C. DeLisi

发表

Towards the identification of essential genes using targeted genome sequencing and comparative analysis

Stephen C. J. Parker, Adam M. Gustafson, S. Kasif, 2006, BMC Genomics.

Hydrophobicity scales and computational techniques for detecting amphipathic structures in proteins.

C. DeLisi, H. Margalit, J. Cornette, 1987, Journal of molecular biology.

Phenotypic connections in surprising places

C. DeLisi, B. Linghu, 2010, Genome Biology.

Integrating genomic data to predict transcription factor binding.

M. Kon, C. DeLisi, D. Holloway, 2005, Genome informatics. International Conference on Genome Informatics.

Genome-wide prioritization of disease genes and identification of disease-disease associations from an integrated human functional linkage network

E. Snitkin, C. DeLisi, B. Linghu, 2009, Genome Biology.

Prediction of protein function from sequence properties. Discriminant analysis of a data base.

M. Kanehisa, C. DeLisi, P. Klein, 1984, Biochimica et biophysica acta.

Prediction of protein structural class from the amino acid sequence

C. DeLisi, P. Klein, 1986, Biopolymers.

Protein structure and evolutionary history determine sequence space topology.

Eric J. Deeds, Boris E. Shakhnovich, C. DeLisi, 2004, Genome research.

Resonant Cavity Imaging: A Means Toward High-Throughput Label-Free Protein Detection

C. DeLisi, B. Goldberg, M. Unlu, 2008, IEEE Journal of Selected Topics in Quantum Electronics.

Prediction of splice junctions in mRNA sequences.

M. Kanehisa, C. DeLisi, K. Nakata, 1985, Nucleic acids research.

A theory of measurement error and its implications for spatial and temporal gradient sensing during chemotaxis

C. DeLisi, F. Marchetti, 1983, Cell Biophysics.

Determining minimum energy conformations of polypeptides by dynamic programming

C. DeLisi, S. Vajda, 1990, Biopolymers.

Some current mathematical topics in cancer research : George W. Swan, University Microfilms International, Ann Arbor, 1977, XXVII, 289 pp.; $16.75 (paperback).

Charles DeLisi, C. DeLisi, 1978 .

Genes linked by fusion events are generally of the same functional category: A systematic analysis of 30 microbial genomes

C. DeLisi, A. Derti, I. Yanai, 2001, Proceedings of the National Academy of Sciences of the United States of America.

Portraits of breast cancer progression

Jill P. Mesirov, Gabriela Alexe, Gyan Bhanot, 2007, BMC Bioinformatics.

A computational framework for optimal masking in the synthesis of oligonucleotide microarrays.

Z. Weng, S. Kasif, C. DeLisi, 2002, Nucleic acids research.

Protein‐protein recognition: exploring the energy funnels near the binding sites

Charles DeLisi, Jing Chen, Chao Zhang, 1999, Proteins.

Determination of atomic desolvation energies from the structures of crystallized proteins.

C. DeLisi, J. Cornette, Chao Zhang, 1997, Journal of molecular biology.

The detection and classification of membrane-spanning proteins.

C DeLisi, M Kanehisa, M. Kanehisa, 1985, Biochimica et biophysica acta.

Genome-wide association studies.

M. Kon, C. DeLisi, Tun-Hsiang Yang, 2013, Methods in molecular biology.

Combinations of newly confirmed Glioma-Associated loci link regions on chromosomes 1 and 9 to increased disease risk

M. Kon, C. DeLisi, Tun-Hsiang Yang, 2011, BMC Medical Genomics.

High expression of lymphocyte-associated genes in node-negative HER2+ breast cancers correlates with lower recurrence rates.

Gabriela Alexe, Gyan Bhanot, Charles DeLisi, 2007, Cancer research.

A network based approach to drug repositioning identifies plausible candidates for breast cancer and prostate cancer

Zhenjun Hu, Charles DeLisi, David H. Sherr, 2016, BMC Medical Genomics.

The biophysics of ligand–receptor interactions

C. DeLisi, Charles DeLisi, 1980, Quarterly Reviews of Biophysics.

Empirical free energy as a target function in docking and design: application to HIV‐1 protease inhibitors

S Vajda, C DeLisi, B L King, 1996, FEBS letters.

The importance of thermodynamic equilibrium for high throughput gene expression arrays.

G. Bhanot, C. DeLisi, Y. Louzoun, 2003, Biophysical journal.

Predictions of gene family distributions in microbial genomes: evolution by gene duplication and modification.

C. DeLisi, I. Yanai, C. Camacho, 2000, Physical review letters.

Analysis of breast cancer progression using principal component analysis and clustering

G. Bhanot, C. DeLisi, G. Alexe, 2007, Journal of Biosciences.

The society of genes: networks of functional links between genes from comparative genomics

C. DeLisi, I. Yanai, 2002, Genome Biology.

Identification of a microRNA panel for clear-cell kidney cancer.

G. Bhanot, C. DeLisi, Huiqing Liu, 2010, Urology.

The COMBREX Project: Design, Methodology, and Initial Results

Michael Y. Galperin, S. Salzberg, R. Greiner, 2013, PLoS biology.

