Juniper A Lake
Senior Bioinformatics Scientist
- juniper.a.lake@gmail.com
- https://juniper-lake.github.io/
- Klamath Falls, Oregon
Juniper Lake is a Senior Bioinformatics Scientist in the Computational Biology group at PacBio, where she develops resources and tools to support and improve human rare genetic disease research. Suggested conversation topics: chicken diabetes, mountain or gravel biking, drywall mudding tips and tricks, swing dance variations, how many dogs is too many, one man band setups.
Work Experience
Senior Bioinformatics Scientist
I work with customers, collaborators, compatible business partners, and internal teams to develop and improve tools and workflows for human rare disease research using highly accurate long-read HiFi sequencing.
- developing tertiary analysis toolset (variant annotation and prioritization) to complement HiFi-specific variants callers such as TRGT and Paraphase
- drove workflow design and development to create a database of human variation from HiFi whole genome sequencing (WGS) in 1000+ samples as part of the Consortium of Long Read Sequencing
- evaluated and guided development of external HiFi-compatible biological interpretation and tertiary analysis tools
- worked with NIST Genome in a Bottle consortium to improve human variant calling benchmarks
- supported commercial teams by leveraging pilot experiments into instrument sales and marketing collateral
- supported customers and collaborators by applying analysis workflows to their data, resulting in publications
- developed workflows for variant calling, filtering, annotation, and prioritization for rare and inherited disease studies
Graduate Research Assistant
Investigated the etiology and pathogenesis of wooden breast (WB) and white striping (WS), two novel and related complex muscle disorders in commercial broiler chickens that cause major economic losses and welfare concerns worldwide.
- developed computational pipelines and machine learning models for analysis of NGS (DNA & RNA) and proteomics data
- proposed a completely new hypothesis linking recently emerged muscle disorders like WB and WS in chickens with type II diabetes in humans
- designed and conducted experiments involving genome-wide association (GWA), differential gene expression (RNA-Seq), and biomarker identification
Graduate Research Assistant
Studied resistance to and transmission of rose rosette disease (RRD), a fatal and widespread disease of landscape roses caused by the multipartite emaravirus rose rosette virus (RRV) vectored by the eriophyid mite Phyllocoptes fructiphilus.
- managed a large, randomized field trial to screen rose genotypes for resistance to RRD
- tested the effectiveness of biological control methods in mitigating spread of the vector mite P. fructiphilus for potential use in greenhouse grow operations
Publications
Pre-Prints
- Wagner J, Olson ND, McDaniel J, Harris L, Pinto BJ, Jáspez D, Muñoz-Barrera A, Rubio-Rodríguez LA, Lorenzo-Salazar J, Flores C, Sahraeian SME, Narzisi G, Byrska-Bishop M, Evani US, Xiao C, Lake JA, Fontana P, Greenberg C, Freed D, Mootor MFE, Boutros PC, Murray L, Shafin K, Carroll A, Sedlazeck FJ, Wilson M, Zook JM, and Genome in a Bottle Consortium. (2023) Small variant benchmark from complete assembly of X and Y chromosomes. bioRxiv.
Papers
- Groza C, Schwendinger-Schreck C, Cheung WA, Farrow EG, Thiffault I, Lake J, Rizzo WB, Evrony G, Curran T, Bourque G, and Pastinen T. (2024) Pangenome graphs improve the analysis of structural variants in rare genetic diseases. Nature Communications 15:657.
- Windham MT, Evans T, Collins S, Lake JA, Lau J, Riera-Lizarazu O, and Byrne DH. (2023) Field resistance to Rose Rosette Disease as determined by multi-year evaluations in Tennessee and Delaware. Pathogens 12(3):439.
- Lake JA, Yan Y, Dekkers JCM, Qiu J, Brannick EM, and Abasht B. (2022) Identification of circulating metabolites associated with wooden breast and white striping. PLoS One 17(9): e0274208.
- Lake JA, Dekkers JCM, and Abasht B. (2021) Genetic basis and identification of candidate genes for wooden breast and white striping in commercial broiler chickens. Scientific Reports 11:6785.
- Tomlinson IV MJ, Polson SW, Qiu J, Lake JA, Lee W, and Abasht B. (2021) Investigation of allele specific expression in various tissues of broiler chickens using the detection tool VADT. Scientific Reports 11:3968.
- Lake JA, Brannick EM, Papah MB, Lousenberg C, Velleman SG, and Abasht B (2020) Blood gas disturbances and disproportionate body weight distribution in broilers with wooden breast. Frontiers in Physiology 11:304.
