PCMI | PCMI Publications

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Learning chemical sensitivity reveals mechanisms of cellular response. bioRxiv [Preprint]. 2023 Aug 28:2023.08.26.554851. doi: 10.1101/2023.08.26.554851. PMID: 37693536; PMCID: PMC10491110.<br></p><p>Hu M, Alkhairy S, Lee I, Pillich RT, Bachelder R, Ideker T, Pratt D. Evaluation of large language models for discovery of gene set function. ArXiv [Preprint]. 2023 Sep 7:arXiv:2309.04019v1. PMID: 37731657; PMCID: PMC10508824.</p><p>Lasser M, Sun N, Xu Y, Wang S, Drake S, Law K, Gonzalez S, Wang B, Drury V, Castillo O, Zaltsman Y, Dea J, Bader E, McCluskey KE, State MW, Willsey AJ, Willsey HR. Pleiotropy of autism-associated chromatin regulators. Development. 2023 Jul 15;150(14):dev201515. doi: 10.1242/dev.201515. Epub 2023 Jul 18. PMID: 37366052; PMCID: PMC10399978.</p><p>Rosenthal SB, Wright SN, Liu S, Churas C, Chilin-Fuentes D, Chen CH, Fisch KM, Pratt D, Kreisberg JF, Ideker T. Mapping the common gene networks that underlie related diseases. Nat Protoc. 2023 Jun;18(6):1745-1759. doi: 10.1038/s41596-022-00797-1. Epub 2023 Jan 18. PMID: 36653526; PMCID: PMC10257754.<br></p><p>Wang B, Vartak R, Zaltsman Y, Naing ZZC, Hennick KM, Polacco BJ, Bashir A, Eckhardt M, Bouhaddou M, Xu J, Sun N, Lasser M, Zhou Y, Guiley KZ, Chan U, Kaye JA, Khare P, Drake S, Drury V, Burke DF, Gonzalez S, Alkhairy S, Morris M, Baum T, Krasnoff R, Wang S, Pham P, Arbalaez J, Pratt D, Chag S, Rolland T, Bourgeron T, Finkbeiner S, Bandyopadhay S, Ideker T, Beltrao P, Willsey HR, Obernier K, Nowakowski TJ, Huttenhain R, State MW, Willsey AJ, Krogan NJ. A foundational atlas of autism protein interactions reveals molecular convergence. bioRxiv. 2023 Dec 3. doi: 10.1101/2023.12.03.569805.<br><br>Wright SN, Leger BS, Rosenthal SB, Liu SN, Jia T, Chitre AS, Polesskaya O, Holl K, Gao J, Cheng R, Garcia Martinez A, George A, Gileta AF, Han W, Netzley AH, King CP, Lamparelli A, Martin C, St Pierre CL, Wang T, Bimschleger H, Richards J, Ishiwari K, Chen H, Flagel SB, Meyer P, Robinson TE, Solberg Woods LC, Kreisberg JF, Ideker T, Palmer AA. Genome-wide association studies of human and rat BMI converge on synapse, epigenome, and hormone signaling networks. Cell Rep. 2023 Aug 29;42(8):112873. doi: 10.1016/j.celrep.2023.112873. Epub 2023 Jul 31. PMID: 37527041; PMCID: PMC10546330.</p><p><b>2022</b></p><p>Allen DE, Donohue KC, Cadwell CR, Shin D, Keefe MG, Sohal VS, Nowakowski TJ. Fate mapping of neural stem cell niches reveals distinct origins of human cortical astrocytes. Science. 2022 Jun 24;376(6600):1441-1446. doi: 10.1126/science.abm5224. Epub 2022 May 19. PMID: 35587512; PMCID: PMC9233096.</p><p>Braberg H, Echeverria I, Kaake RM, Sali A, Krogan NJ. From systems to structure - using genetic data to model protein structures. Nat Rev Genet. 