The Human Genome Project

C. DeLisi, 1988 .

Computational Methods for Analysis of Transcriptional Regulations

M. Kon, C. DeLisi, Yue Fan, 2011 .

Free energy mapping of class I MHC molecules and structural determination of bound peptides

C. DeLisi, S. Vajda, U. Sezerman, 1996, Protein science : a publication of the Protein Society.

Free energy landscapes of encounter complexes in protein-protein association.

S Vajda, C DeLisi, C. DeLisi, 1999, Biophysical journal.

Title : Pathway-Based Classification of Cancer Subtypes Running title : Pathway-based classification of cancer subtypes

M. Kon, C. DeLisi, Shinuk Kim, 2011 .

Pathway-based classification of cancer subtypes

Charles DeLisi, Mark Kon, Shinuk Kim, 2012, Biology Direct.

Kinetics of desolvation-mediated protein-protein binding.

S Vajda, C DeLisi, C. DeLisi, 2000, Biophysical journal.

Toward a predictive understanding of molecular recognition

Z. Weng, C. DeLisi, 1998, Immunological reviews.

The kinetics of aggregation phenomena. I. Minimal models for patch formation of lymphocyte membranes.

C DeLisi, C. DeLisi, A. Perelson, 1976, Journal of theoretical biology.

Receptor cross-linking and histamine release in basophils.

C. DeLisi, R. Chabay, W. Hook, 1980, The Journal of biological chemistry.

Effect of nonspecific forces and finite receptor number on rate constants of ligand--cell bound-receptor interactions.

C DeLisi, C. DeLisi, F. W. Wiegel, 1981, Proceedings of the National Academy of Sciences of the United States of America.

THE WATERS OF LIFE

Z. Weng, C. DeLisi, S. Vajda, 1998 .

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.

C. DeLisi, J. Berzofsky, D. Margulies, 1993, International immunology.

Flexible docking of peptides to class I major-histocompatibility-complex receptors.

S Vajda, C DeLisi, C. DeLisi, 1995, Genetic analysis : biomolecular engineering.

ELISA: a unified, multidimensional view of the protein domain universe.

J. M. Harvey, C. DeLisi, B. Shakhnovich, 2004, Genome informatics. International Conference on Genome Informatics.

Data Perturbation Independent Diagnosis and Validation of Breast Cancer Subtypes Using Clustering and Patterns

C. DeLisi, G. Bhanot, C. DeLisi, 2006, Cancer informatics.

Identification and Characterization of Renal Cell Carcinoma Gene Markers

Charles DeLisi, Dustin T. Holloway, Louis S. Liou, 2007, Cancer informatics.

Computing the structure of bound peptides. Application to antigen recognition by class I major histocompatibility complex receptors.

C. DeLisi, S. Vajda, R. Rosenfeld, 1993, Journal of molecular biology.

Reflections on Mathematical Contributions to Understanding the Molecular Basis of Life: From 1970 to the 21 st Century

C. DeLisi, 1994 .

Companion Diagnostics and Cancer Biomarkers Mutated Pathways as a Guide to Adjuvant Therapy Treatments for Breast Cancer

C. DeLisi, Zhenjun Hu, Yang Liu, 2022 .

Introduction: Stochastic methods in the life sciences: General aspects and specific models

C. DeLisi, M. Iannelli, G. Koch, 1983 .

--2-- Building Transcription Factor Classifiers and Discovering Relevant Biological Features

Dustin T. Holloway, M. Kon, C. DeLisi, 2007 .

Regulatory Analysis for Exploring Human Disease Progression

Dustin T. Holloway, M. Kon, C. DeLisi, 2007 .

Immune surveillance and neoplasia—1 a minimal mathematical model

C. DeLisi, A. Rescigno, 1977 .

Assessing transcription factor motif drift from noisy decoy sequences.

Timothy E. Reddy, Boris E. Shakhnovich, C. DeLisi, 2005, Genome informatics. International Conference on Genome Informatics.

The organization of human leucocyte antigen class I epitopes in HIV genome products: implications for HIV evolution and vaccine design.

C. DeLisi, J. Cornette, J. Berzofsky, 1997, Vaccine.

The dynamics of antibody secreting cell production: regulation of growth and oscillations in the response to T-independent antigens.

C. DeLisi, Z. Grossman, R. Asofsky, 1980, Journal of theoretical biology.

Characterization of receptor affinity heterogeneity by scatchard plots

C. DeLisi, 1978 .

An analysis of the limits of resolution of binding experiments as assays for affinity heterogeneity.

C. DeLisi, A. Thakur, 1978, Immunochemistry.

Analysis of Covid-19 Data for Eight European Countries and the United Kingdom Using a Simplified SIR Model

G. Bhanot, C. DeLisi, 2020, medRxiv.

Protein therapeutics: promises and challenges for the 21st century.

Z. Weng, C. DeLisi, 2002, Trends in biotechnology.

Robust gene network analysis reveals alteration of the STAT5a network as a hallmark of prostate cancer.

