Past Research Reports

2/23 - Steven Lee, Sarah Hilton, Chris Large

Sarah Hilton
"Estimating the age of deep viral lineages using experimentally informed site-specific substitution models"

Chris Large
"Science you can taste: Genomic evolution of beer yeast"

Steven Lee
"Automating Interpretation of Pharmacogenetic Data"

2/16 - Colin McNally, Seungsoo Kim, Cecilia Noecker

Seungsoo Kim
"Systematic genetic dissection of a unique inducible chromosomal contact"

Colin McNally:
"Effect of community composition on the evolutionary potential of microbial species"

Cecilia Noecker
"Model-based study of taxon-metabolite links in microbiomes"

2/9 - Tim Durham, Damon May, Alex Eng

Tim Durham
"Using FACS followed by ATAC-seq to Assess Tissue-Specific Chromatin Accessibility in C. elegans"

Alex Eng
"Taxa-function robustness in microbial communities"

Damon May
"Enriching the interpretation of proteomics experiments by sharing mass spectrum information within the proteomics community"

2/2 - Sam Entwisle

Sam Entwisle
"Cold adaptation remodels the mitochondrial proteome and acetylproteome in mouse brown fat"

1/26/18 -

Anne Clark
"Finding and characterizing introgression in S. cerevisiae"

Juhye Lee
“Distinguishing the evolutionary fates of influenza virus lineages using deep mutational scanning”

Sanjay Srivatsan
"Designing a Single Cell Genetic Screen with a Chromatin Readout" 

1/19/18 -

Ken Jean-Baptiste
"Mechanism of Acquired Thermotolerance in Arabidopsis thaliana"

Kyle Hess
"Mapping protein stability and mutational sensitivity on a proteome-wide scale"

Mitchell Vollger
"Whole genome assembly of Segmental duplications"

1/12/18 -

Claudia Espinoza
"What genes are involved in tube morphogenesis?" 

Anja Ollodart
"A high throughput method to determine mutation rate of DNA fidelity protein variants"

Taylor Ward
"Exploring the connection between genomic organization and cellular fitness with a novel tethering assay"

Tuesday, 12/12/17 -

first year rotation talks: Will DeWitt, Philip Dishuck, Michael Goldberg, Deanna Plubell

12/8/17 -

first year rotation talks: Danielle Boley, Florence Chardon, Emma De Neef, David Read

12/1/17 -

Gesine Cauer
"predicting response to drug combination therapy in acute myeloid leukemia"

April Lo
"A whole transcriptomic approach to functional phenotyping of somatic variants"

11/17/17 -

Kate Dusenbury
"Sequencing by Serology: Characterizing an Individual's Influenza Infection History."

Alberto Rivera
"Strategies for sequencing a repetitive egg coat gene"

11/3/17 -

Nick Popp
"A flexible method for suppression of off-target Cas9 gene editing"

Anthony Valente

Cindy Yeh
"Investigating the role of loss-of-function alleles in evolution"

10/27/17 -

Danny Lawrence
“Using RecA to explore how mutational effects change as proteins evolve”

Xiaojie Qiu
"Learning causal gene regulatory networks from single-cell RNA-seq data with Scribe"

Bianca Ruiz
"Genetic tools for mistranslation"

10/20/17 -

Nick Hasle
“High-throughput Selection of Cells using Microscopy”

Ian Smith
"New Approaches for Global Identification of Functional Phosphorylation Sites"

10/13/17 -

David Bacsik
"Targeted Sequencing of Influenza from Single Cells"

Emma Hoppe
"How does transcription affect splicing?"

Jose Pineda
"Most human branchpoints are redundant and tissue specific"

10/6/17 -

Martin Mathay
"From cells to systems: towards an in vivo map of the worm protein interactome"

Anna Minkina
"On the origin of cell types, by means of single cell lineage tracing"

9/29/17 -

Andria Ellis
"a forward genetic screen for aneuploidy"

Jared Mohr
"Hunting for complexes in their natural habitat: tools for in vivo cross-linking"

Tuesday, 6/6/17 -

first year rotation talks: Gesine Cauer, Emma Hoppe, Alberto Rivera, Bianca Ruiz, Ian Smith, Anthony Valente, Mitchell Vollger, Cindy Yeh

6/2/17 -

first year rotation talks: Andria Ellis, April Lo, Martin Mathay, Anna Minkina, Jared Mohr

5/26/17 -

Daniel Chee

Emily Killingbeck

Amanda Watts
"Modeling schizophrenia using human cerebral organoids"

5/19/17 -

Molly Gasperini
"Massively parallel perturbation of noncoding sequence to connect regulatory elements to their targets"

Abigail Keller
"A genome-wide approach to distinguish models of aneuploid fitness consequences"

Hannah Pliner
"Chromatin accessibility dynamics in skeletal muscle myogenesis"

