Publications by Year:

| 2007 | 2006 | 2005 | 2004 | 2003 | 2002 | 2001 | 2000 |

| 1999 | 1998 | 1997 | 1996 | 1995 | 1994 | 1993 | 1992 | 1991 | 1990 |

____________________________________________________

2007

Reddy TE, Shakhnovich BE, Roberts DS, Russek SJ, DeLisi, C. Positional clustering improves computational binding site detection and identifies novel cis-regulatory sites in mammalian GABAA receptor subunit genes. Nucleic Acids Res. 2007 February;35(3):e20. [Abstract]

Reddy TE, DeLisi C, Shakhnovich, BE. Binding Site Graphs: A New Graph Theoretical Framework for Prediction of Transcription Factor Binding Sites. PLoS Computational Biology, Vol. preprint, No. 2007 (1 April 2007), e90.eor. [Abstract]
[Map of Transcription Factor Binding Motifs in S. cerevisiae]

 

2006

Holloway DT, Kon MA, DeLisi C. Machine Learning methods for transcription data integration. IBM Journal of Research and Development 50(6): 631-643 Nov 2006 [Full Text]

Gustafson AM, Snitkin ES, Parker SCJ, et al. Towards the identification of essential genes using targeted genome sequencing and comparative analysis. BMC Genomics 7:Art. No. OCT 19 2006 [Full Text]

Snitkin ES, Gustafson AM, Mellor J, et al. Comparative assessment of performance and genome dependence among phylogenetic profiling methods. BMC Bioinformatics 7: Art. No. 420 Sep 27 2006 [Full Text]

Wu J, Hu ZJ, DeLisi C. Gene annotation and network inference by phylogenetic profiling. BMC Bioinformatics 7: Art No. 80 Feb 17 2006 [Full Text]

Mellor J. and DeLisi C. An equilibrium partitioning model connecting gene expression and cis-motif content. Vol. 00 no. 00 2006, pages 1–7 doi:10.1093/bioinformatics/btl253 [Full Text]

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]

 

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]

 

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]

 

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.

 

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.

 

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.


1999

Camacho CJ, Weng Z, Vajda S, DeLisi C. Free energy landscapes of encounter complexes in protein-protein association. Biophys J. 1999 Mar;76(3):1166-78. [Abstract] [Full Text]

Zhang C, Chen J, DeLisi C. Protein-protein recognition: exploring the energy funnels near the binding sites. Proteins. 1999 Feb 1;34(2):255-67. [Abstract] [Full Text]

DeLisi C, Vajda S. Computational Problems in the Molecular Biology of the Cell. Computing in Science and Engineering, IEEE. 1999:18-26.

 

1998

Zhang C, DeLisi C. Estimating the number of protein folds. J Mol Biol. 1998 Dec 18;284(5):1301-5. [Full Text]

Weng Z, Gulukota K, Vaughn DE, Bjorkman PJ, DeLisi C. Computational determination of the structure of rat Fc bound to the neonatal Fc receptor. J Mol Biol. 1998 Sep 18;282(2):217-25. [Full Text]

Zhang C, Anderson A, DeLisi C. Structural principles that govern the peptide-binding motifs of class I MHC molecules. J Mol Biol. 1998 Sep 4;281(5):929-47. [Full Text]

Weng Z, DeLisi C. Toward a predictive understanding of molecular recognition. Immunol Rev. 1998 Jun;163:251-66. Review. [Abstract]

 

1997

DeLisi C, Cantor C, Weng Z. Hedgehogs, foxes, and a new science. Nat Biotechnol. 1997 Sep;15(9):819. [Abstract]

Weng Z, Delisi C, Vajda S. Empirical free energy calculation: comparison to calorimetric data. Protein Sci. 1997 Sep;6(9):1976-84. [Abstract] [Full Text]

Zhang C, Cornette JL, Delisi C. Consistency in structural energetics of protein folding and peptide recognition. Protein Sci. 1997 May;6(5):1057-64. [Abstract] [Full Text]

Gulukota K, Sidney J, Sette A, DeLisi C. Two complementary methods for predicting peptides binding major histocompatibility complex molecules. J Mol Biol. 1997 Apr 18;267(5):1258-67. [Full Text]

Zhang C, Vasmatzis G, Cornette JL, DeLisi C. Determination of atomic desolvation energies from the structures of crystallized proteins. J Mol Biol. 1997 Apr 4;267(3):707-26. [Full Text]

DeGroot AS, Meister GE, Cornette JL, Margalit H, DeLisi C, Berzofsky JA. Computer Prediction of T Cell Epitopes. A New Generation of Vaccines, eds. Levine MM, et al.. Marcel Dekker, New York, 1997.

