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Items: 34

1.

tRNA functional signatures classify plastids as late-branching cyanobacteria.

Lawrence TJ, Amrine KC, Swingley WD, Ardell DH.

BMC Evol Biol. 2019 Dec 9;19(1):224. doi: 10.1186/s12862-019-1552-7.

2.

Prediction of regulatory targets of alternative isoforms of the epidermal growth factor receptor in a glioblastoma cell line.

Weinholdt C, Wichmann H, Kotrba J, Ardell DH, Kappler M, Eckert AW, Vordermark D, Grosse I.

BMC Bioinformatics. 2019 Aug 22;20(1):434. doi: 10.1186/s12859-019-2944-9.

3.
4.

Whole RNA-Sequencing and Transcriptome Assembly of Candida albicans and Candida africana under Chlamydospore-Inducing Conditions.

Giosa D, Felice MR, Lawrence TJ, Gulati M, Scordino F, Giuffrè L, Lo Passo C, D'Alessandro E, Criseo G, Ardell DH, Hernday AD, Nobile CJ, Romeo O.

Genome Biol Evol. 2017 Jul 1;9(7):1971-1977. doi: 10.1093/gbe/evx143.

5.
6.

FAST: FAST Analysis of Sequences Toolbox.

Lawrence TJ, Kauffman KT, Amrine KC, Carper DL, Lee RS, Becich PJ, Canales CJ, Ardell DH.

Front Genet. 2015 May 19;6:172. doi: 10.3389/fgene.2015.00172. eCollection 2015.

7.

Dynamic regulation of mRNA decay during neural development.

Burow DA, Umeh-Garcia MC, True MB, Bakhaj CD, Ardell DH, Cleary MD.

Neural Dev. 2015 Apr 21;10:11. doi: 10.1186/s13064-015-0038-6.

8.

Eye movements during listening reveal spontaneous grammatical processing.

Huette S, Winter B, Matlock T, Ardell DH, Spivey M.

Front Psychol. 2014 May 21;5:410. doi: 10.3389/fpsyg.2014.00410. eCollection 2014.

9.

tRNA signatures reveal a polyphyletic origin of SAR11 strains among alphaproteobacteria.

Amrine KC, Swingley WD, Ardell DH.

PLoS Comput Biol. 2014 Feb 27;10(2):e1003454. doi: 10.1371/journal.pcbi.1003454. eCollection 2014 Feb.

10.

CMCpy: Genetic Code-Message Coevolution Models in Python.

Becich PJ, Stark BP, Bhat HS, Ardell DH.

Evol Bioinform Online. 2013;9:111-25. doi: 10.4137/EBO.S11169. Epub 2013 Feb 27.

11.

Computational analysis of tRNA identity.

Ardell DH.

FEBS Lett. 2010 Jan 21;584(2):325-33. doi: 10.1016/j.febslet.2009.11.084. Review.

12.
13.

Structure is three to ten times more conserved than sequence--a study of structural response in protein cores.

Illergård K, Ardell DH, Elofsson A.

Proteins. 2009 Nov 15;77(3):499-508. doi: 10.1002/prot.22458.

PMID:
19507241
14.

De novo search for non-coding RNA genes in the AT-rich genome of Dictyostelium discoideum: performance of Markov-dependent genome feature scoring.

Larsson P, Hinas A, Ardell DH, Kirsebom LA, Virtanen A, Söderbom F.

Genome Res. 2008 Jun;18(6):888-99. doi: 10.1101/gr.069104.107. Epub 2008 Mar 17.

15.

Evolution of genes and genomes on the Drosophila phylogeny.

