| A New Strategy to Reduce Allelic Bias in RNA-Seq Readmapping |
Jan 2012 |
11 pages |
| Authors:
Ravi V Satya; Nela Zavaljevski; Jaques Reifman; ARMY MEDICAL RESEARCH AND MATERIEL COMMAND FORT DETRICK MD TELEMEDICINE AND ADVANCED TECH RESEARCH CENTER
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 | Accurate estimation of expression levels from RNA-Seq data entails precise mapping of the sequence reads to a reference genome. Because the standard reference genome contains only one allele at any given locus, reads overlapping polymorphic loci that carry a non-reference allele are at least one mismatch away from the reference and hence, are less likely to be mapped. This bias in read mapping leads to inaccurate estimates of allele-specific expression ... |
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| AGeS: A Software System for Microbial Genome Sequence Annotation |
07 Mar 2011 |
9 pages |
| Authors:
Kamal Kumar; Valmik Desai; Li Cheng; Maxim Khitrov; Deepak Grover; Ravi V Satya; Chenggang Yu; Nela Zavaljevski; Jaques Reifman; ARMY MEDICAL RESEARCH AND MATERIEL COMMAND FORT DETRICK MD TELEMEDICINE AND ADVANCED TECH RESEARCH CENTER
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| The annotation of genomes from next-generation sequencing platforms needs to be rapid, high-throughput and fully integrated and automated. Although a few Web-based annotation services have recently become available, they may not be the best solution for researchers that need to annotate a large number of genomes, possibly including proprietary data, and store them locally for further analysis. To address this need, we developed a standalone software application, the Annotation of ... |
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| AGeS: A Software System for Microbial Genome Sequence Annotation |
Mar 2011 |
8 pages |
| Authors:
Kamal Kumar; Valmik Desai; Li Cheng; Maxim Khitrov; Deepak Grover; Ravi V Satya; Chenggang Yu; Nela Zavaljevski; Jaques Reifman; ARMY MEDICAL RESEARCH AND MATERIEL COMMAND FORT DETRICK MD TELEMEDICINE AND ADVANCED TECH RESEARCH CENTER
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| The annotation of genomes from next-generation sequencing platforms needs to be rapid, high-throughput,and fully integrated and automated. Although a few Web-based annotation services have recently become available, they may not be the best solution for researchers that need to annotate a large number of genomes, possibly including proprietary data, and store them locally for further analysis. To address this need, we developed a standalone software application, the Annotation of microbial ... |
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| SNIT: SNP Identification for Strain Typing |
Jan 2011 |
6 pages |
| Authors:
Ravi V Satya; Nela Zavaljevski; Jaques Reifman; ARMY MEDICAL RESEARCH AND MATERIEL COMMAND FORT DETRICK MD TELEMEDICINE AND ADVANCED TECH RESEARCH CENTER
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| With ever-increasing numbers of microbial genomes being sequenced, efficient tools are needed to perform strainlevel identification of any newly sequenced genome. Here, we present the SNP identification for strain typing (SNIT) pipeline, a fast and accurate software system that compares a newly sequenced bacterial genome with other genomes of the same species to identify single nucleotide polymorphisms (SNPs) and small insertions/ deletions (indels). Based on this information, the pipeline analyzes ... |
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| QuartetS: A Fast and Accurate Algorithm for Large-Scale Orthology Detection |
2011 |
12 pages |
| Authors:
Chenggang Yu; Nela Zavaljevski; Valmik Desai; Jaques Reifman; ARMY MEDICAL RESEARCH AND MATERIEL COMMAND FORT DETRICK MD TELEMEDICINE AND ADVANCED TECH RESEARCH CENTER
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| The unparalleled growth in the availability of genomic data offers both a challenge to develop orthology detection methods that are simultaneously accurate and high throughput and an opportunity to improve orthology detection by leveraging evolutionary evidence in the accumulated sequenced genomes. Here, we report a novel orthology detection method, termed QuartetS, that exploits evolutionary evidence in a computationally efficient manner. Based on the well-established evolutionary concept that gene duplication events ... |
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| Accelerating Biomedical Research in Designing Diagnostic Assays, Drugs, and Vaccines |
Oct 2010 |
11 pages |
| Authors:
Anders Wallqvist; Nela Zavaljevski; Ravi V Satya; Rajkumar Bondugula; Valmik Desai; Xin Hu; Kamal Kumar; Michael S Lee; In-Chul Yeh; Chenggang Yu; ARMY MEDICAL RESEARCH AND MATERIEL COMMAND FORT DETRICK MD TELEMEDICINE AND ADVANCED TECH RESEARCH CENTER
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| The US Department of Defense Biotechnology High-Performance Computing Software Applications Institute for Force Health Protection develops state-of-the-art high-performance computing applications that accelerate biomedical research in the development of diagnostic assays, drugs, and vaccines. The BHSAI works together with DoD life scientists to develop and integrate HPC software applications into DoD biomedical research programs. |
