Jean-claude Farre

Title(s)Project Scientist, Molecular Biology
SchoolVc-academic Affairs
Address9500 Gilman Drive #
La Jolla CA 92093
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    Altmetrics Details PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. OXPHOS deficiencies affect peroxisome proliferation by downregulating genes controlled by the SNF1 signaling pathway. Elife. 2022 04 25; 11. Farre JC, Carolino K, Devanneaux L, Subramani S. PMID: 35467529; PMCID: PMC9094750.
      View in: PubMed   Mentions: 4     Fields:    Translation:HumansAnimalsCells
    2. Recognition and Chaperoning by Pex19, Followed by Trafficking and Membrane Insertion of the Peroxisome Proliferation Protein, Pex11. Cells. 2022 01 04; 11(1). Zientara-Rytter KM, Mahalingam SS, Farré JC, Carolino K, Subramani S. PMID: 35011719; PMCID: PMC8750153.
      View in: PubMed   Mentions: 5     Fields:    Translation:HumansCells
    3. BiFC Method Based on Intraorganellar Protein Crowding Detects Oleate-Dependent Peroxisomal Targeting of Pichia pastoris Malate Dehydrogenase. Int J Mol Sci. 2021 May 05; 22(9). Farré JC, Li P, Subramani S. PMID: 34063066; PMCID: PMC8124512.
      View in: PubMed   Mentions: 2     Fields:    Translation:AnimalsCells
    4. Balancing the Opposing Principles That Govern Peroxisome Homeostasis. Trends Biochem Sci. 2021 03; 46(3):200-212. Mahalingam SS, Shukla N, Farré JC, Zientara-Rytter K, Subramani S. PMID: 33046344; PMCID: PMC7880872.
      View in: PubMed   Mentions: 19     Fields:    Translation:Cells
    5. The autophagic degradation of cytosolic pools of peroxisomal proteins by a new selective pathway. Autophagy. 2020 01; 16(1):154-166. Wang X, Wang P, Zhang Z, Farré JC, Li X, Wang R, Xia Z, Subramani S, Ma C. PMID: 31007124; PMCID: PMC6984484.
      View in: PubMed   Mentions: 9     Fields:    Translation:AnimalsCells
    6. Peroxisome biogenesis, membrane contact sites, and quality control. EMBO Rep. 2019 01; 20(1). Farré JC, Mahalingam SS, Proietto M, Subramani S. PMID: 30530632; PMCID: PMC6322382.
      View in: PubMed   Mentions: 68     Fields:    Translation:HumansCells
    7. TRIM37 deficiency induces autophagy through deregulating the MTORC1-TFEB axis. Autophagy. 2018; 14(9):1574-1585. Wang W, Xia Z, Farré JC, Subramani S. PMID: 29940807; PMCID: PMC6135569.
      View in: PubMed   Mentions: 21     Fields:    Translation:HumansCells
    8. A New Yeast Peroxin, Pex36, a Functional Homolog of Mammalian PEX16, Functions in the ER-to-Peroxisome Traffic of Peroxisomal Membrane Proteins. J Mol Biol. 2017 11 24; 429(23):3743-3762. Farré JC, Carolino K, Stasyk OV, Stasyk OG, Hodzic Z, Agrawal G, Till A, Proietto M, Cregg J, Sibirny AA, Subramani S. PMID: 29037759; PMCID: PMC5693695.
      View in: PubMed   Mentions: 14     Fields:    Translation:HumansAnimalsCells
    9. TRIM37, a novel E3 ligase for PEX5-mediated peroxisomal matrix protein import. J Cell Biol. 2017 09 04; 216(9):2843-2858. Wang W, Xia ZJ, Farré JC, Subramani S. PMID: 28724525; PMCID: PMC5584156.
      View in: PubMed   Mentions: 35     Fields:    Translation:HumansAnimalsCells
    10. Active Interaction Mapping as a tool to elucidate hierarchical functions of biological processes. Autophagy. 2017 Jul 03; 13(7):1248-1249. Farré JC, Kramer M, Ideker T, Subramani S. PMID: 28486053; PMCID: PMC5529073.
      View in: PubMed   Mentions:    Fields:    Translation:Animals
    11. Active Interaction Mapping Reveals the Hierarchical Organization of Autophagy. Mol Cell. 2017 Feb 16; 65(4):761-774.e5. Kramer MH, Farré JC, Mitra K, Yu MK, Ono K, Demchak B, Licon K, Flagg M, Balakrishnan R, Cherry JM, Subramani S, Ideker T. PMID: 28132844; PMCID: PMC5439305.
