Linghu, Bolan, Snitkin, Evan S, Hu, Zhenjun, Xia, Yu, DeLisi, Charles
Abstract We integrate 16 genomic features to construct an evidence-weighted functional-linkage network comprising 21,657 human genes. The functional-linkage network is used to prioritize candidate...
Hu, Zhenjun, Hung, Jui-Hung, Wang, Yan, Chang, Yi-Chien, Huang, Chia-Ling, Huyck, Matt, ...
Despite its wide usage in biological databases and applications, the role of the gene ontology (GO) in network analysis is usually limited to functional annotation of genes or gene sets with...
BioMed Central Open Access (2008)
Gul S Dalgin, Gabriela Alexe, Daniel Scanfeld, Pablo Tamayo, Jill P Mesirov, Shridar Ganesan, ...
This is an Open Access article distributed under the terms of the Creative Commons Attribution License
In silico regulatory analysis for exploring human disease progression (2008)
Holloway, Dustin T, Kon, Mark, DeLisi, Charles
Abstract Background An important goal in bioinformatics is to unravel the network of transcription factors (TFs) and their targets. This is important in the human genome, where many TFs are involved...
Classifying transcription factor targets and discovering relevant biological features (2008)
Holloway, Dustin T, Kon, Mark, DeLisi, Charles
Abstract Background An important goal in post-genomic research is discovering the network of interactions between transcription factors (TFs) and the genes they regulate. We have previously reported...
Thermodynamic favorability of transcription factor (TF) binding to DNA is a significant factor in the control of gene expression. Theoretical and in vitro measures link the relative equilibrium...
Gabriela Alexe, Gul S. Dalgin, Daniel Scanfeld, Pablo Tamayo, Jill Mesirov, Charles Delisi, ...
expression of lymphocyte-associated genes in node negative HER2+ breast
BIOINFORMATICS Articles (2008)
Thermodynamic favorability of transcription factor (TF) binding to DNA is a significant factor in the control of gene expression. Theoretical and in vitro measures link the relative equilibrium...
High-precision high-coverage functional inference from integrated data sources (2008)
Linghu, Bolan, Snitkin, Evan S, Holloway, Dustin T, Gustafson, Adam M, Xia, Yu, DeLisi, Charles
Abstract Background Information obtained from diverse data sources can be combined in a principled manner using various machine learning methods to increase the reliability and range of knowledge...
Bmc Bioinformatics, Bolan Linghu, Evan S Snitkin, Dustin T Holloway, Adam M Gustafson, Yu Xia, ...
Research article High-precision high-coverage functional inference from integrated data sources
VisANT: an integrative framework for networks in systems biology (2008)
Hu, Zhenjun, Snitkin, Evan S., DeLisi, Charles
The essence of a living cell is adaptation to a changing environment, and a central goal of modern cell biology is to understand adaptive change under normal and pathological conditions. Because the...
In silico regulatory analysis for exploring human disease progression (2008)
Dustin T Holloway, Mark Kon, Charles Delisi
© 2008 Holloway et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License
Biology Direct BioMed Central (2008)
Dustin T Holloway, Mark Kon, Charles Delisi
Classifying transcription factor targets and discovering relevant biological features
Portraits of breast cancer progression (2007)
Dalgin, Gul S, Alexe, Gabriela, Scanfeld, Daniel, Tamayo, Pablo, Mesirov, Jill P, Ganesan, Shridar, ...
Abstract Background Clustering analysis of microarray data is often criticized for giving ambiguous results because of sensitivity to data perturbation or clustering techniques used. In this paper,...
VisANT 3.0: new modules for pathway visualization, editing, prediction and construction (2007)
Hu, Zhenjun, Ng, David M., Yamada, Takuji, Chen, Chunnuan, Kawashima, Shuichi, Mellor, Joe, ...
With the integration of the KEGG and Predictome databases as well as two search engines for coexpressed genes/proteins using data sets obtained from the Stanford Microarray Database (SMD) and Gene...
