Joe Daniele, Ph.D.

Post-doctoral Fellow



I received my Bachelor’s degree in Biology from the Massachusetts Institute of Technology (MIT) and my Ph.D. in Biochemistry from Harvard University in Cambridge, MA. In graduate school, I utilized the Drosophila larval eye disc to study how the protein Hedgehog (Hh) is partitioned for release within photoreceptor neurons. Secretion into the retina regulates eye development while axon transport and release at photoreceptor termini initiates postsynaptic neuron development in the brain. I showed that this binary targeting decision involves a very novel secretory pathway choice controlled by Hedgehog C-terminal proteolysis and non-canonical secretion.

In the Dillin lab, I am interested in developing tools to study the organelle basis for disease. In collaboration with Edgar Arriaga from the University of Minnesota we have developed methods to measure mitochondrial bioenergetics and morphology at the organelle and organismal level. With Anu Wartiovaara, I have applied these methods to understanding the pathogenesis of human heteroplasmic disease. Other interests include developing methods to measure lipid metabolism with respect to aging and lipodystrophy.


Current Collaborations

Dr. Edgar Arriaga, Department of Chemistry, University of Minnesota

Dr. Anu Wartiovaara, Program for Molecular Neurology, University of Helsinki

Union Biometrica, Inc. 



Technique Development

High-Throughput Characterization of Region-Specific Mitochondrial Function and Morphology. Daniele, J.R., Esping, D.J., Garcia, G., Parsons, L.S., Arriaga, E.A., & Dillin, A. Submitted to Scientific Reports.

Identification and characterization of mitochondrial subtypes in C. elegans via analysis of individual mitochondria by flow cytometryDaniele J.R., Heydari, K., Arriaga, E.A., and Dillin, A. Analytical Chemistry 2016, May 23. [PDF]

Label-free Live Cell Imaging of Nucleic Acids using Stimulated Raman Scattering (SRS) Microscopy. Zhang X*, Roeffaers MBJ*, Basu S*, Daniele JR, Fu D, Freudiger CW, Holtom GR, Xie XS. ChemPhysChem. 2012 Feb 24. doi: 10.1002/cphc.201100890. (‘*’ authors contributed equally) [PDF


Biochemistry/ Cell and Developmental Biology / Neuroscience 

A Novel Proteolytic Event Controls Hedgehog Intracellular Sorting and Distribution to Receptive Fields. Daniele J.R., Chu T.Y., Kunes S. Biology Open 2017 Mar 15 [PDF]

Analysis of Axonal Trafficking via a Novel Live Imaging Technique Reveals Distinct Hedgehog Transport Kinetics. Daniele, J.R.*, Baqri, R.M.*, Kunes, S. Biology Open Mar 15 *co-first author* [PDF]

Licensing of primordial germ cells for gametogenesis depends on genital ridge signaling. Hu Y.C., Nicholls P.K., Soh Y.Q., Daniele J.R., Junker J.P., van Oudenaarden A., Page D.C. PLoS Genet. 2015 Mar 4;11(3):e1005019. [PDF] * Built upon my MIT thesis *

Characterization of type IV secretion system mutants of Sinorhizobium meliloti strain 1021. Jones K.M., Lloret J., Daniele J.R., & Walker G.C. J Bacteriol. 2007 Mar;189(5):2133-8. [PDF]


Brain and Cognitive Science

The ‘Rhythmic Fingerprint’: An extension of the nPVI to quantify rhythmic influenceDaniele, J.R. (2017) Empirical Musicology Review 11 (2), 243-260. [PDF]

A tool for the quantitative anthropology of music: Use of the nPVI equation to analyze rhythmic variability within long-term historical patterns in music. Daniele J.R. (2017). Empirical Musicology Review 11 (2), 228-233. [PDF]

Stability and change in rhythmic patterning across a composer’s lifetime: a study of four famous composers using the nPVI equation. Daniele J.R. & Patel, A.D. Music Perception Dec. 2015, Vol. 33 No. 2, pp. 255-265. [PDF]

An empirical study of historical patterns in musical rhythm: Analysis of German & Italian classical music using the nPVI equation. Daniele J.R. & Patel, A.D. Music Perception Sept. 2013, Vol 31, Issue 1, pp. 10–18, ISSN 0730-7829.- featured in a corpus issue on “Empirical Musicology Methods” [PDF]

The interplay of linguistic and historical influences on musical rhythm in different culturesDaniele, J.R. & Patel, A.D. (2004) S.D. Lipscomb et al. (Eds.), pp. 759-762. Adelaide: Causal Productions. [PDF]

Stress-timed vs. syllable-timed music? A comment on Huron and Ollen. Patel, A.D. & Daniele, J.R. Music Perception, 2003 21:273-276.  [PDF]

An empirical comparison of rhythm in language and music. Patel A.D. & Daniele J.R. Cognition. 2003 Feb;87(1):B35-45. [PDF]