​​​Publications

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1. Shiraishi Y, Ochi Y, Sugawa M, Sakamoto Y, Kimura K, Tsujimura T, Okada A, Okuda R, Namba S, Miyauchi T, …, Logsdon GA, Ogawa S. Rare k-mers reveal centromere haplogroups underlying human diversity and cancer translocations. In press at Cell. 2025 July 30. doi: 10.1101/2025.07.26.666712

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2. Hansen NF, Dwarshuis N, Ji HJ, Rhie A, Loucks H, Logsdon GA, Vollger MR, Storer JM, Kim J, Adam E, …, Phillippy AM. A complete diploid human genome benchmark for personalized genomics. Cell. 2026 August 6. doi: 10.1016/j.cell.2026.06.016. PMID: 42561913

• Featured on the cover of Cell

 

3. Gao S*, Oshima KK*, Chuang S-C, Loftus M, Montanari A, Gordon DS, Human Genome Structural Variation Consortium, Human Pangenome Reference Consortium, Hsieh PH, Konkel MK, Ventura M, Logsdon GA†. A global view of human centromere variation and evolution. Nature. 2026 July 29. doi: 10.1038/s41586-026-10841-9. PMID: 42527608

*Authors contributed equally

†Corresponding author

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4. Mastrorosa FK, Rozanski AN, Harvey WT, Knuth J, Garcia G, Munson KMM, Hoekzema K, Logsdon GA†, Eichler EE†. Complete chromosome 21 centromere sequencing of families with Down syndrome. AJHG. 2024 Feb 26. doi: 10.1101/2024.02.25.581464.

†Co-corresponding author

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5. Balzano E, Twayana S, Kosiyatrakul ST, Logsdon GA, Thakur BL, Eichler EE, Bohl B, Koch P, Sidoli S, …, Schildkraut CL. Impact of Tau expression on DNA replication dynamics in centromeres of human neural progenitor cells. iScience. 2026 Jan 15. doi: 10.1016/j.isci.2026.114707. PMCID: PMC12876619

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6. Bruno M, Maisha S, Mitra A, Costello K, Watkins-Chow D, Logsdon GA, Gambogi CW, Dumont BL, Black BE, Keane TM, Ferguson-Smith AC, Dale R, Macfarlan TS. Young KRAB-zinc finger gene clusters are highly dynamic incubators of ERV-driven genetic heterogeneity in mice. Nat Comm. 2025 Oct 30. doi: 10.1101/2025.02.26.640358. PMCID: PMC12575710

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7. Logsdon GA*, Ebert P*, Audana PA*, Loftus M, Porubsky D, Ebler J, Yilmaz F, Hallast P, Prodanov T, Yoo D, …, Marschall T. Complex genetic variation in nearly complete human genomes. Nature. 2025 July 23. doi: 10.1101/2024.09.24.614721. PMID: 3937279
*Authors contributed equally

• Highlighted on Science Friday, a public radio show and podcast with 1.8 million listeners weekly

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8. Yoo D, Rhie A, Hebbar P, Antonacci F, Logsdon GA, Solar SJ, Antipov A, Pickett BD, Safonova Y, Montinaro F, …, Makova KD, Phillippy AM, Eichler EE. Complete sequencing of ape genomes. Nature. 2025 April 9. doi: 10.1038/s41586-025-08816-3. PMID: 40205052

• Featured on the cover of Nature

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9. Porubsky D, Dashnow H*, Sasani TA*, Logsdon GA*, Hallast P*, Noyes MD*, Kronenberg ZN*, Mokveld T*, Koundinya N, …, Eichler EE. Human de novo mutation rates from a four-generation pedigree reference. Nature. 2025 Apr 25. doi: 10.1038/s41586-025-08922-2. PMID: 40269156*Authors contributed equally

 

10. Dubocanin D, Hartley GA, Sedeno Cortes AE, Mao Y, Hedouin S, Ranchalis J, Agarwal A, Logsdon GA, Munson KM, Real T, Mallory BJ, Eichler EE, Biggins S, O’Neill RJ, Stergachis AB. Conservation of dichromatin organization along regional centromeres. Cell Genomics. 2025 April 9. doi: 10.1016/j.xgen.2025.100819. PMCID: PMC12008808

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11. Zhang S, Xu N, Fu L, Yang X, Ma K, Li Y, Yang Z, Li Z, Feng Y, Jiang X, Han J, …, Logsdon GA, Phillippy AM, Su B, Zhang G, Eichler EE, Lu Q, Shi Y, Sun Q, Mao Y. Integrated analysis of the complete sequence of a macaque genome. Nature. 2025 Feb 26. doi: 10.1038/s41586-025-08596-w. PMID: 40011769​

 

12. Mastrorosa FK, Oshima KK, Rozanski AN, Harvey WT, Eichler EE, Logsdon GA†. Identification and annotation of centromeric hypomethylated regions with Centromere Dip Region (CDR)-Finder. Bioinformatics. 2024 Dec 24. doi: 10.1093/bioinformatics/btae733. PMID: 39657946
†Corresponding author

