Past Research Reports

6/6/08 -

First Year Rotation Talks:
Renee George, Alex Nord, Rupali Patwardhan, Dan Skelly, Cailyn Spurrell

5/30/08 -

First Year Rotation Talks:
Sayer Herin, Ray Malfavon-Borja, Sarah Ng

5/9/08 -

Brig Mecham
"Identifying and controlling for sources of heterogeneity in genome- wide association studies"

Abstract:

Microarray technology has been used to measure variation in gene expression for a variety of diseases, including many types of cancer. As this technology becomes cheaper and users more comfortable with analysis of array data there has been a change in the emphasis on small studies consisting of two to six arrays, to larger studies consisting of hundreds to even thousands of samples in a single experiment. Intuition tells us that larger studies are more likely to suffer from spuriously correlated data as the sheer volume of samples requires arrays to be grouped with respect to date of processing, manufactoring lot (or array batch), and even labelling reagent. These factors are examples of Expression Heterogeneity: a general class of factors that confound associations between gene
expression variation and the biological quantity of interest. Controlling for EH is the motivation for all commonly used normalization procedures, including the lowess-dye bias method, quantile normalization, and VSN. In this talk I'll explore expression variation associated with tumor status in three panels of prostate cancer studies. The effects of EH on each study are investigated, and a novel method is described that can account for bias introduced by certain types of EH. The method is applied to these data and shown to considerably increase the consistency across these studies when compared to the results obtained from other common analysis techniques. We also apply this method to other studies that extend its relevance to multiple generations of Affymetrix platform as well as two-color assays.
This work is of direct interest to people involved in the analysis or interpretation of genomic studies using microarray technology. It is probably also of interest to people using the new Solexa data as similar models should apply here as well.

5/2/08 -

Matt Sandel

Troy Zerr
"SCIMM and SCOUT: Model-Based Clustering and Outlier Detection For Copy Number Variation"

4/25/08 -

Carlos Araya
"Randomly addressed protein arrays: Moving towards self-assembly"

Cindy Desmarais
"Approaches to Studying Variation in the Promoter Regions of Human Genes"

4/18/08 -

Will Sheffler
"Validation of Protein Databank Structures Using Rosetta"

Greg Finney
"Label-Free Differential Proteomics: Discovery and Directed LC-MS Methods"

4/11/08 -

Jeff Kidd
"Mapping and sequencing of structural variation from eight human genomes"

4/4/08 -

Mike Hoopmann
"A Sweet Method For Mass Spectrometry: High-Throughput, Site-Specific Identification of Glycosylated Proteins"

Kevin Schutz
"Genomic Approaches to Capturing Chromosome Architecture and Nontraditional RNAs"

3/14/08 - First Year Rotation Talks:
Renee George, Sayer Herin, Ray Malfavon-Borja, Sarah Ng

3/7/08 - First Year Rotation Talks:
Alex Nord, Rupali Patwardhan, Dan Skelly, Cailyn Spurrell

2/15/08 -

Tom Nicholas
"Analysis of Structural Variation in the Modern Domestic Dog"

Angela Poole
"The PINK1/Parkin Pathway Influences Mitochondrial Morphology"

2/8/08 -

Kristen Lewis
"Identification of Individuals through Familial Database Searches" and "Improving DNA Mixture Interpretation"

Steve Salipante
"A Weird Explanation for a Weird Disease: a Novel Protein Implicated in Cyclic Neutropenia"

2/1/08 -

Geoff Findlay
"Proteomic and Evolutionary Analysis of Drosophila Seminal Fluid"

Lazar Dimitrov
"Identifying factors involved in mitochondrial genome instability in S. cerevisiae"

1/25/08 -

Diane Dickel
"A genomic approach to studying repeat instability in schizophrenia"

Max Boeck
"A role for the redundant: the unique functions of the GATA transcription factors end-1 and end-3 in C. elegans endodermal development"

1/18/08 -

Vivian Hawkins
"Origin and spread of dihydrofolate reductase mutant alleles in Plasmodium vivax"

David Spencer
"Applications of haplotype matching"