5/12 /17 -

Clara Amorosi

Serena Liu

Damon May
"Lighting up the “dark matter” of proteomics"

5/5/17 -

Ken Chen

Michael Dorrity
"Exploring mechanisms of temperature-sensing by deep mutational scanning of the HSF1 trimerization domain"

Anja Ollodart

4/28/17 -

Rachel Dam
"Same cells, different tubes: dorsal appendage formation across drosophilids"

Vanessa Gray
"Predicting quantitative effects of protein mutations"

Jason Klein
"Studying the role of regulatory variation on GDF5 dosage and Osteoarthritis Susceptibility"

4/21/17 -

Junyue Cao
"Comprehensive single cell transcriptional profiling of a multicellular organism by combinatorial indexing"

Will Chen

Andrew Hill
"Using scRNA-seq as a readout for high-throughput genetic screens"

4/14/17 -

Heather Machkovech

Han-Yin Yang

4/7/17 -

Ethan Ahler
"Saturation mutagenesis of Src kinase reveals novel inhibitor resistance mechanisms"

Melissa Chiasson

3/31/17 -

Anne Clark
"Identifying introgressed regions in yeast genomes"

Wei Zhou
“Multiplexed identification of genomic targets for Ste12 DNA-binding domain variants”

3/14/17 -

first year rotation talks: Gesine Cauer, Andria Ellis, Emma Hoppe, April Lo, Martin Mathay, Anna Minkina

3/10/17 -

first year rotation talks: Jared Mohr, Alberto Rivera, Bianca Ruiz, Ian Smith, Anthony Valente, Mitchell Vollger, Cindy Yeh

3/3/17 -

Bryan Andrews

Cecilia Noecker

2/24/17 -

Tim Durham
"PREDICTD: PaRallel Epigenomics Data Imputation with Cloud-based Tensor Decomposition"

2/17/17 -

Colin McNally
"Constraints and Mechanisms in the Evolution of Bacterial Metabolic Interaction"

Brian Searle

2/10/17 -

Seungsoo Kim
"Genome engineering of chromosome conformation"

John Lazar
"The interaction between cell identity and chromatin remodelers"

2/3/17 -

Max Dougherty
"Discovery and annotation of young duplicate genes by enrichment and long-read sequencing”

1/27/17 -

Aaron Seo
"Homozygous BRCA1 truncation causes Fanconi Anemia"

1/20/17 -

Kelsey Lynch
"Linking DNA replication initiation defects and genome instability"

Aaron Wolf
"Modeling Archaic-Modern Human Admixture and Depletions of Introgressed Sequence"

1/13/17 - Lindsay Pino, Katherine Xue, Alex Eng

Alex Eng
"Computationally estimating functional robustness to taxonomic changes in microbial communities"

Lindsay Pino
"Building reliable global gene expression profiles from proteomic data"

Katherine Xue
"Influenza evolution displays parallelism at multiple spatiotemporal scales"

12/13/16 -

first year rotation talks: Gesine Cauer, Andria Ellis, Jared Mohr, Alberto Rivera, Bianca Ruiz, Mitchell Vollger, Cindy Yeh

12/9/16 -

first year rotation talks: Emma Hoppe, April Lo, Martin Mathay, Anna Minkina, Ian Smith, Anthony Valente

12/2/16 -

Nick Hasle (Fowler Lab) -
"Expanding the scope of deep mutational scans with in situ sequencing"

Sanjay Srivatsan (Trapnell Lab) -
"Developing a single cell forward genetic screen for the interrogation of regulatory DNA”

11/18/16 -

Madeleine Geisheker (Eichler Lab) -
"Hotspots of missense mutation identify novel neurodevelopment delay genes and functional domains"

Danny Lawrence (Bloom Lab) -
“Using recA to model mutational effects across deep evolutionary lineages”

11/4/16 -

Jolie Carlisle (Queitsch Lab) -
"The role of STE12 DNA-binding in a phenotypic trade-off"

Eliah Overbey (Hawkins Lab) -
"Journey through Embryonic Development: In Vitro Modeling of Gastrulation and Neurulation"

10/28/16 -

Jonathan Packer (Trapnell & Waterston Labs) -
"Tracking cell differentiation in the C. elegans embryo with single cell RNA-seq"

10/21/16 -

Sarah Hilton
"High-throughput mapping of anti-viral immune selection"

10/14/16 -

Juhye Lee
“Improving fitness models of influenza using deep mutational scanning of hemagglutinin”

Andy Lin
"Calibrated score function for scoring high-resolution tandem mass spectrometry data"

10/7/16 -

Khrystyna Dilai
"Understanding the mechanism of mutual exclusivity in splicing factor mutations"

Steven Lee
"Genotyping CYP2D6 with Next-Generation Sequencing"

9/30/16 -

Sam Entwisle
“Phosphoproteome analysis reveals potential crosstalk between mTORC2 and MAP kinases”

Ken Jean-Baptiste
"Mating Efficiency of STE7 Mutant Variants in the Presence of a MAP2K Inhibitor"

Tuesday, 6/7/16, 12:30 - first year rotation talks: Steven Lee, Eliah Overbey, Jonathan Packer

6/3/16 - first year rotation talks: Khrystyna Dilai, Sarah Hilton, Ken Jean-Baptiste, Andy Lin

5/27/16 -

Anne Clark
"Identifying introgressed sequences in S. cerevisiae"

Colby Samstag
"Does selection act on mitochondrial DNA mutations in somatic tissues?"

