Mackenzie Weygandt Mathis

Mackenzie Weygandt Mathis, PhD Swiss Federal Institute of Technology, Lausanne (EPFL) Chemin des Mines 9, 1202 Geneva, Switzerland mackenzie.mathis@epﬂ.ch www.mackenziemathislab.org| google scholar| ORCiD

RESEARCH 8/2020 - Assistant Professor, Bertarelli Foundation Chair of Integrative Neuroscience APPOINTMENTS Swiss Federal Institute of Technology, Lausanne (EPFL) 9/17 - 7/20 Principal Investigator, Rowland Fellow. The Rowland Institute at Harvard, Harvard University (independent group leader position) 4/17 - 8/17 Postdoctoral Fellow. Dept. of Theoretical Physics, Eberhard Karls Universitat Tuebingen | Laboratory of Matthias Bethge Research: Deep learning methods for neural and behavioral quantiﬁcation 3/13 - 4/17 Graduate Researcher. Center for Brain Science, Dept. of Molecular & Cellular Biology, Harvard University | Laboratory of Naoshige Uchida Dissertation: Prediction errors guide learning in a mouse model of motor adaptation 2012 - 2013 PhD Rotation Student, Harvard University Laboratories of Naoshige Uchida, Paola Arlotta, & Takao Hensch 2007 - 2012 Senior Research Technician & Laboratory Manager Project A.L.S. Laboratory for Stem Cell Research, Columbia University, NYC. Laboratory of Christopher E. Henderson and Hynek Wichterle Research: Human stem cell-derived motor neurons as tools for modeling ALS

EDUCATION 2012 - 2017 Harvard University, Ph.D. 2012 - 2014 Harvard University, A.M. 2004 - 2007 University of Oregon, B.S.

FELLOWSHIPS 2019 - 2020 CZI Essential Open Source Software for Science - grant for DeepLabCut AND AWARDS 2019 - ELLIS Society Scholar, Natural Intelligence 2018 Mind, Brain & Behavior Harvard University Faculty Award 2018 eLife Travel Grant Award Winner 2017 NVIDIA GPU Grant 2017 - 2022 Rowland Fellowship 2017 Women & the Brain Fellowship for Advancement of Neuroscience 2013 - 2018 National Science Foundation Graduate Research Fellowship Life Sciences – Neuroscience 2013, ’14, ’16 Harvard University Certiﬁcate of Distinction in Teaching (MCB80, MCB145) 2014 Dr. Ernest Peralta Fund Award for Best Qualifying Exam proposal & defense, Harvard 2012 - 2013 Morris E. Zukerman Graduate Fellowship Awarded to top students in brain sciences at Harvard GSAS

TRAINING Jan. 2016 Neuroimaging Techniques Course, Max Plank Florida Institute for Neuroscience

PUBLICATIONS [1] Alexander Mathis, Steffen Schneider, Jessy Lauer, Mackenzie W Mathis. A Primer on Motion Capture with Deep Learning: Principles, Pitfalls, and Perspectives. Neuron 2020. (pre-print on arXiv)

[2] Mackenzie W. Mathis & Alexander Mathis. Deep learning tools for the measurement of animal behavior in neuroscience. Current Opinion in Neurobiology. Vol 60. (pre-print on arXiv) [3] Mackenzie W. Mathis A new spin on ﬁdgets. Nature Neuroscience (2019) (News & Views)

[4] Tanmay Nath*, Alexander Mathis*, An Chi Chen, Amir Patel, Matthias Bethge, Mackenzie W. Mathis. Using DeepLabCut for 3D markerless pose estimation across species and behaviors. Nature Protocols (2019). (pre-print on BioRxiv; Top 10 neuroscience papers of all-time).