Drosophila 12 Genomes Consortium, 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, Abad JP, Abt DN, Adryan B, Aguade M, Akashi H, Anderson WW, Aquadro CF, Ardell DH, Arguello R, Artieri CG, Barbash DA, Barker D, Barsanti P, Batterham P, Batzoglou S, Begun D, Bhutkar A, Blanco E, Bosak SA, Bradley RK, Brand AD, Brent MR, Brooks AN, Brown RH, Butlin RK, Caggese C, Calvi BR, Bernardo de Carvalho A, Caspi A, Castrezana S, Celniker SE, Chang JL, Chapple C, Chatterji S, Chinwalla A, Civetta A, Clifton SW, Comeron JM, Costello JC, Coyne JA, Daub J, David RG, Delcher AL, Delehaunty K, Do CB, Ebling H, Edwards K, Eickbush T, Evans JD, Filipski A, Findeiss S, Freyhult E, Fulton L, Fulton R, Garcia AC, Gardiner A, Garfield DA, Garvin BE, Gibson G, Gilbert D, Gnerre S, Godfrey J, Good R, Gotea V, Gravely B, Greenberg AJ, Griffiths-Jones S, Gross S, Guigo R, Gustafson EA, Haerty W, Hahn MW, Halligan DL, Halpern AL, Halter GM, Han MV, Heger A, Hillier L, Hinrichs AS, Holmes I, Hoskins RA, Hubisz MJ, Hultmark D, Huntley MA, Jaffe DB, Jagadeeshan S, Jeck WR, Johnson J, Jones CD, Jordan WC, Karpen GH, Kataoka E, Keightley PD, Kheradpour P, Kirkness EF, Koerich LB, Kristiansen K, Kudrna D, Kulathinal RJ, Kumar S, Kwok R, Lander E, Langley CH, Lapoint R, Lazzaro BP, Lee SJ, Levesque L, Li R, Lin CF, Lin MF, Lindblad-Toh K, Llopart A, Long M, Low L, Lozovsky E, Lu J, Luo M, Machado CA, Makalowski W, Marzo M, Matsuda M, Matzkin L, McAllister B, McBride CS, McKernan B, McKernan K, Mendez-Lago M, Minx P, Mollenhauer MU, Montooth K, Mount SM, Mu X, Myers E, Negre B, Newfeld S, Nielsen R, Noor MA, O'Grady P, Pachter L, Papaceit M, Parisi MJ, Parisi M, Parts L, Pedersen JS, Pesole G, Phillippy AM, Ponting CP, Pop M, Porcelli D, Powell JR, Prohaska S, Pruitt K, Puig M, Quesneville H, Ram KR, Rand D, Rasmussen MD, Reed LK, Reenan R, Reily A, Remington KA, Rieger TT, Ritchie MG, Robin C, Rogers YH, Rohde C, Rozas J, Rubenfield MJ, Ruiz A, Russo S, Salzberg SL, Sanchez-Gracia A, Saranga DJ, Sato H, Schaeffer SW, Schatz MC, Schlenke T, Schwartz R, Segarra C, Singh RS, Sirot L, Sirota M, Sisneros NB, Smith CD, Smith TF, Spieth J, Stage DE, Stark A, Stephan W, Strausberg RL, Strempel S, Sturgill D, Sutton G, Sutton GG, Tao W, Teichmann S, Tobari YN, Tomimura Y, Tsolas JM, Valente VL, Venter E, Venter JC, Vicario S, Vieira FG, Vilella AJ, Villasante A, Walenz B, Wang J, Wasserman M, Watts T, Wilson D, Wilson RK, Wing RA, Wolfner MF, Wong A, Wong GK, Wu CI, Wu G, Yamamoto D, Yang HP, Yang SP, Yorke JA, Yoshida K, Zdobnov E, Zhang P, Zhang Y, Zimin AV, Baldwin J, Abdouelleil A, Abdulkadir J, Abebe A, Abera B, Abreu J, Acer SC, Aftuck L, Alexander A, An P, Anderson E, Anderson S, Arachi H, Azer M, Bachantsang P, Barry A, Bayul T, Berlin A, Bessette D, Bloom T, Blye J, Boguslavskiy L, Bonnet C, Boukhgalter B, Bourzgui I, Brown A, Cahill P, Channer S, Cheshatsang Y, Chuda L, Citroen M, Collymore A, Cooke P, Costello M, D'Aco K, Daza R, De Haan G, DeGray S, DeMaso C, Dhargay N, Dooley K, Dooley E, Doricent M, Dorje P, Dorjee K, Dupes A, Elong R, Falk J, Farina A, Faro S, Ferguson D, Fisher S, Foley CD, Franke A, Friedrich D, Gadbois L, Gearin G, Gearin CR, Giannoukos G, Goode T, Graham J, Grandbois E, Grewal S, Gyaltsen K, Hafez N, Hagos B, Hall J, Henson C, Hollinger A, Honan T, Huard MD, Hughes L, Hurhula B, Husby ME, Kamat A, Kanga B, Kashin S, Khazanovich D, Kisner P, Lance K, Lara M, Lee W, Lennon N, Letendre F, LeVine R, Lipovsky A, Liu X, Liu J, Liu S, Lokyitsang T, Lokyitsang Y, Lubonja R, Lui A, MacDonald P, Magnisalis V, Maru K, Matthews C, McCusker W, McDonough S, Mehta T, Meldrim J, Meneus L, Mihai O, Mihalev A, Mihova T, Mittelman R, Mlenga V, Montmayeur A, Mulrain L, Navidi A, Naylor J, Negash T, Nguyen T, Nguyen N, Nicol R, Norbu C, Norbu N, Novod N, O'Neill B, Osman S, Markiewicz E, Oyono OL, Patti C, Phunkhang P, Pierre F, Priest M, Raghuraman S, Rege F, Reyes R, Rise C, Rogov P, Ross K, Ryan E, Settipalli S, Shea T, Sherpa N, Shi L, Shih D, Sparrow T, Spaulding J, Stalker J, Stange-Thomann N, Stavropoulos S, Stone C, Strader C, Tesfaye S, Thomson T, Thoulutsang Y, Thoulutsang D, Topham K, Topping I, Tsamla T, Vassiliev H, Vo A, Wangchuk T, Wangdi T, Weiand M, Wilkinson J, Wilson A, Yadav S, Young G, Yu Q, Zembek L, Zhong D, Zimmer A, Zwirko Z, Jaffe DB, Alvarez P, Brockman W, Butler J, Chin C, Gnerre S, Grabherr M, Kleber M, Mauceli E, MacCallum I.