Zhang C, Kimura SR, Weng Z, Vajda S, Brower R, DeLisi C. The Waters of Life. J Franklin Inst, 1997.

 

1996

Vasmatzis G, Zhang C, Cornette JL, DeLisi C. Computational determination of side chain specificity for pockets in class I MHC molecules. Mol Immunol. 1996 Nov;33(16):1231-9. [Full Text]

Gulukota K, DeLisi C. HLA allele selection for designing peptide vaccines. Genet Anal. 1996 Sep;13(3):81-6. [Abstract]

Vasmatzis G, Cornette J, Sezerman U, DeLisi C. TcR recognition of the MHC-peptide dimer: structural properties of a ternary complex. J Mol Biol. 1996 Aug 9;261(1):72-89. [Full Text]

Sezerman U, Vajda S, DeLisi C. Free energy mapping of class I MHC molecules and structural determination of bound peptides. Protein Sci. 1996 Jul;5(7):1272-81. [Abstract] [Full Text (pdf)]

Frederic T, Rosenfeld R, Cantor CR, DeLisi C. RNA loop structure prediction via bond scaling and relaxation. Biopolymers. 1996 Jun;38(6):769-79. [Abstract]

King BL, Vajda S, DeLisi C. Empirical free energy as a target function in docking and design: application to HIV-1 protease inhibitors. FEBS Lett. 1996 Apr 8;384(1):87-91. [Full Text]

Weng Z, Vajda S, Delisi C. Prediction of protein complexes using empirical free energy functions. Protein Sci. 1996 Apr;5(4):614-26. [Abstract] [Full Text (pdf)]

Gulukota K, Vajda S, DeLisi C. Peptide Docking Using Dynamic Programming. J. Computational Chemistry 17, 1996: 418-428.

 

1995

Vajda S, Weng Z, DeLisi C. Extracting hydrophobicity parameters from solute partition and protein mutation/unfolding experiments. Protein Eng. 1995 Nov;8(11):1081-92. [Abstract]

Cornette JL, Margalit H, Berzofsky JA, DeLisi C. Periodic variation in side-chain polarities of T-cell antigenic peptides correlates with their structure and activity. Proc Natl Acad Sci U S A. 1995 Aug 29;92(18):8368-72. [Abstract] [Full Text (pdf)]

Rosenfeld R, Zheng Q, Vajda S, DeLisi C. Flexible docking of peptides to class I major-histocompatibility-complex receptors. Genet Anal. 1995 Mar;12(1):1-21. [Abstract]

Rosenfeld R, Vajda S, DeLisi C. Flexible docking and design. Annu Rev Biophys Biomol Struct. 1995;24:677-700. Review. [Abstract]



1994

Vasmatzis G, Brower R, Delisi C. Predicting immunoglobulin-like hypervariable loops. Biopolymers. 1994 Dec;34(12):1669-80. [Abstract]

Vajda S, Weng Z, Rosenfeld R, DeLisi C. Effect of conformational flexibility and solvation on receptor-ligand binding free energies. Biochemistry. 1994 Nov 29;33(47):13977-88. [Abstract]

Brower RC, England R, Takeshita T, Kozlowski S, Margulies DH, Berzofsky JA, Delisi C. Minimal requirements for peptide mediated activation of CD8+ CTL. Mol Immunol. 1994 Nov;31(16):1285-93. [Abstract]

Bouzida D, Garnier J, Brower R, Cornette J, DeLisi C. Monte Carlo study of the effect of beta 2-microglobulin on the binding cleft of the HLA-A2 complex. Protein Sci. 1994 Jun;3(6):911-9. [Abstract] [Full Text (pdf)]

Zheng Q, Rosenfeld R, DeLisi C, Kyle DJ. Multiple copy sampling in protein loop modeling: computational efficiency and sensitivity to dihedral angle perturbations. Protein Sci. 1994 Mar;3(3):493-506. [Abstract] [Full Text (pdf)]

DeLisi C. Reflections on Mathematical Contributions to Understanding the Molecular Basis of Life: From 1970 to the 21st Century. Lectures in Biomathematics 100, 1994.

