Matthew F Rose

Assistant Professor, Pathology
School of Medicine

Assistant Professor (Joint Appointment), Developmental & Cell Biology
Charlie Dunlop School of Biological Sciences

Member, Center for Complex Biological Systems

Member, Center for Neural Circuit Mapping, Anatomy & Neurobiology
School of Medicine

Member, Center for Synthetic Biology, Biomedical Engineering
The Henry Samueli School of Engineering

Director, Pathology Advanced Imaging Resource (PAIR), Pathology
School of Medicine

neurodevelopment, neuropathology, bioinformatics, AI, 3D imaging, tool development, gene expression patterns, brainstem, motor neurons, axon targeting, congenital cranial dysinnervation disorders (CCDDs), amyotrophic lateral sclerosis (ALS)

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UCI Profiles

ResearchGate

GitHub: Rose Research Group

-Affiliated Non-Clinical Staff, Engle Lab, F.M. Kirby Neurobiology Center, Boston Children’s Hospital (2021-2023)
-Associated Scientist, Klarman Cell Observatory, The Broad Institute of MIT and Harvard (2016-2023)
-Collaborator-POI, Pathology, Brigham & Women's Hospital (2021-2023)
-Instructor, Harvard Medical School (2016-2023)
-Affiliated Non-Clinical Staff, Engle Lab, Pathology, Boston Children’s Hospital (2014-2021)
-Associate Pathologist, Pathology (Neuropathology), Brigham and Women’s Hospital (2016-2021)
-Research/Clinical Fellow, Pathology, Laboratory of Elizabeth Engle, Boston Children's Hospital and Brigham and Women’s Hospital (2014-2016)
-Affiliated Fellow, Pathology, Boston Children’s Hospital (2014)
-Neuropathology Fellow, Pathology (Neuropathology), Brigham & Women's Hospital, Boston Children’s Hospital, & Beth Israel Deaconess Medical Center (2012-2014)
-Resident, Pathology, Brigham and Women's Hospital (2010-2012)

We study the gene networks driving neuronal diversity during brainstem development to uncover why only specific subsets are differentially affected in a given human neurologic disease. The brainstem controls multiple critical motor and sensory functions, including eye movements, facial expression, speech, hearing, proprioception, arousal, and breathing. Disruption of these functions can lead to profound deficits including in childhood social interaction. The anatomy and gene circuits in the brainstem are highly conserved in mice, providing an ideal model system to investigate neuronal specification and axon growth and guidance in both health and disease. We combine neurodevelopmental tools, 3D imaging, multi-omics/bioinformatic approaches, molecular/synthetic biology, and mouse models of human disease to define developmental differences among various neuronal populations. Through a single cell and spatial transcriptomic atlas of developing motor neurons, we have identified unique genetic fingerprints of each motor neuron population, including novel markers of spatially and temporally distinct subpopulations that contribute to specific aberrant nerve branches in mouse models of childhood disorders. This work provides a new toolbox to study differential neuronal vulnerability in disease.

-The Robert & Sylvia Mapel Research Innovation Award to Mentor and Mentee, University of California Irvine (2024)
-Weil Award for the Best Paper in Experimental Neuropathology, American Association of Neuropathologists (2018)
-Poster of Distinction for Outstanding Achievement In Clinical, Translational, or Basic Science Research, Harvard-Wide Department of Pathology, Harvard Medical School (2018)
-BRASS Scholar (Baylor Research Advocates for Student Scientists) (2002-2008)
-Neurobiology Fellow, Marine Biological Laboratory (MBL) (2003)
-Barry M. Goldwater National Scholar, The Barry Goldwater Scholarship and Excellence in Education Program (1998-2000)
-Echols Scholar, University of Virginia (1996-2000)
-Research Science Institute Fellow, Massachusetts Institute of Technology (1995)

I’ve pursued research since an early age, supported by many wonderful mentors and teachers along the way, and I consider mentoring and training the next generation of scientists one of my primary goals. I have progressively developed approaches in critical thinking, imaging, cell culture, animal work, bioinformatics, and neuropathology through work in the laboratories of Jeff Corwin, PhD (University of Virginia), Huda Zoghbi, MD and Hugo Bellen, PhD (Baylor College of Medicine), Jeff Lichtman, MD/PhD (The Marine Biological Laboratory), Elizabeth Engle, MD (Harvard Medical School), & Aviv Regev, PhD (The Broad Institute of MIT & Harvard), among many others. I’m also a clinical neuropathologist and look for areas to apply our research findings to medicine.