1 of 2 [5] Alexander Mathis, Pranav Mamidanna, Kevin N. Cury, Taiga Abe, Venkatesh N. Murthy, Macken- zie W. Mathis**† & Matthias Bethge**. DeepLabCut: markerless pose estimation of user-defined body parts with deep learning. Nature Neuroscience (2018) 10.1038/s41593-018-0209-y. News & Views: Behavior tracking gets real (Nature Neuroscience), The Atlantic: A Game-Changing AI Tool for Tracking Animal Movements, and The Harvard Gazette. Open Source code: www.deeplabcut.org [6] Mackenzie W. Mathis†, ∪, Alexander Mathis, Naoshige Uchida†. Somatosensory cortex plays an essential role in forelimb motor adaptation in mice. Neuron (2017) 10.1016/j.neuron.2017.02.049 [7] Ritchie Ho, Sam Sances, Genevieve Gowing, Mackenzie W. Amoroso, Jacqueline G. O’Rourke, Anais Sahabian, Hynek Wichterle, Robert H. Baloh, Dhruv Sareen, and Clive N. Svendsen.A transcriptional comparison of iPSC models of ALS defines interactions of spinal motor neuron maturation and aging pathways with disease. Nature Neuroscience (2016) 10.1038/nn.4345 [8] Hai Li, Takaaki Kuwajima, Derek Oakley, Elena Nikulina, Jianwei Hou, Wan Seok Yang, Emily Rhodes Lowry, Nuno Jorge Lamas, Mackenzie W. Amoroso, Raghavendra Hosur, Hynek Wichterle, Said Sebti, Marie T. Filbin, Brent Stockwell, Christopher E. Henderson. Protein prenylation ex- erts a brake on axonal growth and elevated levels are correlated with early onset of amyotrophic lateral sclerosis. Cell Reports (2016) 10.1016/j.celrep.2016.06.013. [9] Jeremiah Y. Cohen, Mackenzie W. Amoroso, Naoshige Uchida. Serotonergic neurons signal re- ward and punishment on multiple timescales. eLife (2015) 10.7554/eLife.06346 Review in eLife (April 2015): Serotonin’s many meanings elude simple theories [10] Diane B. Re*, Virginia Le Verche*, Changhao Yu, Mackenzie W. Amoroso, Burcin Ikiz, Kristin A. Politi, Sudarshan Phani, Lucas Hoffmann, Martijn Koolen, Tetsuya Nagata, Dimitra Papadim- itriou, Peter Nagy, Hiroshi Mitsumoto, Shingo Kariya, Hynek Wichterle, Christopher E. Hender- son & Serge Przedborski. Necroptosis drives motor neuron death in models of both sporadic and familial ALS. Neuron (2014) 81(5):1001-1008. Review article in Neuron (Mar. 2014): Motor Neuron Death in ALS: Programmed by Astrocytes? [11] Mackenzie W. Amoroso*, Gist F. Croft*, Damian Williams, Sean O’Keefe, Monica A. Carassco, Anne R. Davis, Laurent Roybon, Derek Oakley, Tom Maniatis, Christopher E. Henderson, Hynek Wichterle. Accelerated high-yield generation of limb-innervating motor neurons from human stem cells. Journal of Neuroscience (2013) 33(2): 574-586. Review article in J.Neurosci (May 2013): Induced Pluripotent Stem Cells and Motor Neuron Dis- ease: Toward an Era of Individualized Medicine [12] Tomonori Takazawa, Gist F. Croft, Mackenzie W. Amoroso, Lorenz Studer, Hynek Wichterle & Amy B. MacDermott. Maturation of spinal motor neurons derived from human embryonic stem cells. PLoS ONE (2012) 7(7):e40154 [13] Stephane Nedelec, Mirza Peljto, Peng Shi, Mackenzie W. Amoroso, Lance Kam, Hynek Wichterle. Concentration dependent requirement for local protein synthesis in motor neuron subtype spe- cific response to axon guidance cues. Journal of Neuroscience (2012) 32(4): 1496-1506. [14] Gabriella L. Boulting*, Evangelos Kiskinis*, Gist F. Croft*, Mackenzie W. Amoroso*, Derek H. Oakley*, Brian J. Wagner, Damian Williams, David J. Kahler, Mariko Yamaki, Lance Davidow, Christopher T. Rodolfa, John T. Dimos, Shravani Mikkilineni, Amy B. MacDermott, Clifford Woolf, Christopher E. Henderson, Hynek Wichterle & Kevin Eggan. A functionally character- ized test set of human induced pluripotent stem cells. Nature Biotechnology (2011) 29:279-286. Review article in Nature Biotechnology (March 2011): IPSCs put to the test Featured in Harvard Gazette: Two studies prove value of iPS cells [15] Christoph Bock*, Evangelos Kiskinis*, Griet Verstappen*, Hongcang Gu, Gabriella Boulting, Zach D. Smith, Michael Ziller, Gist F. Croft, Mackenzie W. Amoroso, Derek H. Oakley, Andreas Gnirke, Kevin Eggan, & Alexander Meissner. Reference Maps of Human ES and iPS Cell Variation Enable High-Throughput Characterization of Pluripotent Cell Lines. Cell (2011) 144: 439-452. Review article in Nature Methods (April 2011): Testing Pluripotency.Review article in Nature Review Genetics (March 2011): Stem cells: scorecard for pluripotent cell lines

*co-ﬁrst authors, † co-corresponding authors, ∪ lead contact, **co-senior authors

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