Main Body

Center for Bioinformatics

Key Publications

Long, D., Lee, R., Williams, P., Chan, C.Y., Ambros, V. and Ding, Y. (2007) Potent role of target structure in microRNA function. Nat. Struct. Mol. Biol. (To appear).

Ding, Y., Chan, C.Y. and Lawrence, C.E. (2006) Clustering of RNA secondary structures with application to messenger RNAs. J. Mol. Biol. 359, 554-571.

Ding, Y., Chan, C.Y. and Lawrence, C.E. (2005) RNA secondary structure prediction by centroids in a Boltzmann weighted ensemble. RNA 11, 1157-1166.

Thompson, W., Palumbo, M. J., Wasserman, W. W., Liu, J. S. and Lawrence, C. E. (2004) Decoding human regulatory circuits. Genome Res 14:1967-74.

Ding, Y. and Lawrence, C. E. (2003) A statistical sampling algorithm for RNA secondary structure prediction. Nucleic Acids Res31:7280-301.

Qin, Z. S., McCue, L. A., Thompson, W., Mayerhofer, L., Lawrence,C. E. and Liu, J. S. (2003)Identification of co-regulated genes through Bayesian clustering of predicted regulatory binding sites. Nat Biotechnol 21:435-9.

Samso, M., Palumbo, M. J., Radermacher, M., Liu, J. S. and Lawrence, C. E. (2002) A Bayesian method for classification of images from electron micrographs. J Struct Biol 138:157-70.

Ding, Y. and Lawrence, C. E. (2001) Statistical prediction of single-stranded regions in RNA secondary structure and application to predicting effective antisense target sites and beyond. Nucleic Acids Res 29:1034-46.

McCue, L., Thompson, W., Carmack, C., Ryan, M. P., Liu, J. S., Derbyshire, V. and Lawrence, C. E. (2001) Phylogenetic footprinting of transcription factor binding sites in proteobacterial genomes. Nucleic Acids Res 29:774-82.

McCue, L. A., McDonough, K. A. and Lawrence, C. E. (2000) Functional classification of cNMP-binding proteins and nucleotide cyclases with implications for novel regulatory pathways in Mycobacterium tuberculosis. Genome Res 10:204-19.

Wasserman, W. W., Palumbo, M., Thompson, W., Fickett, J. W. and Lawrence, C. E. (2000) Human-mouse genome comparisons to locate regulatory sites. Nat Genet 26:225-8.

Liu, J., Neuwald, A. F. and Lawrence, C. E. (1999) Markovian structures in biological sequence alignments. J Amer Statist Assoc 94:1-15.

Lawrence, C. E., Altschul, S. F., Boguski, M. S., Liu, J. S., Neuwald, A. F. and Wootton, J. C. (1993) Detecting subtle sequence signals: a Gibbs sampling strategy for multiple alignment. Science 262:208-14.

"Web server" Publications

Ding, Y., Chan, C. Y. and Lawrence, C. E. (2004) Sfold web server for statistical folding and rational design of nucleic acids. Nucleic Acids Res 32:W135-41.

Thompson, W., McCue, L. A. and Lawrence, C. E. (2004) Using the Gibbs Motif Sampler to find conserved domains in DNA and protein sequences, Current Protocols in Bioinformatics. John Wiley & Sons, Inc.

Thompson, W., Rouchka, E. C. and Lawrence, C. E. (2003) Gibbs Recursive Sampler: finding transcription factor binding sites. Nucleic Acids Res 31:3580-5.

RNA Structure Prediction Publications

Chan, C.Y. and Ding, Y. (2007) Boltzmann ensemble features of RNA secondary structures: a comparative analysis of biological RNA sequences and random shuffles. J. Math. Biol. (To appear).

Shao, Y., Wu, Y., Chan, C.Y., McDonough, K. and Ding, Y. (2006) Rational design and rapid screening of antisense oligonucleotides for prokaryotic gene modulation. Nucleic Acids Res. 34, 5660-5669.

Ding, Y. (2006) Statistical and Bayesian approaches to RNA secondary structure prediction. RNA 12, 323-331.

Chan, C.Y., Lawrence, C.E. and Ding, Y. (2005) Structure clustering features on the Sfold Web server. Bioinformatics 21, 3926-3928.

Ding, Y. and Lawrence, C.E. (2005) Rational design of siRNAs with the Sfold software. In RNA Interference: from Basic Science to Drug Development, ed. Krishnarao Appasani, Cambridge University Press.

