KM

About me

Thanks for your interest. I am a molecular and computational biologist focused on understanding gene regulatory networks through integrated genomic approaches, including RNA-seq, DAP-seq, and related datasets.

My training spans end-to-end genomics, from DNA and RNA extraction and sequencing library preparation to high-throughput data analysis and modeling. My work emphasizes developing practical, reproducible approaches to analyzing complex biological data.

I am particularly interested in teaching applied bioinformatics, emphasizing clear biological interpretation alongside computational skills, and contributing to the development of collaborative, student-centered research and teaching programs.

— Kirk

Publications

Submitted · Nature Communications

Genome-wide transcription factor binding reveals regulatory logic and evolutionary divergence in grasses

Bahman Khahani, Leo A. Baumgart, Kirk R. Amundson, Ian W. McCahill, Greg A. Gregory, Kirk J.-M. MacKinnon, Xiaocheng Yu, Ritesh Mewalal, Anthony Bortolazzo, Yu Zhang, Madelaine E. Bartlett, John P. Vogel, Ian K. Blaby, Ronan C. O’Malley, Samuel P. Hazen

Submitted · Molecular Systems Biology

Combinatorial effects of transcription factors functionally revealed by single cell TARGET-seq

Amélie Emanuel, Jean-Baptiste Carluer, Will E. Hinckley, Baldwin Dumortier, Samantha Frangos, Kirk MacKinnon, Bruno Guillotin, Tim L. Jeffers, Yitao Long, Manpreet Katari, Dennis Shasha, Angelo Pasquino, Matthew D. Brooks, Stéphanie Pateyron, Myriam Boyer-Clavel, Stéphanie Boireau, Wojciech Szponarski, Hatem Rouached, Sandrine Ruffel, André Mas, Gloria Coruzzi, Bastiaan O. Bargmann, Etienne Delannoy

2024 · Quantitative Plant Biology

Mechanically induced localisation of SECONDARY WALL INTERACTING bZIP is associated with thigmomorphogenic and secondary cell wall gene expression

Joshua H. Coomey, Kirk J.-M. MacKinnon, Ian W. McCahill, Bahman Khahani, Pubudu P. Handakumbura, Gina M. Trabucco, Jessica Mazzola, Nicole A. Leblanc, Rithany Kheam, Miriam Hernandez-Romero, Kerrie Barry, Lifeng Liu, Ji E. Lee, John P. Vogel, Ronan C. O’Malley, James J. Chambers, Samuel P. Hazen

https://doi.org/10.1017/qpb.2024.5

2020 · New Phytologist

Changes in ambient temperature are the prevailing cue in determining Brachypodium distachyon diurnal gene regulation

Kirk J.-M. MacKinnon, Benjamin J. Cole, Chang Yu, Joshua H. Coomey, Nolan T. Hartwick, Marie-Stanislas Remigereau, Tomás Duffy, Todd P. Michael, Steve A. Kay, Samuel P. Hazen

https://doi.org/10.1111/nph.16507

2018 · The Plant Journal

SECONDARY WALL ASSOCIATED MYB1 is a positive regulator of secondary cell wall thickening in Brachypodium distachyon and is not found in the Brassicaceae

Pubudu P. Handakumbura, Kathryn Brow, Ian P. Whitney, Kangmei Zhao, Karen A. Sanguinet, Scott J. Lee, Jennifer Olins, Sandra P. Romero-Gamboa, Michael J. Harrington, Carlisle J. Bascom, Kirk J.-M. MacKinnon, Michael T. Veling, Lifeng Liu, Ji E. Lee, John P. Vogel, Ronan C. O’Malley, Magdalena Bezanilla, Laura E. Bartley, Samuel P. Hazen

https://doi.org/10.1111/tpj.14047

2018 · Frontiers in Plant Science

Secondary Wall Regulating NACs Differentially Bind at the Promoter at a CELLULOSE SYNTHASE A4 Cis-eQTL

Jennifer R. Olins, Li Lin, Scott J. Lee, Gina M. Trabucco, Kirk J.-M. MacKinnon, Samuel P. Hazen

https://doi.org/10.3389/fpls.2018.01895

2014 · PLoS ONE

Daily Changes in Temperature, Not the Circadian Clock, Regulate Growth Rate in Brachypodium distachyon

Dominick A. Matos, Benjamin J. Cole, Ian P. Whitney, Kirk J.-M. MacKinnon, Steve A. Kay, Samuel P. Hazen

https://doi.org/10.1371/journal.pone.0100072

Exploration

Applications

Interactive tools for exploring transcriptional regulation and RNA-seq datasets, designed for intuitive exploration of gene expression dynamics and regulatory behavior.

Timecourse RNA-seq

Interactive exploration of time-course RNA-seq expression patterns.

Open application

Touch Responsive Timecourse RNA-seq

Visualization of gene expression responses following touch/mechanical stimulation.

Open application

Gain and Loss of Function RNA-seq

Exploration of RNA-seq datasets from gain- and loss-of-function transcriptional regulators.

Open application

Visualizations

High-resolution time-lapse imaging of Brachypodium distachyon under controlled light and temperature regimes, capturing diurnal growth dynamics and environmental responses.