Nadav Ahituv, PhD

Professor
Department of Bioengineering and Therapeutic Sciences
Ahituv
[email protected]
Phone: +1 415 476-1838
Fax: +1 415 502-0720
1550 Fourth Street, Rm 584C
UCSF Box 2911
San Francisco, CA 94158
United States

Links

Ahituv Lab UCSF Profiles

Affiliations

Education programs

Biological and Medical Informatics Graduate Program (BMI)
Pharmaceutical Sciences and Pharmacogenomics Graduate Program (PSPG)
PhD program in Biomedical Sciences (BMS), School of Medicine
PhD program in Developmental and Stem Cell Biology (DSCB), School of Medicine
UCSF Tetrad Graduate Program

What I do

My research focuses on understanding how nucleotide variation in gene regulatory elements can lead to human disease and other phenotypes.

Departmental research area

pharmacogenomics and genomics

My research expertise

functional genomics, gene regulation, human genetics, mouse genetic engineering, gene therapy, obesity, neurodevelopment, cancer diagnosis

Professional background

Degrees

PhD, Human Genetics, Tel Aviv University, 2002
BSc, Biology, Tel Aviv University, 1996

Biography

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. In addition, our lab is developing massively parallel reporter assays (MPRAs) that allow for high-throughput functional characterization of gene regulatory elements and the use of gene regulatory elements as therapeutic targets or disease diagnostic markers.

Research keywords

  • enhancers
  • limb malformations
  • autism
  • pharmacogenomics
  • epilepsy
  • noncoding DNA
  • obesity
  • mouse models
  • comparative genomics
  • Human genetics
  • gene regulation
  • genomics
  • scoliosis
  • Zebrafish
  • scoliosis
  • Syndactyly
  • Exons
  • Congenital Limb Deformities
  • Regulatory Elements, Transcriptional
  • Gene Expression Regulation, Developmental
  • transcription factors
  • Enhancer Elements, Genetic
  • Gene Expression Regulation
  • Promoter Regions, Genetic
  • Chiroptera
  • Regulatory Sequences, Nucleic Acid
  • Hand Deformities, Congenital
  • Human Genome
  • Sequence Analysis, DNA
1. Update from the Dean: Putting plans in action
2. Ahituv appointed director of UCSF Institute for Human Genetics
3. UCSF School of Pharmacy leads in NIH funding for the 42nd straight year
4. Update from the Dean: Excellence amidst change
5. Regulatory DNA opens a window through time
6. UCSF School of Pharmacy leads in NIH funding for the 41st straight year
7. Update from the Dean: Community during challenging times
8. Labs juggle community, distance during COVID-19
9. Update from the Dean: We are rising to the challenges presented by COVID-19
10. UCSF School of Pharmacy leads in NIH funding for the 40th straight year
11. For UCSF graduate, DACA gives a chance to fight cancer
12. Update from the Dean – May 2019
13. School of Pharmacy tops pharmacy schools in NIH funding for 39th straight year
14. CRISPR-based obesity treatment shows promise for other diseases
15. UCSF School of Pharmacy leads in NIH funding for 38th year
16. Asthma drug response in racially diverse children
17. Using antibiotics to stop contamination in cell cultures changes them, study finds
18. Team member Sally Brown
19. Update from the Dean - March 2017
20. Koda-Kimble Seed Award recipients explore ‘blue-sky’ projects
21. Ahituv Lab research finds how bats grow wings, with implications for human limb development
22. Ahituv, Kaiser Permanente study identifies genetic susceptibility for hernia
23. Update from the Dean - Spring/Summer 2015
24. Update from the Dean - Fall 2013
25. Ahituv study provides new insights into enhancer gene regulation
26. Update from the Dean - Fall 2012
27. Reflection: 30 years of top NIH funding for UCSF School of Pharmacy
28. Update from the Dean - Fall 2007/Winter 2008
29. Ahituv asks why some DNA is ultraconserved
1. No sign of Pfizer or Moderna COVID-19 vaccines in breast milk
2. Gene expression in archaic humans study lights path towards modern Homo sapiens
3. Astonishing animals that illuminate human health
4. Is “Junk DNA” What Makes Humans Unique?
5. Scientists investigate the weird genetics of bat wings
1. ASCPT Leon I. Goldberg young investigator award, The American Society for Clinical Pharmacology and Therapeutics, 2014
2. Ph.D. with distinction, Tel-Aviv University, 2002

