A5028159435- Topic Modeling
- Genetics, Aging, and Longevity in Model Organisms
- Natural Language Processing Techniques
- Genetics and Neurodevelopmental Disorders
- Autism Spectrum Disorder Research
- Multimodal Machine Learning Applications
- RNA modifications and cancer
- Cell Image Analysis Techniques
- Advanced Fluorescence Microscopy Techniques
- CRISPR and Genetic Engineering
- Single-cell and spatial transcriptomics
- Genomic variations and chromosomal abnormalities
- Bioinformatics and Genomic Networks
- Cancer Cells and Metastasis
- Text Readability and Simplification
- Evolution and Genetic Dynamics
- Genetic Associations and Epidemiology
- Domain Adaptation and Few-Shot Learning
- Genetic Mapping and Diversity in Plants and Animals
- Chromosomal and Genetic Variations
- Cancer-related molecular mechanisms research
- Sentiment Analysis and Opinion Mining
- Epigenetics and DNA Methylation
- Speech Recognition and Synthesis
- Genomics and Chromatin Dynamics
Hebrew University of Jerusalem
2012-2024
University of California, Los Angeles
2016-2023
Technion – Israel Institute of Technology
2020-2022
Illumina (United States)
2022
Howard Hughes Medical Institute
2017-2021
Institute of Life Sciences
2011
Autism spectrum disorders (ASD) are neurodevelopmental with phenotypic and genetic heterogeneity. Recent studies have reported rare de novo mutations in ASD, but the allelic architecture of ASD remains unclear. To assess role common variations we constructed a gene co-expression network based on widespread survey expression human brain. We identified modules associated specific cell types processes. By integrating known results an genome-wide association study (GWAS), two neuronal that...
Selfish genetic interactions in nematodes Identifying the effects and evolution of selfish elements can be difficult because their biased inheritance. Ben-David et al. identified a element that drives maternal-effect lethality nematode Caenorhabditis elegans (see Perspective by Phadnis). This incompatibility stems from interaction between maternally deposited toxin zygotically expressed antidote. Interestingly, antidote is encoded gene pha-1 , which has been described as an essential...
Abstract Natural Language Processing algorithms have made incredible progress, but they still struggle when applied to out-of-distribution examples. We address a challenging and underexplored version of this domain adaptation problem, where an algorithm is trained on several source domains, then examples from unseen domains that are unknown at training time. Particularly, no examples, labeled or unlabeled, any other knowledge about the target available present PADA: An example-based...
Abstract Recombination events are not uniformly distributed and often cluster in narrow regions known as recombination hotspots. Several studies using different approaches have dramatically advanced our understanding of hotspot regulation. Population genetic data been used to map quantify hotspots the human genome. Genetic variation rates usage explored pedigrees, mouse intercrosses, by sperm typing. These pointed central role PRDM9 gene modulation. In this study, we single nucleotide...
Recurrent genomic instability in cancer is attributed to positive selection and/or the sensitivity of specific regions breakage. Among these are fragile sites (FSs), sensitive replication stress conditions induced by DNA polymerase inhibitor aphidicolin. However, basis for majority hotspots remains unclear. Aberrant oncogene expression induces stress, leading breaks and instability. Here we map cytogenetic locations oncogene-induced FSs show that same cells, each creates a unique fragility...
Loss of flight in the Galapagos cormorant Although rare among existing birds, loss appears to have occurred multiple times evolutionary history. However, genetic changes that ground avian species are not well understood. Burga et al . sequenced genomes from three and compared them with flightless (see Perspective by Cooper). They identified variants genes involved primary ciliogenesis. Functional analyses these suggest impaired function may be responsible for skeletal associated cormorant’s...
Abstract The sexual strain of the planarian Schmidtea mediterranea , indigenous to Tunisia and several Mediterranean islands, is a hermaphrodite 1,2 . Here we isolate individual chromosomes use sequencing, Hi-C 3,4 linkage mapping assemble chromosome-scale genome reference. map reveals an extremely low rate recombination on chromosome 1. We confirm suppression 1 by genotyping sperm cells oocytes. show that previously identified genomic regions maintain heterozygosity even after prolonged...
Abstract Genomic imprinting—the non-equivalence of maternal and paternal genomes—is a critical process that has evolved independently in many plant mammalian species 1,2 . According to kinship theory, imprinting is the inevitable consequence conflictive selective forces acting on differentially expressed parental alleles 3,4 Yet, how these epigenetic differences evolve first place poorly understood 3,5,6 Here we report identification molecular dissection parent-of-origin effect gene...
