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Laura L Elnitski, Ph.D.
Investigator, Genome Technology Branch
Head, Genomic Functional Analysis Section
Selected Publications
Hillier LW, Miller W, Birney E, Warren W, Hardison RC, Ponting CP, Bork P, Burt DW, Groenen MA, Delany ME, Dodgson JB, Chinwalla AT, Cliften PF, Clifton SW, Delehaunty KD, Fronick C, Fulton RS, Graves TA, Kremitzki C, Layman D, Magrini V, McPherson JD, Miner TL, Minx P, Nash WE, Nhan MN, Nelson JO, Oddy LG, Pohl CS, Randall-Maher J, Smith SM, Wallis JW, Yang SP, Romanov MN, Rondelli CM, Paton B, Smith J, Morrice D, Daniels L, Tempest HG, Robertson L, Masabanda JS, Griffin DK, Vignal A, Fillon V, Jacobbson L, Kerje S, Andersson L, Crooijmans RP, Aerts J, van der Poel JJ, Ellegren H, Caldwell RB, Hubbard SJ, Grafham DV, Kierzek AM, McLaren SR, Overton IM, Arakawa H, Beattie KJ, Bezzubov Y, Boardman PE, Bonfield JK, Croning MD, Davies RM, Francis MD, Humphray SJ, Scott CE, Taylor RG, Tickle C, Brown WR, Rogers J, Buerstedde JM, Wilson SA, Stubbs L, Ovcharenko I, Gordon L, Lucas S, Miller MM, Inoko H, Shiina T, Kaufman J, Salomonsen J, Skjoedt K, Wong GK, Wang J, Liu B, Wang J, Yu J, Yang H, Nefedov M, Koriabine M, Dejong PJ, Goodstadt L, Webber C, Dickens NJ, Letunic I, Suyama M, Torrents D, von Mering C, Zdobnov EM, Makova K, Nekrutenko A, Elnitski L, et. al. Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature, 432(7018):695-716. 2004. [PubMed]
ENCODE Project Consortium. The ENCODE (ENCyclopedia Of DNA Elements) Project. Science, 306:636-640. 2004. [PubMed]
Giardine, B., Riemer, C., Hardison, R.C., Burhans, R., Elnitski, L., Shah, P., Zhang, Y., Blankenberg, D., Albert, I., Taylor, J., Miller, W., Kent, W.J., Nekrutenko, A. Galaxy: a platform for interactive large-scale genome analysis. Genome Res, 15:1451-5. 2005. [PubMed]
King, D.C., Taylor, J., Elnitski, L., Chiaromonte, F., Miller, W., Hardison, R.C. Evaluation of regulatory potential and conservation scores for detecting cis-regulatory modules in aligned mammalian genome sequences. Genome Res, 15:1051-60. 2005. [PubMed]
Walters E, Altman NS, Elnitski L. Clustering of gene locations. Comput Stat Data Anal, 50:29202932. 2005. [PubMed]
Elnitski, L., King, D., Hardison, R.C. Computational prediction of cis-regulatory modules from multispecies alignments using Galaxy, Table Browser, and GALA.
Methods Mol Biol, 338:91-103. 2006. [PubMed]
Elnitski, L., Jin, V.X., Farnham, P.J., Jones, S.J. Locating mammalian transcription factor binding sites: A survey of computational and experimental techniques.
Genome Res, 16:1455-1464. 2006. [PubMed]
Yang, M.Q., Koehly, L.M., Elnitski, L.L. Comprehensive Annotation of Bidirectional Promoters Identifies Co-Regulation among Breast and Ovarian Cancer Genes. PLOS Computational Biol, 3(4):e72. 2007. [PubMed]
Elnitski, L.L., Shah, P., Umayam, L., Wolfsberg, T.G., and Baxevanis, A.D. The ENCODEdb Portal: Simplified Access to ENCODE Consortium Data. Genome Research, 2007. [PubMed]
Yang MQ and Elnitski LL. Prediction-based approaches to characterize bidirectional promoters in the mammalian genome. BMC Genomics, 9 Suppl 1:S2. 2008. [PubMed]
Yang MQ, Taylor J, Elnitski L. Comparative analyses of bidirectional promoters in vertebrates. BMC Bioinformatics 9 Suppl 6:S9, 2008. [PubMed]
Petrykowska, H.M, Vockley, C.M., and Elnitski, L. Detection and characterization of silencers and enhancer-blockers in the greater CFTR locus. Genome Research, 2008. [PubMed]
Jacox, E. and Elnitski, L. Finding Occurrences of Relevant Functional Elements in Genomic Signatures. International Journal of Computational Science 2008. [In Press]
Book Chapters
Yang, M.Q., and Elnitski, L.L. Feature Characterization and Testing of Bidirectional Promoters in the Human Genome - Significance and Applications in Human Genome Research. Chapter 19 in Machine Learning in Bioinformatics, Yan-Qing Zhang and Jagath C. Rajapakse, eds. John Wiley & Sons, 2007.
Yang, M.Q. and Elnitski, L. A computational study of bidirectional promoters in the human genome. Bioinformatics Research and Applications, Zhang, Y., eds, Heidelberg, pp. 361-371. 2007.
Yang, M.Q. and Elnitski, L. Orthology of Bidirectional Promoters Enables Use of a Multiple Class Predictor for Discriminating Functional Elements in the Human Genome. Proceedings of the 2007 International Conference on Bioinformatics & Computational Biology. Arabnia, Yang, M.Q. and Yang, J.Y., eds. pp. 218-228. 2007.
Yang, M.Q., Taylor, J., and Elnitski, L. Rigorous Mapping of Orthologous Bidirectional Promoters in Vertebrates. Proceedings of Computations in Bioinformatics and Bioscience. BMC Bioinformatics Suppl. Issue. pp. 115-122. 2008. [In Press]
Last Reviewed: March 23, 2009
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