Doctorial Dissertations

Dissertation Title Graduate Student Advisor(s)
May 2015    
“Trade-offs in Bacterial Chemotaxis and the Adaptation of Non-genetic Diversity” Nicholas Frankel Thierry Emonet
“MicroRNAs and the Gene Regulatory Network during Aging” Sachi Inukai Frank Slack
Post-transcriptional Regulation of the KRSA gene through its 3’ Untranslated Region Minlee Kim Frank Slack
Cadherin 2 bimodally regulates ECM assembly through distinct and spatially non-overlapping emchanisms Patrick McMillen Scott Holley
Cellular metabolism fluidizes the Glassy cytoplasm of Bacteria” Bradley Parry Christine Jacobs-Wagner
“Distinct differentiations and Mechanics at Stem Cell Colony Edges” Kathryn Rosowski Valerie Horsley
“Construction and Characterization of Recorded Organisms” Alexis Rovner Farren Isaacs
“Functional Analyses of Bacterial Non-coding RNAs” Zhiyuan Zhou Ronald Breaker
December 2014    
Characterizing the role of adipocytes in skin wound healing Barbara Schmidt Valerie Horsley
“C. elegans as a model for developmental Chanatip Metheetrairut Frank Slack
“Functional investigation of ribozymes and ribozyme candidates Andy Chen Ron Breaker
May 2014    
The Utilization of Genetic Mouse Models to Determine the ntogeny, Identity, and Function of White, Brown, and Bone Marrow Adipocyte Lineage Cells Ryan Berry Matthew Rodeheffer
“Molecular regulation of skin stem Cell function during hair growth tumorigenesis” Jill Goldstein Valerie Horsley
“Manipulating Protein Stability with Small Molecules: applications in studying biological systems and accessing new drug targets”  Devin Noblin Craig Crews
“Riboswitch diversity and distributions suggest ancient origins” Phillip McCown Ronald Breaker
“MicroRNA Function During Aging in Caenorhabditis elegans and Humans” Thaylana Smith-Vikos Frank Slack
“Investigating the Cytosolic Delivery of Biological Therapeutics”  Jonathan LaRochelle Alanna Schepartz
December 2013    
Characterization and Functional Analysis of Sequence and Regulation Variation in Pan troglodytes and Macaca mulatta Akwasi Asabere Michael Snyder
The interaction proteome of the Plant immune receptor “N” Patrick Cournoyer Timothy Nelson
ATG6 Interacting Mitochondrial Protein (AIMP) is Targeted to the Vacuole by Autophagy to Limit Cell Death during Senescence and Defense Responses in Plants Andrew Hayward S.P. Dinesh-Kumar
Chaperone Assisted Proteasome Assembly and Oxidative Stress Resistance Mary Kunjappu Mark Hochstrasser
May 2013    
Characterization and Functional Analysis of Sequence and Regulation Variation in Pan troglodytes and Macaca mulatta Akwasi Asabere Michael Snyder
The interaction proteome of the Plant immune receptor “N” Patrick Cournoyer Timothy Nelson
ATG6 Interacting Mitochondrial Protein (AIMP) is Targeted to the Vacuole by Autophagy to Limit Cell Death during Senescence and Defense Responses in Plants Andrew Hayward S.P. Dinesh-Kumar
Chaperone Assisted Proteasome Assembly and Oxidative Stress Resistance Mary Kunjappu Mark Hochstrasser
Body Elongation: Coherence and Flow in Balance Andrew Lawton Scott Holley
Genomic Variation in Somatic Human Tissues Maeve O’Huallachain Michael Snyder
Ancient Chemoreceptors in Drosophila Larvae Shannon Stewart John Carlson
December 2012    
Early Mammalian Neural Crest Development Erin Betters Martin Garcia-Castro
The expression of Unc5 homologs and their co-receptors in the postnatal cerebellum Jeanne Hansen Elke Stein
Genomic Analysis of STAT3 in Diffuse Large B Cell Lymphoma Jennifer Hardee Michael Snyder
Human Gene Regulation Christopher Heffelfinger Michael Snyder
The Molecular, Cellular and Behavioral Basis of Taste in the Drosophila Tarsi Frederick Ling John Carlson
Centromeric Studies in the Budding Yeast Saccharomyces cerevisiae Phillipe LeFrancois Michael Snyder/Shirleen Roeder
