Projects Submitted by Workshop Participants

This list represents projects developed by participants in a variety of BEDROCK sponsored workshops which varied in length from 3 days to 9 days. Some are in preliminary form, others are more fully developed.

1. The FtsH Proteases of Oryza sativa and Arabidopsis thaliana – Orthologs and Parologs?
2. Molecular Visualization Powerpoint
3. A Study of Tamarix, a Invasive Desert Species or, Another Juicy Hypothesis Bites the Dust
4. Differential gene expression in breast carcinoma
5. Using MAPPfinder to explore connections between microarray data sets, Gene Ontology, and biological pathways
6. Using GenMAPP and MAPPFinder to analyze publicly available cancer microarray data.
7. Three isoforms of human tissue plasminogen activator
8. Functional Genetic Clusters
9. Introducing Database Mining to Molecular Genetics Students (Juniors & Seniors)
10. Bioinformatics in Introductory Biology
11. Links and Resources
12. Exploring Bioinformatics with Insulin
13. Signal transduction molecules
14. Comparison of alpha subunits of phycocyanins and phycoerythrins with the structure of Galdieria sulphuraria phycocyanin
15. Comparision of Homeobox Domains: Plant vs. Engrailed
16. Bioinformatic Assignments in Computer Science Courses
17. Bioinformatics project in conservation genetics
18. Development of a bioinformatics project for high school laboratories
19. Changes in the V3 region of p120 that correlate with a rapid decline in CD4 count
20. Genetic Diversity and Conservation of Pan troglodytes
21. The highly conserved coronavirus RNA polymerase and SARS
22. Molecular phylogeny of a chef salad
23. A Comparison between the Structures of Human Like Chitinase and a bacterial Chitinase
24. Using Microarray Technology to Explore Problems in Systems Biology.
25. Influenza
26. The Phylogenetic Tree Constructor
27. GenMAPP and MAPPFinder for Systems Biology Education
28. Bridges to Structure
29. New Zealand Cyatheaceae Phylogenies?
30. Systems Approaches to Adopting, Teaching and Learning Models
31. Simulating Gene Expression using Netlogo
32. Prion biology problem space: Mad cows, itchy sheep and protein structure
33. Rice Phylogeny Revisited
34. Campus Evolution
35. Metabolic Pathways via Tom Sawyer
36. Tribes within subspecies Pt Verus Chimps
37. Analysis of Whippo Hypothesis
38. Phylogenetic relationships among chimpanzee subspecies
39. Analysis of Mitochondrial DNA from Chimpanzees in Tanzania
40. Maintaining Chimp Genetic Diversity
41. Molecular Evolution of West Nile Virus
42. Helix-loop-helix: Simple is not Boring!
43. Bioinformatic Investigation of Insulin Signalling System
44. Antibiotic Resistance Project Space
45. Introducing Phylogenetics
46. The ABCs of Floral MADSness
47. Icebreaker Introduction to Bioinformatics
48. A bioinformatics simulation of a mutant workup from a model genetic organism
49. Bioinformatics Introductory Module: Use of Bioinformatics Tools in Genome Assembly and Annotation
50. Adaptation of HIV Problem Space to High School Students
51. A Tutorial of Sequence Matching in Oracle
52. Integrating genomics in teaching metabolism
53. Mechanisms of Drug Resistance
54. Evolutionary Relationship of Greenbug Biotypes
55. Searching For New Phylogenetically-Informative Nuclear Genes in Bryophytes
56. Mammalian Evolution Using IRBP Gene
57. Undergraduate Exercises with Trp Cage
58. What is the Evolutionary History and Function of GLP-1?
59. Molecular Evolution: From Sequence to Structure to Function
60. Heat Resistant Amylase
61. Nitrogenase: Enzyme catalyzing N-fixation
62. Aquaporins: Are regions of the protein conserved?
63. Protein Structure of Snake Venom: A Phylogenetic Study
64. Structural Analysis of Amino Acid Sequence Variation of Immunoglobulin Epsilon Heavy Chain
65. Comparison of p53 Structure: Wild type vs. mutant
66. Cuddling with your souieeee-tee: A bad case of the flu
67. Hemoglobin: Soup to Nuts
68. BRCA Mutations and Breast Cancer
69. Verifying Morphologically Based Finch Taxonomy by Appeal to Sequence Data
70. Is the Red Wolf Real?
71. Fundamental methods of computer science and their application to bioinformatics
72. Biomedical Case Studies
73. Student Exploration of Water Transport
74. Transferrins "R US! : An evolutionary look at changes in the structure of this protein
75. Gene Sleuthing
