Past Research Reports

2/3/12 -

Andrew Stergachis
"Circuitry and dynamics of human transcription factor regulatory networks"

Alessandra Sullivan
"Genomic Footprints of a Phenotypic Capacitor"

Nate Peters
"Identification of Tramtrack69 targets required for tube morphogenesis in the Drosophila ovary"

1/27/12 -

Jeff Vierstra
"Fine-scale architecture of human cis-regulatory elements"

Sam Lancaster
"Haploinsufficiency in Hybrid Yeast"

1/13/12 -

Chad Weisbrod, Ray Malfavon-Borja

1/6/12 -

Keolu Fox
"Next Generation Sequence Analysis of Human Blood Group Antigens"

Jeff Staples
"Splice site variants in 5400 exomes"

12/13/11 -

First year rotation talks: Jorgen Nelson, Matthew Snyder, Elyse Hope, Rachel Gittelman

12/9/11 -

First year rotation talks: Stephanie Battle, Alex Mason, Sonia Ting

12/2/11 -

Michael Duyzend
"Autism: A whole-genome approach"

David Young
"The Fitness Landscape of the PAB1 RRM2 Domain"

11/18/11 -

Jennifer Andrie:
"Genome-wide analysis of cis-regulatory variation affecting translation efficiency in Saccharomyces cerevisiae"

Dan Skelly:
"Comprehensive phenomics analysis of Saccharomyces cerevisiae"

11/4/11 -

Benjamin Vernot, Anna Brosius

10/28/11 -

Max Press
'Evolutionary Inference of Function for Bacterial Hsp90'

Matt Rich
"Deep Mutational Scanning of HIV-1 Tat"

10/21/11 -

Alexander Nuttle
“The Evolution of Human-Specific SRGAP2 Duplications”

Jennifer McCreight

10/14/11 -

Tanya Grancharova
"Exploring the Viral Hypothesis: Zinc Finger Binding to LTR Retroelements"

10/7/11 -

Nik Krumm:
"A novel method for discovery and genotyping of CNVs using exome sequencing"

William Edelman:
"Dynamic Changes In Protein Abundance In Response to Oxidative Stress"

9/30/11 -

Josh Burton:
"Algorithms to detect structural mutations in cancer genomes." 

Akash Kumar:
"Hypermutated genomes" in Advanced Prostate Cancer

6/7/11 - First year rotation talks: Josh Burton, Keolu Fox, Jennifer McCreight, Matt Rich, Jeff Staples, Jennifer Wagner

6/3/11 - First year rotation talks: William Edelman, Tanya Grancharova, Alexander Nuttle, Max Press, Benjamin Vernot

5/21/11 -

Ryan Emerson

"Gypsy and the Birth of the SCAN Domain"

Katrina Claw

"Evolution and proteomics of primate seminal fluid"

5/20/11 -

Evelyn Vincow

"Role of the PINK1/Parkin pathway in mitochondrial turnover: an in vivo proteomics approach"

Sarah Ng

"Analysis of variation in a 50Kb locus"

5/13/11 -

Ray Malfavon-Borja -

Functional analysis of a third and ancient TRIMCyp gene fusion

Nate Peters -

"Identification of Tramtrack69 targets required for Drosophila dorsal appendage morphogenesis"

5/6/11 -

Tom Pohl
"Centromeres induce early activation of origins of DNA replication"

Sean Schneider
"Adventures in Virology: Zinc Fingers, Sap Suckers and Blood Suckers"

4/29/11 -

Rupali Patwardhan
"High-resolution enhancer-bashing"

4/22/11 -

Jarrett Egertson

"De novo Correction of Systematic Mass Measurement Error in Low Resolution MS/MS Data"

Melody Palmer

"Characterizing the abalone sperm proteome and the evolution of a newly discovered sperm protein"

4/15/11 -

Jacob Kitzman
"Haplotype-resolved genome sequencing with short reads"

