About

Nicolas Altemose is an Assistant Professor of Genetics and a Chan Zuckerberg Biohub Investigator at Stanford University. His lab develops new experimental and analytical tools to study how chromatin proteins organize and regulate complex regions of the human genome. He completed his PhD in Bioengineering at UC Berkeley and UCSF in 2021, following a DPhil in Statistics from the University of Oxford in 2016, and a Bachelor's degree in Biology from Duke University in 2011. His research focuses on understanding the mechanisms by which chromatin proteins influence genome organization and function.

Research topics

• Biology
• Genetics
• Computational biology
• Evolutionary biology

Selected publications

• From telomere to telomere: The transcriptional and epigenetic state of human repeat elements

  Science · 2022 · 396 citations

  • Biology
  • Genetics
  • Computational biology

  Mobile elements and repetitive genomic regions are sources of lineage-specific genomic innovation and uniquely fingerprint individual genomes. Comprehensive analyses of such repeat elements, including those found in more complex regions of the genome, require a complete, linear genome assembly. We present a de novo repeat discovery and annotation of the T2T-CHM13 human reference genome. We identified previously unknown satellite arrays, expanded the catalog of variants and families for repeats and mobile elements, characterized classes of complex composite repeats, and located retroelement transduction events. We detected nascent transcription and delineated CpG methylation profiles to define the structure of transcriptionally active retroelements in humans, including those in centromeres. These data expand our insight into the diversity, distribution, and evolution of repetitive regions that have shaped the human genome.

  PublisherOA PDFDOI

• The complete sequence of a human genome

  Science · 2022 · 3273 citations

  • Genetics
  • Biology
  • Computational biology

  Since its initial release in 2000, the human reference genome has covered only the euchromatic fraction of the genome, leaving important heterochromatic regions unfinished. Addressing the remaining 8% of the genome, the Telomere-to-Telomere (T2T) Consortium presents a complete 3.055 billion-base pair sequence of a human genome, T2T-CHM13, that includes gapless assemblies for all chromosomes except Y, corrects errors in the prior references, and introduces nearly 200 million base pairs of sequence containing 1956 gene predictions, 99 of which are predicted to be protein coding. The completed regions include all centromeric satellite arrays, recent segmental duplications, and the short arms of all five acrocentric chromosomes, unlocking these complex regions of the genome to variational and functional studies.

  PublisherOA PDFDOI

• DiMeLo-seq: a long-read, single-molecule method for mapping protein–DNA interactions genome wide

  Nature Methods · 2022 · 137 citations

  1st authorCorresponding
  • Computational biology
  • Biology
  • Genetics
  PublisherOA PDFDOI

• Complete genomic and epigenetic maps of human centromeres

  Science · 2022 · 612 citations

  1st authorCorresponding
  • Biology
  • Genetics
  • Computational biology

  Existing human genome assemblies have almost entirely excluded repetitive sequences within and near centromeres, limiting our understanding of their organization, evolution, and functions, which include facilitating proper chromosome segregation. Now, a complete, telomere-to-telomere human genome assembly (T2T-CHM13) has enabled us to comprehensively characterize pericentromeric and centromeric repeats, which constitute 6.2% of the genome (189.9 megabases). Detailed maps of these regions revealed multimegabase structural rearrangements, including in active centromeric repeat arrays. Analysis of centromere-associated sequences uncovered a strong relationship between the position of the centromere and the evolution of the surrounding DNA through layered repeat expansions. Furthermore, comparisons of chromosome X centromeres across a diverse panel of individuals illuminated high degrees of structural, epigenetic, and sequence variation in these complex and rapidly evolving regions.

  PublisherOA PDFDOI

Frequent coauthors

• Simon Myers

  University of Oxford

  32 shared

• Aaron Streets

  University of California, Berkeley

  29 shared

• Adam M. Phillippy

  National Human Genome Research Institute

  24 shared

• Arang Rhie

  National Human Genome Research Institute

  22 shared

• Benjamin Davies

  The Francis Crick Institute

  21 shared

• Evan E. Eichler

  University of Washington

  21 shared

• Emmanuelle Bitoun

  University of Oxford

  21 shared

• Sergey Koren

  National Human Genome Research Institute

  20 shared

Labs

• The Altemose LabPI

Education

• PhD, Bioengineering

  University of California, Berkeley

  2021

• DPhil, Statistics

  University of Oxford

  2016

• B.S. Biology: Genomics, Biology

  Duke University

  2011

Similar researchers at Stanford University

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• Zhenan Baoh-224
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• Michael Snyderh-215
• Roger Blandfordh-205