5/20/16 -

Daniel Chee

Han-Yin Yang

5/13/16 -

Melisa Chiasson

Joe Sanchez
"A Meier-Gorlin Syndrome mutation that impairs replication of the rDNA locus in budding yeast"

5/6/16 -

Ken Chen
"Microfluidics for Yeast Aging"

Alex Mason

5/4/16 -

Matt Rich
"Comprehensive analysis of the yeast promoters through mutagenesis and chemostat selection"

4/29/16 -

Mike Doud
"Towards high-throughput mapping of influenza antibody epitopes"

4/22/16 -

Seungsoo Kim
"The 3D organization of the diploid Saccharomyces genome"

Vijay Ramani
"Multiplex capture of single-cell chromosome conformation by combinatorial Hi-C"

4/15/16 -

Ethan Ahler
"Prospectively mapping resistance mutations in oncogenic kinases"

Kelsey Lynch
"Understanding the consequences of reduced DNA replication initiation"

4/8/16 -

Cecilia Noecker
"Integrative mechanistic analysis of microbiome composition and metabolism"

Aaron Seo
"Genomic Analysis of Inherited Bone Marrow Failure"

4/1/16 -

Colin McNally
"Effect of Community Composition on the Evolutionary Potential of Microbial Species"

Monica Sanchez
"Differential paralog divergence modulates evolutionary outcomes in yeast"

Tuesday, 3/15/16 -

first year rotation talks: Khrystyna Dilai, Sarah Hilton, Ken Jean-Baptiste, Steven Lee

3/11/16 -

first year rotation talks: Andy Lin, Eliah Overbey, Jonathan Packer, Jolie Carlisle

3/4/16 -

Stephanie Battle
"Enhancers and Pluripotency in Naive Embryonic Stem Cells"

Elyse Hope
"Determining genetic mechanisms of cell aggregation using evolved strains of Saccharomyces cerevisiae"

2/26/16 -

Michael Duyzend
"Exploring the genetic basis of phenotype heterogeneity of the autism-associated 16p11.2 CNV"

Vanessa Gray
"Using mutational data to improve models of amyloid β aggregate structure"

2/19/16 -

Bryan Andrews
"Engineering a Phage Retroelement as a New Tool for Experimental Evolution"

Rachel Gittelman
"Signatures of adaptive introgression in diverse populations"

2/12/16 -

Tim Durham
"Imputing Missing Data in the ENCODE and Roadmap Projects"

Xiaojie Qiu
"A novel principal graph approach to reconstruct hierarchical developmental tree from single-cell RNA-seq data"

2/5/16 -

Sam Entwisle
"Phosphoproteomics approaches for studying mTORC2/Akt signaling in adipocytes"

Abigail Keller
"Exploring the fitness costs and benefits of aneuploidy"

1/29/16 -

Sonia Ting
"Exploring the limits of data independent acquisition (DIA) using a state-of-the-art mass spectrometer"

Madeleine Geisheker
"Recurrent missense mutations in neurodevelopmental disorders"

1/22/16 -

Claudia Espinoza
"Understanding a newly proposed source of amplification"

Alex Hu
"A regression model to deconvolve data-independent acquisition mass spectra for peptide identification"

1/15/16 -

Michael Dorrity
"Methods for assigning function to chromatin structure"

1/8/16 -

Aaron McKenna
"Whole organism lineage tracing by multiplex in vivo genome editing"

Matthew Snyder
"Nucleosome footprints in cell-free DNA are evidence of its tissues of origin"

12/15/15 -

first year rotation talks: Steven Lee, Andy Lin, Eliah Overbey, Jonathan Packer

12/11/15 -

first year rotation talks: Jolie Carlisle, Khrystyna Dilai, Sarah Hilton, Ken Jean-Baptiste

12/4/15 -

Juhye Lee
“Improving fitness models of influenza using deep mutational scanning of hemagglutinin”

Aaron Wolf
"Identifying and interpreting human genomic regions depleted of Neandertal ancestry"

Katherine Xue
"Cooperation between distinct viral variants promotes growth of H3N2 influenza in cell culture"

11/20/15 -

Molly Gasperini
"Massively parallel genome editing for discovery of novel regulatory sequences"

Hannah Pliner
"single-cell chromatin accessibility during muscle development"