G. Bhanot, C. DeLisi, Huiqing Liu, 2010, Genome informatics. International Conference on Genome Informatics.

Data Preprocessing Data normalization , Imputation Gene Filtering PCA 85 % variation k-Level Ensemble Consensus Clustering

J. Mesirov, P. Tamayo, G. Bhanot, 2007 .

Resonant cavity imaging biosensor

C. DeLisi, M. Unlu, D. A. Bergstein, 2004, 2005 IEEE LEOS Annual Meeting Conference Proceedings.

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.

C. DeLisi, H. Margalit, J. Cornette, 1987, Proceedings of the National Academy of Sciences of the United States of America.

An immunodominant epitope of the human immunodeficiency virus envelope glycoprotein gp160 recognized by class I major histocompatibility complex molecule-restricted murine cytotoxic T lymphocytes.

C. DeLisi, J. Cornette, K. Cease, 1988, Proceedings of the National Academy of Sciences of the United States of America.

T cell multideterminant regions in the human immunodeficiency virus envelope: toward overcoming the problem of major histocompatibility complex restriction.

C. DeLisi, H. Margalit, J. Cornette, 1989, International immunology.

Deciphering protein network organization using phylogenetic profile groups.

C. DeLisi, Jie Wu, J. Mellor, 2005, Genome informatics. International Conference on Genome Informatics.

Predictions for Europe for the Covid-19 pandemic from a SIR model

G. Bhanot, C. DeLisi, Charles DeLisi, 2020, medRxiv.

Mechanism of binding of multivalent immune complexes to Fc receptors. 2. Kinetics of binding.

C. DeLisi, D. Segal, S. Dower, 1981, Biochemistry.

Mechanism of binding of multivalent immune complexes to Fc receptors. 1. Equilibrium binding.

C. DeLisi, D. Segal, S. Dower, 1981, Biochemistry.

The asymptotic form of partition functions of linear chain molecules: An application of renewal theory☆

W. A. Beyer, C. DeLisi, 1977 .

Quantitative aspects of a unified model of diffusion mediated receptor--cyclase coupling.

C. DeLisi, 1979, Biophysical chemistry.

Multideterminant regions of the HIV-1 envelope with sites seen by murine and human helper T cells: circumventing the MHC restriction problem

C. DeLisi, J. Cornette, K. Cease, 1990 .

A resource for the comparison and integration of heterogeneous microbiome networks

C. DeLisi, Zhenjun Hu, K. Korolev, 2022, bioRxiv.

Non-equilibrium model of liquid column chromatography

C. DeLisi, H. Hethcote, 1982 .

Protein Antigenic Structures Recognized by T Cells; Potential Applications to Vaccine Design

C. DeLisi, H. Margalit, J. Cornette, 1987, Immunological reviews.

Neural network method for predicting peptides that bind major histocompatibility complex molecules.

C. DeLisi, K. Gulukota, 2001, Methods in molecular biology.

Computational problems in cell biology

Charles DeLisi, Sandor Vajda, C. DeLisi, 1999, Comput. Sci. Eng..

An Adaptive Branch-and-Bound Minimization Method Based on Dynamic Programming

Charles DeLisi, Sandor Vajda, C. DeLisi, 1994 .

Ensemble Machine Methods for Analysis of Transcription Factor and DNA Interactions

M. Kon, C. DeLisi, Yue Fan, 2010 .

Non-equilibrium model of liquid column chromatography : II. Explicit solutions and non-ideal conditions

C. DeLisi, H. Hethcote, Jeffrey W. Brettler, 1982 .

Fluctuation analysis in small chemically reacting systems

C. DeLisi, A. K. Thakur, 1980 .

The age incidence of female breast cancer— simple models and analysis of epidemiological patterns

C. DeLisi, 1977 .

The interaction map of yeast: terra incognita?

C. DeLisi, J. Mellor, 2006, Journal of biology.

The influence of cell surface receptor clustering on the thermodynamics of ligand binding and the kinetics of its dissociation.

C. DeLisi, R. Chabay, 1979, Cell biophysics.

Some physical chemical aspects of receptor-ligand interactions.

C. DeLisi, H. Metzger, 1976, Immunological communications.

Evaluation of reaction rate enhancement by reduction in dimensionality.

C. DeLisi, F. W. Wiegel, 1982, The American journal of physiology.

HLA allele selection for designing peptide vaccines.

C DeLisi, K Gulukota, C. DeLisi, 1996, Genetic analysis : biomolecular engineering.

Selecting stable molecular targets for treatment and prevention of AIDS.

C. DeLisi, J. Berzofsky, Yaoyu E. Wang, 2005, Genome informatics. International Conference on Genome Informatics.

Electrostatic contributions to oligonucleotide transitions

C. DeLisi, D. Crothers, Charles Delisi, 1971, Biopolymers.

RNA loop structure prediction via bond scaling and relaxation.

C. DeLisi, C. Cantor, R. Rosenfeld, 1996, Biopolymers.

Binding Site Graphs: A New Graph Theoretical Framework for Prediction of Transcription Factor Binding Sites

Charles DeLisi, Timothy E. Reddy, Boris E. Shakhnovich, 2007, PLoS Comput. Biol..

