Nicolas Altemose

GBZ-base and GAF-base: Indexed pangenome file formats

The paper introduces GBZ-base and GAF-base, indexed pangenome file formats for efficient subgraph and alignment extraction.

Inverted logic of ecDNA localization converts nuclear periphery into oncogenic transcription hubs in cancer

The paper shows ecDNA localizes to the nuclear periphery in cancer, resisting silencing and enhancing transcriptional output through interactions with the nuclear lamina.

Pangenome alignment reveals global diversity and evolution of human centromeric regions

The paper introduces Centrolign, a tool for aligning centromeric regions, revealing mutation dynamics and enabling variant calling in human centromeres.

Evolution and instability of human centromeres are accelerated by heterochromatin boundary loss and CENP-A overexpression

The paper shows that human centromeres and neocentromeres evolve epigenetically, with instability linked to loss of heterochromatin boundaries and CENP-A overexpression.

A complete diploid human genome benchmark for personalized genomics

T2T-HG002v1.1, a complete diploid HG002 assembly lacking detectable errors over 99.4% of its length, enables genome-based benchmarking of assemblies, sequencing reads, and phased variant calls.

A global view of human centromere variation and evolution

The paper assembles and characterizes 2,110 human centromeres, revealing novel haplotypes, mobile element insertions, and mutation rate variation across chromosomes.

Single-molecule variation in telomeric sequence and structure across humans

The paper constructs an atlas of telomere variation across humans using long-read sequencing and reveals heritable telomere variant repeats and telomerase-independent extension mechanisms.

Population differences of chromosome 22q11.2 duplication structure predispose differentially to microdeletion and inversion.

The paper analyzes chromosome 22q11.2 haplotypes to show how structural variations in specific regions correlate with microdeletion and inversion risks across populations.

Haplotype-resolved centromeric chromatin organization from a complete diploid human genome

The paper uses a complete diploid human genome to study centromeric chromatin organization, revealing that DNA methylation regulates centromere structure and plasticity.

Pangenome discovery of missing autism variants

The paper uses long-read sequencing to identify pathogenic variants in autism cases, finding three pathogenic mutations and nine candidate structural variants missed by short-read sequencing.

Heterochromatin boundaries maintain centromere position, size and number

The paper investigates how heterochromatin boundaries maintain centromere position, size, and number through specific histone modifications and methyltransferases.

Integrated analysis of multimodal long-read epigenetic assays

The paper introduces dimelo-toolkit, a Python package for analyzing multimodal long-read epigenetic data, demonstrating its use with a novel DiMeLo-seq protocol to study chromatin state in GM12878 cells.

A telomere-to-telomere map of somatic mutation burden and functional impact in cancer

The paper maps somatic mutation burden and functional impact across the cancer genome using telomere-to-telomere sequencing, revealing novel mutation hotspots and regulatory rewiring mechanisms.

Epigenetic remodeling and 3D chromatin reorganization governed by NKX2-1 drive neuroendocrine prostate cancer

This study identifies NKX2-1-driven epigenetic and 3D chromatin remodeling as key to neuroendocrine prostate cancer progression and reveals CBP/p300 inhibitors as potential therapeutic targets.

DiMeLo-cito: a one-tube protocol for mapping protein-DNA interactions reveals CTCF bookmarking in mitosis

DiMeLo-cito improves DiMeLo-seq by eliminating wash steps, enabling mitotic protein-DNA interaction analysis in diploid human cells and revealing CTCF bookmarking.

Integrating Single-Molecule Sequencing and Deep Learning to Predict Haplotype-Specific 3D Chromatin Organization in a Mendelian Condition

This paper introduces FiberFold, a deep learning model that predicts haplotype-specific 3D chromatin organization using Fiber-seq data, revealing changes in TADs in a Mendelian disease.

Rampant transcription replication conflict creates therapeutic vulnerability in extrachromosomal DNA containing cancers

This paper identifies transcription-replication conflict as a vulnerability in ecDNA-containing cancers and demonstrates that CHK1 inhibition selectively kills these tumors.

Human Satellite 3 DNA encodes megabase-scale transcription factor binding platforms

The paper identifies HSat3 DNA as a platform for transcription factor binding, showing it enhances nucleolar RNA Polymerase I activity through Hippo pathway interactions.

Mapping protein-DNA interactions with DiMeLo-seq

The paper introduces DiMeLo-seq, a method for mapping protein-DNA interactions using long-read sequencing, and provides a protocol and analysis tool.

The complete sequence of a human Y chromosome

The paper presents the complete sequence of a human Y chromosome, correcting errors in the GRCh38 reference and adding over 30 million base pairs.

DiMeLo-seq: a long-read, single-molecule method for mappingprotein-DNA interactions genome-wide

DiMeLo-seq maps protein-DNA interactions genome-wide with single-molecule resolution by methylating DNA near binding sites and using long-read sequencing.

Epigenetic Patterns in a Complete Human Genome

The paper uses a complete human genome assembly to analyze epigenetic patterns in previously uncharacterized genomic regions, revealing methylation and chromatin accessibility features in satellite DNA and centromeres.

The complete sequence of a human genome

A gapless 3.055 billion bp human genome from HiFi and ultra-long nanopore reads resolves all centromeric arrays and acrocentric p-arms, adding 182 Mbp of new sequence.

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

The paper presents the first de novo repeat discovery and annotation of a complete human reference genome, identifying novel satellite arrays and characterizing new classes of complex repeats.

Complete genomic and epigenetic maps of human centromeres

The paper presents a comprehensive analysis of fully assembled human centromeres, revealing their architecture, variation, and evolutionary dynamics at high resolution.

A high-resolution map of non-crossover events reveals impacts of genetic diversity on mammalian meiotic recombination

The paper maps non-crossover events in meiotic recombination, showing how genetic diversity affects repair mechanisms and contributes to hybrid infertility.

Human PRDM9 Can Bind And Activate Promoters, And Other Zinc-Finger Proteins Associate With Reduced Recombination In cis

The paper investigates PRDM9 binding and its effects on meiotic recombination and gene expression in human cells, finding that DNA-binding motifs and histone modifications predict recombination outcomes.