Dan Levy, Ph.D. - Publications

Affiliations: 
2005 University of California, Berkeley, Berkeley, CA 

59 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2016 Wang Z, Andrews P, Kendall J, Ma B, Hakker I, Rodgers L, Ronemus M, Wigler M, Levy D. SMASH, a fragmentation and sequencing method for genomic copy number analysis. Genome Research. PMID 27197213 DOI: 10.1101/gr.201491.115  0.72
2015 Iossifov I, Levy D, Allen J, Ye K, Ronemus M, Lee YH, Yamrom B, Wigler M. Low load for disruptive mutations in autism genes and their biased transmission. Proceedings of the National Academy of Sciences of the United States of America. PMID 26401017 DOI: 10.1073/pnas.1516376112  0.72
2015 MacGregor JT, Frötschl R, White PA, Crump KS, Eastmond DA, Fukushima S, Guérard M, Hayashi M, Soeteman-Hernández LG, Johnson GE, Kasamatsu T, Levy DD, Morita T, Müller L, Schoeny R, et al. IWGT report on quantitative approaches to genotoxicity risk assessment II. Use of point-of-departure (PoD) metrics in defining acceptable exposure limits and assessing human risk. Mutation Research. Genetic Toxicology and Environmental Mutagenesis. 783: 66-78. PMID 25953401 DOI: 10.1016/j.mrgentox.2014.10.008  0.72
2015 MacGregor JT, Frötschl R, White PA, Crump KS, Eastmond DA, Fukushima S, Guérard M, Hayashi M, Soeteman-Hernández LG, Kasamatsu T, Levy DD, Morita T, Müller L, Schoeny R, Schuler MJ, et al. IWGT report on quantitative approaches to genotoxicity risk assessment I. Methods and metrics for defining exposure-response relationships and points of departure (PoDs). Mutation Research. Genetic Toxicology and Environmental Mutagenesis. 783: 55-65. PMID 25953400 DOI: 10.1016/j.mrgentox.2014.09.011  0.72
2015 Ding W, Levy DD, Bishop ME, Pearce MG, Davis KJ, Jeffrey AM, Duan JD, Williams GM, White GA, Lyn-Cook LE, Manjanatha MG. In vivo genotoxicity of estragole in male F344 rats. Environmental and Molecular Mutagenesis. 56: 356-65. PMID 25361439 DOI: 10.1002/em.21918  0.72
2014 Iossifov I, O'Roak BJ, Sanders SJ, Ronemus M, Krumm N, Levy D, Stessman HA, Witherspoon KT, Vives L, Patterson KE, Smith JD, Paeper B, Nickerson DA, Dea J, Dong S, et al. The contribution of de novo coding mutations to autism spectrum disorder. Nature. 515: 216-21. PMID 25363768 DOI: 10.1038/nature13908  0.72
2014 Levy D, Wigler M. Facilitated sequence counting and assembly by template mutagenesis. Proceedings of the National Academy of Sciences of the United States of America. 111: E4632-7. PMID 25313059 DOI: 10.1073/pnas.1416204111  0.72
2014 Ronemus M, Iossifov I, Levy D, Wigler M. The role of de novo mutations in the genetics of autism spectrum disorders. Nature Reviews. Genetics. 15: 133-41. PMID 24430941 DOI: 10.1038/nrg3585  0.72
2014 Warburton D, Ronemus M, Kline J, Jobanputra V, Williams I, Anyane-Yeboa K, Chung W, Yu L, Wong N, Awad D, Yu CY, Leotta A, Kendall J, Yamrom B, Lee YH, ... ... Levy D, et al. The contribution of de novo and rare inherited copy number changes to congenital heart disease in an unselected sample of children with conotruncal defects or hypoplastic left heart disease. Human Genetics. 133: 11-27. PMID 23979609 DOI: 10.1007/s00439-013-1353-9  0.72
2014 Guo X, Zhang S, Dial SL, Boudreau MD, Xia Q, Fu PP, Levy DD, Moore MM, Mei N. In vitro investigation of the mutagenic potential of Aloe vera extracts Toxicology Research. 3: 487-496. DOI: 10.1039/c4tx00053f  0.72