      View in: PubMed   Mentions: 21     Fields:    Translation:HumansAnimals
    12. Mechanistic insights into selective autophagy pathways: lessons from yeast. Nat Rev Mol Cell Biol. 2016 09; 17(9):537-52. Farré JC, Subramani S. PMID: 27381245; PMCID: PMC5549613.
      View in: PubMed   Mentions: 195     Fields:    Translation:HumansAnimalsCells
    13. Peroxisomal Pex3 activates selective autophagy of peroxisomes via interaction with the pexophagy receptor Atg30. J Biol Chem. 2015 Mar 27; 290(13):8623-31. Burnett SF, Farré JC, Nazarko TY, Subramani S. PMID: 25694426; PMCID: PMC4375511.
      View in: PubMed   Mentions: 26     Fields:    Translation:AnimalsCells
    14. Phosphorylation of mitophagy and pexophagy receptors coordinates their interaction with Atg8 and Atg11. EMBO Rep. 2013 May; 14(5):441-9. Farré JC, Burkenroad A, Burnett SF, Subramani S. PMID: 23559066; PMCID: PMC3642380.
      View in: PubMed   Mentions: 86     Fields:    Translation:AnimalsCells
    15. RNA editing in mitochondrial trans-introns is required for splicing. PLoS One. 2012; 7(12):e52644. Farré JC, Aknin C, Araya A, Castandet B. PMID: 23285127; PMCID: PMC3527595.
      View in: PubMed   Mentions: 20     Fields:    Translation:AnimalsCells
    16. Guidelines for the use and interpretation of assays for monitoring autophagy. Autophagy. 2012 Apr; 8(4):445-544. Klionsky DJ, Abdalla FC, Abeliovich H, Abraham RT, Acevedo-Arozena A, Adeli K, Agholme L, Agnello M, Agostinis P, Aguirre-Ghiso JA, Ahn HJ, Ait-Mohamed O, Ait-Si-Ali S, Akematsu T, Akira S, Al-Younes HM, Al-Zeer MA, Albert ML, Albin RL, Alegre-Abarrategui J, Aleo MF, Alirezaei M, Almasan A, Almonte-Becerril M, Amano A, Amaravadi R, Amarnath S, Amer AO, Andrieu-Abadie N, Anantharam V, Ann DK, Anoopkumar-Dukie S, Aoki H, Apostolova N, Arancia G, Aris JP, Asanuma K, Asare NY, Ashida H, Askanas V, Askew DS, Auberger P, Baba M, Backues SK, Baehrecke EH, Bahr BA, Bai XY, Bailly Y, Baiocchi R, Baldini G, Balduini W, Ballabio A, Bamber BA, Bampton ET, Bánhegyi G, Bartholomew CR, Bassham DC, Bast RC, Batoko H, Bay BH, Beau I, Béchet DM, Begley TJ, Behl C, Behrends C, Bekri S, Bellaire B, Bendall LJ, Benetti L, Berliocchi L, Bernardi H, Bernassola F, Besteiro S, Bhatia-Kissova I, Bi X, Biard-Piechaczyk M, Blum JS, Boise LH, Bonaldo P, Boone DL, Bornhauser BC, Bortoluci KR, Bossis I, Bost F, Bourquin JP, Boya P, Boyer-Guittaut M, Bozhkov PV, Brady NR, Brancolini C, Brech A, Brenman JE, Brennand A, Bresnick EH, Brest P, Bridges D, Bristol ML, Brookes PS, Brown EJ, Brumell JH, Brunetti-Pierri N, Brunk UT, Bulman DE, Bultman SJ, Bultynck G, Burbulla LF, Bursch W, Butchar JP, Buzgariu W, Bydlowski SP, Cadwell K, Cahová M, Cai D, Cai J, Cai Q, Calabretta B, Calvo-Garrido J, Camougrand N, Campanella M, Campos-Salinas J, Candi E, Cao L, Caplan AB, Carding SR, Cardoso SM, Carew JS, Carlin CR, Carmignac V, Carneiro LA, Carra S, Caruso RA, Casari G, Casas C, Castino R, Cebollero E, Cecconi F, Celli J, Chaachouay H, Chae HJ, Chai CY, Chan DC, Chan EY, Chang RC, Che CM, Chen CC, Chen GC, Chen GQ, Chen M, Chen Q, Chen SS, Chen