Developmental Biology

Publications

Adhikari, N; Wu, Z; Huang, Y; Lan, Y; Jiang, R. Twist1 Acts Upstream of the Dlx5-Hand2 Pathway to Pattern the Mammalian Jaw. Journal of Dental Research. 2025; 104(3):310-319.

Bartusel, M; Kim, SX; Rehimi, R; Darnell, AM; Nikolić, M; Heggemann, J; Kolovos, P; Van Ijcken, WFJ; Varineau, J; Crispatzu, G; Laugsch, M; Ludwig, KU; Rada-Iglesias, A; Calo, E. A non-syndromic orofacial cleft risk locus links tRNA splicing defects to neural crest cell pathologies. American Journal of Human Genetics. 2025; 112(5):1097-1116.

Bhaskar, S; Gowda, J; Hegde, A; Thumu, SCR; Banerjee, S; M Bellchambers, H; Ramanan, N; Sala, PM; Campbell, K; Ware, S; Prasanna, J; Kumar, A. Zic3 enables bimodal regulation of tyrosine hydroxylase expression in olfactory bulb and midbrain-derived neurons. Cell Death Discovery. 2025; 11(1):165.

Cai, H; Tian, C; Chen, L; Yang, Y; Sun, AX; Mccracken, K; Tchieu, J; Gu, M; Mackie, K; Guo, F. Vascular network-inspired diffusible scaffolds for engineering functional midbrain organoids. Cell Stem Cell. 2025; 32(5):824-837.e5.

Cain, B; Yuan, Z; Thoman, E; Kovall, RA; Gebelein, B. The ALX4 dimer structure provides insight into how disease alleles impact function. Nature Communications. 2025; 16(1):4800.

Cederquist, GY; Oberst, P; Chang, X; Tchieu, J; Studer, L. Generation of Prefrontal Cortex Neurons from Human Pluripotent Stem Cells Under Chemically Defined Conditions. 2025:37-51.

Chang, X; Li, W; Matsui, S; Huynh, C; Erickson, C; Guo, F; Cederquist, GY; Studer, L; Iwafuchi, M; Shillington, A; Chronis, C; Tchieu, J. ZMYND11 functions in bimodal regulation of latent genes and brain-like splicing to safeguard corticogenesis. Nature Communications. 2025; 16(1):9010.

Chen, Z; Zhang, C; Zhang, Y. Chromatin Analyses in Mouse Oocytes and Preimplantation Embryos. Methods in Molecular Biology. 2025; 2923:33-44.

Chu, S; Bell, AJ; Lotay, V; Ly, N; Pells, TJ; Kwon, T; Agalakov, S; Ponferrada, V; Lenz, C; James-Zorn, C; Fisher, M; Karimi, K; Zorn, AM; Vize, PD. Xenbase: 25 years of integrating molecular and biomedical data from Xenopus. Genetics. 2025.

Chung, E; Nosrati, F; Adam, M; Potter, A; Sayed, M; Ahn, C; Humphreys, BD; Lim, H-W; Hu, Y-C; Potter, SS; Park, J-S. Proximal Tubule Cells Contribute to the Thin Descending Limb of the Loop of Henle during Mouse Kidney Development. Journal of the American Society of Nephrology. 2025; 36(10):1928-1938.

Crossen, MJ; Jia, S; Jorgensen, JS; Kelleher, AM; Jiang, R; Zhao, F. Wnt9b enables androgen action to maintain Wolffian ducts in mice. Molecular Human Reproduction. 2025; 31(3).

Edwards, NA; Rankin, SA; Kashyap, A; Warren, A; Agricola, ZN; Kenny, AP; Kofron, M; Shen, Y; Chung, WK; Zorn, AM. Disrupted endosomal trafficking of the Vangl-Celsr polarity complex underlies congenital anomalies in Xenopus trachea-esophageal morphogenesis. Developmental Cell. 2025; 60(18):2487-2502.e4.

Farrow, E; Rao, S; Han, SJY; Chang, X; Huynh, C; Brugmann, SA; Lim, H-W; Tchieu, J; Campbell, K; Gebelein, B. An inducible system to study the regulatory functions of GSX2 in human lateral ganglionic eminence-like progenitors. Developmental Biology. 2026; 532:35-51.

Feuermann, M; Mi, H; Gaudet, P; Muruganujan, A; Lewis, SE; Ebert, D; Mushayahama, T; Thomas, PD. A compendium of human gene functions derived from evolutionary modelling. Nature. 2025; 640(8057):146-154.

Halurkar, MS; Inoue, O; Singh, A; Mukherjee, R; Ginugu, M; Ahn, C; Bonatto Paese, CL; Duszynski, M; Brugmann, SA; Lim, H-W; Sanchez-Gurmaches, J. The widely used Ucp1-Cre transgene elicits complex developmental and metabolic phenotypes. Nature Communications. 2025; 16(1):770.

