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Charles DeLisi - Publications

Affiliations: 
1969-1972 Chemistry Yale University, New Haven, CT 
 1972-1977 Los Alamos National Laboratory, Los Alamos, NM, United States 
 1977-1985 National Institutes of Heath, Bethesda, MD 
 1985-1987 Department of Energy, Washington, DC 
 1987-1890 Mount Sinai School of Medicine, New York, NY 
 1990- Biomedical Engineering Boston University, Boston, MA 
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Year Citation  Score
2023 Kishore D, Birzu G, Hu Z, DeLisi C, Korolev KS, Segrè D. Inferring microbial co-occurrence networks from amplicon data: a systematic evaluation. Msystems. e0096122. PMID 37338270 DOI: 10.1128/msystems.00961-22  0.763
2020 DeLisi C, Patrinos A, MacCracken M, Drell D, Annas G, Arkin A, Church G, Cook-Deegan R, Jacoby H, Lidstrom M, Melillo J, Milo R, Paustian K, Reilly J, Roberts RJ, et al. The Role of Synthetic Biology in Atmospheric Greenhouse Gas Reduction: Prospects and Challenges. Biodesign Research. 2020: 1016207. PMID 37849905 DOI: 10.34133/2020/1016207  0.608
2016 Chen HR, Sherr DH, Hu Z, DeLisi C. A network based approach to drug repositioning identifies plausible candidates for breast cancer and prostate cancer. Bmc Medical Genomics. 9: 51. PMID 27475327 DOI: 10.1186/S12920-016-0212-7  0.688
2016 Granger BR, Chang YC, Wang Y, DeLisi C, Segrè D, Hu Z. Visualization of Metabolic Interaction Networks in Microbial Communities Using VisANT 5.0. Plos Computational Biology. 12: e1004875. PMID 27081850 DOI: 10.1371/Journal.Pcbi.1004875  0.769
2015 Liu Y, Hu Z, DeLisi C. Mutated pathways as a guide to adjuvant therapy treatments for breast cancer. Molecular Cancer Therapeutics. PMID 26625895 DOI: 10.1158/1535-7163.Mct-15-0601  0.688
2015 Liu Y, Tian F, Hu Z, DeLisi C. Evaluation and integration of cancer gene classifiers: identification and ranking of plausible drivers. Scientific Reports. 5: 10204. PMID 25961669 DOI: 10.1038/Srep10204  0.743
2015 Liu Y, Tian F, Hu Z, Delisi C. Evaluation and integration of cancer gene classifiers: Identification and ranking of plausible drivers Scientific Reports. 5. DOI: 10.1038/srep10204  0.715
2013 Anton BP, Chang YC, Brown P, Choi HP, Faller LL, Guleria J, Hu Z, Klitgord N, Levy-Moonshine A, Maksad A, Mazumdar V, McGettrick M, Osmani L, Pokrzywa R, Rachlin J, ... ... DeLisi C, et al. The COMBREX project: design, methodology, and initial results. Plos Biology. 11: e1001638. PMID 24013487 DOI: 10.1371/Journal.Pbio.1001638  0.77
2013 Hu Z, Chang YC, Wang Y, Huang CL, Liu Y, Tian F, Granger B, Delisi C. VisANT 4.0: Integrative network platform to connect genes, drugs, diseases and therapies. Nucleic Acids Research. 41: W225-31. PMID 23716640 DOI: 10.1093/Nar/Gkt401  0.781
2013 Yang TH, Kon M, DeLisi C. Genome-wide association studies. Methods in Molecular Biology (Clifton, N.J.). 939: 233-51. PMID 23192550 DOI: 10.1007/978-1-62703-107-3_15  0.775
2012 Ahn S, Huang CL, Ozkumur E, Zhang X, Chinnala J, Yalcin A, Bandyopadhyay S, Russek S, Unlü MS, DeLisi C, Irani RJ. TATA binding proteins can recognize nontraditional DNA sequences. Biophysical Journal. 103: 1510-7. PMID 23062343 DOI: 10.1016/J.Bpj.2012.08.030  0.776
2012 Kim S, Kon M, DeLisi C. Pathway-based classification of cancer subtypes. Biology Direct. 7: 21. PMID 22759382 DOI: 10.1186/1745-6150-7-21  0.744
2012 Huang CL, Lamb J, Chindelevitch L, Kostrowicki J, Guinney J, Delisi C, Ziemek D. Correlation set analysis: detecting active regulators in disease populations using prior causal knowledge. Bmc Bioinformatics. 13: 46. PMID 22443377 DOI: 10.1186/1471-2105-13-46  0.75
2012 Shigemizu D, Hu Z, Hung JH, Huang CL, Wang Y, DeLisi C. Using functional signatures to identify repositioned drugs for breast, myelogenous leukemia and prostate cancer. Plos Computational Biology. 8: e1002347. PMID 22346740 DOI: 10.1371/Journal.Pcbi.1002347  0.778
2012 Hung JH, Yang TH, Hu Z, Weng Z, DeLisi C. Gene set enrichment analysis: performance evaluation and usage guidelines. Briefings in Bioinformatics. 13: 281-91. PMID 21900207 DOI: 10.1093/Bib/Bbr049  0.791
