Program CTC-RG2023
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Registration still open only for Zoom attendees. Register here
Sessions
- AI, ML, and statistical methods for mapping and causal modeling
- Pangenomics
- Resources and services for systems genetics
- Disease model non-cancer
- Addiction
- Disease model cancer
- Database resources
- Omics
- Aging
- Software for Systems Genetics
- Rat genome
- Metabolism
- Epigenetics and Epigenomics
- Other and Open (e.g. Reduced Complexity Crosses, Indirect Genetic Effects)
Program (Preliminary) Central Time (US and Canada)
October 8 (Sunday): Registration and Reception
- All Day Registration in the Freeman Auditorium at the Hamilton Eye Institute
- 5:00 PM Reception in the University of Tennessee Health Science Center (Mooney Building)
Workshops at the Freeman Auditorium at the Hamilton Eye Institute
In person | On Zoom- 10:00 AM to 12 PM GeneNetwork and AI workshop by Pjotr Prins, Rob Williams, Shelby and David Ashbrook
- 1:00 PM to 3:00 PM: Pangenome workshop. Tools and Applications by Andrea Guarracino and Flavia Villani
October 9 (Monday): Day 1.
Freeman Auditorium at the Hamilton Eye Institute
In person | On Zoom
- 8:50 AM to 9:00 AM: Conference Opening by Rob Williams
- 9:00 AM to 9:15 AM: Genetic locus associated with bleomycin induced lung fibrosis in mice. (Yingping Wang)
- 9:15 AM to 9:30 AM: Rat MIER family member 3 (Mier3) is involved in spermatogenesis. (David J. Samuelson)
- 9:30 AM to 9:45 AM: From genes to proteins: exploring nephron deficiency in the HSRA rat model. (Andrew R Milner)
- 9:45 AM to 10:00 AM: A mutation in Themis contributes to peanut-induced oral anaphylaxis in CC027 mice. (Ellen L. Risemberg)
- 10:00 AM to 10:15 AM: Stroke susceptibility in SHRSP is determined by B cells genes. (Peter A Doris)
- 10:15 AM to 10:30 AM: Genetic mapping of cardiomyocyte ploidy phenotypes that influence basal cardiac physiology and outcomes after myocardial infarction. (Alexandra L Purdy)
- 10:30 AM to 11:00 AM: Coffee break
- 11:00 AM to 11:15 AM: Genome-wide association study of delay discounting in Heterogenous Stock rats. (Montana Kay Lara)
- 11:15 AM to 11:30 AM: Adolescent Social Isolation Increases Vulnerability to Voluntary Opioid Consumption in Adulthood in Rats. (P. LEMEN)
- 11:30 AM to 11:45 AM: Oxycodone addiction model behaviors following brain versus liver viral Zhx2 overexpression and following Zhx2 knockout in BALB/c substrains. (Camron D Bryant)
- 11:45 AM to 12:00 PM: Enhanced alcohol self-administration in rat models of endogenous depression vulnerability versus resistance. (Mallory E. Udell)
- 12:00 PM to 12:15 PM: Genetic analysis of multiple measures of locomotor activity in 7,895 outbred Heterogeneous Stock rats. (Apurva S. Chitre)
- 12:15 PM to 12:30 PM: Spontaneously Hypertensive Rat substrains and the offspring of reciprocal F2 crosses exhibit differences in model risk traits for addiction and cocaine sensitivity. (Britahny M Baskin)
- 12:30 PM to 1:30 PM: Lunch
- 1:30 PM to 1:45 PM: Novel pre-clinical recombinant inbred model to identify genetic modifiers of breast cancer. (Boston W. Simmons)
- 1:45 PM to 2:00 PM: Determining novel gene candidates in breast cancer using a unique pre-clinical model. (Liza Makowski)