Vajda S, DeLisi C. An Adaptive Branch and Bound Method Based on Dynamic Programming. Protein Structure Determinations, eds. Merz K, Le Grand S, Birkhauser, Boston, 1994.

 

1993

Rosenfeld R, Zheng Q, Vajda S, DeLisi C. Computing the structure of bound peptides. Application to antigen recognition by class I major histocompatibility complex receptors. J Mol Biol. 1993 Dec 5;234(3):515-21. [Abstract]

Sezerman U, Vajda S, Cornette J, DeLisi C. Toward computational determination of peptide-receptor structure. Protein Sci. 1993 Nov;2(11):1827-43. [Abstract] [Full Text (pdf)]

Takeshita T, Kozlowski S, England RD, Brower R, Schneck J, Takahashi H, DeLisi C, Margulies DH, Berzofsky JA. Role of conserved regions of class I MHC molecules in the activation of CD8+ cytotoxic T lymphocytes by peptide and purified cell-free class I molecules. Int Immunol. 1993 Sep;5(9):1129-38. [Abstract]

Cornette JL, King BL, Silverman MD, DeLisi C. Graphical representations of the class I MHC cleft. J Mol Graph. 1993 Sep;11(3):174-9, 187. [Abstract]

Zheng Q, Rosenfeld R, Vajda S, DeLisi C. Determining protein loop conformation using scaling-relaxation techniques. Protein Sci. 1993 Aug;2(8):1242-8. [Abstract] [Full Text (pdf)]

Brower RC, Vasmatzis G, Silverman M, Delisi C. Exhaustive conformational search and simulated annealing for models of lattice peptides. Biopolymers. 1993 Mar;33(3):329-34. [Abstract]

Vajda S, Jafri MS, Sezerman OU, DeLisi C. Necessary conditions for avoiding incorrect polypeptide folds in conformational search by energy minimization. Biopolymers. 1993 Jan;33(1):173-92. [Abstract]

Cornette JL, Margalit H, DeLisi C, Berzofsky JA. The Amphipathic Helix as a Structural Feature Inolved in T-Cell Recognition. CRC Press, Boca Raton, 1993.

Qiang Z, Rosenfeld R, Vajda S, DeLisi C. Loop closer via bond scaling and relaxation. Computational Chemistry 14, 1993:556.

 

1992

Brower RC, DeLisi C. Impact of massively parallel computation on protein structure determination. Crit Rev Biomed Eng. 1992;20(5-6):373-89. [Abstract]

DeLisi C, Sezerman U, Rosenfeld R. Problems and progress on computational approaches to the molecular basis of cell recognition. 25th Jerusalem Symposium on Biochemistry and Quantum Chemistry, eds. Pullman, Jortner. Kluwer Academic Publishers, Amsterdam, 1992.

 

1991

Eisenfeld J, Vajda S, Sugar I, DeLisi C. Constrained optimization and protein structure determination. Am J Physiol. 1991 Aug;261(2 Pt 1):C376-86. [Abstract]

 

1990

Vajda S, Delisi C. Determining minimum energy conformations of polypeptides by dynamic programming. Biopolymers. 1990 Dec;29(14):1755-72. [Abstract]

Kim JE, Kojima M, Houghten R, Pendleton CD, Cornette JL, DeLisi C, Berzofsky JA. Characterization of a helper T cell epitope recognized by mice of a low responder major histocompatibility type. Mol Immunol. 1990 Oct;27(10):941-6. [Abstract]

Vajda S, Kataoka R, DeLisi C, Margalit H, Berzofsky JA, Cornette JL. Molecular structure and vaccine design. Annu Rev Biophys Biophys Chem. 1990;19:69-82. Review.

DeLisi C. Computation and the Human Genome Project. Computers and DNA, eds. Bell D, Marr T. Addison Wesley, New York, 1990:13-19.

DeLisi C. Computer Aided Prediction of Protein Structure and Function. Computers in Endocrinology: Recent Advances, eds. Guardobasso V, Rodbard D, Forti G. Raven press, 1990.

Vadja S, DeLisi C. Structural Biology and the Human Genome Project. Structure and Methods, eds. Sarma RH, Sarma MH. Adenine Press, Schenectedy, NY, 1990:7-14.