Publications

2005

Hu Z, Mellor J, Wu J, Yamada T, Holloway D, Delisi C. VisANT: data-integrating visual framework for biological networks and modules. Nucleic Acids Res. 2005 Jul 1;33. [Abstract] [Full Text]

Shakhnovich BE, Deeds E, Delisi C, Shakhnovich E. Protein structure and evolutionary history determine sequence space topology. Genome Res. 2005 Mar;15(3):385-92. [Abstract] [Full Text]

Anderson, R.J., Weng, Z, Campbell, R.K. & Jiang, X. (2005) Main-chain conformational tendencies of amino acids. Proteins, in press.

Mintseris, J. & Weng, Z. (2005). Structure, function, and evolution of transient and obligate protein-protein interactions. PNAS 102(31), 10930-10935.

Mintseris, J., Wiehe, K., Pierce, B., Anderson, R., Chen, R., Janin, J. & Weng, Z. (2005) Protein-Protein Docking Benchmark 2.0: an update. Proteins 60(2), 214-216.

Wiehe, K., Pierce, B., Mintseris, J., Tong, W., Anderson, R., Chen, R. & Weng, Z. (2005) ZDOCK and RDOCK performance in CAPRI rounds 3, 4, and 5. Proteins 60(2), 207-213.

Pierce, B., Tong, W. & Weng, Z. (2005) M-ZDOCK: A Grid-based Approach for Cn Symmetric Multimer Docking. Bioinformatics 21(8), 1472-1476.

Haverty, P. M., Weng, Z. & Hansen, U. (Accepted) Transcriptional Regulatory Networks Activated by PI3K and ERK Transduced Growth Signals in Human Glioblastoma Cells. J. Comput. Sci. & Tech.

Yanai, I.*, Yu, Y.*, Zhu, X., Cantor, C. & Weng, Z. (2005) (*Joint First Authors) An Avidin-like Domain that Does Not Bind Biotin Is Adopted for Oligomerization by the Extracellular Mosaic Protein Fibropellin. Protein Science, Vol 14, 417-423.

Zhu, J. & Weng, Z. (2005) FAST: A Novel Protein Structure Alignment Algorithm. Proteins: Structure Function, and Bioinformatics, Vol 58, 618-627.

Tompa M, Li N, Bailey TL, Church GM, De Moor B, Eskin E, Favorov AV, Frith MC, Fu Y, Kent WJ, Makeev VJ, Mironov AA, Noble WS, Pavesi G, Pesole G, Regnier M, Simonis N, Sinha S, Thijs G, van Helden J, Vandenbogaert M, Weng Z, Workman C, Ye C, Zhu Z. (2005) Assessing computational tools for the discovery of transcription factor binding sites. Nature Biotechnology, Vol 23, 137-144.

Shu-Hsien Sheu, Taner Kaya, David J. Waxman, and Sandor Vajda. Exploring the Binding Site Structure of PPAR? Ligand-Binding Domain by Computational Solvent Mapping. Biochemistry, 2005, 44, 1193-1209.

Shu-Hsien Sheu, David R. Lancia Jr, Karl Clodefelter, Melissa R. Landon and Sandor Vajda. PRECISE: a Database of Predicted and Consensus Interaction Sites in Enzymes. Nucleic Acids Research, 2005 Jan 1; Vol 33 Database Issue:D206-11.

Daniel Segrè, Alexander DeLuna, George M. Church and Roy Kishony. Modular epistasis in yeast metabolism. Nature Genetics (2005), 37(1), 77-83.

Daniel Segrè. Ventimila geni sotto i mari dei tropici (Review, in Italian). Darwin (2005) May-June, 56-61.