Timothy E. Reddy, Charles DeLisi, Boris E. Shakhnovich
Computational prediction of nucleotide binding specificity for transcription factors remains a fundamental and largely unsolved problem. Determination of binding positions is a prerequisite for...
Identification and Characterization of Renal Cell Carcinoma Gene Markers (2007)
Gul S. Dalgin, Dustin T. Holloway, Louis S. Liou, Charles DeLisi
Microarray gene expression profiling has been used to distinguish histological subtypes of renal cell carcinoma (RCC), and consequently to identify specific tumor markers. The analytical procedures...
Reddy, Timothy E., Shakhnovich, Boris E., Roberts, Daniel S., Russek, Shelley J., DeLisi, Charles
Understanding transcription factor (TF) mediated control of gene expression remains a major challenge at the interface of computational and experimental biology. Computational techniques predicting...
Reddy, Timothy E., Shakhnovich, Boris E., Roberts, Daniel S., Russek, Shelley J., DeLisi, Charles
Understanding transcription factor (TF) mediated control of gene expression remains a major challenge at the interface of computational and experimental biology. Computational techniques predicting...
Gustafson, Adam M, Snitkin, Evan S, Parker, Stephen CJ, DeLisi, Charles, Kasif, Simon
Abstract Background The identification of genes essential for survival is of theoretical importance in the understanding of the minimal requirements for cellular life, and of practical importance in...
Snitkin, Evan S, Gustafson, Adam M, Mellor, Joseph, Wu, Jie, DeLisi, Charles
Abstract Background The rapidly increasing speed with which genome sequence data can be generated will be accompanied by an exponential increase in the number of sequenced eukaryotes. With the...
The interaction map of yeast: terra incognita? (2006)
Abstract A systematic curation of the literature on Saccharomyces cerevisiae has yielded a comprehensive collection of experimentally observed interactions. This new resource augments current views...
Gene annotation and network inference by phylogenetic profiling (2006)
Wu, Jie, Hu, Zhenjun, DeLisi, Charles
Abstract Background Phylogenetic analysis is emerging as one of the most informative computational methods for the annotation of genes and identification of evolutionary modules of functionally...
Bmc Genomics, Adam M Gustafson, Evan S Snitkin, Stephen Cj Parker, Charles Delisi, Simon Kasif, ...
Research article Towards the identification of essential genes using targeted genome sequencing and comparative analysis
Jie Wu, Zhenjun Hu, Charles Delisi
Background: Phylogenetic analysis is emerging as one of the most informative computational methods for the annotation of genes and identification of evolutionary modules of functionally related...
An equilibrium partitioning model connecting gene expression and cis-motif content (2006)
Thermodynamic favorability of transcription factor (TF) binding to DNA is a significant factor in the control of gene expression. Theoretical and in vitro measures link the relative equilibrium...
Integrating genomic data to predict transcription factor binding (2005)
Dustin T. Holloway, Mark Kon, Charles Delisi
Transcription factor binding sites (TFBS) in gene promoter regions are often predicted by using position specific scoring matrices (PSSMs), which summarize sequence patterns of experimentally...
Integrating genomic data to predict transcription factor binding (2005)
Dustin T. Holloway, Mark Kon, Charles Delisi
Transcription factor binding sites (TFBS) in gene promoter regions are often predicted by using position specific scoring matrices (PSSMs), which summarize sequence patterns of experimentally...
VisANT: data-integrating visual framework for biological networks and modules (2005)
Hu, Zhenjun, Mellor, Joe, Wu, Jie, Yamada, Takuji, Holloway, Dustin, DeLisi, Charles
VisANT is a web-based software framework for visualizing and analyzing many types of networks of biological interactions and associations. Networks are a useful computational tool for representing...
Protein structure and evolutionary history determine sequence space topology (2005)
Shakhnovich, Boris E., Deeds, Eric, Delisi, Charles, Shakhnovich, Eugene
Understanding the observed variability in the number of homologs of a gene is a very important unsolved problem that has broad implications for research into coevolution of structure and function,...
