CV

Current Affiliations

Previous Affiliations

Education

  • Ph.D. Plant Biology, University of Illinois at Urbana-Champaign - 2012
  • B.S. Integrative Biology, Minor: Chemistry, University of Illinois at Urbana-Champaign - 2007

Grants, Fellowships, and Awards

  • PI: Accenture Global Environmental Change Fellowship ($198,000)- 2021-23

  • PI: NSF- Postdoctoral Fellowships in Biology- Develop a systems level model of resource allocation and partitioning in Brassica rapa to predict growth across multiple genotypes and environments. Plant Genome Research Program ($216,000) - 2014-17

  • PI: Physiological systems biology of secondary metabolism in Brassica rapa leaves. Amaryllis Nucleics Research Grant ($9600)- 2016

  • PI: Developing distributed image processing pipelines for plant growth phenotyping using Docker container based NVIDIA GPU Amazon EC2 instances. Amazon Web Services Research Grant ($5600). - 2015-2016

  • Collaborator: Genotyping by Sequencing and Detection of eQTLs in a Recombinant Inbred Line Population of Brassica rapa. TACC Lonestar4 Super Computer Cluster (260,000 Units). - 2013-14

  • PI: National Science Foundation Graduate Research Fellowship ($135,000) - 2009-12

  • Co-PI: Project Leader, ASPB Education Foundation Grant- Plants iView ($20,000) - 2011-12

  • Co-PI: Project Leader, UIUC Public Engagement Grant- Plants iView ($12,500) - 2011-12

  • Outstanding Teaching Award- UIUC Department of Plant Biology ($400) - 2012

  • Govindjee Award for Excellence in Biological Science ($1000) - 2011

  • PI: Francis M. and Harlie M. Clark Research Grant ($1,000) - 2010

  • PI: Francis M. and Harlie M. Clark Research Grant ($1,000) - 2009

  • Distinction- School of Integrative Biology. Thesis Title: “How will elevated [CO2] alter soil and plant water status of the C3-crop soybean and the C4-crop maize?” Published as part of Hussain et al. (2013). - 2007

  • Total Academic Awards: $600,100

Publications

Google Scholar Profile

  • Holmquist AJ, Markelz RJC, Martinez CC, Gillespie RG (2024). The importance of habitat type and historical fire regimes in arthropod community response following large-scale wildfires. Global Change Biology (30:1). paper

  • Van Tuyl, Steve (Ed.). (2023). Hiring, Managing, and Retaining Data Scientists and Research Software Engineers in Academia: A Career Guidebook from ADSA and US-RSE. Zenodo. Book

  • Baker RL, Leong W, Brock MT, Rubin MJ, Markelz RJC, Welch S, Maloof JN, Weinig C (2019) Integrating transcriptomic network reconstruction and QTL analyses reveals mechanistic connections between genomic architecture and Brassica rapa development. PLoS Genetics 15 (9), e1008367. paper

  • Markelz RJC 1,Covington MF 1, Devisetty UK, Brock M, Weinig C, Ma. oof JN (2017) Using RNA-Seq for genomic scaffold placement, correcting assemblies, and genetic map creation in a common Brassica rapa mapping population. G3. paper 1Equal contribution.

  • Bucksch A, Atta-Boateng A, Azihou AF, Battogtokh D, Baumgartner A, Binder BM, Braybrook SA, Chang C, Coneva V, DeWitt TJ, Fletcher AG, Gehan MA, Diaz -Martinez DH, Hong L, Iyer -Pascuzzi AS, Klein LL, Leiboff S, Li M, Lynch JP, Maizel A, Maloof JN, Markelz RJC, Martinez CC, Miller LA, Mio W, Palubicki W, Poorter H, Pradal C, Price CA, Puttonen E, Reese JB, Rellán-Álvarez R, Spalding EP, Sparks EE, Topp CN, Williams JH and Chitwood DH (2017) Morphological plant modeling: unleashing geometric and topological potential within the plant sciences. Frontiers in Plant Science. 8:900. doi: 10.3389/fpls.2017.00900 paper

