My Research
Complex Disorders We seek to identify the genetic and environmental factors involved in Sudden Infant Death Syndrome (SIDS), Autism, ALS, and Multiple Myeloma. We analyze environmental and genomic (DNA and RNA-seq) data. We carry out genomic and epidemiologic studies, either independently or in collaboration with leading labs in the US, Singapore, and the UK. We ask questions such as:
1. Movert E, et al. 2023. Interplay between human STING genotype and bacterial NADase activity regulates inter-individual disease variability. Nat. Commun. 14:4008. 2. Eachus H, et al. 2023. Glucocorticoid receptor regulates protein chaperone, circadian clock and affective disorder genes in the zebrafish brain. Disease Models & Mechanisms. 16. 3. Zhang S, et al. 2022. Genome-wide identification of the genetic basis of amyotrophic lateral sclerosis. Neuron. 4. Aguiar-Pulido V, et al. 2021. Systems biology analysis of human genomes points to key pathways conferring spina bifida risk. Proc. Natl. Acad. Sci. U.S.A. 118:e2106844118. |
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Population Genetics We develop microarrays, models, and novel tools and apply them to understand population history. We analyze DNA data from modern-day populations, using a diverse range of tools, including our own AI-based tools, to reconstruct their history We ask questions such as:
1. Elhaik E. 2022. Principal Component Analyses (PCA)-based findings in population genetic studies are highly biased and must be reevaluated. Sci. Rep. 12:14683. 2. Elhaik E, Ryan DM. 2019. Pair Matcher (PaM): fast model-based optimisation of treatment/case-control matches. Bioinformatics. 35:2243-2250. 3. Das R, et al. 2017. The Origins of Ashkenaz, Ashkenazic Jews, and Yiddish. Front. Genet. 8. |
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Paleogenetics We develop advanced models and AI-based tools and apply them to ancient DNA data to reconstruct history. We analyze ancient DNA data from humans and non-humans to understand how they migrated and interacted with one another. We ask questions such as:
1. Behnamian S, et al. 2022. Temporal population structure, a genetic dating method for ancient Eurasian genomes from the past 10,000 years. Cell Reports Methods. 2. 2. Esposito U, et al. 2018. Ancient Ancestry Informative Markers for Identifying Fine-Scale Ancient Population Structure in Eurasians. Gene. 9:625. 3. Freeman L, et al. 2020. aYChr-DB: a database of ancient human Y haplogroups. NAR genom. bioinform. 2. |
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Microbiome and Forensics We develop forensic tools to study how to trace microbiome and AMR genes. We analyze microbiome and human metadata to understand where did they come from. We ask questions such as:
1. Zhang Y, et al. 2023. The microbial biodiversity at the archeological site of Tel Megiddo (Israel). Front. microbiol. 14:1253371. 2. Danko D, et al. 2021. A global metagenomic map of urban microbiomes and antimicrobial resistance. Cell. 184:3376-3393.e3317. 3. Robinson JM, et al. 2021. Forensic Applications of Microbiomics: A Review. Front. microbiol. 11. |
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Molecular Evolution We develop and evaluate methods for studying selection and evolution. We analyze genomic data from humans and non-humans and use simulations to understand the evolutionary processes that have affected our genes. We consider ourselves genomic archeologists who seek to dig and date genes using evolutionary approaches. We ask questions such as:
1. Elhaik E, Graur D. 2021. On the Unfounded Enthusiasm for Soft Selective Sweeps III: The Supervised Machine Learning Algorithm That Isn’t. Genes. 12:527. 2. Elhaik E, Graur D. 2014. A Comparative Study and a Phylogenetic Exploration of the Compositional Architectures of Mammalian Nuclear Genomes. PLoS Comput. Biol. 10:e1003925. 3. Graur D, et al. 2013. On the immortality of television sets: "function" in the Human genome according to the evolution-free gospel of ENCODE. Genome Biol. Evol. 5:578-590. |
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