2011 Yang TH, Kon M, Hung JH, Delisi C. Combinations of newly confirmed Glioma-Associated loci link regions on chromosomes 1 and 9 to increased disease risk. Bmc Medical Genomics. 4: 63. PMID 21827660 DOI: 10.1186/1755-8794-4-63  0.773
2011 Roberts RJ, Chang YC, Hu Z, Rachlin JN, Anton BP, Pokrzywa RM, Choi HP, Faller LL, Guleria J, Housman G, Klitgord N, Mazumdar V, McGettrick MG, Osmani L, Swaminathan R, ... ... Delisi C, et al. COMBREX: a project to accelerate the functional annotation of prokaryotic genomes. Nucleic Acids Research. 39: D11-4. PMID 21097892 DOI: 10.1093/Nar/Gkq1168  0.775
2010 Linghu B, DeLisi C. Phenotypic connections in surprising places. Genome Biology. 11: 116. PMID 20423531 DOI: 10.1186/Gb-2010-11-4-116  0.737
2010 Hung JH, Whitfield TW, Yang TH, Hu Z, Weng Z, DeLisi C. Identification of functional modules that correlate with phenotypic difference: the influence of network topology. Genome Biology. 11: R23. PMID 20187943 DOI: 10.1186/Gb-2010-11-2-R23  0.795
2010 Ozkumur E, Ahn S, Yalçin A, Lopez CA, Cevik E, Irani RJ, DeLisi C, Chiari M, Unlü MS. Label-free microarray imaging for direct detection of DNA hybridization and single-nucleotide mismatches. Biosensors & Bioelectronics. 25: 1789-95. PMID 20097056 DOI: 10.1016/J.Bios.2009.12.032  0.771
2009 Linghu B, Snitkin ES, Hu Z, Xia Y, Delisi C. Genome-wide prioritization of disease genes and identification of disease-disease associations from an integrated human functional linkage network. Genome Biology. 10: R91. PMID 19728866 DOI: 10.1186/Gb-2009-10-9-R91  0.781
2009 Hu Z, Hung JH, Wang Y, Chang YC, Huang CL, Huyck M, Delisi C. VisANT 3.5: Multi-scale network visualization, analysis and inference based on the gene ontology Nucleic Acids Research. 37. PMID 19465394 DOI: 10.1093/Nar/Gkp406  0.795
2009 Tadigotla V, Alexe G, Sethi N, Bilal E, Huang C, Monti S, Tamayo P, DeLisi C, Bhanot G, Ganesan S. NF-κB Activation in Breast Cancer Occurs Via Different Mechanisms in Triple Negative and HER2+ Tumors with Lymphocytic Infiltrate. Cancer Research. 69: 1164-1164. DOI: 10.1158/0008-5472.Sabcs-09-1164  0.726
2008 Bergstein DA, Ozkumur E, Wu AC, Yalçin A, Colson JR, Needham JW, Irani RJ, Gershoni JM, Goldberg BB, Delisi C, Ruane MF, Unlü MS. Resonant Cavity Imaging: A Means Toward High-Throughput Label-Free Protein Detection. Ieee Journal of Selected Topics in Quantum Electronics : a Publication of the Ieee Lasers and Electro-Optics Society. 14: 131-139. PMID 19823593 DOI: 10.1109/Jstqe.2007.913397  0.763
2008 Unlü MS, Ozkumur IE, Needham J, Bergstein DA, Goldberg BB, Yalcin A, Spuhler P, Irani R, DeLisi C. Applications of optical resonance to biological imaging and label-free protein microarrays. Conference Proceedings : ... Annual International Conference of the Ieee Engineering in Medicine and Biology Society. Ieee Engineering in Medicine and Biology Society. Annual Conference. 2008: 2643. PMID 19163247 DOI: 10.1109/IEMBS.2008.4649744  0.768
2008 Dalgin GS, Drever M, Williams T, King T, DeLisi C, Liou LS. Identification of novel epigenetic markers for clear cell renal cell carcinoma. The Journal of Urology. 180: 1126-30. PMID 18639284 DOI: 10.1016/J.Juro.2008.04.137  0.757
2008 Holloway DT, Kon M, DeLisi C. In silico regulatory analysis for exploring human disease progression. Biology Direct. 3: 24. PMID 18564415 DOI: 10.1186/1745-6150-3-24  0.785
2008 Holloway DT, Kon M, DeLisi C. Classifying transcription factor targets and discovering relevant biological features. Biology Direct. 3: 22. PMID 18513408 DOI: 10.1186/1745-6150-3-22  0.8
2008 Hu Z, Snitkin ES, DeLisi C. VisANT: an integrative framework for networks in systems biology. Briefings in Bioinformatics. 9: 317-25. PMID 18463131 DOI: 10.1093/Bib/Bbn020  0.787
2008 Linghu B, Snitkin ES, Holloway DT, Gustafson AM, Xia Y, DeLisi C. High-precision high-coverage functional inference from integrated data sources. Bmc Bioinformatics. 9: 119. PMID 18298847 DOI: 10.1186/1471-2105-9-119  0.768