Daniel Segrè. Life as a cellular automaton (Review of the The Principles of Life by Tibor Gánti). Journal of Biogeography (in press)

2004

Shakhnovich BE, Reddy TE, Galinsky K, Mellor J, Delisi C. Comparisons of predicted genetic modules: identification of co-expressed genes through module gene flow. Genome Inform Ser Workshop Genome Inform. 2004;15(1):221-8. [Abstract]

Shakhnovich BE, Harvey JM, Delisi C. ELISA: a unified, multidimensional view of the protein domain universe. Genome Inform Ser Workshop Genome Inform. 2004;15(1):213-20. [Abstract]

Mellor JC, Wu J, Delisi C. Constructing networks with correlation maximization methods. Genome Inform Ser Workshop Genome Inform. 2004;15(1):149-59. [Abstract]

DeLisi C. Systems biology, the second time around. Environ Health Perspect. 2004 Nov;112(16):A926-7. [Full Text]

Hu Z, Mellor J, Wu J, DeLisi C. VisANT: an online visualization and analysis tool for biological interaction data. BMC Bioinformatics. 2004 Feb 19;5(1):17. [Abstract] [Full Text]

The ENCODE Project Consortium (2004) The ENCODE (ENCyclopedia Of DNA Elements) Project Science, Vol 306, 636-640.

Haverty, PM., Hsiao, L., Gullans, SR., Hansen, U. & Weng, Z. (2004) Limited Agreement among Three Global Gene Expression Methods Highlights the Requirement for Non-Global Validation. Bioinformatics. Vol 20, 3431-3441.

Hu, Z. Fu, Y. Halees, A. S. Kielbasa, S. M. & Weng, Z. (2004) SeqVISTA: a New Module of Integrated Computational Tools for Studying Transcriptional Regulation. Nucleic Acids Res., Vol 32, Web Server Issue, W235-W241.

Mintseris, J. & Weng, Z. (2004) Optimizing Protein Representations with Information Theory. Genome Informatics, 15(1):160-169.

Halees, A. S. & Weng, Z. (2004) PromoSer: Improvements on Algorithm, Visualization and Accessibility. Nucleic Acids Res., Vol 32, Web Server Issue, W191-W194.

Fu, Y., Frith, M.C., Haverty, P.M. & Weng, Z. (2004) MotifViz: an Analysis and Visualization Tool for Motif Discovery. Nucleic Acids Res., Vol. 32, Web Server Issue, W420-W423.

Haverty, P.M., Frith, M.C. & Weng, Z. (2004) CARRIE Web Service: Automated Transcriptional Regulatory Network Inference and Interactive Analysis. Nucleic Acids Res., Vol. 32, Web Server Issue, W213-W216.

Leyfer, D., Bond, A., Tworog, E., Perron, D., Maska, S., Brito, A., Kamens, J., Weng, Z. & Voss, J. (2004) Cis-Element Clustering Correlates with Dose-Dependent Pro- and Anti- Signaling Effects of IL18. Genes and Immunity, June 10, 1-9.

Haverty, P.M. & Weng, Z. (2004) CisML, an XML-based Format for Sequence Motif Detection Software .Bioinformatics, 20(11), 1815-1817.

Frith, M. C., Fu, Y., Yu, L., Chen, J. F., Hansen, U. & Weng, Z. (2004) Detection of Functional DNA Motifs via Statistical Overrepresentation. Nucleic Acids Res. 2004 Feb 26; 32(4):1372-1381.

Frith, M. C.*, Halees, A. S.*, Hansen, U. & Weng, Z. (2004) *Joint First Authors Site2genome: Locating Short DNA Sequences in Whole Genomes. Bioinformatics. 20(9):1468-1469.

Haverty, P. M., Hansen, U. & Weng, Z. (2004) Computational Inference of Transcriptional Regulatory Networks from Expression Profiling and Transcription Factor Binding Site Identification . Nucleic Acids Res. 2004 Jan 1;32(1):179-188.

Frith, M. C., Hansen, U., Spouge, J. L. & Weng, Z. (2004) Finding Functional Sequence Elements by Multiple Local Alignment. Nucleic Acids Res. 2004 Jan 1;32(1):189-200.

