46. Macrophage WDFY3, a protector against autoimmunity
Wu X, Wang Z, Croce KR, Li F, Cui J, D’Agati VD, Soni RK, Khalid S, Saleheen D, Tabas I, Yamamoto A, Zhang H. bioRxiv.

45. The tissue-specific autophagic response to nutrient deprivation
Yang YJ, Grosso Jasutkar H, Griffey CJ, Kim K, Melia TJ, Dephoure N, Yamamoto A. bioRxiv.

44. Adult-onset deactivation of autophagy leads to loss of synapse homeostasis and cognitive impairment, with implications for Alzheimer’s disease
Grosso Jasutkar H, Wasserlein EM, Ishola A, Litt N, Staniszewski A, Arancio O, Yamamoto A. Autophagy. (2024).

43. Autophagy at the synapse, an early site of dysfunction in neurodegeneration
Grosso Jasutkar H, Yamamoto A. Curr. Opin. Physiol. (2023).

42. A genome-wide CRISPR screen identifies WDFY3 as a novel regulator of macrophage efferocytosis
Shi J, Wu X, Wang Z, Li F, Meng Y, Moore RM, Cui J, Xue C, Croce KR, Yurdagul A Jr, Doench JG, Li W, Zarbalis KS, Tabas I, Yamamoto A, Zhang H. Nat Commun. (2022).

41. Oligodendroglial macroautophagy is essential for myelin sheath turnover to prevent neurodegeneration and death
Aber ER, Griffey CJ, Davies T, Li AM, Yang YJ, Croce KR, Goldman JE, Grutzendler J, Canman JC, Yamamoto A. Cell Reports. (2022).

40. Macroautophagy in CNS health and disease
Griffey CJ, Yamamoto A. Nat Rev Neurosci. (2022).

39. The distribution and density of Huntingtin inclusions across the Huntington disease neocortex: regional correlations with Huntingtin repeat expansion independent off pathologic grade
Hickman RA, Faust PL, Marder K, Yamamoto A, Vonsattel JP. Acta Neuropathol. Commun. (2022).

38. Living in α-syn: Tackling aggregates in Parkinson’s disease
Griffey CJ, Yamamoto A. Neuron (2022).

37. ALFY localizes to early endosomes and cellular protrusions to facilitate directional cell migration
Søreng K, Pankiv S, Bergsmark C, Haugsten EM, Dahl AK, de la Ballina LR, Yamamoto A, Lystad AH, Simonsen A. J Cell Sci. (2022).

36. Go for the Golgi: Eating selectively with Calcoco1
Yamamoto A. J Cell Biol. (2021).

35. Do changes in synaptic autophagy underlie the cognitive impairments in Huntington’s disease?
Grosso Jasutkar H, Yamamoto A. J. Huntingtons Dis. (2021).

34. Dissolving the complex role aggregation plays in neurodegenerative disease
Croce KR, Yamamoto A. Mov Disord. (2021).

33. A highly conserved glutamic acid in ALFY inhibits membrane binding to aid in aggregate clearance
Reinhart EF, Litt NA, Katzenell S, Pellegrini M, Yamamoto A, Ragusa MJ. Traffic (2020).

32. Huntington’s disease pathogenesis is modified in vivo by Alfy/Wdfy3 and selective macroautophagy
Fox LM, Kim K, Johnson CW, Chen S, Croce KR, Victor MB, Eenjes E, Bosco JR, Randolph LK, Dragatsis I, Dragich JM, Yoo AS, Yamamoto A. Neuron (2020).

31. Cell-type-specific regulation of neuronal intrinsic excitability by macroautophagy
Lieberman OJ, Frier MD, McGuirt AF, Griffey CJ, Rafikian E, Yang M, Yamamoto A, Borgkvist A, Santini E, Sulzer D. eLife (2020).