2022 Jun;23(6):342-354. doi: 10.1038/s41576-021-00441-w. Epub 2022 Jan 10. PMID: 35013567; PMCID: PMC8744059.</p><p>Delgado RN, Allen DE, Keefe MG, Mancia Leon WR, Ziffra RS, Crouch EE, Alvarez-Buylla A, Nowakowski TJ. Individual human cortical progenitors can produce excitatory and inhibitory neurons. Nature. 2022 Jan;601(7893):397-403. doi: 10.1038/s41586-021-04230-7. Epub 2021 Dec 15. PMID: 34912114; PMCID: PMC8994470.</p><p>Dr盲ger NM, Sattler SM, Huang CT, Teter OM, Leng K, Hashemi SH, Hong J, Aviles G, Clelland CD, Zhan L, Udeochu JC, Kodama L, Singleton AB, Nalls MA, Ichida J, Ward ME, Faghri F, Gan L, Kampmann M. A CRISPRi/a platform in human iPSC-derived microglia uncovers regulators of disease states. Nat Neurosci. 2022 Sep;25(9):1149-1162. doi: 10.1038/s41593-022-01131-4. Epub 2022 Aug 11. PMID: 35953545; PMCID: PMC9448678.</p><p>Gonzalez-Teran B, Pittman M, Felix F, Thomas R, Richmond-Buccola D, H眉ttenhain R, Choudhary K, Moroni E, Costa MW, Huang Y, Padmanabhan A, Alexanian M, Lee CY, Maven BEJ, Samse-Knapp K, Morton SU, McGregor M, Gifford CA, Seidman JG, Seidman CE, Gelb BD, Colombo G, Conklin BR, Black BL, Bruneau BG, Krogan NJ, Pollard KS, Srivastava D. Transcription factor protein interactomes reveal genetic determinants in heart disease. Cell. 2022 Mar 3;185(5):794-814.e30. doi: 10.1016/j.cell.2022.01.021. Epub 2022 Feb 18. PMID: 35182466; PMCID: PMC8923057.</p><p>Wang S, Linsley JW, Linsley DA, Lamstein J, Finkbeiner S. Fluorescently labeled nuclear morphology is highly informative of neurotoxicity. Front Toxicol. 2022 Aug 24;4:935438. doi: 10.3389/ftox.2022.935438. PMID: 36093369; PMCID: PMC9449453.</p><p>Willsey HR, Guille M, Grainger RM. Modeling Human Genetic Disorders with CRISPR Technologies in Xenopus. Cold Spring Harb Protoc. 2022 Mar 1;2022(3). doi: 10.1101/pdb.prot106997. PMID: 34531330.</p><p>Winkler EA, Kim CN, Ross JM, Garcia JH, Gil E, Oh I, Chen LQ, Wu D, Catapano JS, Raygor K, Narsinh K, Kim H, Weinsheimer S, Cooke DL, Walcott BP, Lawton MT, Gupta N, Zlokovic BV, Chang EF, Abla AA, Lim DA, Nowakowski TJ. A single-cell atlas of the normal and malformed human brain vasculature. Science. 2022 Mar 4;375(6584):eabi7377. doi: 10.1126/science.abi7377. Epub 2022 Mar 4. PMID: 35084939; PMCID: PMC8995178.</p><p><b>2021</b></p><p>DeJong CS, Dichmann DS, Exner CRT, Xu Y, Harland RM. The atypical RNA-binding protein Taf15 regulates dorsoanterior neural development through diverse mechanisms in Xenopus tropicalis. Development. 2021 Aug 1;148(15):dev191619. doi: 10.1242/dev.191619. Epub 2021 Aug 4. PMID: 34345915; PMCID: PMC8353262.</p><p>Exner CRT, Willsey HR. Xenopus leads the way: Frogs as a pioneering model to understand the human brain. Genesis. 