Rajamani D, Thiel S, Vajda S, Camacho CJ. Anchor residues in protein-protein interactions. Proc. Natl. Acad. Sci. USA. 2004 Aug 3;101(31):11287-92.

Stephen R. Comeau, David W. Gatchell, Sandor Vajda and Carlos J. Camacho. ClusPro: a fully automated algorithm for protein-protein docking. Nucleic Acids Research Vol. 32, Web Server issue.

J.C. Prasad, Camacho C. J., Vajda, S. Consensus alignment server for reliable comparative modeling with distant templates. Nucleic Acids Research Vol. 32, Web Server issue.

Camacho C, and Vajda S. Protein protein docking: is the glass half-full or half-empty? TRENDS in Biotechnology. 2004 Mar;22(3):110-6.

Stephen R. Comeau, David W. Gatchell, Sandor Vajda and Carlos J. Camacho. ClusPro: an automated docking and discrimination method for the prediction of protein complexes. BIOINFORMATICS Vol. 20 no. 1 2004, pages 45-50.

P. E. Warburton, J. Giordano, F. Cheung, Y. Gelfand and G. Benson. Inverted Repeat Structure of the Human Genome: The X-Chromosome Contains a Preponderance of Large, Highly Homologous Inverted Repeats That Contain Testes Genes , Genome Research, 14:1861-1869, 2004.

D. Ahlbrandt, G. Benson, W. Casey. Minimal Entropy Probability Paths Between Genome Families, Journal of Mathematical Biology, 48(5):563-90.

Daniel Segrè. The regulatory software of cellular metabolism (Commentary of Ihmels et al. Nat. Biotech. 2003). Trends in Biotechnology (2004), 22 (6), 261-265.

Daniel Segre' and Doron Lancet. Theoretical and computational approaches to the study of the origins of life. In Origins: Genesis, Evolution and Diversity of Life (2004), COLE series, Vol.6, Kluwer, J. Seckbach (ed.)

2003

Shakhnovich BE, Harvey JM, Comeau S, Lorenz D, DeLisi C, Shakhnovich E. ELISA: structure-function inferences based on statistically significant and evolutionarily inspired observations. BMC Bioinformatics. 2003 Sep 2;4(1):34. [Abstract] [Full Text]

Wu J, Kasif S, DeLisi C. Identification of functional links between genes using phylogenetic profiles. Bioinformatics. 2003 Aug 12;19(12):1524-30. [Abstract] [Full Text (pdf)]

Powell CA, Spira A, Derti A, DeLisi C, Liu G, Borczuk A, Busch S, Sahasrabudhe S, Chen Y, Sugarbaker D, Bueno R, Richards WG, Brody JS. Gene expression in lung adenocarcinomas of smokers and nonsmokers. Am J Respir Cell Mol Biol. 2003 Aug;29(2):157-62. Epub 2003 Feb 21. [Abstract] [Full Text]

Shakhnovich BE, Dokholyan NV, DeLisi C, Shakhnovich EI. Functional fingerprints of folds: evidence for correlated structure-function evolution. J Mol Biol. 2003 Feb 7;326(1):1-9. [Full Text]

Bhanot G, Louzoun Y, Zhu J, DeLisi C. The importance of thermodynamic equilibrium for high throughput gene expression arrays. Biophys J. 2003 Jan;84(1):124-35. [Abstract] [Full Text]

Peters, B., Tong, W., Sidney, J., Sette, A. & Weng, Z. (2003) Examining the Independent Binding Assumption for Binding of Peptide Epitopes to MHC-I Molecules. Bioinformatics. 19:1765-1772.

Halees, A.S., Leyfer, D. & Weng, Z. (2003) PromoSer: A Larger-scale Mammalian Promoter and Transcription Start Site Identification Service. Nucleic Acids Res. 2003 Jul 1;31(13):3554-9.

