Selected Projects 2014

Anthony Chang - Artificial Nerual Networks in Protein Secondary Structure Predictions

Chenxi Chen - Review of Recent NGS Short Reads Alignment Tools

Eva Huang - A critical review of single-cell RNA sequencing-based genetic profiling for human embryo -s

Gergana Vandova - Critical assessment of phylogenetic algorithms

Bing Wu - Review of Computation for RNA-Seq Studies: Development and Improvement

Anne Ye - A Critical Review of Computational Protein Design Strategies: Progress, Limitations, and Improvements

Dana Yeo - Drug Repurposing

Samantha Zarati - A critical review of computational neurological models

Selected Projects 2013

Yang Bi - A critical review on chromatin architecture modeling with high throughput chromosome conformation capture techniques

Devon Chandler-Brown - Molecular Dynamics Simulations: Methods and Value in the Folding Problem

Paul Godden - Machine Learning for Genome-Wide Association Studies: A Critical Review

Yooli Light - Metatranscriptomic Pipeline Draft for Linking Functions to Microbes in Environmental Microbial Community

Lance Middleton - A critical review of MuTaME scoring for ceRNA predictions

Bojan Milic - From Whole-Cell Simulation to WholeCellKB: A Critical Review of Whole-Cell Computational Modeling

Charles Zheng - Frequentist tests of association for imputed genotypes

Simon Zheng - A Critical Review of Natural Language Processing Approaches to Discovering Drug-Drug Interactions from Medical Literature

Selected Projects 2012

Yunqin Lee - Review of the Clustering and Feature Extraction Methods of Mass Cytometry

I. Lin - Discovering Transcription Factor Binding Motif Sequences

Dian Yang - A Critical Review of Gene Set Enrichment Analysis: Development and Improvement

Jake Wang - Critical Review of the Rosetta Algorithm

Alex Wilkinson- Computational Prediction of Protein-protein interaction

Samantha Woodward - A Critical Analysis of DNA Data Compression Methods

Brian Yu - Comparison of Microarrayc and RNA-Seq Analysis Methods for Single Cell Transcriptiomics

Kristen Carnohan - Methods for Transmembrane Protein Topology and Alpha Helix Prediction

Clarence Cheng - Experimentally-guided computational RNA structure modeling

Caroline Townsend - A critical review of ChIP-seq enrichment analysis tools

Selected Projects 2011

Brand, Veronica - Degenerate Primer Design using Computational Tools

Constant, David - Template-Based Modeling of Protein Structure

Gopal, Nikhil - Comparison of Short Read De Novo Alignment Algorithms

Harris, Jason - Using MotifScan to Discover Transcription Factor Binding Sites in Non‐human Genomes

Lee, Ruby - A Critical Review of Strategies for Selecting Haplotype Tag SNPs

Ly, Nina -Evaluating Protein-Protein Docking Web Servers

Mayer-Blackwell, Koshian - Hunting the Monsters in the Database A critical review of computational tools for detecting chimeric 16S PCR amplification

Pauerstein, Philip - RNA-Seq: Current Methods and Potential Applications

Perez, Adam -Predicting Protein Complex Structures: A Review of the Docking Process

Ye, Simon - Considerations and Recent Advances in Molecular Dynamics

Zou, Amy - Multiple Sequence Alignments

 

Selected Projects 2010

Arul, Hari: A Review of Phylogenetic Trees and Their Function in Evolutionary Studies

Bhand, Maneesh: Handling Rearrangements in DNA Sequence Alignment

Blair, Stuart: A review of the Gene Ontology: past developments, present roles, and future possibilities

Boxer, Lisa: Hi-C: Genome-wide Chromosome Conformation Capture

Ghezelayagh, Talayeh: Analysis of the Computational Methods Available for MicroRNA Target Prediction

Guiney, Evan: Evaluation of currently available web-servers for 3D-structure based prediction of protein interface regions

Guo, Ming: Biological Pathways - A pathway to explore diseases mechanism

Hester, Jim: Comprehensive comparison of RNA-­‐Seq alignment packages

Ito, William: A review of recent advances in ab initio protein folding by the Folding@home project

Kuenzel, Laney: Gene clustering methods for time series microarray data

Lee, Jong: Recent Advances in Statistical Methods for Genome-Wide Association Studies

Lim, Jaclyn: ChIP-Seq: The new way to ‘seq’ genome wide for transcription factor binding patterns

Sae-Seaw, Por: A review of graphical models for gene regulatory network inference using microarray data

Shiigi, Stacey: Mathematical models for designing synthetic ribosome binding sites to control protein expression in prokaryotes

Van de Mark, Daniel: The Numerous Caveats of Designing, Implementing, and Interpreting Genome-Wide Association Studies

Youngs, Noah: Progress in the Side-Chain Prediction Problem

 

Selected Projects 2009

Altman, Tomer: Large-Scale Alignment of Encyclopedic Metabolic Networks

Auburn, Mark: Recent Advances in the Determination of Three-­-Dimensional Chromosomal Conformation

Bettinger, Keith: The Phylo-HMM approach to problems in comparative genomics, with examples.

Chung, Christina: Mapping Short Sequencing Reads: Challenges & Solutions

Davies, Kelli: Eukaryotic Gene Prediction

Dow, Graham: The limitation of genome wide association studies

Edris, Badreddin: A comparison of the Oligomap and TargetScan algorithms for miRNA target analysis

Gharegozlou, Roham: Protein Multiple Sequence Alignment: Benchmarks and Comparison

Naul, Brett: A Review of Support Vector Machines in Computational Biology

Singh, Simar: Sequence- and Structure-Based Functional Annotation

Tang, Grace: Critical Review of Functional Site Prediction

Wang, Jennifer: Protein Structure Prediction by Comparative Modeling: An analysis of methodology

Yang, Arthur: Analysis of Methodology in Cophylogenetic Studies

 

Selected Projects 2008

Li, Molong: Computational Methods of Discovering Gene Modules and Constructing Regulatory Networks

Sim, Adeline: Recent Developments in RNA Secondary Structure Prediction

Williams, Brandon: A Review on Common Applications Designed to Optimize the SEQUEST Search Algorithm With Respect to Limiting False Positive Identification

Min, Hye Young: A Review of Computational Methods for miRNA Target Prediction

Sutton, Shirley: Multiple Sequence Alignment: A Critical Comparison of Four Popular Programs

Tan, Meng How: Network Inference from Multiple Data Sources

Vinjamoori, Anant: Using Network Motif Analysis to Explore Transcriptional Regulatory Systems