
Professor
Bioengineering
+1 415 476-1838
Custom People Group
The Ahituv lab is focused on identifying gene regulatory elements and linking nucleotide variation within them to various phenotypes including morphological differences between species, drug response and human disease. It develops and uses massively parallel reporter assays (MPRAs) that allow for high-throughput functional characterization of gene regulatory elements. In addition, the lab pioneered cis-regulation therapy (CRT), the use of gene regulatory elements as therapeutic targets for haploinsufficient disorders, and adipose modulation transplantation (AMT), a novel cancer cell therapy.
Publications
Massively parallel reporter assays and mouse transgenic assays provide correlated and complementary information about neuronal enhancer activity.
Nature communications
Massively parallel jumping assay decodes Alu retrotransposition activity.
Nature communications
Functional characterization of OXTR-associated enhancers.
Human molecular genetics
MPRAbase a Massively Parallel Reporter Assay database.
Genome research
Deletion of an evolutionarily conserved TAD boundary impacts spermatogenesis in mice†.
Biology of reproduction
2024 ASHG Scientific Achievement Award.
American journal of human genetics
Gene therapies for neurogenetic disorders.
Trends in molecular medicine
Implantation of engineered adipocytes suppresses tumor progression in cancer models.
Nature biotechnology
The topography of nullomer-emerging mutations and their relevance to human disease.
Computational and structural biotechnology journal
Multiplex, single-cell CRISPRa screening for cell type specific regulatory elements.
Nature communications
Comprehensive network modeling approaches unravel dynamic enhancer-promoter interactions across neural differentiation.
Genome biology
Deletion of an evolutionarily conserved TAD boundary compromises spermatogenesis in mice.
bioRxiv : the preprint server for biology
Genetic regulation of cell type-specific chromatin accessibility shapes brain disease etiology.
Science (New York, N.Y.)
Massively parallel characterization of regulatory elements in the developing human cortex.
Science (New York, N.Y.)
Comprehensive network modeling approaches unravel dynamic enhancer-promoter interactions across neural differentiation.
bioRxiv : the preprint server for biology
Multiplex, single-cell CRISPRa screening for cell type specific regulatory elements.
bioRxiv : the preprint server for biology
Massively parallel reporter assays and mouse transgenic assays provide complementary information about neuronal enhancer activity.
bioRxiv : the preprint server for biology
Massively parallel jumping assay decodes Alu retrotransposition activity.
bioRxiv : the preprint server for biology
Deletion of Pax1 scoliosis-associated regulatory elements leads to a female-biased tail abnormality.
Cell reports
Author Correction: Genomic and epigenomic mapping of leptin-responsive neuronal populations involved in body weight regulation.
Nature metabolism
Optimizing sequence design strategies for perturbation MPRAs: a computational evaluation framework.
Nucleic acids research
Author Correction: Integrative single-cell characterization of a frugivorous and an insectivorous bat kidney and pancreas.
Nature communications
Characterization of enhancer activity in early human neurodevelopment using Massively Parallel Reporter Assay (MPRA) and forebrain organoids.
Scientific reports
Integrative functional genomic analyses identify genetic variants influencing skin pigmentation in Africans.
Nature genetics
Integrative single-cell characterization of a frugivorous and an insectivorous bat kidney and pancreas.
Nature communications
TAD evolutionary and functional characterization reveals diversity in mammalian TAD boundary properties and function.
Nature communications
Association of an estrogen-sensitive Pax1-Col11a1-Mmp3 signaling axis with adolescent idiopathic scoliosis.
bioRxiv : the preprint server for biology
MPRAbase: A Massively Parallel Reporter Assay Database.
bioRxiv : the preprint server for biology
Best practices for perturbation MPRA-a computational evaluation framework of sequence design strategies.
bioRxiv : the preprint server for biology
Characterization of enhancer activity in early human neurodevelopment using Massively parallel reporter assay (MPRA) and forebrain organoids.
bioRxiv : the preprint server for biology
Impaired cerebellar plasticity hypersensitizes sensory reflexes in SCN2A -associated ASD.
bioRxiv : the preprint server for biology
Three-dimensional genome rewiring in loci with human accelerated regions.
Science (New York, N.Y.)