76. Going Green: Using GFP to Investigate Bioinformatics
77. LIMPET: Leptin, an insular molecule physiologically investigates evolutionary theory.
78. World Population: A Model Approach
79. DIVERSITY OF HIV MEMBRANE PROTEIN gp120 IN INDIVIDUALS WITH DIFFERENT RATES OF CD4 CELL DECLINE
80. Get a Rise out of Life!
81. Making Introductory Biology Labs Cooler: Data Acquisition and Analysis
82. How does Antiretroviral Therapy Affect HIV Mutation?
83. Water - A Coordinated Study Learning Community
84. Exploring Cancer Incidence Rates: Creating the Multi-hit Model of Cancer in STELLA.
85. javaFoodWeb: Bridging the gap between Excel and Niches
86. Orbitals and Wave Functions
87. Confessions of an innovator
88. North Georgia College & State University Biology Curriculum Development
89. Genomics: from gene to conserved function to disease
90. Bio-Medical Informatics - From the Computer Programmer's Perspective
91. Antigenic shift v. drift in avian and mammalian Sino-influenza type A viruses.
92. Comparison of the Olfactory Receptor Genes in Canines and Primates
93. Demonstration file
94. PFK Through The Ages
95. Creating a New Workspace: Genetic Diversity of Mycobacterium tuberculosis
96. Visually Demonstrating the Principles of Protein Folding
97. SARS: A Multi-disciplinary Exploration
98. Bioinformatics Curriculum
99. Exploring Phylogeny in the Introductory Microbiology Lab
100. Using Bioinformatics to Investigate Evolution, Phylogeny, and Virulence in the Human Pathogen Clostridium difficile (with Brad Goodner, institute presenter, as a group member)
101. Seeing the forest for the trees
102. Fat chickens, fat people, fat chance?
103. Microbial Ecology of Kentucky Bourbon
104. Taking the Bite (Byte?) out of Phylogeny
105. A laboratory unit investigating 2,4-dichlorophenoxyacetic acid degradation in soils
106. Bad Hygiene or Bad Bug? (Investigation of C. difficile outbreak and toxicity using bioinformatics tools, case-based approach, and molecular genetics simulation using CaseIt software; linked with Project 2 above)
107. Genetics in your Blood: Hemoglobin Workspace to Illustrate Basic Genetic Concepts
108. Do HIV+ Rapid Progressors Show More Divergenece than Non-Progressors?
109. Poster: The Puzzling Properties of the Permease (PPP)
110. Scholarship of Teaching and Learning resources
111. Projecting Presence of Pecans: Mining Environmental Data to Identify Ecological Limits of Species Distribution
112. Malaria II - Microarray analysis tools
113. Malaria I - Case study and bioinformatics activities
114. STD Case It! The Soldier's Gift
115. Green Scum Up the Bay:Using Linear Modeling to Analyze Algal Blooms in the Chesapeake Bay
116. Citrus Canker Investigation Space
117. Protein Folding in 3-d and 2-d
118. Hedgehog-emony!
119. Taking BioQUEST Home
120. Interactions Among Dissolved Nitrogen, Phosphate, and Dissolved Oxygen at Several Sites in Chesapeake Bay in 2000.
121. The Tree P's: The 'Pistemology of Phylogeny
122. Of Pigs and People on the Potomac
123. Using Esteem-style models to study two-species and three-species interactions in comparison with an in vitro situation
124. Find The Fake Ones
125. HIV Evolution During Infection
126. RNA --> DNA --> RNA --> PROTEIN
127. Globin Genes
128. Comparative Genomics: The Globin Gene in Human and Bats
129. Using mtDNA to trace human geographic origin
130. RNA-Folding Programming Project for High-Performance Computing
131. Interplay between Selective Pressure and Genetic Diversity of Viral Populations in HIV Patients
132. Re-annotation of nitrate reductase gene cluster
133. "Kefir Kommunity: Investigating the Population Composition and Dynamics of the Kefir Grain Consortium."
134. Peanut Butter and Jelly Or Salmonella
135. Conservation and Taxonomic Distribution of Arsenate Detoxification Proteins, ArsA, ArsB, and ArsC
136. Microbes Spanning the World: Exploring Phylogenetic Relationships and Protein Structure
137. Student Research in Microbial Biogeography: Introducing Bioinformatics Tools
138. Bioinformatic modules for Biology instruction
139. Global Malaria Problem Space
140. A Consortium Approach for Introducing Bioinformatics to Undergraduates
141. "A Microbiological and Bioinformatics Safari: Searching for Cellulolytic Prokaryotes from the Environment and Characterization of their Cellulase Genes."