Ding, Y., Chan, C. Y. and Lawrence, C. E. (2004) Sfold web server for statistical folding and rational design of nucleic acids. Nucleic Acids Res 32:W135-41.

Ding, Y. and Lawrence, C. E. (2003) A statistical sampling algorithm for RNA secondary structure prediction. Nucleic Acids Res 31:7280-301.

Ding, Y. (2002) Rational statistical design of antisense oligonucleotides for high throughput functional genomics and drug target validation. Statistica Sinica 12:273-96.

Ding, Y. and Lawrence, C. E. (2001) Statistical prediction of single-stranded regions in RNA secondary structure and application to predicting effective antisense target sites and beyond. Nucleic Acids Res 29:1034-46.

Ding, Y. and Lawrence, C. E. (1999) A bayesian statistical algorithm for RNA secondary structure prediction. Comput Chem 23:387-400.

Prokaryotic Transcription Regulation and Genomics Publications

Wan, X.-F., VerBerkmoes, N. C., McCue, L. A., Stanek, D., Connelly, H., Hauser, L. J., Wu, L., Liu, X., Yan, T., Leaphart, A., Hettich, R. L., Zhou, J. and Thompson, D. K. (2004) Transcriptomic and proteomic characterization of the Fur modulon in the metal-reducing bacterium Shewanella oneidensis. J. Bacteriol. 186:8385-400.

Florczyk, M. A., McCue, L. A., Purkayastha, A., Currenti, E., Wolin, M. J. and McDonough, K. A. (2003) A family of acr-coregulated Mycobacterium tuberculosis genes shares a common DNA motif and requires Rv3133c (dosR or devR) for expression. Infect Immun 71:5332-43.

Qin, Z. S., McCue, L. A., Thompson, W., Mayerhofer, L., Lawrence, C. E. and Liu, J. S. (2003) Identification of co-regulated genes through Bayesian clustering of predicted regulatory binding sites. Nat Biotechnol 21:435-9.

McCue, L. A., Thompson, W., Carmack, C. S. and Lawrence, C. E. (2002) Factors influencing the identification of transcription factor binding sites by cross-species comparison. Genome Res 12:1523-32.

McCue, L., Thompson, W., Carmack, C., Ryan, M. P., Liu, J. S., Derbyshire, V. and Lawrence, C. E. (2001) Phylogenetic footprinting of transcription factor binding sites in proteobacterial genomes. Nucleic Acids Res 29:774-82.

Hu, W. Y., Thompson, W., Lawrence, C. E. and Derbyshire, K. M. (2001) Anatomy of a preferred target site for the bacterial insertion sequence IS903. J Mol Biol 306:403-16.

Barrick, D., Villanueba, K., Childs, J., Kalil, R., Schneider, T. D., Lawrence, C. E., Gold, L. and Stormo, G. D. (1994) Quantitative analysis of ribosome binding sites in E.coli. Nucleic Acids Res 22:1287-95.

Bryk, M., Quirk, S. M., Mueller, J. E., Loizos, N., Lawrence, C. and Belfort, M. (1993) The td intron endonuclease I-TevI makes extensive sequence-tolerant contacts across the minor groove of its DNA target. Embo J 12:2141-9.

Eukaryotic Gene Regulation Publications

Newberg, L. A. and Lawrence, C. E. (2004) Mammalian genomes ease location of human DNA functional segments but not their description. Statist Appl Gen Mol Biol 3:23.

Thompson, W., Palumbo, M. J., Wasserman, W. W., Liu, J. S. and Lawrence, C. E. (2004) Decoding human regulatory circuits. Genome Res 14:1967-74.

Wasserman, W. W., Palumbo, M., Thompson, W., Fickett, J. W. and Lawrence, C. E. (2000) Human-mouse genome comparisons to locate regulatory sites. Nat Genet 26:225-8.

Protein Sequence Analysis & Structure Prediction Publications

Purkayastha, A., McCue, L. A. and McDonough, K. A. (2002) Identification of a Mycobacterium tuberculosis putative classical nitroreductase gene whose expression is coregulated with that of the acr aene within macrophages, in standing versus shaking cultures, and under low oxygen conditions. Infect Immun 70:1518-29.

Shaw, E., McCue, L. A., Lawrence, C. E. and Dordick, J. S. (2002) Identification of a novel class in the alpha/beta hydrolase fold superfamily: the N-myc differentiation-related proteins. Proteins 47:163-8.

