Publication Archives

Publication Archives, 1976 - 2009

Ruggieri, E., T. Herbert, K. T. Lawrence, and C. E. Lawrence (2009), Change point method for detecting regime shifts in paleoclimatic time series: Application to δ-O18 time series of the Plio-Pleistocene, Paleoceanography, 24, PA1204, doi:10.1029/2007PA001568.

Exact Calculation of Distributions on Integers, with Application to Sequence Alignment (2009), Newberg LA. Lawrence CE. Journal of Computational Biology, 16(1): 1-18.

Centroid estimators for inference in high-dimensional discrete spaces (2008) Luis E. Carvalho, and Charles E. Lawrence, PNAS: USA, 105: 3209–3214.

Automated mapping of large-scale chromatin structure in ENCODE.  Lian H, Thompson WA, Thurman R, Stamatoyannopoulos JA, Noble WS, Lawrence CE.Bioinformatics. 2008 Sep 1;24(17):1911-6. Epub 2008 Jun 30.

Measuring Global Credibility with Application to Local Sequence Alignment, (2008) Webb-Robertson BJM. McCue LA. and Lawrence CE.   PLoS Computational Biology 4(5): e1000077 doi:10.1371/journal.pcbi.1000077.

Using the Gibbs Motif Sampler for phylogenetic footprinting. (2007) Thompson W, Conlan S, McCue LA, Lawrence CE.  Methods Mol Biol. 2007;395:403-24.

The Gibbs Centroid Sampler, (2007) Thompson WA.Newberg, LA. Conlan SP.McCue, LA. Lawrence, CE.  Nucleic Acids Res, 2007 35(Web Server issue):W232-W237.

A phylogenetic Gibbs sampler that yields centroid solutions for cis regulatory site prediction (2007) Lee A. Newberg, William A. Thompson, Sean P. Conlan,  Thomas M. Smith, Lee Ann McCue, Charles E. Lawrence. Bioinformatics, 23: 1718-1727; doi:10.1093/bioinformatics/btm241doi:

PhyloScan: Identification of transcription factor binding sites using cross-species evidence (2007) C Steven Carmack, Lee Ann McCue,  Lee A Newberg, and Charles E Lawrence, (in press)  Algorithms for Molecular Biology, 2:1 doi:10.1186/1748-7188-2-1 .

Contribution of the histone H3 and H4 amino termini to Gcn4p- and Gcn5p-mediated transcription in yeast. (2006), Yu C. Palumbo MJ. Lawrence CE. Morse, RH.  J Biol Chem. 281(14):9755-64. Epub 2006 Feb 4.

Clustering of RNA secondary structures with application to messenger RNAs, (2006) Ye Ding YChan CY, and Lawrence CE, Journal of Molecular Biology, 359: 554–571.

Rhodopseudomonas palustris Regulons Detected by Cross-Species Analysis of Alphaproteobacterial Genomes.  (2005) Conlan S, Lawrence C, McCue LA. Appl Environl Microbiol, 71 (11):7442-7452, 2005.

Structure Clustering Features on the Sfold Web server.  Chan CY, Lawrence CE, Ding Y.  Bioinformatics 21 (20):3926-3928, 2005.

RNA Secondary Structure Prediction by Centroids in a Boltzmann Weighted Ensemble.  Ding Y, Chan CY, and Lawrence CE. RNA, 11 (8):1157-1166, 2005.

Using the Gibbs Motif Sampler to Find Conserved Domains in DNA and Protein Sequences. In Current Protocols in Bioinformatics,  (eds. Baxevanis AD, Davison DB, Page RDM, Petsko GA, Stein LD, and GD Stormo),  pp. 2.8.1-2.8.42. John Wiley & Sons, Inc., New York, NY. Thompson, W., McCue, LA., Lawrence, CE. 2005. 

