Final Projects Submitted for Credit in

Selected Projects Autumn 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

Selected Projects Winter 2007

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 Spring 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

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

Selected Projects Winter 2003

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

Almassian, David: Bacterial Diagnostics: From Culture to Chip

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

Neal, Stephen: Analysis and Clustering of Gene Expression Data

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

Scoville, John: Kolmolgorov Complexity Based Distance Phylogenies

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

Mark, Barbara: Trinucleotide Repeats

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

Wu, Shanshan: Characterization of the Thioredoxin Superfamily

Yu, Kristine: Theoretical Determination of Amino Acid Substitution Groups based on Qualitative Physicochemical Properties

Zhang, Nancy: Markov Models for Classification of Protein Helices

Selected Projects from 2000 

Bandic, Zvonimir: Characterization of Human DNA topoisomerase Type I and II Proteins

Basch, Jonathan: A comparison of the CYP105 and CYP107 families

Buturovic, Lubomir: Supervised learning for functional annotation of yeast genome

Cheng, Jason: VZV Orf Web site

DeLano, Patrick: Reusable Objects for Bioinformatics

Flynn, Michael: The Search For Life In Our Solar System

Garvin, Michael: Clustering of GTP-binding proteins: A Bioinformatics Approach

Houghton, John: Using Similarity to Discover Upstream Regulation Sites in Bacteria

Iobst, Susanne: The Nuclear Receptor Superfamily

Ma, Dali: A "Dishevelled" Analysis

Selkirk, Marianne: Interaction of the poliovirus protein 3A with the E1B 19-kDa interacting protein 3 (BNip3)

Shandler, Scott: Theory for Improving Alignments by Using Motif, Domain, and Structural Information to Weight Aligned Regions

Suchorolski, Martin: Nuclear Hormone Receptors: Phylogenetic clustering and HMM Competitive Selection as tools for Data-mining

Wares, John: Analysis of Human Aldose Reductase

Waugh, Allison: Identifying an Evolutionarily Distant Relationship Between P3 and Hexon

Yeh, Iwei: Finding Proteins with Similar Functions between Plasmodia Falciparum and Humans

Zhang, Qi: Phylogenetic Analysis of the Ligand-binding Domains and the DNA-binding Domains of Nuclear Hormone Receptors:?Comparison of Maximum Parsimony and Neighbor-Joining Algorithm

Selected Projects from 1999  

Artuz, Robert & Durrance, Nathaniel: Analysis of Haemophilus influenzae, Escherchia coli, and Vibrio cholerae genomes for biofilm genes using model organism

Chen, Ruoying: Characterization of Multiple Functional Proteins Involved in Beta-Oxidation Systems

Harmon, Erin B.: Identification of Homologues to PDX1

Hunkapillar, Kathryn: Motif Discovery in Estrogen Receptor a and Estrogen Receptor b

Katz, William T.: Protein Secondary Structure Prediction A Review of the Problem and Methods

Kerrigan, Richard W.: A Search for Commonalities among DNA/DNA Class II Transposons at the Protein Level

McGettrick, Owen: Proposed Changes and Enhancements to Existing Protein Databases

Povolones, Michael: Characterization of porcupine: A mysterious gene involved wingless signaling

Saldanha, Alok: Construction of Phylogenies using Multiple BLOSUM Matrices

Sood, Nitin: Characterization of Pancreatic eIF-2 alpha kinase to show its role in linking protein synthesis to protein folding

Stephan, Megan: Use of bioinformatics methods to detect potential functional domains of the serotonin transporter.

Watson, Anjie: Exploring a Chromatin Based Mechanism of TUP1 Repression Using Genomics and Bioinformatics.

Wolinsky, Murray: An Experimental Implementation of the TEIRESIAS Algorithm

Selected Projects from 1998 

Alvarez-Savedra, Ezequiel: How do we smell?

Apaydin, Mehmet Serkin : Ligand-Protein Docking

Budman, Joe : Analysis of the human BRG1 protein

Byrnes, Michael: Intracellular localization and trafficking of proteins and organelles

Chan, Bob: CYRCA: Sequence Similarity Detection Using Graph Theory

Chen, G. Kevin : Computational Analysis of the Sequence Motifs of the Multidrug-resistant P-glycoproteins, A Subfamily of the ABC Transporters

DeFazio, Lisa: Characterization of Human DNA-Dependent Protein Kinase ,Catalytic Subunit

Feng, Peter: A survey of computational algorithms to analyze patterns of gene expression from cDNA/DNA chip Microarray data.

Haverty, Peter: Characterization of a Yeast Multicopper Oxidase

Hurowitz, Evan: Chemotaxis and Motility in Fifteen Organisms with Fully Sequenced Genomes

Konigshofer, Yves: Using Bioinformatics to Uncover Novel Transcription Factor Binding Sites

Liu, Xiaole: Analysis of Yeast Gene Promoter Sequences

Nakorn, Thanyaphong Na: Sequence analysis of C. elegans CED-7 protein

*Rajan, Rahul: Prediction of solvent-accessible helices in the cytoplasmic domains of cftr.

Simon, Alexander: Analysis of Heregulin beta-1 As a prototypic ligand of the Human EGF Receptor Family

Steinmetz, Lars: Identification of Three Regulatory Sequence Elements in Genes Correlated in Expression Level During the Early G1 Phase of the Saccharomyces Cerevisiae Cell Cycle

Swiko, Stefan: The mechanism of RACK-1 (Receptor for Activated C-Kinase)

* Usuka, Jonathan: A Statistical Analysis of the Occurrence of Protein Motifs at the Oligonucleotide Level: a Genomics Approach