Final Projects Submitted for Credit in

Computational Molecular Biology

Biochemistry 218/ BioMedical Informatics 231

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


Selected Projects 2007

Emerson, Tom: Conditional Random Fields for Classification of Protein Families: An Alternative to Hidden Markov Models

Goldstein, Ted: T-Tree, a new tool for taxonomy-based phylogenetic co-evolution analysis

Chen, Jennifer: Biological network analysis by division into modules, motifs, and themes based on physical and functional interactions between genes

Dennis, Steve: Simulating chromatin: Gene prediction at the structural level?

Shelef, Katie: A Critical Analysis of Degenerate Primer Design Programs

Keymer, Daniel: Efficiency and Accuracy of Phylogenetic Trees for Large Sequence Datasets

Li, Li: Pair Stochastic Context-Free Grammar Model in Comparative Sequence Analysis to Identify New Noncoding RNAs

Martinez-Alcantara, Antonio: SCFGs as Predictors of RNA's Secondary Structure

McElwain, Mark: A Critical Review of Gene Prediction Software

McPherson, Selwyn-Lloyd: Investigations Into a Genetic Algorithm for Protein Sequences

Ng, Chung W.: Inexact Pattern Matching Algorithms Via Automata

Peng, Chuang: Distance-Based Methods in Phylogenetic Tree Construction

Reitmaier, Rick: Review of Immunoinformatic Approaches to In-silico B-Cell Epitope Prediction

Verma, Seema: Bioinformatics Approaches to Biomarker Discovery


Selected Projects 2005

Carlson, Scott M.: Sequence Motifs are Necessary but not Sufficient for Predicting Post-translational Modifications

Hild II, Kenneth E. : Critical assessment of microarray analyses for gene identification

Kou, Charles : Analysis of Protein Structure Prediction by Homology Modeling

Patankar, Vishnu: Critical Analysis of the Computational Methods used to Discover Biomarkers to assist in the Early Detection of Disease

Ramamoorthy, Krithika : Critical Review of Methods available for Microarray Data Analysis

Sirota, Marina : Protein Multiple Alignment

Yu, Gang: Multivariate Projection Approaches for Microarray Analysis


Selected Projects 2004

Albert, Istevan: Predicting Protein-Protein Interactions with Collaborative Filtering Algorithms

Chan, Alexander: An Analysis of Pairwise Sequence Alignment Algorithm Complexities: Needleman-Wunsch, Smith-Waterman, FASTA, BLAST and Gapped BLAST

Choi, Jinkuk: A Critical Review of Computational Approaches on Finding Transcriptional Factor Binding Sites

Holbert, Daniel: Detecting motifs with EMOTIF-MAKER and MASIA: A critical comparison of two tools for finding protein motifs

Hwang, Andrew: Genotype Interpretation Algorithms: The Key to Resistance Testing for HIV-1

Lee, Jonathan: Analysis of Fundamental Exact and Inexact Pattern Matching Algorithms

Lo, Frederick: Three Recently Developed Algorithms for Aligning Distantly Related Proteins

Metzger, Ross: Multiple Alignment of Genomic Sequences

Mills, Brad: Towards Virtual Screening: Exploring the Potential (and Pitfalls) of Docking Software

Poon, Andy: Predicting Phosphorylation: A critique of the NetPhos program and potential alternatives

Sherwood, Rich: Trying on Phylogenetic Footprinting Methods

Sourirajan, Jayanthi: Protein Structure Prediction

Truong: A Critical Evaluation of Multiple Sequence Alignment

Watkins, Tara: Full-Atom Refinement Methods: The Key to High Resolution Protein Structure Prediction?


Selected Projects 2003

Ding, Yi : Singular Value Decomposition applied to the building of class predictor

Gunawardena, Shanti : Proteomics for the Discovery of Biomarkers and Diagnosis of Diseases

Huntzicker, Eric: Comparison of multiple sequence alignment algorithms

Knox, Kirstin : An Introduction To Motif Based Functional Classification of Large Protein Families

McGrath, Patrick: Uses of the Singular Value Decompositions in Biology

Moore, Chris Computational Methods of Identifying Novel sRNA Genes in E. coli

Pootakham, Wirulda: Will You Find Me? A Critical Evaluation of Motif Finding Programs: BioProspector, MDscan, andConsensus

Potter, Brian: Improved Methods for Inferring Regulatory Networks from Temporal Expression Data

Silverman, Adam: A Critical Review of Computational Methods for RNA Secondary Structure Prediction

Smetana, Caroline Reiss: Data Analysis Methods for DNA Microarrays: A Critical Review of Applications to Breast Cancer Research

Tan, Elyn C.: A Critical Review of Statistical Methods for Differential Analysis of 2-sample Microarrays

Ching, Wendy: Applying Near-Optimal Alignments to Protein Structure Predictions

Choundhury, Rahul: Application of Evolutionary Algorithms for Multiple Sequence Alignment

Davies, Erin Lane: A Critical Review of Computational Methods Used to Manage Microarray Data Sets

Goepfer, Cecile: Bioinformatics and Learning: Will Machines Outsmart Humans?

Gordon, Michael: Methods of Phylogenetics Analysis: New Improvements on Old Methods

Jacob, Reza: Docking Algorithms of Virtual Ligand Screening

Middleton, Jack Larry: Combinatorial Relationships in Transcription Factors

Mikels, : Can HMMgene Net a Gene Too?: Analysis of Alternative Splicing/Gene Predicting Algorithms

Parker, David William: A Survey of Classification Methods for Protein Domain Motions and Flexibility

Srivastava, Sanjay: Analysis of Methods for Predicting Protein Fold and Remote Homologue Recognition

Zhang, Zhiyong: An Overview of Protein Structure Prediction: From Homology to Ab Initio


Selected Projects from 2002

Almstead, Laura: Secondary Structure Prediction of Proposed RNAi Targets: Can Current Energy Minimization Algorithms Be Used?