30. Examining aggregates through the eyes of WDFY3/Alfy
Fox LM, Yamamoto A. Autophagy (2020).

29. NIPSNAP1 and NIPSNAP2 act as “eat me” signals for mitophagy
Princely AY, Pankiv S, Mathai BJ, Håkon Lystad A, Bindesbøll C, Brenne HB, Yoke Wui Ng M, Thiede B, Yamamoto A, Mutugi Nthiga T, Lamark T, Esguerra CV, Johansen T, Simonsen A. Dev Cell (2019).

28. A role for autophagy in Huntington’s disease
Croce KR, Yamamoto A. Neurobiol Dis. (2019).

27. Monitoring aggregate clearance and formation in cell-based assays
Eenjes E, Yang-Klingler YJ, Yamamoto A. Methods Mol Biol. (2019)

26. Autophagy linked FYVE (Alfy/WDFY3) is required for establishing neuronal connectivity in the mammalian brain
Dragich JM, Kuwajima T, Hirose-Ikeda M, Yoon MS, Eenjes E, Bosco JR, Fox LM, Lystad AH, Oo TF, Yarygina O, Mita T, Waguri S, Ichimura Y, Komatsu M, Simonsen A, Burke RE, Mason CA, Yamamoto A. eLife (2016).

25. Distinguishing aggregate formation and aggregate clearance using cell-based assays
Eenjes E, Dragich JM, Kampinga HH, Yamamoto A. J Cell Sci. (2016).

24. Macroautophagy of aggregation-prone proteins in neurodegenerative disease
Fox LM, Yamamoto A. Autophagy (2015).

23. Loss of mTOR-dependent macroautophagy causes autistic-like synaptic pruning deficits
Tang G, Gudsnuk K, Kuo SH, Cotrina ML, Rosoklija G, Sosunov A, Sonders MS, Kanter E, Castagna C, Yamamoto A, Yue Z, Arancio O, Peterson BS, Champagne F, Dwork AJ, Goldman J, Sulzer D. Neuron (2014).

22. CLEARance wars: PolyQ strikes back
Yang XW, Yamamoto A. Nature Neurosci. (2014).

21. A time course analysis of the electrophysiological properties of neurons differentiated from human induced pluripotent stem cells (iPSCs)
Prè D, Nestor MW, Sproul AA, Jacob S, Koppensteiner P, Chinchalongporn V, Zimmer M, Yamamoto A, Noggle SA, Arancio O. Plos One (2014).

20. Lipidation of the LC3/GABARAP family of autophagy proteins relies on a membrane-curvature-sensing domain in Atg3
Nath S, Dancourt J, Shteyn V, Puente G, Fong WM, Nag S, Bewersdorf J, Yamamoto A, Antonny B, Melia TJ. Nature Cell Biology (2014).

19. Autophagy and its normal and pathogenic states in the brain
Yamamoto A, Yue Z. Annu Rev Neurosci. (2014).

18. Identification of a candidate therapeutic autophagy-inducing peptide
Shoji-Kawata S, Sumpter R, Leveno M, Campbell GR, Zou Z, Kinch L, Wilkins AD, Sun Q, Pallauf K, MacDuff D, Huerta C, Virgin HW, Helms JB, Eerland R, Tooze SA, Xavier R, Lenschow DJ, Yamamoto A, King D, Lichtarge O, Grishin NV, Spector SA, Kaloyanova DV, Levine B. Nature (2013).

17. The membrane raft protein Flotillin-1 is essential in dopamine neurons for amphetamine-induced behavior in Drosophila
Pizzo AB, Karam CS, Zhang Y, Yano H, Freyberg RJ, Karam DS, Freyberg Z, Yamamoto A, McCabe BD, Javitch JA. Mol Psychiatry (2013).

16. Lingo-1 expression is increased in essential tremor cerebellum and is present in the basket cell pinceau
Kuo SH, Tang G, Louis ED, Ma K, Babji R, Balatbat M, Cortes E, Vonsattel JP, Yamamoto A, Sulzer D, Faust PL. Acta Neuropathol. (2013).