Han, SJY; Adani, V; Farrow, E; Parmar, B; Chang, C-F; Cochran, K; Horne, RR; Ramkissoon, PJK; Esteban, E; Elliott, KH; Peterson, KA; Gebelein, B; García-Castro, MI; Brugmann, SA. A dual role for GLI3 signaling in neural crest development. Development. 2026; 153(1).

Heekin, S; Lopez-Nunez, O; Smith, J; Denson, N; Denson, L; Miethke, A; Collins, MH; Dillman, J; Miraldi, E; Kofron, JM; Dhaliwal, J; Erdman, L. Implications of Model Loss and Configuration for Sparse Histological Segmentation. In: Machine Learning Methods in Biomedical Field. Springer Nature; 2026:189-217.

Hendrickson, CL; Blitz, IL; Hussein, A; Paraiso, KD; Cho, JS; Klymkowsky, MW; Kofron, MJ; Cho, KWY. Foxi2 and Sox3 are master transcription regulators that control ectoderm germ layer specification in Xenopus. PLoS Biology. 2025; 23(11):e3003476.

Huang, F; Wang, Y; Zhang, X; Gao, W; Li, J; Yang, Y; Mo, H; Prince, E; Long, Y; Hu, J; Chen, C-W; Chen, J; Huang, H; Weng, H. m6A/IGF2BP3-driven serine biosynthesis fuels AML stemness and metabolic vulnerability. Nature Communications. 2025; 16(1):4214.

Hyatt, BA; Lundberg, E; Eye, R; Rankin, SA; Zorn, AM. Temporal induction of the homeodomain transcription factor Nkx2-1 is sufficient to respecify foregut and hindgut endoderm to a pulmonary fate in Xenopus laevis. microPublication Biology. 2025; 2025.

Jia, Z; Li, B; Matsuo, M; Dewar, A; Mustafaraj, A; Dey, SK; Yuan, J; Sun, X. Foxa2-dependent uterine glandular cell differentiation is essential for successful implantation. Nature Communications. 2025; 16(1):2465.

Lai, C; Chen, K; Huang, H-Z; Huang, X; Zhang, J; Wang, Y-B; Chen, Z; Hu, F; Guo, Z; Man, H-Y; Du, H-Y; Lu, Y-M; Shu, K; Liu, D; Zhu, L-Q. Historical loss weakens competitive behavior by remodeling ventral hippocampal dynamics. Cell Discovery. 2025; 11(1):16.

Li, S-Y; Matsuyama, S; Whiteside, S; Gu, X; Cool, J; Capel, B; Defalco, T. Platelet-derived growth factor receptor alpha regulates fetal testis differentiation via an ERK-CREB axis. Proceedings of the National Academy of Sciences of the United States of America. 2026; 123(4):e2515138123.

Li, S-Y; Whiteside, S; Li, B; Sun, X; Defalco, T. Mesenchymal-to-epithelial transition of perivascular cells contributes to endometrial re-epithelialization. Nature Communications. 2025; 16(1):10174.

Liu, L; Li, J; Cheng, H; Xiang, M; Liu, J; Kidd, B; Li, J; Qin, Y; Peng, H; Ji, J-Y; Kelly, RG; Jiang, R; Zhang, K; Xie, L. Osr1 orchestrates posterior second heart field cell migration for outflow tract formation. Communications Biology. 2025; 8(1):1770.

Matsuyama, S; Defalco, T. Leydig Cell Interaction with Macrophages, Peritubular Cells, and Sertoli Cells. In: Leydig Cells. Springer Nature; 2025:311-336.

Miao, Y; Pek, NM; Tan, C; Jiang, C; Yu, Z; Iwasawa, K; Shi, M; Kechele, DO; Sundaram, N; Pastrana-Gomez, V; Zorn, AM; Chen, Y-W; Guo, M; Gu, M. Co-development of mesoderm and endoderm enables organotypic vascularization in lung and gut organoids. Cell. 2025; 188(16):4295-4313.e27.

Michaels, J-R; Iyyanar, PPR; Husami, A; Vontell, AM; Brugmann, SA; Stottmann, RW. Genetic analysis and functional assessment of a TGFBR2 variant in micrognathia and cleft palate. PLoS ONE. 2025; 20(6):e0324803.

Mirizio, G; Sampson, S; Iwafuchi, M. Interplay between pioneer transcription factors and epigenetic modifiers in cell reprogramming. Regenerative Therapy. 2025; 28:246-252.

Mongan, M; Xiao, B; Christianto, A; Hu, Y-C; Xia, Y. Mitogen-Activated Protein Kinase Kinase Kinase 1 Overexpression Disrupts Development of the Ocular Surface Epithelium. Cells. 2025; 14(12).