Anekonda, Thimmappa: Artificial Neural Networks and Hidden Markov Models for Predicting the Protein Structures: The Secondary Structure Prediction in Caspases

Awan, Ali: In Silico Transfer of Ligand Binding Function between Structurally Analogous Proteins

Bennett, Eric: Utilization of primary and secondary structure elements to predict a protein's propensity to form amyloids

Boerner, Joanna: Improving Structural Superpositions for Complex Protein Structures by Limiting Query to Single Domains

Brandt, Stephanie: R You Out There?: Computational Strategies for Identifying Resistance (R) Genes in Arabidopsis and Beyond

Butler, Thomas: Protein-Ligand Docking: A Critical Review of Molecular Dynamics, Robotics, and Rotamer Library Methods

Cevallos, Randal: A Poor Mans EVA: Examining the Accuracy of Secondary Structure Prediction

Chao, Elizabeth: Critical Analysis of secondary Structure Prediction Algorithms

Chen, William: A comparison of search algorithms in identifying all the proteins from the PROSITE protein database

Doukas, Tammy: Analysis of Ebola Glycoprotein Sequences from Strains of Varying Lethality

Edwards, John D.: Organism specific Amino Acid Substitution Matrices

Evans, Stacy: Horizontal Gene Transfer: Effect and Affect on Computational Methods

Frazier, Tamara: The Use of Computational Methods to Describe and Establish Utility of a DNA Sequence for Purposes of Patenting

Garg, Amit: A Go Model of Proteins and RNA

Gentile, Margaret: Computational Methods for the Design of PCR Primers for the Amplification of functional Markers from Environmental Samples

Hovijitra, Norman Tana: Computational Methods For Predicting Transmembrane Alpha Helices

Jayachandran, Guha: Constructing Nature's Building Blocks: An Analysis of Computational protein Design Today

Ki, Hwangmin: Microarray Data Analysis Methods Comparison : A Review

Koeva, Martina: Strengths and weaknesses of parsimony and distance methods, used in the PHYLIP 3.6 software package

Krishnan, Jagannath: Data Analysis of Villin Headpiece Subdomain Folding

MacDougall, Christina: Determination of Common Motifs in Proteins Found to Interact with TriC/CCT Subunits During Large-Scale Saccharomyces Cerevisiae Pulldown Experiments

Meehan, Joseph Foles III: Using Blocks in Pairwise Sequence Alignment

Patariu, David: A new Method of Analysis and Scoring Gene Expression Data

Radosevich, Jenny: Structural Considerations are Important when Performing Computer-Based Searches for Molecular Mimics

Ren, Pei-Hsien: eMOTIF Maker: Nodally Awesome: Comparing Results of eMOTIF Maker with Neighbor-Joining Trees

Sen, George: Finding genes by computational methods: An analysis of the methods and programs

Shah, Jessica Harendra: A Review of DNA Microarray Data Analysis

Shan, Lu: Analysis of The DQ Family of The Human Leukocyte Antigens

Stickney, Heather: Investigating the Mechanism of Follistatin Function with Bioinformatics

Tam, Stephen: Motif Finding in Upstream Regions of Chaperone Genes Downregulated in Response to Environmental Changes

Taylor, Matthew: A Comparative Analysis of Position Specific Scoring Matrixes for the Identification of Related Proteins

Tenenbaum, Jessica Dale: Integration of the Comprehensive Microbial Resource into the BioSPICE Data Warehouse

Vigdal, Thomas: Insertion Site Similarities in the TC1/Mariner Element Family

Wang, Stream: Prediction of Tight Junction Localization Signal(s) in the Mammalian Systems

Yang, Hang Wai Brian: A Parallel implementation of Smith-Waterman Sequence Comparison Algorithm

Yang, Yong: Comparative Analysis of Methods for Multiple Sequence Alignment

Yeo, Thomas: Using Information Theory to reduce Complexities of Neural Networks in Protein Secondary Structure Prediction


Selected Projects from 2001 

Bair, Eric: An Improved Method for identifying Cell Cycle-regulatored Genes in Yeast

Burpo, John: A critical review of PCR primer design algorithms and crosshybridization case study. 

Chain, Patrick: Examining the Current Problems of Whole Genome Comparison: A Review

Hua, Yuanyuan: A sequence based analysis of the structure of SNARE family N terminal domains

Lalush, David: Clique Scoring for Enhancing Protein Family Classification of Hidden Markov Models

Moraleda, Jorge: New Secondary Structure Prediction software package using automatically trained Bayesian Networks

Pai, Sukesh: A study of tree construction method in Phylogeny

Pulavarthi, Prasanth: Construction of a database of co-occurring eMtotifs based on conditional Probabilities

Reddy, Kirthi: Analysis of Caenorhabditis elegans protein T09E8.2

Segars, Paul: Quantitative Analysis of tRNA Sequences Using Information Theory

Schroeder, Jamie: Characterization of Hypervariability in Conotoxins

Varma, Chris: Molecular Mechanical Force Fields

Wenes, Geert: A Case study of transcriptional regulation in bacteriophage l- infected E. coli cells

Zhang, Nancy: Markov Models for Classification of Protein Helices