Generating, Analyzing, and Understanding Sensory and Sequencing Information

NEWS
  • Congratulations, Julia Labadie! On your successful dissertation defense! 

  • Adam Heck awarded NSF Graduate Research Fellowship.

  • Mike Mangalea and Nadia Vieira Sampaio awarded 2016 Graduate Student Showcase Top Scholar prizes

  • Zach Fox awarded VPR 2017 Fellowship in Scott College of Engineering

  • 2017-2018 GAUSSI fellowships awarded! Caleb Begly, Charlotte Cialek, Shaun Cross, Bridget Eklund, Jessie Filer, Mike Mangalea,  Alex Mauro, & Daniel Jonas.

Current GAUSSI Trainees

heckAdam Heck

Adam Heck is a graduate student in the Cell and Molecular Biology PhD program. His work in Dr. Carol Wilusz and Dr. Jeff Wilusz’s lab deals with the effects of RNA methylation on mRNA stability and gene expression. Specifically, he is utilizing human foreskin fibroblast (HFF) and induced pluripotent stem (iPS) cells as models to examine the differences in RNA methylation that drives cell differentiation.
Five Minutes of Science

 

Alex Mauro

Alex Mauro is a PhD student in Biology and the Graduate Degree Program in Ecology. He is a member of Dr. Cameron Ghalambor’s lab. His research focuses on understanding on how genetic processes and selective pressures interact to influence range limits and local adaption in tropical fishes from the island of Trinidad.

 

beklundBridget Eklund

Bridget is a graduate student in the Microbiology PhD program within the Department of Microbiology, Immunology, and Pathology. Her first rotation lab focuses on cell mediated immune responses to mycobacteria infections. She is also interested in investigating how changes in the microbial community of a person’s microbiome affect the host through RNA sequencing.

 

Caleb Begly

Caleb is a Master’s Degree EE Student at Colorado State University. He received a BS Computer Engineering degree from Colorado State University in May 2017, and an AS Physics degree from Colorado Mountain College in December 2014. The undergraduate degree focused on hardware classes and VLSI to build skills in digital systems design in addition to the core Computer Engineering coursework. For his senior design project, Caleb worked on the interdisciplinary BioBox environmental chamber project which won first place in the CSU 2017 E-Days. This project, coupled with the GAUSSI classes, sparked an interest in biosensing. Caleb is working on sensing applications using the third generation CMOS biosensor chip. Caleb enjoys hiking, biking, playing the mandolin, PC gaming, and working on hardware and software projects in his spare time.

Charlotte Cialek

Charlotte Cialek is a PhD candidate in the Biochemistry and Molecular Biology department. Her project is a collaboration of her co-mentors, Tai Montgomery and Tim Stasevich. She is using Dr. Stasevich’s novel imaging technique to disseminate the mechanism of microRNA and protein Argonaute in gene silencing at the translation level. Her project seeks to further our understanding protein translation regulation and mRNA decay.
Five Minutes of Science

Chloe Stenkamp-Strahm

Chloe is a DVM/PhD student that studies gastrointestinal bacterial pathogen shedding and carriage dynamics in dairy cows. She is currently assessing how GI microbial communities influence colonization of bovine E.coli O157. A future focus of her work is to build models that predict this colonization and shedding, using national USDA samples with machine learning algorithms and GIS mapping.

Daniel Jonas

Daniel Jonas is a doctoral student at Colorado State University in the mathematics department. He is working with Dr. Kirby on connecting mathematical models with biological data. In particular, he will be working with a variety of epidemiological data sets, for which state space reconstruction methods will be applied to uncover underlying dynamical models. Machine learning techniques will also be used to scrutinize data in an attempt to identify properties of key interest such as pathogen tolerance and maintenance, biological mechanisms of tolerance, and the validation of pro-tolerance interventions. The research resources provided by the GAUSSI training program will prove invaluable in his investigations.

dawnDawn Hajdu

Dawn Hajdu is a graduate student in CMB PhD program. Dr. Cris Argueso in the department of BSPM is her advisor. Her research focuses on the role of plant hormone, cytokinin, in plant defense.

 

 

dayton-headshotDayton Pierce

Dayton is a recent graduate of the Master’s B program in Microbiology at CSU and is now a student in the Cell and Molecular Biology PhD program. His current research examines the metabolic processes of cells infected with Dengue viruses.  Specifically, his work revolves around the glycolytic enzyme, hexokinase 2, and its impact on replication of Dengue viruses.

