Eran Elhaik

Eran Elhaik
The University of Sheffield | Sheffield · Department of Animal and Plant Sciences

37.08
 · 
Ph.D

About

99
Publications
27,915
Reads
How we measure 'reads'
A 'read' is counted each time someone views a publication summary (such as the title, abstract, and list of authors), clicks on a figure, or views or downloads the full-text. Learn more
8,698
Citations
Introduction
All my publications are available at my website. Please check out the available positions at my website (under Students) http://www.eranelhaiklab.org/
Research Experience
January 2014 - present
The University of Sheffield
Position
  • Lecturer
July 2013 - present
Johns Hopkins University
Position
  • Research Associate
January 2009 - June 2011
Johns Hopkins Medicine
Position
  • Research Assistant

Publications

Publications (99)
Preprint
The past years saw the rise of genomic biobanks and mega-scale meta-analysis of genomic data that promise to reveal the genetic underpinnings of health and disease. However, the over-representation of Europeans in genomic studies not only limit the global understanding of disease risk and intervention efficacy, but also inhibit viable research into...
Preprint
Full-text available
Advancements in DNA methods and biotechnology have enabled forensic scientists to explore the DNA evidence found as part of a criminal investigation on a much more comprehensive and predictive level. This has led to a rise in research into DNA intelligence tools such as phenotypic prediction (i.e., eye and hair colour) and inference of biogeographi...
Preprint
Full-text available
Recently, Mikheyev et al. (2019) have produced a preprint study describing the genomes of nine Khazars archeologically dated from the 7th to the 9th centuries found in the Rostov county in modern-day Russia. Skull morphology indicated a mix of "Caucasoid" and "Mongoloid" shapes. The authors compared the samples to ancient and contemporary samples t...
Article
Purpose: Multiple myeloma (MM) is a plasma cell (PC) malignancy with an increasing incidence in the US. Epidemiological studies demonstrate a 2-3 fold higher incidence of the pre-malignant monoclonal gammopathy of undetermined significance (MGUS) and MM with a ~4-year younger age of onset among African Americans (AA) compared to European Americans...
Preprint
Full-text available
Radiocarbon dating is the gold-standard in archaeology to estimate the age of skeletons, a key to studying their origins. Half of all published ancient human genomes lack reliable and direct dates, which results in obscure and contradictory reports. We developed Temporal Population Structure (TPS), the first DNA-based dating method for ancient geno...
Article
Full-text available
Gastric cancer (GC) is the fifth most common type of cancer worldwide with high incidences in Asia, Central, and South American countries. This patchy distribution means that GC studies are neglected by large research centers from developed countries. The need for further understanding of this complex disease, including the local importance of epid...
Preprint
Full-text available
Although studies have shown that urban environments and mass-transit systems have geospatially distinct metagenomes, no study has ever systematically studied these dense, human/microbial ecosystems around the world. To address this gap in knowledge, we created a global metagenomic and antimicrobial resistance (AMR) atlas of urban mass transit syste...
Preprint
Full-text available
The Glucocorticoid Receptor (GR) co-ordinates metabolic and behavioural responses to stressors. We hypothesised that GR influences behaviour by modulating specific epigenetic and transcriptional processes in the brain. Using the zebrafish as a model organism, the brain methylomes of wild-type and gr s357 mutant adults were analysed and GR-sensitive...
Article
Full-text available
The rapid accumulation of ancient human genomes from various areas and time periods potentially enables the expansion of studies of biodiversity, biogeography, forensics, population history, and epidemiology into past populations. However, most ancient DNA (aDNA) data were generated through microarrays designed for modern-day populations, which are...
Article
Full-text available
Monoclonal gammopathies, including multiple myeloma (MM), represent a group of plasma cell (PC) disorders that comprise of mostly incurable hematopoietic malignancies with an increasing incidence in the US. Previous epidemiological studies demonstrated a 2-3 fold higher incidence of monoclonal gammopathy of undetermined significance (MGUS) and a si...
Article
Full-text available
Motivation: In clinical trials, individuals are matched using demographic criteria, paired, and then randomly assigned to treatment and control groups to determine a drug's efficacy. A chief cause for the irreproducibility of results across pilot to Phase III trials is population stratification bias caused by the uneven distribution of ancestries...
Article
Full-text available
Multiple myeloma (MM) is two- to three-fold more common in African Americans (AAs) compared to European Americans (EAs). This striking disparity, one of the highest of any cancer, may be due to underlying genetic predisposition between these groups. There are multiple unique cytogenetic subtypes of MM, and it is likely that the disparity is associa...
