Publications

A complete Y chromosome 

Rhie, A., Nurk, S., Cechova, M. et al. The complete sequence of a human Y chromosome. Nature (2023). https://doi.org/10.1038/s41586-023-06457-y

Hallast, P., Ebert, P., Loftus, M. et al. Assembly of 43 human Y chromosomes reveals extensive complexity and variation. Nature (2023). https://doi.org/10.1038/s41586-023-06425-6 

The complete sequence of a human genome

Nurk S, Koren S, Rhie A, Rautiainen M, et al. The complete sequence of a human genome. Science 376. Doi: 10.1126/science.abj6987 (2022) 

Logsdon GA, et al. The structure, function, and evolution of a complete human chromosome 8. Nature, 2021.

Miga KH, Koren S, et al. Telomere-to-telomere assembly of a complete human X chromosome. Nature, 2020.

Analyses of the first complete genome

Vollger MR, et al. Segmental duplications and their variation in a complete human genome. Science 376. Doi: 10.1126/science.abj6965 (2022)

Gershman A, et al. Epigenetic patterns in a complete human genome. Science 376. Doi: 10.1126/science.abj5089 (2022) 

Aganezov S, Yan SM, Soto DC, Kirsche M, Zarate S, et al. A complete reference genome improves analysis of human genetic variation. Science 376. Doi: 10.1126/science.abl3533 (2022)

Hoyt SJ, et al. From telomere to telomere: The transcriptional and epigenetic state of human repeat elements. Science 376. Doi: 10.1126/science.abk3112 (2022)

Altemose N, et al. Complete genomic and epigenetic maps of human centromeres. Science 376. Doi: 10.1126/science.abl4178 (2022)

Companion methods and analyses

McCartney AM, Shafin K, Alonge M, et al. Chasing perfection: validation and polishing strategies for telomere-to-telomere genome assemblies. Nature Methods (2022). https://doi.org/10.1038/s41592-022-01440-3

Formenti G, Rhie A, et al. Merfin: improved variant filtering, assembly evaluation and polishing via k-mer validation. Nature Methods (2022). https://doi.org/10.1038/s41592-022-01445-y.

Alkan C, et al. Implications of the first complete human genome assembly. Genome Research March 31, 2022, doi:10.1101/gr.276723.122

Antonarakis S. Short arms of human acrocentric chromosomes and the completion of the human genome sequence. Genome Research. March 31, 2022, doi:10.1101/gr.275350.121

Talbert P and Henikoff S. The genetics and epigenetics of satellite centromeres. Genome Research. March 31, 2022, doi:10.1101/gr.275351.121

Kirsche M, et al. Jasmine: Population-scale structural variant comparison and analysis. bioRxiv, 2021.

Altemose N, et al. DiMeLo-seq: a long-read, single-molecule method for mapping protein-DNA interactions genome-wide. bioRxiv, 2021.

Kunyavskaya O, et al. HORmon: automated annotation of human centromeres. Genome Research, 2022.

Jain C, et al. A long read mapping method for highly repetitive reference sequences. bioRxiv, 2020.

Wagner J, et al. Curated variation benchmarks for challenging medically relevant autosomal genes. Nature Biotechnology, 2022.

Vollger MR, et al. StainedGlass: Interactive visualization of massive tandem repeat structures with identity heatmaps. Bioinformatics, 2022.

Schatz MC, Philippakis AA, et al. Inverting the model of genomics data sharing with the NHGRI Genomic Data Science Analysis, Visualization, and Informatics Lab-space (AnVIL). Cell Genomics, 2022.

Cheng H, et al. Haplotype-resolved de novo assembly with phased assembly graphs with hifiasm. Nature Methods, 2021.

de Lima LG, et al. PCR amplicons identify widespread copy number variation in human centromeric arrays and instability in cancer. Cell Genomics, 2021.

Dvorkina T, Kunyavskaya O, et al. CentromereArchitect: inference and analysis of the architecture of centromeres. Bioinformatics, 2021.

Grigorev K, Foox J, et al. Haplotype diversity and sequence heterogeneity of human telomeres. Genome Research, 2021.

Rautiainen M, Marschall T. MBG: Minimizer-based sparse de Bruijn Graph construction. Bioinformatics, 2021.

Mikheenko A, et al. TandemTools: mapping long reads and assessing/improving assembly quality in extra-long tandem repeats. Bioinformatics, 2020.

Nurk S, Walenz BP, et al. HiCanu: accurate assembly of segmental duplications, satellites, and allelic variants from high-fidelity long reads. Genome Research, 2020.

Vollger MR, et al. Improved assembly and variant detection of a haploid human genome using single-molecule, high-fidelity long reads. Annals of Human Genetics, 2019.