Peter Sudmant
"The diversity, evolution and expression of human segmental duplications and embedded gene families"

4/8/11 - Keisha Carlson, Ben Whiddon

Keisha Carlson
"Genome-wide role of fast evolving tandem repeats in phenotypic variation"

Ben Whiddon
"Ablating the neurons that release MCH improves some phenotypes of obese leptin-deficient mice"

4/1/11 -

Cailyn Spurrell
"Targeted sequencing of breast cancer families"

Matt Maurano
"Identification of functional regulatory polymorphism in vivo"

3/15/11 -

First year rotation talks: Jeff Staples, Tanya Grancharova, Alexander Nuttle, Max Press, Ben Vernot

3/11/11 -

First year rotation talks: Matt Rich, Jennifer Wagner, Keolu Fox, Jennifer McCreight, Josh Burton

3/4/11 -

Leslie Emery

"Evaluating and improving methods for detecting selection"

Roie Levy

"Assembly of host associated Microbial Communities: A systems approach"

2/25/11 -

Andrew Adey

"Transposase Based DNA Library Construction for High-Throughput Sequencing and Capture of Sequence Contiguity"

2/18/11 - Kyle Siebenthall, Renee George

2/4/11 -

Dan Skelly
"A statistical framework for detecting allele-specific gene expression using RNA-Seq"

Oliver Serang
"A graphical approach to high ploidy SNP genotyping in beautiful Braizilian sugarcane"

1/28/11 -

Jennifer Lachowiec
"HSP90 aids in the maintenance of gene duplicates"

Sara Di Rienzi
"Evolution of the DNA Replication Landscape"

1/21/11 -

Lisa Beutler
"The Striatal Circuitry Underlying Amphetamine Sensitization"

Alan Rubin
"Expression-based genome segmentation"

Jeff Staples
Autumn Quarter rotation presentation

1/7/11 -

Cait Rippey

Alex Nord
"CNV detection using high-coverage targeted sequencing data"

12/14/10 -

First year rotation talks: Alexander Nuttle, Max Press, Matt Rich, Benjamin Vernot, Jennifer Wagner//

12/10/10 -

First year rotation talks: Josh Burton, William Edelman, Keolu Fox, Tanya Grancharova, Jennifer McCreight

12/3/10 -

Nik Krumm
"Recurrent Co-occurring Genomic Deletions in Intellectual Disability"

Akash Kumar
"Discovering candidate genes in prostate cancer using exome sequencing"

11/19/10 -

Rose Okamoto
"Genetic Analysis of a Mitochondrial Quality Control Pathway"

Jeff Vierstra
"In vivo discovery and characterization of DNA binding proteins"

11/12/10 -

Adam Gordon
"Whole-exome resequencing for pharmacogenetic discovery"

Aaron Miller
"In vivo characterization of natural variants"

11/5/10 -

Blake Hovde
"Gene Specific Manipulations with Homing Endonucleases"

Tzitziki Lemus Vergara
"How much of the variation released by HSP90 reduction arises from perturbation of the miRNA pathway"

10/29/10 -

Anna Brosius
"How do point mutations and aneuploides contribute to fitness changes in evolved yeast?"

Joe Hiatt
"Molecular tagging: a versatile approach to extend the read length, accuracy, and utility of massively parallel sequencing"

10/22/10 -

Alessandra Oddone
"Characterization of tissue-specific cis-regulatory elements in Arabidopsis"

Sharon Greenblum
"Network Analysis of the Human Gut Microbiome"

10/15/10 -

Caitlin Connelly
"Evolution of regulatory regions in yeast"

Rachel Diederich
"Detecting Exon Loss in Primates Using Read Depth of Sequencing"

10/8/10 -

Chad Weisbrod
"Accurate Peptide Fragment Mass Analysis: Multiplexed Peptide Identification and Quantification"

Andrew Stergachis
"Genomics beyond the ribosome: Proteomic and genomic tools to elucidate regulatory DNA occupancy and function"

