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Articles 1 - 10 of 10
Full-Text Articles in Bioinformatics
Genome-Wide Detection And Analysis Of Multifunctional Genes, Yuri Pritykin, Dario Ghersi, Mona Singh
Genome-Wide Detection And Analysis Of Multifunctional Genes, Yuri Pritykin, Dario Ghersi, Mona Singh
Interdisciplinary Informatics Faculty Publications
Many genes can play a role in multiple biological processes or molecular functions. Identifying multifunctional genes at the genome-wide level and studying their properties can shed light upon the complexity of molecular events that underpin cellular functioning, thereby leading to a better understanding of the functional landscape of the cell. However, to date, genome-wide analysis of multifunctional genes (and the proteins they encode) has been limited. Here we introduce a computational approach that uses known functional annotations to extract genes playing a role in at least two distinct biological processes. We leverage functional genomics data sets for three organisms—H. sapiens, …
Molblocks: Decomposing Small Molecule Sets And Uncovering Enriched Fragments, Dario Ghersi, Mona Singh
Molblocks: Decomposing Small Molecule Sets And Uncovering Enriched Fragments, Dario Ghersi, Mona Singh
Interdisciplinary Informatics Faculty Publications
The chemical structures of biomolecules, whether naturally occurring or synthetic, are composed of functionally important building blocks. Given a set of small molecules—for example, those known to bind a particular protein—computationally decomposing them into chemically meaningful fragments can help elucidate their functional properties, and may be useful for designing novel compounds with similar properties. Here we introduce molBLOCKS, a suite of programs for breaking down sets of small molecules into fragments according to a predefined set of chemical rules, clustering the resulting fragments, and uncovering statistically enriched fragments. Among other applications, our software should be a great aid in large-scale …
Interaction-Based Discovery Of Functionally Important Genes In Cancers, Dario Ghersi, Mona Singh
Interaction-Based Discovery Of Functionally Important Genes In Cancers, Dario Ghersi, Mona Singh
Interdisciplinary Informatics Faculty Publications
A major challenge in cancer genomics is uncovering genes with an active role in tumorigenesis from a potentially large pool of mutated genes across patient samples. Here we focus on the interactions that proteins make with nucleic acids, small molecules, ions and peptides, and show that residues within proteins that are involved in these interactions are more frequently affected by mutations observed in large-scale cancer genomic data than are other residues. We leverage this observation to predict genes that play a functionally important role in cancers by introducing a computational pipeline (http://canbind.princeton.edu) for mapping large-scale cancer exome data …
Automated Identification Of Binding Sites Forphosphorylated Ligands In Protein Structures, Dario Ghersi, Roberto Sanchez
Automated Identification Of Binding Sites Forphosphorylated Ligands In Protein Structures, Dario Ghersi, Roberto Sanchez
Interdisciplinary Informatics Faculty Publications
Phosphorylation is a crucial step in many cellular processes, ranging from metabolic reactions involved in energy transformation to signaling cascades. In many instances, protein domains specifically recognize the phosphogroup. Knowledge of the binding site provides insights into the interaction, and it can also be exploited for therapeutic purposes. Previous studies have shown that proteins interacting with phosphogroups are highly heterogeneous, and no single property can be used to reliably identify the binding site. Here we present an energy-based computational procedure that exploits the protein three-dimensional structure to identify binding sites involved in the recognition of phosphogroups. The procedure is validated …
Beyond Structural Genomics: Computational Approaches For The Identification Of Ligand Binding Sites In Protein Structures, Dario Ghersi, Roberto Sanchez
Beyond Structural Genomics: Computational Approaches For The Identification Of Ligand Binding Sites In Protein Structures, Dario Ghersi, Roberto Sanchez
Interdisciplinary Informatics Faculty Publications
t Structural genomics projects have revealed structures for a large number of proteins of unknown function. Understanding the interactions between these proteins and their ligands would provide an initial step in their functional characterization. Binding site identification methods are a fast and cost-effective way to facilitate the characterization of functionally important protein regions. In this review we describe our recently developed methods for binding site identification in the context of existing methods. The advantage of energy-based approaches is emphasized, since they provide flexibility in the identifi- cation and characterization of different types of binding sites
Systematic Assessment Of Accuracy Of Comparative Model Of Proteins Belonging To Different Structural Fold Classes, Subrata Chakrabarty, Dario Ghersi, Roberto Sanchez
Systematic Assessment Of Accuracy Of Comparative Model Of Proteins Belonging To Different Structural Fold Classes, Subrata Chakrabarty, Dario Ghersi, Roberto Sanchez
