About

Erez Lieberman Aiden, Ph.D., is a Professor and Chair of the Department of Biochemistry and Molecular Biology at the University of Texas Medical Branch, where he directs the Center for Genome Architecture. He is also a Professor in the Department of Biosciences at Rice University. His work focuses on understanding the three-dimensional structure of the genome and its implications for biology and disease. As the principal investigator of the Aiden Lab, he leads a team that applies experimental and computational approaches to study genome architecture, including the analysis of chromatin structure and gene regulation. His leadership at the Center for Genome Architecture highlights his commitment to advancing knowledge in the field of genome organization and its functional consequences.

Research topics

• Biology
• Genetics
• Evolutionary biology
• Political Science
• Ecology
• Environmental ethics
• Botany
• Environmental science
• Public relations
• Zoology
• Computational biology
• Horticulture
• Environmental resource management

Selected publications

• Diploid dual assemblies reveal the telocentric structure and extensive allelic heterogeneity of canine genomes

  NAR Genomics and Bioinformatics · 2026-03-21

  articleOpen access

  Although an increasing number of long-read genome assemblies have been created from a diverse collection of dogs and wolves, most published assemblies represent the diploid genome as a single primary sequence. Here, we generate and analyze phase-resolved diploid dual assemblies from five canines. The most contiguous assemblies represent over half of the canine chromosomes as single contigs, permitting an assessment of the sequence and structure of canine chromosomes. Consistent with a telocentric classification, we find that the centromeres of canine autosomes begin an average of 59 kb from the start of the chromosome and are flanked by a 35 kb subtelomeric segment that is repeat-rich and shared across autosomes. Analysis of a pangenome graph constructed from the 10 haplotype-resolved assemblies shows that short tandem repeat loci are three times more common than variable number tandem repeat loci and that the landscape of canine structural variation features extensive allelic heterogeneity. The pangenome graph includes examples of complex, nested allelic variation involving SINEC (a carnivore-specific SINE) and LINE-1 mobile elements. Analysis of 3' transductions implicate an uncharacterized source element with high activity and demonstrates the presence of full-length LINE-1s capable of retrotransposition that are segregating among canines.

  PublisherDOI

• Chromosome-level genomics and historical museum collections reveal new insights into the population structure and chromosome evolution of waterbuck

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-03-19

  preprintOpen access

  ) as an emerging model antelope for studying population dynamics and chromosome evolution. Antelope evolutionary history has been shaped by Robertsonian (Rb) fusions, with waterbuck also showing variation in karyotype due to two polymorphic Rb fusions. These polymorphisms are variable between and within the two recognised subspecies, the common and defassa waterbuck. To provide new insights into waterbuck evolution, we firstly assembled a chromosome-level genome assembly for the defassa subspecies using PacBio HiFi and Hi-C sequencing. We then utilised museum collections to carry out whole genome sequencing (WGS) of 24 historical waterbuck skins from both subspecies. Combined with a previous WGS dataset (n = 119), this represents the largest study of waterbuck populations to date. We found novel population structure and gene flow between waterbuck populations and regions across the genome with high genomic differentiation between the two subspecies. Several of these regions were found around the centromeres of fixed and polymorphic Rb fusions, exhibiting signatures of low recombination and local population structure. Interestingly, these regions contain genes involved in development, fertility, and recombination. Our results highlight the importance of assembling genomes to the chromosome-level, the utility and value of historical collections in sampling a wide-ranging species to uncover fine-scale population structure, and the potential impacts of Rb fusions on genomic differentiation and the recombination landscape.

  PublisherOA PDFDOI

• Geometric Diagrams of Genomes: constructing a visual grammar for 3D genomics

  Genome biology · 2025-06-26 · 1 citations

  articleOpen access

  Advances in the field of three-dimensional (3D) genomics have revealed an ever-expanding array of architectural features that were unknown only a few years ago. Just as ribbon diagrams integrate spatial and symbolic representation to communicate the shape of a protein, the representation of genomes in 3D space requires the development and use of new cartographic symbols and visual conventions. Here, we propose a conceptualized grammar that makes it easier to create visual 3D representations of genomes.

  PublisherOA PDFDOI

• The control of prickle formation in <i>Rubus</i>

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-12-23 · 2 citations

  articleOpen access

  Abstract Prickles on blackberry and raspberry canes make pruning, harvesting, and handling more difficult and can increase labor costs for growers. The trait has been challenging to improve in these clonal crops because it is recessive and linked to undesirable agronomic traits. In blackberry and red raspberry, breeding programs have used recessive mutants at the S locus to generate prickleless cultivars for the last century. In this study, we identified independent loss-of-function mutations in a WUSCHEL-LIKE HOMEOBOX transcription factor, WOX1 , as the genetic basis of the prickleless S locus in both blackberry and red raspberry. We mapped the S locus using integrated genome-wide association, bulked segregant analysis, and identity-by-descent analyses informed by breeding pedigrees. Additionally, we generated a genome sequence from Luther Burbank’s prickleless blackberry variety Burbank Thornless that contained an additional allele of WOX1 . To verify the gene’s role, we used gene editing to knock out WOX1 in an elite prickled commercial blackberry line. All edited plants were prickleless and lacked glandular trichomes, confirming that WOX1 controls a joint developmental pathway. Other plant traits were unchanged, indicating WOX1 is a specific and safe target for improvement. Gene editing can enable breeders to remove prickles directly from elite varieties, reducing the need for extensive breeding cycles and delivering safer, easier-to-harvest cultivars to growers.