Global Profiling of Shewanella Oneidensis MR-1: Expression of Hypothetical Genes and Improved Functional Annotations. Kolker E, Picone AF, Galperin MY, Romine MF, Higdon R, Makarova KS, Kolker N, Anderson GA, Qiu X, Auberry KJ, Babnigg G, Beliaev AS, Edlefsen P, Elias DA, Gorby YA, Holzman T, Klappenbach JA, Konstantindis KT, Land ML, Lipton MS, McCue LA, Monroe M, Pasa-Tolic L, Pinchuk G, Purvine S, Serres, MH, Tsapin S, Zakrajsek BA, Zhu W, Zhou J, Larimer FW, Lawrence CE, Riley M, Collart FR, Yates JR 3rd, Smith RD, Giometti CS, Nealson KH, Fredrickson JK, Tiedje JM.   Proc Natl Acad Sci U S A, 8;102(6):2099-2104, 2005.

Mammalian Genomes Ease Location of Human DNA Functional Segments but Not Their Description.  Newberg LA, Lawrence CE.  Statist App Gen Mol Biol, 3:23, 2004. http://www.bepress.com/sagmb/vol3/iss1/art23/

Decoding Human Regulatory Circuits.  Thompson W, Palumbo MJ, Wasserman WW, Liu  JS, Lawrence CE. Genome Res, 14: 1967-1974, 2004.

Sfold Web Server for Statistical Folding and Rational Design of Nucleic Acids. Ding Y, Chan CY, Lawrence CE.  Nucleic Acids Res, 1;32(Web Server issue):W135-141, 2004.

Discussions on a Bayesian Approach to DNA Sequence Segmentation.  Auger I, Lawrence CE.  Biometrics 60(3):581, 2004.

A Statistical Sampling Algorithm for RNA Secondary Structure Prediction.  Ding Y, Lawrence CE.  Nucleic Acids Res, 31(24): 7280-7301, 2003.

Gibbs Recursive Sampler: Finding Transcription Factor Binding Sites.  Thompson W, Rouchka EC, Lawrence CE.  Nucleic Acids Res, (web server issue), 31:3580-3585, 2003.

Comparative Analyses of Multi-Species Sequences from Targeted Genomic Regions.  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.  Nature, 424(6950):788-793, 2003.

Bayesian Clustering with Variable and Transformation Selections (with discussion).  Liu JS, Zhang JL, Palumbo H, Lawrence CE.  Bayesian Statistics, 7:249-275, Bernardo JM, Berger JO, David AP, Smith AFM. (eds). Oxford: Clarendon Press, 2003.

Identification of Co-regulated Genes through Bayesian Clustering of Predicted Regulatory Binding Sites. Qin ZS, McCue LA, Thompson W, Mayerhofer L, Lawrence CE, Liu JS.  Nat Biotechno, 21(4):435-439, 2003.

An Application of Nonlinear Optimization in Molecular Biology.  Ecker JG, Kupferschmid M, Lawrence CE, Reilly AA, Scott ACH.  Eur J Oper Res, 138: 452-458, 2002.

A Bayesian Method for Classification of Images from Electron Micrographs.  Samso M, Palumbo MJ, Radermacher M, Liu JS, Lawrence CE.  J Struct Biol, 138:157-170, 2002.

Identification of a Novel Class in the Alpha/Beta Hydrolase Fold Superfamily: the N-myc Differentiation-Related Proteins.  Shaw E, McCue LA, Lawrence CE, Dordick JS.  Proteins 47(2):163-168, 2002.

Factors Influencing the Identification of Transcription Factor Binding Sites by Cross Species Comparison.  McCue LA, Thompson W, Carmack CS, Lawrence CE.  Genome Res,  12:1523-532, 2002.

BALSA: Bayesian Algorithm for Local Sequence Alignment.  Webb BJ, Liu JS, Lawrence CE.  Nucleic Acids Res, 30(5):1268-1277, 2002.

Bayesian Methodology in Genomics Research.  Liu JS, Liu X, Gupta M, Lawrence CE.  Case Studies in Bayesian Statistics, 2001, Carnegie Mellon University.

