☰

David H. Ardell - Publications

Affiliations: 
School of Natural Sciences University of California, Berkeley, CA, United States 
Tree Info Similar researchers PubMed Report error

31 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
2021 Phillips JB, Ardell DH. Structural and Genetic Determinants of Convergence in the Drosophila tRNA Structure-Function Map. Journal of Molecular Evolution. PMID 33528599 DOI: 10.1007/s00239-021-09995-z  0.324
2020 Kelly P, Hadi-Nezhad F, Liu DY, Lawrence TJ, Linington RG, Ibba M, Ardell DH. Targeting tRNA-synthetase interactions towards novel therapeutic discovery against eukaryotic pathogens. Plos Neglected Tropical Diseases. 14: e0007983. PMID 32106219 DOI: 10.1371/Journal.Pntd.0007983  0.303
2019 Lawrence TJ, Amrine KC, Swingley WD, Ardell DH. tRNA functional signatures classify plastids as late-branching cyanobacteria. Bmc Evolutionary Biology. 19: 224. PMID 31818253 DOI: 10.1186/S12862-019-1552-7  0.317
2019 Collins-Hed AI, Ardell DH. Match fitness landscapes for macromolecular interaction networks: Selection for translational accuracy and rate can displace tRNA-binding interfaces of aminoacyl-tRNA synthetases. Theoretical Population Biology. PMID 31042487 DOI: 10.1016/J.Tpb.2019.03.007  0.4
2016 Ardell DH, Hou YM. Initiator tRNA genes template the 3' CCA end at high frequencies in bacteria. Bmc Genomics. 17: 1003. PMID 27927177 DOI: 10.1186/S12864-016-3314-X  0.422
2015 Lawrence TJ, Kauffman KT, Amrine KC, Carper DL, Lee RS, Becich PJ, Canales CJ, Ardell DH. FAST: FAST Analysis of Sequences Toolbox. Frontiers in Genetics. 6: 172. PMID 26042145 DOI: 10.3389/Fgene.2015.00172  0.361
2014 Amrine KC, Swingley WD, Ardell DH. tRNA signatures reveal a polyphyletic origin of SAR11 strains among alphaproteobacteria. Plos Computational Biology. 10: e1003454. PMID 24586126 DOI: 10.1371/Journal.Pcbi.1003454  0.418
2013 Holloway P, Swenson K, Ardell D, El-Mabrouk N. Ancestral genome organization: An alignment approach Journal of Computational Biology. 20: 280-295. PMID 23560866 DOI: 10.1089/Cmb.2012.0292  0.426
2013 Becich PJ, Stark BP, Bhat HS, Ardell DH. CMCpy: Genetic Code-Message Coevolution Models in Python. Evolutionary Bioinformatics Online. 9: 111-25. PMID 23532367 DOI: 10.4137/Ebo.S11169  0.37
2010 Ardell DH. Computational analysis of tRNA identity. Febs Letters. 584: 325-33. PMID 19944694 DOI: 10.1016/J.Febslet.2009.11.084  0.367
2009 Mallios RR, Ojcius DM, Ardell DH. An iterative strategy combining biophysical criteria and duration hidden Markov models for structural predictions of Chlamydia trachomatis sigma66 promoters. Bmc Bioinformatics. 10: 271. PMID 19715597 DOI: 10.1186/1471-2105-10-271  0.346
2009 Illergård K, Ardell DH, Elofsson A. Structure is three to ten times more conserved than sequence--a study of structural response in protein cores. Proteins. 77: 499-508. PMID 19507241 DOI: 10.1002/Prot.22458  0.31
2008 Larsson P, Hinas A, Ardell DH, Kirsebom LA, Virtanen A, Söderbom F. De novo search for non-coding RNA genes in the AT-rich genome of Dictyostelium discoideum: performance of Markov-dependent genome feature scoring. Genome Research. 18: 888-99. PMID 18347326 DOI: 10.1101/Gr.069104.107  0.456
2007 Clark AG, Eisen MB, Smith DR, Bergman CM, Oliver B, Markow TA, Kaufman TC, Kellis M, Gelbart W, Iyer VN, Pollard DA, Sackton TB, Larracuente AM, Singh ND, ... Ardell DH, et al. Evolution of genes and genomes on the Drosophila phylogeny. Nature. 450: 203-18. PMID 17994087 DOI: 10.1038/Nature06341  0.573
2007 Macvanin M, Gonzalez de Valdivia EI, Ardell DH, Isaksson LA. Transient erythromycin resistance phenotype associated with peptidyl-tRNA drop-off on early UGG and GGG codons. Journal of Bacteriology. 189: 8993-9000. PMID 17951392 DOI: 10.1128/Jb.01004-07  0.309