  PublisherOA PDFDOI

• WITHDRAWN: ChromPhaser: A HiFi Read Phasing Framework Integrating SNPmers and Hi-C Data

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-10-15

  preprintOpen accessSenior authorCorresponding

  Withdrawal Statement The authors have withdrawn this manuscript because [I didn’t get the approval of all authors]. Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author.

  PublisherOA PDFDOI

• Novel chromosome-length genome assemblies of three distinct subspecies of pine marten, sable, and yellow-throated marten (genus <i>Martes</i> , family Mustelidae)

  Journal of Heredity · 2025-12-05

  article

  The genus Martes consists of medium-sized carnivores within the family Mustelidae that are commonly known as martens, many of which exhibit extensive geographic variation and taxonomic uncertainty. Here, we report chromosome-length genome assemblies for three subspecies, each representing a different marten species: the Tobol sable (Martes zibellina zibellina), the Ural pine marten (Martes martes uralensis), and the Far East yellow-throated marten (Martes flavigula aterrima). Using linked-read sequencing and Hi-C scaffolding, we generated assemblies with total lengths of 2.39 to 2.45 Gbp, N50 values of 137 to 145 Mbp, and high BUSCO scores (93.6% to 96.4%). We identified 19 chromosomal scaffolds for sable and pine marten, and 20 for yellow-throated marten, which agrees with the known karyotypes of these species (2n = 38 and 2n = 40, respectively). Annotation predicted ~ 20,000 protein-coding genes per genome, of which > 90% were assigned functional names. Repeats encompass 36.9% to 40.4% of the assemblies, with a prevalence of LINEs and SINEs, and are conservative across the genus. Synteny analysis of our generated and available marten genome assemblies revealed assembly artifacts in previously published assemblies, which we confirmed through investigation of Hi-C contact maps. Among other rearrangements, we verify a sable-specific inversion on chromosome 11 using the published cytogenetic data. Our assemblies broaden the genomic resources available for Martes, extending coverage to geographically distant and taxonomically significant subspecies. Together, they provide a robust framework for assessing intraspecific genetic diversity, identifying signatures of hybridization, and refining the complex taxonomy of the genus. Beyond conservation and evolutionary applications, these references will facilitate comparative genomics across Mustelidae and other carnivorans.

  PublisherDOI

• Chromosome‐Level Genomics and Historical Museum Collections Reveal New Insights Into the Population Structure and Chromosome Evolution of Waterbuck

  Molecular Ecology · 2025-12-22

  articleOpen access

  Advances in sequencing and chromosome-scale assembly have brought non-model animals into focus, deepening our understanding of genome and chromosome evolution. Here, we present the waterbuck (Kobus ellipsiprymnus) as an emerging model antelope for studying population dynamics and chromosome evolution. Waterbuck evolutionary history has been shaped by both climatic and geographic changes, as well as structural chromosome changes, principally Robertsonian (Rb) fusions. To provide new insights into waterbuck evolution, we generated a chromosome-level genome assembly for the species using PacBio HiFi and Hi-C sequencing. We further leveraged museum collections to perform whole genome sequencing (WGS) of 24 historical specimens. Combined with a previous WGS dataset (n = 119), this represents the largest study of waterbuck populations to date and reveals previously unrecognised population structure and gene flow between waterbuck populations, alongside several regions of high genomic differentiation between the two recognised subspecies. Notably, several differentiation hotspots occur near the centromeres of fixed and polymorphic Rb fusions, exhibiting signatures of low recombination and local population structure. These regions contain genes involved in development, fertility, and recombination. Our findings underscore the value of chromosome-level genome assemblies, the critical role of historical collections in capturing fine-scale population structure and gene flow in species with wide-ranging distributions, and the potential evolutionary impacts of Rb fusions on genomic differentiation and recombination landscapes.

