Generating, Analyzing, and Understanding Sensory and Sequencing Information


GAUSSI Trainee Publications


Amanda Koch, et. al., Quantifying the spatiotemporal dynamics of IRES versus Cap translation with single-molecule resolution in living cells. bioRxiv. January 2020.

Steven Lakin, et. al., MEGARes 2.0: a database for classification of antimicrobial drug, biocide and metal resistance determinants in metagenomic sequence data. NUCLEIC ACIDS RESEARCH. January 2020

Alex Mauro, et. al., Distinguishing between active plasticity due to thermal acclimation and passive plasticity due to Q10 effects: Why methodology matters. FUNCTIONAL ECOLOGY. January 2020.

Dylan Parker, Lindsey Winkenbach, et. al., mRNAI localization in the Caenorhabditis elegans early embryo. BioRXIV. January 2020.

Alec Richardson, Luke Schwerdtfeger, Ian McLean, et. al., A microfluidic organotypic device for culture of mammalian intestines ex vivo. ANALYTICAL METHODS. January 2020.

Travis Sanders, Breanna Wenck, et. al., FttA is a CPSF73 homologue that terminates transcription in Archaea. NATURE MICROBIOLOGY. February 2020.

Luke Schwerdtfeger, et. al., Vasoactive Intestinal Peptide Regulates Ileal Goblet Cell Production in Mice. PHYSIOLOGICAL REPORTS. February 2020.


Kailee Reed, Dylan Parker, et. al., Widespread roles for piRNAs and WAGO-class siRNAs in shaping the germline transcriptome of Caenorhabditis elegans. NUCLEIC ACIDES RESIDUES. December 20

Adam Heck, et. al., Zika Virus Noncoding sfRNA Sequesters Multiple RNA Binding Proteins and Impacts mRNA Decay and Splicing. J BIOL CHEM. November 2019.

Julia Labadie, et. al., Immunophenotypic characterization and clinical outcome in cats with lymphocytosis. JOURNAL OF VETERINARY INTERNAL MEDICINE. November 2019.

Steven Lakin, et. al., Horizontal gene transfer and acquired antibiotic resistance in Salmonella enterica serovar Heidelberg following in vitro incubation in broiler ceca. APPLIED AND ENVIRONMENTAL MICROBIOLOGY. October 2019.

Adam Heck, et. al., Small changes, big implications: The impact of m6A RNA methylation on gene expression in pluripotency and development. BIOCHIM BIOSPHYS ACTA GENE REGUL MECH. September 2019.

Steven Lakin, et. al., Characterization of the Microbial Resistome in Conventional and ‘Raised Without Antibiotics’ Beef and Dairy Production Systems. FRONTIERS IN MICROBIOLOGY. September 2019

Reyes Murrieta, et. al., Bat influenza viruses transmit among bats but are poorly adapted to non-bat species. NAT MICROBIOL. September 2019.

Jessica Warren, et. al., Partitioned coalescence support reveals biases in species-tree methods and detects gene trees that determine phylogenomic conflicts. MOL PHYLOGENET EVOL. August 2019.

Steven Lakin, et. al., Hierarchical Hidden Markov models enable accurate and diverse detection of antimicrobial resistance sequences. COMMUNICATIONS BIOLOGY. August 2019.

Steven Lakin, et. al., Comparative diversity of microbiomes and Resistomes in beef feedlots, downstream environments and urban sewage influent. BMC MICROBIOLOGY. August 2019.

Jessica Warren, et. al., The multi-faceted regulation of nuclear tRNA gene transcription. IUBMB LIFE. June 2019.

Julia Labadie, et. al., Evaluation of Region of Interest Digital Cytology Compared to Light Microscopy for Veterinary Medicine. VETRINARY PATHOLOGY. May 2019.

Luke Schwerdtfeger, et. al. Human Colon Function Ex Vivo: Dependence on Oxygen and Sensitivity to Antibiotic. PLoS ONE. May 2019.

Shaun Cross, et. al., RNA regulatory process in RNA virus biology. WIREs RNA. April 2019.

Reyes Murrieta, et. al., Zika viruses of African and Asian lineages cause fetal harm in a mouse model of vertical transmission. PLoS NEGLECTED TROPICAL DISEASES. April 2019.

Zach Fox, et. al., Bayesian Estimation for Stochastic Gene Expression Using Multifidelity Models. THE JOURNAL OF PHYSICAL CHEMISTRY B. February 2019.

Jessica Filer, et. al., A nuclease protection ELISA assay for colorimetric and electrochemical detection of nucleic acids. ANALYTICAL METHODS. January 2019.

Julia Labadie, et. al., Canine CD4+ T-cell lymphoma identified by flow cytometry exhibits a consistent histomorphology and gene expression profile. VETERINARY AND COMPARITIVE ONCOLOGY. January 2019.

Julia Labadie, et. al., Associations of environment, health history, T-zone lymphoma, and T-zone-like cells of undetermined significance: A case-control study of aged Golden Retrievers. JOURNAL OF VETERINARY INTERNAL MEDICINE. January 2019.