Preprint
Full-text available
Sudden Infant Death Syndrome (SIDS) is the most common cause of postneonatal infant death. The allostatic load hypothesis posits that SIDS is the result of perinatal cumulative painful, stressful, or traumatic exposures that tax neonatal regulatory systems. To test it, we explored the relationships between SIDS and two common stressors, male neonat...
Article
Sudden Infant Death Syndrome (SIDS) is the most common cause of postneonatal infant death. The allostatic load hypothesis posits that SIDS is the result of perinatal cumulative painful, stressful, or traumatic exposures that tax neonatal regulatory systems. To test it, we explored the relationships between SIDS and two common stressors, male neonat...
Preprint
Full-text available
The rapid accumulation of ancient human genomes from various places and time periods, mainly from the past 15,000 years, allows us to probe the past with an unparalleled accuracy and reconstruct trends in human biodiversity. Alongside providing novel insights into the population history, population structure permits correcting for population strati...
Article
Full-text available
Background Sudden infant death syndrome (SIDS) is the most common cause of postneonatal unexplained infant death. The allostatic load hypothesis posits that SIDS is the result of cumulative perinatal painful, stressful, or traumatic exposures that tax neonatal regulatory systems. Aims To test the predictions of the allostatic load hypothesis we ex...
Article
Full-text available
The public commonly associates microorganisms with pathogens. This suspicion of microorganisms is understandable, as historically microorganisms have killed more humans than any other agent while remaining largely unknown until the late seventeenth century with the works of van Leeuwenhoek and Kircher. Despite our improved understanding regarding m...
Article
Full-text available
The human population displays wide variety in demographic history, ancestry, content of DNA derived from hominins or ancient populations, adaptation, traits, copy number variation (CNVs), drug response, and more. These polymorphisms are of broad interest to population geneticists, forensics investigators, and medical professionals. Historically, mu...
Article
Full-text available
Recently, the geographical origins of Ashkenazic Jews (AJs) and their native language Yiddish were investigated by applying the Geographic Population Structure (GPS) to a cohort of exclusively Yiddish-speaking and multilingual AJs. GPS localized most AJs along major ancient trade routes in northeastern Turkey adjacent to primeval villages with name...
Article
Full-text available
The Druze are an aggregate of communities in the Levant and Near East living almost exclusively in the mountains of Syria, Lebanon and Israel whose ~1000 year old religion formally opposes mixed marriages and conversions. Despite increasing interest in genetics of the population structure of the Druze, their population history remains unknown. We i...
Article
Full-text available
Nature Communications 5 : Article number: 3513 10.1038/ncomms4513 ( 2014 ); Published: 29 April 2016 ; Updated: 31 October 2016 This article was published without any competing financial interests statement.
Article
Full-text available
Sudden infant death syndrome (SIDS) is the leading cause of death among USA infants under 1 year of age accounting for ~2,700 deaths per year. Although formally SIDS dates back at least 2,000 years and was even mentioned in the Hebrew Bible (Kings 3:19), its etiology remains unexplained prompting the CDC to initiate a sudden unexpected infant death...
Article
Full-text available
The term 'ancient DNA' (aDNA) is coming of age, with over 1,200 hits in the PubMed database, beginning in the early 1980s with the studies of 'molecular paleontology'. Rooted in cloning and limited sequencing of DNA from ancient remains during the pre-PCR era, the field has made incredible progress since the introduction of PCR and next-generation...
Article
Full-text available
The debate as to whether Jewishness is a biological trait inherent from an “authentic” “Jewish type” (jüdische Typus) ancestor or a system of beliefs has been raging for over two centuries. While the accumulated biological and anthropological evidence support the latter argument, recent genetic findings, bolstered by the direct-to-consumer genetic...
Article
Full-text available
Recently, we investigated the geographical origins of Ashkenazic Jews (AJs) and their native language Yiddish by applying a biogeographical tool, the Geographic Population Structure (GPS), to a cohort of 367 exclusively Yiddish-speaking and multilingual AJs genotyped on the Genochip microarray. GPS localized most AJs along major ancient trade route...
Article
Full-text available
The Metagenomics and Metadesign of the Subways and Urban Biomes (MetaSUB) International Consortium is a novel, interdisciplinary initiative comprised of experts across many fields, including genomics, data analysis, engineering, public health, and architecture. The ultimate goal of the MetaSUB Consortium is to improve city utilization and planning...
Article
Full-text available
The Yiddish language is over one thousand years old and incorporates German, Slavic, and Hebrew elements. The prevalent view claims Yiddish has a German origin, whereas the opposing view posits a Slavic origin with strong Iranian and weak Turkic substrata. One of the major difficulties in deciding between these hypotheses is the unknown geographica...