  PublisherOA PDFDOI

• Otolith and Genomic Data Reveal Temporal Insights Into Stocking Across a Large River Basin in a Mobile, Long‐Lived Australian Freshwater Fish Species

  Molecular Ecology · 2025-03-05 · 3 citations

  articleOpen access

  ABSTRACT Freshwater ecosystems and their biota are under increasing pressure from anthropogenic stressors. In response to declining fish stocks, hatchery and stocking programmes are widely implemented as core components of restoration and management strategies, with positive outcomes for some wild populations. Despite this, stocking remains contentious due to potential genetic and ecological risks to wild populations. Monitoring and evaluation of stocking outcomes are critical to ensuring the long‐term sustainability of wild populations, but identification of stocked individuals post‐release remains a key challenge, particularly for mobile species. In this study, we combined otolith (natal origin and age) and genomic data to identify stocked individuals and evaluate the genetic implications of stocking for a culturally and socioeconomically important and mobile freshwater fish, golden perch Macquaria ambigua (family: Percichthyidae), across Australia's Murray–Darling Basin (MDB). We also generated a chromosome‐level genome assembly. Many close kin were detected across the MDB, increasing in prevalence over recent decades and mostly of hatchery origin. Rivers with many close kin were associated with low effective population sizes ( N e &lt; 100). Genetic signatures of stocking varied according to local context, being most pronounced in but not restricted to rivers considered functionally isolated for management purposes. Where fish are stocked into rivers that are part of the connected metapopulation, there is scope to modify current stocking practices to avoid over‐representation of related stocked individuals. Increased focus on the genetic diversity of stocked fish is likely to promote the long‐term persistence of golden perch in the wild.

  PublisherOA PDFDOI

• Chromosome-length genome assembly of the stone marten (<i>Martes foina</i>, Mustelidae): A new view on one of the cornerstones in carnivore cytogenetics

  Journal of Heredity · 2025-01-29 · 5 citations

  article

  The stone marten (Martes foina) is an important species for cytogenetic studies in the order Carnivora. ZooFISH probes created from its chromosomes provided a strong and clean signal in chromosome painting experiments and were valuable for studying the evolution of carnivoran genome architecture. The research revealed that the stone marten chromosome set is similar to the presumed ancestral karyotype of the Carnivora, which added an additional value for the species. Using linked-read and Hi-C sequencing, we generated a chromosome-length genome assembly of a male stone marten (Gansu province, China) from a primary cell line. The stone marten assembly had a length of 2.42 Gbp, scaffold N50 of 144 Mbp, and a 96.2% BUSCO completeness score. We identified 19 chromosomal scaffolds (2n = 38) and assigned them chromosome ids based on chromosome painting data. Annotation identified 20,087 protein-coding gene models, of which 18,283 were assigned common names. Comparison of the stone marten assembly with the cat, dog, and human genomes revealed several small syntenic blocks absent on the published painting maps. Finally, we assessed the heterozygosity and its distribution over the chromosomes. The detected low heterozygosity level (0.4 hetSNPs/kbp) and the presence of long runs of homozygosity require further research and a new evaluation of the conservation status of the stone marten in China. Combined with available carnivoran genomes in large-scale synteny analysis, the stone marten genome will highlight new features and events in carnivoran evolution, hidden from cytogenetic approaches.

  PublisherDOI

• Chromosome-length genome assembly of the critically endangered Mountain bongo (<i>Tragelaphus eurycerus isaaci):</i> a resource for conservation and comparative genomics

  G3 Genes Genomes Genetics · 2025-05-15 · 1 citations

  articleOpen access

  The Mountain bongo (Tragelaphus eurycerus isaaci), a critically endangered tragelaphine antelope native to the montane forests of Kenya, faces significant threats from habitat loss and hunting. Although the Mountain bongo is a flagship species in Kenya, the majority are found in small, isolated populations of less than 100 animals total, making it a species of high conservation concern. In this report, we present a chromosome-length draft genome assembly for the Mountain bongo, generated using a combination of linked-read and proximity ligation (Hi-C) sequencing techniques. The assembly resulted in a 2.96 Gb sized genome with a contig N50 of 79.5 kb and a scaffold N50 of 192 Mb. Assembly completeness was 95.1% based on 12,234 Benchmarking Universal Single-Copy Orthologs (BUSCO) and annotation revealed 29,820 protein-coding genes, of which 27,761 were functionally annotated, and a repetitive content of 47.31%. Synteny analysis against the domestic cattle (Bos taurus) genome assembly revealed numerous chromosomal rearrangements between the 2 species. Our analysis also revealed insights into the evolutionary and demographic history of the Mountain bongo, offering valuable information for conservation management. We also assembled and annotated the mitochondrial genome which showed <1% differences from the Lowland bongo subspecies, T. e. eurycerus. By integrating genomic data with traditional conservation methods, this reference lays the foundation to evaluate and preserve genetic diversity of both in situ and ex situ populations of the Mountain bongo amidst growing environmental pressures.

  PublisherOA PDFDOI

Frequent coauthors

• Olga Dudchenko

  Baylor College of Medicine

  880 shared

• Neva C. Durand

  362 shared

• Suhas S.P. Rao

  251 shared

• Eric S. Lander

  Broad Institute

  236 shared

• Arina D. Omer

  Baylor College of Medicine

  223 shared

• Muhammad S. Shamim

  201 shared

• David Weisz

  Baylor College of Medicine

  186 shared

• Michele Di Pierro

  Northeastern University

  122 shared

Labs

• Aiden LabPI

  The Center for Genome Architecture