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Laura L Elnitski, Ph.D.
Investigator, Genome Technology Branch
Head, Genomic Functional Analysis Section
Selected Publications
Elnitski L, Hardison RC, Li J, Yang S, Kolbe D, Eswara P, O'Connor MJ, Schwartz
S, Miller W, Chiaromonte F. Distinguishing regulatory DNA from neutral sites.
Genome Res, 13:64-72. 2003. [PubMed]
Giardine BM, Elnitski L, Riemer C, Makalowska I, Schwartz S, Miller W, Hardison
RC. GALA, a database for genomic sequence alignments and annotations. Genome
Res, 13:732-741. 2003. [PubMed]
Hardison RC, Chiaromonte F, Kolbe D, Wang H, Petrykowska H, Elnitski L, Yang
S, Giardine B, Zhang Y, Riemer C, Schwartz S, Haussler D, Roskin K, Weber R,
Diekhans M, Kent WJ, Weiss MJ, Welch J, Miller W. Global predictions and tests
of erythroid regulatory regions. Cold Spring Harb Symp Quant Biol, 68:335-344.
2003. [PubMed]
Rijnkel M, Elnitski L, Miller W, Rosen M. Multispecies comparative analysis
of a mammalian-specific genomic domain encoding secretory proteins. Genomics,
4:417-432. 2003. [PubMed]
Schwartz S, Elnitski L, Li M, Weirauch M, Riemer C, Smit A, NISC Comparative
Sequencing Program, Green ED, Hardison RC, Miller W. MultiPipMaker and supporting
tools: Alignments and analysis of multiple genomic DNA sequences. Nucleic
Acids Res, 13:3518-3524. 2003. [PubMed]
Thomas JW, Touchman JW, Blakesley RW, Bouffard GG, Beckstrom-Sternberg SM,
Margulies EH, Blanchette M, Siepel AC, Thomas PJ, McDowell JC, Maskeri B, Hansen
NF, Schwartz MS, Weber RJ, Kent WJ, Karolchik D, Bruen TC, Bevan R, Cutler DJ,
Schwartz S, Elnitski L, Idol JR, Prasad AB, Lee-Lin SQ, Maduro VV, Summers TJ,
Portnoy ME, Dietrich NL, Akhter N, Ayele K, Benjamin B, Cariaga K, Brinkley
CP, Brooks SY, Granite S, Guan X, Gupta J, Haghighi P, Ho SL, Huang MC, Karlins
E, Laric PL, Legaspi R, Lim MJ, Maduro QL, Masiello CA, Mastrian SD, McCloskey
JC, Pearson R, Stantripop S, Tiongson EE, Tran JT, Tsurgeon C, Vogt JL, Walker
MA, Wetherby KD, Wiggins LS, Young AC, Zhang LH, Osoegawa K, Zhu B, Zhao B,
Shu CL, De Jong PJ, Lawrence CE, Smit AF, Chakravarti A, Haussler D, Green P,
Miller W, Green ED. Comparative analyses of multi-species sequences from targeted
genomic regions. Nature, 424:788-793. 2003. [PubMed]
Blanchette M, Kent WJ, Riemer C, Elnitski L, Smit AFA, Roskin KM, Baertsch
R, Rosenbloom K, Clawson H, Green ED, Haussler D, Miller W. Aligning multiple
genomic sequences with the threaded blockset aligner. Genome Res, 14:708-715.
2004. [PubMed]
Kolbe D, Taylor J, Elnitski L, Eswara P, Li J, Miller W, Hardison R, Chiaromonte
F. Regulatory potential scores from genome-wide 3-way alignments of human, mouse,
and rat. Genome Res, 14:700-707. 2004. [PubMed]
The Rat Genome Sequencing Consortium. Genome sequence of the brown Norway rat
yields insights into mammalian evolution. Nature, 428:493-521. 2004.
[PubMed]
Piontkivska H, Zhang Y, Green ED, NISC Comparative Sequencing Program, Elnitski
L. Multi-species sequence comparison reveals dynamic evolution of the elastin
gene that has involved purifying selection and lineage-specific insertions/deletions.
BMC Genomics, 5:31. 2004. [PubMed]
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]
Wu J, Iwata F, Grass JA, Osborne CS, Elnitski L, Fraser P, Ohneda O, Yamamoto M, Bresnick EH. Molecular determinants of NOTCH4 transcription in vascular endothelium. Mol Cell Biol, 25(4):1458-74. 2005. [PubMed]
Elnitski L, Giardine B, Shah P, Zhang Y, Riemer C, Weirauch M, Burhans R, Miller W, Hardison RC. Improvements to GALA and dbERGE II: databases featuring genomic sequence alignment, annotation and experimental results. Nucleic Acids Res, D466-70. 2005.
[PubMed]
Walters, E., Altman, N.S., Elnitski, L. Clustering of Gene Locations. J.Computational Statistics and Data Analysis, 50:2920-2932. 2005.
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]
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]
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]
Giardine, B., Riemer, C., Hefferon, T., Thomas, D., Hsu, F., Zielenski, J., Sang, Y., Elnitski, L., Cutting, G., Trumbower, H., Kern, A., Kuhn, R., Patrinos, G.P., Hughes, J., Higgs, D., Chui, D., Scriver, C., Phommarinh, M., Patnaik, S.K., Blumenfeld, O., Gottlieb, B., Kent, J. Miller, W., Hardison, R.C. PhenCode: Connecting ENCODE Data with Mutations and Phenotype. Human Mutat, 28:554-562. 2007. [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, M.Q., Elnitski L. Promoter studies in the human genome: one perspective on an unfinished story. Proceedings of IEEE international Conference on Bioinformatics and Bioengineering. 2007. [In Press]
Elnitski, L., Welch, L. New Frontiers in Computational Genomics: Identification of Novel Functional Elements and Genome-scale Pattern Analysis. Scalable Computing: Practice and Experience, 8(3): i-vii. 2007.
Yang MQ and Elnitski LL. Prediction-based approaches to characterize bidirectional promoters in the mammalian genome. BMC Genomics, 9 Suppl 1:S2. 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. [In Press]
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. In Press. 2008.
Last Updated: May 9, 2008
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