Webb, B. J., Liu, J. S. and Lawrence, C. E. (2002) BALSA: Bayesian algorithm for local sequence alignment. Nucleic Acids Res 30:1268-77.

Florczyk, M. A., McCue, L. A., Stack, R. F., Hauer, C. R. and McDonough, K. A. (2001) Identification and characterization of mycobacterial proteins differentially expressed under standing and shaking culture conditions, including Rv2623 from a novel class of putative ATP-binding proteins. Infect Immun 69:5777-85.

Chave, K. J., Auger, I. E., Galivan, J. and Ryan, T. J. (2000) Molecular modeling and site-directed mutagenesis define the catalytic motif in human gamma -glutamyl hydrolase. J Biol Chem 275:40365-70.

McCue, L. A., McDonough, K. A. and Lawrence, C. E. (2000) Functional classification of cNMP-binding proteins and nucleotide cyclases with implications for novel regulatory pathways in Mycobacterium tuberculosis. Genome Res 10:204-19.

Qu, K., Martin, D. L. and Lawrence, C. E. (1998) Motifs and structural fold of the cofactor binding site of human glutamate decarboxylase. Protein Sci 7:1092-105.

Qu, K., McCue, L. A. and Lawrence, C. E. (1998) Bayesian protein family classifier. Proc Int Conf Intell Syst Mol Biol 6:131-9.

Neuwald, A. F., Liu, J. S., Lipman, D. J. and Lawrence, C. E. (1997) Extracting protein alignment models from the sequence database. Nucleic Acids Res 25:1665-77.

Qu, K. and Lawrence, C. E. (1997) Extended homology prediction for motif structure by multiple sequence alignment. Math Modeling & Sci Computing 8.

Mannella, C. A., Neuwald, A. F. and Lawrence, C. E. (1996) Detection of likely transmembrane beta strand regions in sequences of mitochondrial pore proteins using the Gibbs sampler. J Bioenerg Biomembr 28:163-9.

Neuwald, A. F., Liu, J. S. and Lawrence, C. E. (1995) Gibbs motif sampling: detection of bacterial outer membrane protein repeats. Protein Sci 4:1618-32.

Lawrence, C. (1994) Toward the unification of sequence and structural data for identification of structural and functional constraints. Comput Chem 18:255-8.

Bryant, S. H. and Lawrence, C. E. (1993) An empirical energy function for threading protein sequence through the folding motif. Proteins 16:92-112.

Bryant, S. H. and Lawrence, C. E. (1991) The frequency of ion-pair substructures in proteins is quantitatively related to electrostatic potential: a statistical model for nonbonded interactions. Proteins 9:108-19.

Lawrence, C. E. and Bryant, S. H. (1991) Hydrophobic potentials from statistical analysis of protein structures. Methods Enzymol 202:20-31.

Auger, I. E. and Lawrence, C. E. (1990) Identification of the most significant amphipathic helix with application to HIV and MHV envelope proteins. Comput Appl Biosci 6:165-71.

Lawrence, C., Auger, I. and Mannella, C. (1987) Distribution of accessible surfaces of amino acids in globular proteins. Proteins 2:153-61.

Bayesian Statistics & Gibbs Sampling Publications

Lawrence, C. and Auger, I. (2004) Discussions on "a bayesian approach to DNA sequence segmentation". Biometrics 60:581-2.

Ding, Y. and Lawrence, C. E. (2003) A statistical sampling algorithm for RNA secondary structure prediction. Nucleic Acids Res 31:7280-301.

Qin, Z. S., McCue, L. A., Thompson, W., Mayerhofer, L., Lawrence, C. E. and Liu, J. S. (2003) Identification of co-regulated genes through Bayesian clustering of predicted regulatory binding sites. Nat Biotechnol 21:435-9.

Thompson, W., Rouchka, E. C. and Lawrence, C. E. (2003) Gibbs Recursive Sampler: finding transcription factor binding sites. Nucleic Acids Res 31:3580-5.

Samso, M., Palumbo, M. J., Radermacher, M., Liu, J. S. and Lawrence, C. E. (2002) A Bayesian method for classification of images from electron micrographs. J Struct Biol 138:157-70.

Webb, B. J., Liu, J. S. and Lawrence, C. E. (2002) BALSA: Bayesian algorithm for local sequence alignment. Nucleic Acids Res 30:1268-77.

Ding, Y. and Lawrence, C. E. (1999) A bayesian statistical algorithm for RNA secondary structure prediction. Comput Chem 23:387-400.

