Michaels Lab
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Todd P. Michael, PhD

Principal Investigator

Todd loves sequencing and analyzing plant genomes. At the Salk his group is part of the Harnessing Plant Initiative (HPI) that aims to develop crop plants that sequester more carbon via extensive root systems containing recalcitrant carbon polymers to fight climate change. Before joining the Salk, Todd directed genome centers at Monsanto, Abbott Laboratories, Rutgers University and the J. Craig Venter Institute (JCVI), where his group sequenced thousands of plant, animal and microbial genomes. He received his PhD on the plant circadian clock from Dartmouth College in the lab of Rob McClung, BA from the University of Virginia where he worked in Michael Timko’s lab, and conducted Postdoctoral research in the lab of Joanne Chory at The Salk Institute for Biological Studies.
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Nicholas “Nick” Allsing

Bioinformatics Analyst

Nick Allsing completed his master’s degree at San Diego State University, using both experimental and metagenomic techniques to study the microbes and viruses found in the Tijuana River. He is now a bioinformatics analyst in the Michael Lab, focusing on genome assembly for a variety of plant species. Outside of the lab, you would most likely find him on a hike, at a Padres baseball game, or binging a new favorite TV show.

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Tony Aylward, PhD

Bioinformatics Analyst

Anthony is a bioinformatics analyst studying plant genomic data generated by the Michael group. He is currently focused on using nanopore sequencing data to detect DNA methylation and building reference-free pan gnomes using chromosome-resolved genomes. Before joining Salk, he completed his PhD at UC San Diego, where he developed software and statistical methods for human epigenomics and diabetes research.
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          Dan Butler

          Bioinformatics Analyst

          Dan is the Data Management Lead for the Harnessing Plants Initiative (HPI). His work focuses on creating software systems for storing large image and genomic datasets, processing them with bioinformatics and AI/ML pipelines, and making the results available via interactive web apps. In 2022 he was a recipient of the Koenderink Prize for fundamental contributions in computer vision. He received an MS from the University of Washington, where he worked on robotics and photogrammetry, and a BS from Brown University. Prior to joining HPI, he was a member of Eiman Azim’s lab at Salk developing new motion capture systems for neuroscience, and he has also worked at the Max Plank Institute for Intelligent Systems and MIT Lincoln Laboratory. Outside of work, he enjoys rock climbing and electronics projects.
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          Heidi Chen, PhD

          Postdoctoral Fellow

          Heidi earned her PhD in the labs of David Kingsley and Gill Bejerano at Stanford University, using computational and functional genomics approaches to understand the sequence basis of vertebrate traits. She is interested in similar research themes but now applied to plant biology – with the aim of supporting socially equitable greenhouse gas drawdown and climate change mitigation. Outside of the lab, you can usually find Heidi throwing at the ceramics studio, attempting a DIY project, playing soccer, or learning to surf at the beach.

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          Kelly Colt

          Research Associate

          Kelly graduated with a BS in Biological Sciences from California State University San Marcos, then worked at SGI-DNA (now Codex) and in the J. Craig Venter Institute Sequencing Core before joining the Michael Lab in 2020. She is skilled in the art of next generation sequencing on multiple platforms; from growing plants to isolation of nucleic acid, library preparation, and managing sequencing projects. Outside of the lab Kelly is an avid reader and gamer who loves to paint and grow lots of fun plants!!
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          Tiffany Duong

          Research Assistant

          Tiffany graduated from UC Berkeley with a BS in Chemistry and a BS in Genetics and Plant Biology, and is now a Research Assistant with the Michael lab. She works on nucleic acid extractions and library preparations for next generation sequencing, as well as plant and general maintenance. In her spare time she enjoys cooking, playing games, and needlework crafts.
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          Nolan Hartwick