Recent work has led to the identification of several susceptibility genes for autism spectrum disorder (ASD) and an increased appreciation importance rare de novo mutations. Some mutations may be very hard detect using current strategies, especially if they are located in regulatory regions. We present a new approach identify functional that exploit fact many disrupt expression from single parental chromosome. The method incorporates measurement relative two copies gene across genome...
Genetic susceptibility to intellectual disability (ID), autism spectrum disorder (ASD), and schizophrenia (SCZ) often arises from mutations in the same genes, suggesting that they share common mechanisms. We studied genes with de novo three disorders implicated SCZ by genome-wide association study (GWAS). Using biological annotations brain gene expression, we show mutation class explains enrichment patterns more than specific disorder. Genes loss-of-function missense were associated...
Genetic studies of complex traits in animals have been hindered by the need to generate, maintain, and phenotype large panels recombinant lines. We developed a new method, C. elegans eXtreme Quantitative Trait Locus (ceX-QTL) mapping, that overcomes this obstacle via bulk selection on millions unique individuals. use ceX-QTL map drug resistance locus with high resolution. also differences gene expression live worms discovered mutations co-chaperone sti-1 upregulate transcription HSP-90....
Pivot-based neural representation models have led to significant progress in domain adaptation for NLP. However, previous research following this approach utilize only labeled data from the source and unlabeled target domains, but neglect incorporate massive corpora that are not necessarily drawn these domains. To alleviate this, we propose PERL: A learning model extends contextualized word embedding such as BERT (Devlin et al., 2019 ) with pivot-based fine-tuning. PERL outperforms strong...
Toxin-antidote elements (TAs) are selfish genetic dyads that spread in populations by selectively killing non-carriers. TAs common prokaryotes, but very few examples known animals. Here, we report the discovery of maternal-effect both C. tropicalis and briggsae, two distant relatives elegans. In tropicalis, multiple combine to cause a striking degree intraspecific incompatibility: five reduce fitness >70% F2 hybrid progeny Caribbean isolates. We identified genes underlying one novel TAs,...
Genetic regulation of gene expression underlies variation in disease risk and other complex traits. The effect quantitative trait loci (eQTLs) varies across cell types; however, the complexity mammalian tissues makes studying cell-type eQTLs highly challenging. We developed a novel approach model nematode Caenorhabditis elegans that uses single-cell RNA sequencing to map at cellular resolution single one-pot experiment. mapped types an extremely large population genetically distinct C....
Marine algae are responsible for half of the world's primary productivity, but this critical carbon sink is often constrained by insufficient iron. One species marine algae, Dunaliella tertiolecta , remarkable its ability to maintain photosynthesis and thrive in low-iron environments. A related species, salina Bardawil, shares attribute an extremophile found hypersaline To elucidate how manage their iron requirements, we produced high-quality genome assemblies transcriptomes both serve as a...
Several different interventions improve depressed mood, including medication and environmental factors such as regular physical exercise. The molecular pathways underlying these effects are still not fully understood. In this study, we sought to identify shared mechanisms antidepressant interventions. We studied three groups of mice: mice treated with a widely used drug--fluoxetine, engaged in voluntary exercise, living an enriched environment. hippocampi were investigated at the cellular...
Understanding the genetic basis of gene expression can shed light on regulatory mechanisms underlying complex traits and diseases. Single-cell resolved measures RNA levels single-cell quantitative trait loci (sc-eQTLs) have revealed regulation that drives sub-tissue cell states types across diverse human tissues. Here, we describe first phase TenK10K, largest-to-date dataset matched whole-genome sequencing (WGS) RNA-sequencing (scRNA-seq). We leverage scRNA-seq data from over 5 million cells...
Transcription factors (TFs) establish cell identity during development by binding regulatory DNA in a sequence-specific manner, often promoting local chromatin accessibility, and regulating gene expression. Mapping accessible offers critical insights into transcriptional control, but available datasets for human are restricted to bulk tissue, single organs, or modalities. Here, we present the Human Development Multiomic Atlas (HDMA), single-cell atlas of accessibility expression from 817,740...
Natural language processing (NLP) algorithms have become very successful, but they still struggle when applied to out-of-distribution examples. In this paper we propose a controllable generation approach in order deal with domain adaptation (DA) challenge. Given an input text example, our DoCoGen algorithm generates domain-counterfactual textual example (D-con) - that is similar the original all aspects, including task label, its changed desired one. Importantly, trained using only unlabeled...
Though extensively characterized clinically, the causes of autism spectrum disorder (ASD) remain a mystery. ASD is known to have strong genetic basis, but it genetically very heterogeneous. Recent studies estimated that de novo disruptive mutations in hundreds genes may contribute ASD. However, unclear how possible for so many different findings suggest disrupt involved transcription regulation are expressed prenatally developing brain. De also more frequent girls with ASD, despite fact...