1/11/08 -

Rori Rohlfs
"Discrete data does not produce continuous test statistics: Ramifications of assuming continuity in HWE testing"

Graham McVicker
"Purifying Selection in Primate Evolution"

12/7/07 - First Year Rotation Talks:
Caitlin Rippey, Sarah Ng, Rupali Patwardhan, Dan Skelly, Cailyn Spurrell

11/30/07 - First Year Rotation Talks:
Andy Itsara, Renee George, Sayer Herin, Ray Malfavon-Borja, Alex Nord,

11/16/07 -

Shameek Biswas
"Describing Population Structure in the Human Genome Diversity Project"

Mark Enstrom
"Genome Scale Phenotyping of Francisella Novicida"

11/9/07 -

Joanna Kelley
"Functional diversification and evolution of antifreeze proteins in the Antarctic fish Lycodichthys dearborni"

Ryan Emerson
"Insights into the Evolutionary History of Poly-ZF Transcription Factors"

11/2/07 -

James Thomp/son
"Comparative Modeling Using Rosetta"

10/26/07 -

Kyle Siebenthall
“In Search of the Molecular Basis of FSHD”

Oliver Serang
"Algorithms for Protein Identification in Mass Spectrometry"

10/19/07 -

Alan Rubin
"Mutation Patterns in Cancer"

Kevin Roach
“Centromere Drive”

10/5/07 -

Dan Blick
"Investigating cell fate specification in the C lineage during C. elegans embryogenesis"

Sara Di Rienzi
"Comparative Analysis of Replication Origins using the Genomes of Pre- and Post- Whole Genome Duplication Yeast Species"

9/28/07 -

Lisa Beutler
"progressive motor deficits in an NMDA receptor knock-out mouse"

Nick Coley
"Zebrafish Lateral Line Enhancer Elucidation Via Comparative Genomics
and a Transgenic Approach" and "A Potential Role for Stat3 in Hair Cell Regeneration"

6/5/07 - First Year Rotation Talks:
Kevin Roach, Sara Di Rienzi, Oliver Serang, Kyle Siebenthall

5/29/07 - First Year Rotation Talks:
Dan Blick, Alan Rubin, Ryan Emerson, Chris Murphy

5/22/07 -

Kiran Dhillon
"Analysis of in vivo functions of WRN and BLM RecQ helicase proteins"

Will Sheffler
"Protein core packing flaws in computationally generated structures
and what to do about it. Plus, the rosetta video Game, coming soon to
an x-box near you!"

5/15/07 -

Charla Lambert -
"Using the FY locus to search for African-specific natural selection in the human genome"

Carlos Araya -
"Towards recording counts on DNA, & Random-address protein arrays"

5/8/07 -

Lazar Dimitrov -
"Mitochondrial genome instability in S. cerevisiae"

Ben Smith -
"Tight junction regulation and Claudin-3 in the blood-testis barrier"

5/1/07 -

Chul Joo Kang
"The full likelihood approach for estimation of recombination rate heterogeneity"

Shobhit Gupta
"Tomtom: Quantifying similarity between motifs"

4/24/07 -

Sara Selgrade -
"Investigating the antimicrobial peptide response in Pseudomonas aeruginosa"

Mark Enstrom -
"Genome Scale Phenotyping of a Bacterial Mutant Library"

4/17/07 -

Zhaoshi Jiang -
"Evolutionary Reconstruction of Segmental Duplications Reveals Punctuated Cores of Human Gene Innovation"

Aaron Klammer -
"Peptide retention time prediction yields improved tandem mass spectrum identification for diverse chromatography conditions"

4/10/07 -

Greg Finney -
"Relative Protein Abundance Levels and Changes in Post-Translational
Modifications using LC-MS and LC-MS/MS"

Michael Boyle -
"Controlling Cell Shapes and Migrations: tramtrack and Gbeta13F are required for multiple events during Drosophila dorsal appendage morphogenesis."

