Lab members
Joanna L. Kelley, PhD, Principal Investigator
Joanna is currently a Professor in the Department of Ecology and Evolutionary Biology at University of California Santa Cruz. She was previously in the School of Biological Sciences at Washington State University. Her research focuses on the genomic basis of adaptation, with a special emphasis on extreme environments. She is a member of the Society for Molecular Biology and Evolution (SMBE).
She received her AB in Mathematics and Biology from Brown University. She received her PhD in Genome Sciences from University of Washington with advisor Willie Swanson and held postdoctoral positions at University of Chicago in Human Genetics and at Stanford University in the Department of Genetics.
email: jokelley-at-ucsc-dot-edu
Google scholar
profile at GenomeWeb
NSF Biosketch
Muh-Ching Yee, PhD, Lab Manager
Muh-ching (M.C.) has worked as a laboratory researcher at Stanford University in the departments of Genetics, Chemical and Systems Biology, Biology, and the Carnegie Institution for Science. M.C.’s childhood passion for solving the New York Times crossword has led to her current work playing with the letters of the genetic code in genomics and synthetic biology in human, animal and plant systems. M.C. received an SB in Chemistry at MIT, and a PhD in Chemistry at UC Berkeley, CA.
Blair Perry, PhD, Postdoctoral Researcher
Blair completed his PhD in Todd Castoe’s lab at the University of Texas at Arlington in April 2021. For his dissertation, he used functional genomics to understand the molecular basis and evolution of adaptations in non-traditional model systems. This included comparative transcriptomic studies of post-feeding regenerative organ growth in multiple snake species and functional genomic studies focused on understanding the regulation and evolution of snake venom systems. Broadly, Blair is interested in understanding how complex adaptations evolve through the integration of functional, population, and comparative genomics data. Blair started in the Kelley Lab as a NSF Office of Polar Programs Postdoctoral Research Fellow studying the genomic basis and evolution of Arctic adaptations in the polar bear. Blair continues to work on this project while also contributing to ongoing efforts to understand the genomic mechanisms of hibernation in brown bears.
Website: blairperry.net
Sam Bogan, PhD, Postdoctoral Researcher
Office: Coastal Biology Building rm 158
Email: snbogan(at)ucsc.edu
Sam is an evolutionary biologist who integrates genomics and ecophysiology to study how genomes and environments interactively shape adaptation. Much of his research has focused on coastal and polar marine animals facing rapid global change. Sam received his PhD from UC Santa Barbara where he studied the evolution and regulation of plastic responses to global change in populations of marine invertebrates. As a postdoc in the Kelley Lab, Sam is leveraging long-read DNA and RNA sequencing to investigate the evolution of antifreeze protein genes in polar fishes. Specifically, he is evaluating how structural genomic variation has shaped the copy number, expression, and function of antifreeze proteins across environmental gradients.
Website: snbogan.github.io
Carlos A. Garita-Alvarado, PhD, Postdoctoral Researcher
Carlos’ research interests are focused on the role of selective pressures on fish diversification using a combination of ecomorphological, behavioral and genetic tools. He received his PhD from UNAM where he studied parallel evolution and the ecological speciation process in Astyanax fish morphotypes from Mexico and Central America. For his Master at the University of Costa Rica, he studied morphological and behavioral variation associated with ecological variables using Costa Rican poeciliids. In the Kelley Lab, Carlos will participate in projects related to the adaptation to extreme sulfidic environments by poeciliids including genomic and field approaches. In parallel, he is also participating in a project in Palkovacs Lab about polymorphism, sexual conflict, and the strength of top-down control in trophic cascades with the sailfin molly.
Kara Ryan, PhD Graduate Student (started August 2020)
Kara graduated from Le Moyne College with a B.S in Biology in 2016. While at Le Moyne, Kara studied primary and secondary succession near retreated glaciers in Iceland. In 2020, she graduated from American University with a M.S in Biology. In Dr. David Carlini’s lab, she used a transcriptomic approach to study adaptation to shallow subterranean environments. During her time in the Kelley lab, Kara hopes to learn more about adaption to extreme and unusual environments. In addition to her research, Kara is working to increase science accessibility in the criminal justice system.
Tina Cai, PhD Graduate Student (started September 2023)
Tina graduated from Middlebury College with a BA in Conservation Biology in 2023. At Middlebury, Tina worked in the Evolutionary Ecosystem Ecology (E3) Lab under the guidance of Eric Moody. Tina has spent most of her undergraduate thinking about stoichiometric constraints in aquatic macroinvertebrates. Tina also completed an honors senior thesis studying the morphological changes associated with diel vertical migration patterns in lanternfishes using micro-CT scan. Tina is currently an NSF GRFP fellow in the Kelley lab and is interested in studying climate change (mal)adaptation in polar fishes. Tina is also always learning about environmental justice.
