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Complete list of publications & preprints

  1. Yang X, Wang X, Zou Y, Zhang S, Xia M, Fu L, Vollger MR, Chen N-C, Taylor DJ, Harvey WT, Logsdon GA, Meng D, Shi J, McCoy RC, Schatz MC, Li W, Eichler EE, Lu Q, Mao Y. A refined characterization of large-scale genomic differences in the first complete human genome. In press at Genome Biology. Available on bioRxiv. doi: 10.1101/2022.12.17.520860
     

  2. Rhie A, Nurk S, Cechova M, Hoyt SJ, Taylor DJ, Altemose N, Hook PW, Koren S, Rautiainen M, Alexandrov IA, . . ., Logsdon GA, . . ., Phillippy AM. The complete sequence of a human Y chromosome. Nature. 2023 Aug 23. doi: 10.1038/s41586-023-06457-y
     

  3. Hallast P, Ebert P, Loftus M, Yilmaz F, Audano PA, Logsdon GA, Bonder MJ, Zhou W, Hops W, Kim K, . . ., Lee C. Assembly of 43 diverse human Y chromosomes reveals extensive complexity and variation. Nature. 2023 Aug 23. doi: 10.1038/s41586-023-06425-6
     

  4. Vollger MR, DeWitt WS, Dishuck PC, Harvey WT, Guitart X, Goldberg ME, Rozanski AN, Lucas J, Asri M, The Human Pangenome Reference Consortium, . . ., Logsdon GA, Porubsky D, Paten B, Harris K, Hsieh PH, Eichler EE. Increased mutation and gene conversion within human segmental duplications. Nature. 2023 May 10. doi: 10.1038/s41586-023-05895-y
     

  5. Rautiainen M, Nurk S, Walenz BP, Logsdon GA, Porubsky D, Rhie A, Eichler EE, Phillippy AM, Koren S. Verkko: telomere-to-telomere assembly of diploid chromosomes. Nature Biotechnology. 2023 February 16. doi: 10.1038/s41587-023-01662-6
     

  6. Logsdon GA and Eichler EE. The dynamic structure and rapid evolution of human centromeric satellite DNA. Genes. 2022 Dec 28. doi: 10.3390/genes14010092. PMCID: PMC9859433
     

  7. Dishuck PC, Rozanski AN, Logsdon GA, Eichler EE. GAVISUNK: Genome assembly validation via inter-SUNK distances in Oxford Nanopore reads. Bioinformatics. 2022 Nov 2. doi: 10.1093/bioinformatics/btac714. PMCID: PMC9805576
     

  8. Jarvis ED, Formenti G, Rhie A, Guarracino A, Yang C, Wood J, Tracey A, Thibaud-Nissen F, Vollger MR, Porubsky D, Cheng H, Asri M, Logsdon GA, …, Eichler EE, Phillippy AM, Paten B, Howe K, Miga KH, Human Pangenome Reference Consortium. Semi-automated assembly of high-quality diploid human reference genomes. Nature. 2022 Oct 19. doi: 10.1038/s41586-022-05325-5. PMCID: PMC9668749
     

  9. Altemose N, Logsdon GA*, Bzikadze AV*, Sidhwani P*, Langley SA*, Caldas GV*, Hoyt SH, Uralsky L, Ryabov FD, Shew CJ, …, Eichler EE, Phillippy AM, Timp W, Dennis MY, O’Neill RJ, Schatz MC, Pevzner PA, Diekhans M, Langley CH, Alexandrov IA, Miga KH. Complete genomic and epigenetic maps of human centromeres. Science. 2022 2022 April 1. doi: 10.1126/science.abl4178
    *Authors contributed equally to the work
     

  10. 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, …, Eichler EE, Miga KH, Phillippy AM. The complete sequence of a human genome. Science. 2022 April 1. doi: 10.1126/science.abj6987​
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  11. Gershman A, Sauria M, Hook PW, Hoyt SJ, Razaghi R, Koren S, Altemose N, Caldas GV, Vollger MR, Logsdon GA, Rhie A, Eichler EE, Schatz MA, O’Neill R, Phillippy AM, Miga KH, Timp W. Epigenetic patterns in a complete human genome. Science. 2022 April 1. doi: 10.1126/science.abj5089
     