Zach Fox, et. al., The finite state projection based Fisher information matrix approach to estimate and maximize the information in single-cell experiments. PLOS COMPUTATIONAL BIOLOGY. January 2019.


Luke Schwerdtfeger, et. al., Spirals of Science. SCIENCE. 362 (6420); 1318. December 2018.

Adam Heck, et. al., Sequences encoding C2H2 zinc fingers inhibit polyadenylation and mRNA export in human cells. SCIENTIFIC REPORTS. November 2018.

Luke Schwerdtfeger, et. al., From organotypic culture to body‐on‐a‐chip: A neuroendocrine perspective. JOURNAL OF NEUROENDOCRINOL. October 2018.

Luke Schwerdtfeger, et. al., High incidence of a third head of biceps brachii in females. TRANSLATIONAL RESEARCH IN ANATOMY. 2018;12:25-27. September 2019.

Lyndsey Gray, et. al., Experimental evaluation of the impact of household aerosolized insecticides on pyrethroid resistant Aedes aegypti. NATURE SCIENTIFIC REPORTS. August 2018.

Jasmine Nejad, Rachel Feeny, Lang Yang, et. al., Electrochemical biosensor system using a CMOS microelectrode array provides high spatially and temporally resolved images. BIOSENSORS AND BIOELECTRONICS. August 2018.

Sean Cross, et. al., Infection Patterns in Individual Ixodes scapularis Ticks Reveal Associations between Viral, Eukaryotic and Bacterial Microorganisms. VIRUSES. July 2018.

Zach Fox, et. al., Distribution shapes govern the discovery of predictive models for gene regulation. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES. July 2018.

Reyes Murrieta, et. al., Variation in competence for ZIKV transmission by Aedes aegypti and Aedes albopictus in Mexico. PLOS NEGLECTED TROPICAL DISEASES. July 2018.

Jessica Warren, Alissa Williams, et. al., Cytonuclear integration and co-evolution. NAT REV GENET. 19(10):635-648. July 2018.

Dylan Parker, et. al., A Strategy To Isolate Modifiers of Caenorhabditis elegans Lethal Mutations: Investigating the Endoderm Specifying Ability of the Intestinal Differentiation GATA Factor ELT-2. G3: GENES, GENOMES, GENETICS. 8(5), 1425-1437. May 2018.

Ian McLean, Luke Schwerdtfeger, et. al., Powering ex vivo tissue models in microfluidic systems. LAB ON A CHIP. April 2018.

Alyssa Melvin, et. al., Nitric oxide generation from S-nitrosoglutathione: new activity of indium and a survey of metal ion effects. NITRIC OXIDE. vol. 84, pp. 16-21, 2019. March 2018.

Aeriel Belk, et. al., Microbiome data accurately predicts the postmortem interval using Random Forest regression models. GENES. February 2018.

Bridget Eklund, et. al., Microbial and Chemical Shelf-Life of Vacuum Steam-Pasteurized Whole Flaxseed and Milled Flaxseed. JOURNAL OF FOOD SCIENCE. January 2018.

Adam Heck, et. al., The Interplay between the RNA Decay and Translation Machinery in Eukaryotes. COLD SPRING HARB PERSPECT BIOL. January 2018.

Julia Labadie, et. al., Preferential use of unmutated immunoglobulin heavy variable region genes in Boxer dogs with chronic lymphocytic leukemia. PLoS ONE. January 2018

Fahad Ullah, et. al., Exploring the relationship between intron retention and chromatin accessibility in plants. BMC GENOMICS. January 2018

Shaun Cross, et. al., RNA regulatory process in RNA virus biology. REVIEWS IN CELL BIOLOGY AND MOLECULAR MEDICINE. 2018 (pending).


Mike R. Mangalea, et. al., A model of chronic equine endometritis involving a Pseudomonas aeruginosa biofilm. INFECTION AND IMMUNITY. October 2017.

Julia Labadie, et al., Increased frequency of CD45 negative T cells (T zone cells) in older Golden retriever dogs. VETERINARY AND COMPARATIVE ONCOLOGY. September 2017.

Mike R. Mangalea, et. al., The current status of extracellular polymeric substances produced by Burkholderia pseudomallei. CURRENT TROPICAL MEDICINE REPORTS. September 2017.

Julia Labadie, et al., Clinicopathologic features of lingual canine T-zone lymphoma. VETERINARY AND COMPARATIVE ONCOLOGY. July 2017.

Mike R. Mangalea, et. al, Nitrate sensing and metabolism inhibit biofilm formation in the opportunistic pathogen Burkholderia pseudomallei by reducing the intracellular concentration of c-di-GMP. FRONTIERS IN MICROBIOLOGY. July 2017.

Mike R. Mangalea, et. al., Genome-scale analysis of the genes that contribute to Burkolderia pseudomallei biofilm formation identifies a crucial exopolysaccharide biosynthesis gene cluster. PLoS NEGLECTED TROPICAL DISEASES. June 2017.