Amanda Watts
"Decoding the spatial regulatory dynamics of the human brain"

11/13/15 -

Serena Liu

Emily Killingbeck

11/6/15 -

Heather Machkovech
"Positive selection on influenza CD8 T-cell epitopes"

Damon May
"Mataproteomics can tell us who's doing how much of what in the ocean"

10/30/15 -

Jason Klein
"Leveraging phylogeny and high-throughput assays to characterize enhancer turnover"

John Lazar
"LSD1 Inhibition in Small Cell Lung Cancer"

10/23/15 -

Andrew Hill
"Analyzing branched single-cell trajectories uncovers regulators of cell-fate decisions"

Lindsay Pino
"A reproducible, scalable method for differential proteomics"

10/16/15 -

Brian Searle
"A New Approach for Quantifying Phosphopeptides"

10/9/15 -

Clara Amorosi
"Testing pharmacogene variants using an engineered yeast strain"

10/2/15 -

Max Dougherty
"Birth of a human-specific neural gene by incomplete duplication and gene fusion"

Greg Findlay
"Efficient generation of sequence diversity at a single genomic locus"

6/9/15 -

first year rotation talks: Damon May, Lindsay Pino, Hannah Pliner, Brian Searle, Aaron Wolf, Katherine Xue

6/5/15 -

first year rotation talks: Clara Amorosi, Claudia Espinoza, Molly Gasperini, Andrew Hill, Emily Killingbeck, Serena Liu, Amanda Watts

6/3/15 -

Barbara Taskinen

Emma Timmins-Schiffman

5/29/15 -

Colby Samstag
"Using Drosophila to Study Mitochondrial DNA Mutations"

Sam Lancaster

5/27/15 -

Damien Wilburn

Kenneth Matreyek

5/22/15 -

Alex Mason
"Increased expressivity and penetrance of new mutations under HSP90-reduced conditions"

Rachel Gittelman
"Adaptive Neanderthal introgression into modern humans"

5/20/15 -

Caitlin Smukowski Heil

Joshua Schraiber

5/13/15 -

Sandra Zimmerman

Calvin Mok

5/8/15 -

Aaron McKenna
"High-contiguity assembly of a de novo mammalian genome using 2nd generation sequencing"

Daniel Kim
“De novo mutational analysis implicates novel genes for Attention Deficit Hyperactivity Disorder (ADHD) risk”

5/6/15 -

Holly Stessman

Tychele Turner

5/1/15 -

Ethan Ahler
"Prospective mapping of resistance mutations in kinases"

Joe Sanchez
"A Meier-Gorlin Syndrome Mutation That Modulates rDNA Copy Number in Yeast"

4/29/15 -

Ben Jester

Evandro Ferrada

4/24/15 -

Daniel Chee
"Efficient Design and Assembly of TALENs for High-throughput Genome Editing"

Kelsey Lynch
"The Economics of DNA Replication"

4/22/15 -

Miguel Martin Perez

Mark Chaisson

4/17/15 -

Jenny Andrie
"A cradle to grave analysis of cis-regulatory variation in yeast"

William Edelman
"LRRK2 Substrate identification by quantitative mass spectrometry phosphoproteomics"

4/15/15 -

Celia Payen

4/10/15 -

Elyse Hope
"The impact of regulatory variation on complex traits in yeast biofilms"

David Young

4/8/15 -

Martin Kircher

Lea Starita
"Massively Parallel Functional Analysis of BRCA1 RING Domain Variants"

4/3/15 -

Vanessa Gray
"Exploring variant effect prediction with deep mutational scanning data"

Michael Dorrity
"Deep mutational scanning links epistasis to shifts in complex trait values"

3/17/15 -

first year rotation talks: Clara Amorosi, Claudia Espinoza, Molly Gasperini, Serena Liu, Amanda Watts, Aaron Wolf

3/13/15 -

first year rotation talks: Damon May, Lindsay Pino, Hannah Pliner, Brian Searle, Katherine Xue, Andrew Hill, Emily Killingbeck

3/6/15 -

Stephanie Battle
"Chromatin Foundation for Human Pluripotency"

Michael Duyzend
"Transmission and Parental Biases of the 16p11.2 Autism CNV"

2/27/15 -

Monica Sanchez
"Functional characterization of a new model yeast species"

Matthew Snyder
"Maternal copy number variants underlie some false-positive results in prenatal aneuploidy screens"

2/20/15 -

Sam Entwisle
"Rapamycin affects the ubiquitination state of membrane permeases in yeast"

Xiaojie Qiu
"Detecting Lineage Specific Genes During Lung Development From Single-cell RNA-seq Experiments"

2/13/15 -

Madeleine Geisheker
"De novo missense mutations in autism spectrum disorder"

Keolu Fox
"True Blood: Fine Scale ABO Blood Typing by High Throughput DNA Sequencing"