2007 Freyhult E, Cui Y, Nilsson O, Ardell DH. New computational methods reveal tRNA identity element divergence between Proteobacteria and Cyanobacteria. Biochimie. 89: 1276-88. PMID 17889982 DOI: 10.1016/J.Biochi.2007.07.013  0.379
2007 Tåquist H, Cui Y, Ardell DH. TFAM 1.0: an online tRNA function classifier. Nucleic Acids Research. 35: W350-3. PMID 17591612 DOI: 10.1093/Nar/Gkm393  0.446
2007 Chang WJ, Addis VM, Li AJ, Axelsson E, Ardell DH, Landweber LF. Intron Evolution and Information processing in the DNA polymerase alpha gene in spirotrichous ciliates: a hypothesis for interconversion between DNA and RNA deletion. Biology Direct. 2: 6. PMID 17270054 DOI: 10.1186/1745-6150-2-6  0.352
2006 Sella G, Ardell DH. The coevolution of genes and genetic codes: Crick's frozen accident revisited. Journal of Molecular Evolution. 63: 297-313. PMID 16838217 DOI: 10.1007/S00239-004-0176-7  0.377
2006 Jin H, Zhao Q, Gonzalez de Valdivia EI, Ardell DH, Stenström M, Isaksson LA. Influences on gene expression in vivo by a Shine-Dalgarno sequence. Molecular Microbiology. 60: 480-92. PMID 16573696 DOI: 10.1111/J.1365-2958.2006.05110.X  0.41
2006 Freyhult E, Moulton V, Ardell DH. Visualizing bacterial tRNA identity determinants and antideterminants using function logos and inverse function logos. Nucleic Acids Research. 34: 905-16. PMID 16473848 DOI: 10.1093/Nar/Gkj478  0.358
2006 Ardell DH, Andersson SG. TFAM detects co-evolution of tRNA identity rules with lateral transfer of histidyl-tRNA synthetase. Nucleic Acids Research. 34: 893-904. PMID 16473847 DOI: 10.1093/Nar/Gkj449  0.393
2005 Ardell DH, Kirsebom LA. The genomic pattern of tDNA operon expression in E. coli. Plos Computational Biology. 1: e12. PMID 16103901 DOI: 10.1371/Journal.Pcbi.0010012  0.37
2005 Fredrik Pettersson BM, Ardell DH, Kirsebom LA. The length of the 5' leader of Escherichia coli tRNA precursors influences bacterial growth. Journal of Molecular Biology. 351: 9-15. PMID 16002088 DOI: 10.1016/J.Jmb.2005.05.022  0.339
2004 Alsmark CM, Frank AC, Karlberg EO, Legault BA, Ardell DH, Canbäck B, Eriksson AS, Näslund AK, Handley SA, Huvet M, La Scola B, Holmberg M, Andersson SG. The louse-borne human pathogen Bartonella quintana is a genomic derivative of the zoonotic agent Bartonella henselae. Proceedings of the National Academy of Sciences of the United States of America. 101: 9716-21. PMID 15210978 DOI: 10.1073/Pnas.0305659101  0.36
2003 Salaneck E, Ardell DH, Larson ET, Larhammar D. Three neuropeptide Y receptor genes in the spiny dogfish, Squalus acanthias, support en bloc duplications in early vertebrate evolution. Molecular Biology and Evolution. 20: 1271-80. PMID 12777532 DOI: 10.1093/Molbev/Msg133  0.338
2002 Ardell DH, Sella G. No accident: genetic codes freeze in error-correcting patterns of the standard genetic code. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 357: 1625-42. PMID 12495519 DOI: 10.1098/Rstb.2002.1071  0.382
2002 Sella G, Ardell DH. The impact of message mutation on the fitness of a genetic code. Journal of Molecular Evolution. 54: 638-51. PMID 11965436 DOI: 10.1007/S00239-001-0060-7  0.353
2001 Ardell DH, Sella G. On the evolution of redundancy in genetic codes. Journal of Molecular Evolution. 53: 269-81. PMID 11675587 DOI: 10.1007/S002390010217  0.389
2001 Ardell DH, Andersen SO. Tentative identification of a resilin gene in Drosophila melanogaster. Insect Biochemistry and Molecular Biology. 31: 965-70. PMID 11483432 DOI: 10.1016/S0965-1748(01)00044-3  0.367
1998 Ardell DH. On error minimization in a sequential origin of the standard genetic code. Journal of Molecular Evolution. 47: 1-13. PMID 9664691 DOI: 10.1007/Pl00006356  0.34
Show low-probability matches.