Study detail Full reference list

Study Detail

Studies

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PARK-seq notes description

Notes cover the following:

  • CONFUSION CLARITY - Notes on oddities in the research tables or text and PARK-seq's best interpretation based on decades of experience in the field (of neurodegenerative disease molecular biology, not of confusion)
  • CROSS-REFERENCE - Information in cross references that is not included and often not even alluded to
  • DETAILS - Information that was a task to clarify due to awkward presentation, over-trimming of manuscript, or disparate
  • ERRORS - Errors in data files or main text and any fixes PARK-seq was able to do
  • METHODS - Verbatim methods from the research paper, sequence archives, or personal communication
  • MISSING - Information that was difficult to track down
  • UNFINISHED - Areas that still need clarity and investigation
  • (?) - explanations for use of the "we think but are not sure" PARK-seq symbol in table

The Study notes are for users and for PARK-seq curation. Despite common structure, scientific papers are incredibly non-uniform in material presented and authors' attention to detail. It makes curation time-consuming and dependent on a manual process (vs training a ML model, the original plan that is now deemed undesirable). Hopefully, having detailed notes will help unify studies and prevent tedious investigation for users.
If you have clarity or suspect an error, please contact us.

References

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  2. Agarwal, Sandor, et al., 2020 Agarwal D, Sandor C, Volpato V, Caffrey TM, Monzón-Sandoval J, Bowden R, Alegre-Abarrategui J, Wade-Martins R, Webber C. A single-cell atlas of the human substantia nigra reveals cell-specific pathways associated with neurological disorders. Nat Commun. 2020 Aug 21;11(1):4183. doi: 10.1038/s41467-020-17876-0. PMID: 32826893; PMCID: PMC7442652.
  3. Aguzzoli Heberle, Brandon, et al., 2025 Aguzzoli Heberle B, Brandon JA, Page ML, Nations KA, Dikobe KI, White BJ, Gordon LA, Fox GA, Wadsworth ME, Doyle PH, Williams BA, Fox EJ, Shantaraman A, Ryten M, Goodwin S, Ghiban E, Wappel R, Mavruk-Eskipehlivan S, Miller JB, Seyfried NT, Nelson PT, Fryer JD, Ebbert MTW. Mapping medically relevant RNA isoform diversity in the aged human frontal cortex with deep long-read RNA-seq. Nat Biotechnol. 2025 Apr;43(4):635-646. doi: 10.1038/s41587-024-02245-9. PMID: 38778214; PMCID: PMC11863200.
  4. Bennett and Keeney, 2018 Bennett JP, Keeney PM. RNA-Sequencing Reveals Similarities and Differences in Gene Expression in Vulnerable Brain Tissues of Alzheimer's and Parkinson's Diseases. J Alzheimers Dis Rep. 2018 Jul 21;2(1):129-137. doi: 10.3233/ADR-180072. PMID: 30480256; PMCID: PMC6159702.
  5. Bressan, Reed, et al., 2023 Bressan E, Reed X, Bansal V, Hutchins E, Cobb MM, Webb MG, Alsop E, Grenn FP, Illarionova A, Savytska N, Violich I, Broeer S, Fernandes N, Sivakumar R, Beilina A, Billingsley KJ, Berghausen J, Pantazis CB, Pitz V, Patel D, Daida K, Meechoovet B, Reiman R, Courtright-Lim A, Logemann A, Antone J, Barch M, Kitchen R, Li Y, Dalgard CL; American Genome Center; Rizzu P, Hernandez DG, Hjelm BE, Nalls M, Gibbs JR, Finkbeiner S, Cookson MR, Van Keuren-Jensen K, Craig DW, Singleton AB, Heutink P, Blauwendraat C. The Foundational Data Initiative for Parkinson Disease: Enabling efficient translation from genetic maps to mechanism. Cell Genom. 2023 Feb 6;3(3):100261. doi: 10.1016/j.xgen.2023.100261. PMID: 36950378; PMCID: PMC10025424.
  6. Cappelletti, Henriksen, et al., 2023 Cappelletti C, Henriksen SP, Geut H, Rozemuller AJM, van de Berg WDJ, Pihlstrøm L, Toft M. Transcriptomic profiling of Parkinson's disease brains reveals disease stage specific gene expression changes. Acta Neuropathol. 2023 Aug;146(2):227-244. doi: 10.1007/s00401-023-02597-7. PMID: 37347276; PMCID: PMC10329075.