6/8/10 - First Year Student Rotation Presentations:
Tzitziki Lemus Vergara, Aaron Miller, Alessandra Oddone, Rose Okamoto, Jeff Vierstra

6/4/10 - First Year Student Rotation Presentations:
Caitlin Connelly, Rachel Diederich, Adam Gordon, Sharon Greenblum, Blake Hovde

5/28/10 -

Max Boeck
"Developmental Delay of the E-Lineage is Caused by Deletions in the GATA Transcription Factors end-1 and end-3"

Alan Rubin
"Expression-based genome segmentation"

5/21/10 -

Evelyn Vincow
"Role of the PINK1/Parkin pathway in mitochondrial quality control: a proteomics approach"

Cailyn Spurrell
"Discovery of rare variants in familial breast cancer"

5/14/10 -

Nick Coley
"The Interplay Between Hair Cell Differentiation and Support Cell Specification"

Sarah Ng
"Exome Sequencing : Promise and Perils"

5/12/10 -

Doug Fowler
"High Resolution Mapping of Protein Sequence–Function Relationships"

Alex Nord
"Enrichment of inherited CNVs in autism"

5/7/10 -

Kevin Roach
"Molecular Evolution of the Primate Kinetochore"

4/23/10 -

Tom Pohl
"Do yeast centromeres advance activation time of nearby origins of DNA replication"

Nate Peters
"The Role of the Tramtrack69 Transcription Factor During Drosophila Dorsal Appendage Morphogenesis"

4/16/10 -

Andy Itsara
"De Novo Rates and Selection of Large Copy-Number Variation"

4/9/10 -

Oliver Serang -
"The relationship between protein identification and peptide detectability in tandem mass spectrometry"

Celia Payen -
"Dissection of Fitness Determinants and Mechanisms Associated with Recurrent Rearrangement in Yeast"

4/2/10 -

Leslie Kim
"The mitochondrial quality control system in mitochondrial DNA heteroplasmy"

Ray Malfavon-Borja
"Ancient and recurrent evolution of the antiviral gene fusion TRIMCyp in primates"

3/16/10 - First Year Student Rotation Presentations:
Caitlin Connelly, Rachel Diederich, Adam Gordon, Sharon Greenblum, Blake Hovde, Tzitziki Lemus Vergara

3/12/10 - First Year Student Rotation Presentations:
Aaron Miller, Alessandra Oddone, Rose Okamoto, Jeff Vierstra

2/26/10 -

Cait Rippey

Jan Aagaard
"Pollen Tube Proteins & Reproductive Isolation in Yellow Monkeyflowers"

2/19/10 -

Janne Lempe
"Hsp90 and other capacitors of phenotypic variation in plants"

Rupali Patwardhan
"High-throughput analysis of DNA regulatory elements"

2/12/10 -

James Thompson
"Using relationships between protein sequences to build structural models of proteins"

2/5/10 -

Tom Nicholas
"Identification of Structural Variation Within and Between Breeds of Dogs"  

Jennifer Lachowiec
"Environmental and Genetic Variation buffered by HSP90"

1/29/10 -

Rori Rohlfs
"Population group-based differential false positive rates in familial forensic identification"

Lisa Beutler
"NMDA Receptor Signaling in Behavioral Sensitization to Amphetamine"

1/22/10 -

Dan Skelly
"Detecting allele-specific gene expression using RNA-Seq"

Renee George
"Evolutionary analysis of primate exomes"

1/15/10 -

Keisha Carlson
"Variable Tandem Repeats as a Mechanism Generating Phenotypic Diversity"

Kyle Siebenthall
"An Allele-Specific Method to Study the Nuclear Organization of the FSHD Locus"

1/8/10 -

Diane Dickel
"Bioinformatic and Experimental Characterization of Microsatellite Repeats in Transcribed Regions of the Human and Chimpanzee Genomes"

Sean Thomas
"The chromatin landscape of drosophila embryo development"

