Dario Boffelli, PhD

Title(s)Professor, Pediatrics
SchoolSchool of Medicine
Address513 Parnassus Avenue, MSB
San Francisco CA 94117
Phone510-476-7766
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    Collapse Research 
    Collapse Research Activities and Funding
    Multigenerational epigenetic programming induced by paternal obesity and prediabetes
    NIH R01DK111035Sep 1, 2016 - Feb 28, 2022
    Role: Co-Principal Investigator
    Transgenerational epigenetic effects induced by paternal preconception ethanol
    NIH R21AA022753Jul 1, 2014 - Jun 30, 2016
    Role: Co-Principal Investigator
    Heritability of gene expression variants in isogenic mice
    NIH R56ES022377Feb 11, 2013 - Jul 31, 2014
    Role: Principal Investigator
    Identification of Primate-Specific Regulatory Elements of Cholesterol Homeostasis
    NIH R01HL084474Apr 4, 2007 - Mar 31, 2013
    Role: Principal Investigator

    Collapse Bibliographic 
    Collapse Publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help. to make corrections and additions.
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    Altmetrics Details PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Application of full-genome analysis to diagnose rare monogenic disorders. NPJ Genom Med. 2021 Sep 23; 6(1):77. Shieh JT, Penon-Portmann M, Wong KHY, Levy-Sakin M, Verghese M, Slavotinek A, Gallagher RC, Mendelsohn BA, Tenney J, Beleford D, Perry H, Chow SK, Sharo AG, Brenner SE, Qi Z, Yu J, Klein OD, Martin D, Kwok PY, Boffelli D. PMID: 34556655.
      View in: PubMed   Mentions:
    2. Towards a reference genome that captures global genetic diversity. Nat Commun. 2020 10 30; 11(1):5482. Wong KHY, Ma W, Wei CY, Yeh EC, Lin WJ, Wang EHF, Su JP, Hsieh FJ, Kao HJ, Chen HH, Chow SK, Young E, Chu C, Poon A, Yang CF, Lin DS, Hu YF, Wu JY, Lee NC, Hwu WL, Boffelli D, Martin D, Xiao M, Kwok PY. PMID: 33127893.
      View in: PubMed   Mentions: 5     Fields:    Translation:HumansCells
    3. The Driver of Extreme Human-Specific Olduvai Repeat Expansion Remains Highly Active in the Human Genome. Genetics. 2020 01; 214(1):179-191. Heft IE, Mostovoy Y, Levy-Sakin M, Ma W, Stevens AJ, Pastor S, McCaffrey J, Boffelli D, Martin DI, Xiao M, Kennedy MA, Kwok PY, Sikela JM. PMID: 31754017.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansAnimalsCells
    4. Single-Cell Transcriptome Analysis of CD34+ Stem Cell-Derived Myeloid Cells Infected With Human Cytomegalovirus. Front Microbiol. 2019; 10:577. Galinato M, Shimoda K, Aguiar A, Hennig F, Boffelli D, McVoy MA, Hertel L. PMID: 30949159.
      View in: PubMed   Mentions:
    5. CRISPR-Cas9 interrogation of a putative fetal globin repressor in human erythroid cells. PLoS One. 2019; 14(1):e0208237. Chung JE, Magis W, Vu J, Heo SJ, Wartiovaara K, Walters MC, Kurita R, Nakamura Y, Boffelli D, Martin DIK, Corn JE, DeWitt MA. PMID: 30645582.
      View in: PubMed   Mentions: 7     Fields:    Translation:HumansCells
    6. Selection-free genome editing of the sickle mutation in human adult hematopoietic stem/progenitor cells. Sci Transl Med. 2016 10 12; 8(360):360ra134. DeWitt MA, Magis W, Bray NL, Wang T, Berman JR, Urbinati F, Heo SJ, Mitros T, Muñoz DP, Boffelli D, Kohn DB, Walters MC, Carroll D, Martin DI, Corn JE. PMID: 27733558.
      View in: PubMed   Mentions: 130     Fields:    Translation:HumansAnimalsCells
    7. Functionally conserved enhancers with divergent sequences in distant vertebrates. BMC Genomics. 2015 Oct 30; 16:882. Yang S, Oksenberg N, Takayama S, Heo SJ, Poliakov A, Ahituv N, Dubchak I, Boffelli D. PMID: 26519295.