  12. ​McCartney 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. Chasing perfection: validation and polishing strategies for telomere-to-telomere genome assemblies. Nat Methods. 2022 April 1. doi: 10.1038/s41592-022-01440-3​
     

  13. Hedouin S, Logsdon GA, Underwood JG, Biggins S. A transcriptional roadblock protects yeast centromeres. Nucleic Acids Res. 2022 Mar 7. doi: doi: 10.1093/nar/gkac117
     

  14. Giannuzzi G, Logsdon GA, Chatron N, Miller DE, Reversat DE, Munson KM, Hoekzema K, Bonnet-Dupeyron M-N, Pierre-Antoine RF, Baker CA, Sanlaville D, Eichler EE, Schluth-Bolard Caroline, Reymond A. Alpha satellite insertion close to an ancestral centromeric region. Mol Biol Evol. 2021 Dec 9. doi: 10.1101/2021.03.10.434819
     

  15. Salinas-Luypaert C, Allu PK, Logsdon GA, Dawicki-McKenna JM, Gambogi CW, Fachinetti D, Black BE. Gene replacement strategies validate the use of functional tags on centromeric chromatin and invalidate an essential role for CENP-AK124ub. Cell Rep. 2021 Nov 2. doi: 10.1016/j.celrep.2021.109924.
     

  16. Logsdon GA, Vollger MR, Hsieh P, Mao Y, Liskovykh MA, Koren S, Nurk S, Mercuri L, Dishuck PC, Rhie A, …, Miga KH, Phillippy AM, Eichler EE. The structure, function and evolution of a complete human chromosome 8. Nature. 2021 April 7. doi: 10.1038/s41586-021-03420-7
     

  17. Nurk S, Walenz BP, Rhie A, Vollger MR, Logsdon GA, Grothe R, Miga KH, Eichler EE, Phillippy AM, Koren S. HiCanu: accurate assembly of segmental duplications and allelic variants from high-fidelity long reads. Genome Res. 2020 August 14. doi: 10.1101/gr.263566.120
     

  18. Miga KH, Koren S, Rhie A, Vollger MR, Gershman A, Bzikadze A, Brooks S, Howe E, Porubsky D, Logsdon GA, . . ., Eichler EE, Phillippy AM. Telomere-to-telomere assembly of a complete human X chromosome. Nature. 2020 July 14. doi: 10.1038/s41586-020-2547-7
     

  19. Logsdon GA, Vollger MR, Eichler EE. Long-read human genome sequencing and its applications. Nat Rev Gen. 2020 June 5. doi: 10.1038/s41576-020-0236-x
     

  20. Gambogi CW, Dawicki-McKenna J, Logsdon GA, Black BE. The unique kind of human artificial chromosome: bypassing the requirement for repetitive centromere DNA. Exp Cell Res. 2020 April 1. doi: 10.1016/j.yexcr.2020.11197
     

  21. Vollger MR*, Logsdon GA*, Audanao PA, Sulovari A, Porubsky D, Peluso P, Wenger AM, Concepcion GT, Kronenberg ZN, Munson KM, Baker C, Sanders AD, Spierings DCJ, Lansdorp PM, Surti U, Hunkapiller MW, Eichler EE. Improved assembly and variant detection of a haploid human genome using single-molecule, high-fidelity long reads. Ann Hum Genet. 2019 November 11. doi: 10.1111/ahg.12364
    *Authors contributed equally to the work
     

  22. Sulovari, A, Li R, Audano PA, Porubsky D, Vollger MR, Logsdon GA, Human Genome Structural Variation Consortium, Warren WC, Pollen AA, Chaisson M, Eichler EE. Human-specific tandem repeat expansion and differential gene expression during primate evolution. PNAS. 2019 October 28. doi: 10.1073/pnas.1912175116
     

  23. Logsdon GA, Gambogi CW, Liskovykh MA, Barrey EJ, Larionov V, Miga KH, Heun P, Black BE. Human artificial chromosomes that bypass centromeric DNA. Cell. 2019 July 25. doi: 10.1016/j.cell.2019.06.006
     