Regulation of Odor receptor Genes in Trichoid Sensilla of the Drosophila antenna Carson Miller John Carlson
Fgf and Wnt Signaling interplay in Zebrafish Tailbud Development Michael Stulberg Scott Holley
RNA-Seq in Yeast and Diverse Transcriptional Landscapes Karl Waern Michael Snyder
May 2012    
Genome-wide mapping and functional Analysis of Copy Number Variation in The Humane Genome Rajini Haraksingh Michael Snyder
Identification and characterization of the ligand for PUNC Su Li Elke Stein
Biochemical Analysis of the Complex Network of Her Dimers During Zebrafish Somitogenesis (Holley Lab) Anna Trofka Scott Holley
Neural crest specification and Pax7 cis-regulation Stephanie Vadasz Martin Garcia-Castro
The Role of Pax7 in Neural Crest Development Casey Walsh-Delconte Martin Garcia-Castro
Neural Crest Induction in the Non-neural Ectodern and The Role of Nfat5 in the Early Neural Crest Development Nathan Yardley Garcia-Castro Lab
December 2011    
A Study of MicroRNA Oncogene-Addiction in Lymphoma and MicroRNA Radiosensitizers in Lung Cancer Imran Ali Babar Frank Slack
Investigations of the Role of the Regeneration Epithelium during Axolotl Limb Regeneration Leah Jean Campbell Craig Crews
Involvement of MiRNAs in Crop Development and Differential And Differential Epigenetic Modifications within co-Expression Clusters Yeqin Ma Xing-Wang Deng
Age Associated Defects in AMP-Activated Protein Kinase and Mitochandrial Biogenesis Richard Resnick Gerald Shulman
FGF Signaling in Early Neural In Early Neural Crest Development Timothy Stuhlmiller Martin Garcia-Castro
A novel mechanism of MicroRNA up Regulation n the timing of stem-cell-fate decisions Michael Turner Frank Slack
A Large, Noncoded RNA Confers Alcohol Stress Tolerance in Extremophilic Bacteria Jason Wallace Braker Lab
May 2011    
Genomic Analysis of the PGC-1alpha Transcriptional Regulatory Network Alexandra Charos Michael Snyder
A Ulp1 Substrate Suggests Roles for the SUMO Pathway in Regulating Inositol Synthesis and Reveals the Significance of the Ulp1 Coiled Coin Domain in Substrate Contact   Rachel Felberbaum Mark Hochstrasser
Variation in Transcription Factor Binding Among Humans Maya Kasowski Sherman Weissman & Michael Snyder
DSCAM: Tails of Two Isoforms Alice Ly Elke Stein
Spatial organization of the flow of genetic information in Bacteria Paula Montero Llopis Christine Jacobs-Wagner
Insights into Chromosome Segregation Dynamics in C. crescentus Whitman Schofield Christine Jacobs-Wagner
December 2010    
The Discovery and Characterization of Novel Riboswitches and Other nc RNA’s Tyler Ames Ronald Breaker
Exploring Complex Noncoding RNAs in Bacteria Kirsten Block Ronald Breaker
Dissecting Kinase Signaling Pathways Using Protein Microarrays Joseph Fasolo Michael Snyder
Riboswitches as Antibiotic Drug Targets and the Characterization of Newly Discovered Riboswitches Elaine Lee Ronald Breaker
Natural Variation of the Hydractinia symbiolongicarpus Allodeterminant  alr2 Rafael Rosengarten Stephan Dellaporta
May 2010    
Bacterial Cell Curvature Through Mechanical Control of Cell Growth Matthew Cabeen Christine Jacobs-Wagner
MicroRNAs and Cancer: A Two Part Study in the Roles of microRNAs in Melanoma and in Oncogenic Virus Infection Sirie Godshalk Frank Slack
Roles of the Arabidopsis COP10-DET1-DDB1 Complex in Plant Development On Sun Lau Xing-Wang Deng
Genomic Investigation of SREBP Family Transcription Factors Using ChIp-chip and ChIP-seq Brian Reed Michael Snyder & Sherman Weissman
Exploring the Sequence Sensitivity And Substrate Specificity of the Processive Viral Helicase NPH-II Sean Taylor Anna Pyle
December 2009    
