Open Access. Powered by Scholars. Published by Universities.®

Bioinformatics Commons

Open Access. Powered by Scholars. Published by Universities.®

2,438 Full-Text Articles 4,092 Authors 213,250 Downloads 89 Institutions

All Articles in Bioinformatics

Faceted Search

2,438 full-text articles. Page 1 of 86.

1. Types Of Alignment: Presentations & Demos Assignment, Sarah O'Leary-Driscoll 2016 Illinois Mathematics and Science Academy

1. Types Of Alignment: Presentations & Demos Assignment, Sarah O'Leary-Driscoll

Sequence Alignments

Pairwise Alignment: DNA

Pairwise Alignment: Protein

Multiple Sequence Alignment: DNA

Multiple Sequence Alignment: Protein


Channa Striatus Tnfr-1: Molecular Cloning, Characterization And Gene Expression, Rajesh Palanisamy 2016 SRM Institute of Science and Technology

Channa Striatus Tnfr-1: Molecular Cloning, Characterization And Gene Expression, Rajesh Palanisamy

2nd International Conference of Fish & Shellfish Immunology

No abstract provided.


A Comparative Statement On Molecular Approach Of Large Hsps From Macrobrachium Rosenbergii, MUKESH KUMAR CHAURASIA 2016 SRM UNIVERSITY

A Comparative Statement On Molecular Approach Of Large Hsps From Macrobrachium Rosenbergii, Mukesh Kumar Chaurasia

2nd International Conference of Fish & Shellfish Immunology

No abstract provided.


Homeolog Specific Expression Bias, Ronald D. Smith 2016 College of William and Mary

Homeolog Specific Expression Bias, Ronald D. Smith

Biology and Medicine Through Mathematics Conference

No abstract provided.


Dawn Or Doom: The Risks And Rewards Of Emerging Technologies, Diana Hancock, Steve Tally, Gerry McCartney, Michele Arthur 2016 Purdue University

Dawn Or Doom: The Risks And Rewards Of Emerging Technologies, Diana Hancock, Steve Tally, Gerry Mccartney, Michele Arthur

Purdue P-12 Networking Summit & Poster Session

Dawn or Doom is a free and open to the public conference at Purdue where we focus on benefits and risks surrounding some of the technologies that are both the most disruptive to current practices and being adopted the fastest. A collection of Purdue faculty experts and some outside speakers showcase their many perspectives related to this technology explosion, explore conditions that will foster innovation and investment into the next generation, and address the big-picture issues where both optimism and pessimism are warranted.


Beyond Structural Genomics: Computational Approaches For The Identification Of Ligand Binding Sites In Protein Structures, Dario Ghersi, Roberto Sanchez 2016 University of Nebraska at Omaha

Beyond Structural Genomics: Computational Approaches For The Identification Of Ligand Binding Sites In Protein Structures, Dario Ghersi, Roberto Sanchez

Dario Ghersi

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


Molblocks: Decomposing Small Molecule Sets And Uncovering Enriched Fragments, Dario Ghersi, Mona Singh 2016 University of Nebraska at Omaha

Molblocks: Decomposing Small Molecule Sets And Uncovering Enriched Fragments, Dario Ghersi, Mona Singh

Dario Ghersi

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 ...


Systematic Assessment Of Accuracy Of Comparative Model Of Proteins Belonging To Different Structural Fold Classes, Subrata Chakrabarty, Dario Ghersi, Roberto Sanchez 2016 South Dakota State University

Systematic Assessment Of Accuracy Of Comparative Model Of Proteins Belonging To Different Structural Fold Classes, Subrata Chakrabarty, Dario Ghersi, Roberto Sanchez

Dario Ghersi

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 the ...


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 2016 New York University School of Medicine

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

Dario Ghersi

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 ...


Easymifs And Sitehound: A Toolkit For The Identification Of Ligand-Binding Sites In Protein Structures, Dario Ghersi, Roberto Sanchez 2016 University of Nebraska at Omaha

Easymifs And Sitehound: A Toolkit For The Identification Of Ligand-Binding Sites In Protein Structures, Dario Ghersi, Roberto Sanchez

Dario Ghersi

Summary: SITEHOUND uses Molecular Interaction Fields (MIFs) produced by EASYMIFS to identify protein structure regions that show a high propensity for interaction with ligands. The type of binding site identified depends on the probe atom used in the MIF calculation. The input to EASYMIFS is a PDB file of a protein structure; the output MIF serves as input to SITEHOUND, which in turn produces a list of putative binding sites. Extensive testing of SITEHOUND for the detection of binding sites for drug-like molecules and phosphorylated ligands has been carried out.