2013 Regulski M, Lu Z, Kendall J, Donoghue MT, Reinders J, Llaca V, Deschamps S, Smith A, Levy D, McCombie WR, Tingey S, Rafalski A, Hicks J, Ware D, Martienssen RA. The maize methylome influences mRNA splice sites and reveals widespread paramutation-like switches guided by small RNA. Genome Research. 23: 1651-62. PMID 23739895 DOI: 10.1101/gr.153510.112  0.72
2013 Brookmire L, Chen JJ, Levy DD. Evaluation of the highest concentrations used in the in vitro chromosome aberrations assay. Environmental and Molecular Mutagenesis. 54: 36-43. PMID 23076808 DOI: 10.1002/em.21738  0.72
2012 Stadler ZK, Esposito D, Shah S, Vijai J, Yamrom B, Levy D, Lee YH, Kendall J, Leotta A, Ronemus M, Hansen N, Sarrel K, Rau-Murthy R, Schrader K, Kauff N, et al. Rare de novo germline copy-number variation in testicular cancer. American Journal of Human Genetics. 91: 379-83. PMID 22863192 DOI: 10.1016/j.ajhg.2012.06.019  0.72
2012 Iossifov I, Ronemus M, Levy D, Wang Z, Hakker I, Rosenbaum J, Yamrom B, Lee YH, Narzisi G, Leotta A, Kendall J, Grabowska E, Ma B, Marks S, Rodgers L, et al. De novo gene disruptions in children on the autistic spectrum. Neuron. 74: 285-99. PMID 22542183 DOI: 10.1016/j.neuron.2012.04.009  0.72
2012 Lee YH, Ronemus M, Kendall J, Lakshmi B, Leotta A, Levy D, Esposito D, Grubor V, Ye K, Wigler M, Yamrom B. Reducing system noise in copy number data using principal components of self-self hybridizations. Proceedings of the National Academy of Sciences of the United States of America. 109: E103-10. PMID 22207624 DOI: 10.1073/pnas.1106233109  0.72
2011 Abdel-Rahman A, Anyangwe N, Carlacci L, Casper S, Danam RP, Enongene E, Erives G, Fabricant D, Gudi R, Hilmas CJ, Hines F, Howard P, Levy D, Lin Y, Moore RJ, et al. The safety and regulation of natural products used as foods and food ingredients. Toxicological Sciences : An Official Journal of the Society of Toxicology. 123: 333-48. PMID 21821733 DOI: 10.1093/toxsci/kfr198  0.72
2011 Ding W, Levy DD, Bishop ME, Lyn-Cook Lascelles E, Kulkarni R, Chang CW, Aidoo A, Manjanatha MG. Methyleugenol genotoxicity in the Fischer 344 rat using the comet assay and pathway-focused gene expression profiling. Toxicological Sciences : An Official Journal of the Society of Toxicology. 123: 103-12. PMID 21659616 DOI: 10.1093/toxsci/kfr153  0.72
2011 Gilman SR, Iossifov I, Levy D, Ronemus M, Wigler M, Vitkup D. Rare de novo variants associated with autism implicate a large functional network of genes involved in formation and function of synapses. Neuron. 70: 898-907. PMID 21658583 DOI: 10.1016/j.neuron.2011.05.021  0.72
2011 Levy D, Ronemus M, Yamrom B, Lee YH, Leotta A, Kendall J, Marks S, Lakshmi B, Pai D, Ye K, Buja A, Krieger A, Yoon S, Troge J, Rodgers L, et al. Rare de novo and transmitted copy-number variation in autistic spectrum disorders. Neuron. 70: 886-97. PMID 21658582 DOI: 10.1016/j.neuron.2011.05.015  0.72
2011 Navin N, Kendall J, Troge J, Andrews P, Rodgers L, McIndoo J, Cook K, Stepansky A, Levy D, Esposito D, Muthuswamy L, Krasnitz A, McCombie WR, Hicks J, Wigler M. Tumour evolution inferred by single-cell sequencing. Nature. 472: 90-4. PMID 21399628 DOI: 10.1038/nature09807  0.72