15. Modulating macroautophagy: a neuronal perspective
Johnson CW, Melia TJ, Yamamoto A. Future Med Chem. (2012).

14. Receptor protein complexes are in control of autophagy
Mijaljica D, Nazarko TY, Brumell JH, Huang WP, Komatsu M, Prescott M, Simonsen A, Yamamoto A, Zhang H, Klionsky DJ, Devenish RJ. Autophagy (2012).

13. Flotillin-1 is essential for PKC-triggered endocytosis and membrane microdomain localization of DAT
Cremona ML, Matthies HJ, Pau K, Bowton E, Speed N, Lute BJ, Anderson M, Sen N, Robertson SD, Vaughan RA, Rothman JE, Galli A, Javitch JA, Yamamoto A. Nature Neurosci. (2011)

12. The elimination of accumulated and aggregated proteins: A role for aggrephagy in neurodegeneration
Yamamoto A, Simonsen A. Neurobiol Dis. (2011)

11. Alfy-dependent elimination of aggregated proteins by macroautophagy: can there be too much of a good thing?
Yamamoto A, Simonsen A. Autophagy (2010).

10. The selective macroautophic degradation of aggregated proteins requires the PI3P-binding protein Alfy
Filimonenko M, Isakson P, Finley KD, Anderson M, Jeong H, Melia TJ, Bartlett BJ, Myers KM, Birkeland HC, Lamark T, Krainc D, Brech A, Stenmark H, Simonsen A, Yamamoto A. Mol Cell. (2010).

9. Mutant huntingtin alters cell fate in response to microtubule depolymerization via the GEF-H1-RhoA-ERK pathway
Varma H, Yamamoto A, Sarantos MR, Hughes RE, Stockwell BR. J Biol Chem. (2010).

8. Acetylation targets mutant huntingtin to autophagosomes for degradation
Jeong H, Then F, Melia TJ Jr, Mazzulli JR, Cui L, Savas JN, Voisine C, Paganetti, P, Tanese N, Hart AC, Yamamoto A, Krainc D. Cell (2009).

7. PINK1 defect causes mitochondrial dysfunction, proteasomal deficit and a-synuclein aggregation in cell culture models of Parkinson’s disease
Liu W, Vives-Bauza C, Acín-Peréz R, Yamamoto A, Tan Y, Li Y, Magrané J, Stavarache MA, Shaffer S, Chang S, Kaplitt MG, Huang XY, Beal MF, Manfredi G, Li C. Plos One (2009).

6. Potent inhibitors of huntingtin protein aggregation in a cell-based assay
Rinderspacher A, Cremona ML, Liu Y, Deng SX, Xie Y, Gong G, Aulner N, Többen U, Myers K, Chung C, Andersen M, Vidović D, Schürer S, Brandén L, Yamamoto A, Landry DW. Bioorg Med Chem Lett. (2009).

5. Functional multivesicular bodies are required for autophagic clearance of protein aggregates associated with neurodegenerative disease
Filimonenko M, Stuffers S, Raiborg C, Yamamoto A, Malerød L, Fisher EM, Isaacs A, Brech A, Stenmark H, Simonsen A. J Cell Biol. (2007).

4. Autophagy-mediated clearance of huntingtin aggregates triggered by the insulin-signaling pathway
Yamamoto A, Cremona ML, Rothman JE. J Cell Biol. (2006).

3. The ons and offs of inducible transgenic technology: a review
Yamamoto A, Hen R, Dauer WT. Neurobiol Dis. (2001).

2. Proteasomal-dependent aggregate reversal and absernce of cell death in a conditional mouse model of Huntington’s disease
Martín-Aparicio E, Yamamoto A, Hernández F, Hen R, Avila J, Lucas JJ. J. Neurosci. (2001).

1. Reversal of neuropathology and motor dysfunction in a conditional model of Huntington’s disease
Yamamoto A, Lucas JJ, Hen R. Cell (2000).