Quasi-prime peptides: identification of the shortest peptide sequences unique to a species.
NAR genomics and bioinformatics
Transcription factor binding site orientation and order are major drivers of gene regulatory activity.
Nature communications
Deletion of Pax1 scoliosis-associated regulatory elements leads to a female-biased tail abnormality.
bioRxiv : the preprint server for biology
Implantation of engineered adipocytes that outcompete tumors for resources suppresses cancer progression.
bioRxiv : the preprint server for biology
TAD Evolutionary and functional characterization reveals diversity in mammalian TAD boundary properties and function.
bioRxiv : the preprint server for biology
Massively parallel characterization of transcriptional regulatory elements in three diverse human cell types.
bioRxiv : the preprint server for biology
Genetic regulation of cell-type specific chromatin accessibility shapes the etiology of brain diseases.
bioRxiv : the preprint server for biology
Massively parallel characterization of psychiatric disorder-associated and cell-type-specific regulatory elements in the developing human cortex.
bioRxiv : the preprint server for biology
Integrative single-cell characterization of frugivory adaptations in the bat kidney and pancreas.
bioRxiv : the preprint server for biology
Characterization of De Novo Promoter Variants in Autism Spectrum Disorder with Massively Parallel Reporter Assays.
International journal of molecular sciences
Risk scoring based on DNA methylation-driven related DEGs for colorectal cancer prognosis with systematic insights.
Life sciences
Milk antibody response after 3rd dose of COVID-19 mRNA vaccine and SARS-CoV-2 breakthrough infection and implications for infant protection.
medRxiv : the preprint server for health sciences
Genomic characterization and therapeutic utilization of IL-13-responsive sequences in asthma.
Cell genomics
Ancestry- and sex-specific effects underlying inguinal hernia susceptibility identified in a multiethnic genome-wide association study meta-analysis.
Human molecular genetics
Cellular and transcriptional diversity over the course of human lactation.
Proceedings of the National Academy of Sciences of the United States of America
Massively parallel reporter perturbation assays uncover temporal regulatory architecture during neural differentiation.
Nature communications
High-throughput characterization of the role of non-B DNA motifs on promoter function.
Cell genomics
COVID-19 mRNA Vaccination in Lactation: Assessment of Adverse Events and Vaccine Related Antibodies in Mother-Infant Dyads.
Frontiers in immunology
Evaluation of Messenger RNA From COVID-19 BTN162b2 and mRNA-1273 Vaccines in Human Milk.
JAMA pediatrics
COVID-19 mRNA Vaccination in Lactation: Assessment of adverse effects and transfer of anti-SARS-CoV2 antibodies from mother to child.
medRxiv : the preprint server for health sciences
Absent from DNA and protein: genomic characterization of nullomers and nullpeptides across functional categories and evolution.
Genome biology
Author Correction: lentiMPRA and MPRAflow for high-throughput functional characterization of gene regulatory elements.
Nature protocols
Deletion of CTCF sites in the SHH locus alters enhancer-promoter interactions and leads to acheiropodia.
Nature communications
Publisher Correction: Human-chimpanzee fused cells reveal cis-regulatory divergence underlying skeletal evolution.
Nature genetics
Human-chimpanzee fused cells reveal cis-regulatory divergence underlying skeletal evolution.
Nature genetics
Genomic characterization of the adolescent idiopathic scoliosis associated transcriptome and regulome.
Human molecular genetics
Asymmetron: a toolkit for the identification of strand asymmetry patterns in biological sequences.
Nucleic acids research
A systematic evaluation of the design and context dependencies of massively parallel reporter assays.
Nature methods
Modulating gene regulation to treat genetic disorders.
Nature reviews. Drug discovery
Co-option of the lineage-specific LAVA retrotransposon in the gibbon genome.
Proceedings of the National Academy of Sciences of the United States of America
lentiMPRA and MPRAflow for high-throughput functional characterization of gene regulatory elements.
Nature protocols
Noncoding SNPs associated with increased GDF15 levels located in a metformin-activated enhancer region upstream of GDF15.
Pharmacogenomics
Characterization of functional transposable element enhancers in acute myeloid leukemia.
Science China. Life sciences
Comparative Genomic Characterization of the Multimammate Mouse Mastomys coucha.