Analysis of Covid-19 Data for Eight European Countries and the United Kingdom Using a Simplified SIR Model

G. Bhanot, C. DeLisi, 2020, Research square.

Determination of equilibrium and rate constants by affinity chromatography

C. DeLisi, H. Hethcote, 1982 .

In silico regulatory analysis for exploring human disease progression

Charles DeLisi, Mark Kon, Dustin T. Holloway, 2008, Biology Direct.

Classifying transcription factor targets and discovering relevant biological features

Charles DeLisi, Mark Kon, Dustin T. Holloway, 2008, Biology Direct.

Machine learning for regulatory analysis and transcription factor target prediction in yeast

Charles DeLisi, Mark Kon, Dustin T. Holloway, 2006, Systems and Synthetic Biology.

Synthesis of photolabile 2-(2-nitrophenyl)propyloxycarbonyl protected amino acids

C. DeLisi, R. Laursen, K. Bhushan, 2003 .

Minimal requirements for peptide mediated activation of CD8+ CTL.

R C Brower, C. DeLisi, J. Berzofsky, 1994, Molecular immunology.

The effect of cell size and receptor density on ligand--receptor reaction rate constants.

C. DeLisi, 1981, Molecular immunology.

Model for kinetic and steady state analysis of receptor mediated endocytosis

Charles DeLisi, C. DeLisi, Marianne Gex-Fabry, 1984 .

Cell surface receptors: physical chemistry and cellular regulation.

D. Lauffenburger, C. DeLisi, 1983, International review of cytology.

The kinetics of hemolytic plaque formation. IV. IgM plaque inhibition.

C DeLisi, C. DeLisi, 1975, Journal of theoretical biology.

10 – The Role of MHC and Amphipathic Structures in T Cell Recognition: Features Determining Immunodominance

C. DeLisi, H. Margalit, J. Cornette, 1988 .

Immunodominance of Amphipathic Peptides and Their Localization on the Cell Surface for Antigen Presentation to Helper T Cells

C. DeLisi, H. Margalit, J. Cornette, 1986 .

Structural and Conformational Requirements for Ir-Gene-Controlled Myoglobin Epitope Recognition by Ia-Restricted T Cells and Clones

C. DeLisi, K. Cease, J. Berzofsky, 1986 .

Molecular features of class II MHC-restricted T-cell recognition of protein and peptide antigens: the importance of amphipathic structures.

C. DeLisi, H. Margalit, J. Cornette, 1986, Current topics in microbiology and immunology.

Positional clustering improves computational binding site detection and identifies novel cis-regulatory sites in mammalian GABAA receptor subunit genes

Charles DeLisi, Timothy E. Reddy, Boris E. Shakhnovich, 2007, Nucleic acids research.

Positional clustering improves computational binding site detection and identifies novel cis -regulatory sites in mammalian GABA A receptor subunit genes.

Charles DeLisi, Timothy E Reddy, Timothy E. Reddy, 2007, Nucleic acids research.

Determining protein loop conformation using scaling‐relaxation techniques

S Vajda, C DeLisi, C. DeLisi, 1993, Protein science : a publication of the Protein Society.

Breast cancer stratification from analysis of micro-array data of micro-dissected specimens.

J. Mesirov, P. Tamayo, G. Bhanot, 2007, Genome informatics. International Conference on Genome Informatics.

Gene set enrichment analysis: performance evaluation and usage guidelines

Zhiping Weng, Zhenjun Hu, Charles DeLisi, 2012, Briefings Bioinform..

Correlation set analysis: detecting active regulators in disease populations using prior causal knowledge

C. DeLisi, J. Lamb, L. Chindelevitch, 2012, BMC Bioinformatics.

Identification of functional modules that correlate with phenotypic difference: the influence of network topology

Zhiping Weng, Zhenjun Hu, Charles DeLisi, 2010, Genome Biology.

VisANT 3.5: multi-scale network visualization, analysis and inference based on the gene ontology

Yan Wang, Chia-Ling Huang, Zhenjun Hu, 2009, Nucleic Acids Res..

Meetings that changed the world: Santa Fe 1986: Human genome baby-steps

Charles DeLisi, C. DeLisi, 2008, Nature.

Pathway-based classification of cancer subtypes

M. Kon, C. DeLisi, Shinuk Kim, 2012, Biology Direct.

The NIH National Center for Integrative Biomedical Informatics (NCIBI)

H. V. Jagadish, Charles DeLisi, Matthias Kretzler, 2012, J. Am. Medical Informatics Assoc..

VisANT 3.0: new modules for pathway visualization, editing, prediction and construction

Zhenjun Hu, Charles DeLisi, Minoru Kanehisa, 2007, Nucleic Acids Res..

Functional fingerprints of folds: evidence for correlated structure-function evolution.

Charles DeLisi, Eugene I Shakhnovich, Nikolay V Dokholyan, 2003, Journal of molecular biology.

Micrometastases formation: a probabilistic model.

C. DeLisi, L. Liotta, G. Saidel, 1977, Cancer letters.

Computers in molecular biology: current applications and emerging trends.