Protein Structure and Evolutionary History Determine Sequence Space Topology (2004)
Shakhnovich, Boris, Deeds, Eric, Delisi, Charles, Shakhnovich, Eugene
Understanding the observed variability in the number of homologs of a gene is a very important, unsolved problem that has broad implications for research into co-evolution of structure and function,...
VisANT: an online visualization and analysis tool for biological interaction data (2004)
Hu, Zhenjun, Mellor, Joseph, Wu, Jie, DeLisi, Charles
Abstract Background New techniques for determining relationships between biomolecules of all types – genes, proteins, noncoding DNA, metabolites and small molecules – are now making a substantial...
BMC Bioinformatics Methodology article (2004)
Zhenjun Hu, Joseph Mellor, Jie Wu, Charles Delisi
VisANT: an online visualization and analysis tool for biological interaction data
Shakhnovich, Boris E, Harvey, John M, Comeau, Steve, Lorenz, David, DeLisi, Charles, Shakhnovich, Eugene
Abstract The problem of functional annotation based on homology modeling is primary to current bioinformatics research. Researchers have noted regularities in sequence, structure and even chromosome...
Boris E Shakhnovich, John M Harvey, Steve Comeau, David Lorenz, Charles Delisi, Eugene Shakhnovich, ...
The problem of functional annotation based on homology modeling is primary to current bioinformatics research. Researchers have noted regularities in sequence, structure and even chromosome...
The society of genes: networks of functional links between genes from comparative genomics (2002)
Abstract Background Comparative genomics provides at least three methods beyond traditional sequence similarity for identifying functional links between genes: the examination of common phylogenetic...
Predictome: a database of putative functional links between proteins (2002)
Mellor, Joseph C., Yanai, Itai, Clodfelter, Karl H., Mintseris, Julian, DeLisi, Charles
The current deluge of genomic sequences has spawned the creation of tools capable of making sense of the data. Computational and high-throughput experimental methods for generating links between...
Harrison, Rhonda, DeLisi, Charles
Motivation: We demonstrate a computational process by which transcription factor binding sites can be elucidated using genome-wide expression and binding profiles. The profiles direct us to the...
A computational framework for optimal masking in the synthesis of oligonucleotide microarrays (2002)
Kasif, Simon, Weng, Zhiping, Derti, Adnan, Beigel, Richard, DeLisi, Charles
High‐throughput genomic technologies are revolutionizing modern biology. In particular, DNA microarrays have become one of the most powerful tools for profiling global mRNA expression in...
and peptide recognition (1996)
Email Alerting, Chao Zhang, James L. Coriwti'e, Charles Delisi
Consistency in structural energetics of protein folding and peptide recognition
Vajda, Sandor, Weng, Zhiping, DeLisi, Charles
Hydrophobicity values for amino acids obtained from protein unfolding experiments are about twice as large as those obtained from data on the partitioning of amino acids between water and octanol....
Prediction of protein function by discriminant analysis (1986)
Klein, Petr, Jacquez, John A., Delisi, Charles
Approximately 53% the protein sequences in the National Biomedical Research Foundation (NBRF) database can be allocated to one of 26 functional classes, each of which can be characterized by the...
Predictlon of splice junctions in mRNA sequences (1985)
Nakata, Kotoko, Kanehisa, Minoru, DeLisi, Charles
A general method based on the statistical technique of discriminant analysis is developed to distinguish boundaries of coding and non-coding regions in nucleic acid sequences. In parular, the method...
DeLisi, Charles, Blumenthal, Robert
Incluye bibliografía e índice
Yanai, Itai, Derti, Adnan, DeLisi, Charles
Recent work in computational genomics has shown that a functional association between two genes can be derived from the existence of a fusion of the two as one continuous sequence in another genome....
Predictome: a database of putative functional links between proteins
Mellor, Joseph C., Yanai, Itai, Clodfelter, Karl H., Mintseris, Julian, DeLisi, Charles
The current deluge of genomic sequences has spawned the creation of tools capable of making sense of the data. Computational and high-throughput experimental methods for generating links between...
