A5069844269- Real-Time Systems Scheduling
- Embedded Systems Design Techniques
- Distributed systems and fault tolerance
- Distributed and Parallel Computing Systems
- Parallel Computing and Optimization Techniques
- Advanced Software Engineering Methodologies
- Genomics and Phylogenetic Studies
- Genetics, Bioinformatics, and Biomedical Research
- Petri Nets in System Modeling
- Genomics and Chromatin Dynamics
- Software System Performance and Reliability
- Software Engineering Research
- Gene expression and cancer classification
- RNA and protein synthesis mechanisms
- Plant Reproductive Biology
- Formal Methods in Verification
- Polysaccharides and Plant Cell Walls
- Biomedical and Engineering Education
- Advanced Database Systems and Queries
- Machine Learning in Bioinformatics
- Software Reliability and Analysis Research
- Chromosomal and Genetic Variations
- Algorithms and Data Compression
- Cloud Computing and Resource Management
- Epigenetics and DNA Methylation
Ohio University
2015-2024
Ohio University Lancaster
2010
The Ohio State University
1990-2010
National Institutes of Health
2010
The University of Texas at Austin
2006
Dependable Computing (United States)
2004-2005
New Jersey Institute of Technology
1993-2003
The University of Texas at Arlington
1996-2003
Athens University of Economics and Business
2003
University School
2000
The Arabidopsis Gene Regulatory Information Server (AGRIS; http://arabidopsis.med.ohio-state.edu/ ) provides a comprehensive resource for gene regulatory studies in the model plant thaliana . Three interlinked databases, AtTFDB, AtcisDB and AtRegNet, furnish updated information on transcription factors (TFs), predicted experimentally verified cis -regulatory elements (CREs) their interactions, respectively. In addition to significant contributions identification of entire set TF–DNA which...
Abstract Hydroxyproline-rich glycoproteins (HRGPs) are a superfamily of plant cell wall proteins that function in diverse aspects growth and development. This consists three members: hyperglycosylated arabinogalactan (AGPs), moderately glycosylated extensins (EXTs), lightly proline-rich (PRPs). Hybrid chimeric versions HRGP molecules also exist. In order to “mine” genomic databases for HRGPs facilitate guide research the field, BIO OHIO software program was developed identifies classifies...
The three-dimensional (3D) structure of chromatin is intrinsically associated with gene regulation and cell function1-3. Methods based on conformation capture have mapped structures in neuronal systems such as vitro differentiated neurons, neurons isolated through fluorescence-activated sorting from cortical tissues pooled different animals dissociated whole hippocampi4-6. However, changes organization captured by imaging, the relocation Bdnf away nuclear periphery after activation7, are...
Rapid advances in the life sciences and related information technologies necessitate ongoing refinement of bioinformatics educational programs order to maintain their relevance. As discipline computational biology expands matures, it is important characterize elements that contribute success professionals this field. These individuals work a wide variety settings, including core facilities, biological medical research laboratories, software development organizations, pharmaceutical...
Bioinformatics is recognized as part of the essential knowledge base numerous career paths in biomedical research and healthcare. However, there little agreement field over what that entails or how best to provide it. These disagreements are compounded by wide range populations need bioinformatics training, with divergent prior backgrounds intended application areas. The Curriculum Task Force International Society Computational Biology (ISCB) Education Committee has sought a framework for...
Although bioinformatics is becoming increasingly central to research in the life sciences, skills and knowledge are not well integrated into undergraduate biology education. This curricular gap prevents students from harnessing full potential of their education, limiting career opportunities slowing innovation. To advance integration sciences a framework core competencies needed. that end, we here report results survey faculty United States about teaching scientists. Responses were received...
Abstract Technology for measuring 3D genome topology is increasingly important studying gene regulation, assembly and mapping of rearrangements. Hi-C other ligation-based methods have become routine but specific biases. Here, we develop multiplex-GAM, a faster more affordable version architecture (GAM), ligation-free technique that maps chromatin contacts genome-wide. We perform detailed comparison multiplex-GAM using mouse embryonic stem cells. When examining the strongest detected by...
Bioinformatics, a discipline that combines aspects of biology, statistics, mathematics, and computer science, is becoming increasingly important for biological research. However, bioinformatics instruction not yet generally integrated into undergraduate life sciences curricula. To understand why we studied how being included in biology education the US by conducting nationwide survey faculty at two- four-year institutions. The asked several open-ended questions probed barriers to...
Extensins (EXTs) are a family of plant cell wall hydroxyproline-rich glycoproteins (HRGPs) that implicated to play important roles in growth, development, and defense. Structurally, EXTs characterized by the repeated occurrence serine (Ser) followed three five prolines (Pro) residues, which hydroxylated as hydroxyproline (Hyp) glycosylated. Some have Tyrosine (Tyr)-X-Tyr (where X can be any amino acid) motifs responsible for intramolecular or intermolecular cross-linkings. divided into...
Filarial nematodes can cause debilitating diseases in humans. They have complicated life cycles involving an insect vector and mammalian hosts, they go through a number of developmental molts. While whole genome sequences parasitic worms are now available, very little is known about transcription factor (TF) binding sites their cognate factors that play role regulating development. To address this gap, we developed novel motif prediction pipeline, Emotif Alpha, integrates ten different...