Interdisciplinary Informatics Faculty Publications
In the absence of experimental structures, comparative modeling continues to be the chosen method for retrieving structural information on target proteins. However, models lack the accuracy of experimental structures. Alignment error and structural divergence (between target and template) influence model accuracy the most. Here, we examine the potential additional impact of backbone geometry, as our previous studies have suggested that the structural class (all-α, αβ, all-β) of a protein may influence the accuracy of its model. In the twilight zone (sequence identity ≤ 30%) and at a similar level of target-template divergence, the accuracy of protein models does indeed follow …
Computer Simulations Of Heterologous Immunity: Highlights Of An Interdisciplinary Cooperation, Claudia Calcagno, Roberto Puzone, Yanthe E. Pearson, Yiming Cheng, Dario Ghersi, Liisa K. Selin, Raymond M. Welsh, Franco Celada
Computer Simulations Of Heterologous Immunity: Highlights Of An Interdisciplinary Cooperation, Claudia Calcagno, Roberto Puzone, Yanthe E. Pearson, Yiming Cheng, Dario Ghersi, Liisa K. Selin, Raymond M. Welsh, Franco Celada
Interdisciplinary Informatics Faculty Publications
The relationship between biological research and mathematical modeling is complex, critical, and vital. In this review, we summarize the results of the collaboration between two laboratories, exploring the interaction between mathematical modeling and wet-lab immunology. During this collaboration several aspects of the immune defence against viral infections were investigated, focusing primarily on the subject of heterologous immunity. In this manuscript, we emphasize the topics where computational simulations were applied in conjunction with experiments, such as immune attrition, the growing and shrinking of cross-reactive T cell repertoires following repeated infections, the short and long-term effects of cross-reactive immunological memory, and the …
A Parallel Graph Sampling Algorithm For Analyzing Gene Correlation Networks, Kathryn Dempsey Cooper, Kanimathi Duraisamy, Hesham Ali, Sanjukta Bhowmick
A Parallel Graph Sampling Algorithm For Analyzing Gene Correlation Networks, Kathryn Dempsey Cooper, Kanimathi Duraisamy, Hesham Ali, Sanjukta Bhowmick
Interdisciplinary Informatics Faculty Publications
Effcient analysis of complex networks is often a challenging task due to its large size and the noise inherent in the system. One popular method of overcoming this problem is through graph sampling, that is extracting a representative subgraph from the larger network. The accuracy of the sample is validated by comparing the combinatorial properties of the subgraph and the original network. However, there has been little study in comparing networks based on the applications that they represent. Furthermore, sampling methods are generally applied agnostically, without mapping to the requirements of the underlying analysis. In this paper,we introduce a parallel …
Biochemical Profiling Of Histone Binding Selectivity Of The Yeast Bromodomain Family, Qiang Zhang, Suvobrata Chakravarty, Dario Ghersi, Lei Zeng, Alexander N. Plotnikov, Roberto Sanchez, Ming-Ming Zhou
Biochemical Profiling Of Histone Binding Selectivity Of The Yeast Bromodomain Family, Qiang Zhang, Suvobrata Chakravarty, Dario Ghersi, Lei Zeng, Alexander N. Plotnikov, Roberto Sanchez, Ming-Ming Zhou
Interdisciplinary Informatics Faculty Publications
Background: It has been shown that molecular interactions between site-specific chemical modifications such as acetylation and methylation on DNA-packing histones and conserved structural modules present in transcriptional proteins are closely associated with chromatin structural changes and gene activation. Unlike methyl-lysine that can interact with different protein modules including chromodomains, Tudor and MBT domains, as well as PHD fingers, acetyl-lysine (Kac) is known thus far to be recognized only by bromodomains. While histone lysine acetylation plays a crucial role in regulation of chromatin-mediated gene transcription, a high degree of sequence variation of the acetyl-lysine binding site in the bromodomains has …
Sitehound-Web: A Server For Ligand Binding Site Identification In Protein Structures, Marylens Hernandez, Dario Ghersi, Roberto Sanchez
Sitehound-Web: A Server For Ligand Binding Site Identification In Protein Structures, Marylens Hernandez, Dario Ghersi, Roberto Sanchez
Interdisciplinary Informatics Faculty Publications
SITEHOUND-web (http://sitehound.sanchezlab.org) is a binding-site identification server powered by the SITEHOUND program. Given a protein structure in PDB format SITEHOUND-web will identify regions of the protein characterized by favorable interactions with a probe molecule. These regions correspond to putative ligand binding sites. Depending on the probe used in the calculation, sites with preference for different ligands will be identified. Currently, a carbon probe for identification of binding sites for drug-like molecules, and a phosphate probe for phosphorylated ligands (ATP, phoshopeptides, etc.) have been implemented. SITEHOUND-web will display the results in HTML pages including an interactive 3D representation of …