2021 Feb;59(1-2):e23405. doi: 10.1002/dvg.23405. Epub 2020 Dec 27. PMID: 33369095; PMCID: PMC8130472.</p><p>Fabius JM, Krogan NJ. Creating collaboration by breaking down scientific barriers. Cell. 2021 Apr 29;184(9):2271-2275. doi: 10.1016/j.cell.2021.02.022. Epub 2021 Mar 24. PMID: 33765441; PMCID: PMC8630979.</p><p>Lew BJ, Schantell MD, O'Neill J, Morsey B, Wang T, Ideker T, Swindells S, Fox HS, Wilson TW. Reductions in Gray Matter Linked to Epigenetic HIV-Associated Accelerated Aging. Cereb Cortex. 2021 Jul 5;31(8):3752-3763. doi: 10.1093/cercor/bhab045. PMID: 33822880; PMCID: PMC8258439.</p><p>Linsley JW, Linsley DA, Lamstein J, Ryan G, Shah K, Castello NA, Oza V, Kalra J, Wang S, Tokuno Z, Javaherian A, Serre T, Finkbeiner S. Superhuman cell death detection with biomarker-optimized neural networks. Sci Adv. 2021 Dec 10;7(50):eabf8142. doi: 10.1126/sciadv.abf8142. Epub 2021 Dec 8. PMID: 34878844; PMCID: PMC8654296.</p><p>Linsley JW, Shah K, Castello N, Chan M, Haddad D, Doric Z, Wang S, Leks W, Mancini J, Oza V, Javaherian A, Nakamura K, Kokel D, Finkbeiner S. Genetically encoded cell-death indicators (GEDI) to detect an early irreversible commitment to neurodegeneration. Nat Commun. 2021 Sep 6;12(1):5284. doi: 10.1038/s41467-021-25549-9. PMID: 34489414; PMCID: PMC8421388.</p><p>Ly VT, Baudin PV, Pansodtee P, Jung EA, Voitiuk K, Rosen YM, Willsey HR, Mantalas GL, Seiler ST, Selberg JA, Cordero SA, Ross JM, Rolandi M, Pollen AA, Nowakowski TJ, Haussler D, Mostajo-Radji MA, Salama SR, Teodorescu M. Picroscope: low-cost system for simultaneous longitudinal biological imaging. Commun Biol. 2021 Nov 4;4(1):1261. doi: 10.1038/s42003-021-02779-7. PMID: 34737378; PMCID: PMC8569150.</p><p>Naert T, 脟i莽ek 脰, Ogar P, B眉rgi M, Shaidani NI, Kaminski MM, Xu Y, Grand K, Vujanovic M, Prata D, Hildebrandt F, Brox T, Ronneberger O, Voigt FF, Helmchen F, Loffing J, Horb ME, Willsey HR, Lienkamp SS. Deep learning is widely applicable to phenotyping embryonic development and disease. Development. 2021 Nov 1;148(21):dev199664. doi: 10.1242/dev.199664. Epub 2021 Nov 5. PMID: 34739029; PMCID: PMC8602947.</p><p>Qin Y, Huttlin EL, Winsnes CF, Gosztyla ML, Wacheul L, Kelly MR, Blue SM, Zheng F, Chen M, Schaffer LV, Licon K, B盲ckstr枚m 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. A multi-scale map of cell structure fusing protein images and interactions. Nature. 2021 Dec;600(7889):536-542. doi: 10.1038/s41586-021-04115-9. Epub 2021 Nov 24. PMID: 34819669; PMCID: PMC9053732.</p><p>Richards AL, Eckhardt M, Krogan NJ. Mass spectrometry-based protein-protein interaction networks for the study of human diseases. Mol Syst Biol. 2021 Jan;17(1):e8792. doi: 10.15252/msb.20188792. PMID: 33434350; PMCID: PMC7803364.