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| A High-Throughput Pipeline for the Design of Real-Time PCR Signatures |
23 Jun 2010 |
33 pages |
| Authors:
Ravi V Satya; Kamal Kumar; Nela Zavaljevski; Jaques Reifman; BIOTECHNOLOGY HPC SOFTWARE APPLICATIONS INST FORT DETRICK MD
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| Pathogen diagnostic assays based on polymerase chain reaction (PCR) technology provide high sensitivity and specificity. However, the design of these diagnostic assays is computationally intensive, requiring high-throughput methods to identify unique PCR signatures in the presence of an ever increasing availability of sequenced genomes. |
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| Large-Scale Orthology Predictions for Inferring Gene Functions Across Multiple Species |
Jun 2010 |
6 pages |
| Authors:
Chenggang Yu; Valmik Desai; Nela Zavaljevski; Jaques Reifman; ARMY MEDICAL RESEARCH AND MATERIEL COMMAND FORT DETRICK MD
|
| An effective approach to infer the functions of genes is to use the concept of gene orthology. Because orthologous genes are likely to share similar functions the functions of genes in an unstudied species can be inferred through the functions of their orthologs in a studied model species. To infer gene functions for a multitude of species, we developed a high-throughput orthology prediction method, termed PhyloTrace. PhyloTrace is both highly ... |
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| PSPP: A Protein Structure Prediction Pipeline for Computing Clusters |
Jul-2009 |
10 pages |
| Authors:
Jaques Reifman; Nela Zavaljevski; Anders Wallqvist; In-Chul Yeh; Valmik Desai; Michael S Lee; Rajkumar Bondugula; ARMY MEDICAL RESEARCH AND MATERIEL COMMAND FORT DETRICK MD
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| Background: Protein structures are critical for understanding the mechanisms of biological systems and, subsequently, for drug and vaccine design. Unfortunately, protein sequence data exceed structural data by a factor of more than 200 to 1. This gap can be partially filled by using computational protein structure prediction. While structure prediction Web servers are a notable option, they often restrict the number of sequence queries and/or provide a limited set of ... |
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| Parallel Implementation of a Bioinformatics Pipeline for the Design of Pathogen Diagnostic Assays |
19 Jun 2009 |
8 pages |
| Authors:
Ravi V Satye; Kamal Kumar; Nela Zavaljevski; Jaques Reifman; ARMY MEDICAL RESEARCH AND MATERIEL COMMAND FORT DETRICK MD TELEMEDICINE AND ADVANCED TECH RESEARCH CENTER
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| The genomes of hundreds of pathogens and their near neighbors are now available and many more are being sequenced. With the availability of this genome information, sequence-based pathogen identification has become an increasingly important tool for clinical diagnostics and environmental monitoring of biological threat agents. Chief among sequence-based identification tools are DNA microarrays, which have the ability to test for thousands of pathogens in a single diagnostic test. The design ... |
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| A Web-Accessible Protein Structure Prediction Pipeline |
Jun 2009 |
8 pages |
| Authors:
Michael S Lee; Rajkumar Bondugula; Valmik Desai; Nela Zavaljevski; In-Chul Yeh; Anders Wallqvist; Jaques Reifman; ARMY MEDICAL RESEARCH AND MATERIEL COMMAND FORT DETRICK MD TELEMEDICINE AND ADVANCED TECH RESEARCH CENTER
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| Proteins are the molecular basis of nearly all structural, catalytic, sensory, and regulatory functions in living organisms. The biological function of a protein is inextricably linked to its three-dimensional (3D) atomic structure. Traditional structure determination methods, such as X-ray and nuclear magnetic resonance techniques, are time-consuming, expensive, and infeasible for the millions of proteins that have been sequenced so far from various organisms. Alternatively computational structure prediction methods provide a ... |
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| In silico Microarray Probe Design for Diagnosis of Multiple Pathogens |
21 Oct 2008 |
12 pages |
| Authors:
Ravi V Satya; Nela Zavaljevski; Kamal Kumar; Elizabeth Bode; Susana Padilla; Leonard Wasieloski; Jeanne Geyer; Jaques Reifman; BIOTECHNOLOGY HPC SOFTWARE APPLICATIONS INST FORT DETRICK MD
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| With multiple strains of various pathogens being sequenced, it is necessary to develop high-throughput methods that can simultaneously process multiple bacterial or viral genomes to find common fingerprints as well as fingerprints that are unique to each individual genome. We present algorithmic enhancements to an existing single-genome pipeline that allows for efficient design of microarray probes common to groups of target genomes. The enhanced pipeline takes advantage of the similarities ... |
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| PIPA: A High-Throughput Pipeline for Protein Function Annotation |
Jul 2008 |
12 pages |
| Authors:
Chenggang Yu; Valmik Desai; Nela Zavaljevski; Jaques Reifman; BIOTECHNOLOGY HPC SOFTWARE APPLICATIONS INST FORT DETRICK MD
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| Traditional experimental methods to determine the functions of proteins encoded in genomic sequences cannot keep pace with the avalanche of sequence data produced by new high-throughput sequencing technologies. This prompted the development of numerous bioinformatics approaches for automated protein function annotation. However, different function classification terminologies are frequently used by these different approaches, precluding the integration of multisource predictions. We developed Pipeline for Protein Annotation (PIPA), a genome-wide protein function ... |
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| A High-Throughput Pipeline for Designing Microarray-Based Pathogen Diagnostic Assays |
10 APR 2008 |
15 pages |
| Authors:
Ravi Vijaya Satya; Nela Zavaljevski; Kamal Kumar; Jaques Reifman; ARMY MEDICAL RESEARCH AND MATERIEL COMMAND FORT DETRICK MD TELEMEDICINE AND ADVANCED TECH RESEARCH CENTER
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| Background: We present a methodology for high-throughput design of oligonucleotide fingerprints for microarray-based pathogen diagnostic assays. The oligonucleotide fingerprints, or DNA microarray probes, are designed for identifying target organisms in environmental or clinical samples. The design process is implemented in a high-performance computing software pipeline that incorporates major algorithmic improvements over a previous version to both reduce computation time and improve specificity assessment. Results: The algorithmic improvements result in significant ... |
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| The Development of PIPA: An Integrated and Automated Pipeline for Genome-Wide Protein Function Annotation |
25 JAN 2008 |
13 pages |
| Authors:
Chenggang Yu; Nela Zavaljevski; Valmik Desai; Seth Johnson; Fred J. Stevens; Jaques Reifman; BIOTECHNOLOGY HPC SOFTWARE APPLICATIONS INST FORT DETRICK MD
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| Background: Automated protein function prediction methods are needed to keep pace with high-throughput sequencing. With the existence of many programs and databases for inferring different protein functions, a pipeline that properly integrates these resources will benefit from the advantages of each method. However, integrated systems usually do not provide mechanisms to generate customized databases to predict particular protein functions. Here, we describe a tool termed PIPA (Pipeline for Protein Annotation) ... |
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| A Software Pipeline for Protein Structure Prediction |
NOV 2006 |
25 pages |
| Authors:
Michael S. Lee; In-Chul Yeh; Nela Zavaljevski; Paul Wilson; Jaques Reifman; ARMY RESEARCH LAB FREDERICK MD COMPUTATIONAL SCIENCES AND ENGINEERING BRANCH
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| We have developed a software suite to predict protein structures from sequence through the integration of multiple non-commercial programs. The Army and DoD medical and scientific communities will be able to use this software to annotate structures of sequenced pathogenic and host genomes. Such structural predictions can be used in therapeutic and vaccine design as well as many areas of basic biological research. In this work, initial assessments of the ... |
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| Oligonucleotide Fingerprint Identification for Microarray-Based Pathogen Diagnostic Assays |
OCT 2006 |
10 pages |
| Authors:
Tembe Waibhav; Nela Zavaljevski; Elizabeth Bode; Catherine Chase; Jeanne Geyer; Leonard Wasieloski; Gary Benson; Jaques Reifman; ARMY MEDICAL RESEARCH INST OF INFECTIOUS DISEASES FORT DETRICK MD
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| Advances in DNA microarray technology and computational methods have unlocked new opportunities to identify "DNA fingerprints," i.e., oligonucleotide sequences that uniquely identify a specific genome. We present an integrated approach for the computational identification of DNA fingerprints for design of microarray-based pathogen diagnostic assays. We provide a quantifiable definition of a DNA fingerprint stated both from a computational as well as an experimental point of view, and the analytical proof ... |
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| Classifying Noisy Protein Sequence Data: A Case Study of Immunoglobulin Light Chains |
2005 |
9 pages |
| Authors:
Chenggang Yu; Nela Zavaljevski; Fred J. Stevens; Kelly Yackovich; Jaques Reifman; ARGONNE NATIONAL LAB IL
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| Summary: The classification of protein sequences obtained from patients with various immunoglobulin-related conformational diseases may provide insight into structural correlates of pathogenicity. However, clinical data are very sparse and, in the case of antibody-related proteins, the collected sequences have large variability with only a small subset of variations relevant to the protein pathogenicity (function). On this basis, these sequences represent a model system for development of strategies to recognize the ... |
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