Publications

Chardon FM, McDiarmid TA, Page NF, Daza RM, Martin BK, Domcke S, Regalado SG, Lalanne JB, Calderon D, Li X, Starita LM, Sanders SJ, Ahituv N, Shendure J. Multiplex, single-cell CRISPRa screening for cell type specific regulatory elements. Nat Commun. 2024 Sep 18; 15(1):8209.
DeGroat W, Inoue F, Ashuach T, Yosef N, Ahituv N, Kreimer A. Comprehensive network modeling approaches unravel dynamic enhancer-promoter interactions across neural differentiation. Genome Biol. 2024 Aug 14; 25(1):221.
Lima AC, Okhovat M, Stendahl AM, VanCampen J, Nevonen KA, Herrera J, Li W, Harshman L, Yang R, Fedorov LM, Vigh-Conrad KA, Ahituv N, Conrad DF, Carbone L. Deletion of an evolutionarily conserved TAD boundary compromises spermatogenesis in mice. bioRxiv. 2024 Jul 10.
Zeng B, Bendl J, Deng C, Lee D, Misir R, Reach SM, Kleopoulos SP, Auluck P, Marenco S, Lewis DA, Haroutunian V, Ahituv N, Fullard JF, Hoffman GE, Roussos P. Genetic regulation of cell type-specific chromatin accessibility shapes brain disease etiology. Science. 2024 May 24; 384(6698):eadh4265.
Deng C, Whalen S, Steyert M, Ziffra R, Przytycki PF, Inoue F, Pereira DA, Capauto D, Norton S, Vaccarino FM, PsychENCODE Consortium‡, Pollen AA, Nowakowski TJ, Ahituv N, Pollard KS, PsychENCODE Consortium. Massively parallel characterization of regulatory elements in the developing human cortex. Science. 2024 May 24; 384(6698):eadh0559.
DeGroat W, Inoue F, Ashuach T, Yosef N, Ahituv N, Kreimer A. Comprehensive network modeling approaches unravel dynamic enhancer-promoter interactions across neural differentiation. bioRxiv. 2024 May 23.
Chardon FM, McDiarmid TA, Page NF, Daza RM, Martin B, Domcke S, Regalado SG, Lalanne JB, Calderon D, Li X, Starita LM, Sanders SJ, Ahituv N, Shendure J. Multiplex, single-cell CRISPRa screening for cell type specific regulatory elements. bioRxiv. 2024 Apr 30.
Kosicki M, Cintrón DL, Page NF, Georgakopoulos-Soares I, Akiyama JA, Plajzer-Frick I, Novak CS, Kato M, Hunter RD, von Maydell K, Barton S, Godfrey P, Beckman E, Sanders SJ, Pennacchio LA, Ahituv N. Massively parallel reporter assays and mouse transgenic assays provide complementary information about neuronal enhancer activity. bioRxiv. 2024 Apr 23.
Matharu N, Zhao J, Sohota A, Deng L, Hung Y, Li Z, Sims J, Rattanasopha S, Meyer J, Carbone L, Kircher M, Ahituv N. Massively parallel jumping assay decodes Alu retrotransposition activity. bioRxiv. 2024 Apr 19.
Ushiki A, Sheng RR, Zhang Y, Zhao J, Nobuhara M, Murray E, Ruan X, Rios JJ, Wise CA, Ahituv N. Deletion of Pax1 scoliosis-associated regulatory elements leads to a female-biased tail abnormality. Cell Rep. 2024 Mar 26; 43(3):113907.
Inoue F, Eckalbar WL, Wang Y, Murphy KK, Matharu N, Vaisse C, Ahituv N. Author Correction: Genomic and epigenomic mapping of leptin-responsive neuronal populations involved in body weight regulation. Nat Metab. 2024 Mar; 6(3):598.
Liu J, Ashuach T, Inoue F, Ahituv N, Yosef N, Kreimer A. Optimizing sequence design strategies for perturbation MPRAs: a computational evaluation framework. Nucleic Acids Res. 2024 Feb 28; 52(4):1613-1627.
Gordon WE, Baek S, Nguyen HP, Kuo YM, Bradley R, Fong SL, Kim N, Galazyuk A, Lee I, Ingala MR, Simmons NB, Schountz T, Cooper LN, Georgakopoulos-Soares I, Hemberg M, Ahituv N. Author Correction: Integrative single-cell characterization of a frugivorous and an insectivorous bat kidney and pancreas. Nat Commun. 2024 Feb 27; 15(1):1777.
Wang C, Derderian KD, Hamada E, Zhou X, Nelson AD, Kyoung H, Ahituv N, Bouvier G, Bender KJ. Impaired cerebellar plasticity hypersensitizes sensory reflexes in SCN2A-associated ASD. Neuron. 2024 May 01; 112(9):1444-1455.e5.
Capauto D, Wang Y, Wu F, Norton S, Mariani J, Inoue F, Crawford GE, Ahituv N, Abyzov A, Vaccarino FM. Characterization of enhancer activity in early human neurodevelopment using Massively Parallel Reporter Assay (MPRA) and forebrain organoids. Sci Rep. 2024 02 16; 14(1):3936.
Hao Yu, Anas M Khanshour, Aki Ushiki, Nao Otomo, Yoshinao Koike, Elisabet Einarsdottir, Yanhui Fan, Lilian Antunes, Yared H Kidane, Reuel Cornelia, Rory R Sheng, Yichi Zhang, Jimin Pei, Nick V Grishin, Bret M Evers, Jason Pui Yin Cheung, John A Herring, Chikashi Terao, You-qiang Song, Christina A Gurnett, Paul Gerdhem, Shiro Ikegawa, Jonathan J Rios, Nadav Ahituv, Carol A Wise. Association of genetic variation in COL11A1 with adolescent idiopathic scoliosis. eLife. 2024 Jan 26; 12.
Yu H, Khanshour AM, Ushiki A, Otomo N, Koike Y, Einarsdottir E, Fan Y, Antunes L, Kidane YH, Cornelia R, Sheng RR, Zhang Y, Pei J, Grishin NV, Evers BM, Cheung JPY, Herring JA, Terao C, Song YQ, Gurnett CA, Gerdhem P, Ikegawa S, Rios JJ, Ahituv N, Wise CA. Association of genetic variation in COL11A1 with adolescent idiopathic scoliosis. Elife. 2024 Jan 26; 12.
Feng Y, Xie N, Inoue F, Fan S, Saskin J, Zhang C, Zhang F, Hansen MEB, Nyambo T, Mpoloka SW, Mokone GG, Fokunang C, Belay G, Njamnshi AK, Marks MS, Oancea E, Ahituv N, Tishkoff SA. Integrative functional genomic analyses identify genetic variants influencing skin pigmentation in Africans. Nat Genet. 2024 Feb; 56(2):258-272.
Gordon WE, Baek S, Nguyen HP, Kuo YM, Bradley R, Fong SL, Kim N, Galazyuk A, Lee I, Ingala MR, Simmons NB, Schountz T, Cooper LN, Georgakopoulos-Soares I, Hemberg M, Ahituv N. Integrative single-cell characterization of a frugivorous and an insectivorous bat kidney and pancreas. Nat Commun. 2024 01 09; 15(1):12.
Okhovat M, VanCampen J, Nevonen KA, Harshman L, Li W, Layman CE, Ward S, Herrera J, Wells J, Sheng RR, Mao Y, Ndjamen B, Lima AC, Vigh-Conrad KA, Stendahl AM, Yang R, Fedorov L, Matthews IR, Easow SA, Chan DK, Jan TA, Eichler EE, Rugonyi S, Conrad DF, Ahituv N, Carbone L. TAD evolutionary and functional characterization reveals diversity in mammalian TAD boundary properties and function. Nat Commun. 2023 Dec 07; 14(1):8111.
Arnould C, Rocher V, Saur F, Bader AS, Muzzopappa F, Collins S, Lesage E, Le Bozec B, Puget N, Clouaire T, Mangeat T, Mourad R, Ahituv N, Noordermeer D, Erdel F, Bushell M, Marnef A, Legube G. Author Correction: Chromatin compartmentalization regulates the response to DNA damage. Nature. 2023 Dec; 624(7990):E1.