The society of genes: networks of functional links between genes from comparative genomics
Comparative genomics provides at least three methods for identifying functional links between genes: examination of phylogenetic distributions, analysis of conserved proximity and observations of...
A computational framework for optimal masking in the synthesis of oligonucleotide microarrays
Kasif, Simon, Weng, Zhiping, Derti, Adnan, Beigel, Richard, DeLisi, Charles
High-throughput genomic technologies are revolutionizing modern biology. In particular, DNA microarrays have become one of the most powerful tools for profiling global mRNA expression in different...
Shakhnovich, Boris E, Harvey, John M, Comeau, Steve, Lorenz, David, DeLisi, Charles, Shakhnovich, Eugene
The problem of functional annotation based on homology modeling is primary to current bioinformatics research. Researchers have noted regularities in sequence, structure and even chromosome...
Prediction of RNA Secondary Structure
Delisi, Charles, Crothers, Donald M.
Calculations of the free energy required to close single-strand loops by formation of a base pair in double-helical nucleic acids are reported. These results can be used to estimate the free energy...
VisANT: data-integrating visual framework for biological networks and modules
Hu, Zhenjun, Mellor, Joe, Wu, Jie, Yamada, Takuji, Holloway, Dustin, DeLisi, Charles
VisANT is a web-based software framework for visualizing and analyzing many types of networks of biological interactions and associations. Networks are a useful computational tool for representing...
The Importance of Thermodynamic Equilibrium for High Throughput Gene Expression Arrays
Bhanot, Gyan, Louzoun, Yoram, Zhu, Jianhua, DeLisi, Charles
We present an analysis of physical chemical constraints on the accuracy of DNA micro-arrays under equilibrium and nonequilibrium conditions. At the beginning of the article we describe an algorithm...
Protein structure and evolutionary history determine sequence space topology
Shakhnovich, Boris E., Deeds, Eric, Delisi, Charles, Shakhnovich, Eugene
Understanding the observed variability in the number of homologs of a gene is a very important unsolved problem that has broad implications for research into coevolution of structure and function,...
The interaction map of yeast: terra incognita?
A systematic curation of the literature on Saccharomyces cerevisiae has yielded a comprehensive collection of experimentally observed interactions. This new resource augments current views of the...
Comparative assessment of performance and genome dependence among phylogenetic profiling methods
Snitkin, Evan S, Gustafson, Adam M, Mellor, Joseph, Wu, Jie, DeLisi, Charles
Yanai, Itai, Derti, Adnan, DeLisi, Charles
Recent work in computational genomics has shown that a functional association between two genes can be derived from the existence of a fusion of the two as one continuous sequence in another genome....
Predictome: a database of putative functional links between proteins
Mellor, Joseph C., Yanai, Itai, Clodfelter, Karl H., Mintseris, Julian, DeLisi, Charles
The current deluge of genomic sequences has spawned the creation of tools capable of making sense of the data. Computational and high-throughput experimental methods for generating links between...
The society of genes: networks of functional links between genes from comparative genomics
Comparative genomics provides at least three methods for identifying functional links between genes: examination of phylogenetic distributions, analysis of conserved proximity and observations of...
A computational framework for optimal masking in the synthesis of oligonucleotide microarrays
Kasif, Simon, Weng, Zhiping, Derti, Adnan, Beigel, Richard, DeLisi, Charles
High-throughput genomic technologies are revolutionizing modern biology. In particular, DNA microarrays have become one of the most powerful tools for profiling global mRNA expression in different...
Shakhnovich, Boris E, Harvey, John M, Comeau, Steve, Lorenz, David, DeLisi, Charles, Shakhnovich, Eugene
The problem of functional annotation based on homology modeling is primary to current bioinformatics research. Researchers have noted regularities in sequence, structure and even chromosome...
Prediction of RNA Secondary Structure
Delisi, Charles, Crothers, Donald M.
Calculations of the free energy required to close single-strand loops by formation of a base pair in double-helical nucleic acids are reported. These results can be used to estimate the free energy...