2011 Sanders ME, Levy DD. The science and regulations of probiotic food and supplement product labeling. Annals of the New York Academy of Sciences. 1219: E1-E23. PMID 21332758 DOI: 10.1111/j.1749-6632.2010.05956.x  0.72
2011 Galloway S, Lorge E, Aardema MJ, Eastmond D, Fellows M, Heflich R, Kirkland D, Levy DD, Lynch AM, Marzin D, Morita T, Schuler M, Speit G. Workshop summary: Top concentration for in vitro mammalian cell genotoxicity assays; and report from working group on toxicity measures and top concentration for in vitro cytogenetics assays (chromosome aberrations and micronucleus). Mutation Research. 723: 77-83. PMID 21255675 DOI: 10.1016/j.mrgentox.2011.01.003  0.72
2011 Kamalakaran S, Varadan V, Giercksky Russnes HE, Levy D, Kendall J, Janevski A, Riggs M, Banerjee N, Synnestvedt M, Schlichting E, KÃ¥resen R, Shama Prasada K, Rotti H, Rao R, Rao L, et al. DNA methylation patterns in luminal breast cancers differ from non-luminal subtypes and can identify relapse risk independent of other clinical variables. Molecular Oncology. 5: 77-92. PMID 21169070 DOI: 10.1016/j.molonc.2010.11.002  0.72
2011 Dearfield KL, Thybaud V, Cimino MC, Custer L, Czich A, Harvey JS, Hester S, Kim JH, Kirkland D, Levy DD, Lorge E, Moore MM, Ouédraogo-Arras G, Schuler M, Suter W, et al. Follow-up actions from positive results of in vitro genetic toxicity testing. Environmental and Molecular Mutagenesis. 52: 177-204. PMID 20963811 DOI: 10.1002/em.20617  0.72
2011 Levy D, Pachter L. The neighbor-net algorithm Advances in Applied Mathematics. 47: 240-258. DOI: 10.1016/j.aam.2010.09.002  0.72
2010 Sanders ME, Akkermans LM, Haller D, Hammerman C, Heimbach J, Hörmannsperger G, Huys G, Levy DD, Lutgendorff F, Mack D, Phothirath P, Solano-Aguilar G, Vaughan E. Safety assessment of probiotics for human use. Gut Microbes. 1: 164-85. PMID 21327023 DOI: 10.4161/gmic.1.3.12127  0.72
2010 Navin N, Krasnitz A, Rodgers L, Cook K, Meth J, Kendall J, Riggs M, Eberling Y, Troge J, Grubor V, Levy D, Lundin P, MÃ¥nér S, Zetterberg A, Hicks J, et al. Inferring tumor progression from genomic heterogeneity. Genome Research. 20: 68-80. PMID 19903760 DOI: 10.1101/gr.099622.109  0.72
2009 Elespuru RK, Agarwal R, Atrakchi AH, Bigger CA, Heflich RH, Jagannath DR, Levy DD, Moore MM, Ouyang Y, Robison TW, Sotomayor RE, Cimino MC, Dearfield KL. Current and future application of genetic toxicity assays: the role and value of in vitro mammalian assays. Toxicological Sciences : An Official Journal of the Society of Toxicology. 109: 172-9. PMID 19336498 DOI: 10.1093/toxsci/kfp067  0.72
2009 Mihaescu R, Levy D, Pachter L. Why neighbor-joining works Algorithmica (New York). 54: 1-24. DOI: 10.1007/s00453-007-9116-4  0.72
2007 Levy D, Reeder C, Loucas B, Hlatky L, Chen A, Cornforth M, Sachs R. Interpreting chromosome aberration spectra. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 14: 144-55. PMID 17456013 DOI: 10.1089/cmb.2006.0127  0.72
2006 Levy D, Yoshida R, Pachter L. Beyond pairwise distances: neighbor-joining with phylogenetic diversity estimates. Molecular Biology and Evolution. 23: 491-8. PMID 16280538 DOI: 10.1093/molbev/msj059  0.72
2004 Levy D, Vazquez M, Cornforth M, Loucas B, Sachs RK, Arsuaga J. Comparing DNA damage-processing pathways by computer analysis of chromosome painting data Journal of Computational Biology. 11: 626-641. PMID 15579235 DOI: 10.1089/cmb.2004.11.626  0.72