  • An N, Welch SM, Markelz RJC, Baker RL, Palmer CM, Ta J, Maloof JN, Weinig C (2017) Using photogrammetry and plant modeling techniques to quantify 2D and 3D rossette area for time-series high-throughput phenotyping. Computers and Electronics in Agriculture. 135: 222-232 paper

  • An N, Palmer CM, Baker RL, Markelz RJC, Ta JT, Covington MF, Maloof JN, Welch SM, Weinig C (2016) Plant High-Throughput Phenotyping Using Photogrammetry and imaging Techniques to Measure Leaf Length and Rosette Area. Computers and Electronics in Agriculture. 127:376-394 paper

  • Brock MT, Lucas L, Anderson N, Rubin M, Markelz RJC, Covington MF, Devisetty UK, Chapple C, Maloof JN, Weinig C (2016) Genetic architecture, biochemical underpinnings, and ecological impact of floral UV patterning. Molecular Ecology. 25:1122-1140 paper

  • Baker RL, Leong WF, Brock MT, Markelz RJC, Covington MF, Devisetty UK, Maloof JN, Welch S, Weinig C (2015) Modeling development and quantitative trait mapping reveal independent genetic modules for leaf size and shape. New Phytologist. 208: 257–268. paper

  • Markelz RJC, Vosseller LN, Leakey ADB (2014) Elevated CO2 concentration induces transcriptional reprogramming of respiration and a stimulation of dark respiration as Arabidopsis thaliana leaves transition from sinks to sources. Plant, Cell, and Environment. 37:2542-2552. paper

  • Markelz RJC, Lai LX, Vosseller LN, Leakey ADB (2014) The stimulation of leaf respiration and transcriptional reprogramming by elevated CO2 concentration is diminished, but not eliminated, under limiting nitrogen supply. Plant, Cell, and Environment. 37:886-898. paper

  • Hussain MZ, VanLoocke A, Markelz RJC, Leakey ADB, Ort DO, Bernacchi CJ (2013) Future carbon dioxide concentration decreases canopy evapotranspiration and soil water depletion by field-grown maize. Global Change Biology. 19:1572–1584. paper

  • Walters KR, Rupassara SI, Markelz RJC, Leakey ADB, Muir W, Pittendrigh B (2012) Methamphetamine causes anorexia in Drosophila melanogaster, exhausting metabolic reserves and contributing to mortality. The Journal of Toxicological Sciences. 4:773-790. paper

  • Gillespie KM, Xu F, Richter KT, McGrath JM, Markelz RJC, Ort DR, Leakey DB, Ainsworth EA (2012) Greater antioxidant and respiratory metabolism in field-grown soybean exposed to elevated O3 under both ambient and elevated CO2 Concentrations. Plant, Cell, and Environment. 35:164-184. paper

  • Markelz RJC, Strellner RS, Leakey ADB (2011) Impairment of C4 photosynthesis by drought is exacerbated by limiting nitrogen and ameliorated by elevated [CO2] in maize. Journal of Experimental Botany. 62:3235-3246. paper

  • Leakey ADB, Ainsworth EA, Bernard SM, Markelz RJC, Ort DR, Placella S, Rogers A, Smith MD, Sudderth EA, Weston DJ, Wullschleger SD, Yuan S (2009) Gene expression profiling – opening the black box of plant ecosystem responses to global change. Global Change Biology. 15:1201-1213. paper

Invited Talks

  • Scaling Fire - Merging Satellite data with eDNA to understand fire recovery in California Ecosystems (2023) - Ethical AI and Generative AI Leadership Summit. UC Berkeley, CA
  • Using Data Science to Understand California Ecosystem Responses to Fire (2022) Data & AI Innovation Day - Accenture. San Francisco, CA
  • The impact of fire on California Arthropods and fire data science techniques (2022) USFS Region 5 Hydrology Meeting, Online.
  • The impact of fire on California Arthropods (2021) UC Berkeley Accenture Day. Berkeley, CA.
  • Full Stack Biology: Moving freely between biological layers with databases, statistics, and network modeling (2017) Phenome 2017. Tucson, AZ.
  • Whole plant systems biology: a Brassica rapa exemplar (2016). Plant Research Lab- Michigan State University. East Lansing, MI.
  • Connecting genotype to phenotype in Brassica rapa using statistical and computational techniques (2015). University of Minnesota, St. Paul, MN.
  • Systems biology of plant competition in Brassica rapa (2014). Plant Genome Research Program- National Science Foundation. Arlington, VA.
  • Adapting crops to global climate change (2009). Darwin 200: A South American celebration. Maldonado, Uruguay.