      View in: PubMed   Mentions: 6     Fields:    Translation:AnimalsCells
    8. piRNA-like small RNAs mark extended 3'UTRs present in germ and somatic cells. BMC Genomics. 2015 Jun 16; 16:462. Yamtich J, Heo SJ, Dhahbi J, Martin DI, Boffelli D. PMID: 26076733.
      View in: PubMed   Mentions: 8     Fields:    Translation:Animals
    9. Deep Sequencing of Serum Small RNAs Identifies Patterns of 5' tRNA Half and YRNA Fragment Expression Associated with Breast Cancer. Biomark Cancer. 2014; 6:37-47. Dhahbi JM, Spindler SR, Atamna H, Boffelli D, Martin DI. PMID: 25520563.
      View in: PubMed   Mentions:
    10. Now you see it: genome methylation makes a comeback in Drosophila. Bioessays. 2014 Dec; 36(12):1138-44. Boffelli D, Takayama S, Martin DI. PMID: 25220261.
      View in: PubMed   Mentions: 12     Fields:    Translation:AnimalsCells
    11. Genome methylation in D. melanogaster is found at specific short motifs and is independent of DNMT2 activity. Genome Res. 2014 May; 24(5):821-30. Takayama S, Dhahbi J, Roberts A, Mao G, Heo SJ, Pachter L, Martin DI, Boffelli D. PMID: 24558263.
      View in: PubMed   Mentions: 59     Fields:    Translation:AnimalsCells
    12. Deficiency of MIWI2 (Piwil4) induces mouse erythroleukemia cell differentiation, but has no effect on hematopoiesis in vivo. PLoS One. 2013; 8(12):e82573. Jacobs JE, Wagner M, Dhahbi J, Boffelli D, Martin DI. PMID: 24376547.
      View in: PubMed   Mentions: 6     Fields:    Translation:AnimalsCells
    13. Statin-induced changes in gene expression in EBV-transformed and native B-cells. Hum Mol Genet. 2014 Mar 01; 23(5):1202-10. Bolotin E, Armendariz A, Kim K, Heo SJ, Boffelli D, Tantisira K, Rotter JI, Krauss RM, Medina MW. PMID: 24179175.
      View in: PubMed   Mentions: 8     Fields:    Translation:HumansCells
    14. A role for epigenetic inheritance in modern evolutionary theory? A comment in response to Dickins and Rahman. Proc Biol Sci. 2013 Nov 22; 280(1771):20130903; discussion 20131820. Suter CM, Boffelli D, Martin DI. PMID: 24089330.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansAnimals
    15. 5'-YRNA fragments derived by processing of transcripts from specific YRNA genes and pseudogenes are abundant in human serum and plasma. Physiol Genomics. 2013 Nov 01; 45(21):990-8. Dhahbi JM, Spindler SR, Atamna H, Boffelli D, Mote P, Martin DI. PMID: 24022222.
      View in: PubMed   Mentions: 59     Fields:    Translation:HumansAnimalsCells
    16. Activation-induced cytidine deaminase (AID) is necessary for the epithelial-mesenchymal transition in mammary epithelial cells. Proc Natl Acad Sci U S A. 2013 Aug 06; 110(32):E2977-86. Muñoz DP, Lee EL, Takayama S, Coppé JP, Heo SJ, Boffelli D, Di Noia JM, Martin DI. PMID: 23882083.
      View in: PubMed   Mentions: 28     Fields:    Translation:HumansAnimalsCells
    17. 5' tRNA halves are present as abundant complexes in serum, concentrated in blood cells, and modulated by aging and calorie restriction. BMC Genomics. 2013 May 02; 14:298. Dhahbi JM, Spindler SR, Atamna H, Yamakawa A, Boffelli D, Mote P, Martin DI. PMID: 23638709.
      View in: PubMed   Mentions: 96     Fields:    Translation:AnimalsCells
    18. Deep sequencing identifies circulating mouse miRNAs that are functionally implicated in manifestations of aging and responsive to calorie restriction. Aging (Albany NY). 2013 Feb; 5(2):130-41. Dhahbi JM, Spindler SR, Atamna H, Yamakawa A, Guerrero N, Boffelli D, Mote P, Martin DI. PMID: 23470454.