Yu H, Khanshour AM, Ushiki A, Otomo N, Koike Y, Einarsdottir E, Fan Y, Antunes L, Kidane YH, Cornelia R, Sheng R, Zhang Y, Pei J, Grishin NV, Evers BM, Cheung JPY, Herring JA, Terao C, Song YQ, Gurnett CA, Gerdhem P, Ikegawa S, Rios JJ, Ahituv N, Wise CA. Association of genetic variation in COL11A1 with adolescent idiopathic scoliosis. bioRxiv. 2023 Nov 22.
Zhao J, Baltoumas FA, Konnaris MA, Mouratidis I, Liu Z, Sims J, Agarwal V, Pavlopoulos GA, Georgakopoulos-Soares I, Ahituv N. MPRAbase: A Massively Parallel Reporter Assay Database. bioRxiv. 2023 Nov 22.
Arnould C, Rocher V, Saur F, Bader AS, Muzzopappa F, Collins S, Lesage E, Le Bozec B, Puget N, Clouaire T, Mangeat T, Mourad R, Ahituv N, Noordermeer D, Erdel F, Bushell M, Marnef A, Legube G. Chromatin compartmentalization regulates the response to DNA damage. Nature. 2023 Nov; 623(7985):183-192.
Liu J, Ashuach T, Inoue F, Ahituv N, Yosef N, Kreimer A. Best practices for perturbation MPRA-a computational evaluation framework of sequence design strategies. bioRxiv. 2023 Sep 29.
Golan Y, Ilala M, Li L, Gay C, Hunagund S, Lin CY, Cassidy AG, Jigmeddagva U, Matsui Y, Ozarslan N, Asiodu IV, Ahituv N, Flaherman VJ, Gaw SL, Prahl M. Milk antibody response after 3rd COVID-19 vaccine and SARS-CoV-2 infection and implications for infant protection. iScience. 2023 Oct 20; 26(10):107767.
Capauto D, Wang Y, Wu F, Norton S, Mariani J, Inoue F, Crawford GE, PsychENCODE Consortium, Ahituv N, Abyzov A, Vaccarino FM. Characterization of enhancer activity in early human neurodevelopment using Massively parallel reporter assay (MPRA) and forebrain organoids. bioRxiv. 2023 Aug 14.
Wang C, Derderian KD, Hamada E, Zhou X, Nelson AD, Kyoung H, Ahituv N, Bouvier G, Bender KJ. Impaired cerebellar plasticity hypersensitizes sensory reflexes in SCN2A-associated ASD. bioRxiv. 2023 Jun 07.
Keough KC, Whalen S, Inoue F, Przytycki PF, Fair T, Deng C, Steyert M, Ryu H, Lindblad-Toh K, Karlsson E, Zoonomia Consortium§, Nowakowski T, Ahituv N, Pollen A, Pollard KS. Three-dimensional genome rewiring in loci with human accelerated regions. Science. 2023 04 28; 380(6643):eabm1696.
Mouratidis I, Chan CSY, Chantzi N, Tsiatsianis GC, Hemberg M, Ahituv N, Georgakopoulos-Soares I. Quasi-prime peptides: identification of the shortest peptide sequences unique to a species. NAR Genom Bioinform. 2023 Jun; 5(2):lqad039.
Georgakopoulos-Soares I, Deng C, Agarwal V, Chan CSY, Zhao J, Inoue F, Ahituv N. Transcription factor binding site orientation and order are major drivers of gene regulatory activity. Nat Commun. 2023 04 22; 14(1):2333.
Ushiki A, Sheng RR, Zhang Y, Zhao J, Nobuhara M, Murray E, Ruan X, Rios JJ, Wise CA, Ahituv N. Deletion of Pax1 scoliosis-associated regulatory elements leads to a female-biased tail abnormality. bioRxiv. 2023 Apr 13.
Ofer Yizhar Barnea, Ilias Georgakopoulos-Soares, Nadav Ahituv, Jocelyn Chapman, Martin Hemberg, Ioannis Mouratidis, Konstantinos Syrigos, Nikolaos Syrigos, Ioannis Vathiotis, Mayank Mahajan, Emmanouil Panagiotou, Andriani Charpidou, Mark Kvale, Candace S. Chan, Ryder Easterlin. Abstract 991: Leveraging sequences missing from the human genome to detect cancer. Cancer Research. 2023 Apr 4; 83(7_Supplement):991-991.
Nguyen HP, Sheng R, Murray E, Ito Y, Bruck M, Biellak C, An K, Lynce F, Dillon DA, Magbanua MJM, Huppert LA, Hammerlindl H, Esserman L, Rosenbluth JM, Ahituv N. Implantation of engineered adipocytes that outcompete tumors for resources suppresses cancer progression. bioRxiv. 2023 Mar 29.
Okhovat M, VanCampen J, Lima AC, Nevonen KA, Layman CE, Ward S, Herrera J, Stendahl AM, Yang R, Harshman L, Li W, Sheng RR, Mao Y, Fedorov L, Ndjamen B, Vigh-Conrad KA, Matthews IR, Easow SA, Chan DK, Jan TA, Eichler EE, Rugonyi S, Conrad DF, Ahituv N, Carbone L. TAD Evolutionary and functional characterization reveals diversity in mammalian TAD boundary properties and function. bioRxiv. 2023 Mar 07.
Agarwal V, Inoue F, Schubach M, Martin BK, Dash PM, Zhang Z, Sohota A, Noble WS, Yardimci GG, Kircher M, Shendure J, Ahituv N. Massively parallel characterization of transcriptional regulatory elements in three diverse human cell types. bioRxiv. 2023 Mar 06.
Zeng B, Bendl J, Deng C, Lee D, Misir R, Reach SM, Kleopoulos SP, Auluck P, Marenco S, Lewis DA, Haroutunian V, Ahituv N, Fullard JF, Hoffman GE, Roussos P. Genetic regulation of cell-type specific chromatin accessibility shapes the etiology of brain diseases. bioRxiv. 2023 Mar 02.
Deng C, Whalen S, Steyert M, Ziffra R, Przytycki PF, Inoue F, Pereira DA, Capauto D, Norton S, Vaccarino FM, Pollen A, Nowakowski TJ, Ahituv N, Pollard KS. Massively parallel characterization of psychiatric disorder-associated and cell-type-specific regulatory elements in the developing human cortex. bioRxiv. 2023 Feb 16.
Gordon WE, Baek S, Nguyen HP, Kuo YM, Bradley R, Galazyuk A, Lee I, Ingala MR, Simmons NB, Schountz T, Cooper LN, Georgakopoulos-Soares I, Hemberg M, Ahituv N. Integrative single-cell characterization of frugivory adaptations in the bat kidney and pancreas. bioRxiv. 2023 Feb 13.
Koesterich J, An JY, Inoue F, Sohota A, Ahituv N, Sanders SJ, Kreimer A. Characterization of De Novo Promoter Variants in Autism Spectrum Disorder with Massively Parallel Reporter Assays. Int J Mol Sci. 2023 Feb 09; 24(4).
Liu Z, Georgakopoulos-Soares I, Ahituv N, Wong KC. Risk scoring based on DNA methylation-driven related DEGs for colorectal cancer prognosis with systematic insights. Life Sci. 2023 Mar 01; 316:121413.
Whalen S, Inoue F, Ryu H, Fair T, Markenscoff-Papadimitriou E, Keough K, Kircher M, Martin B, Alvarado B, Elor O, Laboy Cintron D, Williams A, Hassan Samee MA, Thomas S, Krencik R, Ullian EM, Kriegstein A, Rubenstein JL, Shendure J, Pollen AA, Ahituv N, Pollard KS. Machine learning dissection of human accelerated regions in primate neurodevelopment. Neuron. 2023 03 15; 111(6):857-873.e8.
Golan Y, Ilala M, Gay C, Hunagund S, Lin CY, Cassidy AG, Jigmeddagva U, Li L, Ozarslan N, Asiodu IV, Ahituv N, Flaherman VJ, Gaw SL, Prahl M. Milk antibody response after 3rd dose of COVID-19 mRNA vaccine and SARS-CoV-2 breakthrough infection and implications for infant protection. medRxiv. 2022 Dec 14.
