Bioinformatics Commons^™

From Questions To Effective Answers: On The Utility Of Knowledge-Driven Querying Systems For Life Sciences Data, Amir H. Asiaee, Prashant Doshi, Todd Minning, Satya S. Sahoo, Priti Parikh, Amit P. Sheth, Rick L. Tarleton

Kno.e.sis Publications

We compare two distinct approaches for querying data in the context of the life sciences. The first approach utilizes conventional databases to store the data and intuitive form-based interfaces to facilitate easy querying of the data. These interfaces could be seen as implementing a set of 'pre-canned' queries commonly used by the life science researchers that we study. The second approach is based on semantic Web technologies and is knowledge (model) driven. It utilizes a large OWL ontology and same datasets as before but associated as RDF instances of the ontology concepts. An intuitive interface is provided that allows the …

Improved Detection Of Bartonella Dna In Mammalian Hosts And Arthropod Vectors By Real-Time Pcr Using The Nadh Dehydrogenase Gamma Subunit (Nuog), James M. Colborn, Michael Y. Kosoy, Vladimir L. Motin, Maxim V. Telepnev, Gustavo Valbuena, Khin S. Myint, Yuri Fofanov, Catherine Putonti, Chen Feng, Leonard Peruski

Bioinformatics Faculty Publications

We used a whole-genome scanning technique to identify the NADH dehydrogenase gamma subunit (nuoG) primer set that is sensitive and specific enough to detect a diverse number of Bartonella species in a wide range of environmental samples yet maintains minimal cross-reactivity to mammalian host and arthropod vector organisms.

Adaptive Evolution And Inherent Tolerance To Extreme Thermal Environments, Jennifer Cox, Alyxandria Schubert, Michael Travisano, Catherine Putonti

Bioinformatics Faculty Publications

Background

When introduced to novel environments, the ability for a species to survive and rapidly proliferate corresponds with its adaptive potential. Of the many factors that can yield an environment inhospitable to foreign species, phenotypic response to variation in the thermal climate has been observed within a wide variety of species. Experimental evolution studies using bacteriophage model systems have been able to elucidate mutations, which may correspond with the ability of phage to survive modest increases/decreases in the temperature of their environment.

Results

Phage ΦX174 was subjected to both elevated (50°C) and extreme (70°C+) temperatures for anywhere from a few …

Mechanisms Responsible For A Φx174 Mutant's Ability To Infect Escherichia Coli By Phosphorylation, Jennifer Cox, Catherine Putonti

Bioinformatics Faculty Publications

The ability for a virus to expand its host range is dependent upon a successful mode of viral entry. As such, the host range of the well-studied ΦX174 bacteriophage is dictated by the presence of a particular lipopolysaccharide (LPS) on the bacterial surface. The mutant ΦX174 strain JACS-K, unlike its ancestor, is capable of infecting both its native host Escherichia coli C and E. coli K-12, which does not have the necessary LPS. The conversion of an alanine to a very reactive threonine on its virion surface was found to be responsible for the strain's expanded host range.

Cspcr: A Computational Tool For The Simulation Of The Polymerase Chain Reaction, Sandhya Dasu, April Williams, Yuriy Fofanov, Catherine Putonti

Bioinformatics Faculty Publications

Dasu S, Williams A, Fofanov Y, Putonti C., csPCR: A computational tool for the simulation of the Polymerase Chain Reaction, Online J Bioinformatics, 11 (1): 30-33, 2010. Herein we present a computational simulation package PCR (csPCR) which models the PCR reaction, taking into consideration the issues of specificity, sensitivity, potential mishybridizations throughout the primer sequence as well as at the 3’ end, and primer interactions, including selfcomplementarity and primer-primer interactions. A single target sequence or multiple target sequences can be considered simultaneously in addition to multiple primer sequences; thus a complex community and/or a multiplex assay can be simulated in …

Provenance Aware Linked Sensor Data, Harshal Kamlesh Patni, Satya S. Sahoo, Cory Andrew Henson, Amit P. Sheth

Kno.e.sis Publications

Provenance, from the French word “provenir”, describes the lineage or history of a data entity. Provenance is critical information in the sensors domain to identify a sensor and analyze the observation data over time and geographical space. In this paper, we present a framework to model and query the provenance information associated with the sensor data exposed as part of the Web of Data using the Linked Open Data conventions. This is accomplished by developing an ontology-driven provenance management infrastructure that includes a representation model and query infrastructure. This provenance infrastructure, called Sensor Provenance Management System (PMS), is …

Getting Code Near The Data: A Study Of Generating Customized Data Intensive Scientific Workflows With Domain Specific Language, Ashwin Manjunatha, Ajith Harshana Ranabahu, Paul E. Anderson, Amit P. Sheth

Kno.e.sis Publications

The amount of data produced in modern biological experiments such as Nuclear Magnetic Resonance (NMR) analysis far exceeds the processing capability of a single machine. The present state-of-the-art is taking the ”data to code”, the philosophy followed by many of the current service oriented workflow systems. However this is not feasible in some cases such as NMR data analysis, primarily due to the large scale of data.