      View in: PubMed   Mentions: 29     Fields:    Translation:Animals
    19. Epigenetic inheritance: a contributor to species differentiation? DNA Cell Biol. 2012 Oct; 31 Suppl 1:S11-6. Boffelli D, Martin DI. PMID: 22966965.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansAnimalsCells
    20. mRNA-Seq reveals complex patterns of gene regulation and expression in the mouse skeletal muscle transcriptome associated with calorie restriction. Physiol Genomics. 2012 Mar 19; 44(6):331-44. Dhahbi JM, Atamna H, Boffelli D, Martin DI, Spindler SR. PMID: 22274562.
      View in: PubMed   Mentions: 3     Fields:    Translation:AnimalsCells
    21. Identification and correction of systematic error in high-throughput sequence data. BMC Bioinformatics. 2011 Nov 21; 12:451. Meacham F, Boffelli D, Dhahbi J, Martin DI, Singer M, Pachter L. PMID: 22099972.
      View in: PubMed   Mentions: 104     Fields:    Translation:HumansCells
    22. Phyloepigenomic comparison of great apes reveals a correlation between somatic and germline methylation states. Genome Res. 2011 Dec; 21(12):2049-57. Martin DI, Singer M, Dhahbi J, Mao G, Zhang L, Schroth GP, Pachter L, Boffelli D. PMID: 21908772.
      View in: PubMed   Mentions: 22     Fields:    Translation:HumansAnimalsCells
    23. VISTA Region Viewer (RViewer)--a computational system for prioritizing genomic intervals for biomedical studies. Bioinformatics. 2011 Sep 15; 27(18):2595-7. Lukashin I, Novichkov P, Boffelli D, Paciorkowski AR, Minovitsky S, Yang S, Dubchak I. PMID: 21791533.
      View in: PubMed   Mentions: 6     Fields:    Translation:HumansAnimals
    24. Deep sequencing reveals novel microRNAs and regulation of microRNA expression during cell senescence. PLoS One. 2011; 6(5):e20509. Dhahbi JM, Atamna H, Boffelli D, Magis W, Spindler SR, Martin DI. PMID: 21637828.
      View in: PubMed   Mentions: 46     Fields:    Translation:HumansCells
    25. MetMap enables genome-scale Methyltyping for determining methylation states in populations. PLoS Comput Biol. 2010 Aug 19; 6(8):e1000888. Singer M, Boffelli D, Dhahbi J, Schönhuth A, Schroth GP, Martin DI, Pachter L. PMID: 20856582.
      View in: PubMed   Mentions: 6     Fields:    Translation:HumansCells
    26. LPA and PLG sequence variation and kringle IV-2 copy number in two populations. Hum Hered. 2008; 66(4):199-209. Crawford DC, Peng Z, Cheng JF, Boffelli D, Ahearn M, Nguyen D, Shaffer T, Yi Q, Livingston RJ, Rieder MJ, Nickerson DA. PMID: 18612205.
      View in: PubMed   Mentions: 10     Fields:    Translation:HumansCells
    27. Phylogenetic shadowing: sequence comparisons of multiple primate species. Methods Mol Biol. 2008; 453:217-31. Boffelli D. PMID: 18712305.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansAnimals
    28. Detection of weakly conserved ancestral mammalian regulatory sequences by primate comparisons. Genome Biol. 2007; 8(1):R1. Wang QF, Prabhakar S, Chanan S, Cheng JF, Rubin EM, Boffelli D. PMID: 17201929.
      View in: PubMed   Mentions: 17     Fields:    Translation:AnimalsCells
    29. Symbiosis insights through metagenomic analysis of a microbial consortium. Nature. 2006 Oct 26; 443(7114):950-5. Woyke T, Teeling H, Ivanova NN, Huntemann M, Richter M, Gloeckner FO, Boffelli D, Anderson IJ, Barry KW, Shapiro HJ, Szeto E, Kyrpides NC, Mussmann M, Amann R, Bergin C, Ruehland C, Rubin EM, Dubilier N. PMID: 16980956.
      View in: PubMed   Mentions: 160     Fields:    Translation:AnimalsCells
    30. Primate-specific evolution of an LDLR enhancer. Genome Biol. 2006; 7(8):R68. Wang QF, Prabhakar S, Wang Q, Moses AM, Chanan S, Brown M, Eisen MB, Cheng JF, Rubin EM, Boffelli D. PMID: 16884525.
      View in: PubMed   Mentions: 9     Fields:    Translation:HumansAnimalsCells
    31. Intraspecies sequence comparisons for annotating genomes. Genome Res. 2004 Dec; 14(12):2406-11. Boffelli D, Weer CV, Weng L, Lewis KD, Shoukry MI, Pachter L, Keys DN, Rubin EM. PMID: 15545499.