Koh KD, Bonser LR, Eckalbar WL, Yizhar-Barnea O, Shen J, Zeng X, Hargett KL, Sun DI, Zlock LT, Finkbeiner WE, Ahituv N, Erle DJ. Genomic characterization and therapeutic utilization of IL-13-responsive sequences in asthma. Cell Genom. 2023 Jan 11; 3(1):100229.
Georgakopoulos-Soares I, Chan CSY, Ahituv N, Hemberg M. Author Correction: High-throughput techniques enable advances in the roles of DNA and RNA secondary structures in transcriptional and post-transcriptional gene regulation. Genome Biol. 2022 Jul 27; 23(1):164.
Georgakopoulos-Soares I, Chan CSY, Ahituv N, Hemberg M. High-throughput techniques enable advances in the roles of DNA and RNA secondary structures in transcriptional and post-transcriptional gene regulation. Genome Biol. 2022 07 18; 23(1):159.
Choquet H, Li W, Yin J, Bradley R, Hoffmann TJ, Nandakumar P, 23 and Me Research Team, Mostaedi R, Tian C, Ahituv N, Jorgenson E. Ancestry- and sex-specific effects underlying inguinal hernia susceptibility identified in a multiethnic genome-wide association study meta-analysis. Hum Mol Genet. 2022 07 07; 31(13):2279-2293.
Nyquist SK, Gao P, Haining TKJ, Retchin MR, Golan Y, Drake RS, Kolb K, Mead BE, Ahituv N, Martinez ME, Shalek AK, Berger B, Goods BA. Cellular and transcriptional diversity over the course of human lactation. Proc Natl Acad Sci U S A. 2022 04 12; 119(15):e2121720119.
Kreimer A, Ashuach T, Inoue F, Khodaverdian A, Deng C, Yosef N, Ahituv N. Massively parallel reporter perturbation assays uncover temporal regulatory architecture during neural differentiation. Nat Commun. 2022 03 21; 13(1):1504.
Georgakopoulos-Soares I, Victorino J, Parada GE, Agarwal V, Zhao J, Wong HY, Umar MI, Elor O, Muhwezi A, An JY, Sanders SJ, Kwok CK, Inoue F, Hemberg M, Ahituv N. High-throughput characterization of the role of non-B DNA motifs on promoter function. Cell Genom. 2022 Apr 13; 2(4).
Golan Y, Prahl M, Cassidy AG, Gay C, Wu AHB, Jigmeddagva U, Lin CY, Gonzalez VJ, Basilio E, Chidboy MA, Warrier L, Buarpung S, Li L, Murtha AP, Asiodu IV, Ahituv N, Flaherman VJ, Gaw SL. COVID-19 mRNA Vaccination in Lactation: Assessment of Adverse Events and Vaccine Related Antibodies in Mother-Infant Dyads. Front Immunol. 2021; 12:777103.
Krause WC, Rodriguez R, Gegenhuber B, Matharu N, Rodriguez AN, Padilla-Roger AM, Toma K, Herber CB, Correa SM, Duan X, Ahituv N, Tollkuhn J, Ingraham HA. Oestrogen engages brain MC4R signalling to drive physical activity in female mice. Nature. 2021 11; 599(7883):131-135.
Ziffra RS, Kim CN, Ross JM, Wilfert A, Turner TN, Haeussler M, Casella AM, Przytycki PF, Keough KC, Shin D, Bogdanoff D, Kreimer A, Pollard KS, Ament SA, Eichler EE, Ahituv N, Nowakowski TJ. Single-cell epigenomics reveals mechanisms of human cortical development. Nature. 2021 10; 598(7879):205-213.
Golan Y, Prahl M, Cassidy A, Lin CY, Ahituv N, Flaherman VJ, Gaw SL. Evaluation of Messenger RNA From COVID-19 BTN162b2 and mRNA-1273 Vaccines in Human Milk. JAMA Pediatr. 2021 10 01; 175(10):1069-1071.
Golan Y, Prahl M, Cassidy AG, Gay C, Wu AHB, Jigmeddagva U, Lin CY, Gonzalez VJ, Basilio E, Warrier L, Buarpung S, Li L, Murtha AP, Asiodu IV, Ahituv N, Flaherman VJ, Gaw SL. COVID-19 mRNA Vaccination in Lactation: Assessment of adverse events and vaccine related antibodies in mother-infant dyads. medRxiv. 2021 Sep 16.
Georgakopoulos-Soares I, Yizhar-Barnea O, Mouratidis I, Hemberg M, Ahituv N. Absent from DNA and protein: genomic characterization of nullomers and nullpeptides across functional categories and evolution. Genome Biol. 2021 08 25; 22(1):245.
Gordon MG, Inoue F, Martin B, Schubach M, Agarwal V, Whalen S, Feng S, Zhao J, Ashuach T, Ziffra R, Kreimer A, Georgakopoulos-Soares I, Yosef N, Ye CJ, Pollard KS, Shendure J, Kircher M, Ahituv N. Author Correction: lentiMPRA and MPRAflow for high-throughput functional characterization of gene regulatory elements. Nat Protoc. 2021 Jul; 16(7):3736.
Weiss CV, Harshman L, Inoue F, Fraser HB, Petrov DA, Ahituv N, Gokhman D. The cis-regulatory effects of modern human-specific variants. Elife. 2021 04 22; 10.
Ushiki A, Zhang Y, Xiong C, Zhao J, Georgakopoulos-Soares I, Kane L, Jamieson K, Bamshad MJ, Nickerson DA, University of Washington Center for Mendelian Genomics, Shen Y, Lettice LA, Silveira-Lucas EL, Petit F, Ahituv N. Deletion of CTCF sites in the SHH locus alters enhancer-promoter interactions and leads to acheiropodia. Nat Commun. 2021 04 16; 12(1):2282.
Gokhman D, Agoglia RM, Kinnebrew M, Gordon W, Sun D, Bajpai VK, Naqvi S, Chen C, Chan A, Chen C, Petrov DA, Ahituv N, Zhang H, Mishina Y, Wysocka J, Rohatgi R, Fraser HB. Publisher Correction: Human-chimpanzee fused cells reveal cis-regulatory divergence underlying skeletal evolution. Nat Genet. 2021 Apr; 53(4):587.
Gokhman D, Agoglia RM, Kinnebrew M, Gordon W, Sun D, Bajpai VK, Naqvi S, Chen C, Chan A, Chen C, Petrov DA, Ahituv N, Zhang H, Mishina Y, Wysocka J, Rohatgi R, Fraser HB. Human-chimpanzee fused cells reveal cis-regulatory divergence underlying skeletal evolution. Nat Genet. 2021 04; 53(4):467-476.
Makki N, Zhao J, Liu Z, Eckalbar WL, Ushiki A, Khanshour AM, Wu J, Rios J, Gray RS, Wise CA, Ahituv N. Genomic characterization of the adolescent idiopathic scoliosis-associated transcriptome and regulome. Hum Mol Genet. 2021 01 21; 29(22):3606-3615.
Georgakopoulos-Soares I, Mouratidis I, Parada GE, Matharu N, Hemberg M, Ahituv N. Asymmetron: a toolkit for the identification of strand asymmetry patterns in biological sequences. Nucleic Acids Res. 2021 01 11; 49(1):e4.
Klein JC, Agarwal V, Inoue F, Keith A, Martin B, Kircher M, Ahituv N, Shendure J. A systematic evaluation of the design and context dependencies of massively parallel reporter assays. Nat Methods. 2020 11; 17(11):1083-1091.
Matharu N, Ahituv N. Modulating gene regulation to treat genetic disorders. Nat Rev Drug Discov. 2020 11; 19(11):757-775.
Okhovat M, Nevonen KA, Davis BA, Michener P, Ward S, Milhaven M, Harshman L, Sohota A, Fernandes JD, Salama SR, O'Neill RJ, Ahituv N, Veeramah KR, Carbone L. Co-option of the lineage-specific LAVA retrotransposon in the gibbon genome. Proc Natl Acad Sci U S A. 2020 08 11; 117(32):19328-19338.
Gordon MG, Inoue F, Martin B, Schubach M, Agarwal V, Whalen S, Feng S, Zhao J, Ashuach T, Ziffra R, Kreimer A, Georgakopoulos-Soares I, Yosef N, Ye CJ, Pollard KS, Shendure J, Kircher M, Ahituv N. lentiMPRA and MPRAflow for high-throughput functional characterization of gene regulatory elements. Nat Protoc. 2020 08; 15(8):2387-2412.