(Selected Publications)

Riffle D*, Shirooni N*, Vijay V, Sureshkumar P, Rose MF. (2026) CARIBOU: Computational AI research interface for bioinformatics, omics, and unifying agents. bioRxiv. (*equal contribution). https://doi.org/10.64898/2026.05.25.727730

Almpani K, Devine KR, Liberton DK, Mishra R, Bassim C, Van Ryzin C, Facio FM, Webb BD, Barry BJ, Engle EC, Wang Jabs E, Collins FS, Manoli I, Lee JS, Moebius Syndrome Research Consortium‡. (2026) Multimodality Craniofacial Phenotyping of Congenital Facial Weakness Disorders. The Cleft Palate Craniofacial Journal. 63(6):1455-1468. (‡contributed as part of consortium). PMCID: PMC12826332. https://doi.org/10.1177/10556656251344128.

Shirooni N, Whedon I, Padisetti V, Wang L, Sureshkumar P, Vijay V, Ramos J, Yang X, Li J, Munawar F, Kermani K, Barroga A, Chi L, Zabrocki C, Shenoy A, Thayer S, Raychaudhuri U, Rose MF. (2026) An optimized transcriptomic toolbox for rare cell types in neurodevelopment. In: American Association of Neuropathologists, Inc. Abstracts of the 102nd Annual Meeting June 4-7, 2026, Cambridge, MD. Journal of Neuropathology and Experimental Neurology. 85(6):652. (Published Abstract) https://doi.org/10.1093/jnen/nlag044.

Shirooni N, Wu M, Weiss L, Robson N, Shmara A, Kimonis V, Rose MF. (2026) High-Fat Diet Ameliorates Transcriptional Changes in R155H/R155H VCP Disease. In: American Association of Neuropathologists, Inc. Abstracts of the 102nd Annual Meeting June 4-7, 2026, Cambridge, MD. Journal of Neuropathology and Experimental Neurology. 85(6):605. (Published Abstract) https://doi.org/10.1093/jnen/nlag044.

Monuki WE, Hevner RF, Rose MF. (2024) Normal Development of the Nervous System. In: Smith C, Perry A, Kovacs G, Jacques T, editors. Greenfield’s Neuropathology, 10th Edition. Boca Raton (FL): CRC Press. Vol. 1, p. 247-294. https://doi.org/10.1201/9781003389699

Lee AS, Ayers LJ, Kosicki M, Chan WM, Fozo LN, Pratt BM, Collins T, Zhao B, Rose MF, Sanchis-Juan A, Fu JM, Wong I, Zhao X, Tenney AP, Lee C, Laricchia KM, Barry BJ, Bradford VR, Lek M, MacArthur DG, Lee EA, Talkowski ME, Brand H, Pennacchio LA, Engle EC. (2024) A cell type-aware framework for nominating non-coding variants in Mendelian regulatory disorders. Nature Communications. 15(1):8268. PCMID: PMC11436875. https://doi.org/10.1038/s41467-024-52463-7.

Rose MF, Tenney AP, Ray TP, Creighton D, Gelber A, Tischfield MA, Murray E, Collins T, Nugent AA, Ang P, Izen S, Bauer MR, Huang W, Satija R, Rozenblatt-Rosen O, Chen F, Macosko EZ, Regev A, Engle EC. (2021). Developing hindbrain motor neurons show spatial and temporal transcriptomic diversity mapping to wiring decisions. In: American Association of Neuropathologists, Inc. Abstracts of the 97th Annual Meeting June 10–13, 2021, St. Louis, MO. Journal of Neuropathology and Experimental Neurology. 80(6):564. (Published Abstract) https://doi.org/10.1093/jnen/nlab042.

An D, Fujiki R, Iannitelli DE, Smerdon SW, Maity S, Wanaselja EK, Yagudayeva I, Lee JY, Rose MF, Vogel C, Wichterle H, Engle EC, Mazzoni EO. (2019) Stem cell-derived cranial and spinal neurons reveal proteostatic differences between ALS resistant and sensitive motor neurons. eLife. 8:e44423. PMCID: PMC6594754. https://doi.org/10.7554/elife.44423.

Di Gioia SA, Connors S**, Matsunami N**, Cannavino J**, Rose MF**, Gilette NM, Artoni P, de Macena Sobreira NL, Chan WM, Webb BD, Robson CD, Cheng L, Van Ryzin C, Ramirez-Martinez A, Mohassel P, Leppert M, Scholand MB, Grunseich C, Ferreira CR, Hartman T, Hayes IM, Morgan T, Markie DM, Fagiolini M, Swift A, Chines PS, Speck-Martins CE, Collins FS, Jabs EW, Bönnemann CG, Olson EN; Moebius Syndrome Research Consortium, Carey JC, Robertson SP, Manoli I, Engle EC. (2017) A defect in myoblast fusion underlies Carey-Fineman-Ziter syndrome. Nature Communications. 8:16077. PMCID: PMC5504296. https://doi.org/10.1038/ncomms16077. (**equal contribution).