Frith, M.C., Li, M.C. & Weng, Z. (2003) Cluster-Buster: Finding Dense Clusters of Motifs in DNA Sequences. Nucleic Acids Res. 2003 Jul 1;31(13):3666-8.

Li, L.*, Chen, R.* & Weng, Z. (2003) *Joint First Authors RDOCK: Refinement of Rigid-body Protein Docking Predictions. Proteins. 53:693-707.

Mintseris, J. & Weng, Z. (2003) Atomic Contact Vectors in Protein-Protein Recognition. Proteins. 53:629-639.

Chen, R., Tong, W., Mintseris, J., Li, L. & Weng, Z. (2003) ZDOCK Predictions for the CAPRI Challenge. Proteins. 2003 Jul 1;52(1):68-73.

Chen, R., Li, L. & Weng, Z. (2003) ZDOCK: An Initial-stage Protein Docking Algorithm. Proteins. 2003 Jul 1;52(1):80-7.

Chen, R., Mintseris, J., Janin, J. & Weng, Z. (2003) A Protein-Protein Docking Benchmark. Proteins. 2003 Jul 1;52(1):88-91.

Chen, R. & Weng, Z. (2003) A Novel Shape Complementarity Scoring Function For Protein-Protein Docking. Proteins. 2003 May 15;51(3):397-408.

Hu, Z., Frith, M., Niu, T. & Weng, Z. (2003) SeqVISTA: A Graphical Tool for Sequence Feature Visualization and Comparison BMC Bioinformatics 4: 1.

J.C. Prasad, S.R. Comeau, S. Vajda and C.J. Camacho. Consensus alignment for reliable framework prediction in homology modeling. BIOINFORMATICS Vol. 19 no. 13 2003, pages 1682-1691.

Michael Silberstein, Sheldon Dennis, Lawrence Brown, Tamas Kortvelyesi Karl Clodfelter and Sandor Vajda. Identification of Substrate Binding Sites in Enzymes by Computational Solvent Mapping. J. Mol. Biol., 332, 1095-113, 2003.

Janin J, Henrick K, Moult J, Eyck L, Sternberg M, Vajda S, Vakser I, and Wodak S. CAPRI: A critical assessment of predicted interactions. Proteins, 52:2-9, 2003.

Murphy J, Gatchell D, Prasad J, and Vajda S. Combination of scoring functions improves discrimination in protein-protein docking. Proteins, 3 :840-854, 2003.

Kortvelyesi T, Silberstein M, Dennis S, and Vajda S. Improved mapping of protein binding sites. Journal of Computer-Aided Molecular Design, 17: 173-186, 2003.

Kortvelyesi T, Dennis S, Silberstein M, Brown III L, and Vajda S. Algorithms for computational solvent mapping of proteins. Proteins, 51: 340-351, 2003.

Camacho C, and Gatchell D. Successful discrimination of protein interactions. Proteins, 52:92-97, 2003.

G. Benson. Composition Alignment, Proceedings of the Workshop on Algorithms in Bioinformatics 2003, Budapest, Hungary, September 2003.

Daniel Segrè, Jeremy Zucker, Jeremy Katz, Xiaoxia Lin, Patrik D'haeseleer, Wayne P. Rindone, Peter Kharchenko, Dat Nguyen, Matthew A. Wright and George M. Church. From annotated genomes to metabolic flux models and kinetic parameter fitting. Omics (2003), 7(3), 301-316.

Daniel Segre', Dennis Vitkup and George Church. Analysis of optimality in natural and perturbed metabolic networks. Proc. Natl. Acad. Sci. USA (2002), 99(23), 15112-15117.

Barak Shenhav, Daniel Segre' and Doron Lancet. Mesobiotic emergence: molecular and ensemble complexity in early evolution. Advances in Complex Systems (2003), 6 (1), 15-35.