Lexi Enstrom, Masters Graduate Student (started October 2024)
Lexi graduated from Santa Clara University in 2021 with a BS in Bioengineering, where she focused on biomolecular engineering and designing micro needles for encapsulated cell extrusion. Afterwards, she worked at a biotech company based in San Francisco called GigaGen where she worked on developing recombinant polyclonal antibody therapeutics to fight infectious diseases and cancer. Her work also involved advancing a novel microfluidic single-cell droplet-based tool for characterizing recombinant polyclonal therapeutics through the application of protein and cellular engineering and bioinformatics. Lexi is currently a Bioinformatics Master’s student at UCSC in the Kelley Lab and is interested in investigating the transcriptional changes in brown bears during hibernation.
Nathan Surendran, Junior Specialist (March 2023 – present)
Nathan is a graduate of UCSC with a degree in Biology B.S. He is currently assisting in bioinformatic tasks for the lab and in the past has instructed undergraduate students joining the lab on the use of the hummingbird cluster used to perform bioinformatic analyses. He is attending a pre health post baccalaureate program in the ‘24-’25 academic year in preparation for applying to medical school programs.
Undergraduate Researchers
Itzel Pedraza, Undergraduate Researcher (Winter 2024 – Present)
Itzel is an undergraduate student at the University of California Santa Cruz, majoring in Biology with a minor in Bioinformatics. She has done field research collecting resight data and data collection for procedures on the elephant seals at Ano Nuevo along with the Beltran Lab. Shas also done field research collecting population data on small mammals in Santa Cruz. She is currently investigating the evolutionary relationships between hibernating species and closely related non-hibernators through comparative transcriptomic analyses. After graduation, Itzel plans to pursue a degree in veterinary medicine as well as a PhD program.
Dalya Salih, Undergraduate Researcher (Spring 2024 – Present) Dalya is an undergraduate student at the University of California, Santa Cruz, majoring in Biomolecular Engineering and Bioinformatics with a concentration in Bioinformatics and a minor in Computer Science. She has worked on integrating sequencing data with bioinformatics pipelines to analyze genetic variants. Dalya is currently utilizing advanced computational tools to explore microsatellite markers in genomic data. She has always had a passion for understanding the complexities of genomics and looks forward to continuing her exploration in the field as well as computational biology.
Owen Moosman, Undergraduate Researcher (Spring 2024 – Present)
Owen is an undergraduate student at University of California, Santa Cruz with a major in Molecular, Cell, and Developmental Biology. He has done research on genetic variants in RNA sequencing data that are clinically relevant for pediatric cancer. Currently, he works on untangling copy number variation of antifreeze protein genes in polar fish. After graduation, he plans to pursue a graduate degree in genetics.
Emma Tashi, Undergraduate Researcher (Spring 2024 – Present)
Emma is an undergraduate majoring in Molecular, Cell, and Developmental Biology at the University of California, Santa Cruz. After graduation, she plans on further pursuing her interests by obtaining a graduate degree in the field of biology.
Alumni
Postdoctoral Researchers
Ellie Armstrong
Position: Postdoctoral Researcher (2021-2024)
Research focus: Population and conservation genomics of bears
Current position: Assistant professor at UC Riverside
Rishi De-Kayne
Position: Postdoctoral Researcher (2023-2024)
Research focus: Adaptation to extreme environments in Poeciliid fishes
Current position: Postdoctoral Researcher at UC Berkeley
Scott Hotaling
Position: Postdoctoral Researcher (2017-2022)
Research focus: Adaptation to cold and high-altitude environments
Current position: Assistant Professor at Utah State University
Luana Lins
Position: Postdoctoral Researcher (2016-2018)
Research focus: genome variation in Kryptolebias marmoratus
Current position: Post-doctoral scholar at CSIRO in Australia
Website: https://www.drluanalins.com/
Graduate Students
Tait Algayer
Position: Masters student (2021-2023)
Research focus: Genomics of seasonal run timing in salmon
Current position: Research Associate at the Cooperative Institute for Great Lakes Research
Kerry McGowan
Position: PhD student (2017-2023)
Research focus: Functional genomics of hydrogen sulfide adaptation in Poeciliid fish
Current position: Data Scientist at A-Alpha Bio
Alexandra Fraik
Position: PhD student (2015-2021)
Research focus: Conservation genomics of Tasmanian devils and salmonids
Current position: Research biologist at the Rocky Mountain Research Station
Michael Saxton
Position: PhD student (2014-2021, co-advised with Dr. Charles Robbins)
Research focus: Genomic mechanisms of hibernation physiology in brown bears
Current position: Wildlife biologist at Katmai National Park
Anthony Brown
Position: PhD student (2014-2019)
Research focus: Genomics of hydrogen sulfide adaptation in Poeciliid fish
Current position: Bioinformatics programmer at UC Davis
Shawn Trojahn
Position: Masters student (Jan 2017 – Nov 2020)
Research focus: genetic causes of coloration variation in Rainbow Trout.