2004 Levy DD, Sharma B, Cebula TA. Single-nucleotide polymorphism mutation spectra and resistance to quinolones in Salmonella enterica serovar Enteritidis with a mutator phenotype. Antimicrobial Agents and Chemotherapy. 48: 2355-63. PMID 15215081 DOI: 10.1128/AAC.48.7.2355-2363.2004  0.72
2004 Sachs RK, Levy D, Hahnfeldt P, Hlatky L. Quantitative analysis of radiation-induced chromosome aberrations Cytogenetic and Genome Research. 104: 142-148. PMID 15162028 DOI: 10.1159/000077479  0.72
2003 Chorny M, Levy D, Schumacher I, Lichaa C, Gruzman B, Livshits O, Lomnicky Y. Development and validation of a stability-indicating high performance liquid chromatographic assay for benoxinate Journal of Pharmaceutical and Biomedical Analysis. 32: 189-196. PMID 12852462 DOI: 10.1016/S0731-7085(03)00052-9  0.72
2002 Kotewicz ML, Li B, Levy DD, LeClerc JE, Shifflet AW, Cebula TA. Evolution of multi-gene segments in the mutS-rpoS intergenic region of Salmonella enterica serovar Typhimurium LT2. Microbiology (Reading, England). 148: 2531-40. PMID 12177346 DOI: 10.1099/00221287-148-8-2531  0.72
2002 Orlandi PA, Lampel KA, South PK, Assar SK, Carter L, Levy DD. Analysis of flour and food samples for cry9C from bioengineered corn. Journal of Food Protection. 65: 426-31. PMID 11848580  0.72
2001 Chizhikov V, Rasooly A, Chumakov K, Levy DD. Microarray analysis of microbial virulence factors. Applied and Environmental Microbiology. 67: 3258-63. PMID 11425749 DOI: 10.1128/AEM.67.7.3258-3263.2001  0.72
2001 Levy DD, Cebula TA. Fidelity of replication of repetitive DNA in mutS and repair proficient Escherichia coli Mutation Research - Fundamental and Molecular Mechanisms of Mutagenesis. 474: 1-14. PMID 11239958 DOI: 10.1016/S0027-5107(00)00169-X  0.72
2000 Sachs RK, Levy D, Chen AM, Simpson PJ, Cornforth MN, Ingerman EA, Hahnfeldt P, Hlatky LR. Random breakage and reunion chromosome aberration formation model; an interaction-distance version based on chromatin geometry. International Journal of Radiation Biology. 76: 1579-88. PMID 11133039  0.72
1999 Igoucheva O, Peritz AE, Levy D, Yoon K. A sequence-specific gene correction by an RNA-DNA oligonucleotide in mammalian cells characterized by transfection and nuclear extract using a lacZ shuttle system Gene Therapy. 6: 1960-1971. PMID 10637447 DOI: 10.1038/sj.gt.3301042  0.72
1999 Levy DD, Cebula TA. Mutagenesis patterns in a tRNA mutation marker gene altered to include repetitive sequence replicated in mutS E. coli Annals of the New York Academy of Sciences. 870: 392-395. PMID 10415506 DOI: 10.1111/j.1749-6632.1999.tb08911.x  0.72
1999 Tobi SE, Levy DD, Seidman MM, Kraemer KH. Sequence-dependent mutations in a shuttle vector plasmid replicated in a mismatch repair deficient human cell line Carcinogenesis. 20: 1293-1301. PMID 10383903 DOI: 10.1093/carcin/20.7.1293  0.72
1999 Rubnov S, Shats I, Levy D, Amisar S, Schneider H. Autocatalytic degradation and stability of obidoxime Journal of Pharmacy and Pharmacology. 51: 9-14. PMID 10197411  0.72
1999 Lacroix L, Lacoste J, Reddoch JF, Mergny JL, Levy DD, Seidman MM, Matteucci MD, Glazer PM. Triplex formation by oligonucleotides containing 5-(1-propynyl)-2'-deoxyuridine: decreased magnesium dependence and improved intracellular gene targeting. Biochemistry. 38: 1893-901. PMID 10026270 DOI: 10.1021/bi982290q  0.72