2007 Dalgin GS, Holloway DT, Liou LS, DeLisi C. Identification and characterization of renal cell carcinoma gene markers. Cancer Informatics. 3: 65-92. PMID 19455236 DOI: 10.4137/Cin.S0  0.785
2007 Holloway DT, Kon M, Delisi C. Machine learning for regulatory analysis and transcription factor target prediction in yeast. Systems and Synthetic Biology. 1: 25-46. PMID 19003435 DOI: 10.1007/S11693-006-9003-3  0.804
2007 Alexe G, Dalgin GS, Scanfeld D, Tamayo P, Mesirov JP, Ganesan S, Delisi C, Bhanot G. Breast cancer stratification from analysis of micro-array data of micro-dissected specimens. Genome Informatics. International Conference On Genome Informatics. 18: 130-40. PMID 18546481 DOI: 10.11234/Gi1990.18.130  0.789
2007 Alexe G, Dalgin GS, Scanfeld D, Tamayo P, Mesirov JP, DeLisi C, Harris L, Barnard N, Martel M, Levine AJ, Ganesan S, Bhanot G. High expression of lymphocyte-associated genes in node-negative HER2+ breast cancers correlates with lower recurrence rates. Cancer Research. 67: 10669-76. PMID 18006808 DOI: 10.1158/0008-5472.Can-07-0539  0.782
2007 Alexe G, Dalgin GS, Ganesan S, Delisi C, Bhanot G. Analysis of breast cancer progression using principal component analysis and clustering. Journal of Biosciences. 32: 1027-39. PMID 17914245 DOI: 10.1007/S12038-007-0102-4  0.783
2007 Dalgin GS, Alexe G, Scanfeld D, Tamayo P, Mesirov JP, Ganesan S, DeLisi C, Bhanot G. Portraits of breast cancer progression. Bmc Bioinformatics. 8: 291. PMID 17683614 DOI: 10.1186/1471-2105-8-291  0.77
2007 Hu Z, Ng DM, Yamada T, Chen C, Kawashima S, Mellor J, Linghu B, Kanehisa M, Stuart JM, DeLisi C. VisANT 3.0: new modules for pathway visualization, editing, prediction and construction. Nucleic Acids Research. 35: W625-32. PMID 17586824 DOI: 10.1093/Nar/Gkm295  0.778
2007 Reddy TE, DeLisi C, Shakhnovich BE. Binding site graphs: a new graph theoretical framework for prediction of transcription factor binding sites. Plos Computational Biology. 3: e90. PMID 17500587 DOI: 10.1371/Journal.Pcbi.0030090  0.793
2007 Hu Z, Mellor J, Wu J, Kanehisa M, Stuart JM, DeLisi C. Towards zoomable multidimensional maps of the cell. Nature Biotechnology. 25: 547-54. PMID 17483841 DOI: 10.1038/Nbt1304  0.796
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 Research. 35: e20. PMID 17204484 DOI: 10.1093/Nar/Gkl1062  0.797
2007 Kirca G, Holloway DT, Kang JS, Shen L, Drever M, Lee C, Delisi C, Liou LS. 449: Hypermethylation of Genes in Clear Cell Carcinoma of the Kidney. Utilization of Novel Bioinformatics Methods and Correlation with Protein Expression Journal of Urology. 177: 150-151. DOI: 10.1016/S0022-5347(18)30702-X  0.79
2006 Wang YE, DeLisi C. Inferring protein-protein interactions in viral proteins by co-evolution of conserved side chains. Genome Informatics. International Conference On Genome Informatics. 17: 23-35. PMID 17503353 DOI: 10.11234/Gi1990.17.23  0.622
2006 Gustafson AM, Snitkin ES, Parker SC, DeLisi C, Kasif S. Towards the identification of essential genes using targeted genome sequencing and comparative analysis. Bmc Genomics. 7: 265. PMID 17052348 DOI: 10.1186/1471-2164-7-265  0.797
2006 Snitkin ES, Gustafson AM, Mellor J, Wu J, DeLisi C. Comparative assessment of performance and genome dependence among phylogenetic profiling methods. Bmc Bioinformatics. 7: 420. PMID 17005048 DOI: 10.1186/1471-2105-7-420  0.784
2006 Mellor J, DeLisi C. An equilibrium partitioning model connecting gene expression and cis-motif content. Bioinformatics (Oxford, England). 22: e368-74. PMID 16873495 DOI: 10.1093/Bioinformatics/Btl253  0.637
2006 Mellor J, DeLisi C. The interaction map of yeast: terra incognita? Journal of Biology. 5: 10. PMID 16762048 DOI: 10.1186/Jbiol44  0.58
2006 Wu J, Hu Z, DeLisi C. Gene annotation and network inference by phylogenetic profiling. Bmc Bioinformatics. 7: 80. PMID 16503966 DOI: 10.1186/1471-2105-7-80  0.728
2006 Alexe G, Dalgin G, Ramaswamy R, Delisi C, Bhanot G. Data Perturbation Independent Diagnosis and Validation of Breast Cancer Subtypes Using Clustering and Patterns Cancer Informatics. 2: 117693510600200. DOI: 10.1177/117693510600200006  0.774