4/3/07 -

Mike Hoopmann
"18O-labeling techniques and peptide isotope distribution identification in mass spectra"

3/27/07 -

Shameek Biswas
"Characterizing Variance Components of Gene Expression Variation in Humans"

3/13/07 - First Year Rotation Talks:
Dan Blick, Sara Di Rienzi, Ryan Emerson, Chris Murphy

3/6/07 - First Year Rotation Talks:
Kevin Roach, Alan Rubin, Oliver Serang, Kyle Siebenthall

2/27/07 -

Cindy Desmarais
"Exploring Evolution and Diversity in the Human Genome Using the HKA Test"

Brig Mecham
"Investigating Prostate Cancer using Mouse Models"

2/20/07 -

Nathan Clark
"Tracing Protein-protein Co-evolution through Correlated Selective Pressure"

Jian Qiu
"Prediction of the structural quality of predicted protein structural models"

2/13/07 -

David Spencer
"Exploring new technologies for resequencing"

Vivian Hawkins
"Analysis of the origin and spread of mutations in Plasmodium vivax dihydrofolate reductase"

2/6/07 -

Andrew Sharp
"Discovery of novel recurrent genomic disorders from the duplication architecture of the human genome"

Zhihong Zhang
"Genomewide identification of spliced introns using a tiling microarray"

1/30/07 -

Diane Genereux
"When are a few errors better than none?: Assessing the fidelity of epigenetic information"

Lukas Kall
"A semi-supervised machine learning technique for peptide identification from shotgun proteomics datasets"

12/12/06 -

First Year Rotation Talks:
Lisa Beutler, Kevin Roach, Alan Rubin, Oliver Serang, Kyle Siebenthall

12/5/06 -

First Year Rotation Talks:
Dan Blick, Sara Di Rienzi, Ryan Emerson, Nick Coley, Chris Murphy

11/28/06 -

Angela Poole
"Proteomic Analysis Of Parkin and PINK1"

Rori Rohlfs
"Demonstrating single-stage association studies' superior power"

11/21/06 -

Diane Dickel -
"A Genomic Approach to Studying Repeat Instability in Schizophrenia"

Marianna Ivanov -
"Characterizing Mechanisms of Normal Gene Expression Variation in the Mouse Prostate"

11/14/06 -

Karen Chisholm -
"Mutator genes permissive for genomic rearrangements at Alu repeats"

Troy Zerr -

11/7/06 -

Tom Nicholas -
"Ascertainment of Interbreed Variation across Breeds of the Modern Domestic Dog"

James Thompson -
"Ab-initio structure prediction in CASP7"

10/31/06 -

Max Boeck -
"Dissecting GATA Factor Redundancy in the C. Elegans Endoderm"

James Ronald -
"The evolution of gene expression QTL in Saccharomyces cerevisiae"

10/24/06 -

Joanna Kelley -
"Positive selection in primate tooth enamelin and evidence for human population specific adaptation"

Kristen Lewis -
"Identification of Criminals and Mass Disaster Victims through Kinship DNA Database Searches"

10/17/06 -

Geoff Findlay -
"Cooperation, Competition and Coercion in Drosophila Reproduction"

Jeff Kidd -
"Extended Haplotype Homozygosity and Population Stratification of a Common APOBEC Gene Deletion Polymorphism"

10/10/06 -

Laura Certain -
"Population Genetics of Drug Resistance in P. falciparum"

Graham McVicker -
"Exploring the relationship between mutational asymmetry and germline transcription in primates"

10/3/06 -
Steve Salipante
"Phylogenetic Fate Mapping: What Somatic Mutations can Tell Us About Embryogenesis"

Matt Sandel
"Dissecting redundancy in a C. elegans developmental pathway"

6/6/06 -

Chung-Ying Huang
"Profiling Response and Resistance Mechanisms to Taxane-Based Chemotherapy in Prostate Cancer"

5/30/06 -

Nathan Clark
"Female-male Co-evolution: Following a Protein-protein Interaction over Time"

5/23/06 -

Greg Finney
"Label-free Relative Quantitation of Protein Expression Levels Using LC/MS"

5/16/06 -

5/9/06 -

Mark Enstrom
"High Throughput Methods for Screening Bacterial Gene Disruption Libraries"

5/2/06 -

Angela Poole
"What Does Parkin Do?"