  7. Craig, Hutchins, et al., 2021 Craig DW, Hutchins E, Violich I, Alsop E, Gibbs JR, Levy S, Robison M, Prasad N, Foroud T, Crawford KL, Toga AW, Whitsett TG, Kim S, Casey B, Reimer A, Hutten SJ, Frasier M, Kern F, Fehlman T, Keller A, Cookson MR, Van Keuren-Jensen K; Parkinson Progression Marker Initiative. RNA sequencing of whole blood reveals early alterations in immune cells and gene expression in Parkinson's disease. Nat Aging. 2021 Aug;1(8):734-747. doi: 10.1038/s43587-021-00088-6. PMID: 37117765.
  8. Dick, Johanson, et al., 2025 Dick F, Johanson GAS, Tysnes OB, Alves G, Dölle C, Tzoulis C. Brain Proteome Profiling Reveals Common and Divergent Signatures in Parkinson's Disease, Multiple System Atrophy, and Progressive Supranuclear Palsy. Mol Neurobiol. 2025 Mar;62(3):2801-2816. doi: 10.1007/s12035-024-04422-y. PMID: 39164482; PMCID: PMC11790761.
  9. Dick, Nido, et al., 2020 Dick F, Nido GS, Alves GW, Tysnes OB, Nilsen GH, Dölle C, Tzoulis C. Differential transcript usage in the Parkinson's disease brain. PLoS Genet. 2020 Nov 2;16(11):e1009182. doi: 10.1371/journal.pgen.1009182. PMID: 33137089; PMCID: PMC7660910.
  10. Dick, Tysnes, et al., 2023 Dick F, Tysnes OB, Alves GW, Nido GS, Tzoulis C. Altered transcriptome-proteome coupling indicates aberrant proteostasis in Parkinson's disease. iScience. 2023 Jan 4;26(2):105925. doi: 10.1016/j.isci.2023.105925. PMID: 36711240; PMCID: PMC9874017.
  11. Fan, Yang, et al., 2023 Fan LY, Yang J, Liu RY, Kong Y, Guo GY, Xu YM. Integrating single-nucleus sequence profiling to reveal the transcriptional dynamics of Alzheimer's disease, Parkinson's disease, and multiple sclerosis. J Transl Med. 2023 Sep 21;21(1):649. doi: 10.1186/s12967-023-04516-6. PMID: 37735671; PMCID: PMC10515258. [Correction/erratum is for author affiliations.]
  12. Fernandes, Patikas, et al., 2020 Fernandes HJR, Patikas N, Foskolou S, Field SF, Park JE, Byrne ML, Bassett AR, Metzakopian E. Single-Cell Transcriptomics of Parkinson's Disease Human In Vitro Models Reveals Dopamine Neuron-Specific Stress Responses. Cell Rep. 2020 Oct 13;33(2):108263. doi: 10.1016/j.celrep.2020.108263. PMID: 33053338;
  13. Gao, Takenaka, et al., 2025 Gao Y, Takenaka K, Santucci K, Lindner G, Xu SM, Cheng Y, Janitz M. Dysregulated circRNA-miRNA-mRNA networks reveal stage-specific mRNA expression changes in Parkinson's disease. Mol Brain. 2025 Dec 1;19(1):4. doi: 10.1186/s13041-025-01262-2. PMID: 41327336; PMCID: PMC12798134.
  14. Grubman, Chew, et al., 2019 Grubman A, Chew G, Ouyang JF, Sun G, Choo XY, McLean C, Simmons RK, Buckberry S, Vargas-Landin DB, Poppe D, Pflueger J, Lister R, Rackham OJL, Petretto E, Polo JM. A single-cell atlas of entorhinal cortex from individuals with Alzheimer's disease reveals cell-type-specific gene expression regulation. Nat Neurosci. 2019 Dec;22(12):2087-2097. doi: 10.1038/s41593-019-0539-4. PMID: 31768052.
  15. Hemmings, Swart, et al., 2022 Hemmings SMJ, Swart P, Womersely JS, Ovenden ES, van den Heuvel LL, McGregor NW, Meier S, Bardien S, Abrahams S, Tromp G, Emsley R, Carr J, Seedat S. RNA-seq analysis of gene expression profiles in posttraumatic stress disorder, Parkinson's disease and schizophrenia identifies roles for common and distinct biological pathways. Discov Ment Health. 2022 Mar 3;2(1):6. doi: 10.1007/s44192-022-00009-y. PMID: 37861850; PMCID: PMC10501040.
  16. Hooshmand, Halliday, et al., 2022 Hooshmand K, Halliday GM, Pineda SS, Sutherland GT, Guennewig B. Overlap between Central and Peripheral Transcriptomes in Parkinson's Disease but Not Alzheimer's Disease. Int J Mol Sci. 2022 May 6;23(9):5200. doi: 10.3390/ijms23095200. PMID: 35563596; PMCID: PMC9104085.
  17. Irmady, Hale, et al., 2023 Irmady K, Hale CR, Qadri R, Fak J, Simelane S, Carroll T, Przedborski S, Darnell RB. Blood transcriptomic signatures associated with molecular changes in the brain and clinical outcomes in Parkinson's disease. Nat Commun. 2023 Jul 5;14(1):3956. doi: 10.1038/s41467-023-39652-6. PMID: 37407548; PMCID: PMC10322907.