          Bioinformatics Analyst

          Nolan is a bioinformatics scientist advancing de novo plant genome assembly and annotation methods for the Michael group. Creating a high quality chromosome scale genomes is an important first step for working with non-model organisms. Before joining the Michael group, he completed a BS at UCSD in bioinformatics where he worked to develop plasmid identification and assembly methods for the SPAdes genome assembler.
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          Neil Hauser

          Lab Technician I

          Neil Hauser recently graduated from San Diego State University with a bachelor’s degree in chemistry, with an emphasis in biochemistry. During his undergraduate studies, he engaged in research experiences in both a structural biochemistry lab and an exercise and nutritional science lab. His involvement in a study investigating the impact of almond consumption on overall health and immune function sparked Neil’s keen interest in plant-related research. This enthusiasm dovetailed seamlessly with Neil’s personal research in plant biology, fueled by his frustration and struggle with maintaining houseplants. These experiences eventually led him to discover HPI and Todd Michael’s lab. Now, Neil contributes to the genotyping team, focusing on introducing genetic modifications into plants to enhance root length and increase suberin content.

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                  Jenni Kao

                  Research Assistant

                  Jenni Kao is an undergraduate at UC Riverside studying Plant Biology with an emphasis on plant genetics and biotechnology. Her research projects consisted of utilizing bioinformatics to investigate the grape phylloxera aphid gene evolution and the effects of climate change on the Arctostaphylos species distribution in California. Kao spends her free time painting, gardening, and spending time with her cats and dog.

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                  Justine Kitony, PhD

                  Postdoctoral Fellow

                  Justine Kitony is a postdoctoral fellow from Kenya. Before joining Salk, he worked as a scientist at Kenya Agricultural and Livestock Research Organization (KALRO). Kitony earned his PhD in Agricultural Science from Nagoya University in Japan, where he developed and analyzed rice nested association mapping populations (aus-NAM). Kitony is working on identifying genetic signatures for improving crop productivity utilizing high-quality genomic sequences and phenotype data from Michael’s group. Currently, Kitony is constructing a sorghum pan-genome for genetic analysis of agronomic traits. Kitony’s research, in a nutshell, aims to provide genomic resources to be used in modern plant breeding programs while also expanding our understanding of plant biology in the face of the world’s growing population and changing climate.

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                  Ryan Lynch, PhD

                  Postdoctoral Fellow

                  Ryan is a plant biologist focused on utilizing genomic data to understand and improve crop species with the Michael group. His current projects focus on dormancy, stress tolerance and carbon storage traits. Prior to joining Salk, he worked as a plant breeder and technology developer, primarily focused on the re-emerging hemp industry. Ryan completed his PhD at the University of Colorado, Boulder, where he worked with a variety of plant and microbial species.
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                  Allen Mamerto

                  Bioinformatics Analyst

                  Allen received his Master’s in Biological and Medical Informatics from San Diego State University where he was introduced to plant genomic research focusing on genome assembly and phylogenetic analysis. As a bioinformatics analyst with the Michael group, he is currently working with haplotype phasing of soy genes and analysis using reference-free pan genomes. In his free time, he enjoys hosting tabletop games for friends and family.
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                  Jeremiah Minich, PhD

                  Postdoctoral Fellow

                  Jake received his Ph.D. from UCSD Scripps Institution of Oceanography in Marine Biology in 2020 under the supervision of Rob Knight and Eric Allen. During his PhD, he developed molecular and computational microbiome tools to study the microbial communities associated with marine and freshwater fish. He joined the Michael lab in Jan 2021 as a recipient of the NSF Postdoctoral Fellowship in Biology “Rules of Life” where he will apply multi-omic methods in eukaryotic genomes and microbiomes primarily utilizing long read sequencing technology. Jake’s passion is to solve childhood food security problems in LMIC and continues to work in Malawi Africa at the intersection of aquaculture and integrated agriculture.
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                  Emily Murray

                  GRADUATE STUDENT, SIO

                  Emily Murray graduated from UC San Diego with a BS in Microbiology. She conducted her undergraduate research investigating the microbiota-gut-brain axis, specifically, microbiota and metabolites associated with aging, longevity, and Alzheimer’s disease. She joined the Michael lab in 2022 as a research assistant, working on plant nucleic acid extractions and library preparations, including HMW DNA for long-read sequencing technologies. Outside of the lab, Murray enjoys surfing, gardening, and hiking with her family, friends, and wiener dog.