2006 Holloway DT, Kon MA, DeLisi C. Machine learning methods for transcription data integration Ibm Journal of Research and Development. 50: 631-643. DOI: 10.1147/Rd.506.0631  0.803
2005 Wang YE, Zhang C, Berzofsky J, DeLisi C. Selecting stable molecular targets for treatment and prevention of AIDS. Genome Informatics. International Conference On Genome Informatics. 16: 254-61. PMID 16362928 DOI: 10.11234/Gi1990.16.254  0.631
2005 Dalgin GS, DeLisi C. Simple discriminant functions identify small sets of genes that distinguish cancer phenotype from normal. Genome Informatics. International Conference On Genome Informatics. 16: 245-53. PMID 16362927  0.794
2005 Wu J, Mellor JC, DeLisi C. Deciphering protein network organization using phylogenetic profile groups. Genome Informatics. International Conference On Genome Informatics. 16: 142-9. PMID 16362916 DOI: 10.11234/Gi1990.16.142  0.621
2005 Holloway DT, Kon M, DeLisi C. Integrating genomic data to predict transcription factor binding. Genome Informatics. International Conference On Genome Informatics. 16: 83-94. PMID 16362910 DOI: 10.11234/Gi1990.16.83  0.803
2005 Reddy TE, DeLisi C, Shakhnovich BE. Assessing transcription factor motif drift from noisy decoy sequences. Genome Informatics. International Conference On Genome Informatics. 16: 59-67. PMID 16362907 DOI: 10.11234/Gi1990.16.59  0.786
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 Research. 33: W352-7. PMID 15980487 DOI: 10.1093/Nar/Gki431  0.783
2005 Shakhnovich BE, Deeds E, Delisi C, Shakhnovich E. Protein structure and evolutionary history determine sequence space topology. Genome Research. 15: 385-92. PMID 15741509 DOI: 10.1101/Gr.3133605  0.758
2004 Hu Z, Mellor J, DeLisi C. Analyzing networks with VisANT. Current Protocols in Bioinformatics / Editoral Board, Andreas D. Baxevanis ... [Et Al.]. Unit 8.8. PMID 18428738 DOI: 10.1002/0471250953.Bi0808S08  0.776
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 Informatics. International Conference On Genome Informatics. 15: 221-8. PMID 15712124  0.789
2004 Shakhnovich BE, Harvey JM, Delisi C. ELISA: a unified, multidimensional view of the protein domain universe. Genome Informatics. International Conference On Genome Informatics. 15: 213-20. PMID 15712123 DOI: 10.11234/Gi1990.15.213  0.73
2004 Mellor JC, Wu J, Delisi C. Constructing networks with correlation maximization methods. Genome Informatics. International Conference On Genome Informatics. 15: 149-59. PMID 15712118  0.582
2004 Hu Z, Mellor J, Wu J, DeLisi C. VisANT: an online visualization and analysis tool for biological interaction data. Bmc Bioinformatics. 5: 17. PMID 15028117 DOI: 10.1186/1471-2105-5-17  0.784
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:Identification of Co-Expressed Genes through Module Gene Flow Genome Informatics. 15: 221-228. DOI: 10.11234/Gi1990.15.221  0.785
2004 Mellor JC, DeLisi C. Circuits of the cell Drug Discovery Today: Biosilico. 2: 120-126. DOI: 10.1016/S1741-8364(04)02401-1  0.615
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. 4. PMID 12952559 DOI: 10.1186/1471-2105-4-34  0.757
2003 Wu J, Kasif S, DeLisi C. Identification of functional links between genes using phylogenetic profiles. Bioinformatics (Oxford, England). 19: 1524-30. PMID 12912833 DOI: 10.1093/Bioinformatics/Btg187  0.358
2003 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. American Journal of Respiratory Cell and Molecular Biology. 29: 157-62. PMID 12600827 DOI: 10.1165/Rcmb.2002-0183Rc  0.773
2003 Shakhnovich BE, Dokholyan NV, DeLisi C, Shakhnovich EI. Functional fingerprints of folds: evidence for correlated structure-function evolution. Journal of Molecular Biology. 326: 1-9. PMID 12547186 DOI: 10.1016/S0022-2836(02)01362-1  0.735
2003 Bhanot G, Louzoun Y, Zhu J, DeLisi C. The importance of thermodynamic equilibrium for high throughput gene expression arrays. Biophysical Journal. 84: 124-35. PMID 12524270 DOI: 10.1016/S0006-3495(03)74837-1  0.311