Reyes Murrieta, et. al., American Aedes vexans Mosquitoes are Competent Vectors of Zika Virus.  THE AMERICAN JOURNAL OF TROPICAL MEDICINE AND HYGIENE. June 2017.

Jessica Warren, et. al., The Mitonuclear Dimension of Neanderthal and Denisovan Ancestry in Modern Human Genomes. GENOME BIOLOGY AND EVOLUTION. June 2017.

Reyes Murrieta, et. al., Impact of simultaneous exposure to arboviruses on infection and transmission by Aedes aegypti mosquitoes. NATURE COMMUNICATIONS. May 2017.

Reyes Murrieta, et. al., Mosquitoes transmit unique West Nile virus populations during each feeding episode. CELL REPORTS. April 2017.

Hailey Sedam, Nadia Sampaio, et. al., Both R-loop removal and ribonucleotide excision repair activities of RNase H2 contribute substantially to chromosome stability. DNA REPAIR. April 2017.

Adam Heck, et. al., Metabolic labeling and recovery of nascent RNA to accurately quantify mRNA stability. METHODS. February 2017.

Adam Heck, et al., The CELF1 RNA-Binding Protein Regulates Decay of Signal Recognition Particle mRNAs and Limits Secretion in Mouse Myoblasts. PLoS ONE. January 2017.

Kate Rockenbach, et al., Phylogenetic and population genetic evidence for positive selection in rapidly evolving plastid-nuclear enzyme complexes. GENETICS. January 2017.

Chloe Stenkamp-Strahm, et al., Climate, lactation, and treatment factors influence faecal shedding of Escherichia coli O157 pathotypes in dairy cows. EPIDEMIOLOGY & INFECTION. January 2017.


Katherine Schuamberg, et al., Changes in cell shape are e correlated with metastatic potential in murine and human osteosarcomas. BIOLOGY OPEN. 2016.

Nadia Sampaio, et al., Unraveling the genetic basis of xylose consumption in engineered Saccharomyces cerevisiae strains. SCIENTIFIC REPORTS. December 2016.

Christopher Dean, et al., MEGARes: an antimicrobial resistance database for high throughput sequencing. NUCLEIC ACIDS RESEARCH. November 2016.

Mike Mangalea, et al., Clay Components in Soil Dictate Environmental Stability and Bioavailability of Cervid Prions in Mice. FRONT MICROBIOL. November 2016.

Yusra Obeidat, et al., Characterization of an O2 Sensor Using Microelectrodes. IEEE SENSORS. October 2016.

William Tedjo, Rachel Feeny, Stacy Willett, et al., Design of an Integrated Microelectrode Array System for High Spatiotemporal Resolution Chemical Imaging. IEEE TRANSACTIONS ON BIOMEDICAL CIRCUITES AND SYSTEMS, Special Issue BioCAS. October 2016.

Lang Yang, et al., A Compact Signal Generation and Acquisition Circuit for Electrochemical Impedance Spectroscopy. IEEE TRANSACTIONS ON BIOMEDICAL CIRCUITES AND SYSTEMS, Special Issue BioCAS. October 2016.

Shannon Stiverson, et al., Explorations in Very Early Prognosis of the Human Immune Response to Influenza. ACM International Workshop on Big Data in Life Sciences, October, 2016.

Julia Labadie, et al., BCL2 and MYC are expressed at high levels in canine diffuse large B-cell lymphoma but are not predictive for outcome in dogs treated with CHOP chemotherapy. VETERINARY AND COMPARATIVE ONCOLOGY. August 2016.

Zachary Fox, et al., Finite state projection based bounds to compare chemical master equation models using single-cell data. THE JOURNAL OF CHEMICAL PHYSICS. August 2016.

Chloe Stenkamp-Strahm, et al.,  Antimicrobial Resistance Profiles in Escherichia coli O157 Isolates from Northern Colorado Dairies. JOURNAL OF FOOD PROTECTION. March 2016.

Julia Labadie, et al., Breed distribution and clinical characteristics of B cell chronic lymphocytic leukemia in dogs. JOURNAL OF VETERINARY INTERNAL MEDICINE. January 2016.

Jessice Warren, et al., Linear plasmids and the rate of sequence evolution in plant mitochondrial genomes. GENOME BIOLOGY AND EVOLUTION. January 2016.


Rachel Feeny, et al., Spatiotemporal Norepinephrine Mapping Using a High-Density CMOS Microelectrode Array. ROYAL SOCIETY OF CHEMISTRY. 2015.

Katherine A Schaumberg, et al., Quantitative characterization of genetic parts and circuits for plant synthetic biology. NATURE METHODS. November 2015.

Lang Yang, et al., A Low Power 64-point Bit-Serial FFT Engine for Implantable Biomedical Applications. EUROMICRO CONFERENCE ON DIGITAL SYSTEM DESIGN. August 2015.

Zachary Fox, et al., Integrating single-molecule experiments and discrete stochastic models to understand heterogeneous gene transcription dynamics. METHODS. September 2015.