- 2:00 PM to 2:15 PM: High fat diet induced obesity and identification of genetic modifiers of breast cancer using novel recombinant inbred strains. (Sandesh J. Marathe)
- 2:15 PM to 2:30 PM: Unsupervised clustering of tumors from preclinical models of triple-negative breast cancer reveals distinct patterns of gene expression and pathway enrichment that associate with BXD strain and immunity. (Jeremiah R. Holt)
- 2:30 PM to 2:45 PM: Exploring the Impact of Methylation Genetics on Tumor Suppressors in BXD Preclinical Mouse Models. (Samson Eugin Simon)
- 2:45 PM to 3:00 PM: Coffee break
- 3:00 PM to 3:15 PM: Upgraded genome browsers at the Rat Genome Database support comparative and translational studies. (Jennifer R Smith)
- 3:15 PM to 3:30 PM: Rat Genome Database: An Integrated Rat Phenomics and Genomics Data Resource. (Shur-Jen Wang)
- 3:30 PM to 3:45 PM: Enhanced Hybrid Rat Diversity Panel resources at RGD. (Mary L. Kaldunski)
- 3:45 PM to 4:00 PM: Expansion of Rat Expression Data at the Rat Genome Database. (Wendy M. Demos)
- 4:00 PM to 4:15 PM: RATTACA: a new paradigm for examining genetic correlations in outbred rats. (Abraham A Palmer)
- 4:15 PM to 5:30 PM: HRDP workshop by Laura Saba
Session 1: Disease model non-cancer (Chair: Rob Williams)
Session 2: Addiction (Chair: Abraham Palmer)
Session 3: Disease model cancer (Chair: David Ashbrook)
Session 4: Database resources (Chair: Pjotr Prins and Shelby Solomon Darnell)
October 10 (Tuesday): Day 2.
Freeman Auditorium at the Hamilton Eye Institute
In person | On Zoom
- 7:45 AM to 8:30 AM: Mentoring sessions (via zoom: by Amelie Baud)
- 9:00 AM to 9:15 AM: Genetic Regulation of Protein Expression in Rat Brain. (Xusheng Wang)
- 9:15 AM to 9:30 AM: Genetic basis of cecum metabolome composition in heterogeneous stock rats identifies ABC and SLC transporters and enzymes including CES, CYP, and UGT as associated with metabolome abundance. (Joel D Leal-Gutiérrez)
- 9:30 AM to 9:45 AM: Renal multi-omics analysis of UMOD knockout mouse in response to salt. (Manshi Zhou)
- 9:45 AM to 10:00 AM: Assessment of different microbiome profiling approaches for host genetic effects analyses in outbred rats. (Felipe M S Dias)
- 10:00 AM to 10:15 AM: Dominance is common in mammals and is associated with trans-acting gene expression and alternative splicing. (Richard Mott)
- 10:15 AM to 10:30 AM: Genetic Integration of Multi-Omics Data: Realizing the Promise of Genetical Genomics. (Gary A. Churchill)
- 10:30 AM to 11:00 AM: Coffee break
- 11:00 AM to 11:15 AM: Genetics of epigenetics, entropy increase, and aging. (Khyobeni Mozhui)
- 11:15 AM to 11:30 AM: Interactions in the BXD metagenome, metatranscriptome, and tissue gene expression across genotype, age, diet, and tissues. (Evan Williams)
- 11:30 AM to 11:45 AM: MACHINE LEARNING FOR QUANTIFICATION OF BEHAVIOR IN RODENT MODELS OF AGING AND ALZHEIMER’S DISEASE. (Joy Afolabi)
- 11:45 AM to 12:00 PM: Heterogeneity in the impact of dietary protein on metabolic health highlights the importance of precision dietetics. (Cara Green)
- 12:00 PM to 12:15 PM: Charting the genetic loci linked to lifespan and variable response to high fat diet in the BXD family. (Rob Williams)
- 12:15 PM to 12:30 PM: Mitochondrial phenotypes in BXD models of aging and Alzheimer’s disease (Mikhail Tiumentsev)
