Selected Publications for David C. King

1. Ogg, H.A., Mikol, Z.M., King, D.C. et al. Altered histone modifications in Aedes aegypti midguts following Rift Valley fever virus exposure. Sci Rep (2026).
doi: 10.1038/s41598-026-37729-y. PMID: 41611818.

2. Williams RTP, King DC, Mastroianni IR, Hill JL, Apenes NW, Ramirez G, Miner EC, Moore A, Coleman K, Nishimura EO. Transcriptome profiling of the Caenorhabditis elegans intestine reveals that ELT-2 negatively and positively regulates intestinal gene expression within the context of a gene regulatory network. Genetics. 2023 Aug 9;224(4):iyad088.
doi:10.1093/genetics/iyad088. PMID: 37183501; PMCID: PMC10411582.

3. Herman JA, Romain RR, Hoellerbauer P, Shirnekhi HK, King DC, DeLuca KF, Osborne Nishimura E, Paddison PJ, DeLuca JG. Hyper-active RAS/MAPK introduces cancer-specific mitotic vulnerabilities. Proc Natl Acad Sci U S A. 2022 Oct 11;119(41):e2208255119.
doi: 10.1073/pnas.2208255119. Epub 2022 Oct 3. PMID: 36191188; PMCID: PMC9565228.

4. Cascarina SM, King DC, Osborne Nishimura E, Ross ED. LCD-Composer: an intuitive, composition-centric method enabling the identification and detailed functional mapping of low-complexity domains. NAR Genom Bioinform. 2021 May 26;3(2):lqab048.
doi: 10.1093/nargab/lqab048. PMID: 34056598; PMCID: PMC8153834.

5. Kapuscinski ML, Bergren NA, Russell BJ, Lee JS, Borland EM, Hartman DA, King DC, Hughes HR, Burkhalter KL, Kading RC, Stenglein MD. Genomic characterization of 99 viruses from the bunyavirus families Nairoviridae, Peribunyaviridae, and Phenuiviridae, including 35 previously unsequenced viruses. PLoS Pathog. 2021 Mar 1;17(3):e1009315.
doi: 10.1371/journal.ppat.1009315. PMID: 33647063; PMCID: PMC7951987.

6. Cheng Y, Wu W, Kumar SA, Yu D, Deng W, Tripic T, King DC, Chen KB, Zhang Y, Drautz D, Giardine B, Schuster SC, Miller W, Chiaromonte F, Zhang Y, Blobel GA, Weiss MJ, Hardison RC. Erythroid GATA1 function revealed by genome-wide analysis of transcription factor occupancy, histone modifications, and mRNA expression. Genome Res. 2009 Dec;19(12):2172-84.
doi: 10.1101/gr.098921.109. Epub 2009 Nov 3. PMID: 19887574; PMCID: PMC2792182.

8. Zhang Y, Wu W, Cheng Y, King DC, Harris RS, Taylor J, Chiaromonte F, Hardison RC. Primary sequence and epigenetic determinants of in vivo occupancy of genomic DNA by GATA1. Nucleic Acids Res. 2009 Nov;37(21):7024-38.
doi: 10.1093/nar/gkp747. PMID: 19767611; PMCID: PMC2790884.

9. Cheng Y, King DC, Dore LC, Zhang X, Zhou Y, Zhang Y, Dorman C, Abebe D, Kumar SA, Chiaromonte F, Miller W, Green RD, Weiss MJ, Hardison RC. Transcriptional enhancement by GATA1-occupied DNA segments is strongly associated with evolutionary constraint on the binding site motif. Genome Res. 2008 Dec;18(12):1896-905.
doi: 10.1101/gr.083089.108. Epub 2008 Sep 25. PMID: 18818370; PMCID: PMC2593580.

10. Miller W, Rosenbloom K, Hardison RC, Hou M, Taylor J, Raney B, Burhans R, King DC, Baertsch R, Blankenberg D, Kosakovsky Pond SL, Nekrutenko A, Giardine B, Harris RS, Tyekucheva S, Diekhans M, Pringle TH, Murphy WJ, Lesk A, Weinstock GM, Lindblad-Toh K, Gibbs RA, Lander ES, Siepel A, Haussler D, Kent WJ. 28-way vertebrate alignment and conservation track in the UCSC Genome Browser. Genome Res. 2007 Dec;17(12):1797-808.
doi: 10.1101/gr.6761107. Epub 2007 Nov 5. PMID: 17984227; PMCID: PMC2099589.

11. ENCODE Project Consortium; Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature. 2007 Jun 14;447(7146):799-816.
doi: 10.1038/nature05874. PMID: 17571346; PMCID: PMC2212820.

12. King DC, Taylor J, Zhang Y, Cheng Y, Lawson HA, Martin J; ENCODE groups for Transcriptional Regulation and Multispecies Sequence Analysis; Chiaromonte F, Miller W, Hardison RC. Finding cis-regulatory elements using comparative genomics: some lessons from ENCODE data. Genome Res. 2007 Jun;17(6):775-86.
doi: 10.1101/gr.5592107. PMID: 17567996; PMCID: PMC1891337.

13. Taylor J, Tyekucheva S, King DC, Hardison RC, Miller W, Chiaromonte F. ESPERR: learning strong and weak signals in genomic sequence alignments to identify functional elements. Genome Res. 2006 Dec;16(12):1596-604.
doi: 10.1101/gr.4537706. Epub 2006 Oct 19. PMID: 17053093; PMCID: PMC1665643.

14. Wang H, Zhang Y, Cheng Y, Zhou Y, King DC, Taylor J, Chiaromonte F, Kasturi J, Petrykowska H, Gibb B, Dorman C, Miller W, Dore LC, Welch J, Weiss MJ, Hardison RC. Experimental validation of predicted mammalian erythroid cis-regulatory modules. Genome Res. 2006 Dec;16(12):1480-92.
doi: 10.1101/gr.5353806. Epub 2006 Oct 12. PMID: 17038566; PMCID: PMC1665632.

15. King DC, Taylor J, Elnitski L, Chiaromonte F, Miller W, Hardison RC. Evaluation of regulatory potential and conservation scores for detecting cis-regulatory modules in aligned mammalian genome sequences. Genome Res. 2005 Aug;15(8):1051-60.
doi: 10.1101/gr.3642605. Epub 2005 Jul 15. PMID: 16024817; PMCID: PMC1182217.

16. International Chicken Genome Sequencing Consortium. Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature. 2004 Dec 9;432(7018):695-716.
doi: 10.1038/nature03154. Erratum in: Nature. 2005 Feb 17;433(7027):777. PMID: 15592404.

17. Putta S, Smith JJ, Walker JA, Rondet M, Weisrock DW, Monaghan J, Samuels AK, Kump K, King DC, Maness NJ, Habermann B, Tanaka E, Bryant SV, Gardiner DM, Parichy DM, Voss SR. From biomedicine to natural history research: EST resources for ambystomatid salamanders. BMC Genomics. 2004 Aug 13;5(1):54.
doi: 10.1186/1471-2164-5-54. PMID: 15310388; PMCID: PMC509418.

18. Shah NH, King DC, Shah PN, Fedoroff NV. A tool-kit for cDNA microarray and promoter analysis. Bioinformatics. 2003 Sep 22;19(14):1846-8.
doi: 10.1093/bioinformatics/btg253. PMID: 14512358.