C DeLisi, C. DeLisi, 1988, Science.

Identification of novel epigenetic markers for clear cell renal cell carcinoma.

C. DeLisi, G. Dalgin, L. Liou, 2008, The Journal of urology.

Thymus-independent immunogenicity in vitro of the divalent antigen DNP-polyethylene oxide.

C. DeLisi, J. Hiernaux, B. Barisas, 1983, Cellular immunology.

Identifying functional links between genes using conserved chromosomal proximity.

Charles DeLisi, Itai Yanai, Joseph C Mellor, 2002, Trends in genetics : TIG.

VisANT: an online visualization and analysis tool for biological interaction data

Zhenjun Hu, Charles DeLisi, Jie Wu, 2004, BMC Bioinformatics.

VisANT: data-integrating visual framework for biological networks and modules

Zhenjun Hu, Charles DeLisi, Jie Wu, 2005, Nucleic Acids Res..

Computationa 21. Computational Methods for Analysis of Transcriptional Regulation

Charles DeLisi, Mark Kon, Yue Fan, 2014 .

Computational Methods for Analysis of Transcriptional Regulation

Charles DeLisi, Mark Kon, Yue Fan, 2014 .

Estimating the number of protein folds.

C DeLisi, C. DeLisi, Chao Zhang, 1998, Journal of molecular biology.

The Role of Synthetic Biology in Atmospheric Greenhouse Gas Reduction: Prospects and Challenges

Richard J. Roberts, Charles DeLisi, George Church, 2020 .

Transcription factor-DNA binding via machine learning ensembles

Charles DeLisi, Yue Fan, Mark Kon, 2018, 1805.03771.

Modulation of the immune response to lipopolysaccharide.

C. DeLisi, J. Hiernaux, P. Baker, 1982, Journal of immunology.

Prediction of immunodominant helper T cell antigenic sites from the primary sequence.

J L Cornette, C. DeLisi, H. Margalit, 1987, Journal of immunology.

Predictome: a database of putative functional links between proteins

Charles DeLisi, Julian Mintseris, Itai Yanai, 2002, Nucleic Acids Res..

Gene expression in lung adenocarcinomas of smokers and nonsmokers.

Avrum Spira, Charles DeLisi, Charles A Powell, 2003, American journal of respiratory cell and molecular biology.

VisANT 4.0: Integrative network platform to connect genes, drugs, diseases and therapies

Yang Liu, Yan Wang, Feng Tian, 2013, Nucleic Acids Res..

Visant: an Integrative Framework for Networks in Systems Biology

Zhenjun Hu, Charles DeLisi, Evan S. Snitkin, 2008 .

Lack of involvement of auto-anti-idiotypic antibody in the regulation of oscillations and tolerance in the antibody response to levan.

C. DeLisi, J. Hiernaux, P. Baker, 1982, Cellular immunology.

Secretion rate independent evaluation of IgM antibody avidity at the level of single immunocytes.

C. DeLisi, G. Doria, C. Mancini, 1978, Journal of immunology.

Towards zoomable multidimensional maps of the cell

Zhenjun Hu, Charles DeLisi, Minoru Kanehisa, 2007, Nature Biotechnology.

Identification of functional links between genes using phylogenetic profiles

Simon Kasif, Charles DeLisi, Jie Wu, 2003, Bioinform..

Identification of T-cell epitopes and use in construction of synthetic vaccines.

C. DeLisi, H. Margalit, J. Cornette, 1989, Methods in enzymology.

T-cell antigenic sites tend to be amphipathic structures.

C DeLisi, C. DeLisi, J. Berzofsky, 1985, Proceedings of the National Academy of Sciences of the United States of America.

Prediction of protein complexes using empirical free energy functions

S Vajda, Z. Weng, C. DeLisi, 1996, Protein science : a publication of the Protein Society.

Machine learning methods for transcription data integration

Charles DeLisi, Mark A. Kon, Dustin T. Holloway, 2006, IBM J. Res. Dev..

Two complementary methods for predicting peptides binding major histocompatibility complex molecules.

A Sette, C DeLisi, K Gulukota, 1997, Journal of molecular biology.

Structural principles that govern the peptide-binding motifs of class I MHC molecules.

C DeLisi, C. DeLisi, C. Zhang, 1998, Journal of molecular biology.

Receptor cross-linking and histamine release. I. The quantitative dependence of basophil degranulation on the number of receptor doublets.

C. DeLisi, R. Siraganian, 1979, Journal of immunology.

Visualization of Metabolic Interaction Networks in Microbial Communities Using VisANT 5.0

Yan Wang, Zhenjun Hu, Charles DeLisi, 2016, PLoS Comput. Biol..

COMBREX: a project to accelerate the functional annotation of prokaryotic genomes

Richard J. Roberts, Stanley Letovsky, Simon Kasif, 2010, Nucleic Acids Res..

Theory of ligand binding to heterogeneous receptor populations: Characterization of the free‐energy distribution function

C. DeLisi, A. K. Thakur, 1978 .

Some mathematical problems in the initiation and regulation of the immune response

Charles DeLisi, C. DeLisi, 1977 .