Molecular biology and evolution
Identification and Massively Parallel Characterization of Regulatory Elements Driving Neural Induction.
Cell stem cell
A novel ZRS variant causes preaxial polydactyly type I by increased sonic hedgehog expression in the developing limb bud.
Genetics in medicine : official journal of the American College of Medical Genetics
Saturation mutagenesis of twenty disease-associated regulatory elements at single base-pair resolution.
Nature communications
Integration of multiple epigenomic marks improves prediction of variant impact in saturation mutagenesis reporter assay.
Human mutation
Meta-analysis of massively parallel reporter assays enables prediction of regulatory function across cell types.
Human mutation
Genomic and epigenomic mapping of leptin-responsive neuronal populations involved in body weight regulation.
Nature metabolism
Reply to Liu et al.: Tissue specificity of SIM1 gene expression and erectile dysfunction.
Proceedings of the National Academy of Sciences of the United States of America
Genome-wide de novo risk score implicates promoter variation in autism spectrum disorder.
Science (New York, N.Y.)
CRISPR-mediated activation of a promoter or enhancer rescues obesity caused by haploinsufficiency.
Science (New York, N.Y.)
Genome-wide meta-analysis and replication studies in multiple ethnicities identify novel adolescent idiopathic scoliosis susceptibility loci.
Human molecular genetics
A multidisciplinary review of triphalangeal thumb.
The Journal of hand surgery, European volume
Genetic variation in the SIM1 locus is associated with erectile dysfunction.
Proceedings of the National Academy of Sciences of the United States of America
Whole-Genome Sequencing of Pharmacogenetic Drug Response in Racially Diverse Children with Asthma.
American journal of respiratory and critical care medicine
Corrigendum: A systematic comparison reveals substantial differences in chromosomal versus episomal encoding of enhancer activity.
Genome research
Functional Characterization of Gene Regulatory Elements.
The FASEB Journal
Mutations in the fourth ß-propeller domain of LRP4 are associated with isolated syndactyly with fusion of the third and fourth fingers.
Human mutation
A point mutation in the pre-ZRS disrupts sonic hedgehog expression in the limb bud and results in triphalangeal thumb-polysyndactyly syndrome.
Genetics in medicine : official journal of the American College of Medical Genetics
Rare Variants in the ABCG2 Promoter Modulate In Vivo Activity.
Drug metabolism and disposition: the biological fate of chemicals
ABCG2 regulatory single-nucleotide polymorphisms alter in vivo enhancer activity and expression.
Pharmacogenetics and genomics
CRISPR-Cas9-mediated functional dissection of 3'-UTRs.
Nucleic acids research
Variant Interpretation: Functional Assays to the Rescue.
American journal of human genetics
Use antibiotics in cell culture with caution: genome-wide identification of antibiotic-induced changes in gene expression and regulation.
Scientific reports
Gene Regulatory Elements, Major Drivers of Human Disease.
Annual review of genomics and human genetics
Limb development: a paradigm of gene regulation.
Nature reviews. Genetics
Genomic Characterization of Metformin Hepatic Response.
PLoS genetics
In Vivo Hepatic Enhancer Elements in the Human ABCG2 Locus.
Drug metabolism and disposition: the biological fate of chemicals
A systematic comparison reveals substantial differences in chromosomal versus episomal encoding of enhancer activity.
Genome research
Prenatal ß-catenin/Brn2/Tbr2 transcriptional cascade regulates adult social and stereotypic behaviors.
Molecular psychiatry
A genome-wide association study identifies four novel susceptibility loci underlying inguinal hernia.
Nature communications
Uncovering drug-responsive regulatory elements.
Pharmacogenomics
Identification of novel Fgf enhancers and their role in dental evolution.
Evolution & development
A PAX1 enhancer locus is associated with susceptibility to idiopathic scoliosis in females.
Nature communications
Genome-wide identification of signaling center enhancers in the developing limb.
Development (Cambridge, England)
Genome-wide distribution of Auts2 binding localizes with active neurodevelopmental genes.
Translational psychiatry
Integrating diverse datasets improves developmental enhancer prediction.
PLoS computational biology
A novel ZRS mutation leads to preaxial polydactyly type 2 in a heterozygous form and Werner mesomelic syndrome in a homozygous form.