</p><p>Rosenthal SB, Willsey HR, Xu Y, Mei Y, Dea J, Wang S, Curtis C, Sempou E, Khokha MK, Chi NC, Willsey AJ, Fisch KM, Ideker T. A convergent molecular network underlying autism and congenital heart disease. Cell Syst. 2021 Nov 17;12(11):1094-1107.e6. doi: 10.1016/j.cels.2021.07.009. Epub 2021 Aug 18. PMID: 34411509; PMCID: PMC8602730.</p><p>Willsey HR, Exner CRT, Xu Y, Everitt A, Sun N, Wang B, Dea J, Schmunk G, Zaltsman Y, Teerikorpi N, Kim A, Anderson AS, Shin D, Seyler M, Nowakowski TJ, Harland RM, Willsey AJ, State MW. Parallel in vivo analysis of large-effect autism genes implicates cortical neurogenesis and estrogen in risk and resilience. Neuron. 2021 Mar 3;109(5):788-804.e8. doi: 10.1016/j.neuron.2021.01.002. Epub 2021 Jan 25. Erratum in: Neuron. 2021 Apr 21;109(8):1409. PMID: 33497602; PMCID: PMC8132462.</p><p>Willsey HR. Whole-Mount RNA In Situ Hybridization and Immunofluorescence of Xenopus Embryos and Tadpoles. Cold Spring Harb Protoc. 2021 Oct 1;2021(10):pdb.prot105635. doi: 10.1101/pdb.prot105635. PMID: 33827967; PMCID: PMC8487899.</p><p>Ziffra RS, Kim CN, Ross JM, Wilfert A, Turner TN, Haeussler M, Casella AM, Przytycki PF, Keough KC, Shin D, Bogdanoff D, Kreimer A, Pollard KS, Ament SA, Eichler EE, Ahituv N, Nowakowski TJ. Single-cell epigenomics reveals mechanisms of human cortical development. Nature. 2021 Oct;598(7879):205-213. doi: 10.1038/s41586-021-03209-8. Epub 2021 Oct 6. PMID: 34616060; PMCID: PMC8494642.</p><p><b>2020</b></p><p>Finkbeiner S. Functional genomics, genetic risk profiling and cell phenotypes in neurodegenerative disease. Neurobiol Dis. 2020 Dec;146:105088. doi: 10.1016/j.nbd.2020.105088. Epub 2020 Sep 23. PMID: 32977020; PMCID: PMC7686089.</p><p>Kampmann M. CRISPR-based functional genomics for neurological disease. Nat Rev Neurol. 2020 Sep;16(9):465-480. doi: 10.1038/s41582-020-0373-z. Epub 2020 Jul 8. Review. PubMed PMID: 32641861; <a href="NIHMSID:NIHMS1612053.">NIHMSID:NIHMS1612053.</a> </p><p>Wang F, Yu Z, Betegon M, Campbell MG, Aksel T, Zhao J, Li S, Douglas SM, Cheng Y, Agard DA. Amino and PEG-amino graphene oxide grids enrich and protect samples for high-resolution single particle cryo-electron microscopy. J Struct Biol. 2020 Feb 1;209(2):107437. doi: 10.1016/j.jsb.2019.107437. Epub 2019 Dec 19. PubMed PMID: 31866389; PubMed Central PMCID: PMC7272056.</p><p>Wang F, Liu Y, Yu Z, Li S, Feng S, Cheng Y, Agard DA. General and robust covalently linked graphene oxide affinity grids for high-resolution cryo-EM. Proc Natl Acad Sci U S A. 2020 Sep 29;117(39):24269-24273. doi: 10.1073/pnas.2009707117. Epub 2020 Sep 10. PMID: 32913054; PMCID: PMC7533693.</p><p>Willsey HR, Xu Y, Everitt A, Dea J, Exner CRT, Willsey AJ, State MW, Harland RM. The neurodevelopmental disorder risk gene DYRK1A is required for ciliogenesis and control of brain size in Xenopus embryos. Development. 