The objective of this research is to bring ”code to data”, preferred in the cases when the data is extremely large. We present a DSL based approach to develop customized data intensive scientific …

Scale: A Scalable Framework For Efficiently Clustering Transactional Data, Hua Yan, Keke Chen, Ling Liu, Zhang Yi

Kno.e.sis Publications

This paper presents SCALE, a fully automated transactional clustering framework. The SCALE design highlights three unique features. First, we introduce the concept of Weighted Coverage Density as a categorical similarity measure for efficient clustering of transactional datasets. The concept of weighted coverage density is intuitive and it allows the weight of each item in a cluster to be changed dynamically according to the occurrences of items. Second, we develop the weighted coverage density measure based clustering algorithm, a fast, memory-efficient, and scalable clustering algorithm for analyzing transactional data. Third, we introduce two clustering validation metrics and show that these domain …

Tracking Profiles Of Genomic Instability In Spontaneous Transformation And Tumorigenesis, Lesley Lawrenson

Wayne State University Dissertations

The dominant paradigm for cancer research focuses on the identification of specific genes for cancer causation and for the discovery of therapeutic targets. Alternatively, the current data emphasize the significance of karyotype heterogeneity in cancer progression over specific gene-based causes of cancer. Variability of a magnitude significant to shift cell populations from homogeneous diploid cells to a mosaic of structural and numerical chromosome alterations reflects the characteristic low-fidelity genome transfer of cancer cell populations. This transition marks the departure from micro-evolutionary gene-level change to macro-evolutionary change that facilitates the generation of many unique karyotypes within a cell population. Considering cancer …

Genbank, Dennis A. Benson, Ilene Karasch-Mizrachi, David J. Lipman, James Ostell, Eric W. Sayers

Harold W. Manter Laboratory: Library Materials

GenBank(R) is a comprehensive database that contains publicly available nucleotide sequences for more than 380,000 organisms named at the genus level or lower, obtained primarily through submissions from individual laboratories and batch submissions from large-scale sequencing projects, including whole genome shotgun (WGS) and environmental sampling projects. Most submissions are made using the web-based BankIt or standalone Sequin programs, and accession numbers are assigned by GenBank staff upon receipt. Daily data exchange with the European Nucleotide Archive (ENA) and the DNA Data Bank of Japan (DDBJ) ensures worldwide coverage. GenBank is accessible through the NCBI Entrez retrieval system that integrates data …

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 …

The 3rd Computational Structural Bioinformatics Workshop, Jing He, Di Wu

Computer Science Faculty Publications

As many other domains in biology, molecular structures have proposed challenging but interesting computational problems. The unique challenge of the 3-dimensional molecular structures comes from the combination of the fundamental concepts of physics, chemistry, biology and geometry, and it is often computationally intensive to search for the correct structure. The Computational Structural Bioinformatics Workshop (CSBW) is a workshop that focuses on the fundamental computational work that is related to 3-dimensional molecular structures. This workshop aims to bring together researchers with expertise in bioinformatics, computational biology, structural biology, data mining, optimization and high performance computing to discuss recent results, new techniques, …

Bayesmotif: De Novo Protein Sorting Motif Discovery From Impure Datasets, Jianjun Hu, F. Zhang

Faculty Publications

Background

Protein sorting is the process that newly synthesized proteins are transported to their target locations within or outside of the cell. This process is precisely regulated by protein sorting signals in different forms. A major category of sorting signals are amino acid sub-sequences usually located at the N-terminals or C-terminals of protein sequences. Genome-wide experimental identification of protein sorting signals is extremely time-consuming and costly. Effective computational algorithms for de novo discovery of protein sorting signals is needed to improve the understanding of protein sorting mechanisms.

Methods

We formulated the protein sorting motif discovery problem as a classification problem …

An Intelligent Data-Centric Approach Toward Identification Of Conserved Motifs In Protein Sequences, Kathryn Dempsey Cooper, Benjamin Currall, Richard Hallworth, Hesham Ali

Interdisciplinary Informatics Faculty Proceedings & Presentations

The continued integration of the computational and biological sciences has revolutionized genomic and proteomic studies. However, efficient collaboration between these fields requires the creation of shared standards. A common problem arises when biological input does not properly fit the expectations of the algorithm, which can result in misinterpretation of the output. This potential confounding of input/output is a drawback especially when regarding motif finding software. Here we propose a method for improving output by selecting input based upon evolutionary distance, domain architecture, and known function. This method improved detection of both known and unknown motifs in two separate case studies. …

Polyphyly Of The Pikeminnows (Teleostei: Cyprinidae) Inferred Using Mitochondrial Dna Sequences, T. Heath Ogden

T. Heath Ogden

The phylogenetic relationships of the Colorado pikeminnow Ptychocheilus lucius, northern pikeminnow P. oregonensis, Sacramento pikeminnow P. grandis, Umpqua pikeminnow P. umpquae, and hardhead Mylopharodon conocephalus were examined by using molecular data to investigate monophyly of the genus Ptychocheilus. Phylogenies generated using DNA sequence data from the cytochrome b and 16S ribosomal DNA genes of the mitochondrial genome reveal that Ptychocheilus is a polyphyletic genus and suggest that the taxonomy of the group is in need of further revision. These data yield insights into the evolution of the pikeminnows and help place the significant evolutionary events in context with the geological …