Linhares ND, Pereira DA, Conceição IM, Franco GR, Eckalbar WL, Ahituv N, Luizon MR. Noncoding SNPs associated with increased GDF15 levels located in a metformin-activated enhancer region upstream of GDF15. Pharmacogenomics. 2020 06; 21(8):509-520.
Wise CA, Sepich D, Ushiki A, Khanshour AM, Kidane YH, Makki N, Gurnett CA, Gray RS, Rios JJ, Ahituv N, Solnica-Krezel L. The cartilage matrisome in adolescent idiopathic scoliosis. Bone Res. 2020; 8:13.
Zeng Y, Cao Y, Halevy RS, Nguyen P, Liu D, Zhang X, Ahituv N, Han JJ. Characterization of functional transposable element enhancers in acute myeloid leukemia. Sci China Life Sci. 2020 May; 63(5):675-687.
Hardin A, Nevonen KA, Eckalbar WL, Carbone L, Ahituv N. Comparative Genomic Characterization of the Multimammate Mouse Mastomys coucha. Mol Biol Evol. 2019 12 01; 36(12):2805-2812.
Liu Z, Easson GWD, Zhao J, Makki N, Ahituv N, Hilton MJ, Tang SY, Gray RS. Dysregulation of STAT3 signaling is associated with endplate-oriented herniations of the intervertebral disc in Adgrg6 mutant mice. PLoS Genet. 2019 10; 15(10):e1008096.
Inoue F, Kreimer A, Ashuach T, Ahituv N, Yosef N. Identification and Massively Parallel Characterization of Regulatory Elements Driving Neural Induction. Cell Stem Cell. 2019 Nov 07; 25(5):713-727.e10.
Matharu N, Rattanasopha S, Tamura S, Maliskova L, Wang Y, Bernard A, Hardin A, Eckalbar WL, Vaisse C, Ahituv N. CRISPR-mediated activation of a promoter or enhancer rescues obesity caused by haploinsufficiency. . 2019 Sep 12.
Ashuach T, Fischer DS, Kreimer A, Ahituv N, Theis FJ, Yosef N. MPRAnalyze: statistical framework for massively parallel reporter assays. Genome Biol. 2019 09 02; 20(1):183.
Xu C, Yang X, Zhou H, Li Y, Xing C, Zhou T, Zhong D, Lian C, Yan M, Chen T, Liao Z, Gao B, Su D, Wang T, Sharma S, Mohan C, Ahituv N, Malik S, Li QZ, Su P. A novel ZRS variant causes preaxial polydactyly type I by increased sonic hedgehog expression in the developing limb bud. Genet Med. 2020 01; 22(1):189-198.
Kircher M, Xiong C, Martin B, Schubach M, Inoue F, Bell RJA, Costello JF, Shendure J, Ahituv N. Saturation mutagenesis of twenty disease-associated regulatory elements at single base-pair resolution. Nat Commun. 2019 08 08; 10(1):3583.
Shigaki D, Adato O, Adhikari AN, Dong S, Hawkins-Hooker A, Inoue F, Juven-Gershon T, Kenlay H, Martin B, Patra A, Penzar DD, Schubach M, Xiong C, Yan Z, Boyle AP, Kreimer A, Kulakovskiy IV, Reid J, Unger R, Yosef N, Shendure J, Ahituv N, Kircher M, Beer MA. Integration of multiple epigenomic marks improves prediction of variant impact in saturation mutagenesis reporter assay. Hum Mutat. 2019 09; 40(9):1280-1291.
Kreimer A, Yan Z, Ahituv N, Yosef N. Meta-analysis of massively parallel reporter assays enables prediction of regulatory function across cell types. Hum Mutat. 2019 09; 40(9):1299-1313.
Inoue F, Eckalbar WL, Wang Y, Murphy KK, Matharu N, Vaisse C, Ahituv N. Genomic and epigenomic mapping of leptin-responsive neuronal populations involved in body weight regulation. Nat Metab. 2019 04; 1(4):475-484.
Gasperini M, Hill AJ, McFaline-Figueroa JL, Martin B, Kim S, Zhang MD, Jackson D, Leith A, Schreiber J, Noble WS, Trapnell C, Ahituv N, Shendure J. A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens. Cell. 2019 Mar 07; 176(6):1516.
Jorgenson E, Matharu N, Palmer MR, Yin J, Shan J, Hoffmann TJ, Thai KK, Zhou X, Hotaling JM, Jarvik GP, Ahituv N, Wessells H, Van Den Eeden SK. Reply to Liu et al.: Tissue specificity of SIM1 gene expression and erectile dysfunction. Proc Natl Acad Sci U S A. 2019 02 26; 116(9):3349-3350.
Gasperini M, Hill AJ, McFaline-Figueroa JL, Martin B, Kim S, Zhang MD, Jackson D, Leith A, Schreiber J, Noble WS, Trapnell C, Ahituv N, Shendure J. A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens. Cell. 2019 01 10; 176(1-2):377-390.e19.
An JY, Lin K, Zhu L, Werling DM, Dong S, Brand H, Wang HZ, Zhao X, Schwartz GB, Collins RL, Currall BB, Dastmalchi C, Dea J, Duhn C, Gilson MC, Klei L, Liang L, Markenscoff-Papadimitriou E, Pochareddy S, Ahituv N, Buxbaum JD, Coon H, Daly MJ, Kim YS, Marth GT, Neale BM, Quinlan AR, Rubenstein JL, Sestan N, State MW, Willsey AJ, Talkowski ME, Devlin B, Roeder K, Sanders SJ. Genome-wide de novo risk score implicates promoter variation in autism spectrum disorder. Science. 2018 12 14; 362(6420).
Matharu N, Rattanasopha S, Tamura S, Maliskova L, Wang Y, Bernard A, Hardin A, Eckalbar WL, Vaisse C, Ahituv N. CRISPR-mediated activation of a promoter or enhancer rescues obesity caused by haploinsufficiency. Science. 2019 01 18; 363(6424).
Khanshour AM, Kou I, Fan Y, Einarsdottir E, Makki N, Kidane YH, Kere J, Grauers A, Johnson TA, Paria N, Patel C, Singhania R, Kamiya N, Takeda K, Otomo N, Watanabe K, Luk KDK, Cheung KMC, Herring JA, Rios JJ, Ahituv N, Gerdhem P, Gurnett CA, Song YQ, Ikegawa S, Wise CA. Genome-wide meta-analysis and replication studies in multiple ethnicities identify novel adolescent idiopathic scoliosis susceptibility loci. Hum Mol Genet. 2018 11 15; 27(22):3986-3998.
Potuijt JWP, Galjaard RH, van der Spek PJ, van Nieuwenhoven CA, Ahituv N, Oberg KC, Hovius SER. A multidisciplinary review of triphalangeal thumb. J Hand Surg Eur Vol. 2019 Jan; 44(1):59-68.
Jorgenson E, Matharu N, Palmer MR, Yin J, Shan J, Hoffmann TJ, Thai KK, Zhou X, Hotaling JM, Jarvik GP, Ahituv N, Wessells H, Van Den Eeden SK. Genetic variation in the SIM1 locus is associated with erectile dysfunction. Proc Natl Acad Sci U S A. 2018 10 23; 115(43):11018-11023.
Mak ACY, White MJ, Eckalbar WL, Szpiech ZA, Oh SS, Pino-Yanes M, Hu D, Goddard P, Huntsman S, Galanter J, Wu AC, Himes BE, Germer S, Vogel JM, Bunting KL, Eng C, Salazar S, Keys KL, Liberto J, Nuckton TJ, Nguyen TA, Torgerson DG, Kwok PY, Levin AM, Celedón JC, Forno E, Hakonarson H, Sleiman PM, Dahlin A, Tantisira KG, Weiss ST, Serebrisky D, Brigino-Buenaventura E, Farber HJ, Meade K, Lenoir MA, Avila PC, Sen S, Thyne SM, Rodriguez-Cintron W, Winkler CA, Moreno-Estrada A, Sandoval K, Rodriguez-Santana JR, Kumar R, Williams LK, Ahituv N, Ziv E, Seibold MA, Darnell RB, Zaitlen N, Hernandez RD, Burchard EG, NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium. Whole-Genome Sequencing of Pharmacogenetic Drug Response in Racially Diverse Children with Asthma. Am J Respir Crit Care Med. 2018 06 15; 197(12):1552-1564.