Article
Full-text available
In general, community similarity is thought to decay with distance; however, this view may be complicated by the relative roles of different ecological processes at different geographical scales, and by the compositional perspective (e.g. species, functional group and phylogenetic lineage) used. Coastal salt marshes are widely distributed worldwide...
Conference Paper
Full-text available
The Yiddish language is a curious amalgam of Hebrew, German, and Slavonic. It is written in Hebrew characters and spoken primarily by European Jews of Central and Eastern Europe. Due to its mixed nature, it is very difficult to trace the origin of this language using traditional linguistic approaches. Given the close association between languages,...
Article
Full-text available
For the past four decades the compositional organization of the mammalian genome posed a formidable challenge to molecular evolutionists attempting to explain it from an evolutionary perspective. Unfortunately, most of the explanations adhered to the "isochore theory," which has long been rebutted. Recently, an alternative compositional domain mode...
Article
Full-text available
Earlier this year, we published a scathing critique of a paper by Mendez et al. (2013) in which the claim was made that a Y chromosome was 237,000-581,000 years old. Elhaik et al. (2014) also attacked a popular article in Scientific American by the senior author of Mendez et al. (2013), whose title was "Sex with other human species might have been...
Article
Full-text available
The search for a method that utilizes biological information to predict humans' place of origin has occupied scientists for millennia. Over the past four decades, scientists have employed genetic data in an effort to achieve this goal but with limited success. While biogeographical algorithms using next-generation sequencing data have achieved an a...
Article
Full-text available
The search for a method that utilizes biological information to predict humans’ place of origin has occupied scientists for millennia. Over the past four decades, scientists have employed genetic data in an effort to achieve this goal but with limited success. While biogeographical algorithms using next-generation sequencing data have achieved an a...
Article
Full-text available
The first generation of genome sequence assemblies and annotations have had a significant impact upon our understanding of the biology of the sequenced species, the phylogenetic relationships among species, the study of populations within and across species, and have informed the biology of humans. As only a few Metazoan genomes are approaching fin...
Article
Full-text available
Mendez and colleagues reported the identification of a Y chromosome haplotype (the A00 lineage) that lies at the basal position of the Y chromosome phylogenetic tree. Incorporating this haplotype, the authors estimated the time to the most recent common ancestor (TMRCA) for the Y tree to be 338 000 years ago (95% CI=237 000-581 000). Such an extrao...
Article
Full-text available
The methylation of cytosines at CpG dinucleotides, which plays an important role in gene expression regulation, is one of the most studied epigenetic modifications. Thus far, the detection of DNA methylation has been determined mostly by experimental methods, which are not only prone to bench effects and artifacts but are also time-consuming, expen...
Article
Full-text available
Background. The GC-content in the third codon position (GC3) exhibits a unimodal distribution in many plant and animal genomes. Interestingly, grasses and homeotherm vertebrates exhibit a unique bimodal distribution. High GC3 was previously found to be associated with variable expression, higher frequency of upstream TATA boxes, and an increase of...
Article
Full-text available
The Genographic Project is an international effort aimed at charting human migratory history. The project is nonprofit and non-medical, and, through its Legacy Fund, supports locally led efforts to preserve indigenous and traditional cultures. Although the first phase of the project was focused on uniparentally inherited markers on the Y-chromosome...
Article
Full-text available
Genomes of eusocial insects code for dramatic examples of phenotypic plasticity and social organization. We compared the genomes of seven ants, the honeybee, and various solitary insects to examine whether eusocial lineages share distinct features of genomic organization. Each ant lineage contains ~4,000 novel genes, but only 64 of these genes are...
Article
Full-text available
Eukaryotic genomes, particularly animal genomes, have a complex, nonuniform, and nonrandom internal compositional organization. The compositional organization of animal genomes can be described as a mosaic of discrete genomic regions, called “compositional domains,” each with a distinct GC content that significantly differs from those of its upstre...
Article
Full-text available
A recent slew of ENCODE Consortium publications, specifically the article signed by all Consortium members, put forward the idea that more than 80% of the human genome is functional. This claim flies in the face of current estimates according to which the fraction of the genome that is evolutionarily conserved through purifying selection is under 1...
Article
Full-text available
The Genographic Project is an international effort using genetic data to chart human migratory history. The project is non-profit and non-medical, and through its Legacy Fund supports locally led efforts to preserve indigenous and traditional cultures. In its second phase, the project is focusing on markers from across the entire genome to obtain a...