2/6/15 -

Max Libbrecht
"Joint annotation of chromatin state and chromatin conformation reveals relationships among domain types and identifies domains of cell type-specific expression"

Alex Hu
"A regularized linear regression model to identify peptides from data-independent mass spectra"

1/30/15 -

Jorgen Nelson
“Using high-throughput genomics techniques to improve protein design"

Sonia Ting
"Data-Independent Acquisition (DIA)-based Mass Spectrometry: PECAN Validation and Applications"

1/23/15 -

Rob Lawrence
"Integrative analysis of the breast cancer proteome leads to new insights in cancer biology and drug sensitivity"

Benjamin Vernot
"Patterns of Archaic Introgression in Papuans and other Non-Africans"

1/16/15 -

Matt Rich
"Functional annotation of the SUL1 promoter at single base resolution"

Han-Yin Yang
"Mass spectrometry based clinic testing for Amyloidosis"

1/9/15 -

Jennifer McCreight
"Discovery of microRNA across the primate lineage"

Max Press
"Evolutionary assembly patterns of prokaryotic genomes"

Tuesday, 12/9/14 -

first year rotation talks: Damon May, Lindsay Pino, Brian Searle, Aaron Wolf, Katherine Xue, Emily Killingbeck, Clara Amorosi, Molly Gasperini, Serena Liu

12/5/14 -

first year rotation talks: Claudia Espinoza, Andrew Hill, Hannah Pliner, Amanda Watts

11/21/14 -

Tim Durham
"Investigating gene regulatory networks in C. elegans embryogenesis"

11/14/14 -

John Lazar
"Epigenetic Signatures of Early Development in Cancer "

Heather Machkovech
"Does alternative translation initiation contribute to immune epitopes in influenza?"

11/7/14 -

Greg Findlay
”Saturation Genome Editing by Multiplex Homology-Directed Repair”

Jason Klein
"How do enhancers evolve? Reconstructing orthologous and ancestral enhancers"

10/31/14 -

Aaron Seo
“Identification and Characterization of Genes for Inherited Bone Marrow Failure Syndromes” 

Max Dougherty
"Evolution of a Human-specific Neural Gene"


Cecilia Noecker
"Integrative analysis of microbiome metabolism"

Vijay Ramani
"Resolving RNA Structure Through Proximity Ligation"

10/17/14 -

Seungsoo Kim
"Functional and molecular consequences of chromosomal rearrangements"

Colin McNally
“The emergence of mutualism during bacterial co-evolution”

10/10/14 -

Alex Eng
"Designing microbial communities with a targeted metabolism"

10/3/14 -

Anne Clark
"Correcting for population structure in budding yeast GWA studies"

Mike Doud
"In-vivo deep mutational scanning to map viral epitopes"

9/26/14 -

Melissa Chiasson
"Interpreting variation in VKORC1, a critical pharmacogene"

Ken Chen
"Microfluidics for Yeast Aging"

6/10/14 -

first year rotation talks: Melissa Chiasson, Seungsoo Kim, Colin McNally, Vijay Ramani

6/6/14 -

first year rotation talks: Anne Clark, Timothy Durham, Alexander Eng, Cecilia Noecker

6/4/14 -

Dr. Adam Warner
"C. elegans embryogenesis: profiling tissue specific gene expression over time."

Dr. Lea Starita

5/30/14 -

Stephanie Battle
"Characterization of Ovarian Cancer Stem Cell Enhancers"

Keolu Fox
"Next Generation Blood Typing" 

5/28/14 -

Dr. Celia Payen
"High-throughput functional screening of driver mutations"

Dr. Sandra Zimmerman
"Tubular cells: A story of tubulogenesis in Drosophila melanogaster"

5/23/14 -

David Young
"Uncovering the Structural Basis of GPCR Functional Selectivity through Deep Mutational Scanning"

5/21/14 -

Dr. Calvin Mok
"Developing a High-Throughput Genetic Interaction Screen in C. elegans"

Dr. Osnat Penn
"The discovery of integrated gene networks for neurologic diseases"

5/14/14 -

Dr. Josh Cuperus
“Genome engineering in Saccharomyces cerevisiae”

Dr. Danielle Swaney
"Phosphorylation of ubiquitin adds a new dimension to ubiquitin signaling"

5/9/14 -

Sonia Ting
"Peptide detection and quantification using data-independent acquisition (DIA): In-depth characterization of cardiac proteome response in mice"

Joe Sanchez
"Functional study of conserved Meier-Gorlin Syndrome mutations in Saccharomyces cerevisiae"

5/7/14 -

Dr. Ivan Liachko
"Species-Level Deconvolution of Metagenome Assemblies with Contact Probability Maps"

Dr. Elizabeth Kwan

Dr. Matthew Maurano
"Pinpointing functional regulatory variation"

4/25/14 -

Sharon Greenblum
"Copy Number Variation in the Human Gut Microbiome"