Liu, J., Neuwald, A. F. and Lawrence, C. E. (1999) Markovian structures in biological sequence alignments. J Amer Statist Assoc 94:1-15.

Liu, J. S. and Lawrence, C. E. (1999) Bayesian inference on biopolymer models. Bioinformatics 15:38-52.

Zhu, J., Luthy, R. and Lawrence, C. E. (1999) Database search based on Bayesian alignment. Proc Int Conf Intell Syst Mol Biol 297-305.

Qu, K., McCue, L. A. and Lawrence, C. E. (1998) Bayesian protein family classifier. Proc Int Conf Intell Syst Mol Biol 6:131-9.

Zhu, J., Liu, J. S. and Lawrence, C. E. (1998) Bayesian adaptive sequence alignment algorithms. Bioinformatics 14:25-39.

Zhu, J., Liu, J. and Lawrence, C. (1997) Bayesian adaptive alignment and inference. Proc Int Conf Intell Syst Mol Biol 5:358-68.

Lawrence, C. E. and Reilly, A. A. (1996) Likelihood Inferences for permuted data with application to gene regulation. J Amer Statist Assoc 91:76-85.

Liu, J. S. and Lawrence, C. E. (1996) Statistical models for multiple sequence alignment: unifications and generalizations, p. 1-8, Proc Amer Statist Assoc.

Liu, J. S., Neuwald, A. F. and Lawrence, C. E. (1995) Bayesian models for multiple local sequence alignment and Gibbs sampling strategies. J Amer Statist Assoc 90:1156-70.

Neuwald, A. F., Liu, J. S. and Lawrence, C. E. (1995) Gibbs motif sampling: detection of bacterial outer membrane protein repeats. Protein Sci 4:1618-32.

Lawrence, C. E., Altschul, S. F., Wootton, J. C., Boguski, M. S., Neuwald, A. F. and Liu, J. (1994) A Gibbs sampler for the detection of subtle motifs in multiple sequences, p. 245-54, Proc 27th Ann Hawaii Int Conf Syst Sci. IEEE Computer Society.

Lawrence, C. E., Altschul, S. F., Boguski, M. S., Liu, J. S., Neuwald, A. F. and Wootton, J. C. (1993) Detecting subtle sequence signals: a Gibbs sampling strategy for multiple alignment. Science 262:208-14.

Lawrence, C. E. and Reilly, A. A. (1990) An expectation maximization (EM) algorithm for the identification and characterization of common sites in unaligned biopolymer sequences. Proteins 7:41-51.

Auger, I. E. and Lawrence, C. E. (1989) Algorithms for the optimal identification of segment neighborhoods. Bull Math Biol 51:39-54.

Lawrence, C. E. and Reilly, A. A. (1985) Maximum likelihood estimation of subsequence conservation. J Theor Biol 113:425-39.

Computational Molecular Biology and Statistics Core Facility Collaborative Publications

Kim, D., Reilly, A. and Lawrence, D. A. (2001) Relationships between IFNgamma, IL-6, corticosterone, and Listeria monocytogenes pathogenesis in BALB/c mice. Cell Immunol 207:13-8.

Parsons, P. J., Reilly, A. A., Esernio-Jenssen, D., Werk, L. N., Mofenson, H. C., Stanton, N. V. and Matte, T. D. (2001) Evaluation of blood lead proficiency testing: comparison of open and blind paradigms. Clin Chem 47:322-30.

Spivack, S. D., Hurteau, G. J., Reilly, A. A., Aldous, K. M., Ding, X. and Kaminsky, L. S. (2001) CYP1B1 expression in human lung. Drug Metab Dispos 29:916-22.

Walsh, A. C., Feulner, J. A. and Reilly, A. (2001) Evidence for functionally significant polymorphism of human glutamate cysteine ligase catalytic subunit: association with glutathione levels and drug resistance in the National Cancer Institute tumor cell line panel. Toxicol Sci 61:218-23.

Bolivar, V. J., Caldarone, B. J., Reilly, A. A. and Flaherty, L. (2000) Habituation of activity in an open field: A survey of inbred strains and F1 hybrids. Behav Genet 30:285-93.

Chave, K. J., Auger, I. E., Galivan, J. and Ryan, T. J. (2000) Molecular modeling and site-directed mutagenesis define the catalytic motif in human gamma -glutamyl hydrolase. J Biol Chem 275:40365-70.

