Generating, Analyzing, and Understanding Sensory and Sequencing Information

NEWS
  • GAUSSI Faculty in the News, Professor Dan Sloan investigates plant genomes with two new grants!

  • 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

Aeriel Belk

Aeriel is a doctoral student in the department of Animal Science in the College of Agriculture. She is working under Dr. Jessica Metcalf to investigate the decomposition-associated microbiome. Specifically, she is modeling the postmortem succession of microbes to estimate the time of death in human cadavers and using the microbiome to evaluate mechanisms to modify the shelf-life of meat and poultry products. She obtained a B.S. in Animal Science from CSU and a Master’s in Animal Science with certificates in meat science and food safety from Texas A&M University.

 

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.
  

Alyssa MelvinAlyssa Melvin

Alyssa Melvin is a doctoral student in the Department of Chemistry in the College of Natural Sciences. She received her B.S. in Chemistry at Gannon University in May 2017. She is working under Dr. Melissa Reynolds developing biosensors that incorporate metal-organic frameworks (MOFs) into various aspects of the design to address common deficiencies of enzymatic biosensors. The first part of her project is focused on enhancing the biocompatibility of an in vivo glucose biosensor using MOFs. The second part of her project, in collaboration with Dr. Tom Chen, is focused on using MOFs to improve the signal transduction in the biosensor.

 

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.

Heather DeelHeather Deel

Heather is a doctoral student in the department of Animal Sciences and the Cell and Molecular Biology Graduate Program. She received her B.S. in Biology at Sam Houston State University, where she researched the core microbiome of human cadavers at an anthropological facility. Currently, she is working on characterizing microbial succession in human cadaver rib bones. She will then use this microbiome data to build a microbial clock for estimating the postmortem interval of human cadavers.

jasmine

Jasmine 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.

 

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.

Luke Schwerdtfeger

Luke Schwerdtfeger is a PhD student in the Biomedical Sciences program.  He works under Dr. Stuart Tobet.  Luke’s research uses an in vitro culture model for mammalian intestine, coupled with ongoing development of a microfluidic system to regulate environmental conditions of the intestine more accurately.  Coupling these cultures with both microbiome and metabolome analysis, he hopes to further understand how the innate bacterial – immune – neural signaling of the intestines occurs in both health and disease.

Lyndsey Gray

Lyndsey Gray is a PhD student in CSU’s Microbiology, Immunology, and Pathology Department. Working in Dr. Brian Foy’s lab, her research investigates how mass drug administration of ivermectin among human populations affects entomological indices of malaria transmission in children under five years of age. Specifically, she will be studying if ivermectin disrupts the age structure and causes novel, genetic variations or genetic bottlenecks in wild Anopheles gambiae populations.

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.
 
 

Michael MayMichael May

Michael May received two Bachelors degrees in Chemical Biological Engineering and Biomedical Engineering at Colorado State University in 2017 and is currently a doctoral student in the School of Biomedical Engineering who is co-advised by Dr. Munsky and Dr. Stasevich. Michael works on problems characterizing variability in single-cell, single-molecule experiments using computational and mathematical tools, with future directions moving towards using control theory with stochastic processes in cell populations. His current work examines the ability to identify proteins involved in translation using imaging techniques developed by Tim Stasevich using stochastic models and his next project is developing optogenetic controllers to control gene expression in cell populations.

 

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.

Seré Williams

Seré Williams Seré Williams is passionate about understanding abiotic stress response in plants. Working with the Reddy Lab in the Department of Biology, she is looking at drought stress response in rice. A specific transcription factor is known to be involved in cold, herbivory, and salt stress response. In rice, a knock-out mutant of this transcription factor shows wilting while the wild type is still standing strong. Seré is generating complimented and overexpression lines to verify that this drought response phenotype is linked to this hypothesized transcription factor. She is also performing RNA-seq to identify specific gene products differentially regulated in drought stress response. With the GAUSSI program, Seré is analyzing big data to help solve complex problems, and ultimately, help farmers grow crops in a changing world.

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.

 

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.

Michael May
Alyssa Melvin
Amanda Koch
Kristen Jackson
Lang Yang
Bryce Asay
Cary Mundell
Daniel Ball
Evan Conaway
Heather Deel
Julius Stuart
Lyndah Chow
Neha Ahuja
Robert Williams
Steven Lakin
Suzanne Gallagher