CompGen Fellowship Program
The CompGen Fellowship program awards predoctoral fellowships, funded by NSF and the University of Illinois, to promote interdisciplinary research in computational genomics. Fellows can be either computationally focused doctoral students with a biology co-advisor, or biologically focused doctoral students with a computational co-advisor. The fellowships were initially founded to support research directly relevant to the NSF-funded CompGen instrument, a supercomputer designed exclusively for genomic biology. The fellowship program now also supports fellows in any branch of interdisciplinary computational genomics.
Examples of focus areas in biology and genomics include accurate detection of genomic variation, development of statistical methods and methodologies for metagenomics, improvements in phylogeny reconstruction, enabling drug discovery through the use of microbial genomes, genotype-to-phenotype associations, and behavioral and neurological genomic biology. Computational projects may include topics such as reduction of data volume, optimization of storage hierarchy, identification of primitives that are common across algorithms, visualization and toolkits for computational genomic tools, construction of flexible software platforms that simplify the use of important statistical tools such as HMMs, tool flow optimization, mathematical simulations of genomic problems, and performance and reliability assessment of existing software.
2014–2015 CompGen Fellows
Emad Amin was enrolled in the Electrical and Computer Engineering (ECE) Ph.D. program. Previous degrees earned were a B.S. in electrical engineering from Sharif University of Technology, Tehran, Iran and an M.S. in electrical engineering from the University of Alberta, Edmonton, Canada. Amin’s research interests involved developing novel computational methods and algorithms, using information theory, applied mathematics, and signal processing to address various problems in computational biology. A research focus was developing novel specialized lossless and lossy compression algorithms for emerging genomic big-data formats. Professor Olgica Milenkovic (ECE) and Professor Jian Ma (BIOE) were his co-mentors.
Adam Hamilton is enrolled in the Neuroscience Program Ph.D. program. Previous degrees are a B.S. in psychology and a B.S. in genomics and molecular genetics, both from Michigan State University. Adam is interested in how interactions between the genome and environment result in contextually specific patterns of gene expression that can organize behavior (social, aggressive, food gathering, and otherwise) in honey bees. In the framework of CompGen, this entails developing novel techniques capable of combining gene expression data (both microarray and RNAseq) from behavioral experiments with computationally derived predictions of transcription factor binding sites to generate accurate and functionally relevant predictions of the transcriptional regulatory networks that underlie behavior. The architecture of these networks can then inform us about what transcription factors might be critical for organizing specific behaviors as well as whether a common set of transcription factors exists that can influence behavior in a more general sense. Adam is co-mentored by Professor and Director Gene Robinson (Carl R. Woese Institute for Genomic Biology) and Professor Saurabh Sinha (Computer Science). Adam served as a CompGen Fellow in 2013–2014 and his fellowship was renewed for 2014–2015.
Anand Ramachandran is enrolled in the Electrical and Computer Engineering (ECE) Ph.D. program. Previously, he earned a B. Tech in ECE from the National Institute of Technology, Calicut. Anand’s research focuses on adapting and optimizing graph-based techniques to compare genome data against a database of thousands of genomes using specialized hardware, aiming to achieve significant improvements in performance. Professor Deming Chen (ECE) and Professor Jian Ma (BIOE) and are his co-mentors. Anand served as a 2013–2014 CompGen Fellow; his fellowship was renewed for 2014–2015.
Zachary Stephens is enrolled in the Electrical and Computer Engineering (ECE) Ph.D. program. He received his B.S. in electrical engineering from The Pennsylvania State University, with two minors in mathematics and music technologies. Zachary is interested in estimating accuracy bounds in genomics problems (including read alignment, SNP calling) as affected by sequencing platform characteristics and reference genome repeat content. As a CompGen Fellow, his co-mentors are Professor Ravi Iyer (ECE) and Professor Bryan White (Animal Sciences).
Joseph Troy is enrolled in the Illinois Informatics Institute, Informatics Ph.D. program. He earned a B.S. in finance degree from UIUC and a M.S. in computer science degree from North Central College in Naperville. Using tools developed at UIUC, Joseph’s CompGen project determined new transcription factor genes in the honey bee genome and, additionally, the DNA binding sites of discovered transcription factor genes were studied to understand their evolutionarily history. Professor Lisa Stubbs (Molecular and Cellular Biology) and Professor Jian Ma (Bioengineering—BIOE) are his co-mentors.
Kedir Turi was enrolled in the Kinesiology and Community Health, Community Health Ph.D. program, having previously earned a master’s degree in applied economics from UIUC. Kedir’s research spanned a range of socioeconomic determinants of population health and health disparities. His investigations encompassed the macro-level determinants of population health (e.g., income inequality, economic activity, social capital, urbanization) to the meso-level (neighborhood contextual influences such as retail food environment, crime, and land use mix) down to the individual level (stress, psychosocial risk factors for cardiovascular disease). He used noble methods in econometrics, spatial analysis, epidemiology, and genomics to investigate the interrelationship between socioeconomic and psychological risk factors and genes in determining health status. Kedir’s co-mentors were Professor Ruby Mendenhall (African American Studies), Professor Sandra Rodriguez-Zas (Animal Sciences), and Professor Olgica Milenkovic (ECE).