1999 Rubnov S, Levy D, Schneider H. Liquid chromatographic analysis of physostigmine salicylate and its degradation products Journal of Pharmaceutical and Biomedical Analysis. 18: 939-945. PMID 9925328 DOI: 10.1016/S0731-7085(98)00099-5  0.72
1999 Rubnov S, Amisar S, Levy D, Muchtar S, Schneider H. Stability of trimedoxime in concentrated acidic injectable solutions Military Medicine. 164: 55-58. PMID 9922646  0.72
1997 Wanidworanun C, Levy DD, Shear HL. Plasmodium chabaudi: cDNa of Pc96, a protective antigen associated with the erythrocyte membrane of infected erythrocytes Experimental Parasitology. 85: 92-98. PMID 9024207 DOI: 10.1006/expr.1996.4122  0.72
1996 Levy DD, Magee AD, Seidman MM. Single nucleotide positions have proximal and distal influence on UV mutation hotspots and coldspots Journal of Molecular Biology. 258: 251-260. PMID 8627623 DOI: 10.1006/jmbi.1996.0247  0.72
1996 Levy DD, Magee AD, Namiki C, Seidman MM. The influence of single base changes on UV mutational activity at two translocated hotspots Journal of Molecular Biology. 255: 435-445. PMID 8568888 DOI: 10.1006/jmbi.1996.0036  0.72
1995 Wang G, Levy DD, Seidman MM, Glazer PM. Targeted mutagenesis in mammalian cells mediated by intracellular triple helix formation Molecular and Cellular Biology. 15: 1759-1768. PMID 7862165  0.72
1995 Levy DD, Saijo M, Tanaka K, Kraemer KH. Expression of a transfected DNA repair gene (XPA) in xeroderma pigmentosum group A cells restores normal DNA repair and mutagenesis of UV-treated plasmids Carcinogenesis. 16: 1557-1563. PMID 7614689  0.72
1994 Parris CN, Levy DD, Jessee J, Seidman MM. Proximal and distal effects of sequence context on ultraviolet mutational hotspots in a shuttle vector replicated in xeroderma cells Journal of Molecular Biology. 236: 491-502. PMID 8107135 DOI: 10.1006/jmbi.1994.1160  0.72
1994 Kraemer KH, Levy DD, Parris CN, Gozukara EM, Moriwaki S, Adelberg S, Seidman MM. Xeroderma pigmentosum and related disorders: Examining the linkage between defective DNA repair and cancer Journal of Investigative Dermatology. 103: 96S-101S. PMID 7963692  0.72
1992 Levy DD, Groopman JD, Lim SE, Seidman MM, Kraemer KH. Sequence specificity of aflatoxin B1-induced mutations in a plasmid replicated in xeroderma pigmentosum and DNA repair proficient human cells Cancer Research. 52: 5668-5673. PMID 1394191  0.72
1991 Levy DD, Teebor GW. Site directed substitution of 5-hydroxymethyluracil for thymine in replicating ∅X-174am3 DNA via synthesis of 5-hydroxymethyl-2'-deoxyuridine-5'-triphosphate Nucleic Acids Research. 19: 3337-3343. PMID 2062651  0.72
1987 Boorstein RJ, Levy DD, Teebor GW. Toxicity of 3-aminobenzamide to Chinese hamster cells containing 5-hydroxymethyluracil in their DNA Cancer Research. 47: 4372-4377. PMID 3607769  0.72
1987 Boorstein RJ, Levy DD, Teebor GW. 5-Hydroxymethyluracil-DNA glycosylase activity may be a differentiated mammalian function Mutation Research Dna Repair Reports. 183: 257-263. PMID 3553917 DOI: 10.1016/0167-8817(87)90008-3  0.72
1981 Wigler M, Levy D, Perucho M. The somatic replication of DNA methylation. Cell. 24: 33-40. PMID 6263490 DOI: 10.1016/0092-8674(81)90498-0  0.72
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