Superfund Research Program

Nucleic Acids Research (impact factor: 16.971)

2023

• Wang Y, Risteski P, Yang Y, Chen H, Droby G, Walens A, Jayaprakash D, Troester MA, Herring L, Chernoff J, Tolic IM, Bowser J, Vaziri C. 2023. The TRIM69-MST2 signaling axis regulates centrosome dynamics and chromosome segregation. Nucleic Acids Res doi:10.1093/nar/gkad766 PMID:37739411
• Zhou H, Arapoglou T, Li X, Li Z, Zheng X, Moore JE, Asok A, Kumar S, Blue EE, Buyske S, Cox NJ, Felsenfeld A, Gerstein M, Kenny E, Li B, Matise T, Philippakis A, Rehm HL, Sofia HJ, Snyder G, Weng Z, Neale BM, Sunyaev SR, Lin X. 2023. FAVOR: functional annotation of variants online resource and annotator for variation across the human genome. Nucleic Acids Res 51:1300-1311. doi:10.1093/nar/gkac966 PMID:36350676 PMCID:9825437

2022

• Leuthner T, Benzing L, Kohrn BF, Bergemann CM, Hipp MJ, Hershberger KA, Mello DF, Sokolskyi T, Stevenson K, Merutka IR, Seay SA, Gregory SG, Kennedy SR, Meyer JN. 2022. Resistance of mitochondrial DNA to cadmium and Aflatoxin B1 damage-induced germline mutation accumulation in C. elegans. Nucleic Acids Res 50(15):8696-8642. doi:10.1093/nar/gkac666 PMID:35947695 PMCID:PMC9410910
• Nault R, Saha S, Bhattacharya S, Dodson J, Sinha S, Maiti T, Zacharewski TR. 2022. Benchmarking of a Bayesian single cell RNAseq differential gene expression test for dose-response study designs. Nucleic Acids Res doi:10.1093/nar/gkac019 PMID:35061903

2021

• Hung Y, Huang S, Dame MK, Yu Q, Yu QC, Zeng Y, Camp JG, Spence JR, Sethupathy P. 2021. Chromatin regulatory dynamics of early human small intestinal development using a directed differentiation model. Nucleic Acids Res 49(2):726-744. doi:10.1093/nar/gkaa1204 PMID:33406262 PMCID:PMC7826262
• Reed E, Monti S. 2021. Multi-resolution characterization of molecular taxonomies in bulk and single-cell transcriptomics data. Nucleic Acids Res 49(17):doi:10.1093/nar/gkab552 PMID:34226941 (ahead of print)

2020

• Ngo LP, Owiti NA, Swartz C, Winters J, Su Y, Ge J, Xiong A, Han J, Recio L, Samson LD, Engelward BP. 2020. Sensitive CometChip assay for screening potentially carcinogenic DNA adducts by trapping DNA repair intermediates. Nucleic Acids Res 48(3):e13. doi:10.1093/nar/gkz1077 PMID:31822921 PMCID:PMC7026589
• Stossi F, Dandekar RD, Mancini MG, Gu G, Fuqua SA, Nardone A, De Angelis C, Fu X, Schiff R, Bedford MT, Xu W, Johansson HE, Stephan C, Mancini MA. 2020. Estrogen-induced transcription at individual alleles is independent of receptor level and active conformation but can be modulated by coactivators activity. Nucleic Acids Res 48:1800-1810. doi:10.1093/nar/gkz1172 PMID:31930333 PMCID:PMC7039002

2016

• Jensen KL, Russell P. 2016. Ctp1-dependent clipping and resection of DNA double-strand breaks by Mre11 endonuclease complex are not genetically separable. Nucleic Acids Res 44(17):8241-8249. doi:10.1093/nar/gkw557 PMID:27325741 PMCID:PMC5041466

2015

• Hirota K, Yoshikiyo K, Guilbaud G, Tsurimoto T, Murai J, Tsuda M, Phillips LG, Narita T, Nishihara K, Kobayashi K, Yamada K, Nakamura J, Pommier Y, Lehmann A, Sale JE, Takeda S. 2015. The POLD3 subunit of DNA polymerase δ can promote translesion synthesis independently of DNA polymerase ζ. Nucleic Acids Res 43(3):1671-1683. doi:10.1093/nar/gkv023 PMID:25628356 PMCID:PMC4330384
• Lee S, Muench MO, Fomin ME, Xiao J, Zhou M, de Smith AJ, Martin-Subero JI, Heath S, Houseman EA, Roy R, Wrensch MR, Wiencke JK, Metayer C, Wiemels JL. 2015. Epigenetic remodeling in B-cell acute lymphoblastic leukemia occurs in two tracks and employs embryonic stem cell-like signatures. Nucleic Acids Res 43(5):2590-2602. doi:10.1093/nar/gkv103 PMID:25690899 PMCID:PMC4357708