W, Chen X, Chen X, Chen X, Chen YG, Chen Y, Chen Y, Chen YJ, Chen Z, Cheng A, Cheng CH, Cheng Y, Cheong H, Cheong JH, Cherry S, Chess-Williams R, Cheung ZH, Chevet E, Chiang HL, Chiarelli R, Chiba T, Chin LS, Chiou SH, Chisari FV, Cho CH, Cho DH, Choi AM, Choi D, Choi KS, Choi ME, Chouaib S, Choubey D, Choubey V, Chu CT, Chuang TH, Chueh SH, Chun T, Chwae YJ, Chye ML, Ciarcia R, Ciriolo MR, Clague MJ, Clark RS, Clarke PG, Clarke R, Codogno P, Coller HA, Colombo MI, Comincini S, Condello M, Condorelli F, Cookson MR, Coombs GH, Coppens I, Corbalan R, Cossart P, Costelli P, Costes S, Coto-Montes A, Couve E, Coxon FP, Cregg JM, Crespo JL, Cronjé MJ, Cuervo AM, Cullen JJ, Czaja MJ, D'Amelio M, Darfeuille-Michaud A, Davids LM, Davies FE, De Felici M, de Groot JF, de Haan CA, De Martino L, De Milito A, De Tata V, Debnath J, Degterev A, Dehay B, Delbridge LM, Demarchi F, Deng YZ, Dengjel J, Dent P, Denton D, Deretic V, Desai SD, Devenish RJ, Di Gioacchino M, Di Paolo G, Di Pietro C, Díaz-Araya G, Díaz-Laviada I, Diaz-Meco MT, Diaz-Nido J, Dikic I, Dinesh-Kumar SP, Ding WX, Distelhorst CW, Diwan A, Djavaheri-Mergny M, Dokudovskaya S, Dong Z, Dorsey FC, Dosenko V, Dowling JJ, Doxsey S, Dreux M, Drew ME, Duan Q, Duchosal MA, Duff K, Dugail I, Durbeej M, Duszenko M, Edelstein CL, Edinger AL, Egea G, Eichinger L, Eissa NT, Ekmekcioglu S, El-Deiry WS, Elazar Z, Elgendy M, Ellerby LM, Eng KE, Engelbrecht AM, Engelender S, Erenpreisa J, Escalante R, Esclatine A, Eskelinen EL, Espert L, Espina V, Fan H, Fan J, Fan QW, Fan Z, Fang S, Fang Y, Fanto M, Fanzani A, Farkas T, Farré JC, Faure M, Fechheimer M, Feng CG, Feng J, Feng Q, Feng Y, Fésüs L, Feuer R, Figueiredo-Pereira ME, Fimia GM, Fingar DC, Finkbeiner S, Finkel T, Finley KD, Fiorito F, Fisher EA, Fisher PB, Flajolet M, Florez-McClure ML, Florio S, Fon EA, Fornai F, Fortunato F, Fotedar R, Fowler DH, Fox HS, Franco R, Frankel LB, Fransen M, Fuentes JM, Fueyo J, Fujii J, Fujisaki K, et al. PMID: 22966490; PMCID: PMC3404883.
      View in: PubMed   Mentions: 1831     Fields:    Translation:HumansAnimals
    17. Atg35, a micropexophagy-specific protein that regulates micropexophagic apparatus formation in Pichia pastoris. Autophagy. 2011 Apr; 7(4):375-85. Nazarko VY, Nazarko TY, Farré JC, Stasyk OV, Warnecke D, Ulaszewski S, Cregg JM, Sibirny AA, Subramani S. PMID: 21169734; PMCID: PMC3127218.
      View in: PubMed   Mentions: 19     Fields:    
    18. Rallying the exocyst as an autophagy scaffold. Cell. 2011 Jan 21; 144(2):172-4. Farré JC, Subramani S. PMID: 21241888; PMCID: PMC3030914.
      View in: PubMed   Mentions: 8     Fields:    
    19. A yeast MAPK cascade regulates pexophagy but not other autophagy pathways. J Cell Biol. 2010 Apr 19; 189(2):303-10. Manjithaya R, Jain S, Farré JC, Subramani S. PMID: 20385774; PMCID: PMC2856896.
      View in: PubMed   Mentions: 39     Fields:    Translation:AnimalsCells
    20. Molecular mechanism and physiological role of pexophagy. FEBS Lett. 2010 Apr 02; 584(7):1367-73. Manjithaya R, Nazarko TY, Farré JC, Subramani S. PMID: 20083110; PMCID: PMC2843806.
