and J.A.M. Graves. 1999. Genome evolution:  Role of methylation in eutherian hybrids. Nature 401: 131-132.
    115. Martin, J., E*. Herniou, J*. Cook, J.Waugh O’Neill, and M. Tristem. 1999. Inter-class transmission and phyletic host tracking in murine leukaemia-related retroviruses.  J. Virology  73: 2442-9.
    116. O’Neill, R.J.Waugh, M.D.B. Eldridge, M.A. Ferguson-Smith, P.C. O’Brien, J.A.M. Graves. 1999. Chromosome evolution in kangaroos (Marsupialia:  Macopodidae):  Cross species chromosome painting between the tammar wallaby and rock wallaby spp. with the 2n=22 ancestral karyotype. Genome 42: 525-530.
    117. Toder, R., J.Waugh O’Neill and J.A.M. Graves. 1999. Chromosome painting in marsupials. ILAR Journal 39(2,3): 92-95.

     

    Before starting laboratory at UConn

    1. O’Neill, R.J.Waugh, M.J. O’Neill and J.A.M. Graves. 1998. Undermethylation associated with retroelement activation and chromosome remodelling in an interspecific mammalian hybrid. Nature 393: 68-72.
    2. O'Neill, R.J.Waugh, F.Brennan, M.L. Delbridge, and J.A.M. Graves. 1998. De novo insertion of an intron into the mammalian sex determining gene, SRY. Proceedings of the National Academy of SciencesUSA 95:1653-1657.
    3. O'Neill, R.J.Waugh, M.D.B. Eldridge, R.H. Crozier, and J.A.M. Graves. 1997. Low levels of sequence divergence in Rock Wallabies (Petrogale) suggest a lack of positive directional selection in SRY.  Molecular Biology and Evolution 14(3): 350-353.
    4. Martin, J., E. Herniou, J. Cook, J.Waugh O’Neill, and M. Tristem. 1997. Human endogenous retrovirus type-I related viruses have an apparently widespread distribution within vertebrates.  Journal of Virology 71(1) 437-443.
    5. Graves, J.A.M., S.I. Cook, J.Waugh O’Neill, R. Glass, A. Pask, and M.L. Delbridge. 1997. Biological control of possums. Proceedings of the New Zealand Royal Society (misc series 45) 62-72.
    6. Watson, C.M., P.G. Johnston, K.A. Rodger, L.M. McKenzie, J. Waugh O’Neill, and D.W. Cooper. 1997. Sex chromosome complements and Sry status of two intersexual marsupials and one abnormal marsupial. Reproduction, Fertility and Development 9(2): 233-241.
    7. Graves, J.A.M. and J.Waugh O'Neill. 1997. Sex chromosomes and Haldane’s Rule. Journal of Heredity 88(5): 358-360.
    8. Toder, R., R.J.Waugh O’Neill, J. Wienberg, L. Voillaire and J.A.M. Graves. 1997. Comparative chromosome painting between two marsupial species: origins of an XX/XY1Y2 sex chromosome system. Mammalian Genome 8(6): 418-422.
    9. Delbridge, M.L., J.L. Harry, J.Waugh O’Neill, R. Toder, K. Ma, A.C. Chandley, and J.A.M. Graves. 1996.  A human candidate spermatogenesis gene RBM1 is conserved and amplified on the marsupial Y chromosome.  Nature Genetics 15(2): 131-136.
    10. Pamilo, P. and J.Waugh O'Neill. 1996. Evolution of the Sry genes. Molecular Biology and Evolution 14(1): 49-55.