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13. 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. Nature. 2024 Apr 3. doi: 10.1038/s41586-024-07278-3. PMID: 38570684

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14. 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. Science. 2024 Mar 24. doi: 10.1126/science.adj3566. PMID: 38513017

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15. 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. Cell. 2024 Mar 14. doi: 10.1016/j.cell.2024.01.052. PMID: 38428424

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16. 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. Sci Adv. 2023 Nov 17. doi: 10.1126/sciadv.adi5764. PMCID: PMC10651114
 

17. 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. Nat Biotechnol. 2023 Oct 24. doi: 10.1038/s41587-023-01662-6. PMCID: PMC10422740
 

18. 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. PMCID: PMC10752217
 

19. 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. PMCID: PMC10726138
 

20. 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. Characterization of large-scale genomic differences in the first complete human genome. Genome Biol. 2023 Jul 4. doi: 10.1101/2022.12.17.520860. PMCID: PMC10320979
 

21. 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. PMCID: PMC10172114
 

22. 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

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23. 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
 

24. 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

 

25. Hedouin S, Logsdon GA, Underwood JG, Biggins S. A transcriptional roadblock protects yeast centromeres. Nucleic Acids Res. 2022 Aug 12. doi: 10.1093/nar/gkac117. PMCID: PMC9371891

•    Selected as a Nucleic Acids Research Breakthrough Article

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26. 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 Mar 31. doi: 10.1038/s41592-022-01440-3. PMCID: PMC9812399

•    Featured on the cover of Nature Methods

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27. 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. PMCID: PMC9233505
*Authors contributed equally to the work
 

28. 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​. PMCID: PMC9186530

•    Featured on the cover of Science

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29. 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. PMCID: PMC9170183
 

​30. 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. PMCID: PMC8662618
 

31. 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. PMCID: PMC8643106

 

32. Logsdon GA, Eichler EE. Mining the gaps of chromosome 8. Nature. 2021 May 14. doi: 10.1038/d41586-021-01095-8. PMCID: PMC8590702

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33. 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. PMCID: PMC7877196

 

34. 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. PMCID: PMC7545148
 

35. 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. PMCID: PMC7484160
 

36. 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. PMCID: PMC7877196
 

37. 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. PMCID: PMC725333

 

38. 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
 

39. 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
 

40. 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
 

41. 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​

 

42. 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
 

43. 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
 

44. 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
 

45. 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
 

46. 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
 

47. 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

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Preprints
 

1. Yang Z, Zhang S, Logsdon GA, Mao Y. VAMPIRE: Analyzing variation and motif pattern in tandem repeats. bioRxiv. 2025 June 15. doi: 10.1101/2025.06.15.659631

 

2. Hoyt SJ, Hartley GA, Antopia MC, Tullius TW, Taylor D, Tillquist NM, Neph S, Pauloski N, Munson KM, Hoekzema K, Eichler EE, Stergachis AB*, Logsdon GA*, O’Neill RJ. Haplotype-resolved genomics reveals conserved chromatin architecture and epigenetic constraints of human neocentromeres. bioRxiv. 2025 Dec 23.

*Authors contributed equally

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3. Birchak GJ, Allu PK, Kashyap P, Anbalagan GK, Chuang S-C, Logsdon GA, Gibson DG, Glass JI, Black BE. Protein-only centromeric chromatin assembly streamlines human artificial chromosome formation. bioRxiv. 2026 Jan 29. doi: 10.64898/2026.01.28.702397. PMCID: PMC12873790

 

4. De Gennaro L, Yoo D, Pistacchia L, Magrone R, Daponte A, Perrone F, Ravasini F, Mastrorosa FK, Oshima KK, Polano C, Hoekzema K, Munson KM, Wertz J, Marroni F, Catacchio CR, Antonacci F, Noordermeer D, Montinaro F, Logsdon GA, Trombetta B, Eichler EE, Ventura M. A segmental duplication-mediated deletion leads to neocentromere formation in orangutans. bioRxiv. 2026 April 11. doi: 10.64898/2026.04.09.717302. PMCID: PMC13081907

 

5. Wagner J*, Keskus AG*, Oshima KK*, Ranallo-Benavidez R*, McDaniel J, Sikic M, Lin D, Paulin LF, English AC, …, Barthel FP, Xiao C, Logsdon GA, Kolmogorov M, Zook JM. A complete human pancreatic cancer genome. bioRxiv. 2026 May 10. doi: 10.64898/2026.05.01.722316. PMCID: PMC13174521
*Authors contributed equally

 

6. Hallast P*, Rhie A*, Loftus M*, Mazzetto M, Ebert P, Gao S, Martino GV, Audana PA, Ashraf H, Pal K., …, Konkel MK, Marschall T, Cechova M, Logsdon GA, Phillippy AM, Lee C. Population-scale assemblies reveal recurrent remodeling and functional constraint on the human Y chromosome. bioRxiv. 2026 May 10. doi: 10.64898/2026.05.01.722316. PMCID: PMC13252187​​

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