Michael Lab
Todd-Michael-767×767-1

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.
Nicholas-Allsing-20221006-551A1471

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.

aaylward-cv-cropped

Tony Alyward, 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.
          Kelly-Colt-767

          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!!
          Tiffany-Duong-20221006-551A1268

          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.
          Nolan-Hartwick-767

          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.

          Jenni Kao

          Lab Technician

          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.

          Justine-Kitony-20221006-551A1441

          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.

          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.
          Allen-Mamerto-767

          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.
          Jeremiah-Minich-767

          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.
          Emily-Murray-20221006-551A1381

          Emily Murray

          Research Assistant

          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.

          Malia-Moore-767

          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.
          Ashot-Papikian-20221006-551A1318

          Ashot Papikian, PhD

          Staff 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.
          Rachel-Rattner-Norris-20221006-551A1331

          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.

          Dharmendra-Singh

          Dharmendra Singh, PhD

          CRoPS Transform Project Manager

          Dharmendra Singh has a PhD from Pennsylvania State University, where he studied the function of a plastoglobuli localized protein in plant physiology and defense against biotic and abiotic stress in the apple and Arabidopsis. He did a postdoc fellowship at Cornell, where he identified plant defense-associated kinase proteins using large-scale protein-protein interaction. As a postdoctoral fellowship at Noble Foundation, he studied plant defense against viral and bacterial pathogens in sorghum, cassava, and tomato. As a global discovery pathologist for Solanaceae at HM Clause (Limagrain), his work involved discovering and deploying genes against several pathogens of tomato, pepper, and tomatillo. He joined the Michael lab in 2022 as a CRoPS Translation Project Manager. Singh is developing strategies and managing a translational team to validate gene function in several crops for improving their carbon sequester potential.

          Ying-Sun-767

          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 is starting an affinity group to support Asian