Availability: EASYMIFS and SITEHOUND executables for Linux, Mac OS X ...


Automated Identification Of Binding Sites Forphosphorylated Ligands In Protein Structures, Dario Ghersi, Roberto Sanchez 2016 University of Nebraska at Omaha

Automated Identification Of Binding Sites Forphosphorylated Ligands In Protein Structures, Dario Ghersi, Roberto Sanchez

Dario Ghersi

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 ...


Genome-Wide Compensatory Changes Accompany Drug-Selected Mutations In The Plasmodium Falciparum Crt Gene, Hongying Jiang, Jigar J. Patel, Ming Yi, Jianbing Mu, Jinhui Ding, Robert Stephens, Roland A. Cooper, Michael T. Ferdig, Xin-zhuan Su 2016 Old Dominion University

Genome-Wide Compensatory Changes Accompany Drug-Selected Mutations In The Plasmodium Falciparum Crt Gene, Hongying Jiang, Jigar J. Patel, Ming Yi, Jianbing Mu, Jinhui Ding, Robert Stephens, Roland A. Cooper, Michael T. Ferdig, Xin-Zhuan Su

Roland A. Cooper

Mutations in PfCRT (Plasmodium falciparum chloroquine-resistant transporter), particularly the substitution at amino acid position 76, confer chloroquine (CQ) resistance in P. falciparum. Point mutations in the homolog of the mammalian multidrug resistance gene (pfmdr1) can also modulate the levels of CQ response. Moreover, parasites with the same pfcrt and pfmdr1 alleles exhibit a wide range of drug sensitivity, suggesting that additional genes contribute to levels of CQ resistance (CQR). Reemergence of CQ sensitive parasites after cessation of CQ use indicates that changes in PfCRT are deleterious to the parasite. Some CQR parasites, however, persist in the field and grow well ...


Design, Implementation And Evaluation Of A Medical Library Program To Support Biomedical Research In The Omics Era, Rolando Garcia-Milian, John Gallagher, Janis Glover 2016 Yale University

Design, Implementation And Evaluation Of A Medical Library Program To Support Biomedical Research In The Omics Era, Rolando Garcia-Milian, John Gallagher, Janis Glover

Rolando Garcia-Milian


Objectives
Design and implement a sustainable program that supports biomedical research at Yale University. Our program responds to the challenges posed by omics (e.g. genomics, transcriptomics, proteomics, etc.) technologies, identifies the role and place of the Yale Cushing/Whitney Medical Library in the high-throughput omics research cycle, and is based on the organizational culture of the institution.

Methods
Key challenges posed by omics technologies on preclinical and clinical research are: rapidly generating high amount of diverse omics data; integrating these diverse data; exponential increase in the biomedical literature and databases; use of pathway and network-based methods to analyze and ...


Design, Implementation And Evaluation Of A Medical Library Program To Support Biomedical Research In The Omics Era, Rolando Garcia-Milian 2016 Yale University

Design, Implementation And Evaluation Of A Medical Library Program To Support Biomedical Research In The Omics Era, Rolando Garcia-Milian

Rolando Garcia-Milian


Objectives
Design and implement a sustainable program that supports biomedical research at Yale University. Our program responds to the challenges posed by omics (e.g. genomics, transcriptomics, proteomics, etc.) technologies, identifies the role and place of the Yale Cushing/Whitney Medical Library in the high-throughput omics research cycle, and is based on the organizational culture of the institution.

Methods
Key challenges posed by omics technologies on preclinical and clinical research are: rapidly generating high amount of diverse omics data; integrating these diverse data; exponential increase in the biomedical literature and databases; use of pathway and network-based methods to analyze and ...


Identification Of Candidate Genes Underlying An Iron Efficiency Quantitative Trait Locus In Soybean, Gregory A. Peiffer, Keith E. King, Andrew J. Severin, Gregory D. May, Silvia R. Cianzio, Shun Fu Lin, Nicholas C. Lauter, Randy C. Shoemaker 2016 Iowa State University

Identification Of Candidate Genes Underlying An Iron Efficiency Quantitative Trait Locus In Soybean, Gregory A. Peiffer, Keith E. King, Andrew J. Severin, Gregory D. May, Silvia R. Cianzio, Shun Fu Lin, Nicholas C. Lauter, Randy C. Shoemaker

Andrew Severin

Prevalent on calcareous soils in the United States and abroad, iron deficiency is among the most common and severe nutritional stresses in plants. In soybean (Glycine max) commercial plantings, the identification and use of iron-efficient genotypes has proven to be the best form of managing this soil-related plant stress. Previous studies conducted in soybean identified a significant iron efficiency quantitative trait locus (QTL) explaining more than 70% of the phenotypic variation for the trait. In this research, we identified candidate genes underlying this QTL through molecular breeding, mapping, and transcriptome sequencing. Introgression mapping was performed using two related near-isogenic lines ...