Inoue F, Kircher M, Martin B, Cooper GM, Witten DM, McManus MT, Ahituv N, Shendure J. Corrigendum: A systematic comparison reveals substantial differences in chromosomal versus episomal encoding of enhancer activity. Genome Res. 2018 05; 28(5):766.3.
Nadav Ahituv. Functional Characterization of Gene Regulatory Elements. The FASEB Journal. 2018 Apr 1; 32:20.2-20.2.
Sukenik Halevy R, Chien HC, Heinz B, Bamshad MJ, Nickerson DA, University of Washington Center for Mendelian Genomics, Kircher M, Ahituv N. Mutations in the fourth β-propeller domain of LRP4 are associated with isolated syndactyly with fusion of the third and fourth fingers. Hum Mutat. 2018 06; 39(6):811-815.
Potuijt JWP, Baas M, Sukenik-Halevy R, Douben H, Nguyen P, Venter DJ, Gallagher R, Swagemakers SM, Hovius SER, van Nieuwenhoven CA, Galjaard RH, van der Spek PJ, Ahituv N, de Klein A. A point mutation in the pre-ZRS disrupts sonic hedgehog expression in the limb bud and results in triphalangeal thumb-polysyndactyly syndrome. Genet Med. 2018 11; 20(11):1405-1413.
Eclov RJ, Kim MJ, Smith R, Ahituv N, Kroetz DL. Rare Variants in the ABCG2 Promoter Modulate In Vivo Activity. Drug Metab Dispos. 2018 05; 46(5):636-642.
Eclov RJ, Kim MJ, Chhibber A, Smith RP, Ahituv N, Kroetz DL. ABCG2 regulatory single-nucleotide polymorphisms alter in vivo enhancer activity and expression. Pharmacogenet Genomics. 2017 Dec; 27(12):454-463.
Zhao W, Siegel D, Biton A, Tonqueze OL, Zaitlen N, Ahituv N, Erle DJ. CRISPR-Cas9-mediated functional dissection of 3'-UTRs. Nucleic Acids Res. 2017 Oct 13; 45(18):10800-10810.
Starita LM, Ahituv N, Dunham MJ, Kitzman JO, Roth FP, Seelig G, Shendure J, Fowler DM. Variant Interpretation: Functional Assays to the Rescue. Am J Hum Genet. 2017 Sep 07; 101(3):315-325.
Ryu AH, Eckalbar WL, Kreimer A, Yosef N, Ahituv N. Use antibiotics in cell culture with caution: genome-wide identification of antibiotic-induced changes in gene expression and regulation. Sci Rep. 2017 08 08; 7(1):7533.
Chatterjee S, Ahituv N. Gene Regulatory Elements, Major Drivers of Human Disease. Annu Rev Genomics Hum Genet. 2017 08 31; 18:45-63.
Petit F, Sears KE, Ahituv N. Limb development: a paradigm of gene regulation. Nat Rev Genet. 2017 04; 18(4):245-258.
Luizon MR, Eckalbar WL, Wang Y, Jones SL, Smith RP, Laurance M, Lin L, Gallins PJ, Etheridge AS, Wright F, Zhou Y, Molony C, Innocenti F, Yee SW, Giacomini KM, Ahituv N. Genomic Characterization of Metformin Hepatic Response. PLoS Genet. 2016 Nov; 12(11):e1006449.
Eclov RJ, Kim MJ, Smith RP, Liang X, Ahituv N, Kroetz DL. In Vivo Hepatic Enhancer Elements in the Human ABCG2 Locus. Drug Metab Dispos. 2017 02; 45(2):208-215.
Inoue F, Kircher M, Martin B, Cooper GM, Witten DM, McManus MT, Ahituv N, Shendure J. A systematic comparison reveals substantial differences in chromosomal versus episomal encoding of enhancer activity. Genome Res. 2017 01; 27(1):38-52.
Booker BM, Friedrich T, Mason MK, VanderMeer JE, Zhao J, Eckalbar WL, Logan M, Illing N, Pollard KS, Ahituv N. Bat Accelerated Regions Identify a Bat Forelimb Specific Enhancer in the HoxD Locus. PLoS Genet. 2016 Mar; 12(3):e1005738.
Eckalbar WL, Schlebusch SA, Mason MK, Gill Z, Parker AV, Booker BM, Nishizaki S, Muswamba-Nday C, Terhune E, Nevonen KA, Makki N, Friedrich T, VanderMeer JE, Pollard KS, Carbone L, Wall JD, Illing N, Ahituv N. Transcriptomic and epigenomic characterization of the developing bat wing. Nat Genet. 2016 05; 48(5):528-36.
Ahituv N. Exonic enhancers: proceed with caution in exome and genome sequencing studies. Genome Med. 2016 Feb 08; 8(1):14.
Belinson H, Nakatani J, Babineau BA, Birnbaum RY, Ellegood J, Bershteyn M, McEvilly RJ, Long JM, Willert K, Klein OD, Ahituv N, Lerch JP, Rosenfeld MG, Wynshaw-Boris A. Prenatal β-catenin/Brn2/Tbr2 transcriptional cascade regulates adult social and stereotypic behaviors. Mol Psychiatry. 2016 10; 21(10):1417-33.
Jorgenson E, Makki N, Shen L, Chen DC, Tian C, Eckalbar WL, Hinds D, Ahituv N, Avins A. A genome-wide association study identifies four novel susceptibility loci underlying inguinal hernia. Nat Commun. 2015 Dec 21; 6:10130.
Matharu N, Ahituv N. Minor Loops in Major Folds: Enhancer-Promoter Looping, Chromatin Restructuring, and Their Association with Transcriptional Regulation and Disease. PLoS Genet. 2015 Dec; 11(12):e1005640.
Hesse RG, Kouklis GK, Ahituv N, Pomerantz JH. The human ARF tumor suppressor senses blastema activity and suppresses epimorphic tissue regeneration. Elife. 2015 Nov 17; 4.
Luizon MR, Ahituv N. Uncovering drug-responsive regulatory elements. Pharmacogenomics. 2015 Nov; 16(16):1829-41.
Yang S, Oksenberg N, Takayama S, Heo SJ, Poliakov A, Ahituv N, Dubchak I, Boffelli D. Functionally conserved enhancers with divergent sequences in distant vertebrates. BMC Genomics. 2015 Oct 30; 16:882.
Tapaltsyan V, Charles C, Hu J, Mindell D, Ahituv N, Wilson GM, Black BL, Viriot L, Klein OD. Identification of novel Fgf enhancers and their role in dental evolution. Evol Dev. 2016 Jan-Feb; 18(1):31-40.
Inoue F, Ahituv N. Decoding enhancers using massively parallel reporter assays. Genomics. 2015 Sep; 106(3):159-164.
Sharma S, Londono D, Eckalbar WL, Gao X, Zhang D, Mauldin K, Kou I, Takahashi A, Matsumoto M, Kamiya N, Murphy KK, Cornelia R, TSRHC Scoliosis Clinical Group, Japan Scoliosis Clinical Research Group, Herring JA, Burns D, Ahituv N, Ikegawa S, Gordon D, Wise CA. A PAX1 enhancer locus is associated with susceptibility to idiopathic scoliosis in females. Nat Commun. 2015 Mar 18; 6:6452.
Markenscoff-Papadimitriou E, Allen WE, Colquitt BM, Goh T, Murphy KK, Monahan K, Mosley CP, Ahituv N, Lomvardas S. Enhancer interaction networks as a means for singular olfactory receptor expression. Cell. 2014 Oct 23; 159(3):543-57.
Birnbaum RY, Patwardhan RP, Kim MJ, Findlay GM, Martin B, Zhao J, Bell RJ, Smith RP, Ku AA, Shendure J, Ahituv N. Systematic dissection of coding exons at single nucleotide resolution supports an additional role in cell-specific transcriptional regulation. PLoS Genet. 2014 Oct; 10(10):e1004592.