  18. Jäkel, Agirre, et al., 2019 Jäkel S, Agirre E, Mendanha Falcão A, van Bruggen D, Lee KW, Knuesel I, Malhotra D, Ffrench-Constant C, Williams A, Castelo-Branco G. Altered human oligodendrocyte heterogeneity in multiple sclerosis. Nature. 2019 Feb;566(7745):543-547. doi: 10.1038/s41586-019-0903-2. PMID: 30747918; PMCID: PMC6544546.
  19. Jang, Pletnikova, et al., 2023 Jang Y, Pletnikova O, Troncoso JC, Zhang Z, Pantelyat AY, Dawson TM, Rosenthal LS, Na CH. Mass Spectrometry-Based Proteomics Analysis of Human Substantia Nigra From Parkinson's Disease Patients Identifies Multiple Pathways Potentially Involved in the Disease. Mol Cell Proteomics. 2023 Jan;22(1):100452. doi: 10.1016/j.mcpro.2022.100452. PMID: 36423813; PMCID: PMC9792365. Erratum in: Mol Cell Proteomics. 2023 Jun;22(6):100570. doi: 10.1016/j.mcpro.2023.100570. [Erratum pertains to authors: "In the published article, there was an error in the author list and the author Dr. Zhen Zhang was erroneously excluded."]
  20. Jang, Thuraisamy, et al., 2023 Jang Y, Thuraisamy T, Redding-Ochoa J, Pletnikova O, Troncoso JC, Zhang Z, Rosenthal LS, Dawson TM, Pantelyat AY, Na CH. Mass spectrometry-based proteomics analysis of human globus pallidus from progressive supranuclear palsy patients discovers multiple disease pathways. Clin Transl Med. 2022 Nov;12(11):e1076. doi: 10.1002/ctm2.1076. PMID: 36354133; PMCID: PMC9647849. Erratum in: Clin Transl Med. 2023 May;13(5):e1275. doi: 10.1002/ctm2.1275. [Erratum pertains to authors: "The sixth author's name and affiliation has been included. The online article has been amended. The authors apologize for this error."]
  21. Jerber, Seaton, et al., 2021 Jerber J, Seaton DD, Cuomo ASE, Kumasaka N, Haldane J, Steer J, Patel M, Pearce D, Andersson M, Bonder MJ, Mountjoy E, Ghoussaini M, Lancaster MA; HipSci Consortium; Marioni JC, Merkle FT, Gaffney DJ, Stegle O. Population-scale single-cell RNA-seq profiling across dopaminergic neuron differentiation. Nat Genet. 2021 Mar;53(3):304-312. doi: 10.1038/s41588-021-00801-6. PMID: 33664506; PMCID: PMC7610897.
  22. Jin, Chen, et al., 2026 Jin Y, Chen K, Wixom AQ, Li Z, Koga S, Sekiya H, Xhafkollari G, Castanedes-Casey M, Santhakumar H, Meneses AD, Neff AJ, Bu G, Heckman MG, Liu Y, Ross OA, Dickson DW, Zhao N. Spatially resolved molecular signatures of Lewy body dementia. Acta Neuropathol. 2026 Jan 26;151(1):10. doi: 10.1007/s00401-026-02981-z. PMID: 41588135; PMCID: PMC12835040.
  23. Keo, Mahfouz, et al., 2020 Keo A, Mahfouz A, Ingrassia AMT, Meneboo JP, Villenet C, Mutez E, Comptdaer T, Lelieveldt BPF, Figeac M, Chartier-Harlin MC, van de Berg WDJ, van Hilten JJ, Reinders MJT. Transcriptomic signatures of brain regional vulnerability to Parkinson's disease. Commun Biol. 2020 Mar 5;3(1):101. doi: 10.1038/s42003-020-0804-9. PMID: 32139796; PMCID: PMC7058608.
  24. Kong, Lv, et al., 2021 Kong F, Lv Z, Wang L, Zhang K, Cai Y, Ding Q, Sun Z, Zhen H, Jiao F, Ma Q, Nie C, Yang Y. RNA-sequencing of peripheral blood circular RNAs in Parkinson disease. Medicine (Baltimore). 2021 Jun 11;100(23):e25888. doi: 10.1097/MD.0000000000025888. PMID: 34114985; PMCID: PMC8202568.
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  28. Martirosyan, Ansari, et al., 2024 Martirosyan A, Ansari R, Pestana F, Hebestreit K, Gasparyan H, Aleksanyan R, Hnatova S, Poovathingal S, Marneffe C, Thal DR, Kottick A, Hanson-Smith VJ, Guelfi S, Plumbly W, Belgard TG, Metzakopian E, Holt MG. Unravelling cell type-specific responses to Parkinson's Disease at single cell resolution. Mol Neurodegener. 2024 Jan 20;19(1):7. doi: 10.1186/s13024-023-00699-0. PMID: 38245794; PMCID: PMC10799528. Erratum in: Mol Neurodegener. 2024 Mar 25;19(1):28. doi: 10.1186/s13024-024-00717-9. [Erratum pertains to affiliations: "The original article contained an error whereby the production team handling the article mistakenly omitted the company of affiliation #8 (‘ bit.bio’)."]
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