Publications

Towards CRISPR-based editing of the mitochondrial genome in yeast.

Yin S, Jarosz DF, Ting AY. Proc Natl Acad Sci U S A. 2026 Jan 20;123(3):e2505894123. doi: 10.1073/pnas.2505894123. Epub 2026 Jan 16. PMID: 41543903 [PubMed]

Protein structure shapes natural genetic variation and de novo adaptation.

Jakobson CM, Van Elgort A, Aguilar-Rodríguez J, Jarosz DF. bioRxiv [Preprint]. 2025 Dec 22:2025.12.19.695599. doi: 10.64898/2025.12.19.695599. PMID: 41509306 Free PMC article. Preprint. [PubMed]

Fibroblasts of disparate developmental origins harbor anatomically variant scarring potential.

Griffin MF, Li DJ, Chen K, Parker JBL, Guo JL, Kim S, Kraft K, Downer M, Morgan AG, Kuhnert MM, Jing SL, Yao H, Valencia C, Cotterell A, Januszyk M, Gurtner GC, Chang HY, Wysocka J, Wan DC, Longaker MT. Cell. 2026 Jan 22:S0092-8674(25)01427-8. doi: 10.1016/j.cell.2025.12.014. Online ahead of print. PMID: 41576949 [PubMed]

The craniofacial shape of modern humans embodies genomic signatures of evolution, diversity, and clinical conditions.

Goovaerts S, Devine J, Claessens N, Gabbita S, Deprest J, Pauwels K, Herrick N, Mohammed J, Mounier A, Sofer T, Long HK, Bartsch U, Hallgrímsson B, Lewis SJ, Richmond S, Bauermeister S, Walsh S, Shaffer JR, Shriver MD, Naqvi S, Wysocka J, Kivisild T, Weinberg SM, Claes P. bioRxiv [Preprint]. 2026 Jan 3:2025.12.29.696848. doi: 10.64898/2025.12.29.696848. PMID: 41509417 Free PMC article. Preprint. [PubMed]

BACH2 regulates T cell lineage state to enhance CAR T cell function.

Chang TC, Heard A, Lattin J, Warrington JM, Barrett A, Landmann JH, Tenzin Y, Ganesh V, Thompson B, Afrin S, Gupta DK, Chang JF, Ritchey J, Selli ME, Hsu YS, Song H, Federico AJ, Horn A, Meers MP, Weber EW, Wandless TJ, Crawford JC, Thomas PG, DiPersio JF, Gottschalk S, Singh N. Nat Immunol. 2026 Jan 16. doi: 10.1038/s41590-025-02391-5. Online ahead of print. PMID: 41545540 [PubMed]

Stress-driven emergence of heritable non-genetic drug resistance.

Xie JL, Yin S, Yang TS, Chandrasekher K, Hanson L, Kim SH, Esqueda L, Hogan CA, Banaei N, Round JL, Ost KS, Berman J, Jarosz DF. Res Sq [Preprint]. 2025 Nov 28:rs.3.rs-5744219. doi: 10.21203/rs.3.rs-5744219/v1. PMID: 41356366 Free PMC article. Preprint. [PubMed]

How does cytoplasmic crowding affect reaction rates?

Huang JH, Ferrell JE Jr. Mol Cell. 2025 Dec 30:S1097-2765(25)00981-5. doi: 10.1016/j.molcel.2025.12.007. Online ahead of print. PMID: 41475345 Review. [PubMed]

The future of academia-pharma partnerships for novel drug discovery: a better path to success?

Romeo M, Ehrenkaufer G, Kim J, Mochly-Rosen D. Expert Opin Drug Discov. 2025 Dec 2:1-5. doi: 10.1080/17460441.2025.2594638. Online ahead of print. PMID: 41332242 No abstract available. [PubMed]

Genetic and chromatin regulation of Pvt1 monoallelic expression.

Luong C, Chen M, Belk JA, Kraft K, Gendrel AV, Heard E, Wysocka J, Chang HY. Cell Rep. 2025 Nov 25;44(11):116554. doi: 10.1016/j.celrep.2025.116554. Epub 2025 Nov 11. PMID: 41223055 [PubMed]

Low Alanine Aminotransferase Levels in Alcohol Consuming Male Subjects, Carriers of the Common ALDH2 Deficient Variant, ALDH2*2.

Seike T, Chen CH, Mizukoshi E, Mochly-Rosen D. Hepatol Res. 2025 Oct 27. doi: 10.1111/hepr.70061. Online ahead of print. PMID: 41144869 Review. [PubMed]

A default silencing mechanism restrains stress-induced genes in C. elegans.

Ilbay O, Gama AR, Jarosz DF, Morimoto RI, Fire A. bioRxiv [Preprint]. 2025 Nov 14:2025.10.22.683740. doi: 10.1101/2025.10.22.683740. PMID: 41279874 Free PMC article. Preprint. [PubMed]

A human-specific regulatory mechanism revealed in a pre-implantation model.

Fueyo R, Wang S, Crocker OJ, Swigut T, Nakauchi H, Wysocka J. Nature. 2025 Oct 1. doi: 10.1038/s41586-025-09571-1. Online ahead of print. PMID: 41034587 [PubMed]

Geometrical compartmentalization of trigger waves.

Li Z, Zhang KS, Chen Y, Tang SKY, Ferrell JE Jr. Proc Natl Acad Sci U S A. 2025 Oct 7;122(40):e2512872122. doi: 10.1073/pnas.2512872122. Epub 2025 Oct 2. PMID: 41037632 [PubMed]

Mechanistic origins of temperature scaling in the early embryonic cell cycle.

Rombouts J, Tavella F, Vandervelde A, Phong C, Ferrell JE Jr, Yang Q, Gelens L. Nat Commun. 2025 Aug 28;16(1):8045. doi: 10.1038/s41467-025-62918-0. PMID: 40877323 Free PMC article. [PubMed]

Promoter strength and position govern promoter competition.

Koska M, Swigut T, Boettiger AN, Wysocka J. bioRxiv [Preprint]. 2025 May 7:2025.05.06.652547. doi: 10.1101/2025.05.06.652547. PMID: 40654859 Free PMC article. Preprint. [PubMed]

Mouse lemur cell atlas informs primate genes, physiology and disease.

Ezran C, Liu S, Chang S, Ming J, Guethlein LA, Wang MFZ, Dehghannasiri R, Olivieri J, Frank HK, Tarashansky A, Koh W, Jing Q, Botvinnik O, Antony J; Tabula Microcebus Consortium; Pisco AO, Karkanias J, Yang C, Ferrell JE Jr, Boyd SD, Parham P, Long JZ, Wang B, Salzman J, De Vlaminck I, Wu AR, Quake SR, Krasnow MA. Nature. 2025 Jul 30. doi: 10.1038/s41586-025-09114-8. Online ahead of print. PMID: 40739355 [PubMed]

A molecular cell atlas of mouse lemur, an emerging model primate.

Tabula Microcebus Consortium; Ezran C, Liu S, Chang S, Ming J, Botvinnik O, Penland L, Tarashansky A, de Morree A, Travaglini KJ, Zhao J, Wang G, Hasegawa K, Sin H, Sit R, Okamoto J, Sinha R, Zhang Y, Karanewsky CJ, Pendleton JL, Morri M, Perret M, Aujard F, Stryer L, Artandi S, Fuller MT, Weissman IL, Rando TA, Ferrell JE Jr, Wang B, De Vlaminck I, Yang C, Casey KM, Albertelli MA, Pisco AO, Karkanias J, Neff N, Wu AR, Quake SR, Krasnow MA. Nature. 2025 Jul 30. doi: 10.1038/s41586-025-09113-9. Online ahead of print. PMID: 40739356 [PubMed]

Corrigendum: Novel and prevalent non-East Asian ALDH2 variants; implications for global susceptibility to aldehydes’ toxicity EBioMedicine.

Chen CH, Ferreira JCB, Joshi AU, Stevens MC, Li SJ, Hsu JH, Maclean R, Ferreira ND, Cervantes PR, Martinez DD, Barrientos FL, Quintanares GHR, Mochly-Rosen D. EBioMedicine. 2025 Jun 11;117:105798. doi: 10.1016/j.ebiom.2025.105798. Online ahead of print. PMID: 40505418 No abstract available. [PubMed]

DNA binding and mitotic phosphorylation protect polyglutamine proteins from assembly formation.

Saad S, Swigut T, Tabatabaee S, Lalgudi P, Jarosz DF, Wysocka J. Cell. 2025 May 29;188(11):2974-2991.e20. doi: 10.1016/j.cell.2025.03.031. Epub 2025 Apr 15. PMID: 40239647 [PubMed]

Evaluation of Benzo[cd]indol-2(1H)-ones as Downstream Hedgehog Pathway Inhibitors.

Tsakoumagkos IA, Pasquer QTL, Guillod CL, Rossion C, Bagka M, Torche S, Sakata-Kato T, Chen JK, Hoogendoorn S. ChemistryOpen. 2025 May;14(5):e202500119. doi: 10.1002/open.202500119. Epub 2025 Apr 14. PMID: 40227130 [PubMed]

A hidden cysteine in Fis1 targeted to prevent excessive mitochondrial fission and dysfunction under oxidative stress.

Pokhrel S, Heo G, Mathews I, Yokoi S, Matsui T, Mitsutake A, Wakatsuki S, Mochly-Rosen D. Nat Commun. 2025 May 6;16(1):4187. doi: 10.1038/s41467-025-59434-6. PMID: 40328741 [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. 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]