Abstract Sex determination mechanisms often differ even between related species yet the evolution of sex chromosomes remains poorly understood in all but a few model organisms. Some nematodes such as Caenorhabditis elegans have an XO system while others, filarial parasite Brugia malayi , XY mechanism. We present complete B. genome assembly and define Nigon elements shared with C. which we then map to genomes other more distantly nematodes. find remarkable plasticity chromosome several...
Hydroxyproline-rich glycoproteins (HRGPs) constitute a plant cell wall protein superfamily that functions in diverse aspects of growth and development. This contains three members: the highly glycosylated arabinogalactan-proteins (AGPs), moderately extensins (EXTs), lightly proline-rich proteins (PRPs). Chimeric hybrid HRGPs, however, also exist. A bioinformatics approach is employed here to identify classify AGPs, EXTs, PRPs, chimeric HRGPs from predicted by completed genome sequence poplar...
Tbx15 is a member of the T-box gene family mesodermal developmental genes. We have recently shown that plays critical role in formation and metabolic programming glycolytic myofibers skeletal muscle. also differentially expressed among white adipose tissue (WAT) different body depots. In current study, using three independent methods, we show even within single WAT depot, high expression restricted to subset preadipocytes mature adipocytes. Gene profiling demonstrate Tbx15Hi preadipocyte...
Time constrained systems which operate in dynamic environments may have unknown worst case scenarios, large variances the sizes of data and event sets that they process (and thus, execution latencies resource requirements), not be statically characterizable, even by time invariant statistical distributions. The paper presents a specification language for describing environment dependent features. Also presented is an abstract model constructed (statically) from specifications, augmented...
DNA repair genes provide an important contribution towards the surveillance and of damage. These produce a large network interacting proteins whose mRNA expression is likely to be regulated by similar regulatory factors. Full characterization promoters similarities among them will more fully elucidate networks that activate or inhibit their expression. To address this goal, authors introduce technique find genomic signatures, which represents specific application signature methodology...
White adipose tissue (WAT) is composed of mature adipocytes and a stromal vascular fraction (SVF), which contains variety cells, including immune cells that vary among the different WAT depots. Growth hormone (GH) impacts function adiposity in an depot-specific manner. However, its effects on cell populations remain unstudied. Bovine GH transgenic (bGH) mice are commonly used to study vivo GH. These giant have excess action, impaired glucose metabolism, decreased adiposity, increased lean...
The paper presents DynBench, a benchmark suite that is representative of the emerging generation dynamic real time distributed systems. characteristics and architecture application are described. Additionally, discusses DynBench environment, which includes: (1) technique for specification "repeatable" execution scenarios; (2) mechanisms control (start, stop, replicate move) applications; (3) interfaces collection QoS metrics from (4) an infrastructure assessment adaptive resource management...
Genome sequences can be conceptualized as arrangements of motifs or words. The frequencies and positional distributions these words within particular non-coding genomic segments provide important insights into how the function in processes such mRNA stability regulation gene expression. Using an enumerative word discovery approach, we investigated all 65,536 different 8-letter genome Arabidopsis thaliana. Focusing on promoter regions, introns, 3' 5' untranslated regions (3'UTRs 5'UTRs),...
Recent epidemiological studies indicate that only 30–50% of undiagnosed type 2 diabetes mellitus (T2DM) patients are identified using glycated hemoglobin (HbA1c) and elevated fasting plasma glucose (FPG) levels. Thus, novel biomarkers for early diagnosis prognosis urgently needed providing personalized treatment. Here, we studied the glycation degrees 27 sites representing nine proteins in 48 newly diagnosed male T2DM non-diabetic men matched age (range 35–65 years). Samples were digested...
The Curriculum Task Force (CTF) of ISCB’s Education Committee seeks to define curricular guidelines for those who educate or train bioinformatics professionals at all career stages. A recent report the CTF [1] presented a draft set core competencies, derived from results surveys (1) facility directors, (2) opportunities, and (3) existing curricula. Since publication its 2014 report, has focused on application in varied contexts identify areas where refinement is needed. As first step,...
Eukaryotic core promoters are often characterized by the presence of consensus motifs such as TATA box or initiator elements, which attract and direct transcriptional machinery to transcription start site. However, many human have none known promoter motifs, suggesting that undiscovered exist in genome. We previously identified a mutation Ankyrin-1 ( ANK -1) causes disease ankyrin-deficient Hereditary Spherocytosis (HS). Although -1 is CpG rich, no discernable basal elements had been...
Summary Technologies for measuring 3D genome topology are increasingly important studying mechanisms of gene regulation, assembly and mapping rearrangements. Hi-C other ligation-based methods have become routine but specific biases. Here, we develop multiplex-GAM, a faster more affordable version Genome Architecture Mapping (GAM), ligation-free technique to map chromatin contacts genome-wide. We perform detailed comparison obtained by multiplex-GAM using mouse embryonic stem (mES) cells....
For widespread reuse in a component-based software industry, component must be designed and developed to reused. Benefits of are maximized when is reused “as is” (possibly with provisions for expected customization, such as through parameters), based only on its specification. The expression the specification crucial this setting. formal, yet understandable, well abstract implementation-independent. also make it possible demonstrate correctness an implementation permit formal reasoning about...