Nature. 2007 Nov 8;450(7167):203-18.

PMID:
17994087
16.

Transient erythromycin resistance phenotype associated with peptidyl-tRNA drop-off on early UGG and GGG codons.

Macvanin M, Gonzalez de Valdivia EI, Ardell DH, Isaksson LA.

J Bacteriol. 2007 Dec;189(24):8993-9000. Epub 2007 Oct 19.

17.

New computational methods reveal tRNA identity element divergence between Proteobacteria and Cyanobacteria.

Freyhult E, Cui Y, Nilsson O, Ardell DH.

Biochimie. 2007 Oct;89(10):1276-88. Epub 2007 Jul 31.

PMID:
17889982
18.

TFAM 1.0: an online tRNA function classifier.

Tåquist H, Cui Y, Ardell DH.

Nucleic Acids Res. 2007 Jul;35(Web Server issue):W350-3. Epub 2007 Jun 25.

20.

The coevolution of genes and genetic codes: Crick's frozen accident revisited.

Sella G, Ardell DH.

J Mol Evol. 2006 Sep;63(3):297-313. Epub 2006 Jul 12. Review.

PMID:
16838217
21.

Influences on gene expression in vivo by a Shine-Dalgarno sequence.

Jin H, Zhao Q, Gonzalez de Valdivia EI, Ardell DH, Stenström M, Isaksson LA.

Mol Microbiol. 2006 Apr;60(2):480-92.

22.

Visualizing bacterial tRNA identity determinants and antideterminants using function logos and inverse function logos.

Freyhult E, Moulton V, Ardell DH.

Nucleic Acids Res. 2006 Feb 9;34(3):905-16. Print 2006.

23.

TFAM detects co-evolution of tRNA identity rules with lateral transfer of histidyl-tRNA synthetase.

Ardell DH, Andersson SG.

Nucleic Acids Res. 2006 Feb 9;34(3):893-904. Print 2006.

24.

The genomic pattern of tDNA operon expression in E. coli.

Ardell DH, Kirsebom LA.

PLoS Comput Biol. 2005 Jun;1(1):e12. Epub 2005 Jun 24.

25.

The length of the 5' leader of Escherichia coli tRNA precursors influences bacterial growth.

Fredrik Pettersson BM, Ardell DH, Kirsebom LA.

J Mol Biol. 2005 Aug 5;351(1):9-15.

PMID:
16002088
26.

The louse-borne human pathogen Bartonella quintana is a genomic derivative of the zoonotic agent Bartonella henselae.

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.

Proc Natl Acad Sci U S A. 2004 Jun 29;101(26):9716-21. Epub 2004 Jun 21.

27.

SCANMS: adjusting for multiple comparisons in sliding window neutrality tests.

Ardell DH.

Bioinformatics. 2004 Aug 12;20(12):1986-8. Epub 2004 Apr 1.

PMID:
15059827
29.

Three neuropeptide Y receptor genes in the spiny dogfish, Squalus acanthias, support en bloc duplications in early vertebrate evolution.

Salaneck E, Ardell DH, Larson ET, Larhammar D.

Mol Biol Evol. 2003 Aug;20(8):1271-80. Epub 2003 May 30.

PMID:
12777532
30.

No accident: genetic codes freeze in error-correcting patterns of the standard genetic code.

Ardell DH, Sella G.

Philos Trans R Soc Lond B Biol Sci. 2002 Nov 29;357(1427):1625-42.

31.

The impact of message mutation on the fitness of a genetic code.

Sella G, Ardell DH.

J Mol Evol. 2002 May;54(5):638-51.

PMID:
11965436
32.

On the evolution of redundancy in genetic codes.

Ardell DH, Sella G.

J Mol Evol. 2001 Oct-Nov;53(4-5):269-81.

PMID:
11675587
33.

Tentative identification of a resilin gene in Drosophila melanogaster.

Ardell DH, Andersen SO.

Insect Biochem Mol Biol. 2001 Sep;31(10):965-70.

PMID:
11483432
34.

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