12/15/09 - First Year Student Rotation Presentations:
Tzitziki Lemus Vergara, Aaron Miller, Alessandra Oddone, Rose Okamoto, Rachel Diederich

12/11/09 - First Year Student Rotation Presentations:
Caitlin Connelly, Adam Gordon, Sharon Greenblum, Blake Hovde, Jeff Vierstra

12/4/09 - First Year Student Research Presentations:
Anna Brosius, Joe Hiatt, Andrew Stergachis, Chad Weisbrod

11/20/09 -

Ivan Liachko
"Discovery of novel DNA replication initiation mechanisms through ARS mapping in different yeast species"

Veronika Glukhova
“Characterization of Werner protein interactions and modifications to elucidate its role in DNA damage repair and genome stability”

11/13/09 -

Michael Hoffman -
"Segway: pattern discovery in multitrack functional genomics data"

11/6/09 -

Ben Whiddon -
"Gene targeted ablation of neurons expressing melanin-concentrating hormone"

Melody Rynerson -
"The Abalone Sperm Proteome"

10/30/09 -

Sean Schneider

Peter Sudmant
"The Diversity of Copy Number Variation Across Hundreds of Sequenced Human Genomes"

10/23/09 -

Matt Maurano -
"The insulator CTCF as a model for protein-DNA recognition"

Ben Smith -

10/16/09 -

Leslie Emery
"Sex-biased demographic processes in the human expansion out of Africa"

Jacob Kitzman
"Genome-scale functional profiling of non-coding sequence elements"

10/9/09 -

Katrina Claw
"Adaptive Evolution of Gamete Fusion Proteins in Primates"

Jarrett Egertson
"Deconvolution of MS/MS Spectra Acquired by Data-Independent-Acquisition"

6/9/09 -

first year student rotation presentations:
Katrina Claw, Melody Rynerson, Peter Sudmant, Keisha Carlson, Jarrett Egertson

6/5/09 -

first year student rotation presentations:
Jacob Kitzman, Leslie Emery, Matt Maurano, Sean Schneider

5/22/09 -

Shameek Biswas -
"Genetic Analysis of TLR7 Mediated Innate Immune Response"

Kevin Roach -
"Evolution of the Primate Kinetochore"

5/15/09 -

Dan Blick
"Strategies for studying C. elegans embryogenesis with 4D imaging"

Angela Poole
"The effects of the PINK1/Parkin pathway on neuronal integrity"

5/8/09 -

Alan Rubin -
"Mutation Patterns in Cancer Genomes"

Carlos Araya -
"Whole genome sequencing in evolved and suppressor yeasts"

5/1/09 -

Brig Mecham -
"Supervised Normalization of Microarray Data"

4/24/09 -

Leslie Kim
"Selective mitochondrial turnover"

Geoff Findlay
"Drosophila Seminal Fluid Proteins: Proteomic Identification and Functional Analysis"

4/17/09 -

Ryan Emerson
"Polymorphic Gain and Loss of Protein Domains in Zinc Finger Transcription Factors"

Graham McVicker
"Genomic Signatures of Germline Gene Expression"

4/10/09 -

Kevin Schutz
"Novel ends justify novel means:  developing tRNA ligase to isolate and identify RNAs with 2'-3' cyclic phosphates"

Kristen Lewis
"Improving DNA Mixture Interpretation: Evaluating the Use of Amplification-Specific Parameters"

4/3/09 -

Mike Hoopmann:
"Maximizing sample coverage with post analysis data acquisition"

3/17/09 -

first year rotation presentations:
Melody Rynerson, Leslie Emery, Matt Maurano, Sean Schneider, Peter Sudmant

3/13/09 -

first year rotation presentations:
Katrina Claw, Jacob Kitzman, Keisha Carlson, Jarrett Egertson

2/20/09 -

Oliver Serang
"A Statistical Procedure for Identifying Proteins Directly from Spectra in a Tandem Mass Spectrometry Experiment"

2/13/09 -

Tom Nicholas
"The Genomic Architecture of Segmental Duplications and Copy Number Variation in Dogs"

Rori Rohlfs

2/6/09 -

Sara Di Rienzi
"Do replication origins promote genome instability?"