Statistical Prediction of Single-Stranded Regions in RNA Secondary Structure and Application to Predicting Effective Antisense Target Sites and Beyond.  Ding Y, Lawrence CE.  Nucleic Acids Res, 29(5):1034-1046, 2001.

Phylogenetic Footprinting of Transcription Factor Binding Sites in Proteobacterial Genomes. McCue LA, Thompson W, Carmack CS, Ryan MP, Liu JS, Derbyshire V, Lawrence CE.  Nucleic Acids Res, 29:774-782, 2001.

Anatomy of a Preferred Target Site for the Bacterial Insertion Site IS903.  Hu W, Thompson W, Lawrence CE, Derbyshire KM.  J Mol Biol, 306(3): 397-402, 2000.

Human-Mouse Genome Comparison to Locate Human Regulatory Sites.  Wasserman WW, Palumbo M, Thompson W, Fickett JW, Lawrence CE.  Nature-Genetics, 26(2):225-228, 2000.

Functional Classification of cNMP-Binding Proteins and Nucleotide Cyclases with Implications for Novel Regulatory Pathways in Mycobacterium Tuberculosis.  McCue LA, McDonough KA, Lawrence CE.  Genome Res, 10:204-219, 2000.

Database Search Based on Bayesian Alignment.  Zhu J, Luthy R, Lawrence CE.  Proceedings of the Seventh International Conference on Intelligent Systems for Molecular Biology, ISMB, 7:297-305, 1999.

A Bayesian Statistical Algorithm for RNA Secondary Structure Prediction.  Ding Y, Lawrence CE.  Computers & Chemistry, 23:387-400, 1999.

Bayesian Inference on Biopolymer Models.  Liu JS, Lawrence CE.  Bioinformatics, (invited paper) 15:38-52, 1999.

Markovian Structures in Biological Sequence Alignments.  Liu JS, Neuwald AF, Lawrence CE.  J Am Stat Assoc, 94:1-15, 1999.

Bayesian Protein Family Classifier.  Qu K, McCue LA, Lawrence CE.  Proceedings of the Sixth International Conference on Intelligent Systems for Molecular Biology, ISMB, 6:131-139, 1998.

Motifs and Structural Fold of the Cofactor Binding Site of Human Glutamate Decarboxylase.  Qu K, Martin DL, Lawrence CE.  Protein Sci, 7:1092-1105, 1998.

Bayesian Adaptive Sequence Alignment Algorithms.  Zhu J, Liu JS, Lawrence CE.  Bioinformatics, 14:25-39, 1998.

Bayesian Adaptive Alignment and Inference.  Zhu J, Liu J, Lawrence CE.  Proceedings of the Fifth International Conference on Intelligent Systems for Molecular Biology, ISMB, 5:358-368, 1997.

Extended Homology Prediction for Motif Structure by Multiple Sequence Alignment.  Qu K, Lawrence CE.  Mathematical Modeling & Scientific Computing,Vol. 8, 1997.

Identification and Characterization of Two Groups of Congenital Hypothyroid Infants: Implications for Newborn Screening.  Auger IE, Bellisario R, Koerner-Rabatoy S, Lawrence CE.  Early Human Develop, 44:235-245, 1997.

Extracting Protein Alignment Models from the Sequence Database.  Neuwald AF, Liu JS, Lipman DJ, Lawrence CE.  Nucleic Acids Res, 25(9):1665-1677, 1997.

Extent and Nature of Contacts Between Protein Molecules in Crystal Lattices and Between Subunits of Protein Oligomers.  Dasgupta S, Iyer GH, Bryant SH, Lawrence CE, Bell J.  Proteins: Structure, Function and Genetics, 28:494-514, 1997.

Detection of Likely Transmembrane Beta-Strand Regions in Sequences of Mitochondrial Pore Proteins Using the Gibbs Sampler.  Mannella CA, Neuwald AF, Lawrence CE.  J Bioenerg Biomembr, 28:163-169, 1996.