TATA binding proteins can recognize nontraditional DNA sequences.

Charles DeLisi, Sunmin Ahn, Xirui Zhang, 2012, Biophysical journal.

Hemolytic plaque inhibition: the physical chemical limits on its use as an affinity assay.

C DeLisi, C. DeLisi, 1976, Journal of immunology.

Effect of conformational flexibility and solvation on receptor-ligand binding free energies.

S Vajda, C DeLisi, C. DeLisi, 1994, Biochemistry.

Consistency in structural energetics of protein folding and peptide recognition

J L Cornette, C. DeLisi, J. Cornette, 1997, Protein science : a publication of the Protein Society.

Computational determination of side chain specificity for pockets in class I MHC molecules.

C DeLisi, J L Cornette, C. DeLisi, 1996, Molecular immunology.

Peptide docking using dynamic programming

Charles DeLisi, Sandor Vajda, Kamalakar Gulukota, 1996, J. Comput. Chem..

A method for determining whether the descending limb of a biphasic histamine release curve reflects insufficient cross-linking.

C. DeLisi, A. Perelson, R. Siraganian, 1982, Molecular immunology.

The magnitude of signal amplification by ligand-induced receptor clustering

C. DeLisi, 1981, Nature.

Receptor cross-linking and histamine release. II. Interpretation and analysis of anomalous dose response patterns.

C. DeLisi, R. Siraganian, 1979, Journal of immunology.

Amino Acid Substitutions: Effects on Protein Stability

Z. Weng, C. DeLisi, 2001 .

Computational determination of the structure of rat Fc bound to the neonatal Fc receptor.

Z. Weng, C. DeLisi, P. Bjorkman, 1998, Journal of molecular biology.

Biological sciences: mRNA is expected to form stable secondary structures

C. DeLisi, J. Gralla, 1974, Nature.

An equilibrium partitioning model connecting gene expression and cis-motif content

Charles DeLisi, Joseph C. Mellor, C. DeLisi, 2006, ISMB.

A network based approach to drug repositioning identifies plausible candidates for breast cancer and prostate cancer

C. DeLisi, Zhenjun Hu, Hsiao-Rong Chen, 2016, BMC Medical Genomics.

Assessing the significance of local sequence homologies

M. Kanehisa, C. DeLisi, 1984 .

Antigen binding to receptors on immunocompetent cells. II. Thermodynamic and biological implications of the receptor cross-linking requirement for B-cell activation.

C DeLisi, C. DeLisi, A. Thakur, 1977, Cellular immunology.

Antigen binding to receptors on immunocompetent cells. I. Simple models and interpretation of experiments.

C. DeLisi, G. I. Bell, G I Bell, 1974, Cellular immunology.

Strong conformational propensities enhance T cell antigenicity.

C DeLisi, J L Cornette, H. Guy, 1987, Journal of immunology.

Monte Carlo study of the effect of β2‐microglobulin on the binding cleft of the HLA‐A2 complex

C. DeLisi, J. Garnier, J. Cornette, 1994, Protein science : a publication of the Protein Society.

Toward computational determination of peptide‐receptor structure

S Vajda, C DeLisi, C. DeLisi, 1993, Protein science : a publication of the Protein Society.

Characterization of a helper T cell epitope recognized by mice of a low responder major histocompatibility type.

C. DeLisi, J. Cornette, J. Berzofsky, 1990, Molecular immunology.

Flexible docking and design.

S Vajda, C DeLisi, R Rosenfeld, 1995, Annual review of biophysics and biomolecular structure.

Mathematical analysis of the reaction of EAC1-8 with C9: identification of parameters defining conditions for molecular titration.

C. DeLisi, T. Borsós, M. Boyle, 1980, Journal of immunology.

Antigen Antibody Interactions

Charles DeLisi, C. DeLisi, 1976 .

Protein folds: molecular systematics in three dimensions

C. DeLisi, C. Zhang, Charles DeLisi, 2001, Cellular and Molecular Life Sciences CMLS.

Comparative assessment of performance and genome dependence among phylogenetic profiling methods

Charles DeLisi, Evan S. Snitkin, Jie Wu, 2006, BMC Bioinformatics.

Theory of clustering of cell surface receptors by ligands of arbitrary valence: dependence of dose response patterns on a coarse cluster characteristic

C. DeLisi, 1980 .

Theory of the influence of oligonucleotide chain conformation on double helix stability

C. DeLisi, D. Crothers, 1971 .

SVMotif: A Machine Learning Motif Algorithm

Charles DeLisi, Yue Fan, Mark A. Kon, 2007, Sixth International Conference on Machine Learning and Applications (ICMLA 2007).

On the mechanism of hemolytic plaque inhibition.

C DeLisi, C. DeLisi, B. Goldstein, 1974, Immunochemistry.

Igf1 and Pacap rescue cerebellar granule neurons from apoptosis via a common transcriptional program

C. DeLisi, M. Ciotti, S. Cavallaro, 2015, Cell Death Discovery.

Inferring microbial co-occurrence networks from amplicon data: a systematic evaluation

C. DeLisi, Zhenjun Hu, K. Korolev, 2020, bioRxiv.

Receptor-mediated endocytosis: a model and its implications for experimental analysis.