2002

Yanai I, DeLisi C. The society of genes: networks of functional links between genes from comparative genomics. Genome Biol. 2002 Oct 25;3(11):research0064. Epub 2002 Oct 25. [Abstract] [Full Text]

Kasif S, Weng Z, Derti A, Beigel R, DeLisi C. A computational framework for optimal masking in the synthesis of oligonucleotide microarrays. Nucleic Acids Res. 2002 Oct 15;30(20):e106. [Abstract] [Full Text]

Harrison R, DeLisi C. Condition specific transcription factor binding site characterization in Saccharomyces cerevisiae. Bioinformatics. 2002 Oct;18(10):1289-96. [Abstract] [Full Text (pdf)]

Yanai I, Mellor JC, DeLisi C. Identifying functional links between genes using conserved chromosomal proximity. Trends Genet. 2002 Apr;18(4):176-9. [Full Text]

Mellor JC, Yanai I, Clodfelter KH, Mintseris J, DeLisi C. Predictome: a database of putative functional links between proteins. Nucleic Acids Res. 2002 Jan 1;30(1):306-9. [Abstract] [Full Text]

Weng Z, DeLisi C. Protein therapeutics: promises and challenges for the 21st century. Trends Biotechnol. 2002 Jan;20(1):29-35. Review. [Full Text]

Harrison R, DeLisi C. A hypothesis driven approach to condition specific transcription factor binding site characterization in S.C. SAC 2002:151-158.

Yanai I, Mellor JC, DeLisi C. Beyond Sequence Similarity: Functional Analysis in the Age of the Genome. Evolution of Genomic Technologies, Functional Genomics Series, vol 1, eds. McCormack S, Galas D. 2002.

Kasif, S., Weng, Z. Derti, A., Beigel, R. & DeLisi, C. (2002) A Computational Framework for Optimal Masking in the Synthesis of Oligonucleotide Microarrays. Nucleic Acid Research 30(20): e106.

Wong, J. Y., Weng, Z., Moll, S., Kim, S. & Brown, C. (2002) Identification and validation of a novel cell-recognition site (KNEED) on the 8th type III domain of fibronectin. Biomaterials 23: 3865-3870.

Brown, C.T., Weng, Z., Zhang, H. & Wong, J.Y. (2002) Mutational Analysis Verifies that "KNEED" Sequence of Fibronectin Participates in Cell-substrate Interactions. Polym. Prep. 43(2): 754.

Frith, M.C., Hansen, U. & Weng, Z. (2002) A Gibbs Sampling Algorithm to Detect Clustered Cis-elements. Proceedings of the Third International Conference on Bioinformatics of Genome Regulation and Structure (1) 59-61.

Anderson, R. & Weng, Z. Bioinformatics. Encyclopedia of Sciences, 2002.

J.D. Szustakowski and Z. Weng. (2002) K2: Protein structure comparison and their statistical significance. Evolutionary Computation in Bioinformatics. Edited by G. Fogel and D. Corne, Morgan Kaufman.

Betley JN, Frith MC, Graber JH, Choo S, Deshler JO. (2002) A ubiquitous and conserved signal for RNA localization in chordates. Curr Biol. 12(20):1756-61.

Yu Zheng, Joseph D. Szustakowski, Lance Fortnow, Rich Roberts, Simon Kasif. (2002) Computational identification of operons in microbial genomes. Genome Research 12(8):1221-30.

Martin C. Frith, John L. Spouge, Ulla Hansen, Zhiping Weng. (2002) Statistical significance of clusters of motifs represented by position specific scoring matrices in nucleotide sequences. Nucleic Acids Research 30(14):3214-24.

Chen, R. & Weng, Z. (2002) Docking Unbound Proteins Using Shape Complementarity, Desolvation, and Electrostatics. Proteins: Structure, Function, and Genetics. 47:281-294.