Human mutation
Identification of three novel FGF16 mutations in X-linked recessive fusion of the fourth and fifth metacarpals and possible correlation with heart disease.
Molecular genetics & genomic medicine
Functional characterization of SIM1-associated enhancers.
Human molecular genetics
Functional analysis of limb enhancers in the developing fin.
Development genes and evolution
The role of AUTS2 in neurodevelopment and human evolution.
Trends in genetics : TIG
Massively parallel decoding of mammalian regulatory sequences supports a flexible organizational model.
Nature genetics
A compact, in vivo screen of all 6-mers reveals drivers of tissue-specific expression and guides synthetic regulatory element design.
Genome biology
Sequence signatures extracted from proximal promoters can be used to predict distal enhancers.
Genome biology
The hydrodynamic tail vein assay as a tool for the study of liver promoters and enhancers.
Methods in molecular biology (Clifton, N.J.)
Functional characterization of tissue-specific enhancers in the DLX5/6 locus.
Human molecular genetics
A novel ZRS mutation in a Balochi tribal family with triphalangeal thumb, pre-axial polydactyly, post-axial polydactyly, and syndactyly.
American journal of medical genetics. Part A
Studies of TBX4 and chromosome 17q23.1q23.2: an uncommon cause of nonsyndromic clubfoot.
American journal of medical genetics. Part A
Massively parallel functional dissection of mammalian enhancers in vivo.
Nature biotechnology
Cis-Regulatory Enhancer Mutations are a Cause of Human Limb Malformations.
Gene Regulatory Sequences and Human Disease
Gene Regulatory Elements.
Gene Regulatory Sequences and Human Disease
Location, location, cis-mutation.
Human mutation
Functional characterization of liver enhancers that regulate drug-associated transporters.
Clinical pharmacology and therapeutics
cis-regulatory mutations are a genetic cause of human limb malformations.
Developmental dynamics : an official publication of the American Association of Anatomists
Identification and characterization of novel polymorphisms in the basal promoter of the human transporter, MATE1.
Pharmacogenetics and genomics
Institutional Profile: The University of California Pharmacogenomics Center: at the interface of genomics, biological mechanisms and drug therapy.
Pharmacogenomics
Identification and characterization of proximal promoter polymorphisms in the human concentrative nucleoside transporter 2 (SLC28A2).
The Journal of pharmacology and experimental therapeutics
Association of functionally significant Melanocortin-4 but not Melanocortin-3 receptor mutations with severe adult obesity in a large North American case-control study.
Human molecular genetics
Introduction to Computational Genomics: A Case Studies Approach Nello Cristianini and Matthew W. Hahn.
Briefings in bioinformatics
A new mouse mutant for the LDL receptor identified using ENU mutagenesis.
Journal of lipid research
Alternative approach to a heavy weight problem.
Genome research
Medical sequencing at the extremes of human body mass.
American journal of human genetics
A PYY Q62P variant linked to human obesity.
Human molecular genetics
Mapping cis-regulatory domains in the human genome using multi-species conservation of synteny.
Human molecular genetics
Comparative genomic analysis reveals a distant liver enhancer upstream of the COUP-TFII gene.
Mammalian genome : official journal of the International Mammalian Genome Society
Exploiting human--fish genome comparisons for deciphering gene regulation.
Human molecular genetics
An ENU-induced mutation in AP-2alpha leads to middle ear and ocular defects in Doarad mice.
Mammalian genome : official journal of the International Mammalian Genome Society
Myosin VI.
Genetic Hearing Loss
Mouse models for human deafness: current tools for new fashions.
Trends in molecular medicine
MYO6, the human homologue of the gene responsible for deafness in Snell's waltzer mice, is mutated in autosomal dominant nonsyndromic hearing loss.
American journal of human genetics
The Notch ligand Jagged1 is required for inner ear sensory development.
Proceedings of the National Academy of Sciences of the United States of America
Auditory and vestibular mouse mutants: models for human deafness.
Journal of basic and clinical physiology and pharmacology
Mutation in transcription factor POU4F3 associated with inherited progressive hearing loss in humans.
Science (New York, N.Y.)
Devising a cooperation policy for emergency networks.
The Journal of the Operational Research Society