      View in: PubMed   Mentions: 17     Fields:    Translation:AnimalsCells
    32. eShadow: a tool for comparing closely related sequences. Genome Res. 2004 Jun; 14(6):1191-8. Ovcharenko I, Boffelli D, Loots GG. PMID: 15173121.
      View in: PubMed   Mentions: 23     Fields:    Translation:HumansAnimalsCells
    33. Comparative genomics at the vertebrate extremes. Nat Rev Genet. 2004 Jun; 5(6):456-65. Hanna RF, Ward TJ, Chow DS, Lagana SM, Moreira RK, Emond JC, Weintraub JL, Prince MR, Boffelli D, Nobrega MA, Rubin EM. PMID: 15153998.
      View in: PubMed   Mentions: 103     Fields:    Translation:HumansAnimalsCells
    34. Obesity in BSB mice is correlated with expression of genes for iron homeostasis and leptin. Obes Res. 2004 Feb; 12(2):191-204. Farahani P, Chiu S, Bowlus CL, Boffelli D, Lee E, Fisler JS, Krauss RM, Warden CH. PMID: 14981211.
      View in: PubMed   Mentions: 10     Fields:    Translation:Animals
    35. Convergent evolution in primates and an insectivore. Genomics. 2004 Jan; 83(1):19-23. Boffelli D, Cheng JF, Rubin EM. PMID: 14667805.
      View in: PubMed   Mentions: 3     Fields:    Translation:Animals
    36. Phylogenetic shadowing of primate sequences to find functional regions of the human genome. Science. 2003 Feb 28; 299(5611):1391-4. Boffelli D, McAuliffe J, Ovcharenko D, Lewis KD, Ovcharenko I, Pachter L, Rubin EM. PMID: 12610304.
      View in: PubMed   Mentions: 213     Fields:    Translation:HumansAnimalsCells
    37. Functional annotation of a full-length mouse cDNA collection. Nature. 2001 Feb 08; 409(6821):685-90. Kawai J, Shinagawa A, Shibata K, Yoshino M, Itoh M, Ishii Y, Arakawa T, Hara A, Fukunishi Y, Konno H, Adachi J, Fukuda S, Aizawa K, Izawa M, Nishi K, Kiyosawa H, Kondo S, Yamanaka I, Saito T, Okazaki Y, Gojobori T, Bono H, Kasukawa T, Saito R, Kadota K, Matsuda H, Ashburner M, Batalov S, Casavant T, Fleischmann W, Gaasterland T, Gissi C, King B, Kochiwa H, Kuehl P, Lewis S, Matsuo Y, Nikaido I, Pesole G, Quackenbush J, Schriml LM, Staubli F, Suzuki R, Tomita M, Wagner L, Washio T, Sakai K, Okido T, Furuno M, Aono H, Baldarelli R, Barsh G, Blake J, Boffelli D, Bojunga N, Carninci P, de Bonaldo MF, Brownstein MJ, Bult C, Fletcher C, Fujita M, Gariboldi M, Gustincich S, Hill D, Hofmann M, Hume DA, Kamiya M, Lee NH, Lyons P, Marchionni L, Mashima J, Mazzarelli J, Mombaerts P, Nordone P, Ring B, Ringwald M, Rodriguez I, Sakamoto N, Sasaki H, Sato K, Schönbach C, Seya T, Shibata Y, Storch KF, Suzuki H, Toyo-oka K, Wang KH, Weitz C, Whittaker C, Wilming L, Wynshaw-Boris A, Yoshida K, Hasegawa Y, Kawaji H, Kohtsuki S, Hayashizaki Y, RIKEN Genome Exploration Research Group Phase II Team and the FANTOM Consortium . PMID: 11217851.
      View in: PubMed   Mentions: 235     Fields:    Translation:HumansAnimalsCells
    38. Genomic interval engineering of mice identifies a novel modulator of triglyceride production. Proc Natl Acad Sci U S A. 2000 Feb 01; 97(3):1137-42. Zhu Y, Jong MC, Frazer KA, Gong E, Krauss RM, Cheng JF, Boffelli D, Rubin EM. PMID: 10655497.
      View in: PubMed   Mentions: 8     Fields:    Translation:HumansAnimalsCells
    39. Estrogen modulation of apolipoprotein(a) expression. Identification of a regulatory element. J Biol Chem. 1999 May 28; 274(22):15569-74. Boffelli D, Zajchowski DA, Yang Z, Lawn RM. PMID: 10336452.