Barbara L. Resendes, Nahid G. Robertson, Joseph D. Szustakowski, Robert J. Resendes, Zhiping Weng, and Cynthia C. Morton (2002) Gene Discovery in the Auditory System: Characterization of Additional Cochlear-Expressed Sequences Journal of the Association for Research in Otolaryngology 3(1):45-53. Haverty, PM., Weng, Z., Hsiao, L., Best, N., Auerbach, K., Jensen, RV., Gullans, SR. (2002) HugeIndex: A Database of High Density Oligonucleotide Array Data from Normal Human Tissues Nucleic Acids Research. 30(1): 214-217.

Camacho C, and Vajda S. Protein-protein association kinetics and protein docking. Curr Opin Struct Biol. 12(1):36-40, 2002.

Dennis S, Kortvelyesi T, and Vajda S. Computational mapping identifies the binding sites of organic solvents on proteins. Proc. Natl. Acad. Sci. USA. 99(7): 4290-4295, 2002.

Dennis S, and Vajda S. Semi-global simplex optimization and its application to determining the preferred solvation sites of proteins. J. Comp. Chem. 23(3): 319-334, 2002.

Peter P. Valko, and Sandor Vajda. Inversion of Noise-free Laplace Transforms: Towards a Standardized Set of Test Problems. Inverse Problems in Engineering Volume 10, Number 5, Year 2002, pp. 467 - 483.

G. Benson. A new distance measure for comparing sequence profiles based on path lengths along an entropy surface, Proceedings of the European Conference on Computational Biology 2002, Bioinformatics, 18: Supplement 2, S44-S52, 2002.

D. Marras, L. Bruggeman, N. Tanji, M. Mansukhani, A. Cara, M. Ross, G. Benson, V. D'Agati, M. Klotman, and P. Klotman. Evolution of HIV-1 quasispecies in kidney epithelium in HIV-associated nephropathy, Nature Medicine, 8:522-526, 2002.

J. Walewski, J. Gutierrez, W. Branch-Elliman, D. Stump, T. Keller, A. Rodriguez, G. Benson, and A. Branch. Mutation Master: Profiles of Substitutions in Hepatitis C Virus RNA of the Core, Alternate Reading Frame and NS2 Coding Regions, RNA, 8:557-571, 2002.

2001

Yanai I, Derti A, DeLisi C. Genes linked by fusion events are generally of the same functional category: a systematic analysis of 30 microbial genomes. Proc Natl Acad Sci U S A. 2001 Jul 3;98(14):7940-5. [Abstract] [Full Text]

Zhang C, DeLisi C. Protein folds: molecular systematics in three dimensions. Cell Mol Life Sci. 2001 Jan;58(1):72-9. Review. [Abstract]

Gulukota K, DeLisi C. Neural network method for predicting peptides that bind major histocompatibility complex molecules. Methods Mol Biol. 2001;156:201-9.

Weng, Z. (2001) Bioinformatics. Macmillan's Biology.

Frith, MC., Hansen, U., Weng, Z. (2001) Detection of cis-element clusters in higher eukaryotic DNA Bioinformatics 17(10):878-889.

Hsiao, L.L., Dangond, F., Yoshida, T., Hong, R., Jensen, R.V., Misra, J., Dillon, W., Lee, K.F., Clark, K.E., Haverty, P., Weng, Z., Mutter, G.L., Frosch, M.P., Macdonald, M.E., Milford, E.L., Crum, C.P., Bueno, R., Pratt, R.E., Mahadevappa, M., Warrington, J.A., Stephanopoulos, G., Stephanopoulos, G., Gullans, S.R. (2001) A Compendium of Gene Expression in Normal Human Tissues. Physiological Genomics. 7: 97-104.

Lander ES, Szustakowski J,et al. (2001) Initial sequencing and analysis of the human genome. Nature 409(6822):860-921.