2014

• Cole JR, Wang Q, Fish JA, Chai B, McGarrell DM, Sun Y, Brown C, Porras-Alfaro A, Kuske CR, Tiedje JM. 2014. Ribosomal Database Project: data and tools for high throughput rRNA analysis. Nucleic Acids Res 42(Databaseissue):D633-D642. doi:10.1093/nar/gkt1244 PMID:24288368 PMCID:PMC3965039

2013

• Shuga J, Zeng Y, Novak R, Lan Q, Tang X, Rothman N, Vermeulen R, Li L, Hubbard AE, Zhang L, Mathies RA, Smith MT. 2013. Single molecule quantitation and sequencing of rare translocations using microfluidic nested digital PCR. Nucleic Acids Res 41(16):e159. doi:10.1093/nar/gkt613 PMID:23873959 PMCID:PMC3763562

2007

• Heacock M, Idol RA, Friesner JD, Britt AB, Shippen DE. 2007. Telomere dynamics and fusion of critically shortened telomeres in plants lacking DNA ligase IV. Nucleic Acids Res 35(19):6490-6500. PMID:17897968
• Reynolds M, Stoddard L, Bespalov I, Zhitkovich A. 2007. Ascorbate acts as a highly potent inducer of chromate mutagenesis and clastogenesis: linkage to DNA breaks in G2 phase by mismatch repair. Nucleic Acids Res 35(2):465-476. doi:10.1093/nar/gkl1069 PMID:17169990 PMCID:PMC1802609

2006

• Sartor MA, Zorn AM, Schwanekamp J, Halbleib D, Karyala S, Howell ML, Dean GE, Medvedovic M, Tomlinson CR. 2006. A new method to remove hybridization bias for interspecies comparison of global gene expression profiles uncovers an association between mRNA sequence divergence and differential gene expression in Xenopus. Nucleic Acids Res 34(1):185-200. doi:10.1093/nar/gkj413 PMID:16397297 PMCID:PMC1325202

2005

• Burgoon LD, Eckel-Passow JE, Gennings C, Boverhof DR, Burt JW, Fong C, Zacharewski TR. 2005. Protocols for the assurance of microarray data quality and process control. Nucleic Acids Res 33(19):e172. PMID:16272462
• Jeong Y, Nakamura J, Upton PB, Swenberg JA. 2005. Pyrimido[1,2-a]-purin-10(3H)-one, M1G, is less prone to artifact than base oxidation. Nucleic Acids Res 33(19):6426-6434. doi:10.1093/nar/gki944 PMID:16282591 PMCID:PMC1283527
• Sheu S, Lancia DR, Clodfelter KH, Landon MR, Vajda S. 2005. PRECISE: a database of predicted and consensus interaction sites in enzymes. Nucleic Acids Res 33(Databaseissue):D206-D211. doi:10.1093/nar/gki091 PMID:15608178 PMCID:PMC540045
• Wetmur JG, Kumar M, Zhang L, Palomeque C, Wallenstein S, Chen J. 2005. Molecular haplotyping by linking emulsion PCR: analysis of paraoxonase 1 haplotypes and phenotypes. Nucleic Acids Res 33(8):2615-2619. PMID:15886392

2004

• Comeau SR, Gatchell DW, Vajda S, Camacho CJ. 2004. ClusPro: A fully automated algorithm for protein-protein docking. Nucleic Acids Res 32:W96-W99. PMID:15215358
• Prasad JC, Vajda S, Camacho CJ. 2004. Consensus alignment server for reliable comparative modeling with distant templates. Nucleic Acids Res 32:W50-W54. PMID:15215349

2003

• Nakamura J, Asakura S, Hester SD, de Murcia G, Caldecott KW, Swenberg JA. 2003. Quantitation of intracellular NAD(P)H can monitor an imbalance of DNA single strand break repair in base excision repair deficient cells in real time. Nucleic Acids Res 31(17):e104. PMID:12930978
• Nakamura J, Purvis ER, Swenberg JA. 2003. Micromolar concentrations of hydrogen peroxide induce oxidative DNA lesions more efficiently than millimolar concentrations in mammalian cells. Nucleic Acids Res 31(6):1790-1795. PMID:12626721

2001

• Brown K, Guenther EA, Dingley KH, Cosman M, Harvey CA, Shields SJ, Turteltaub KW. 2001. Synthesis and spectroscopic characterization of site-specific 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine oligodeoxyribonucleotide adducts. Nucleic Acids Res 29:1951-1959. PMID:11328879

1998

• Khrapko K, Coller HA, Hanekamp JS, Thilly WG. 1998. Identification of point mutations in mixtures by capillary electrophoresis hybridization. Nucleic Acids Res 26(24):5738-5740. PMID:9838007

1990

• Hassett C, Omiecinski CJ. 1990. Sequence and gene expression of rabbit cytochrome P450 IIC16: comparison to highly related family members. Nucleic Acids Res 18(6):1429-1434. PMID:2326187 PMCID:PMC330507