Alex Mason
"Characterizing stress-induced lesions in an Arabidopsis thaliana small RNA mutant"

4/18/14 -

Caitlin Gamble
"Codon Context and Translation Efficiency in a Yeast GFP Assay"

Adam Gordon
"Rare variation in clinical pharmacogenetics"

4/11/14 -

Michael Duyzend
"The genetic bases of phenotype variability of the 16p11.2 CNV"

Xander Nuttle
"Human-specific duplicate genes: new frontiers for disease and evolution"

4/9/14 -

Dr. Benjamin Logsdon
"Sparse coding identifies driver genes in cancer"

Dr. Holly Stessman
"Identifying genetic subtypes of autism"

Dr. Habil Zare
"How to infer clonal composition of a tumor from multiple tissue samples?"

4/4/14 -

Rob Lawrence
"Large scale, systematic analysis of the HeLa phosphoproteome"

4/2/14 -

Dr. Attila Kertesz-Farkas
"Peptide identification in tandem mass spectrometry data via cascade search"

Tuesday, 3/18/14 -

first year rotation talks: Melissa Chiasson, Anne Clark, Timothy Durham, Alexander Eng

3/14/14 -

first year rotation talks: Seungsoo Kim, Colin McNally, Cecilia Noecker, Vijay Ramani

3/7/14 -

Tzitziki Lemus Vergara
"Buffering of phenotypic variation: interplays between HSP90 and miRNAs"

Rachel Gittelman
"Rapid evolution of regulatory DNA in humans"

2/28/14 -

Billy Edelman

Jorgen Nelson

2/21/14 -

Anna Sunshine
"How does aneuploidy affect fitness?"

2/14/14 -

Matthew Snyder
"Methods and applications of targeted interrogation of cell-free DNA"

Elyse Hope
"Biofilm-related phenotypes in natural isolates of S. cerevisiae"

2/7/14 -

Matt Rich
"Modulating yeast flocculation through DNA shuffling"

Michael Dorrity
"A Model System for Complex Trait Genetics"

1/31/14 -

Aaron Miller
"Multiplexed evolution and inference of mutation rate in chemostats"

Max Press
"Epistasis and the ELF3 polyglutamine"

1/24/14 -

Kelsey Lynch
"Characterizing the cis- and trans- regulators of DNA replication initiation"

Jeff Staples
"Pedigree Reconstruction from IBD estimates"

1/17/14 -

Alessandra Sullivan
"Mapping and dynamics of light-responsive regulatory DNA in A. thaliana"

Ethan Ahler
"Mapping resistance to targeted cancer therapy"

1/10/14 -

Monica Mascarenas
"yeast evolutionary genetics: A tool to unveil novel gene function"

Sam Lancaster
"Evolution of hybrid yeast genomes"

12/10/13 -

first year rotation talks: Mike Doud, Alexander Eng, Seungsoo Kim, Cecilia Noecker, Vijay Ramani, Tim Durham

12/6/13 -

first year rotation talks: Melissa Chiasson, Anne Clark, Ken Chen, Aaron Seo, Colin McNally

11/22/13 -

Keisha Carlson

Jenny Andrie

11/15/13 -

Josh Burton
"Assembling genomes in three dimensions using Hi-C"

11/8/13 -

Max Libbrecht
"Interpreting domain-scale regulation by integrating histone modification, replication timing and chromatin architecture"

Daniel Kim
"Rare variation in PON1 is associated with ischemic stroke in the NHLBI GO Exome Sequencing Project (ESP)"

10/25/13 -

Aaron McKenna
"Cell lineage reconstruction using single cell transcriptomics and genome engineering"

Alex Hu
"A new pipeline to analyze mass spectra from data-independent acquisition"

10/18/13 -

Daniel Chee
"Exploring the Dynamic Interplay of Human miRNA-Transcription Factor Regulatory Cycles"

10/11/13 -

Vanessa Gray
"Mutational analyses to study protein aggregation and chaperone-client interactions"

Han-Yin Yang
"Analysis of unidentified spectra in proteomic data using high-resolution mass spectrometry"

9/27/13 -

Benjamin Vernot
"Resurrecting surviving Neanderthal lineages from modern human genomes"

6/11/13 -

first year rotation reports: Alex Hu, Daniel Kim, Aaron McKenna, Han-Yin Yang

6/7/13 -

first year rotation reports: Julia Behnen, Daniel Chee, Vanessa Gray

6/5/13 -

Calvin Mok

Adam Warner

5/31/13 -

Jennifer McCreight
"MicroRNA diversity within humans and across primates"

Adam Gordon
"Targeted pharmacogenetic sequencing for research and clinical use"

5/29/13 -

Kyle Siebenthall
“Developmental dynamics of human regulatory DNA”

Stuart Davidson
“Genetic variation in a high-functioning Dutch cohort implicates genes involved in Asperger syndrome”