Smith RP, Eckalbar WL, Morrissey KM, Luizon MR, Hoffmann TJ, Sun X, Jones SL, Force Aldred S, Ramamoorthy A, Desta Z, Liu Y, Skaar TC, Trinklein ND, Giacomini KM, Ahituv N. Genome-wide discovery of drug-dependent human liver regulatory elements. PLoS Genet. 2014 Oct; 10(10):e1004648.
VanderMeer JE, Smith RP, Jones SL, Ahituv N. Genome-wide identification of signaling center enhancers in the developing limb. Development. 2014 Nov; 141(21):4194-8.
Oksenberg N, Haliburton GD, Eckalbar WL, Oren I, Nishizaki S, Murphy K, Pollard KS, Birnbaum RY, Ahituv N. Genome-wide distribution of Auts2 binding localizes with active neurodevelopmental genes. Transl Psychiatry. 2014 Sep 02; 4:e431.
Erwin GD, Oksenberg N, Truty RM, Kostka D, Murphy KK, Ahituv N, Pollard KS, Capra JA. Integrating diverse datasets improves developmental enhancer prediction. PLoS Comput Biol. 2014 Jun; 10(6):e1003677.
VanderMeer JE, Lozano R, Sun M, Xue Y, Daentl D, Jabs EW, Wilcox WR, Ahituv N. A novel ZRS mutation leads to preaxial polydactyly type 2 in a heterozygous form and Werner mesomelic syndrome in a homozygous form. Hum Mutat. 2014 Aug; 35(8):945-8.
Laurell T, Nilsson D, Hofmeister W, Lindstrand A, Ahituv N, Vandermeer J, Amilon A, Annerén G, Arner M, Pettersson M, Jäntti N, Rosberg HE, Cattini PA, Nordenskjöld A, Mäkitie O, Grigelioniene G, Nordgren A. Identification of three novel FGF16 mutations in X-linked recessive fusion of the fourth and fifth metacarpals and possible correlation with heart disease. Mol Genet Genomic Med. 2014 Sep; 2(5):402-11.
Evans DS, Calton MA, Kim MJ, Kwok PY, Miljkovic I, Harris T, Koster A, Liu Y, Tranah GJ, Ahituv N, Hsueh WC, Vaisse C. Genetic association study of adiposity and melanocortin-4 receptor (MC4R) common variants: replication and functional characterization of non-coding regions. PLoS One. 2014; 9(5):e96805.
Zhang Y, Wong CH, Birnbaum RY, Li G, Favaro R, Ngan CY, Lim J, Tai E, Poh HM, Wong E, Mulawadi FH, Sung WK, Nicolis S, Ahituv N, Ruan Y, Wei CL. Chromatin connectivity maps reveal dynamic promoter-enhancer long-range associations. Nature. 2013 Dec 12; 504(7479):306-310.
Kim MJ, Oksenberg N, Hoffmann TJ, Vaisse C, Ahituv N. Functional characterization of SIM1-associated enhancers. Hum Mol Genet. 2014 Apr 01; 23(7):1700-8.
Booker BM, Murphy KK, Ahituv N. Functional analysis of limb enhancers in the developing fin. Dev Genes Evol. 2013 Nov; 223(6):395-9.
Zhao J, Shi H, Ahituv N. Classification of topological domains based on gene expression and regulation. Genome. 2013 Jul; 56(7):415-23.
Oksenberg N, Ahituv N. The role of AUTS2 in neurodevelopment and human evolution. Trends Genet. 2013 Oct; 29(10):600-8.
Smith RP, Taher L, Patwardhan RP, Kim MJ, Inoue F, Shendure J, Ovcharenko I, Ahituv N. Massively parallel decoding of mammalian regulatory sequences supports a flexible organizational model. Nat Genet. 2013 Sep; 45(9):1021-1028.
Smith RP, Riesenfeld SJ, Holloway AK, Li Q, Murphy KK, Feliciano NM, Orecchia L, Oksenberg N, Pollard KS, Ahituv N. A compact, in vivo screen of all 6-mers reveals drivers of tissue-specific expression and guides synthetic regulatory element design. Genome Biol. 2013 Jul 18; 14(7):R72.
Oksenberg N, Stevison L, Wall JD, Ahituv N. Function and regulation of AUTS2, a gene implicated in autism and human evolution. PLoS Genet. 2013; 9(1):e1003221.
Taher L, Smith RP, Kim MJ, Ahituv N, Ovcharenko I. Sequence signatures extracted from proximal promoters can be used to predict distal enhancers. Genome Biol. 2013; 14(10):R117.
Kim MJ, Ahituv N. The hydrodynamic tail vein assay as a tool for the study of liver promoters and enhancers. Methods Mol Biol. 2013; 1015:279-89.
Andersson LS, Larhammar M, Memic F, Wootz H, Schwochow D, Rubin CJ, Patra K, Arnason T, Wellbring L, Hjälm G, Imsland F, Petersen JL, McCue ME, Mickelson JR, Cothran G, Ahituv N, Roepstorff L, Mikko S, Vallstedt A, Lindgren G, Andersson L, Kullander K. Mutations in DMRT3 affect locomotion in horses and spinal circuit function in mice. Nature. 2012 Aug 30; 488(7413):642-6.
Birnbaum RY, Everman DB, Murphy KK, Gurrieri F, Schwartz CE, Ahituv N. Functional characterization of tissue-specific enhancers in the DLX5/6 locus. Hum Mol Genet. 2012 Nov 15; 21(22):4930-8.
Clarke SL, VanderMeer JE, Wenger AM, Schaar BT, Ahituv N, Bejerano G. Human developmental enhancers conserved between deuterostomes and protostomes. PLoS Genet. 2012; 8(8):e1002852.
VanderMeer JE, Afzal M, Alyas S, Haque S, Ahituv N, Malik S. A novel ZRS mutation in a Balochi tribal family with triphalangeal thumb, pre-axial polydactyly, post-axial polydactyly, and syndactyly. Am J Med Genet A. 2012 Aug; 158A(8):2031-5.
Lu W, Bacino CA, Richards BS, Alvarez C, VanderMeer JE, Vella M, Ahituv N, Sikka N, Dietz FR, Blanton SH, Hecht JT. Studies of TBX4 and chromosome 17q23.1q23.2: an uncommon cause of nonsyndromic clubfoot. Am J Med Genet A. 2012 Jul; 158A(7):1620-7.
Smith RP, Lam ET, Markova S, Yee SW, Ahituv N. Pharmacogene regulatory elements: from discovery to applications. Genome Med. 2012 May 25; 4(5):45.
Laurell T, Vandermeer JE, Wenger AM, Grigelioniene G, Nordenskjöld A, Arner M, Ekblom AG, Bejerano G, Ahituv N, Nordgren A. A novel 13 base pair insertion in the sonic hedgehog ZRS limb enhancer (ZRS/LMBR1) causes preaxial polydactyly with triphalangeal thumb. Hum Mutat. 2012 Jul; 33(7):1063-6.
Birnbaum RY, Clowney EJ, Agamy O, Kim MJ, Zhao J, Yamanaka T, Pappalardo Z, Clarke SL, Wenger AM, Nguyen L, Gurrieri F, Everman DB, Schwartz CE, Birk OS, Bejerano G, Lomvardas S, Ahituv N. Coding exons function as tissue-specific enhancers of nearby genes. Genome Res. 2012 Jun; 22(6):1059-68.
Patwardhan RP, Hiatt JB, Witten DM, Kim MJ, Smith RP, May D, Lee C, Andrie JM, Lee SI, Cooper GM, Ahituv N, Pennacchio LA, Shendure J. Massively parallel functional dissection of mammalian enhancers in vivo. Nat Biotechnol. 2012 Feb 26; 30(3):265-70.
Julia E. VanderMeer, Nadav Ahituv. Cis-Regulatory Enhancer Mutations are a Cause of Human Limb Malformations. Gene Regulatory Sequences and Human Disease. 2012 Jan 1; 73-93.
Nadav Ahituv. Gene Regulatory Elements. Gene Regulatory Sequences and Human Disease. 2012 Jan 1; 1-17.