Protein structure and evolutionary history determine sequence space topology
Shakhnovich, Boris E., Deeds, Eric, Delisi, Charles, Shakhnovich, Eugene
Understanding the observed variability in the number of homologs of a gene is a very important unsolved problem that has broad implications for research into coevolution of structure and function,...
VisANT: data-integrating visual framework for biological networks and modules
Hu, Zhenjun, Mellor, Joe, Wu, Jie, Yamada, Takuji, Holloway, Dustin, DeLisi, Charles
VisANT is a web-based software framework for visualizing and analyzing many types of networks of biological interactions and associations. Networks are a useful computational tool for representing...
The Importance of Thermodynamic Equilibrium for High Throughput Gene Expression Arrays
Bhanot, Gyan, Louzoun, Yoram, Zhu, Jianhua, DeLisi, Charles
We present an analysis of physical chemical constraints on the accuracy of DNA micro-arrays under equilibrium and nonequilibrium conditions. At the beginning of the article we describe an algorithm...
The interaction map of yeast: terra incognita?
A systematic curation of the literature on Saccharomyces cerevisiae has yielded a comprehensive collection of experimentally observed interactions. This new resource augments current views of the...
Comparative assessment of performance and genome dependence among phylogenetic profiling methods
Snitkin, Evan S, Gustafson, Adam M, Mellor, Joseph, Wu, Jie, DeLisi, Charles
Reddy, Timothy E., Shakhnovich, Boris E., Roberts, Daniel S., Russek, Shelley J., DeLisi, Charles
Understanding transcription factor (TF) mediated control of gene expression remains a major challenge at the interface of computational and experimental biology. Computational techniques predicting...
Reddy, Timothy E, DeLisi, Charles, Shakhnovich, Boris E
Computational prediction of nucleotide binding specificity for transcription factors remains a fundamental and largely unsolved problem. Determination of binding positions is a prerequisite for...
VisANT 3.0: new modules for pathway visualization, editing, prediction and construction
Hu, Zhenjun, Ng, David M., Yamada, Takuji, Chen, Chunnuan, Kawashima, Shuichi, Mellor, Joe, ...
With the integration of the KEGG and Predictome databases as well as two search engines for coexpressed genes/proteins using data sets obtained from the Stanford Microarray Database (SMD) and Gene...
Portraits of breast cancer progression
Dalgin, Gul S, Alexe, Gabriela, Scanfeld, Daniel, Tamayo, Pablo, Mesirov, Jill P, Ganesan, Shridar, ...
High-precision high-coverage functional inference from integrated data sources
Linghu, Bolan, Snitkin, Evan S, Holloway, Dustin T, Gustafson, Adam M, Xia, Yu, DeLisi, Charles
Machine learning for regulatory analysis and transcription factor target prediction in yeast
Holloway, Dustin T., Kon, Mark, DeLisi, Charles
High throughput technologies, including array-based chromatin immunoprecipitation, have rapidly increased our knowledge of transcriptional maps—the identity and location of regulatory binding sites...
Identification and Characterization of Renal Cell Carcinoma Gene Markers
Dalgin, Gul S., Holloway, Dustin T., Liou, Louis S., DeLisi, Charles
Microarray gene expression profiling has been used to distinguish histological subtypes of renal cell carcinoma (RCC), and consequently to identify specific tumor markers. The analytical procedures...
VisANT 3.5: multi-scale network visualization, analysis and inference based on the gene ontology
Hu, Zhenjun, Hung, Jui-Hung, Wang, Yan, Chang, Yi-Chien, Huang, Chia-Ling, Huyck, Matt, ...
Despite its wide usage in biological databases and applications, the role of the gene ontology (GO) in network analysis is usually limited to functional annotation of genes or gene sets with...
Linghu, Bolan, Snitkin, Evan S, Hu, Zhenjun, Xia, Yu, DeLisi, Charles
An evidence-weighted functional-linkage network of human genes reveals associations among diseases that share no known disease genes and have dissimilar phenotypes