C DeLisi, C. DeLisi, M. Gex-fabry, 1984, The American journal of physiology.

The contribution of proximity and orientation to catalytic reaction rates

C. DeLisi, D. Crothers, 1973 .

Label-free microarray imaging for direct detection of DNA hybridization and single-nucleotide mismatches.

Charles DeLisi, Marcella Chiari, Sunmin Ahn, 2010, Biosensors & bioelectronics.

Interaction between proteins localized in membranes.

C DeLisi, C. DeLisi, A. Minton, 1986, Proceedings of the National Academy of Sciences of the United States of America.

ELISA: Structure-Function Inferences based on statistically significant and evolutionarily inspired observations

Charles DeLisi, Eugene I. Shakhnovich, David Lorenz, 2003, BMC Bioinformatics.

Inferring protein-protein interactions in viral proteins by co-evolution of conserved side chains.

C. DeLisi, Yaoyu E. Wang, Charles DeLisi, 2006, Genome informatics. International Conference on Genome Informatics.

Ligand binding to multiple equivalent sites with steric hindrance.

M. Pincus, C. DeLisi, M. Rendell, 1981, Biochimica et biophysica acta.

Cooperative phenomena in homopolymers. An alternative formulation of the partition function

C. DeLisi, 1974 .

Graphical representations of the class I MHC cleft.

C DeLisi, J L Cornette, B L King, 1993, Journal of molecular graphics.

Mean residence time—theoretical development, experimental determination, and practical use in tracer analysis☆

Charles DeLisi, David G. Covell, C. DeLisi, 1984 .

The kinetics of hemolytic plaque formation V. The influence of geometry on plaque growth

C. DeLisi, Ch. DeLisi, 1975 .

The kinetics of hemolytic plaque formation. III. Inhibition of plaques by antigen.

C DeLisi, C. DeLisi, 1975, Journal of theoretical biology.

Inhibition of plaque-forming cells with anti-idiotope or hapten: variation due to hapten density on indicator red cells.

C. DeLisi, R. Cronkhite, J. Černý, 1984, Journal of immunological methods.

Immunodiffusion in gels containing erythrocyte antigen. I. Theory for diffusion of antiserum from a circular well.

C DeLisi, C. DeLisi, B. Goldstein, 1975, Journal of theoretical biology.

Membrane fluidity and the probability of complement fixation.

C. DeLisi, F. W. Wiegel, 1983, Journal of theoretical biology.

Some mathematical aspects of mapping DNA cosmids

James L. Cornette, Charles Delisi, C. DeLisi, 2008, Cell Biophysics.

Gene annotation and network inference by phylogenetic profiling

Zhenjun Hu, Charles DeLisi, Jie Wu, 2006, BMC Bioinformatics.

Analyzing Networks with VisANT

Zhenjun Hu, Joseph Mellor, Charles DeLisi, 2004, Current protocols in bioinformatics.

A theory of precipitation and agglutination reactions in immunological systems.

C. DeLisi, 1974, Journal of theoretical biology.

The role of synthetic biology in climate change mitigation

Charles DeLisi, C. DeLisi, 2019, Biology Direct.

Analysis of the rate-limiting step in a ligand-cell receptor interaction: the immunoglobulin E system.

C. DeLisi, H. Metzger, S. Wank, 1983, Biochemistry.

Analysis of the rate-limiting step in a ligand-cell receptor interaction: the IgE system

C. DeLisi, H. Metzger, S. Wank, 1983 .

Cell surface dynamics : concepts and models

F. W. Wiegel, C. DeLisi, A. Perelson, 1984 .

Learning Methods for DNA Binding in Computational Biology

Charles DeLisi, Yue Fan, Mark A. Kon, 2007, 2007 International Joint Conference on Neural Networks.

Regulation of interacting populations during endocytosis: models of growth factor-tumor promoter dynamics.

C. DeLisi, M. Gex-fabry, 1986, The American journal of physiology.

- 1-AMINO ACID SUBSTITUTIONS : EFFECTS ON PROTEIN STABILITY

Z. Weng, C. DeLisi, 1999 .

Exhaustive conformational search and simulated annealing for models of lattice peptides

R C Brower, C. DeLisi, R. Brower, 1993, Biopolymers.

Multiple copy sampling in protein loop modeling: Computational efficiency and sensitivity to dihedral angle perturbations

C DeLisi, D J Kyle, C. DeLisi, 1994, Protein science : a publication of the Protein Society.

Data Mining for Systems Biology

Hiroshi Mamitsuka, Minoru Kanehisa, Charles DeLisi, 2012, Methods in Molecular Biology.

Data Mining for Systems Biology

Charles DeLisi, Minoru Kanehisa, Hiroshi Mamitsuka, 2013, Methods in Molecular Biology.

Ensemble Machine Methods for DNA Binding

Charles DeLisi, Yue Fan, Mark A. Kon, 2008, 2008 Seventh International Conference on Machine Learning and Applications.