- 12:30 PM to 1:30 PM: Lunch
- 1:30 PM to 1:50 PM: A revamped rat reference genome improves the discovery of genetic diversity in laboratory rats. (Jun Li)
- 1:50 PM to 2:10 PM: Reference Genome Assemblies Built from PacBio HiFi long reads, Proximity Ligation, and Optical Mapping Technologies for Inbred Rat Strains Important as Models of Complex Disease. (Kai Li)
- 2:10 PM to 2:30 PM: Quality and Completeness Assessments of Reference Genome Assemblies for Inbred Rat Strains Important as Models of Complex Disease. (Ted Kalbfleisch)
- 2:30 PM to 2:50 PM: A reference rat assembly from HiFi reads and long range scaffolding (Peter A Doris)
- 2:50 PM to 3:00 PM: Coffee break
- 3:00 PM to 3:20 PM: Structural variants calling in extended rat pedigree using PacBio HiFi sequencing. (Denghui Chen)
- 3:20 PM to 3:40 PM: The HS rats lineage maintains genetic diversity of founder strains after 100 generations. (Thiago Missfeldt Sanches)
- 3:40 PM to 4:00 PM: Quantifying Allo-Coprophagy In Laboratory Rats From Deep Shotgun Sequencing Data Of The Gut. (Kauthar M. Omar)
- 4:00 PM to 4:20 PM: Unveiling genetic complexity in rats through pangenome graphs and genome-phenome analysis. (Flavia Villani)
- 4:20 PM to 4:40 PM: Unlocking Rat Genomics through the NIH Comparative Genomics Resource (CGR) at NCBI. (Vamsi K. Kodali)
- 4:40 PM: Coffee break and end of day 2
Session 1: Omics (Chair: Kyobeni Mozhui))
Session 2: Aging (Chair: Megan Mulligan)
Session 3: Rat genome (Chair: Hao Chen)
October 11 (Wednesday): Day 3.
University of Tennessee Health Science Center (Mooney Building)
In person | On Zoom
- 7:45 AM to 8:30 AM: Mentoring sessions (via zoom: by Amelie Baud)
- 9:00 AM to 9:15 AM: GBAM: a new high performance simple and extensible format for fast column-based processing of aligned sequence reads for interactive tools and pangenome graphs. (Nick Rozinsky)
- 9:15 AM to 9:30 AM: CCQTL: facilitating QTL mapping in the Collaborative Cross. (Victoire Baillet, Rémi Planel)
- 9:30 AM to 9:45 AM: 2023 Update on GeneNetwork.org. (Pjotr Prins)
- 9:45 AM to 10:00 AM: GenomeMUSter: A comprehensive mouse variation analytical resource for complex trait analysis. (Robyn L Ball)
- 10:00 AM to 10:15 AM: Real-Time Interactive Application for Large-Scale Genetic Data Analysis. (Harper Kolehmainen)
- 10:15 AM to 10:30 AM: Julia software for genetic analysis and omics data. (Śaunak Sen)
- 10:30 AM to 11:00 AM Coffee break
- 11:00 AM to 11:15 AM: Physiological variability in mitochondrial rRNA predisposes to metabolic syndrome in the rat. (Michal Pravenec)
- 11:15 AM to 11:30 AM: Transmembrane domain mutation in Adcy3 causes obesity in rats via altered food intake or energy expenditure depending on sex. (Mackenzie Fitzpatrick)
- 11:30 AM to 11:45 AM: Genetic Variation Drives Differences in the mRNA and Protein Levels of Key Hepatic Drug Metabolizing Enzymes and Transporters in Collaborative Cross Mice. (Teresa McGee)
- 11:45 AM to 12:00 PM: High-dimensional mediation analysis identifies heritable transcriptomic signatures associated with metabolic traits in diversity outbred mice. (Anna L Tyler)
- 12:00 PM to 12:15 PM: Striking Survival Outcomes after Vertical Sleeve Gastrectomy Bariatric Surgery in Different Strains of Mice. (Arvind V. Ramesh)