Contributed Talks

  • Cross-Domain Workshops (XDs) - ImageXD, AudioXD, TextXD - ADSA Annual meeting. San Antonio, TX. - 2023
  • ASPB Annual Meeting. Austin, TX. - 2016
  • North American Arabidopsis Steering Committee Focus Group- Training the next generation of quantitative plant biologists. Phoenix, AZ. - 2016
  • UC Davis Postdoctoral Research Symposium– Big Data Session. Davis, CA. - 2015
  • UC Davis Plant Cell Biology Retreat. Davis, CA. - 2015
  • UC Davis Plant Cell Biology Retreat. Marconi Historic Park, CA. - 2014
  • UC Davis Postdoctoral Seminar Series. Davis, CA. - 2013
  • UC Davis Plant Cell Biology Retreat. Asilomar, CA. - 2013
  • ASPB Annual Meeting. Austin, TX. - 2012
  • UIUC Graduate Students in Ecology and Evolutionary Biology Symposium, Urbana, Illinois. - 2010
  • Proctor and Gamble Student Research Competition. Urbana, IL. - 2007

Contributed Posters

  • ASPB Annual Meeting. Austin, TX. - 2016
  • UC Davis Postdoctoral Research Symposium. Davis, CA. - 2016
  • Probabilistic Modeling in Genomics, CSHL, NY. - 2015
  • National Science Foundation, Arlington, VA. - 2015
  • ASPB Annual Meeting, Minneapolis, MN - 2015
  • Plant Animal Genome, San Diego, CA. Poster Presentation. - 2015
  • National Science Foundation, Arlington, VA. - 2014
  • ASPB Annual Meeting. Portland, OR. Poster- 2014
  • Keystone Symposium: Plant Abiotic Stress and Sustainable Agriculture. Taos, NM. - 2013
  • ASPB Annual Meeting. Austin, TX. - 2012
  • World Crop FACE Workshop, Tsukuba, Japan. - 2012
  • University of Illinois Public Engagement Symposium: Transforming Our Society. Champaign, IL. - 2012
  • 8th Okazaki Biology Conference, Okazaki, Japan.- 2012
  • UIUC Plant Biology Departmental Fall Welcome. Urbana, IL. - 2011
  • Institute for Genomic Biology Fellows Symposium. Poster Presentation. - 2011
  • Plant respiration and climate change. Oxford, United Kingdom. - 2010
  • ASPB Annual Meeting. Honolulu, Hawaii. - 2009
  • ASPB Annual Meeting. Merida, Mexico. - 2008

Teaching

  • Guest Lecturer - Biogeography of the Bay Area- Fire Ecology Field Course 2023
  • Critiques- Landscape Architecture Graduate Design Studio 438- University of Illinois - Experimental Design Thinking 2022
  • Guest Lecturer- Landscape Architecture Graduate Design Studio 438- University of Illinois - Experimental Design Thinking 2021
  • Guest Lecturer- Emerging Technologies- Kent School of Law - Biotech approaches to improving crops for a changing world 2020
  • Co-instructor- PBI200C- Plant Biology Graduate Group Core, Plant Primary Productivity: Environmental Impacts on C-Fixation. Mathematical model based instruction using photosynthesis simulations. 2016
  • Guest Instructor- BIS180L- Undergraduate Bioinformatics Lab. Genetic Networks 1: Clustering, Genetic Networks 2: Co-expression, 2015
  • Guest Lecturer- Plant Biology 220: Plant Developmental Biology. QTL mapping with -omics scale data - 2015
  • Co-instructor and Discussion Leader of General Education Class- Integrative Biology 107: Global Warming, Biofuels, and Food - 2011 List of Teachers Ranked Excellent by Their Students; Outstanding Teaching Award Department of Plant Biology
  • Teaching Assistant- Integrative Biology 440: Plants and Global Change. Developed science communication module- Graduate students and undergraduates created Podcasts for primary climate change literature. - 2009