Circuits of the cell

C. DeLisi, J. Mellor, 2004 .

High-precision high-coverage functional inference from integrated data sources

Charles DeLisi, Yu Xia, Evan S. Snitkin, 2008, BMC Bioinformatics.

Condition specific transcription factor binding site characterization in Saccharomyces cerevisiae

Charles DeLisi, Rhonda Harrison, C. DeLisi, 2002, Bioinform..

A hypothesis driven approach to condition specific transcription factor binding site characterization in S.c.

Charles DeLisi, Rhonda Harrison, C. DeLisi, 2002, SAC '02.

Data Perturbation Independent Diagnosis and Validation of Breast Cancer Subtypes Using Clustering and Patterns

G. Bhanot, C. DeLisi, G. Alexe, 2007, Cancer Informatics.

Data Perturbation Independent Diagnosis and Validation of Breast Cancer Subtypes Using Clustering and Patterns

G. Bhanot, C. DeLisi, G. Alexe, 2006, Cancer informatics.

Portraits of breast cancer progression

J. Mesirov, P. Tamayo, G. Bhanot, 2007, BMC Bioinform..

Computer analysis and structure prediction of nucleic acids and proteins

Charles DeLisi, Minoru Kanehisa, P. Klein, 1984, Nucleic Acids Res..

TcR recognition of the MHC-peptide dimer: structural properties of a ternary complex.

C DeLisi, C. DeLisi, J. Cornette, 1996, Journal of molecular biology.

Smoothing Gene Expression Using Biological Networks

Charles DeLisi, Yue Fan, Mark A. Kon, 2010, 2010 Ninth International Conference on Machine Learning and Applications.

Regularization Techniques for Machine Learning on Graphs and Networks with Biological Applications

Mark Kon, Yue Fan, Shinuk Kim, 2010 .

Constrained optimization and protein structure determination.

C. DeLisi, S. Vajda, J. Eisenfeld, 1991, The American journal of physiology.

Receptor Cross-Linking and Histamine Release

C. DeLisi, R. Siraganian, 1979, The Journal of Immunology.

Nonrandom recurrence of consecutive repeats in noncoding mammalian sequences

R. Nussinov, M. Kanehisa, C. DeLisi, 1986 .

Immune surveillance and neoplasia. I. A minimal mathematical model.

C DeLisi, A Rescigno, C. DeLisi, 1977, Bulletin of mathematical biology.

VisANT: an online visualization and analysis tool for biological interaction data

C. DeLisi, Jie Wu, Zhenjun Hu, 2004, BMC Bioinform..

Identification of a microRNA panel for clear-cell kidney cancer.

G. Bhanot, C. DeLisi, Huiqing Liu, 2010, Urology.

Empirical free energy calculation: Comparison to calorimetric data

S Vajda, Z. Weng, C. DeLisi, 1997, Protein science : a publication of the Protein Society.

VisANT: an integrative framework for networks in systems biology

E. Snitkin, C. DeLisi, Zhenjun Hu, 2008, Briefings Bioinform..

Role of diffusion regulation in receptor--ligand interactions.

C. DeLisi, 1983, Methods in enzymology.

Stochastic problems in information transfer across the plasma membrane

C. DeLisi, 1983 .

A systematic and graphical method for generating the kinetic equations governing the growth of aggregates

C. DeLisi, A. Perelson, 1975 .

Statistical thermodynamics of oligomer–polymer interactions

C. DeLisi, Charles Delisi, 1974, Biopolymers.

Theory of a Helix‐to‐Coil Transition in a Triple‐Stranded Macromolecule

C. DeLisi, B. Goldstein, 1969 .

Degradation of nucleic acid in aqueous solution by ionizing radiation. III. The correlation of radiation damage with change in melting transition--model experiments.

C. DeLisi, W. Goad, D. Hoard, 1978, Biophysical chemistry.

Necessary conditions for avoiding incorrect polypeptide folds in conformational search by energy minimization

C. DeLisi, C. DeLisi, S. Vajda, 1993, Biopolymers.

Correlation set analysis: detecting active regulators in disease populations using prior causal knowledge

Chia-Ling Huang, Charles DeLisi, Justin Guinney, 2012, BMC Bioinformatics.

Mathematics and Computers in Biomedical Applications

Charles DeLisi, Jerome Eisenfeld, Jerome Eisenfeld, 1985 .

Evaluation and integration of cancer gene classifiers: identification and ranking of plausible drivers

Feng Tian, Zhenjun Hu, Charles DeLisi, 2015, Scientific Reports.

The NIH National Center for Integrative Biomedical Informatics (NCIBI)

H. V. Jagadish, C. DeLisi, G. Omenn, 2012, J. Am. Medical Informatics Assoc..

Using Functional Signatures to Identify Repositioned Drugs for Breast, Myelogenous Leukemia and Prostate Cancer

Yajie Wang, Chia-Ling Huang, Zhenjun Hu, 2012, PLoS Comput. Biol..

A theory of measurement error and its implications for spatial and temporal gradient sensing during chemotaxis

C. DeLisi, F. Marchetti, G. Grosso, 1982, Cell Biophysics.