Computational

Utilities 

Bioinformatics Tools:

• CAPRG: Sequence Assembling Pipeline for Next-Generation Sequencing of Non-Model Organisms. (Rawat et al 2012)
• ResistanceAlert is a novel genetics-enabled and molecular modeling-based computational tool for predicting undocumented or unknown resistance conferred by genetic mutations in invasive aquatic plants to herbicides. It includes a macromolecular structural biology-based software package that predicts resistance-conferring mutations in invasive aquatic plants. This product (prototype) will be released in FY18 and its primary users include USACE field managers involved in aquatic invasive plant management. No other tool with similar features is available. It can be easily adapted and tailored to customer-specified toxicity targets and thus has a great potential of attracting reimbursable customers.
• miRDisc is a novel computational program for discovery of predicted animal microRNAs (see https://pinfish.cs.usm.edu/earthworm/miRDisc/). MicroRNAs are a group of small non-coding RNAs that regulate gene expression and affect cellular functions. I designed the framework and led the coding of miRDisc, which overcame limitations of existing tools (e.g., the requirement of a complete reference genome) and improved prediction accuracy by using transcriptomic sequencing data.
• Integrated Statistical and Machine Learning (ISML) pipeline is a bioinformatool to identify biomarker genes from multiple classes of microarray data sets. This tool (published in 2010 in PLoS One 5(10): e13715) has so far been cited in 18 articles according to Google Scholar Citations.
• BLOM (Bayesian Learning and Optimization Model) and Web-BLOM (Web-based implementation of BLOM) (see https://pinfish.cs.usm.edu/earthworm/blom2/ and https://pinfish.cs.usm.edu/earthworm/blom/blom.jsp) both are products from my collaboration with the Computational Biology and Bioinformatics Laboratory (CBBL) led by Prof. Joe Zhang at School of Computing, University of Southern Mississippi (USM). I participated in and guided the development of BLOM and Web-BLOM for their targeted application in reverse engineering of gene regulatory networks.
• SeqAssist (https://pinfish.cs.usm.edu/earthworm/SeqAssist/) is a bioinformatics tool designed to serve as a valuable “assistant” to a broad range of researchers who conduct genome re-sequencing, transcriptomic sequencing (RNA-Seq), or de novo genome sequencing and assembly experiments. It generates basic statistics about a mega-dataset of millions of short sequencing reads, estimates the breadth, depth and evenness of genome-wide coverage, and compares two mega-datasets to determine the redundancy or overlapping rate.
• Earthworm Toxicogenomics KnowledgeBase (ETKB) was designed to serve as an open-source, web-accessible repository for the curation and integration of structural and functional analysis of earthworm toxicogenomics data (https://pinfish.cs.usm.edu/earthworm/etkb/). This portal is a product of collaboration between Dr. Nan Wang, School of Computing, USM and me. As a component of this portal, we also developed RefNetBuilder, a platform for construction of integrated reference gene regulatory networks from expressed sequence tags. Currently, both ETKB and RefNetBuilder are under construction.
• BeCow is a web-based tool dedicated to correction of sequencing errors in next generation sequencing (NGS) data. NGS dataset are often error-prone. Many error correction algorithms are available but each has pros and cons. BeCow provides users an opportunity to assess the best correction method for their datasets. This tool was developed by Isaac Akogwu under my supervision. Currently, the website (https://pinfish.cs.usm.edu/becow/) is under construction.
• Bioinformatic pipeline for discovery of chemosensory receptors (CRs) from transcriptomic data is a computational tool I developed to identify putative olfaction-related CR genes from an RNA-Seq dataset collected from the olfactory tissue of the northern leopard frog. I have applied this pipeline to other amphibian species (publication in preparation). This work can lead to the development of a non-invasive, olfactory attraction-based conservation strategy for protecting the endangered or at-risk amphibian species currently residing on military installations.

Also, be sure to check out our Knowledgebases.

References:Rawat A, Elasri MO, Gust KA, George G, Pham D, Scanlan L, Vulpe C, Perkins EJ (2012) CAPRG: Sequence assembling pipeline for next generation sequencing for non-model organisms. PLoS-ONE 7(2): e30370.