Driver EC, Sillers L, Coate TM, Rose MF, Kelley MW. (2013) The Atoh1-lineage gives rise to hair cells and supporting cells within the mammalian cochlea. Developmental Biology. 376(1):86-98. PMCID: PMC3652277. https://doi.org/10.1016/j.ydbio.2013.01.005.

Rose MF*, Ren J*, Ahmad KA*, Chao HT, Klisch TJ, Flora A, Greer JJ, Zoghbi HY. (2009) Math1 is essential for the development of hindbrain neurons critical for perinatal breathing. Neuron. 64(3):341-54. PMCID: PMC2818435. https://doi.org/10.1016/j.neuron.2009.10.023. (*equal contribution)

Rose MF, Ahmad KA, Thaller C, Zoghbi HY. (2009) Excitatory neurons of the proprioceptive, interoceptive, and arousal hindbrain networks share a developmental requirement for Math1. Proceedings of the National Academy of Sciences. 106(52):22462-7. PMCID: PMC2799716. https://doi.org/10.1073/pnas.0911579106.

England C, Kowalczyk T, Dagan A, Daza RAM, Lau C, Rose MF, Hevner RF. (2006) Unipolar Brush Cells of the Cerebellum are Produced in the Rhombic Lip and Migrate through Developing White Matter. Journal of Neuroscience. 26(36):9184-95. PMCID: PMC6674506. https://doi.org/10.1523/jneurosci.1610-06.2006.

Chizhikov VV, Lindgren A, Currle DS, Rose MF, Monuki ES, Millen KJ. (2006) The roof plate regulates cerebellar cell-type specification and proliferation. Development. 133(15):2793-2804. PMID: 16790481. https://doi.org/10.1242/dev.02441.

Young JI, Hong EP, Castle JC, Crespo-Barreto J, Bowman AB, Rose MF, Kang D, Richman R, Johnson JM, Berget S, Zoghbi HY. (2005) Regulation of RNA splicing by the methylation-dependent transcriptional repressor MeCP2. Proceedings of the National Academy of Sciences. 102(49):17551-8. PMCID: PMC1266160. https://doi.org/10.1073/pnas.0507856102.

Wang VY*, Rose MF*, Zoghbi HY. (2005) Math1 expression redefines the rhombic lip and reveals novel lineages within the brainstem and cerebellum. Neuron. 48:31-43. PMID: 16202707. https://doi.org/10.1016/j.neuron.2005.08.024. (*equal contribution)

Tsuda H, Jafar-Nejad H, Patel AJ, Sun Y, Chen HK, Rose MF, Venken KJT, Botas J, Orr HT, Bellen HJ, Zoghbi HY. (2005) The AXH domain of Ataxin-1 mediates neurodegeneration through its interaction with Gfi-1/Senseless proteins. Cell. 122:633-644. PMID: 16122429. https://doi.org/10.1016/j.cell.2005.06.012.

Frankfort BJ, Pepple KL, Mamlouk M, Rose MF, Mardon G. (2004) Senseless is required for pupal retinal development in Drosophila. Genesis. 38:182-194. PMID: 15083519. https://doi.org/10.1002/gene.20018.

Rose MF, Rose SR. (1998) Melatonin accelerates metamorphosis in Xenopus laevis. Journal of Pineal Research. 24:90-95. PMID: 9510433. https://doi.org/10.1111/j.1600-079x.1998.tb00372.x.

Mapping Brainstem Motor Neuron Subtypes and Genetic Pathways Involved in their Differential Susceptibility to Disease NIHK08NS099502; Dec 1, 2016 - Nov 30, 2023; Role: Principal Investigator

Role of Math1 in brain stem & cerebellar development NIHF31NS051046; Sep 30, 2004 - Oct 31, 2007; Role: Principal Investigator

American Association of Neuropathologists (AANP)

Society for Neuroscience (SfN)

Cellular and Molecular Biosciences

Experimental Pathology (PTH)

Interdepartmental Neuroscience Program

Mathematical, Computational and Systems Biology

Neuropathology (PTH)

Center for Complex Biological Systems

Center for Neural Circuit Mapping

Center for Synthetic Biology

Link to this profile
https://faculty.uci.edu/profile/?facultyId=7066

Last updated
03/15/2022