Analysis of the Spatio-temporal Distribution and Function of the Caulobacter crescentus Essential Histidine Kinase CckA Peter Angelastro Christine Jacobs-Wagner
Acj6, a Dual Regulator of Olfactory Receptor Genes Lei Bai John Carlson
Slit/Robo Signaling in Neuronal Morphogenesis Jennifer Round Elke Stein
The Molecular and Cellular Basis of Bitter Taste in Drosophila Linnea Weiss John Carlson
May 2009    
Role for MKL1 in Megakaryocytic Maturation Ee-Chun Cheng Diane Krause
A Study of microRNA Complementary Sites in the 3’ UTRs of Lung Cancer-associated Oncogenes Lena Chin Frank Slack
Myo2 Regulation in S. pombe Janice Friend Thomas Pollard
Remodeling Miniature Proteins that Target EVH1 Domains with High Affinity and Specificity Jennifer Holtzman Alanna Schepartz
Spatial Organization of Gene Expression in Caulobacter crescentus Audrey Jackson Christine Jacobs-Wagner
Discovery and Applications of Purine-sensing Riboswitches Jane Kim Ronald Breaker
Functional Analysis of Agamous Clade Genes in Tomato Irvin Pan Vivian Irish
A Legionella pneumophila Dot/Icm Substrate Protein that Interferes with Vesicular Transport Xiaoxiao Pan Craig Roy
December 2008    
Investigating the Role of tasselseed1 and silkless1 in the Sex Determination Process of Maize Ivan Acosta Stephen Dellaporta
Serine Proteases and Serpins Involved in Drosophila Immune Melanization Huaping Tang Carl Hashimoto
A Novel Drosophila POU Gene, pdm3, Acts in Olfactory Receptor Neuron Development Andrea Tichy John Carlson
May 2008    
Chloroplastic Protein NRIP1 is Required for N Immune Receptor Recognition of Tobacco Mosaic Virus Jeffrey Caplan S.P. Dinesh-Kumar
Temporal Regulation of Neuronal Maturation in C. elegans Katherine  Olsson Carter Frank Slack
Molecular Mechanisms Linking Inflammation, Cancer and Chemoresistance Rui Chen Gil Mor/Harold Behrman
Differential Delta Signaling During Zebrafish Somitogenesis and Midline Development Andrew Mara Scott Holley
Identification and Characterization of Targets of APETALA3 and PISTILLATA Chloe Diamond Mara Vivian Irish
Identification and Characterization of Riboswitches that Sense PreQ1 and Molybdenum Cofactor Elizabeth Regulski Meyer Ronald Breaker
Analysis of Mechanisms that Regulate Neurotransmitter Release from a Pair of Motor Neurons in Caenorhabditis elegans Jessica Tanis Michael Koelle
Identification of Regulators of Neuronal Differentiation by High Throughput Screening of Embryonic Stem Cells Elias Theodorou Michael Snyder
December 2007    
Neuronal Growth Cone Actomyosin II Contractile Systems: Dynamic Barriers Controlling Microtubule Distribution and Function Dylan Burnette Paul Forscher
Unraveling Signaling Pathways Activated by VH1, an Arabidopsis Provascular/Procambial Specific Receptor-like Kinase Teresa Ceserani Timothy Nelson
The Role of CPEB1 Mediated and mRNA Translation in Astrocytes Kendrick Jones David Wells
Functional Characterization of the Mammalian COP9 Signalosome Suchithra Menon Xing-Wang Deng
Taste Coding in Drosophila Jennifer Perry John Carlson
Analysis of Aberrant and Normal Copy-Number Variation of Human Chromosome 22 Alexander Urban Michael Snyder
Sherman Weissman
May 2007    
Pathway of Actin Filament Branch Formation by Arp2/3 Complex Christopher Beltzner Thomas Pollard
A Developmental Timing microRNA and its Target Regulate Lifespan in C. elegans Michelle Boehm Frank Slack
The Molecular Mechanisms of TRAPP Mediated Vesicle Tethering Huaqing Cai Susan Ferro-Novick
Genetic Variation and Linkage Disequilibrium in ADH Genes Yi Han Kenneth Kidd
The Molecular Basis of Olfaction in the Drosophila Larva Scott Kreher John Carlson
CPEB1-mediated mRNA Translation in Purkinje Neurons is Required for Cerebellar Long-term Depression and Motor Coordination Michael McEvoy David Wells