Likelihood Inferences for Permuted Data with Application to Gene Regulation.  Lawrence CE, Reilly AA.  J. Am Stat Assoc, 91:76-85, 1996.

Bayesian Models for Multiple Local Sequence Alignment and Gibbs Sampling Strategies.  Liu JS, Neuwald AF, Lawrence CE.  J. Am Stat Assoc, 90:1156-1170, 1995.

Gibbs Motif Sampling: Detecting Bacterial Outer Membrane Protein Repeats.  Neuwald AF, Liu JS, Lawrence CE.  Protein Sci, 4:1618-1632, 1995.

Statistical Models for Multiple Sequence Alignment: Unification and Generalizations.  Liu JS, Lawrence CE.  Proceedings American Statistical Association, Statistical Computing Section, 21:1-8, 1995.

Quantitative Analysis of Ribosome Binding Sites in E. coli.  Barrick, D, Villaneuba K, Childs J, Kalil R, Schneider T, Lawrence CE, Gold L, Stormo G.  Nucleic Acids Res, 22: 1287-1295, 1994.

Toward the Unification of Sequence and Structural Data for the Identification of Structural and Functional Constraints.  Lawrence CE.  Computers & Chemistry, 18: 255-258 1994.

Gibbs Sampler for the Detection of Subtle Motifs in Multiple Sequences.  Lawrence C, Altschul S, Wootton J, Boguski M, Neuwald AF, Liu JS.  IEEE Computer Society, 27:245-254, 1994.

Risk Profile for Chlamydia Infection in Women from Public Health Clinics in New York State. Han Y, Morse DL, Lawrence CE, Murphy D, Hipp S.  J. Community Health, 18:1-9, 1993.

An Empirical Energy Function of Threading Protein Sequence through the Folding Motif. Bryant SH, Lawrence CE. Proteins: Structure, Function and Genetics, 16:92-112, 1993.

Detecting Subtle Sequence Signals: A Gibbs Sampling Strategy for Multiple Alignment. Lawrence CE, Altschul SF, Boguski MS, Liu JS, Neuwald AF, Wootton JC.  Science, 262:208-214, 1993. 

The td Intron Endonuclease I-Tevl Makes Extensive Sequence-Tolerant Contacts Across the Minor Groove of its DNA Target.  Bryk M, Quirk SM, Mueller JE, Loizos N, Lawrence CE, Belfort M. EMBO J, 12:2141-2149, 1993.

Quantitative PCR: Procedures and Precisions.  Nedelman J, Heagerty P, Lawrence CE.  Bull Math Biol, 54:477-507, 1992.

Quantitative PCR with Internal Controls.  Nedelman J, Heagerty P, Lawrence C.  CABIOS, 8:65-70, 1992.

Polychlorinated Biphenyls: Estimated Serum Half Lives.  Taylor PR, Lawrence CE.  Br J Ind Med, 49(7):527-528, 1992.

Estimating Serum Polychlorinated Biphenyl Levels in Highly Exposed Workers: an Empirical Model.  Taylor PR, Reilly AA, Stelma JM, Lawrence CE.  J Toxicol Environ Health, 34(4):413-422, 1991.

Hydrophobic Potentials from Statistical Analysis of Protein Structures.  Lawrence CE, Bryant SH.  "Molecular Design and Modeling: Concepts and Applications", MethodsEnzymol, 202:20-31, 1991.

Modeling Length Bias in Longitudinal Linked Record System HIV Cases.  Nedelman J, Burns A, Cleary J, Gordon D, Vernon P, Lawrence CE.  Stat Med, 10:423-431, 1991.

The Frequency of Ion-Pair Substructures in Proteins is Quantitatively Related to Electrostatic Potential. A Statistical Model for Non-Bonded Interactions.  Bryant SH, Lawrence CE.  Proteins: Structure, Function, and Genetics, 9:108-119, 1991.