- Lake JA and Abasht B. (2020) Glucolipotoxicity: A proposed etiology for wooden breast and related myopathies in commercial broiler chickens. Frontiers in Physiology 11:169.
- Lake JA, Papah MB, and Abasht B. (2019) Increased expression of lipid metabolism genes in early stages of wooden breast links myopathy of broilers to metabolic syndrome in humans. Genes 10(10):746.
- Wax J, Zhuo Z, Bower A, Cooper J, Gachara S, Kamweru I, Mhora T, Neerukonda SN, Novick D, Winkeler J, Yoder T, and Wisser RJ. (2018) A problem-based learning exercise on food security: understanding the role of genomic variation and plant breeding. Genetics Society of America Peer-Reviewed Education Portal 004.
- Byrne DH, Klein P, Yan M, Young E, Lau J, Ong K, Shires M, Olson J, Windham M, Evans T, and Novick D. (2018) Challenges of breeding rose rosette resistant roses. HortScience 53(5), 604-608.
Book Chapters
- Abasht B., Mignon-Grasteau S., Bottje W., and Lake JA. (2020) “Genetics and genomics of feed utilization efficiency traits in poultry species,” in Advances in Poultry Genetics and Genomics, eds. S. E. Aggrey, H. Zhou, M. Tixier-Boichard, and D. D. Rhoads.. Burleigh Dodds Science Publishing, pp. 183-220.
Presentations
- Lake JA, Dekkers JCM, Velleman SG, Brannick EM, and Abasht B. (2019) Preliminary results from genome wide association study of wooden breast in commercial broilers. Poultry Science Association Annual Meeting. 2019 Jul 15-18; Montreal, QC, Canada.
Posters
- Lake JA, Rowell WJ, Eberle MA. (2022) De novo variant detection with HiFi reads. American Society of Human Genetics Annual Meeting; October 25-29; Los Angeles, CA.
- Dolzhenko E, Billingsley KJ, Jerez PA, Rowell WJ, Kronenberg Z, Saunders CT, Wenger A, Portik D, Harting J, Weisburd B, Erwin G, Lake J, and M Eberle. (2022) Whole-genome analysis of mutations and epigenetic changes in tandem repeat regions using PacBio HiFi sequencing data. Sequencing to Function: Analysis and Applications for the Future (SFAF) conference; June 21-23, Santa Fe, NM, USA.
- Lake JA, Walugembe M, Kramer L, Dekkers JCM, and Abasht B. (2020) Genetic basis of wooden breast and white striping in commercial broilers. Plant and Animal Genome Conference XXVIII; January 11-15; San Diego, CA.
- Lake JA, Velleman S, Brannick E, and Abasht B. (2019) Blood analysis and proportional muscle and organ weights in broilers with wooden breast. Plant and Animal Genome Conference XXVII; January 12-16; San Diego, CA.
- Lake JA, Tomlinson IV MJ, and Abasht B. (2018) FastqBLAST: A tool to quickly assess the organismal and genomic diversity present in a FASTQ file. 26th Conference on Intelligent Systems for Molecular Biology; July 6-10; Chicago, IL.
- Behnam A, Dekkers JCM, Velleman SG, Schmidt C, and Lake JA. (2018) Genome wide identification and functional validation of genes causing susceptibility to wooden breast in commercial broiler chickens. 2018 NIFA Joint Animal Nutrition, Growth and Lactation and Early Concept Grants for Exploratory Research (EAGERs) Project Director Meeting; June 12-13; Washington, DC.
- Novick DN, Tomlinson IV MJ, Papah MB, Chazi Capelo JD, and Abasht B. (2018) A new tool to prioritize candidate genes and characterize sample behavior in differential expression analysis of transcriptomic data. Plant and Animal Genome Conference XXVI; January 13-17; San Diego, CA.
- Novick DN and Evans T. (2017) Evaluation of rose germplasm for resistance to rose rosette disease. American Phytopathological Society Potomac Division Meeting; March 22-24; Morgantown, WV.
Dissertations & Theses
- Ph.D. Dissertation. (2021) Characterization of the systemic metabolic dysfunction underlying wooden breast and white striping in chickens. University of Delaware, Research Advisor: Behnam Abasht.
- M.S. Thesis. (2017) Evaluation of rose germplasm for resistance to rose rosette disease and studies of disease transmission and vector control. University of Delaware, Research Advisor: Tom Evans.
- B.S. Honors Thesis. (2013) Smallholder agroforestry programs: An instrument for mitigating supply chain risk. Wharton School of the University of Pennsylvania, Research Advisor: R. Scott Poethig.