      View in: PubMed   Mentions: 64     Fields:    
    21. Roles of Pichia pastoris Uvrag in vacuolar protein sorting and the phosphatidylinositol 3-kinase complex in phagophore elongation in autophagy pathways. Autophagy. 2010 Jan; 6(1):86-99. Farré JC, Mathewson RD, Manjithaya R, Subramani S. PMID: 19946209; PMCID: PMC2945526.
      View in: PubMed   Mentions: 12     Fields:    
    22. Peroxisome size provides insights into the function of autophagy-related proteins. Mol Biol Cell. 2009 Sep; 20(17):3828-39. Nazarko TY, Farré JC, Subramani S. PMID: 19605559; PMCID: PMC2735482.
      View in: PubMed   Mentions: 39     Fields:    Translation:HumansAnimalsCells
    23. Turnover of organelles by autophagy in yeast. Curr Opin Cell Biol. 2009 Aug; 21(4):522-30. Farré JC, Krick R, Subramani S, Thumm M. PMID: 19515549; PMCID: PMC2725217.
      View in: PubMed   Mentions: 54     Fields:    
    24. PpAtg30 tags peroxisomes for turnover by selective autophagy. Dev Cell. 2008 Mar; 14(3):365-76. Farré JC, Manjithaya R, Mathewson RD, Subramani S. PMID: 18331717; PMCID: PMC3763908.
      View in: PubMed   Mentions: 168     Fields:    
    25. A ubiquitin-like protein involved in membrane fusion. Cell. 2007 Jul 13; 130(1):18-20. Subramani S, Farré JC. PMID: 17632052.
      View in: PubMed   Mentions: 6     Fields:    
    26. A cytoplasm to vacuole targeting pathway in P. pastoris. Autophagy. 2007 May-Jun; 3(3):230-4. Farré JC, Vidal J, Subramani S. PMID: 17329961.
      View in: PubMed   Mentions: 12     Fields:    
    27. Autophagy-related pathways and specific role of sterol glucoside in yeasts. Autophagy. 2007 May-Jun; 3(3):263-5. Nazarko TY, Farré JC, Polupanov AS, Sibirny AA, Subramani S. PMID: 17329963.
      View in: PubMed   Mentions: 6     Fields:    
    28. Localization of proteins and organelles using fluorescence microscopy. Methods Mol Biol. 2007; 389:239-50. Farre JC, Shirahama-Noda K, Zhang L, Booher K, Subramani S. PMID: 17951647.
      View in: PubMed   Mentions: 2     Fields:    
    29. In organello gene expression and RNA editing studies by electroporation-mediated transformation of isolated plant mitochondria. Methods Enzymol. 2007; 424:483-500. Farré JC, Choury D, Araya A. PMID: 17662855.
      View in: PubMed   Mentions: 6     Fields:    Translation:AnimalsCells
    30. Atg28, a novel coiled-coil protein involved in autophagic degradation of peroxisomes in the methylotrophic yeast Pichia pastoris. Autophagy. 2006 Jan-Mar; 2(1):30-8. Stasyk OV, Stasyk OG, Mathewson RD, Farré JC, Nazarko VY, Krasovska OS, Subramani S, Cregg JM, Sibirny AA. PMID: 16874081.
      View in: PubMed   Mentions: 14     Fields:    Translation:AnimalsCells
    31. Gene expression studies in isolated mitochondria: Solanum tuberosum rps10 is recognized by cognate potato but not by the transcription, splicing and editing machinery of wheat mitochondria. Nucleic Acids Res. 2005; 33(22):7058-65. Choury D, Farré JC, Jordana X, Araya A. PMID: 16352866; PMCID: PMC1312363.
      View in: PubMed   Mentions: 7     Fields:    Translation:AnimalsCells
    32. Different patterns in the recognition of editing sites in plant mitochondria. Nucleic Acids Res. 2004; 32(21):6397-406. Choury D, Farré JC, Jordana X, Araya A. PMID: 15585663; PMCID: PMC535677.
      View in: PubMed   Mentions: 24     Fields:    Translation:AnimalsCells
    33. Peroxisome turnover by micropexophagy: an autophagy-related process. Trends Cell Biol. 2004 Sep; 14(9):515-23. Farré JC, Subramani S. PMID: 15350980.
      View in: PubMed   Mentions: 52     Fields:    Translation:HumansAnimalsCells
    34. RNA splicing in higher plant mitochondria: determination of functional elements in group II intron from a chimeric cox II gene in electroporated wheat mitochondria. Plant J. 2002 Jan; 29(2):203-13. Farré JC, Araya A. PMID: 11851920.
      View in: PubMed   Mentions: 11     Fields:    Translation:AnimalsCells
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