Nunley, H; Xue, X; Fu, J; Lubensky, DK. Generation of fate patterns via intercellular forces. Physical Review Research. 2025; 7(2):l022051.

Paulding, D; Han, SJY; Timmons, J; Caye, M; Riedel, A; Brugmann, SA; Barske, L. Cranial neural crest shortage leads to extensive craniofacial anomalies in mice mutant for the NR2F1/2 nuclear receptors. Developmental Biology. 2026; 530:102-118.

Peter, J; Caldwell, KCN; Mcclain, L; Tchieu, J; Ross, AE; Luo, Y. Inhibition of PTPRS function does not affect the survival or regeneration of dopaminergic neurons but alters synaptic function in the nigrostriatal pathway. Neurobiology of Disease. 2025; 213:107023.

Pimentel, L; Ha, S; Yang, Y; Cochran, K; Chang, C-F; Houghtaling, S; Gombart, SK; Beier, DR; Brugmann, SA. Centriolar protein PIBF1 is required for craniofacial and forebrain development. Developmental Biology. 2025; 527:55-64.

Rezvani, M; Quach, S; Lewis, K; Saiki, N; Xue, C; Kimura, M; Iwasawa, K; Weihs, J; Elzobair, T; Al Reza, H; Zorn, A; Wells, JM; Yoshimoto, M; Takebe, T. Modeling Immune Lineage Co-Development in Human Pluripotent Stem Cell-derived Liver Organoids. Journal of Hepatology. 2025.

Roy, K; Warmflash, A. Pattern Formation in Cell Cultures. Annual Review of Biophysics. 2026.

Rui, T-Y; Huang, H-Z; Zheng, K; Fan, H-W; Zhang, J; Guo, Z-Y; Man, H-Y; Brazhe, N; Semyanov, A; Lu, Y-M; Liu, D; Zhu, L-Q. Tau Pathology Drives Disease-Associated Astrocyte Reactivity in Salt-Induced Neurodegeneration. Advanced Science. 2025; 12(11):e2410799.

Setayesh, T; Chi, M; Oestreicher, Z; Sakabe, M; Seu, K; Zhu, Z; Kaur, H; Tijani, A; Xin, M; Shova, A; Balla, J; Vandenheuvel, K; Hu, Y-C; Malik, P. A novel mouse model of hemoglobin SC disease reveals mechanisms underlying beneficial effects of hydroxyurea. Blood. 2025; 146(1):13-28.

Shen, C; Che, Y; Zhou, K; Wang, K; Li, W; Xue, D; Wu, T; Yang, L; Chen, M; Sheng, Y; Marcucci, G; He, C; Deng, X; Chen, J. ALKBH1 Drives Tumorigenesis and Drug Resistance via tRNA-decoding Reprogramming and Codon-biased Translation. Cancer Discovery. 2025; 15(11):2298-2325.

Shi, M; Crouse, B; Sundaram, N; Pode Shakked, N; Thorner, K; King, NM; Dutta, P; Ester, L; Zhang, W; Govindarajah, V; Mayhew, CN; Helmrath, MA; Bonventre, JV; Mccracken, KW. Integrating collecting systems in human kidney organoids through fusion of distal nephron to ureteric bud. Cell Stem Cell. 2025; 32(7):1055-1070.e8.

Showpnil, IA; Feinstein-Goren, N; Greenbaum, L; Barel, O; Koboldt, DC; Brugmann, SA; Weaver, KN; Slavotinek, A; Pode-Shakked, B; Stottmann, RW. Detection of the Heterozygous Recurrent MAX p.(Arg60Gln) Variant in Two Females Confirms and Expands the Phenotypic Spectrum of Polydactyly-Macrocephaly Syndrome. Clinical Genetics. 2025.

Singh, AK; D'alessandro, A; Wellendorf, AM; Gonzalez-Nieto, D; Kofron, M; Dzieciatkowska, M; Mejia, L; Barrio, LC; Filippi, M-D; Cancelas, JA. Metabolic adaptation of regenerative hematopoiesis depends on docking-independent mitochondrial connexin 43. Blood. 2025; 146(19):2306-2321.

Solano, AF; Preusse, K; Cain, B; Hotz, R; Gavini, P; Yuan, Z; Bowen, B; Maco, G; Neal, H; Gagliani, EK; Southgate, L; Kovall, RA; Kopan, R; Gebelein, B. Defective Notch1 signaling in endothelial cells drives pathogenesis in a mouse model of Adams-Oliver syndrome. Journal of Clinical Investigation. 2025; 135(23).

Tominaga, K; Kechele, DO; Sanchez, JG; Vales, S; Jurickova, I; Roman, L; