Publications

Transfer learning reveals sequence determinants of the quantitative response to transcription factor dosage.

Naqvi S, Kim S, Tabatabaee S, Pampari A, Kundaje A, Pritchard JK, Wysocka J. Cell Genom. 2025 Mar 12;5(3):100780. doi: 10.1016/j.xgen.2025.100780. Epub 2025 Feb 27. PMID: 40020686 Free PMC article. [PubMed]

Enhanced insights into the genetic architecture of 3D cranial vault shape using pleiotropy-informed GWAS.

Goovaerts S, Naqvi S, Hoskens H, Herrick N, Yuan M, Shriver MD, Shaffer JR, Walsh S, Weinberg SM, Wysocka J, Claes P. Commun Biol. 2025 Mar 15;8(1):439. doi: 10.1038/s42003-025-07875-6. PMID: 40087503 Free PMC article. [PubMed]

Long-range regulation of transcription scales with genomic distance in a gene-specific manner.

Jensen CL, Chen LF, Swigut T, Crocker OJ, Yao D, Bassik MC, Ferrell JE Jr, Boettiger AN, Wysocka J. Mol Cell. 2024 Nov 19:S1097-2765(24)00861-X. doi: 10.1016/j.molcel.2024.10.021. Online ahead of print. PMID: 39626660 [PubMed]

p53 engagement is a hallmark of an unfolded protein response in the nucleus of mammalian cells.

Park JH, Wandless TJ. bioRxiv [Preprint]. 2024 Nov 8:2024.11.08.622663. doi: 10.1101/2024.11.08.622663. PMID: 39574672 Free PMC article. Preprint. [PubMed]

Massively parallel experimental interrogation of natural variants in ancient signaling pathways reveals both purifying selection and local adaptation.

Aguilar-Rodríguez J, Vila J, Chen SA, Razo-Mejia M, Ghosh O, Fraser HB, Jarosz DF, Petrov DA. bioRxiv [Preprint]. 2024 Oct 31:2024.10.30.621178. doi: 10.1101/2024.10.30.621178. PMID: 39553990 Free PMC article. Preprint. [PubMed]

A genome-to-proteome atlas charts natural variants controlling proteome diversity and forecasts their fitness effects.

Jakobson CM, Hartl J, Trébulle P, Mülleder M, Jarosz DF, Ralser M. bioRxiv [Preprint]. 2024 Oct 22:2024.10.18.619054. doi: 10.1101/2024.10.18.619054. PMID: 39484408 Free PMC article. Preprint. [PubMed]

The Hsp90 molecular chaperone as a global modifier of the genotype-phenotype-fitness map: An evolutionary perspective.

Aguilar-Rodríguez J, Jakobson CM, Jarosz DF. J Mol Biol. 2024 Oct 29:168846. doi: 10.1016/j.jmb.2024.168846. Online ahead of print. PMID: 39481633 Review. [PubMed]

Catalytic asymmetric synthesis of meta benzene isosteres.

Zhang M, Chapman M, Sarode BR, Xiong B, Liang H, Chen JK, Weerapana E, Morken JP. Nature. 2024 Aug 21. doi: 10.1038/s41586-024-07865-4. Online ahead of print. PMID: 39169193 [PubMed]

HLTF resolves G4s and promotes G4-induced replication fork slowing to maintain genome stability.

Bai G, Endres T, Kühbacher U, Mengoli V, Greer BH, Peacock EM, Newton MD, Stanage T, Dello Stritto MR, Lungu R, Crossley MP, Sathirachinda A, Cortez D, Boulton SJ, Cejka P, Eichman BF, Cimprich KA. Mol Cell. 2024 Aug 22;84(16):3044-3060.e11. doi: 10.1016/j.molcel.2024.07.018. Epub 2024 Aug 13. PMID: 39142279 [PubMed]

Cardiac troponin I directly binds and inhibits mitochondrial ATP synthase with a noncanonical role in the post-ischemic heart.

Elezaby A, Lin AJ, Vijayan V, Pokhrel S, Kraemer BR, Bechara LRG, Larus I, Sun J, Baena V, Syed ZA, Murphy E, Glancy B, Ostberg NP, Queliconi BB, Campos JC, Ferreira JCB, Haileselassie B, Mochly-Rosen D. Nat Cardiovasc Res. 2024 Aug;3(8):987-1002. doi: 10.1038/s44161-024-00512-1. Epub 2024 Jul 18. PMID: 39196031 [PubMed]

Uncovering newly identified aldehyde dehydrogenase 2 genetic variants that lead to acetaldehyde accumulation after an alcohol challenge.

Rwere F, White JR, Hell RCR, Yu X, Zeng X, McNeil L, Zhou KN, Angst MS, Chen CH, Mochly-Rosen D, Gross ER. J Transl Med. 2024 Jul 29;22(1):697. doi: 10.1186/s12967-024-05507-x. PMID: 39075523 Free PMC article. [PubMed]

Genome dilution by cell growth drives starvation-like proteome remodeling in mammalian and yeast cells.

Lanz MC, Zhang S, Swaffer MP, Ziv I, Götz LH, Kim J, McCarthy F, Jarosz DF, Elias JE, Skotheim JM. Nat Struct Mol Biol. 2024 Jul 24. doi: 10.1038/s41594-024-01353-z. Online ahead of print. PMID: 39048803 [PubMed]

Transfer learning reveals sequence determinants of the quantitative response to transcription factor dosage.

Naqvi S, Kim S, Tabatabaee S, Pampari A, Kundaje A, Pritchard JK, Wysocka J. bioRxiv [Preprint]. 2024 May 29:2024.05.28.596078. doi: 10.1101/2024.05.28.596078. PMID: 38853998 Free PMC article. Preprint. [PubMed]

Cleavage of Hsp70.1 causes lysosomal cell death under stress conditions.

Yamashima T, Mochly-Rosen D, Wakatsuki S, Mizukoshi E, Seike T, Larus IM, Chen CH, Takemura M, Saito H, Ohashi A. Front Mol Biosci. 2024 May 27;11:1378656. doi: 10.3389/fmolb.2024.1378656. eCollection 2024. PMID: 38859931 Free PMC article. Review. [PubMed]

AAV-mediated genome editing is influenced by the formation of R-loops.

Puzzo F, Crossley MP, Goswami A, Zhang F, Pekrun K, Garzon JL, Cimprich KA, Kay MA. bioRxiv [Preprint]. 2024 May 9:2024.05.07.592855. doi: 10.1101/2024.05.07.592855. PMID: 38766176 Free PMC article. Preprint. [PubMed]

Tissue-specific landscape of protein aggregation and quality control in an aging vertebrate.

Chen YR, Harel I, Singh PP, Ziv I, Moses E, Goshtchevsky U, Machado BE, Brunet A, Jarosz DF. Dev Cell. 2024 May 24:S1534-5807(24)00266-1. doi: 10.1016/j.devcel.2024.04.014. Online ahead of print. PMID: 38810654 [PubMed]

Identification of protein aggregates in the aging vertebrate brain with prion-like and phase-separation properties.

Harel I, Chen YR, Ziv I, Singh PP, Heinzer D, Navarro Negredo P, Goshtchevsky U, Wang W, Astre G, Moses E, McKay A, Machado BE, Hebestreit K, Yin S, Sánchez Alvarado A, Jarosz DF, Brunet A. Cell Rep. 2024 May 24:112787. doi: 10.1016/j.celrep.2023.112787. Online ahead of print. PMID: 38810650 [PubMed]

Extracellular release of mitochondria induced by pre-hematopoietic stem cell transplant conditioning exacerbates GVHD.

Vijayan V, Yan H, Lohmeyer JK, Prentiss KA, Patil RV, Barbarito G, Lopez I, Elezaby A, Peterson K, Baker J, Ostberg NP, Bertaina A, Negrin RS, Mochly-Rosen D, Weinberg KI, Haileselassie B. Blood Adv. 2024 May 3:bloodadvances.2023012328. doi: 10.1182/bloodadvances.2023012328. Online ahead of print. PMID: 38701354 [PubMed]

An organism-wide atlas of hormonal signaling based on the mouse lemur single-cell transcriptome.

Liu S, Ezran C, Wang MFZ, Li Z, Awayan K; Tabula Microcebus Consortium; Long JZ, De Vlaminck I, Wang S, Epelbaum J, Kuo CS, Terrien J, Krasnow MA, Ferrell JE Jr. Nat Commun. 2024 Mar 11;15(1):2188. doi: 10.1038/s41467-024-46070-9. PMID: 38467625 Free PMC article. [PubMed]

Viscosity-dependent control of protein synthesis and degradation.

Chen Y, Huang JH, Phong C, Ferrell JE Jr. Nat Commun. 2024 Mar 8;15(1):2149. doi: 10.1038/s41467-024-46447-w. PMID: 38459041 Free PMC article. [PubMed]

A common cis- regulatory variant impacts normal-range and disease-associated human facial shape through regulation of PKDCC during chondrogenesis.

Mohammed J, Arora N, Matthews HS, Hansen K, Bader M, Walsh S, Shaffer JR, Weinberg SM, Swigut T, Claes P, Selleri L, Wysocka J. Elife. 2024 Mar 14;13:e82564. doi: 10.7554/eLife.82564. PMID: 38483448 Free PMC article. [PubMed]

Author Correction: A selective inhibitor of mitofusin 1-βIIPKC association improves heart failure outcome in rats.

Ferreira JCB, Campos JC, Qvit N, Qi X, Bozi LHM, Bechara LRG, Lima VM, Queliconi BB, Disatnik MH, Dourado PMM, Kowaltowski AJ, Mochly-Rosen D. Nat Commun. 2024 Apr 3;15(1):2889. doi: 10.1038/s41467-024-47288-3. PMID: 38570501 Free PMC article. No abstract available. [PubMed]

Changes of neurofilament light chain in patients with alcohol dependence following withdrawal and the genetic effect from ALDH2 Polymorphism.

Huang MC, Tu HY, Chung RH, Kuo HW, Liu TH, Chen CH, Mochly-Rosen D, Liu YL. Eur Arch Psychiatry Clin Neurosci. 2024 Mar;274(2):423-432. doi: 10.1007/s00406-023-01635-5. Epub 2023 Jun 14. PMID: 37314537 Free PMC article. [PubMed]

In vivo protein turnover rates in varying oxygen tensions nominate MYBBP1A as a mediator of the hyperoxia response.

Chen X, Haribowo AG, Baik AH, Fossati A, Stevenson E, Chen YR, Reyes NS, Peng T, Matthay MA, Traglia M, Pico AR, Jarosz DF, Buchwalter A, Ghaemmaghami S, Swaney DL, Jain IH. Sci Adv. 2023 Dec 8;9(49):eadj4884. doi: 10.1126/sciadv.adj4884. Epub 2023 Dec 8. PMID: 38064566 Free PMC article. [PubMed]

Author Correction: R-loop-derived cytoplasmic RNA-DNA hybrids activate an immune response.

Crossley MP, Song C, Bocek MJ, Choi JH, Kousouros JN, Sathirachinda A, Lin C, Brickner JR, Bai G, Lans H, Vermeulen W, Abu-Remaileh M, Cimprich KA. Nature. 2024 Jan 23. doi: 10.1038/s41586-024-07064-1. Online ahead of print. PMID: 38263519 No abstract available. [PubMed]