Principal Investigator

Andy Perkins is an Associate Professor of Computer Science and Engineering at Mississippi State University. His research is in the areas of computational biology and bioinformatics, high performance computing, and graph theory. Recent research has focused on developing novel algorithms for accurate mapping and analysis of high throughput sequence data in applications such as RNA-Seq, metagenomic/metatranscriptomic studies, and investigation of small RNAs.

Current students

Adam Thrash is an MS student in Computer Science. He is working on the development and testing of algorithms for metatranscriptomic sequence analysis.

Former students

	Tamer Aldwairi graduated with his PhD in Computational Engineering in fall 2014. His research involved analysis of high throughput sequence data for the investigation of single nucleotide polymorphisms and small RNAs.			Ankit Arya was an undergraduate student working with collaborators at the USDA-ARS during spring 2013 on identifying insertion and deletion polymorphisms in genotyping-by-sequencing (GBS) data.
	Raghunandan Avula is an undergraduate student at Carnegie-Mellon University. He was jointly advised by Dr. Perkins and Dr. Federico Hoffmann (in the Department of Biochemistry and Molecular Biology) while a participant in in the Research Experiences for Undergraduates program during summer 2012.			Rajhkeem Beck was an undergraduate student in Biological Sciences and former Undergraduate Research and Mentoring (URM) fellow. He was with the lab during spring 2010-spring 2012. His work focused on the functional annotation of disease resistance-linked genes in maize.
	Tanmay Bhowmik worked with the team as a MS student in Computer Science with a research interest in Software Engineering. He developed software for mapping high throughput sequence reads to splice sites during fall 2009-summer 2010.			Joe Buza was an undergraduate student in Computer Science and worked in the lab fall 2010-spring 2011. He worked on algorithms for SNP analysis in high throughput sequence data.
	Kortni Dees worked with us during fall 2014-spring 2015 while an undergraduate in Computer Science. She investigated genome similarity and its relationship to cross-mapping in high throughput sequencing studies.			Ben Elam worked in the lab during spring 2014-summer 2014 while an undergraduate student in Mathematics. He developed software and user interfaces to help analyze various genomic features.
	Jesse Farek earned his MS in Computer Science in spring 2015. His work was on random forest algorithms to analyse SNP associations.			Trey Gaines was an undergraduate computer science major and worked with the lab during fall 2010-spring 2011. His project was on the proper assignment of genomic sequences in metagenomic and metatranscriptomic studies using high throughput sequencing technologies.
	Dilip Gautam was a MS student in Computer Science working on improved high throughput sequence mapping techniques. Dilip graduated with an MS in Computer Science in spring 2012. This work focused upon statistical and probabilistic methods for handing ambiguous mappings and metagenomic samples.			Kate Haynes worked in the lab during fall 2010 while she was an undergraduate Software Engineering major. Her project involved the functional integration of heterogeneous data types.
	Michael Johnson was a Research Experiences for Undergraduates in Computational Biology participant during summer 2010 and a student at Tennessee Tech University. He worked on applying statistical methods to ambiguous sequence reads.			Ian Johnston was an undergraduate student in Biochemistry and worked in the lab spring 2009-summer 2010. His project involved the development of a pipeline for the detection of alternative splicing events from EST data.
	Glen Luker was a participant in the Computational Biology Research Experiences for Undergraduates site during summer 2010 while a student at Itawamba Community College. He analyzed differential expression methods for RNA-Seq experiments.			Ianna May was an undergraduate student in Biological Sciences and is currently pursing graduate studies at Jackson State University. She worked  with Dr. Perkins and Dr. Memili (in the Department of Animal and Dairy Sciences) using computational tools to investigate certain microRNAs.
	Maya May was a participant in the Computational Biology Research Experiences for Undergraduates site during summer 2011. Maya is also a student at Tougaloo College. Her project involved the analysis of ambiguous sequence mappings in high throughput sequence data.			Abiola Olaniyan graduated with a BS in Computer Science in fall 2013. He worked on novel statistical algorithms for improved sequencing mapping in RNA-Seq studies.
	Jonathan Rice is an undergraduate student at Wofford College and a summer 2015 participant in our NSF-funded REU site in computational biology. He investigated genome similarity and its effects in metatranscriptomic studies.			Pummi Singh, while an MS student in Electrical Engineering, worked on developing stand-alone code for the functional integration of heterogeneous data types during spring-summer 2010.
	Wei Wang earned his MS in Computer Science in spring 2014. He worked to develop algorithms for mapping high throughput sequence data in metatranscriptomic applications.