Article
Full-text available
The question of Jewish ancestry has been the subject of controversy for over two centuries and has yet to be resolved. The "Rhineland Hypothesis" depicts Eastern European Jews as a "population isolate" that emerged from a small group of German Jews who migrated eastward and expanded rapidly. Alternatively, the "Khazarian Hypothesis" suggests that E...
Article
Full-text available
Studies of the apportionment of human genetic variation have long established that most human variation is within population groups and that the additional variation between population groups is small but greatest when comparing different continental populations. These studies often used Wright's F(ST) that apportions the standardized variance in a...
Data
FST values of SNPs from the continental dataset versus their expected exponential values. FST values were calculated for all SNPs (red), excluding rare ones (MAF <0.05) (blue) for autosomal (a) and X-chromosomal (b) SNPs. (TIF)
Data
A histogram of the distances between adjacent F ST>threshold SNPs for five allele frequency groups. (TIF)
Data
Assessing data quality, F-statistics for measuring population differentiation, and Supporting Information References. (DOC)
Data
Fitting the expected cumulative distribution function of an exponential distribution to the FST distribution. The two distributions largely overlap. (TIF)
Data
LD for five allele frequency groups as a function of physical distance in Asians. LD (r2) in Asian populations is plotted as a function of physical distance on a log-scale for five allele frequency groups (a–e). To simplify the presentation, the mean and standard error of the mean r2 for the FST >threshold SNPs (blue) and FST<threshold (red) are pr...
Data
Summary of HapMap phase 3 (second draft) data used in our analyses. The number of SNPs that passed or failed QC++ (top) and the number of unrelated samples that passed or failed QC++ (bottom). (DOC)
Data
Summary of SNP statistics per chromosome. Number of SNPs segregating in all samples within the continental dataset, SNPs density, mean and standard deviation of MAF, and mean and standard deviation of FST for each chromosome. (DOC)
Data
Distribution of genetic variation per HapMap population and phase. SNPs were classified in ten minor allele groups based on their frequency in each population and further subdivided by HapMap phases: 1 (blue), 2 (green), and 3 (red). The number of SNPs genotyped in each phase (n1..3) and the total number of SNPs (ntot) are marked. (TIF)
Data
Distribution of locus-specific FST in eight populations (CEU, CHB, CHD, JPT, LWK, MKK, YRI, and TSI). FST values were obtained for a. 1,100,484 autosomal SNPs, and b. 32,650 SNPs on the non-recombining region of the X chromosome. The histograms show bin distribution as indicated on the x-axis and the cumulative distribution (line). (TIF)
Data
LD for five allele frequency groups as a function of physical distance in Europeans. LD (r2) in European populations is plotted as a function of physical distance on a log-scale for five allele frequency groups (a–e). To simplify the presentation, the mean and standard error of the mean r2 for the FST >threshold SNPs (blue) and FST<threshold (red)...
Article
Full-text available
The rapidly growing amount of genomic sequence data being generated and made publicly available necessitate the development of new data storage and archiving methods. The vast amount of data being shared and manipulated also create new challenges for network resources. Thus, developing advanced data compression techniques is becoming an integral pa...
Article
Full-text available
We describe the distribution of Guanine and Cytosine (GC) content in the third codon position (GC3) distributions in different species, analyze evolutionary trends and discuss differences between genes and organisms with distinct GC3 levels. We scrutinize previously published theoretical frameworks and construct a unified view of GC3 biology in euk...
Article
Full-text available
The Neuregulin-ErbB4 pathway plays a crucial role in brain development and constitutes one of the most biologically plausible signaling pathways implicated in schizophrenia and, to a lesser extent, in bipolar disorder (BP). However, recent genome-wide association analyses have not provided evidence for common variation in NRG1 or ERBB4 influencing...
Article
Full-text available
Ants are some of the most abundant and familiar animals on Earth, and they play vital roles in most terrestrial ecosystems. Although all ants are eusocial, and display a variety of complex and fascinating behaviors, few genomic resources exist for them. Here, we report the draft genome sequence of a particularly widespread and well-studied species,...
Article
Full-text available
We report the draft genome sequence of the red harvester ant, Pogonomyrmex barbatus. The genome was sequenced using 454 pyrosequencing, and the current assembly and annotation were completed in less than 1 y. Analyses of conserved gene groups (more than 1,200 manually annotated genes to date) suggest a high-quality assembly and annotation comparabl...
Article
Full-text available
Leaf-cutter ants are one of the most important herbivorous insects in the Neotropics, harvesting vast quantities of fresh leaf material. The ants use leaves to cultivate a fungus that serves as the colony's primary food source. This obligate ant-fungus mutualism is one of the few occurrences of farming by non-humans and likely facilitated the forma...