5/24/13 -

Sharon Greenblum
"Strain Variation in the Human Gut Microbiome"

Keisha Carlson
"Measuring robustness and its effects in natural populations"

5/22/13 -

James Urton
"Chromatin Landscape Diversity in Arabidopsis thaliana"

5/17/13 -

Matt Rich
"Modulating yeast alcohol tolerance through transcriptional engineering"

Max Press
"Evolutionary inference of bacterial Hsp90 clients"

Sean Schneider
"Large scale search for endogenous viral elements"

5/15/13 -

Celia Payen
“Mechanism of formation of large inverted duplications”

Megan Dennis
“Characterization of human-specific duplicated genes implicated in neurocognitive traits”

5/10/13 -

Caitlin Connelly
"The genetic architecture of chromatin accessibility in yeast"

5/3/13 -

Peter Sudmant
"Great ape genomic diversity and copy number variation"

Rachel Diederich
"Gene Loss in Old World Monkeys"

5/8/13 -

Sarah Zanders
"Cheating Chromosomes in Meiosis and Mitosis"

Ivan Liachko
"Next Generation Genetics: Merging Classic and Next-Generation Tools to Dissect Functional DNA Elements in Diverse Yeasts"

5/1/13 -

Sandra Zimmerman
"Proteomics meets tubulogenesis: Regulation of tube elongation during dorsal appendage formation"

4/26/13 -

Jeff Vierstra
"Of mice and men: comparative analysis of the mouse and human regulatory landscapes"

Keolu Fox
"Next Generation ABO Genomics"

4/24/13 -

Ferhat Ay

Martin Kircher

4/19/13 -

Anna Brosius
"How does aneuploidy affect cellular fitness?"

4/17/13 -

Jonathon Burman
"Using Drosophila to study mitochondrial dysfunction and neurodegenerative disease" 

4/12/13 -

Caitlin Gamble
"Non-optimal codon usage and translation: experimental measurements using a sequencing-based approach"

Sam Lancaster
"Genetic Incompatibilities in Hybrid Yeast"

4/10/13 - Rogan Carr, Hsuan-Chao Chiu

4/5/13 -

Leslie Emery
"Improving methods for fine-scale mapping signatures of adaptive evolution in the human genome"

Jennifer Lachowiec
"Gene Family Divergence and the Protein Chaperone Hsp90"

3/19/13 -

first year rotation reports: Julia Behnen, Daniel Chee, Vanessa Gray

3/15/13 -

first year rotation reports: Alex Hu, Daniel Kim, Aaron McKenna, Han-Yin Yang

3/8/13 -

Tzitziki Lemus-Vergara
"HSP90 and AGO1 in the buffering of phenotypic variation"

Tanya Grancharova
"Evolution of the F-box gene superfamily in plants"

3/1/13 -

Josh Burton
"How to Construct a Genome"

Andrew Adey
"The haplotype-resolved genome and epigenome of the aneuploid HeLa cancer cell line"

2/22/13 -

Blake Hovde
"The Draft Genome of Chrysochromulina tobin"

2/15/13 -

Monica Sanchez
"Yeast evolutionary genetics: A tool to unveil novel gene functions"

Joe Sanchez
"Investigating Human Dwarfism Using Yeast"

2/8/13 -

Xander Nuttle
“Rapid and accurate large-scale genotyping of duplicated genes

Andrew Stergachis
"Regulatory DNA patterning in development, cellular memory, and oncogenesis"

2/1/13 -

Melody Palmer
"The characterization of novel abalone sperm protein sp6"

Jenny Andrie
"Characterization of cis-regulatory variation influencing mRNA decay rate in yeast"

1/25/13 -

Akash Kumar
"Preimplantation Genomic Diagnosis"

1/18/13 -

Jeff Staples
"PRIMUS - Pedigree Reconstruct and Identification of Maximum Unrelated Set"

1/11/13 -

Billy Edelman
"Proteomic signals in response to oxidative stress in S. cerevisiae"

Benjamin Vernot
"Genetic Archaeology: Reconstructing Archaic Genomes"

12/11/12 -

first year rotation reports: Alex Hu, Daniel Kim, Aaron McKenna, Han-Yin Yang

12/7/12 -

first year rotation reports: Julia Behnen, Daniel Chee, Vanessa Gray

11/30/12 -

Tom Pohl
"A DNA Sequence Element that Advances Replication Origin Activation"

Jorgen Nelson
"Deep mutational scanning to improve designed protein function"

11/16/12 -

Nate Peters
"Tramtrack69 regulates epithelial tube expansion in the Drosophila ovary through Paxillin and the homeobox protein Mirror"

Alessandra Oddone
"A high-resolution chromatin landscape of Arabidopsis thaliana"

11/9/12 -

Rob Lawrence
"Proteomic dissection of signaling pathways in mammalian cells"

11/2/12 -

Max Libbrecht
"Semi-automated genome annotation of multiple cell types"

Nik Krumm
"Exome-based discovery and characterization of inherited CNVs in simplex autism families"

10/26/12 -

Stephanie Battle
"Epigenetic Profiling of Ovarian Cancer Stem Cells"

Alex Mason
"Characterization of stress induced lesions in Arabidopsis thaliana ago1 mutants"

10/19/12 -

Sonia Ting
"Hypothesis-Driven Analysis: A New Concept for Investigating Tandem Mass Spectrometry Data."