A ZIP1 Separation-of-Function Mutation Triggers Meiotic Arrest with Synapsed Chromosomes Neal Mitra Shirleen Roeder
Unraveling the Developmental Pathways of Cardiovascular Morphogenesis and the Pathogenic Mechanisms of Congenital Heart Defects Through Classical and Proteomic Approaches Anjali Nath Michael Snyder
Joseph Madri
The Regulation of Adipose Mass by DeltaFosB Isoforms Glenn Rowe Roland Baron
Autophagy-Dependent and –Independent Roles of ATG1 in the Coordination of Cell Differentiation, Cell Survival, and Cell Death Montrell Seay Savithramma Dinesh-Kumar
December 2006     
The Role of the F-box Protein UFO in Regulation of the Floral Homeotic APETALA3 Gene Eunyoung Chae Vivian Irish
Functional Analyses of the B Class Genes in Tomato Gemma de Martino Vivian Irish
Genomic Landscapes and Hormone Action in Drosophila Zareen Gauhar Kevin White
Wrestling with Meiotic Chromosomes: A Role for Sumoylation in Meiotic Chromosome Synapsis Gillian Hooker Shirleen Roeder
Analysis of Transcriptome in Rice and Arabidopsis Yuling Jiao Xing-Wang Deng
Nuclear Localization of Met, the HGF Receptor, in Cell Signaling and Breast Cancer Sharon Moulis David Rimm
Spatiotemporal Regulation of Arabidopsis Petal and Stamen Differentiation Naomi Nakayam Vivian Irish
Post-embryonic Characterization of puf-9, a C. elegans Puf Family Protein Mona Nolde Frank Slack
Leaf Vascular Patterning Mutants in Arabidopsis thaliana: Making Connections Jalean Petricka Timothy Nelson
A Role for the Heterochronic Gene lin-41 During Vertebrate Development Betsy Schulman Frank Slack
May 2006     
Mechanism of Action of ADF/cofilin Proteins Ernesto Adrianantoandro Thomas Pollard
The N Resistance Protein Recognizes its Tobacco Mosaic Virus Elicitor Through a Novel Mechanism Tessa Burch-Smith Savithramma Dinesh-Kumar
Studies on the Regulation of Normal Trophoblast Apoptosis and Survival During Pregnancy Shawn Chavez Harold Behrman/Gil Mor
Statistical Modeling of Transcription Regulation in Eukaryotes Liang Cheng Hongyu Zhao
Identification of Yeast Kinase Substrates Using Proteome Arrays Geeta Devgan Michael Snyder
Regulation of SCF-type E3 Ubiquitin Ligases by the COP9 Signalosome and CAND1 Suhua Feng Xing-Wang Deng
Global Analyses of STAT Target Selection and Transcription Regulation Stephen Hartman Michael Snyder
Regulation of Polarity and Cell Cycle Progression in Caulobacter Crescentus Hubert Lam Christine Jacobs-Wagner
Characterization of Meiosis-Specific Mer2 in Double-Strand Break Formation and Ssp2 and Ssp3 in Spore Morphogenesis Jing Li Shirleen Roeder
Cloning of RCY1 and Characterization of its Role in Cucumber Mosaic Virus Resistance in Arabidopsis Thaliana Jennifer Soosaar Savithramma Dinesh-Kumar
Mechanisms of Chromosome Synapsis and Crossover Distribution During Meiosis in S. cerevisiae Tomomi Tsubouchi Shirleen Roeder
December 2005     
Deletion Mutations Caused by DNA Strand Slippage in Acinetobacter baylyi Jeremy M. Gore L. Nicholas Ornston
Conserved Molecules and Mechanisms of Neuronal Signaling Revealed by the Analysis of Simple Nematode Behaviors Antony M. Jose Michael Koelle
May 2005    
Microarray Approaches to Experimental Genome Annotation Paul N. Bertone Michael Snyder/Mark Gerstein
Control of Immunity by Toll-like Receptors and Semaphorins Agnieszka K. Czopik Ruslan Medzhitov
Functional and Biochemical Characterization of Sec15p, a Subunit of the Exocyst Complex Yen Kang Ellen France Peter Novick
Odor Receptor Gene Choice in Drosophila Anandasankar Ray John Carlson
Characterization of the Mammalian Homologue of an Arabidopsis Developmental Switch Protein – COP1 Chunling Yi Xing-Wang Deng
December 2004    
Vascular Patterning and Leaf Development in Arabidopsis Nicole Kho Clay Vivian Irish
The Molecular Basis of Odor Coding in the Drosophila Maxillary Palp Aaron L. Goldman John Carlson