Predicting Dna Methylation State Of Cpg Dinucleotide Using Genome Topological Features And Deep Networks, Yiheng Wang 2016 University of Southern Mississippi

Predicting Dna Methylation State Of Cpg Dinucleotide Using Genome Topological Features And Deep Networks, Yiheng Wang

Master's Theses

The hypo- or hyper-methylation of the human genome is one of the epigenetic features of leukemia. However, experimental approaches have only determined the methylation state of a small portion of the human genome. We developed deep learning based (stacked denoising autoencoders, or SdA) software named “DeepMethyl” to predict the methylation state of DNA CpG dinucleotides using features inferred from three-dimensional genome topology (based on Hi-C) and DNA sequence patterns. We used the experimental data from immortalised myelogenous leukemia (K562) and healthy lymphoblastoid (GM12878) cell lines to train the learning models and assess prediction performance. We have tested various SdA architectures ...


Genomic Drivers Of Cutaneous Squamous Cell Carcinoma Development, Vida Chitsazzadeh 2016 The University of Texas Graduate School of Biomedical Sciences at Houston

Genomic Drivers Of Cutaneous Squamous Cell Carcinoma Development, Vida Chitsazzadeh

UT GSBS Dissertations and Theses (Open Access)

Skin cancer is the most common malignancy in humans. Annually, in U.S. there are over 3 million cases with an estimated overall economic impact of $2 billion. Cutaneous Squamous Cell Carcinoma (cuSCC) comprises 15-20% of all skin cancers. cuSCC has the best-defined progression from a distinct precancerous lesion, the Actinic Keratosis (AK), to invasive cuSCC. Destructive therapies for AK treatment must be used repetitively, causing significant morbidity. There is a tremendous need for targeted diagnostics and therapy for AKs, representing an important opportunity for secondary skin cancer prevention. Our knowledge of the molecular and cellular events that lead to ...


Accurate Mutation Annotation And Functional Prediction Enhance The Applicability Of -Omics Data In Precision Medicine, Tenghui Chen 2016 The University of Texas Graduate School of Biomedical Sciences at Houston

Accurate Mutation Annotation And Functional Prediction Enhance The Applicability Of -Omics Data In Precision Medicine, Tenghui Chen

UT GSBS Dissertations and Theses (Open Access)

Clinical sequencing has been recognized as an effective approach for enhancing the accuracy and efficiency of cancer patient management and therefore achieve the goals of personalized therapy. However, the accuracy of large scale sequencing data in clinics has been constrained by many different aspects, such as clinical detection, annotation and interpretation of the variants that are observed in clinical sequencing data. In my Ph.D thesis work, I mainly investigated how to comprehensively and efficiently apply high dimensional -omics data to enhance the capability of precision cancer medicine. Following this motivation, my dissertation has been focused on two important topics ...


Mrub_2874 Is Homologous To B3386 And Mrub_1349 Is Homologous To B2914, But Mrub_1349 Is Not Homologous To B4090, Samantha Murad, Dr. Lori Scott 2016 Augustana College, Rock Island Illinois

Mrub_2874 Is Homologous To B3386 And Mrub_1349 Is Homologous To B2914, But Mrub_1349 Is Not Homologous To B4090, Samantha Murad, Dr. Lori Scott

Meiothermus ruber Genome Analysis Project

ABSTRACT. This project is part of the Meiothermus ruber genome analysis project, which uses the bioinformatics tools associated with the Guiding Education through Novel Investigation – Annotation Collaboration Toolkit (GENI-ACT) to predict gene function. We investigated the biological function of the genes Mrub_2874 and Mrub_1349. We predict that Mrub_2874 encodes the enzyme ribulose-5-phosphate 3-epimerase (DNA coordinates 2912530..2913204 on the reverse strand), which is the first step of the pentose phosphate pathway (KEGG map number 00030). It catalyzes the conversion of D-ribulose 5-phosphate to D-xylulose 5-phosphate. The E. coli K12 MG1655 ortholog is predicted to be b3386, which has the gene ...


Darwin Core Archive File, Stover-Ebinger Herbarium, Eastern Illinois University 2016 Eastern Illinois University

Darwin Core Archive File, Stover-Ebinger Herbarium, Eastern Illinois University

Darwin Core Archive Download

ZIP file contains occurrences.csv, identivications.csv, and images.csv. The meta.xml document describes the content. Fields within the occurrences.csv file are defined by the Darwin Core exchange standard.


Digital Commons powered by bepress