Identification of the Most Significant Amphipathic Helix with Application to HIV and MHV Envelope Proteins.  Auger IE, Lawrence CE.  CABIOS, 6:165-171, 1990.

AIDS Behind Bars. Epidemiology of New York State Prison Inmate Cases, 1980-1988.  Morse DL, Truman BI, Hanrahan JP, Mikl J, Broaddus RK, Maguire BH, Grabau JC, Kain-Hyde S, Han Y, Lawrence CE.  N Y State J Med, 90(3):133-138, 1990.

An Expectation Maximization (EM) Algorithm for the Identification and Characterization of Common Sites in Unaligned Biopolymers Sequence.  Lawrence CE, Reilly AA.  Proteins: Structure, Function, and Genetics, 7:41-51, 1990.

Advanced Stage-Endometrial Cancer: Contributions of Estrogen Use, Smoking, and Other Risk Factors. Lawrence C., Tessaro I, Durgerian S, Caputo T, Richart RM, Greenwald P.  Gynecologic Oncology, 32:41-45, 1989.

Algorithms for the Optimal Identification of Segment Neighborhoods.  Auger IE, Lawrence CE.  Bull Math Biol, 51:39-54, 1989.

The Relation of Polychlorinated Biphenyls to Birth Weight and Gestational Age in the Offspring of Occupationally Exposed Mothers.  Taylor PR, Stelma JM, Lawrence CE. Am J Epidemiol, 129:395-406, 1989.

Incubation Periods for Paediatric AIDS patients.  Auger I, Thomas P, DeGruttola V. Morse D, Moore D, Williams R, Truman B, Lawrence CE.  Nature, 336:575-577, 1988.

Effects of Reagent and Instrument on Prothrombin Times, Activated Partial Thromboplastin Times and Patient/Control Ratios.  Naghibi F, Han Y, Dodds WJ, Lawrence CE.  Thromb Haemost, 59:455-463, 1988.

Distribution of Accessible Surfaces of Amino Acids in Globular Proteins.  Lawrence C, Auger I, Mannella C. Proteins: Structure, Function, and Genetics, 2:153-161, 1987.

Smoking, Body Weight, and Early-Stage Endometrial Cancer.  Lawrence CE, Tessaro I, Durgerian S, Caputo T, Richart R, Jacobson H, Greenwald P.  Cancer, 59:1665-1669, 1987.

Prothrombin Time Proficiency Testing: A Robust Grading Method.  Han Y, Lawson WB, Dodds WJ, Lawrence CE.  Thromb Haemost, 54(3):704-708, 1985.

Maximum Likelihood Estimation of Subsequence Conservation.  Lawrence CE, Reilly AA.  J Theor Biol, 113:425-439, 1985.

Mortality Patterns of New York State Vietnam Veterans.  Lawrence CE, Reilly AA, Quickenton P, Greenwald P, Page WF, Kuntz AJ.  Am J Public Health, 75(3):277-279, 1985.

Broken Appointments at a Neighborhood Health Center: Emphasis on Weather.  Morse D, Coulter M, Napodano RJ, Hwang HL, Lawrence CE.  Med Care, 22(9):813, 1984.

Polychlorinated Biphenyls: Influence on Birthweight and Gestation.  Taylor PR, Lawrence CE, Hwang HL, Paulson AS.  Am J Public Health, 74(10):1153-1154, 1984

Trihalomethanes in Drinking Water and Human Colorectal Cancer.  Lawrence CE, Taylor PR, Trock BJ, Reilly AA.  J Natl Cancer Inst, 72(3):563-568, 1984.

Breast Cancer and Oral Contraceptive Use: a Case-Control Study. Janerich DT, Polednak AP, Glebatis DM, Lawrence CE.  J Chronic Dis, 1983;36(9):639-646.

A Queuing Network Approach to Health Care Planning with an Application to Burn Care in New York State.  Blair EL, Lawrence CE.  Journal of Socio-Economic Planning Science, 15(1):207-216, 1981.