2002 Yanai I, DeLisi C. The society of genes: networks of functional links between genes from comparative genomics. Genome Biology. 3: research0064. PMID 12429063 DOI: 10.1186/Gb-2002-3-11-Research0064  0.653
2002 Kasif S, Weng Z, Derti A, Beigel R, DeLisi C. A computational framework for optimal masking in the synthesis of oligonucleotide microarrays. Nucleic Acids Research. 30: e106. PMID 12384608 DOI: 10.1093/Nar/Gnf105  0.782
2002 Harrison R, DeLisi C. Condition specific transcription factor binding site characterization in Saccharomyces cerevisiae. Bioinformatics (Oxford, England). 18: 1289-96. PMID 12376372 DOI: 10.1093/Bioinformatics/18.10.1289  0.61
2002 Yanai I, Mellor JC, DeLisi C. Identifying functional links between genes using conserved chromosomal proximity. Trends in Genetics : Tig. 18: 176-9. PMID 11932011 DOI: 10.1016/S0168-9525(01)02621-X  0.747
2002 Mellor JC, Yanai I, Clodfelter KH, Mintseris J, DeLisi C. Predictome: a database of putative functional links between proteins. Nucleic Acids Research. 30: 306-9. PMID 11752322 DOI: 10.1093/Nar/30.1.306  0.805
2002 Weng Z, DeLisi C. Protein therapeutics: promises and challenges for the 21st century. Trends in Biotechnology. 20: 29-35. PMID 11742675 DOI: 10.1016/S0167-7799(01)01846-7  0.512
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 Proceedings of the National Academy of Sciences of the United States of America. 98: 7940-7945. PMID 11438739 DOI: 10.1073/Pnas.141236298  0.804
2001 Zhang C, DeLisi C. Protein folds: molecular systematics in three dimensions. Cellular and Molecular Life Sciences : Cmls. 58: 72-9. PMID 11229818 DOI: 10.1007/Pl00000779  0.331
2001 Gulukota K, DeLisi C. Neural network method for predicting peptides that bind major histocompatibility complex molecules. Methods in Molecular Biology (Clifton, N.J.). 156: 201-9. PMID 11068761 DOI: 10.1385/1-59259-062-4:201  0.728
2000 Yanai I, Camacho CJ, DeLisi C. Predictions of gene family distributions in microbial genomes: evolution by gene duplication and modification. Physical Review Letters. 85: 2641-4. PMID 10978127 DOI: 10.1103/Physrevlett.85.2641  0.732
2000 Camacho CJ, Kimura SR, DeLisi C, Vajda S. Kinetics of desolvation-mediated protein-protein binding. Biophysical Journal. 78: 1094-105. PMID 10692300 DOI: 10.1016/S0006-3495(00)76668-9  0.593
1999 Camacho CJ, Weng Z, Vajda S, DeLisi C. Free energy landscapes of encounter complexes in protein-protein association. Biophysical Journal. 76: 1166-78. PMID 10049302 DOI: 10.1016/S0006-3495(99)77281-4  0.651
1999 Zhang C, Chen J, DeLisi C. Protein-protein recognition: exploring the energy funnels near the binding sites. Proteins. 34: 255-67. PMID 10022360 DOI: 10.1002/(Sici)1097-0134(19990201)34:2<255::Aid-Prot10>3.0.Co;2-O  0.415
1999 Zhang C, DeLisi C. Estimating the number of protein folds. Journal of Molecular Biology. 284: 1301-5. PMID 9878351 DOI: 10.1006/Jmbi.1998.2282  0.373
1998 Weng Z, Gulukota K, Vaughn DE, Bjorkman PJ, DeLisi C. Computational determination of the structure of rat Fc bound to the neonatal Fc receptor. Journal of Molecular Biology. 282: 217-25. PMID 9735282 DOI: 10.1006/Jmbi.1998.2020  0.76
1998 Zhang C, Anderson A, DeLisi C. Structural principles that govern the peptide-binding motifs of class I MHC molecules. Journal of Molecular Biology. 281: 929-47. PMID 9719645 DOI: 10.1006/Jmbi.1998.1982  0.725
1998 Weng Z, DeLisi C. Toward a predictive understanding of molecular recognition. Immunological Reviews. 163: 251-66. PMID 9700515 DOI: 10.1111/J.1600-065X.1998.Tb01201.X  0.508
1998 Zhang C, Kimura SR, Weng Z, Vajda S, Brower RC, Delisi C. The waters of life Journal of the Franklin Institute. 335: 213-240. DOI: 10.1016/S0016-0032(97)00020-3  0.562
1997 DeLisi C, Cantor C, Weng Z. Hedgehogs, foxes, and a new science. Nature Biotechnology. 15: 819. PMID 9306387 DOI: 10.1038/Nbt0997-819  0.556
1997 Zhang C, Cornette JL, Berzofsky JA, DeLisi C. The organization of human leucocyte antigen class I epitopes in HIV genome products: Implications for HIV evolution and vaccine design Vaccine. 15: 1291-1302. PMID 9302734 DOI: 10.1016/S0264-410X(97)00040-6  0.374