- 12:15 PM to 12:30 PM: Gene-by-PCOS interactions in cardio-metabolic traits on a panel of genetically diverse strains of mice. (Leandro M Velez)
- 12:30 PM to 1:30 PM: Lunch
- 1:30 PM to 1:45 PM: Conditional inference trees to visualize dense systems genetics data. (Jason A. Bubier)
- 1:45 PM to 2:00 PM: A Bayesian model selection approach to mediation analysis. (William Valdar)
- 2:00 PM to 2:15 PM: Data cleaning principles. (Karl W. Broman)
- 2:15 PM to 2:30 PM: Haplotype reconstruction using low-pass whole-genome sequencing in genetically diverse mouse populations. (Samuel J. Widmayer)
- 2:30 PM to 2:45 PM: Real-time Linear Mixed Model Implementation for Association Mapping on Large Numbers of Quantitative Traits. (Zifan Yu)
- 2:45 PM to 3:00 PM: Learning heritable endophenotypes from high-dimensional data using a causal mediation heuristic. (J. Matthew Mahoney)
- 3:00 PM to 3:15 PM: Comparison of linear mixed model genome scans using individual level data vs strain mean data. (Gregory Farage)
- 3:15 PM: to 3:30 PM: Coffee break
- 3:30 PM to 3:45 PM: Homeostatic behavior quantification of mice in a social context using machine vision (Jaycee Choi)
- 3:45 PM to 4:00 PM: A machine-vision-based frailty index for diversity-outbred mice (Gautam Sabnis)
- 4:00 PM to 4:15 PM: Who's who: Tracking multiple mice over multiple days (Brian Geuther)
- 4:15 PM to 4:30 PM: Mouse Homes and Hotels (Vivek Kumar)
- 4:30 PM: end of day 3
Session 1: Software (Chair: Erik Garrison)
Session 2: Metabolism (Chair: Evan Williams)
Session 3: Statistics methods (Chair: Saunak Sen)
Session 4: Machine learning for rodent behavior (Chair: David Ashbrook)
October 12 (Thursday): Day 4.
University of Tennessee Health Science Center (Mooney Building)
In person | On Zoom
- 9:00 AM to 9:15 AM: Identifying Genetic Modifiers of Sickle Cell Disease by Backcrossing Genetically Diverse BXD Inbred Strains with preclinical Townes Sickle Cell Mice. (Jacqueline Harris)
- 9:15 AM to 9:30 AM: Quantifying the Early Cardiac Transcriptome in Rat Models of Left Ventricular Hypertrophy with or without Predisposition to Hypertension. (Cara Trivett)
- 9:30 AM to 9:45 AM: Cell-type specific co-expression network analysis in single nuclei RNA-Seq heart tissue data from inbred HRDP strains. ( Jack Pattee)
- 9:45 AM to 10:00 AM: Coffee break
- 10:00 AM to 10:15 AM: Genome-wide association study finds multiple loci associated with age-related hearing loss in CFW mice. (Oksana Polesskaya)
- 10:15 AM to 10:30 AM: Determining Significant Polymorphisms in the Choline Metabolic Pathway in the Liver of BXD Mice for Greater Efficacy in the Treatment of Fetal Alcohol Spectrum Disorders (Tasfia Chowdhury)
- 10:30 AM to 10:45 AM: The connectome- a complex genetic trait. (G. Allan Johnson)
- 10:45 AM to 11:00 AM: A Rapid Workflow for Cell Quantification in Combined Light Sheet Microscopy and Magnetic Resonance Histology. (Yuqi Tian)
- 11:00 AM to 11:15 AM: Genetic Modifiers Cause Chronic Epilepsy in a Haploinsufficiency Mouse Model of Tuberous Sclerosis Complex. (Montana Kay Lara)
- 11:15 AM to 11:30 AM: Oxycodone oral self-administration in inbred rats identifies different patterns of vulnerability. (Hao Chen)
- 11:30 AM to 12:30 PM Lunch
- 12:30 PM to 1:30 PM: Conference closing. (Rob Williams, David Ashbrook)