4/25/06 -

Charla Lambert
"Inferring the evolutionary history of the Duffy-O mutation"

4/18/06

Aaron Hinz
"Regulation of a Pseudomonas aeruginosa efflux pump important for aminoglycoside resistance"

Sara Selgrade
"Investigating the antimicrobial peptide response in Pseudomonas aeruginosa"

4/11/06 -

Steve Voght
"Analysis of Drosophila NPC1b, an essential cholesterol absorption gene"

4/4/06 -

3/28/06 -

Cindy Desmarais
"Exploring Diversity in the Human Genome Using the HKA Test"

Jennifer Gogarten
"Evolutionary Dynamics of the Olfactory Receptor Subgenome"

3/7/06 -

Wenyi Feng
"When forks go bad: replication under stress"

Laurence Rohmer
"Search for the genome polymorphisms responsible for the virulence attenuation of the live vaccine strain Francisella tularensis ssp. holarctica strain LVS."

2/28/06 -

Tushar Bhangale
"Automating resequencing based detection of insertion-deletion polymorphisms"

Bob Thurman
"Discovery of higher-order functional features in large genomes"

2/21/06 -

Rhiju Das
"New tricks in predicting global protein folds"

Barry Lutz
"Development of Single-cell Suspension Traps for Measurement of Leukocyte Adhesion Dynamics."

2/14/06 -

John Murray
"Single-Cell Expression Profiling in C. elegans"

Jian Qiu
"Protein Complex Co-membership Prediction and Protein Structure Quality Prediction"

2/7/06 -

Michael Eberle
"Frequency-Matching SNPs Reveals Extended Linkage Disequilibrium and Evidence for Natural Selection"

Tera Newman
"Polymorphic human structural variation: New insights into genomic structure and genetic impact"

1/31/06 -

Wade Smith
"Towards Understanding MHC Disease Associations: Analysis of Common, Extended MHC Haplotypes"

1/24/06 -

Jan Aagaard
"Identification and Evolution of Abalone Egg Coat Proteins"

1/17/06 -

Max Robinson
"Mapping mRNA sequences back to the genome to identify introns"

Will Sheffler
"the good the bad and the ugly (in protein structure prediction)"

1/10/06 -

Larry Gallagher
"Comprehensive transposon mutagenesis and analysis of essential genes in Francisella novicida."

Katie Rudd
"Elevated rates of sister chromatid exchange at chromosome ends"

12/6/05 -

Laura Certain
"Separating mixed samples of P. falciparum DNA"

11/29/05 -

Ross Centers
"A Selection for Arbitrary Protein Secretion by Yeast"

11/22/05 -

11/15/05 -

Ben Smith
"Spermatogenesis 101: the role of androgen receptor in seminiferous tubules"

Laura Flinn
"Genomic analysis of HIN200 gene family and lupus susceptibility"

11/8/05 -

Brig Mecham
"Analyzing expression data to identify pathways involved in prostate cancer and normal prostate development identifies an activation of developmental pathways in tumors"

Divya Bhat
"Protein Structure Prediction: Characterizing the Energy Landscape for Improved Sampling"

11/1/05 -

Megan Fluegel
"Drosophila NPC1a is required for proper sterol trafficking and metabolism"

Mike Hoopmann
"Automated mass spectrometry analysis with Hardklor"

10/25/05 -

Shameek Biswas
"Singular Value Decomposition for studying QTL mapping in Yeast"

10/18/05 -

Carlos Araya
"Remix Biology: Exploring cells as a substrate for engineering"

Karen Chisholm
Genetic backgrounds susceptible to genomic deletions: Alu-mediated mutations of BRCA1 as a model

10/11/05 -

Zhaoshi Jiang
"A global phylogenetic recontruction of human segmental duplications"

Jon Bleyhl
"Gene Innovation via Segmental Duplications"

10/4/05 -

James Ronald
"Local regulatory variation in Saccharomyces cerevisiae"

David Spencer
"Detecting disease causing mutations by haplotype matching"