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Happy to announce that Hankum, Qing, Frances, Joao, Julia and Sharan’s paper on Endo-IP is out Congratulations to all!


Excited that our collaboration with the Farese and Walther lab on Frontotemporal Dementia is now out in Nature Communications. Congratulations to Sebastian and Sharan!

Excited to announce that Melissa was named the 2022 Goldberg Fellow at Harvard Medical School, a fellowship program made possible by Fred and Joan Goldberg! Congratulations Melissa!!

Excited to post a copy of Ellen and Felix's new review in Molecular Cell on the role of ubiquitin in selective autophagy of mitochondria and intracellular bacteria. And its Open Access:…

Congratulations to Hankum, Qing, Frances, Joao, Julia and Sharan for posting of the Endo-IP paper on BioRxiv. We are also very grateful to Katie Overmyer in Josh Coon's lab for lipidomics of endosomes! This paper also demonstrates our ability to do targeted proteomics of APP processing products in purified endosomes and lysosomes using TOMAHAQ proteomics.

A big WELCOME to:

Ian Smith who joined the lab recently as a post-doctorial fellow and comes to us from the Villen lab at the University of Washington;


Enya Whelan who joined us recently as a Master's student intern from the University Francisco de Vitoria, in Madrid.

Just out - exciting collaboration with Erika Holzbaur's lab defining the proteome of autophagosomes purified from the mouse brain in Neuron. Great work from Juliet in the Holzbaur lab and Alban before he moved to MSK. Brain-derived autophagosome profiling reveals the engulfment of nucleoid-enriched mitochondrial fragments by basal autophagy in neurons. 



Happy to announce our joint publication with Trey Ideker which uses BioPlex and large-scale imaging to provide a map of human proteins interactions across cellular scales.

A multi-scale map of cell structure fusing protein images and interactions. Qin Y, Huttlin EL, Winsnes CF, Gosztyla ML, Wacheul L, Kelly MR, Blue SM, Zheng F, Chen M, Schaffer LV, Licon K, Bäckström A, Vaites LP, Lee JJ, Ouyang W, Liu SN, Zhang T, Silva E, Park J, Pitea A, Kreisberg JF, Gygi SP, Ma J, Harper JW, Yeo GW, Lafontaine DLJ, Lundberg E, Ideker T. Nature. 2021 Nov 24. doi: 10.1038/s41586-021-04115-9. Online ahead of print.

Happy to announce that Ana Galesic has joined the lab as a post-doctoral fellow. Ana did her PhD in chemistry with Matt Pratt at USC on alpha-synuclein. Welcome Ana!

Happy to announce that Miguel Gonzalez-Lozano (from the Smit lab in Vrije Universiteit Amsterdam) is joining the lab this week!! We are excited to have you and look forward to lots of fun and cool experiments.

Excited that our collaboration with the Mugit lab on Parkin targets in primary neurons is now out! Really fun to work with Miratul and Odetta!

Global ubiquitylation analysis of mitochondria in primary neurons identifies endogenous Parkin targets following activation of PINK1. Antico O, Ordureau A, Stevens M, Singh F, Nirujogi RS, Gierlinski M, Barini E, Rickwood ML, Prescott A, Toth R, Ganley IG, Harper JW, Muqit MMK. Science Advances. 2021 Nov 12;7(46):eabj0722. doi: 10.1126/sciadv.abj0722. Epub 2021 Nov 12.

Happy to announce the publication of Alban's last major paper from the lab - tour-de-force proteomic analysis of neurogenesis and examination of the role of autophagy. With major contributions by Felix, Heeseon, Joao and Jill.


Temporal proteomics during neurogenesis reveals large-scale proteome and organelle remodeling via selective autophagy.

Ordureau A, Kraus F, Zhang J, An H, Park S, Ahfeldt T, Paulo JA, Harper JW. Molecular Cell. 2021 Oct 15:S1097-2765(21)00800-5. doi: 10.1016/j.molcel.2021.10.001. Online ahead of print.

Happy to announce that Vinay, Melissa, Sharan's and Joao's paper on the role of TAX1BP1 and TBK1 in lysophagic flux appeared in Elife. Check it out:

Eapen, V., Swarup, S., Hoyer, M. J., Paulo, J. A. & Harper, J. W. Quantitative proteomics reveals the selectivity of ubiquitin-binding autophagy receptors in the turnover of damaged lysosomes by lysophagy. Elife 10, e72328., doi:doi: 10.7554/eLife.72328. (2021).

Happy to announce that Bobby Hollingsworth (recently graduated from HMS BCMP and Hao Wu's lab) and Chan Lee (recently graduated from Mike Overholtzer's lab at MSKCC) are joining the lab this week!! We are excited to have you and look forward to lots of fun and cool experiments.

Our collaborative paper with Danielle Garshott and Eric Bennett @UCSD describing iRQC - a surveillance pathway for 40S ribosome quality control during mRNA translation initiation is now out in Cell Reports. Interesting use of Ribo-Halo and Ribo-Keima developed previously in the lab by Heeseon An to decode mechanisms of 40S degradation occuring likely as a result of ribosome collisions during translation initiation. Check it out at:

We are sorry to see Hankum leave the lab to start his Assistant Professor position in South Korea but we are excited about his new opportunities! Good luck with everything Hankum - it was great to have you in the lab these last 3 years!

Just released on BioRxiv - our latest work from Team Lysophagy (Vinay, Sharan, and Melissa) describing a proteomic analysis of lysophagy using proximity biotinylation and lyso-IP. We identified TAX1BP1 as a critical cargo adaptor involved in lysophagic flux, as measured using a new lyso-Keima assay. {}

Introducing Frances Hundley, a new postdoc in the lab who comes to us from the Toczyski lab at UCSF, and Julia Paoli, a research assistant, who comes to us from the University of Illinois. Welcome to you both!!

Many CONGRATULATIONS! to Walter, who has been named a 2020 STAT Wunderkinds! Great news...​​

Check out out paper with Rachel Green identifying EDF1 as a key regulator of ribosome collisions - great application fo TMT proteomics to discovery new proteins in polysomes (EDF1).