Reilly, M., Mix, D., Reilly, A. A., Yang Ye, X. and Winslow, G. M. (2000) Intercellular transfer of a soluble viral superantigen. J Virol 74:8262-7.

Winslow, G. M., Yager, E., Shilo, K., Volk, E., Reilly, A. and Chu, F. K. (2000) Antibody-mediated elimination of the obligate intracellular bacterial pathogen Ehrlichia chaffeensis during active infection. Infect Immun 68:2187-95.

Caggana, M., Walker, K., Reilly, A. A., Conroy, J. M., Duva, S. and Walsh, A. C. (1999) Population-based studies reveal differences in the allelic frequencies of two functionally significant human interleukin-4 receptor polymorphisms in several ethnic groups. Genet Med 1:267-71.

Fox, M. P., Reilly, A. A. and Schneider, E. (1999) Effect of the ratio of free to total prostate-specific antigen on interassay variability in proficiency test samples. Clin Chem 45:1181-9.

Meng, Q., Henderson, R. F., Chen, T., Heflich, R. H., Walker, D. M., Bauer, M. J., Reilly, A. A. and Walker, V. E. (1999) Mutagenicity of 1,3-butadiene at the Hprt locus of T-lymphocytes following inhalation exposures of female mice and rats. Mutat Res 429:107-25.

Meng, Q., Henderson, R. F., Walker, D. M., Bauer, M. J., Reilly, A. A. and Walker, V. E. (1999) Mutagenicity of the racemic mixtures of butadiene monoepoxide and butadiene diepoxide at the Hprt locus of T-lymphocytes following inhalation exposures of female mice and rats. Mutat Res 429:127-40.

Reilly, A. A., Salkin, I. F., McGinnis, M. R., Gromadzki, S., Pasarell, L., Kemna, M., Higgins, N. and Salfinger, M. (1999) Evaluation of mycology laboratory proficiency testing. J Clin Microbiol 37:2297-305.

Walker, V. E., Jones, I. M., Crippen, T. L., Meng, Q., Walker, D. M., Bauer, M. J., Reilly, A. A., Tates, A. D., Nakamura, J., Upton, P. B. and Skopek, T. R. (1999) Relationships between exposure, cell loss and proliferation, and manifestation of Hprt mutant T cells following treatment of preweanling, weanling, and adult male mice with N-ethyl-N-nitrosourea. Mutat Res 431:371-88.

Meng, Q., Recio, L., Reilly, A. A., Wong, B. A., Bauer, M. and Walker, V. E. (1998) Comparison of the mutagenic potency of 1,3-butadiene at the hprt locus of T-lymphocytes following inhalation exposure of female B6C3F1 mice and F344 rats. Carcinogenesis19:1019-27.

Reilly, A. A., Bellisario, R. and Pass, K. A. (1998) Multivariate discrimination for phenylketonuria (PKU) and non-PKU hyperphenylalaninemia after analysis of newborns' dried blood-spot specimens for six amino acids by ion-exchange chromatography. Clin Chem 44:317-26.

Parsons, P. J., Reilly, A. A. and Esernio-Jenssen, D. (1997) Screening children exposed to lead: an assessment of the capillary blood lead fingerstick test. Clin Chem 43:302-11.

Iskenderian, A. C., Huang, L., Reilly, A., Stenberg, R. M. and Anders, D. G. (1996) Four of eleven loci required for transient complementation of human cytomegalovirus DNA replication cooperate to activate expression of replication genes. J Virol 70:383-92.

Parsons, P. J., Reilly, A. A. and Hussain, A. (1991) Observational study of erythrocyte protoporphyrin screening test for detecting low lead exposure in children: impact of lowering the blood lead action threshold. Clin Chem 37:216-25.

Hechemy, K. E., Harris, H. L., Wethers, J. A., Stevens, R. W., Stock, B. R., Reilly, A. A. and Benach, J. L. (1989) Fluoroimmunoassay studies with solubilized antigens from Borrelia burgdorferi. J Clin Microbiol 27:1854-8.

Parsons, P. J., Stanton, N. V., Gunter, E. W., Huff, D., Meola, J. R. and Reilly, A. A. (1989) An interlaboratory comparison of control materials for use with hematofluorometers. Clin Chem 35:2059-65.

Rich, S. A. and Reilly, A. A. (1989) Evidence that the interferon-induced Daudi cell human lupus inclusions are de novo synthesized complexes of ribonucleoprotein and membrane. J Biol Chem 264:3529-37.