10/12/12 -

Rachel Gittelman
"Characterizing the size, abundance and evolutionary history of regulatory hotspots"

10/5/12 -

Michael Duyzend
"Generating a catalog of human genetic variation from 16 high-coverage autism trios"

Elyse Hope
"Linking allelic variation to phenotypic variation in Saccharomyces cerevisiae biofilms"

9/28/12 -

David Young
"A Deep Mutational Scan of tRNA"

6/5/12 -

First year rotation talks: Jorgen Nelson, Matthew Snyder, Sonia Ting

6/1/12 -

First year rotation talks: Stephanie Battle, Rachel Gittelman, Elyse Hope, Alex Mason

5/30/12 -

Postdoctoral Research Talks: Soyeon Lippman, Celia Payen, Soledad Undurraga

5/25/12 -

Jacob Kitzman
"Massively parallel functional genomics"

Joe Hiatt
"Detection of sub-clonal variation in clinical tumor samples"

Katrina Claw
"Sex and Evolution: the effects of mating strategies on primate reproductive protein evolution"

5/23/12 -

Postdoctoral Research Talks: Lea Starita, Karyn Meltz Steinberg

5/18/12 -

Aaron Miller
"Fitness in evolution"

Adam Gordon

Wednesday, 5/16/12 - Postdoctoral Research Talks: Danielle Swaney, Michael Hoffman

Michael Hoffman
"Semi-automated annotation of the human genome using RNA-seq"

5/11/12 -

Cait Rippey
"Towards a neuronal phenotype of rare fusion proteins in schizophrenia"

Leslie Kim
"Using Drosophila to study factors that influence mitochondrial DNA heteroplasmy"

Wednesday, 5/9/12 - Postdoctoral Research Talks: Beth Dumont
1:30, Foege Auditorium

Wednesday, 5/2/12 -

Postdoctoral Research Talks: Jerrod Schwartz, Brian O'Roak

Wednesday, 4/25/12 -

Postdoctoral Research Talks: Catarina Campbell, Megan Dennis

4/20/12 -

Melody Palmer
"The abalone sperm proteome and sp6, a new, rapidly evolving sperm protein"

Peter Sudmant
"Characterization of Great Ape genetic diversity by whole genome sequencing"

4/18/12 - Postdoctoral Research Talks:

Ivan Liachko

4/13/12 -

Keisha Carlson
"Phenotypic robustness: from plants to humans"

Jennifer Lachowiec
"HSP90 effects on protein evolution"

Caitlin Connelly
"The evolution of noncoding DNA in yeast"

4/11/12 - Postdoctoral Research Talks:

Jonathon Burman
"Analysis of neural subtypes reveals selective mitochondrial dysfunction in dopaminergic neurons from parkin mutants"

Kirsten Beck
"System-wide study of TrkB signaling in neuroblastoma cell lines"

4/6/12 -

Sean Schneider
"Large scale searching for endogenous viral elements in eukaryotes"

4/4/12 - Postdoctoral Research Talks:

Xia Wu
"Quantitate the proteome of Pseudomonas aeruginosa in cystic fibrosis patients by mass spectrometry"

Bradley Coe
"The Copy Number Variation Landscape of Neurodevelopmental Conditions"

3/30/12 -

Tzitziki Lemus-Vergara
"Interaction of HSP90 and miRNAs in the buffering of phenotypic variation in Arabidopsis thaliana"

Caitlin Gamble
"Synonymous Variation and Fitness in a Yeast Model Gene"

3/13/12 -

First year rotation talks: Stephanie Battle, Rachel Gittelman, Elyse Hope, Alex Mason, Jorgen Nelson, Matthew Snyder

3/2/12 -

Leslie Emery
"Improving methods for fine-scale mapping complex signatures of adaptive evolution on the X chromosome"

Rachel Diederich

2/24/12 -

Blake Hovde
"A molecular toolbox for targeted genetic modification"

Sharon Greenblum
"Genomes and Genes: Strain Variability in the Human Gut Microbiome"

2/17/12 -

Matt Maurano, Jarrett Egertson

2/10/12 -

Ben Whiddon
"MCH-expressing neurons (but not MCH) regulate blood glucose homeostasis"

Andrew Adey
"Tn5mC-Seq: Ultra-low-input, tagmentation-based whole genome bisulfite sequencing"

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"


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"


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"