Short Courses and Workshops

  • United Bicycle Institute - Advanced Bicycle Repair - Certified Bicycle Mechanic - 2023
  • Species distribution modeling with Bayesian statistics in R - 2021
  • Merging Crop Models and Genetics, University of Florida - 2015
  • Pathway Tools for Metabolic Modeling, SRI International - 2015
  • Summer Institute in Statistical Genetics, University of Washington - 2014
  • Computing in the Cloud: What Every Computational Life Scientist Should Know, NIMBioS, University of Tennessee - 2014
  • Frontiers and Techniques in Plant Science- Cold Spring Harbor Laboratory - 2010

Mentoring

  • Anna Holmquist (ESPM PhD Student, UC Berkeley) - 2021-2023
  • Lakshmi Pabbisetty (Biology, UC Davis) - 2015-2017
  • Christina Day (Biology, UC Davis) - 2013-2017
  • Amanjot Kaur (Biotechnology, UC Davis) - 2014-2015
  • Neije Mukherjee-Roy (Microbiology, UC Davis) - 2015
  • James Ta (Junior Specialist, UC Davis) - Graduate Student Biophysics UC Davis 2014-2015
  • Tiffany Ho (Genetics, Bioinformatics, UC Davis) - Graduate Student at Cornell University - 2014-2015
  • Shweta Dash (Biology, UC Davis) - 2015
  • Kamalpreet Sahota (Religious Studies, Biology- UC Davis) – Graduate Student at Touro University - 2013-14
  • Navi Singh (Biology- UC Davis) - 2013-14
  • William Landel (Plant Biology- UC Davis) - 2013
  • Kisha Thayapran (High School Student) - UC Davis Young Scholar - 2013
  • Natalia Rodriquez (High School Student - Puerto Rico) RAP2 Program 2012
  • Lauren Vosseller (Molecular and Cellular Biology- University of Illinois) - Co-Author, Graduate Student University of Illinois- Chicago - 2010-12
  • Alexander Petit (History- University of Illinois) - James Scholar Program
  • Brian Zehr (IB- University of Illinois)- India rural eye-care network - 2010-11
  • Ryan Boyd (IB- University of Illinois) - Graduate student at Washington State University - 2009-10
  • Reid Strellner (IB- University of Illinois) - Co-author, Graduate student at Northwestern University - 2008-10
  • Derek Haselhorst (IB- University of Illinois) - Graduate Student at University of Illinois- Urbana - 2008

Professional and Volunteer Service

  • Manuscript Reviewer: eLife; American Journal of Botany; Journal of Experimental Botany; Photosynthesis Research; Plant, Cell, and Environment- 2009-
  • Moderator : Data Science by Design 2021
  • Technical Editor: Bioinformatics Data Skills, Vince Buffalo, O’Reilly Publishing - 2013-2015
  • Organizer and Leader of Graduate Student Grant Writing: Plants iView - Middle School Plant Science Outreach ; successfully obtained funding from ASPB and UIUC. 2011-2012
  • Creator: Plant Carbon Allocation Relay Race for K-12 Science Teachers Workshop for Ecosystem Ecology - 2012
  • The Art of Science 2.0 - I collaborated with an artist to blend disciplines and create art by visualizing biological processes using confocal microscopy. - 2012
  • Presenter: Microscopy Outreach Event- Mahomet Seymour Junior High School Science Club - 2012
  • Organizer: National Pollinator Week - 2010 and 2011
  • Chair: Plant Biology Graduate Student Association - 2010-11
  • Roots and Shoots, University of Illinois Branch - 2010
  • Departmental Colloquium Coordinator: Plant Biology Graduate Student Association - 2009-10
  • Threatened Species Survey, Grampians National Park, Victoria, Australia - 2008
  • International Impact, fund raising and school building project for small Ecuadorian Indigenous communities - 2005-07

Unpaid Science Consulting