1997 Weng Z, Delisi C, Vajda S. Empirical free energy calculation: Comparison to calorimetric data Protein Science. 6: 1976-1984. PMID 9300497 DOI: 10.1002/Pro.5560060918  0.497
1997 Gulukota K, Sidney J, Sette A, DeLisi C. Two complementary methods for predicting peptides binding major histocompatibility complex molecules. Journal of Molecular Biology. 267: 1258-67. PMID 9150410 DOI: 10.1006/Jmbi.1997.0937  0.733
1997 Zhang C, Cornette JL, Delisi C. Consistency in structural energetics of protein folding and peptide recognition Protein Science. 6: 1057-1064. PMID 9144777 DOI: 10.1002/Pro.5560060512  0.383
1997 Zhang C, Vasmatzis G, Cornette JL, DeLisi C. Determination of atomic desolvation energies from the structures of crystallized proteins Journal of Molecular Biology. 267: 707-726. PMID 9126848 DOI: 10.1006/Jmbi.1996.0859  0.564
1997 Gulukota K, DeLisi C. HLA allele selection for designing peptide vaccines. Genetic Analysis : Biomolecular Engineering. 13: 81-6. PMID 8931995 DOI: 10.1016/1050-3862(95)00156-5  0.713
1996 Vasmatzis G, Zhang C, Cornette JL, DeLisi C. Computational determination of side chain specificity for pockets in class I MHC molecules Molecular Immunology. 33: 1231-1239. PMID 9129159 DOI: 10.1016/S0161-5890(96)00090-9  0.573
1996 Weng Z, Vajda S, Delisi C. Prediction of protein complexes using empirical free energy functions Protein Science. 5: 614-626. PMID 8845751 DOI: 10.1002/Pro.5560050406  0.527
1996 Sezerman U, Vajda S, Delisi C. Free energy mapping of class I MHC molecules and structural determination of bound peptides Protein Science. 5: 1272-1281. PMID 8819160 DOI: 10.1002/Pro.5560050706  0.656
1996 King BL, Vajda S, DeLisi C. Empirical free energy as a target function in docking and design: Application to HIV-1 protease inhibitors Febs Letters. 384: 87-91. PMID 8797810 DOI: 10.1016/0014-5793(96)00276-1  0.314
1996 Vasmatzis G, Cornette J, Sezerman U, DeLisi C. TcR recognition of the MHC-peptide dimer: structural properties of a ternary complex. Journal of Molecular Biology. 261: 72-89. PMID 8760503 DOI: 10.1006/Jmbi.1996.0442  0.713
1996 Frederic T, Rosenfeld R, Cantor CR, DeLisi C. RNA loop structure prediction via bond scaling and relaxation Biopolymers. 38: 769-779. PMID 8652797 DOI: 10.1002/(Sici)1097-0282(199606)38:6<769::Aid-Bip8>3.0.Co;2-P  0.765
1996 Gulukota K, Vajda S, Delisi C. Peptide docking using dynamic programming Journal of Computational Chemistry. 17: 418-428. DOI: 10.1002/(Sici)1096-987X(199603)17:4<418::Aid-Jcc4>3.0.Co;2-X  0.724
1995 Vajda S, Weng Z, Delisi C. Extracting hydrophobicity parameters from solute partition and protein mutation/unfolding experiments Protein Engineering, Design and Selection. 8: 1081-1092. PMID 8819974 DOI: 10.1093/Protein/8.11.1081  0.5
1995 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 Proceedings of the National Academy of Sciences of the United States of America. 92: 8368-8372. PMID 7667297 DOI: 10.1073/Pnas.92.18.8368  0.588
1995 Rosenfeld R, Vajda S, DeLisi C. Flexible docking and design Annual Review of Biophysics and Biomolecular Structure. 24: 677-700. PMID 7663131 DOI: 10.1146/Annurev.Bb.24.060195.003333  0.771
1995 Rosenfeld R, Zheng Q, Vajda S, DeLisi C. Flexible docking of peptides to class I major-histocompatibility-complex receptors Genetic Analysis: Biomolecular Engineering. 12: 1-21. PMID 7648466 DOI: 10.1016/1050-3862(95)00107-7  0.782
1994 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 Science : a Publication of the Protein Society. 3: 911-9. PMID 8069222 DOI: 10.1002/Pro.5560030606  0.764
1994 Zheng Q, Rosenfeld R, DeLisi C, Kyle DJ. Multiple copy sampling in protein loop modeling: computational efficiency and sensitivity to dihedral angle perturbations. Protein Science : a Publication of the Protein Society. 3: 493-506. PMID 8019420 DOI: 10.1002/Pro.5560030315  0.781
1994 Vajda S, Weng Z, Rosenfeld R, DeLisi C. Effect of conformational flexibility and solvation on receptor - Ligand binding free energies Biochemistry. 33: 13977-13988. PMID 7947806 DOI: 10.1021/Bi00251A004  0.779