Identification of Nuclear Factor-KappaB Binding Sites on Chromosome 22 Rebecca B. Martone Michael Snyder
The Role of Mouse Numb and Numblike During Mammalian Development and Neurogenesis Petur H. Petersen Weimin Zhong
In vivo Validation and Architecture of a microRNA::Target Interaction in C. elegans Monica C. Vella Frank Slack
May 2004    
The Ig Protein Turtle is a Genetic Inhibitor of the EGFR Pathway that Functions in Axonal Guidance and Rhabdomere Morphology in Drosophila melanogaster Badar F. Al-Anzi Robert Wyman
Unconventional Myosin Function in the Immune System Jeffrey P. Holt Mark Mooseker
Regulation and Role of C. elegans let-7 Family of MicroRNAs Steven M. Johnson Frank Slack
December 2003    
Cytoskeletal Activation of a Checkpoint Kinase: Delineation of the Functional Domains of Hsl1 Jessie Hanrahan Michael Snyder
Extragenic Suppressor of Growth Defects in msbB Salmonella Sean R. Murray Brooks Low
Isolation and Characterization of the Homeodomain Protein 137, a Putative Regulator of APETALA3 Khoon Ghee QueenieTan Vivian Irish
Information Unavailable Dhara N. Amin David Stern
Information Unavailable Stephanie L. Brewer Trevor Williams
Information Unavailable Anna A. Dobritsa John Carlson
Information Unavailable Gail A. Emilsson Ronald Breaker
Information Unavailable Eun-Jin Hong Shirleen Roeder
Information Unavailable Christine E. Horak Michael Snyder
Information Unavailable Hsin Juan Frank Ruddle
Information Unavailable Danielle K. Nelson Trevor Williams
Information Unavailable John C. Shires Adrian Hayday
Dec-02    
Expansion of an “Island of Catabolic Diversity”: Genetic Analysis of Hydroxycinnamate Catabolism in Acinetobacter sp. Strain ADP1 Michael A. Smith L. Nicholas Ornston
May 2002    
Transcription Factor AP-2 g: Genetic Insight into Placental Development Heidi J. Auman Trevor Williams
Studies on Developmental Transitions During Drosophila Oogenesis Michael H. Buszczak Lynn Cooley
William Segraves
Mode of Action Study of the Anti-inflammatory Sesquiterpene Lactone Partheonolide Benjamin H.B. Kwok Craig Crews
Mechanistic Understanding of Nucleoside Inhibitors of Human Immunodeficiency Virus Adrian S. Ray Karen Anderson
Molecular and functional Analysis of the COP9 Signalsome in Arabidopsis Giovanna Serino Xing-Wang Deng
Biological and Genetic Characterization of a Naturally Transformable Acinetobacter strain David M. Young L. Nicholas Ornston
Mutagenesis Induced by the Tumor Microenvironment – Implications of Increased DNA Damage and Diminished DNA Repair Jianling Yuan Peter Glazer
(MD/PhD)
December 2001    
Requirements for the c-Myc Proto-Oncogene in Physiologic T Cell Development Nataki C. Douglas Alfred Bothwell
(MD/PhD) Adrian Hayday
The Role of the Ecdysone Early-Response Gene E75 in Drosophila Development Alycia N. Shilton William Segraves
Cloning and Characterization of Drosophila Filamin Nicholas S. Sokol Lynn Cooley
A Study of Anti-Angiogenic Agent TNP-470: Revealing a Unique Mechanism of Endothelial Cell Cycle Control and Genetic Targeting of Methionine Aminopeptidase-2, the Binding Protein of TNP-470 Jing-Ruey Joanna Yeh Craig Crews
May 2001    
The Role of Regulator of G-protein Signaling (RGS9) Proteins in Drug Addiction Zia Ur Rahman Eric Nestler
December 2000      
Analysis of the Cis-Regulatory System of the Arabidopsis Floral Homeotic Gene APETALA3 Theresa A. Hill Vivian Irish
Clonal and Mosaic Analyses of the Floral Homeotic Gene APETELA3 in Arabidopsis Pablo D. Jenik Vivian Irish
Studies on the Regulation of Final Cytoplasm Transport During Oocyte Development in Drosophila melanogaster Nina M. Matova Lynn Cooley
Eponemycin and Epoxomicin as Probes of the 20S Proteasome Function Lihao Meng Craig Crews