      View in: PubMed   Mentions: 6     Fields:    Translation:HumansCells
    40. Identification of a receptor mediating absorption of dietary cholesterol in the intestine. Biochemistry. 1998 Dec 22; 37(51):17843-50. Hauser H, Dyer JH, Nandy A, Vega MA, Werder M, Bieliauskaite E, Weber FE, Compassi S, Gemperli A, Boffelli D, Wehrli E, Schulthess G, Phillips MC. PMID: 9922151.
      View in: PubMed   Mentions: 40     Fields:    Translation:HumansAnimalsCells
    41. Apolipoprotein(a) gene enhancer resides within a LINE element. J Biol Chem. 1998 Jan 09; 273(2):891-7. Yang Z, Boffelli D, Boonmark N, Schwartz K, Lawn R. PMID: 9422746.
      View in: PubMed   Mentions: 31     Fields:    Translation:HumansCells
    42. Reconstitution and further characterization of the cholesterol transport activity of the small-intestinal brush border membrane. Biochemistry. 1997 Sep 02; 36(35):10784-92. Boffelli D, Weber FE, Compassi S, Werder M, Schulthess G, Hauser H. PMID: 9271510.
      View in: PubMed   Mentions: 3     Fields:    Translation:AnimalsCells
    43. Molecular cloning of a peroxisomal Ca2+-dependent member of the mitochondrial carrier superfamily. Proc Natl Acad Sci U S A. 1997 Aug 05; 94(16):8509-14. Weber FE, Minestrini G, Dyer JH, Werder M, Boffelli D, Compassi S, Wehrli E, Thomas RM, Schulthess G, Hauser H. PMID: 9238007.
      View in: PubMed   Mentions: 11     Fields:    Translation:HumansAnimalsCells
    44. The uptake of cholesterol at the small-intestinal brush border membrane is inhibited by apolipoproteins. FEBS Lett. 1997 Jul 07; 411(1):7-11. Boffelli D, Compassi S, Werder M, Weber FE, Phillips MC, Schulthess G, Hauser H. PMID: 9247133.
      View in: PubMed   Mentions: 2     Fields:    Translation:HumansAnimalsCells
    45. Comparison of cholesterol and sitosterol uptake in different brush border membrane models. Biochemistry. 1997 Jun 03; 36(22):6643-52. Compassi S, Werder M, Weber FE, Boffelli D, Hauser H, Schulthess G. PMID: 9184144.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansAnimalsCells
    46. A comparative study of sterol absorption in different small-intestinal brush border membrane models. J Lipid Res. 1996 Nov; 37(11):2405-19. Schulthess G, Compassi S, Boffelli D, Werder M, Weber FE, Hauser H. PMID: 8978492.
      View in: PubMed   Mentions: 5     Fields:    Translation:HumansAnimalsCells
    47. Cholesteryl ester absorption by small intestinal brush border membrane is protein-mediated. Biochemistry. 1995 Dec 19; 34(50):16473-82. Compassi S, Werder M, Boffelli D, Weber FE, Hauser H, Schulthess G. PMID: 8845376.
      View in: PubMed   Mentions: 2     Fields:    Translation:AnimalsCells
    48. Absorption of monoacylglycerols by small intestinal brush border membrane. Biochemistry. 1994 Apr 19; 33(15):4500-8. Schulthess G, Lipka G, Compassi S, Boffelli D, Weber FE, Paltauf F, Hauser H. PMID: 8161504.
      View in: PubMed   Mentions: 9     Fields:    Translation:AnimalsCells
    49. A theoretical method to predict DNA permutation gel electrophoresis from the sequence. FEBS Lett. 1992 Mar 30; 300(2):175-8. Boffelli D, De Santis P, Palleschi A, Risuleo G, Savino M. PMID: 1314197.
      View in: PubMed   Mentions: 7     Fields:    Translation:Cells
    50. The curvature vector in nucleosomal DNAs and theoretical prediction of nucleosome positioning. Biophys Chem. 1991 Feb; 39(2):127-36. Hanna RF, Ward TJ, Chow DS, Lagana SM, Moreira RK, Emond JC, Weintraub JL, Prince MR, Boffelli D, De Santis P, Palleschi A, Savino M. PMID: 1647823.
      View in: PubMed   Mentions: 2     Fields:    Translation:Cells
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