Alexia Gee
Position: Masters student (Aug 2019 – Dec 2020)
Research focus: Gene expression in hibernating bears.
Other Lab Members
Anne Nakamoto
Position: PhD rotation student (Fall 2023)
Research focus: Comparative transcriptomics of mammalian hibernation
Current position: PhD student in the Corbett-Detig Lab
Isabel Kline
Position: Lab Technician (2022-2024)
Marc Palmada Flores
Position: Visiting PhD Student (Spring 2023)
Research focus: Comparative genomics of vertebrates.
Xiaomeng Tian
Position: SMBE Virtual Lab Meeting Training Program participant, PhD Student at University of Konstanz (Fall 2022 – Spring 2023)
Research focus: Genomic mechanisms of phenotypic variation and adaptation.
Małgorzata Gazda (Gosia)
Position: SMBE Virtual Lab Meeting Training Program participant, Postdoctoral Researcher at Institut Pasteur (Fall 2022 – Spring 2023)
Research focus: Molecular evolution of menstruation.
Paul Wheeler
Position: Fish guru (Washington State University)
Corey Quackenbush
Position: Lab Manager (2013-2017)
Laura Helou
Position: Intern and Master’s Student in Montpellier, France (April 2017 – August 2017)
Research focus: Comparative genomics, impacts of structural variation on evolution.
Current position: PhD student in at the INRA of Tours, France.
Graduate Students / Visiting Scientists:
John Coffin, PhD student at KSU (Summer 2018)
Annabelle Vesterman, visiting veterinary student (Summer 2017)
Ryan Greenway, PhD student at KSU (Summer 2015)
Kyle Taylor, Non-thesis Master’s (Fall 2014-Fall 2015)
Luca Giordani, Volunteer (Spring 2014)
Undergraduates:
Breeana Barnes, WSU Undergraduate (Spring 2015)
Julian Bennett Ponsford, WSU Undergraduate (2013-2015), Now graduate student at University of Wyoming with Cynthia Weinig
Connor Carrillo, School of Molecular Biosciences STARS student (Fall 2014)
Emma Cordray, WSU Undergraduate (2017)
Kayla Cribbin, WSU Undergraduate (2013-2016), Now studying with the Seattle Children’s Research Institute
Chris Cornelius, University of Alabama Tuscaloosa Undergraduate (Summer 2014)
Jarod Herrera, WSU Undergraduate (Spring 2018 – Fall 2018)
Samantha Kallinen, WSU Undergraduate (Spring 2017 – Spring 2018)
Nicholas Kelly, WSU Undergraduate (Summer 2018 – Fall 2018)
Allegra Sundstrom, WSU Undergraduate (Fall 2015 – Summer 2017)
Samantha Varrelman, WSU Undergraduate (2013-2014), Now a Registered Nurse at Mid-Valley Hospital
Bineeta Veach, WSU Undergraduate (2015-2016), Now a Manufacturing Associate at Infectious Disease Research Institute
Charlotte Walker, WSU Undergraduate (Fall 2017)
Courtney Jensen, WSU Undergraduate (2017-2019)
Anna McDonald, WSU Undergraduate (2019-2020)
Caitlyn Patel, WSU Undergraduate (2019-2020)
Maddi Bibby, WSU Undergraduate (2019-2020)
Lili Bahrami, WSU Undergraduate & Lab Technician (2019-2020)
Keegan Paras, WSU Undergraduate (2019-2020)
Kiersey Nielsen, WSU Undergraduate (2020)
Jake Landers, WSU Undergraduate (2019 – 2022)
Bridget McDonald, WSU Undergraduate (2021 – 2022)
Abigail Lehmann, WSU Undergraduate (2022 – 2024)
Jeremy Davis, UCSC Undergraduate (2024)
Alegria Jeremias-Lin, UCSC Undergraduate (2024)