Laura L Elnitski, Ph.D.

Senior Investigator, Genome Technology Branch
Head, Genomic Functional Analysis Section

Selected Publications

The International Chicken Genome Consortium, Hillier, LW, et. al., including Elnitski L. Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. 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, 17(6):954-9. 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, 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, 18(8):1238-46. 2008. [PubMed]

Jacox, E. and Elnitski, L. Finding Occurrences of Relevant Functional Elements in Genomic Signatures. International Journal of Computational Science, 1;2(5):599-606. 2008. [PubMed]

Piontkivska H, Yang MQ, Larkin DM, Lewin HA, Reecy J, Elnitski L. Cross-species mapping of bidirectional promoters enables prediction of unannotated 5' UTRs and identification of species-specific transcripts. BMC Genomics, 10:189. 2009. [PubMed]

Bovine Genome Sequencing and Analysis Consortium, Elsik CG, Tellam RL, Worley KC, Gibbs RA, Muzny DM, Weinstock GM, Adelson DL, Eichler EE, Elnitski L, et al. The genome sequence of taurine cattle: a window to ruminant biology and evolution. Science, 324:522-8. 2009. [PubMed]

Woolfe A, Mullikin JC, Elnitski L. Genomic features defining exonic variants that modulate splicing. Genome Biol, 11(2):R20. 2010. [PubMed]

Laflamme K, Owen AN, Devlin EE, Yang MQ, Wong C, Steiner LA, Garrett LJ, Elnitski L, Gallagher PG, Bodine DM. Functional analysis of a novel cis-acting regulatory region within the human ankyrin gene (ANK-1) promoter. Mol Cell Biol, 30:3493-502. 2010. [PubMed]

Jacox E, Gotea V, Ovcharenko I, Elnitski L. Tissue-specific and ubiquitous expression patterns from alternative promoters of human genes. PLosOne, 5:e12274 2010. [PubMed Central]

ENCODE Project Consortium, et. al. including Elnitski, L. A user's guide to the encyclopedia of DNA elements (ENCODE). PLoS Biol, 9:e1001046. 2011. [PubMed]

Yang MQ, Laflamme K, Gotea V, Joiner CH, Seidel NE, Wong C, Petrykowska HM, Lichtenberg J, Lee S, Welch L, Gallagher PG, Bodine DM, Elnitski L. Genome-wide detection of a TFIID localization element from an initial human disease mutation. Nucleic Acids Res, 39:2175-87. 2011 [PubMed]

Lichtenberg J, Kurz K, Liang X, Al-ouran R, Neiman L, Nau LJ, Welch JD, Jacox E, Bitterman T, Ecker K, Elnitski L, Drews F, Lee SS, Welch LR. WordSeeker: concurrent bioinformatics software for discovering genome-wide patterns and word-based genomic signatures. BMC Bioinformatics, 11 Suppl 12:S6. 2011. [PubMed]

Kolbe DL, DeLoia JA, Porter-Gill P, Strange M, Guirguis A, Krivak TC, Brody LC, Elnitski L. Genomic analysis of site-specific DNA methylation patterns in primary epithelial ovarian cancers and endometrial metastases to the ovary. 2011. [Under Revision]

Scott, A, Petrykowska HM, Gotea V, Hefferon T, Elnitski L. Functional analysis of synonymous substitutions predicted to affect splicing of the CFTR gene. 2011. [Under Revision]

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.

Elnitski L, Burhans R, Riemer C, Hardison R, Miller W. MultiPipMaker: A comparative alignment server for multiple DNA sequences. Current Protocols in Bioinformatics. Wiley & Sons Inc., pp. 10.4.1-10.4.14. 2010.

Welch LR, Koehly LM, Elnitski L. Shared regulatory motifs in promoters of human DNA repair genes. DNA Repair / Book 4, Inna Kruman (Ed.), InTech Publishers. 2011.

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Last Updated: December 7, 2012