142. Incorporation of class discussions to strengthen bioinformatic concepts Example: Re-examining phylogenies, a discussion
143. Microbial Mystery: Identification of Microbes Present in Soil
144. INTRODUCTION TO BIOINFORMATICS BACTERIAL IDENTIFICATION USING 16s rDNA SEQUENCE ANALYSIS
145. Introduction to Interdisciplinary Problem Solving
146. Using BLAST to investigate genes expressed during loblolly pine embryogenesis
147. Avian Influenza
148. Dolphin Phylogeny
149. HIV Envelope Mutations and Onset of AIDS
150. HIV Strain Variation in Africa
151. Insulin binding to the receptor
152. Acetylcholine Receptor Binding Toxins
153. Molecule Informatics Portfolio
154. Seeing the Trees Through the Forest : Arthropod phylogeny based on morphology and molecular data
155. Anthrax toxin: Examining the relationship between structure and function
156. Escherichia coli O157:H7 Outbreak from Fresh Spinach
157. Protein Chronometers
158. Distributions of Extinction Events through the Cenozoic
159. Evolution within Australian Salmonella strains
160. Click Clack - Milk Attack??
161. Don’t Kiss a Chicken in Cairo or Human and Avian Influenza Virus Hemagglutinin 5 Protein Phylogeny
162. The Molecular Genetics Explorer: a simulation that unifies Genetics, Biochemistry, and Molecular Biology
163. Food for Sex: or how to attract a pollinator.
164. Lactase evolution problem space
165. Pathway-Pondering: Metabolic Engineering Problem Space
166. Modeling selection for lactase persistence in African pastoralist and agro-pastoralist societies
167. Trees from the Seas
168. Hyper-accumulation capability of Silene vulgaris in relation to its phylogeny
169. Biostatistics Data & Lab Search Tool (BiDLaST)
170. Global Health
171. Desiccation Tolerance: Can Mosses Help Feed And Fuel The World
172. Grant Project: Resurrecting Math
173. Modeling haplotype mutation rates
174. Cooperative Learning
175. POSTER: Do other organisms have chalcone isomerase?
176. What does that phylogeny really mean?
177. Integrating (Comparing?) Plant and Animal Physiology
178. Anthocyanin as an Acid/Base Indicator--Activity Series
179. A Model of Factors Related to Tradeoffs in Cyanogenesis and Seed Production in Trifolium repens
180. 4-H Presentation: Using Drugs 2CoPE
181. BioMorph ESTEEM Module
182. Ethnobotany as a Hook to Generate Interest in Plant Research
183. A Model to Describe the Effect of the Timing of Herbivory on Subsequent Leaf Growth
184. Spice Invaders
185. An Exercise in Leaf Growth Modeling based on Wisconsin Fast Plants
186. BlueberryBlues
187. Resources from Yaffa Grossman
188. MASE: A Model of Mutation and Selection: Evolution
189. Insertion Events:Integrating Bioinformatics Into Existing Biology Courses
190. Loss of Adhesion Phenotype Correlated with Loss of Conservation of Extracellular Region and C-terminus in Cadherin
191. pfam01617Erhlichia
192. Structural and Phylogenetic Relationships of Eukaryotic and Some Prokaryotic NAD+ and NADP+ Isocitrate Dehydrogenases
193. Tryptophan Biosynthesis in Chlamydia
194. Show Me the Way to Go Home: Evolution of chemotaxis proteins MCP and CheA in the transition from a free-living to pathogenic life style in Bordetella
195. CRISPR: Clustered regularly interspaced short palindromic repeats
196. Around the world in 800 proteorhodopsins
197. Variations in among TrpG and TrpD among the Proteobacteria
198. Distribution of an Extracellular Protein Motif Across the Domains
199. A Metagenomic Analysis of Polymicrobial Environments in the Undergraduate Laboratory
200. Incorporating inquiry using bioinformatics across the biology curriculum
201. Introducing Bioinformatics Using the Nitrogen Cycle
202. Introductory Course in Bioinformatics
203. Demonstrating Biodiverstiy through Bioinformatics
204. Preparing Students for Annotation Projects
205. What's in a Genome?

Copyright ©2008 BioQUEST Curriculum Consortium, All Rights Reserved. This material is based upon work supported by the National Science Foundation under Grant No. 0127498. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.