 

dylanDylan Parker

Dylan Parker earned his B.S. in Biochemistry from the University of Oregon in 2014 and began work as a graduate student in the department of Biochemistry and Molecular Biology at CSU in 2015. Working in the laboratory of Dr. Erin Nishimura, his research focuses on the developmental role of mRNA localization and dynamics in the C. elegans early embryo. He is currently using single-cell RNA sequencing as well as a variety of microscopy techniques to identify and perturb key mRNA developmental determinants to better understand the mechanisms of developmental regulation and cell-fate determination.

garethGareth Halladay

Gareth Halladay is a graduate student pursuing her Master’s degree in Computer Science as part of Dr. Ben-Hur’s research group. She has a B.S. in Biomedical Sciences from Colorado State University. Gareth plans to analyze and identify global patterns of alternative splicing over a large collection of RNA-seq data for Arabidopsis thaliana. She is passionate about teaching and taught an introductory computer science course at CSU this summer.

hailey-conoverHailey Conover

Hailey is a PhD candidate in the Cell and Molecular Biology graduate program. She works in Dr. Lucas Argueso’s lab studying the mechanisms of formation and genetic predisposition to genetic Copy Number Variations.

 

ianIan Mclean

Ian McLean is a MS student in the Biomedical Engineering Program at CSU. His research in the Tobet Lab focuses on utilizing microfluidic principles to create a more useful and physiologically accurate “tissue-on-a-chip” device. Prior to attending CSU, Ian earned a BS in Bioengineering from Washington State University, and then worked as an engineer for a Seattle-based flow cytometry manufacturing company

jasmineJasmine Nejad

Jasmine Nejad is a PhD student in the Biomedical Engineering program at CSU. Her work is focused on software and microfluidics systems for a high-density microelectrode array for quantitative spatial mapping of electrochemical signals in live tissue. This type of sensor system could provide a platform for characterizing efficacy of chemotherapeutic for personalized medicine.

 

jessica-warrenJessica Warren

Jessica Warren is a graduate student in the Department of Biology working in Dr. Dan Sloan’s lab. Her research focuses on the evolution of mitochondrial translational machinery by studying the cytonuclear response to transfer RNA (tRNA) gene loss. This work will provide unique insight into cellular mechanisms required for eukaryotic translation and involves the sequencing, assembly and comparison of multiple mitochondrial genomes, tRNA-seq libraries, and transcriptomes.

j-filerJessie Filer

Jessie finished her MS in Microbiology here at CSU and is now a PhD candidate in the Cell and Molecular Biology program.  Her research focuses on assay development for viral detection and she is currently collaborating with engineers and chemists for her work with biosensors.

 

Colorado State UniversityJulia Labadie

Julia Labadie is a DVM/PhD student in the Department of Environmental and Radiological Health Sciences pursuing her PhD in cancer epidemiology. Her research focuses on understanding genetic and environmental risk factors for canine lymphoma. Prior to attending CSU, Julia earned her MSPH in Epidemiology at Emory University and her BS in Biological Sciences at UC Davis.

 

j-walkerJulie Walker

Julie Walker is a Ph.D. student in Tom Santangelo’s lab. Her research focuses on characterizing transcription termination as well as investigating global RNA methylation patterns in the archaeal model organism Thermococcus kodakarensis.  Specifically, her work investigating methylation patterns is focused on the RNA modification 5-methylcytosine and the function of the aforementioned RNA modification both in vitro and in vivo.

leddyK.A. Leddy

Leddy’s research with Dr. Jane Stewart is focused on white pine blister rust disease; caused by an invasive fungal pathogen affecting North American white pines. She works in collaboration with USFS Forest Health Protection and USFS Rocky Mountain Research Station to apply molecular and bioinformatic techniques to study the evolutionary relationship between pines conferring resistance to the exotic pathogen and various fungal populations across the Rocky Mountains.

mike-fMichael Friedman

Michael is a graduate student at Colorado State University in the department of biology studying within Dr. Daniel Bush’s Lab. His work focuses on enhancing crop production to support bioenergy technology and food security needs through plant molecular biology, biotechnology, and gene discovery.