  24. Barra V, Logsdon GA, Scelfo A, Hoffman S, Hervé S, Aslanian A, Nechemia-Arbely Y, Cleveland DW, Black BE, Fachinetti D. Phosphorylation of CENP-A on serine 7 does not control centromere function. Nat Commun. 2019 Jan 11. doi: 10.1038/s41467-018-08073-1
     

  25. Logsdon GA and Black BE. The new normal of structure/function studies in the era of CRISPR/Cas9. Biochem J. 2018 May 15. doi: 10.1042/BCJ20170025
     

  26. Wanat JJ, Logsdon GA, Driskill JH, Deng Z, Lieberman PM, Johnson FB. TERRA and the histone methyltransferase Dot1 cooperate to regulate replicative senescence in budding yeast. PLoS One. 2018 April 12. doi: 10.1371/journal.pone.019569
     

  27. Guo LY, Allu PK, Zandarashvili L, McKinley KL, Sekulic N, Dawicki-McKenna JM, Fachinetti D, Logsdon GA, Jamiolkowski RM, Cleveland DW, Cheeseman IM, Black BE. Centromere maintenance is achieved by fastening CENP-A to DNA and directing an arginine anchor-dependent nucleosome structural transition. Nat Commun. 2017 June 9. doi: 10.1038/ncomms15775
     

  28. Fachinetti D*, Logsdon GA*, Abdullah A, Selzer EB, Cleveland DW, Black BE. CENP-A modifications on Ser68 and Lys124 are dispensable for establishment, maintenance, and long-term function of human centromeres. Dev Cell. 2017 January 9. doi: 10.1016/j.devcel.2016.12.014
    *Authors contributed equally to the work
     

  29. Falk SJ, Guo LY, Sekulic N, Smoak EM, Mani T, Logsdon GA, Gupta K, Jansen LET, Van Duyne GD, Vinogradov SA, Lampson MA, Black BE. CENP-C reshapes and stabilizes CENP-A nucleosomes at the centromere. Science. 2015 May 8. doi: 10.1126/science.1259308
     

  30. Logsdon GA, Barrey EJ, Bassett EA, DeNizio JE, Guo LY, Panchenko T, Dawicki-McKenna JM, Heun P, Black BE. Both tails and the centromere targeting domain of CENP-A are required for centromere establishment. J Cell Biol. 2015 March 2. doi: 10.1083/jcb.201412011


Preprints
 

  1. Gambogi CW, Mer E, Brown DM, Arora UP, Yankson G, Gavade JN, Logsdon GA, Heun P, Glass JI, Black BE. Efficient formation of single-copy human artificial chromosomes. bioRxiv. 2023 June 30. doi: 10.1101/2023.06.30.547284
     

  2. ​Logsdon GA, Rozanski AN, Ryabov F, Potapova T, Shepelev VA, Mao Y, Rautiainen M, Koren S, Nurk S, Porubsky D, Lucas JK, Hoekzema K, Munson KM, Gerton JL, Phillippy AM, Alexandrov IA, Eichler EE. The variation and evolution of complete human centromeres. bioRxiv. 2023 May 30. doi: 10.1101/2023.05.30.542849
     

  3. Gambogi CW, Pandey N, Dawick-McKenna JM, Arora UP, Liskovykh MA, Ma J, Lamelza P, Larionov V, Lampson MA, Logsdon GA, Dumont BL, Black BE. Centromere innovations within a mouse species. bioRxiv. 2023 May 13. doi: 10.1101/2023.05.11.540353
     

  4. Dubocanin D, Sedeno Cortes AE, Hartley GA, Ranchalis J, Agarwal A, Logsdon GA, Munson KM, Real T, Mallory BJ, Eichler EE, O’Neill RJ, Stergachis AB. Conservation of chromatin organization within human and primate centromeres. bioRxiv. 2023 April 20. doi: 10.1101/2023.04.20.537689
     

  5. Mao Y, Harvey WT, Porubsky D, Munson KM, Hoekzema K, Lewis AP, Audano PA, Rozanski A, Yang X, Zhang S, . . ., Logsdon GA, . . ., Eichler EE. Structurally divergent and recurrently mutated regions of primate genomes. bioRxiv. 2023 March 7. doi: 10.1101/2023.03.07.531415

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