Camacho C, and Vajda S. Protein docking along smooth association pathways. Proc. Natl. Acad. Sci. USA. 98: 10636-10641, 2001.

Kimura R, Brower R, Vajda S, and Camacho C. Dynamical view of the positions of key side chains in protein-protein recognition. Biophys. J., 80: 635-642, 2001.

G. Benson. Tandem Cyclic Alignment. Proceedings of the 12th Annual Symposium on Combinatorial Pattern Matching (CPM 2001), LNCS, 2089:118-130, 2001.

P. Le Fleche, Y. Hauck, L. Onteniente, A. Prieur, F. Denoeud, V. Ramisse, P. Sylvestre, G. Benson, F. Ramisse, G. Vergnaud. A Tandem Repeats Database for Bacterial Genomes: Application to the Genotyping of Yersinia pestis and Bacillus anthracis. BioMed Central Microbiology 1:2-15, 2001.

Daniel Segre', Barak Shenhav, Ron Kafri and Doron Lancet. The molecular roots of compositional inheritance. Journal of Theoretical Biology (2001), 213, 481-491.

Daniel Segre', Dafna Ben-Eli, David Deamer and Doron Lancet. The Lipid World. Origins Life Evol. Biosphere (2001) 31, 119-145.

2000

Yanai I, Camacho CJ, DeLisi C. Predictions of gene family distributions in microbial genomes: evolution by gene duplication and modification. Phys Rev Lett. 2000 Sep 18;85(12):2641-4. [Abstract]

Camacho CJ, Kimura SR, DeLisi C, Vajda S. Kinetics of desolvation-mediated protein-protein binding. Biophys J. 2000 Mar;78(3):1094-105. [Abstract] [Full Text]

DeLisi C. The First Technological Revolution of the 21st Century. J. Biolaw and Business. 2000. [Abstract]

Weng Z, DeLisi C. Amino Acid Substitutions: Effects on Protein Stability. Encylopedia of Life Sciences. 2000.

Szustakowski JD, Weng Z (2000) Protein structure alignment using a genetic algorithm. Proteins. 38(4):428-40.

Dennis S, Camacho CJ, and Vajda S. Continuum electrostatic analysis of preferred solvation sites around proteins in solution. Proteins, 38: 176-188, 2000.

Camacho C, Kimura SR, DeLisi C, and Vajda S. Kinetics of desolvation-mediated protein-protein binding. Biophys. J., 78: 1094-1105, 2000.

Camacho C, Gatchell D, Kimura R, and Vajda S. Scoring docked conformations generated by rigid body protein-protein docking. Proteins, 40: 525-537, 2000.

Gatchell D, Dennis S, and Vajda S. Discrimination of near-native protein structures from misfolded models by empirical free energy functions. Proteins, 41: 518-534, 2000.

F. Denoeud, G. Vergnaud and G. Benson. Predicting Human Minisatellite Polymorphism, Genome Research, 13(5):856-867, 2000.

Yoav Gilad, Daniel Segre', Karl Skorecki, Michael W. Nachman, Doron Lancet and Dror Sharon. Dichotomy of single-nucleotide polymorphism haplotypes in olfactory receptor genes and pseudogenes. Nature Genetics (2000) 26, 221-224.

Daniel Segre', Dafna Ben-Eli and Doron Lancet. Compositional genomes: prebiotic information transfer in mutually catalytic noncovalent assemblies. Proc. Natl. Acad. Sci. USA (2000), 97(8), 4112-4117.

Daniel Segre', Dafna Ben-Eli and Doron Lancet. Prebiotic evolution of amphiphilic assemblies far from equilibrium: from compositional information to sequence-based biopolymers. Astronomical Society of the Pacific Conference Series Vol.213, Sheridan Books, Michigan, 2000, 373-378.

Daniel Segre' and Doron Lancet. Composing Life. EMBO Reports (2000), 1(3), 217-222.