Andy Perkins, Principal Investigator

Dr. 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

Nicole is currently working toward a MS in Computer Science and expects to graduate in December 2019.

MS Student

Nicole Liu

Mary Lee is an undergraduate student in Biological Engineering. Her project involves developing methods for analyzing gene co-expression networks associated with brain disease or injury.

Undergraduate Researcher

Mary Lee

Daniel is currently working toward a MS in Computer Science and expects to graduate in December 2019.

MS Student

Daniel Rayborn

CJ Nguyen is an undergraduate in Software Engineering. He is using computational methods to studying and compare the spectral properties of various biological networks.

Undergraduate Researcher

CJ Nguyen

PhD Graduates

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.

PhD Graduate

Tamer Aldwairi

Adam Thrash graduated with his PhD in Computer Science in summer 2019. His work was on machine learning methods for genome quality assessment.

PhD Graduate

Adam Thrash

MS Graduates

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.

Graduate Student Worker

Tanmay Bhowmik

Jesse Farek earned his MS in Computer Science in spring 2015. His work was on random forest algorithms to analyse SNP associations.

MS Graduate

Jesse Farek

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.

Graduate Student Worker

Pummi Singh

Jia Zhou completed her MS in Computer Science while pursing her PhD in Biological Sciences. She graduated in spring 2018.

MS Graduate

Jia Zhou

Raghu Chinni completed his MS in Computer Science in spring 2012.

MS Graduate

Raghu Chinni

Dilip Gautam earned his MS in Computer Science in spring 2012. His work focused upon statistical and probabilistic methods for handling ambiguous sequence mappings and metagenomic samples.

MS Graduate

Dilip Gautam

Wei Wang earned his MS in Computer Science in spring 2014. He worked to develop algorithms for more accurate mapping of high throughput sequence data in metatranscriptomic applications.

MS Graduate

Wei Wang

Undergraduate Alumni

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.

Undergraduate Student

Ankit Arya

Meagan Bratton was a 2017 participant in the REU in Computational Biology that worked with collaborators in the College of Veterinary Medicine to identify genes possibly associated with equine asthma.

Undergraduate Student

Meagan Bratton

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.

Undergraduate Student

Kortni Dees

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.

Undergraduate Student

Kate Haynes

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.

Undergraduate Student

Trey Gaines

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.

Undergraduate Student

Ian Johnston

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.

Undergraduate Student

Ianna May

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.

Undergraduate Student

Abiola Olaniyan

Nisha Tripathi was an undergraduate student that worked with the lab during fall 2016-spring 2017 to build a computational pipeline for differential gene expression analysis and comparison of results from various software.

Undergraduate Student

Nisha Tripathi

Dakota Williams was a 2019 participant in the NIH R25 Bridges to the Baccalaureate program from East Mississippi Community College. His work involved automating comparison of results among various sequence mapping and differential expression software.

Undergraduate Student

Dakota Williams

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.

Undergraduate Student

Rajhkeem Beck

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.

Undergraduate Student

Joe Buza

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.

Undergraduate Student

Ben Elam

Baylee Holt was a 2019 participant in the Computational Biology REU from Alcorn State University. Her work focused on identifying the effects of various sequencing mapping programs on transcriptomic data.

Undergraduate Student

Baylee Holt

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.

Undergraduate Student

Michael Johnson

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

Undergraduate Student

Glen Luker

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.

Undergraduate Student

Maya May

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.

Undergraduate Student

Jonathan Rice

Jacob Wall was a summer 2016 participant in the REU in Computational Biology from The Evergreen State College. His was focused on investigating various methods for identification of differentially expressed genes to determine their suitability for use with small sample size

Undergraduate Student

Jacob Wall