Evelyn Vincow
"Oxidative stress, mitochondrial dynamics, and mitochondrial turnover in a Drosophila model of Parkinson disease"

1/30/09 -

Will Sheffler
"Protein Core Packing and Model Quality in the Protein Data Bank"

James Thompson
"Comparative Modeling of Protein Structures"

1/23/09 -

Kyle Siebenthall
"Examining the Role of Nuclear Organization in Facioscapulohumeral Dystrophy”

1/16/09 -

Lisa Beutler
"Striatal NMDA receptors in amphetamine sensitization and structural plasticity"

Max Boeck
"Deletion of the redundant GATA factor end-3 causes defects in cell movement, division timing and downstream gene expression."

1/9/09 -

Diane Dickel
"A Genomic Approach to Studying Repeat Expansions: Transcribed Microsatellite Repeats in Psychiatric Disease"

12/5/08 - first year rotation presentations: Jacob Kitzman, Matt Maurano, Melody Rynerson, Sean Schneider, Peter Sudmant

11/21/08 - reserved for first year rotation presentations: Ben Whiddon, Keisha Carlson, Katrina Claw, Jarrett Egertson, Leslie Emery

11/14/08 -

Sayer Herin
"Evolution of Cis-Regulation in Primates"

Tom Pohl
"Centromere’s influence on activation of nearby origins of replication"

11/7/08 -

Steve Salipante
"In Hodgkin's Lymphoma, Experiment Watches You!"

Alex Nord

10/31/08 -

Jeff Kidd
"Sequencing structurally variant haplotypes reveals mechanisms of genomic rearrangement"

Sarah Ng
"Resequencing the Protein Coding Genome"

10/24/08 -

Cailyn Spurrell
"Inherited Structural Variants in Familial Breast Cancer"

Andy Itsara
"Population Analysis of Large Copy Number Variants"

10/17/08 -

Rupali Patwardhan
"Parallel subassembly of locally derived shotgun microreads"

Dan Skelly
"Population genomics of intron splicing in 38 Saccharomyces cerevisiae genomes"

10/3/08 -

Renee George
"Identification of interacting primate fertilization proteins using coevolution"

Ray Malfavon-Borja
"Exploring the Role of CyclophilinA in Retroviral Restriction"

9/26/08 - Caitlin Rippey
"Rare structural genomic variants in schizophrenia: analysis of an interesting case"

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"

Adele Mitchell
"Using Markov Chain Monte Carlo to map deletions in trios"

5/23/06 -

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

Andy Sharp
"Structural Variation of the Human Genome: Polymorphism and Disease"

5/16/06 -

Rachel Mackelprang
"Evolution of the T Cell Receptor Alpha Locus: A Within and Between Species Approach"

5/9/06 -

Lazar Dimitrov
"Age Induced Genetic Instability in Budding Yeast"

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

5/2/06 -

Tobias Mann
"Adding DNA binding predictions to PCR primer design"

Angela Poole
"What Does Parkin Do?"

4/25/06 -

Kiran Dhillon
"Analysis of the in vivo functions of the Werner syndrome protein"

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 -

Chul Joo Kang
"Estimation of heterogeneity of recombination rate using full-likelihood model"

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

4/4/06 -

Aaron Klammer
"Probabilistic models of peptide fragmentation in tandem mass spectrometry"

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 -

Mary Kuhner
"Population genetics in a pre-cancer condition"

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 -

Michael Boyle
"twinpeaks and G Proteins in Drosophila Dorsal Appendage Morphogenesis"

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"

Joanna Kelley
"Understanding the Adaptive Evolution of enamelin in Primates"

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"