2020 Jun 22;147(21). doi: 10.1242/dev.189290. PubMed PMID: 32467234.</p><p><b>2019</b></p><p>Andrews MG, Nowakowski TJ. Human brain development through the lens of cerebral organoid models. Brain Res. 2019 Dec 15;1725:146470. doi: 10.1016/j.brainres.2019.146470. Epub 2019 Sep 19. Review. PubMed PMID: 31542572; PubMed Central PMCID: PMC6887101.</p><p>Blackburn ATM, Bekheirnia N, Uma VC, Corkins ME, Xu Y, Rosenfeld JA, Bainbridge MN, Yang Y, Liu P, Madan-Khetarpal S, Delgado MR, Hudgins L, Krantz I, Rodriguez-Buritica D, Wheeler PG, Al-Gazali L, Mohamed Saeed Mohamed Al Shamsi A, Gomez-Ospina N, Chao HT, Mirzaa GM, Scheuerle AE, Kukolich MK, Scaglia F, Eng C, Willsey HR, Braun MC, Lamb DJ, Miller RK, Bekheirnia MR. DYRK1A-related intellectual disability: a syndrome associated with congenital anomalies of the kidney and urinary tract. Genet Med. 2019 Dec;21(12):2755-2764. doi: 10.1038/s41436-019-0576-0. Epub 2019 Jul 2. PubMed PMID: 31263215; PubMed Central PMCID: PMC6895419.</p><p>Bouhaddou M, Eckhardt M, Chi Naing ZZ, Kim M, Ideker T, Krogan NJ. Mapping the protein-protein and genetic interactions of cancer to guide precision medicine. Curr Opin Genet Dev. 2019 Feb;54:110-117. doi: 10.1016/j.gde.2019.04.005. Epub 2019 Jul 6. Review. PubMed PMID: 31288129; PubMed Central PMCID: PMC6746583.</p><p>Carlin DE, Fong SH, Qin Y, Jia T, Huang JK, Bao B, Zhang C, Ideker T. A Fast and Flexible Framework for Network-Assisted Genomic Association. iScience. 2019 Jun 28;16:155-161. doi: 10.1016/j.isci.2019.05.025. Epub 2019 May 24. PubMed PMID: 31174177; PubMed Central PMCID: PMC6554232.<br></p><p>Flint J, Ideker T. The great hairball gambit. PLoS Genet. 2019 Nov;15(11):e1008519. doi: 10.1371/journal.pgen.1008519. eCollection 2019 Nov. PubMed PMID: 31770365; PubMed Central PMCID: PMC6910700.</p><p>Linsley JW, Tripathi A, Epstein I, Schmunk G, Mount E, Campioni M, Oza V, Barch M, Javaherian A, Nowakowski TJ, Samsi S, Finkbeiner S. Automated four-dimensional long term imaging enables single cell tracking within organotypic brain slices to study neurodevelopment and degeneration. Commun Biol. 2019;2:155. doi: 10.1038/s42003-019-0411-9. eCollection 2019. PubMed PMID: 31069265; PubMed Central PMCID: PMC6494885. </p><p>Stanley SY, Borges AL, Chen KH, Swaney DL, Krogan NJ, Bondy-Denomy J, Davidson AR. Anti-CRISPR-Associated Proteins Are Crucial Repressors of Anti-CRISPR Transcription. Cell. 2019 Sep 5;178(6):1452-1464.e13. doi: 10.1016/j.cell.2019.07.046. Epub 2019 Aug 29. PubMed PMID: 31474367; PubMed Central PMCID: PMC6754177. </p><p><b>2018-19</b></p><p>Palovcak E, Wang F, Zheng SQ, Yu Z, Li S, Betegon M, Bulkley D, Agard DA, Cheng Y. A simple and robust procedure for preparing graphene-oxide cryo-EM grids. 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