Ahituv N. Location, location, cis-mutation. Hum Mutat. 2011 Dec; 32(12):iv.
Kim MJ, Skewes-Cox P, Fukushima H, Hesselson S, Yee SW, Ramsey LB, Nguyen L, Eshragh JL, Castro RA, Wen CC, Stryke D, Johns SJ, Ferrin TE, Kwok PY, Relling MV, Giacomini KM, Kroetz DL, Ahituv N. Functional characterization of liver enhancers that regulate drug-associated transporters. Clin Pharmacol Ther. 2011 Apr; 89(4):571-8.
VanderMeer JE, Ahituv N. cis-regulatory mutations are a genetic cause of human limb malformations. Dev Dyn. 2011 May; 240(5):920-30.
Ha Choi J, Wah Yee S, Kim MJ, Nguyen L, Ho Lee J, Kang JO, Hesselson S, Castro RA, Stryke D, Johns SJ, Kwok PY, Ferrin TE, Goo Lee M, Black BL, Ahituv N, Giacomini KM. Identification and characterization of novel polymorphisms in the basal promoter of the human transporter, MATE1. Pharmacogenet Genomics. 2009 Oct; 19(10):770-80.
Kroetz DL, Ahituv N, Burchard EG, Guo S, Sali A, Giacomini KM. Institutional Profile: The University of California Pharmacogenomics Center: at the interface of genomics, biological mechanisms and drug therapy. Pharmacogenomics. 2009 Oct; 10(10):1569-76.
Yee SW, Shima JE, Hesselson S, Nguyen L, De Val S, Lafond RJ, Kawamoto M, Johns SJ, Stryke D, Kwok PY, Ferrin TE, Black BL, Gurwitz D, Ahituv N, Giacomini KM. Identification and characterization of proximal promoter polymorphisms in the human concentrative nucleoside transporter 2 (SLC28A2). J Pharmacol Exp Ther. 2009 Mar; 328(3):699-707.
Calton MA, Ersoy BA, Zhang S, Kane JP, Malloy MJ, Pullinger CR, Bromberg Y, Pennacchio LA, Dent R, McPherson R, Ahituv N, Vaisse C. Association of functionally significant Melanocortin-4 but not Melanocortin-3 receptor mutations with severe adult obesity in a large North American case-control study. Hum Mol Genet. 2009 Mar 15; 18(6):1140-7.
Nadav Ahituv. Introduction to Computational Genomics: A Case Studies Approach Nello Cristianini and Matthew W. Hahn. Briefings in Bioinformatics. 2008 Dec 6; 10(3):341-341.
Svenson KL, Ahituv N, Durgin RS, Savage H, Magnani PA, Foreman O, Paigen B, Peters LL. A new mouse mutant for the LDL receptor identified using ENU mutagenesis. J Lipid Res. 2008 Nov; 49(11):2452-62.
Goren A, Kim E, Amit M, Bochner R, Lev-Maor G, Ahituv N, Ast G. Alternative approach to a heavy weight problem. Genome Res. 2008 Feb; 18(2):214-20.
Ahituv N, Akiyama J, Chapman-Helleboid A, Fruchart J, Pennacchio LA. In vivo characterization of human APOA5 haplotypes. Genomics. 2007 Dec; 90(6):674-9.
Costford SR, Kavaslar N, Ahituv N, Chaudhry SN, Schackwitz WS, Dent R, Pennacchio LA, McPherson R, Harper ME. Gain-of-function R225W mutation in human AMPKgamma(3) causing increased glycogen and decreased triglyceride in skeletal muscle. PLoS One. 2007 Sep 19; 2(9):e903.
Ahituv N, Zhu Y, Visel A, Holt A, Afzal V, Pennacchio LA, Rubin EM. Deletion of ultraconserved elements yields viable mice. PLoS Biol. 2007 Sep; 5(9):e234.
Ahituv N, Kavaslar N, Schackwitz W, Ustaszewska A, Martin J, Hebert S, Doelle H, Ersoy B, Kryukov G, Schmidt S, Yosef N, Ruppin E, Sharan R, Vaisse C, Sunyaev S, Dent R, Cohen J, McPherson R, Pennacchio LA. Medical sequencing at the extremes of human body mass. Am J Hum Genet. 2007 Apr; 80(4):779-91.
Pennacchio LA, Ahituv N, Moses AM, Prabhakar S, Nobrega MA, Shoukry M, Minovitsky S, Dubchak I, Holt A, Lewis KD, Plajzer-Frick I, Akiyama J, De Val S, Afzal V, Black BL, Couronne O, Eisen MB, Visel A, Rubin EM. In vivo enhancer analysis of human conserved non-coding sequences. Nature. 2006 Nov 23; 444(7118):499-502.
Bejerano G, Lowe CB, Ahituv N, King B, Siepel A, Salama SR, Rubin EM, Kent WJ, Haussler D. A distal enhancer and an ultraconserved exon are derived from a novel retroposon. Nature. 2006 May 04; 441(7089):87-90.
Ahituv N, Kavaslar N, Schackwitz W, Ustaszewska A, Collier JM, Hébert S, Doelle H, Dent R, Pennacchio LA, McPherson R. A PYY Q62P variant linked to human obesity. Hum Mol Genet. 2006 Feb 01; 15(3):387-91.
Ahituv N, Prabhakar S, Poulin F, Rubin EM, Couronne O. Mapping cis-regulatory domains in the human genome using multi-species conservation of synteny. Hum Mol Genet. 2005 Oct 15; 14(20):3057-63.
Baroukh N, Ahituv N, Chang J, Shoukry M, Afzal V, Rubin EM, Pennacchio LA. Comparative genomic analysis reveals a distant liver enhancer upstream of the COUP-TFII gene. Mamm Genome. 2005 Feb; 16(2):91-5.
Ahituv N, Rubin EM, Nobrega MA. Exploiting human--fish genome comparisons for deciphering gene regulation. Hum Mol Genet. 2004 Oct 01; 13 Spec No 2:R261-6.
Ahituv N, Erven A, Fuchs H, Guy K, Ashery-Padan R, Williams T, de Angelis MH, Avraham KB, Steel KP. An ENU-induced mutation in AP-2alpha leads to middle ear and ocular defects in Doarad mice. Mamm Genome. 2004 Jun; 15(6):424-32.
Nadav Ahituv, Orit Ben-David, Paolo Gasparini, Karen Avraham. Myosin VI. Genetic Hearing Loss. 2003 Oct 17.
Ahituv N, Avraham KB. Mouse models for human deafness: current tools for new fashions. Trends Mol Med. 2002 Sep; 8(9):447-51.
Melchionda S, Ahituv N, Bisceglia L, Sobe T, Glaser F, Rabionet R, Arbones ML, Notarangelo A, Di Iorio E, Carella M, Zelante L, Estivill X, Avraham KB, Gasparini P. MYO6, the human homologue of the gene responsible for deafness in Snell's waltzer mice, is mutated in autosomal dominant nonsyndromic hearing loss. Am J Hum Genet. 2001 Sep; 69(3):635-40.
Kiernan AE, Ahituv N, Fuchs H, Balling R, Avraham KB, Steel KP, Hrabé de Angelis M. The Notch ligand Jagged1 is required for inner ear sensory development. Proc Natl Acad Sci U S A. 2001 Mar 27; 98(7):3873-8.
Ahituv N, Sobe T, Robertson NG, Morton CC, Taggart RT, Avraham KB. Genomic structure of the human unconventional myosin VI gene. Gene. 2000 Dec 31; 261(2):269-75.
Ahituv N, Avraham KB. Auditory and vestibular mouse mutants: models for human deafness. J Basic Clin Physiol Pharmacol. 2000; 11(3):181-91.
Vahava O, Morell R, Lynch ED, Weiss S, Kagan ME, Ahituv N, Morrow JE, Lee MK, Skvorak AB, Morton CC, Blumenfeld A, Frydman M, Friedman TB, King MC, Avraham KB. Mutation in transcription factor POU4F3 associated with inherited progressive hearing loss in humans. Science. 1998 Mar 20; 279(5358):1950-4.
Ahituv N, Berman O. Devising a cooperation policy for emergency networks. J Oper Res Soc. 1987 Nov; 38(11):1015-29.