1994 Vasmatzis G, Brower R, Delisi C. Predicting immunoglobulin-like hypervariable loops Biopolymers - Peptide Science Section. 34: 1669-1680. PMID 7849228 DOI: 10.1002/Bip.360341211  0.554
1993 Brower RC, Vasmatzis G, Silverman M, Delisi C. Exhaustive conformational search and simulated annealing for models of lattice peptides Biopolymers. 33: 329-334. PMID 8461447 DOI: 10.1002/Bip.360330302  0.611
1993 Vajda S, Jafri MS, Sezerman OU, DeLisi C. Necessary conditions for avoiding incorrect polypeptide folds in conformational search by energy minimization. Biopolymers. 33: 173-92. PMID 8427934 DOI: 10.1002/Bip.360330117  0.547
1993 Zheng Q, Rosenfeld R, Vajda S, DeLisi C. Determining protein loop conformation using scaling-relaxation techniques Protein Science. 2: 1242-1248. PMID 8401209 DOI: 10.1002/Pro.5560020806  0.779
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 Journal of Molecular Biology. 234: 515-521. PMID 8254656 DOI: 10.1006/Jmbi.1993.1607  0.779
1993 Sezerman U, Vajda S, Cornette J, DeLisi C. Toward computational determination of peptide-receptor structure Protein Science. 2: 1827-1843. PMID 7505681 DOI: 10.1002/Pro.5560021105  0.651
1993 Zheng Q, Rosenfeld R, Vajda S, DeLisi C. Loop closure via bond scaling and relaxation Journal of Computational Chemistry. 14: 556-565. DOI: 10.1002/Jcc.540140508  0.775
1991 Eisenfeld J, Vajda S, Sugar I, DeLisi C. Constrained optimization and protein structure determination American Journal of Physiology - Cell Physiology. 261. PMID 1872378 DOI: 10.1152/Ajpcell.1991.261.2.C376  0.668
1990 Gex-Fabry M, Marchetti F, Nakata K, DeLisi C. Identifying weak signals in the presence of noise: a new method of locating potential ligand contact residues in immunoglobulin-related molecules. Molecular Immunology. 26: 1169-78. PMID 2517315 DOI: 10.1016/0161-5890(89)90061-8  0.311
1990 Vajda S, Kataoka R, DeLisi C, Margalit H, Berzofsky JA, Cornette JL. Molecular structure and vaccine design Annual Review of Biophysics and Biophysical Chemistry. 19: 69-82. PMID 1694668 DOI: 10.1146/annurev.bb.19.060190.000441  0.65
1989 Hale PM, Cease KB, Houghten RA, Ouyang C, Putney S, Javaherian K, Margalit H, Cornette JL, Spouge JL, Delisi C, Berzofsky1 JA. T cell multideterminant regions in the human immunodeficiency virus envelope: Toward overcoming the problem of major histocompatibility complex restriction International Immunology. 1: 409-415. PMID 2484961 DOI: 10.1093/Intimm/1.4.409  0.709
1989 Cornette JL, Margalit H, DeLisi C, Berzofsky JA. Identification of T-cell epitopes and use in construction of synthetic vaccines Methods in Enzymology. 178: 611-634. PMID 2481216 DOI: 10.1016/0076-6879(89)78042-3  0.574
1987 Cornette JL, Cease KB, Margalit H, Spouge JL, Berzofsky JA, DeLisi C. Hydrophobicity scales and computational techniques for detecting amphipathic structures in proteins Journal of Molecular Biology. 195: 659-685. PMID 3656427 DOI: 10.1016/0022-2836(87)90189-6  0.709
1987 Berzofsky JA, Cornette J, Margalit H, Berkower I, Cease K, DeLisi C. Molecular features of class II MHC-restricted T-cell recognition of protein and peptide antigens: the importance of amphipathic structures. Current Topics in Microbiology and Immunology. 130: 13-24. PMID 3536326 DOI: 10.1007/978-3-642-71440-5_2  0.584
1987 Berzofsky JA, Cease KB, Cornette JL, Spouge JL, Margalit H, Berkower IJ, Good MF, Miller LH, DeLisi C. Protein antigenic structures recognized by T cells: potential applications to vaccine design. Immunological Reviews. 98: 9-52. PMID 2443443 DOI: 10.1111/J.1600-065X.1987.Tb00518.X  0.717
1987 Cease KB, Margalit H, Cornette JL, Putney SD, Robey WG, Ouyang C, Streicher HZ, Fischinger PJ, Gallo RC, DeLisi C. Helper T-cell antigenic site identification in the acquired immunodeficiency syndrome virus gp120 envelope protein and induction of immunity in mice to the native protein using a 16-residue synthetic peptide Proceedings of the National Academy of Sciences of the United States of America. 84: 4249-4253. PMID 2438696 DOI: 10.1073/Pnas.84.12.4249  0.574