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                  Malia Moore

                  Graduate Student

                  Malia is a PhD student in the Marine Chemical Biology program at Scripps Institution of Oceanography, and is sequencing and exploring seagrass genomes with the Michael group. She received her B.S. in Chemical Biology from UC Berkeley in 2019, where her undergraduate research included study of bioorthogonal copper click chemistry in the College of Chemistry, and Cas9 gene therapies at the Innovative Genomics Institute. Outside of the lab, Malia enjoys open water swimming, gardening, and hanging out with her cat.
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                  Lillian Padgitt-Cobb, PHD

                  Postdoctoral Fellow

                  Lillian joined the Michael lab as a postdoctoral fellow in 2022. She is a recipient of the NSF PRFB “Plant Genome Postdoctoral Research Fellowship” to study the regulation of metabolic pathways in the glandular trichomes of hemp (Cannabis sativa) flowers. Lillian received her PhD from Oregon State University in July 2022. Her PhD research focused on genomic data science of hop (Humulus lupulus), which is a close relative of hemp. Lillian received a USDA-NIFA Predoctoral Fellowship (2020-2022) to study time-course gene expression of hop flowers and the chromosome-resolved genome assembly of hop. Outside of research, Lillian enjoys coffee and contemplation, spending time at the beach and in the woods, roller skating, and collecting books about the cultivation and history of hop and hemp.

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                  Ashot Papikian, PhD

                  COMPUTATIONAL SCIENTIST

                  Ashot completed his PhD at UCLA in Dr. Steve Jacobsen’s lab, where he studied gene regulation and developed novel CRISPR-based tools for specifically modulating gene expression by targeting and altering epigenetic marks to elucidate mechanisms regulating gene activation and gene silencing. After his PhD, he began work at start-up company Inari where he was a project leader, leading a team focused on optimizing and developing novel tools for precise genome modifications. Ashot joined the Michael lab in late 2020 and is leading genome engineering efforts across HPI, where he is developing strategies and novel approaches for editing plant genomes.
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                  Rachel Rattner-Norris, PhD

                  Research Assistant

                  Rachel Rattner-Norris completed her PhD at UC Riverside in Dr. Mikeal Roose’s lab, investigating the relationship between gene expression and fruit quality during fruit development in grafted citrus trees. After her PhD, she completed a postdoc with the USDA in Dr. Raymond Yokomi’s lab where she assembled and annotated new strains of Spiroplasma citri, the causal agent of citrus stubborn disease. During her time there, she also helped develop a fast, effective, field-deployable assay for early detection of Huanglongbing (HLB) in citrus. Rattner-Norris joined the Michael lab in 2022 and is contributing to genome engineering projects within HPI. In her free time, Rachel enjoys playing roller derby and playing her trombone.

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                  Ying Sun, PhD

                  Postdoctoral Fellow

                  Ying is an immigrant from Changchun, China and first-gen and/or low-income (FLI) student who grew up in Las Vegas. She received her PhD from Stanford University from the lab of Dr. José Dinneny where she studied variation in ABA response in stress-sensitive and stress-tolerant Brassicaceae species. In her postdoc, Ying is interested in the evolution of gene regulatory networks that govern root form and depth in soybean and other legume relatives. Ying is also active in building community to support the success of diverse scholars at Salk. Ying started the affinity group Asian Pacific Islander and Desi at Salk (APIDAS) which aims to foster a greater understanding of the diverse identities that comprise the Asian diaspora.