Diagnostic Sensitivity Bias -- an Epidemiologic Explanation for an Apparent Brain Tumor Excess. Greenwald P, Friedlander BR, Lawrence CE, Hearn T, Earle K.  J Occup Med, 23(10):690-694, 1981.

Tonsillectomy and Childhood Hodgkin's Disease.  Vianna NJ, Lawrence CE, Davies JN, Arbuckle J, Harris S, Marani W, Wilkinson J.  Lancet , No. 8190, 1:338-340, 1980.

A Systems Model for Burn Care.  Feck G, Blair EL, Lawrence CE.  Med Care, 18:211-218, 1980.

Relationship of Hair Dye Use, Benign Breast Disease and Breast Cancer.  Nasca PC, Lawrence CE, Greenwald P, Chorost S, Arbuckle JT, Paulson A. J Natl Cancer Inst, 64:23-28, 1980.

Burn-care Facilities; Recommendations for New York.  Feck G, Lawrence CE, Blair EL.  N Y State J Med, 79(12):1926-1929, 1979. No abstract available.

Estimated Effect of Breast Self-Examination and Routine Physician Examinations on Breast Cancer Mortality. Greenwald P, Nasca PC, Lawrence CE, Horton J, McGarrah RP, Gabriele T, Carlton K.  N Engl J Med, 299(6):271-273, 1978.

Evaluation of Burn Care (Letter).  Feck G, Lawrence CE.  N Engl J Med, 296:1415-1416, 1977.

PCB and Melanoma (Letter). Lawrence CE.  N Engl J Med, 296:108, 1977.

Female Family Size Ideals as Population Policy Objectives for Latin America, Demographic and Methodological Considerations.  Lawrence CE, Mundigo AI.  Policy Sci, 8 (4):437-454, 1977.

Stable Population Analysis in Periodic Environments.  Gourley RS, Lawrence CE.  Theor Popul Biol, 11:49-59, 1977.

Fertility Patterns Following Oral Contraceptive Use.  Janerich DT, Lawrence CE, Jacobson HI.  Lancet, No. 7968, 2:1051-1053, 1976.

Epidemiological Strategies for Identifying Carcinogens.  Janerich DT, Lawrence CE, Jacobson HI  Mutat Research, 33:55-63, 1975.

REALPOP: A Mathematical Model for Resource Allocation in Population Programs - Results from a Test in the Dominican Republic.  Lawrence CE, Mundigo AI.  Stud Fam Plann, 6(3):64-71, 1975.

Natural Selection of Life History Attributes.  Taylor HM, Gourley RS, Lawrence CE, Kaplan RS.  Theor Popul Biol, 5(1):104-122, 1974.

Analysis of Allocation of Resources in Family Planning Programs.  Lawrence CE, Mundigo AI, ReVelle CS.  Manage Sci, 20(5):520-531, 1973.

A Mathematical Model for Resource Allocation in Population Programs. Lawrence CE, Mundigo AI, ReVelle CS.  Demography, 9(3):465-483, 1972.

Chapters in books 

A Gibbs Sampler for the Detection of Subtle Motifs in Multiple Sequences.  Lawrence CE, Altschul S, Wootton J, Boguski M, Neuwald AF, Liu JS.  Proceedings of the Twenty Seventh Annual Hawaii International Conference on System Sciences, 5:245-254, 1994. 

Empirical Estimation of Exposure in Retrospective Epidemiologic Studies.  Lawrence, CE, Taylor, P. Environmental Epidemiology, Lewis Publishers, Inc., Kopfler F., Craun G. eds., 1986. 

Cigarette Smoke: Cancer Risk at Low Doses. Lawrence CE, Paulson A.  The Analysis of Actual Versus Perceived Risks. Plenum Press, Covello V, Flamm W, Rodricks J, Tardiff R. eds., 1983.

Cohort Related Factors and Congenital Malformation: A Computer Graphics Methodology. Lawrence CE, Blair E. Birth Defects: Risk and Consequences, Academic Press, New York and London, 1976.