1986 Klein P, Delisi C. Prediction of protein structural class from the amino acid sequence. Biopolymers. 25: 1659-72. PMID 3768479 DOI: 10.1002/Bip.360250909  0.768
1986 Greif PC, Nussinov R, Kanehisa M, Delisi C. Nonrandom recurrence of consecutive repeats in noncoding mammalian sequences Mathematical Biosciences. 81: 43-52. DOI: 10.1016/0025-5564(86)90162-8  0.489
1986 Klein P, Jacquez JA, Delisi C. Prediction of protein function by discriminant analysis Mathematical Biosciences. 81: 177-189. DOI: 10.1016/0025-5564(86)90116-1  0.772
1985 Nakata K, Kanehisa M, DeLisi C. Prediction of splice junctions in mRNA sequences. Nucleic Acids Research. 13: 5327-40. PMID 4022782 DOI: 10.1093/Nar/13.14.5327  0.776
1985 Klein P, Kanehisa M, DeLisi C. The detection and classification of membrane-spanning proteins. Biochimica Et Biophysica Acta. 815: 468-76. PMID 3838905 DOI: 10.1016/0005-2736(85)90375-X  0.772
1985 Kanehisa M, DeLisi C. The prediction of a protein and nucleic acid structure: Problems and prospects Acta Applicandae Mathematicae. 4: 115-137. DOI: 10.1007/978-94-009-5426-7_1  0.516
1984 Klein P, Kanehisa M, DeLisi C. Prediction of protein function from sequence properties. Discriminant analysis of a data base. Biochimica Et Biophysica Acta. 787: 221-6. PMID 6547351 DOI: 10.1016/0167-4838(84)90312-1  0.783
1984 Kanehisa M, Klein P, Greif P, DeLisi C. Computer analysis and structure prediction of nucleic acids and proteins. Nucleic Acids Research. 12: 417-28. PMID 6546426 DOI: 10.1093/Nar/12.1Part1.417  0.78
1984 DeLisi C, Kanehisa M. Assessing the significance of local sequence homologies Mathematical Biosciences. 69: 77-85. DOI: 10.1016/0025-5564(84)90015-4  0.499
1983 Peacock JS, Bush J, Krakauer H, Hiernaux J, DeLisi C, Barisas BG. Thymus-independent immunogenicity in vitro of the divalent antigen DNP-polyethylene oxide. Cellular Immunology. 79: 220-31. PMID 6347397 DOI: 10.1016/0008-8749(83)90065-5  0.629
1983 DeLisi C, Wiegel FW. Membrane fluidity and the probability of complement fixation. Journal of Theoretical Biology. 102: 307-22. PMID 6308354 DOI: 10.1016/0022-5193(83)90368-5  0.761
1982 Hiernaux JR, Chiang J, Baker PJ, Delisi C, Prescott B. Lack of involvement of auto-anti-idiotypic antibody in the regulation of oscillations and tolerance in the antibody response to levan. Cellular Immunology. 67: 334-45. PMID 7044574 DOI: 10.1016/0008-8749(82)90225-8  0.612
1980 Grossman Z, Asofsky R, DeLisi C. The dynamics of antibody secreting cell production: regulation of growth and oscillations in the response to T-independent antigens. Journal of Theoretical Biology. 84: 49-92. PMID 6968005 DOI: 10.1016/S0022-5193(80)81037-X  0.629
1974 Gralla J, DeLisi C. mRNA is expected to form stable secondary structures. Nature. 248: 330-2. PMID 4594696 DOI: 10.1038/248330a0  0.406
1973 Delisi C, Crothers DM. The contribution of proximity and orientation to catalytic reaction rates Biopolymers. 12: 1689-1704. DOI: 10.1002/bip.1973.360120719  0.422
1972 Delisi C, Crothers DM. Prediction of RNA secondary structure. Proceedings of the National Academy of Sciences of the United States of America. 68: 2682-5. PMID 5288243 DOI: 10.1073/Pnas.68.11.2682  0.498
1972 Delisi C, Crothers DM. Electrostatic contributions to oligonucleotide transitions. Biopolymers. 10: 2323-43. PMID 5118659 DOI: 10.1002/Bip.360101123  0.49
1972 DeLisi C, Shamos MH. On the occurrence of an exothermic transition in Achilles' heel bovine tendon. Gerontologia. 18: 22-7. PMID 5076744 DOI: 10.1159/000211916  0.601
1972 Delisi C, Shamos MH. Hydration-dependent enthalpy changes in the helix–coil transition in tendon Journal of Polymer Science Part a-2: Polymer Physics. 10: 673-683. DOI: 10.1002/Pol.1972.160100409  0.625
1971 Delisi C, Crothers DM. Theory of the influence of oligonucleotide chain conformation on double helix stability Biopolymers. 10: 1809-1827. DOI: 10.1002/bip.360101006  0.405
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