Bioinformatics Commons^™

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 …

High-Density Screening Reveals A Different Spectrum Of Genomic Aberrations In Chronic Lymphocytic Leukemia Patients With ‘Stereotyped’ Ighv3-21 And Ighv4-34 B-Cell Receptors, Millaray Marincevic, Nicola Cahill, Rebeqa Gunnarsson, Anders Isaksson, Mahmoud Mansouri, Hanna Göransson, Markus Rasmussen, Mattias Jansson, Fergus Ryan, Karin Karlsson, Hans-Olov Adami, Fred Davi, Jesper Jurlander, Gunnar Juliusson, Kostas Stamatopoulos, Richard Rosenquist

Articles

Background The existence of multiple subsets of chronic lymphocytic leukemia expressing ‘stereotyped’ Bcell receptors implies the involvement of antigen(s) in leukemogenesis. Studies also indicate that ‘stereotypy’ may influence the clinical course of patients with chronic lymphocytic leukemia, for example, in subsets with stereotyped IGHV3-21 and IGHV4-34 B-cell receptors; however, little is known regarding the genomic profile of patients in these subsets. Design and Methods We applied 250K single nucleotide polymorphism-arrays to study copy-number aberrations and copy-number neutral loss-of-heterozygosity in patients with stereotyped IGHV3-21 (subset #2, n=29), stereotyped IGHV4-34 (subset #4, n=17; subset #16, n=8) and non-subset #2 IGHV3-21 (n=13) and …

Food Consumption Trends And Drivers, John Kearney

Articles

A picture of food consumption (availability) trends and projections to 2050, both globally and for different regions of the world along with the drivers largely responsible for these observed consumption trends are the subject of this review. Throughout the world, major shifts in dietary patterns are occurring, even in the consumption of basic staples towards more diversified diets. Accompanying these changes in food consumption at a global and regional level have been considerable health consequences. Populations in those countries undergoing rapid transition are experiencing nutritional transition. The diverse nature of this transition may be the result of differences in socio …

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 …

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 …

Nominal Schemas For Integrating Rules And Ontologies, Frederick Maier, Adila A. Krisnadhi, Pascal Hitzler

Computer Science and Engineering Faculty Publications

We propose a description-logic style extension of OWL DL, which includes DL-safe variable SWRL and seamlessly integrates datalog rules. Our language also sports a tractable fragment, which we call ELP 2, covering OWL EL, OWL RL, most of OWL QL, and variable restricted datalog.

Detecting Phenotype-Specific Interactions Between Biological Processes From Microarray Data And Annotations, Nadeem Ahmed Ansari

Wayne State University Dissertations

The development of high throughput technologies such as DNA microarrays has enabled researchers to measure expression levels on a genomic scale. Correct and efficient biological interpretation of the voluminous data generated by these technologies, however, remains a challenging problem. A commonly used approach in interpreting the results of such high throughput experiments is to map the list of differentially expressed (DE) genes to gene ontology (GO) terms, which provides a list of biological processes, biochemical functions, and cellular locations associated with the DE genes. A previously unexplored aspect is the identifications of unusual associations between biological processes. Such associations may …

Approximate Instance Retrieval On Ontologies, Tuvshintur Tserendorj, Stephan Grimm, Pascal Hitzler

Computer Science and Engineering Faculty Publications

With the development of more expressive description logics (DLs) for the Web Ontology Language OWL the question arises how we can properly deal with the high computational complexity for efficient reasoning. In application cases that require scalable reasoning with expressive ontologies, non-standard reasoning solutions such as approximate reasoning are necessary to tackle the intractability of reasoning in expressive DLs. In this paper, we are concerned with the approximation of the reasoning task of instance retrieval on DL knowledge bases, trading correctness of retrieval results for gain of speed. We introduce our notion of an approximate concept extension and we provide …

Semantic Web – Interoperability, Usability, Applicability, Pascal Hitzler, Krzysztof Janowicz

Computer Science and Engineering Faculty Publications

No abstract provided.

A Reasonable Semantic Web, Pascal Hitzler, Frank Van Harmelen

Computer Science and Engineering Faculty Publications

The realization of Semantic Web reasoning is central to substantiating the Semantic Web vision. However, current mainstream research on this topic faces serious challenges, which forces us to question established lines of research and to rethink the underlying approaches. We argue that reasoning for the Semantic Web should be understood as "shared inference," which is not necessarily based on deductive methods. Model-theoretic semantics (and sound and complete reasoning based on it) functions as a gold standard, but applications dealing with large-scale and noisy data usually cannot afford the required runtimes. Approximate methods, including deductive ones, but also approaches based on …

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, …

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 …