 

Mike Mangalea

mike-mMike Mangalea is a PhD student in the Department of Microbiology, Immunology, and Pathology working with Dr. Brad Borlee. His research focuses on the bacterium Burkholderia pseudomallei, which is found in tropical and subtropical regions worldwide and causes the deadly disease known as melioidosis in humans and animals.  Specifically, he is interested in biofilm dynamics and hopes to better understand how bacterial pathogens transition from an environmental reservoir to establish persistent infections within susceptible hosts.

 

nadiaNadia Sampaio

Nadia Sampaio is a PhD candidate in the Cell and Molecular Biology Program. Since joining Dr. Lucas Argueso’s lab, Nadia has been investigating different aspects of the influence of widespread heterozygous alleles on yeast phenotype. Specifically, her project focuses on the characterization of frequent genome instability mechanisms that lead to loss-of-heterozygosity in yeast and also on the identification of specific heteroalleles associated with the vigorous growth of industrial yeast strains.

Reyes Murrieta

Reyes is a graduate student pursuing his PhD in Microbiology, Immunology, and Pathology working under Dr. Greg Ebel. His research uses computation biology and experimental virology to study how different ecological and environmental conditions can impactFlavivirus population diversity. Through GAUSSI Reyes is looking forward to advancing his skill set as a computational biologist and establish new interdisciplinary collaborations for future projects.

richard-berlRichard Berl

Richard Berl is a doctoral student in the Department of Human Dimensions of Natural Resources with a research focus on the dynamics of the transmission and evolution of culture. In the past, Richard has worked on the behavioral ecology of wild white-faced capuchin monkeys (Cebus capucinus), social behavior in captive and wild gray wolves (Canis lupus), and imitation and emulation in hunter-gatherers and horticulturalists of the Congo Basin. Current projects include evaluating the drivers of “prestige” and its influence on cultural transmission processes, and investigating the genetic and linguistic history of the Chabu, an isolated group of hunter-gatherers in the highland rainforest of Ethiopia.

Shannon Stiverson

stiversonShannon Stiverson is a PhD student in the mathematics department at CSU.  Her work focuses on the application of manifold learning techniques to biological data sets.  She is currently exploring techniques for early diagnosis of influenza A based on changes in host genetic expression.

 

 

shauncross-2

Shaun Cross

Shaun is a graduate student in the Department of Microbiology, Immunology, and Pathology. He is currently doing his rotations with several faculty, most recently with Mark Stenglein. His current research is to identify and characterize virus segments in Anopheles gambiae mosquitoes via RNA FISH that were discovered from previous sequencing.

 

shea-moore-farrell-headshot

Shea Moore-Farrell

Shea Moore-Farrell is a graduate student pursuing his PhD through the Cell and Molecular Biology program at CSU. His research is focused on developing a computational model of photosynthesis and carbon metabolism in the food and energy crop Sorghum bicolor. Such a model can be used to predict bottlenecks in the flow of carbon to desired chemical products in silico, identify candidate genes to be further studied in vivo, and act as a guide for future metabolic engineering efforts.
Five Minutes of Science

foxZach Fox

Zack has an interest in data-driven modeling of gene regulation. Specifically focusing on two different cells of the same population that behave heterogeneously. Often times average, population level dynamics of gene expression do not provide sufficient information to identify underlying molecular mechanisms of gene transcription. By incorporating single-cell, single-molecule data into mathematical models, we make quantitative predictions about how cells behave in response to different stimuli.

Afnan Shazwan Nasaruddin
Akash Shrestha
Ali Ebrahimpour
Alissa Williams
Amanda Koch
Amy Sheflin
Ashley Malmlov
Bryce Asay
Carlos Matos e Silva
Cary Mundell
Charles McDonald
Christopher Dean
Daniel Hartman
Dawn Hajdu
Devanshu Upadhyay
Devashish Vedre
Fahad Ullah
Harmonie Akers
Hend Ibrahim
James Hansen
Julie Moreno
Keagan Collins
Kristen Jackson
Lang Yang
Lei Yang
Lyndah Chow
Madeline Maher
Maria Irianni Renno
Medora Huseby
Michael Itgen
Michael May
Neha Ahuja
Nick Grant
Rebecca Foos
Sere Williams
Stephen Cohen
Suzanne Gallagher
Swapnil Sneham
Thenessa Savitsky
Travis Sanders
YoungSeok Song