A Computational Pipeline for Comparative Study of Guide RNAs for CRISPR-CAS Genome Editing Systems

CRISPR-Cas (Clustered Regularly Interspaced Short Palindromic Repeats- CRISPR Associated Proteins ) systems were recently developed into genome editing tools. Given their strength in multiplex targeting and  easy programmability, CRISPR-CAS systems are already widely applied in academia and industry. While existing detection approaches could capture CRISPR arrays based on prior knowledge of sequence features, such predicted CRISPR arrays may lack essential structural features to enable RNA-processing for further immunity mechanism.  Moreover,  for efficient design of single guided RNA, unmet needs may remain to comprehensively discover structural features of CAS-nuclease/guide RNA complexes Here, we discuss a two-step seed-and-extend approach using a distributed computing environment, to detect CRISPR…

A Deep Neural Network Method for Predicting Mitochondria-Localized Proteins in Plants

Targeting and translocation of proteins to the appropriate subcellular compartments is crucial for cell organization and function. Newly synthesized proteins are transported to mitochondria with the assistance of targeting sequences, which are complex, containing either an N-terminal presequence or a multitude of internal signals to target this organelle. Compared with experimental approaches, computational predictions provide an efficient and cost-effective way to infer subcellular localization for any given protein. However, it is still challenging to predict plant mitochondrial localized proteins accurately due to various limitations, and the performance of current tools is unsatisfactory. We present a novel computational approach for large-scale…

An embarrassingly parallel application: High accuracy mapping of copy number variable regions

Finding gene copy number variation in a species is the cornerstone of genomic research. Most CNV finding tools and methods rely on comparing samples to the reference genome and on detecting certain signatures in the alignment data. These methods are robust and are significantly accurate, however they are not perfect. Different tools have various levels of success. Early research had access to few genome samples and these disadvantages could be overcome by using multiple tools for each study. With the development of significantly fast and cheap sequencing machines, a large numbers of samples can be produced in a short amount of time.

Measuring the Speed and Efficacy of Clinical Decision Making through Medication History Visualizations

The rapid advancements in our ability to store, extract, and analyze data in the 20th and 21st century is overwhelming care providers.  Large, diverse, complex and/or longitudinal datasets are continuously generated from a variety of instruments, sensors and/or computer-based transactions.  Considering increased use of electronic medical records (EMRs) as a result of the American Recovery and Reinvestment Act of 2009, combined with a high frequency of poly-pharmacy patients, the number of mismanaged patients and medication errors has increased.  Our study, holding all other things constant, hypothesizes that modifying the visual representation of the medication history within an EMR will increase…

Identification of the causal mutation for a congenital limb abnormality in Mediterranean river buffalo

Mediterranean river buffalo have recently undergone strong selection for increased quality and quantity of milk for mozzarella cheese production. Strong selection for traits such as milk production are often associated with increased inbreeding, leading to decreased genetic diversity and an increase in genetic disease prevalence. Transverse hemimelia (TH) is a congenital developmental abnormality characterized by the absence of a variable portion of the distal limbs. It occurs at the rate of approximately 2-5% in Mediterranean river buffalo populations and causes significant production loss in affected animals as well as in carriers of the disease, which are eliminated from the breeding…

Promoting Population Health Through mHealth: Can Personal Health Management System Alter Personal Health Behavior?

Abstract:  mHealth provides unprecedented medium to collect valuable information on patients, which was otherwise hard to collect and incorporate into management decision making. Several interventions conducted by a leading university school of medicine to measure the health outcome of its population showed significant positive impact on improving population health outcomes.  Caroline et al., (2013) conducted a meta-analysis and outlined a number of questions for investigating the effect of mHealth. These questions are related to investigating functions that make mHealth most effective, the type of behavior change technique that are effective, and whether the effectiveness of interventions is influenced by setting…

Operational Taxonomic Units classification: Diving into Phenetics Approach with the 16S Subunit

Operational Taxonomic Units (or OTUs) are useful approximations for taxonomic species in groups where classification is difficult. As such, OTU classifications based on DNA sequences are commonly used in metagenomics studies to describe sample diversity. Since there are no a priori definitions of what constitutes an OTU, a number of different methods have been applied for defining them. We analyze 20,229 16S rDNA subunit sequences to explore the nature of several OTU classification approaches. In order to do so, we first perform all possible pairwise comparisons with the Needleman-Wunsch alignment algorithm. We then constructed OTU clusters using several different sampling…

Researching the communication structure of online health communities with social network analysis and computational linguistics, a group informatics approach

Online communities are virtual social structures that promote communication among Internet users on various discussion subjects.  Research has found that online communities make communication possible for every person and are highly active with almost every Web user being a member of a forum.  Online health communities connect people facing health concerns, exchange health information, and offer emotional support.  In health care, online support fora are shown to enable emotional support and information sharing. Objective: This research analyzes the interactions of an online health community and study its participants’ interests and level of engagement.  The objective is to develop an informatics…

Large-scale biomedical image analysis using Big Data Infrastructure

Biomedical imaging informatics involves the analysis, manipulation, and computational calculation of digitally acquired biomedical images to gain knowledge and insights. Informatics technologies are being developed to assist biomedical researchers to identify meaningful objects from raw images, extract content, process information, discover relationships, and share knowledge. However, as the ‘Big Data’ era arrives, the ever-exploding image quantity, resolution, and imaging modalities are challenging the already computationally intensive methods. Big Data Ecosystem is expected to accelerate the computing speed and therefore leaves more room to improve the efficiency and accuracy of image analysis, storage, retrieval and sharing. Last but not least, researchers…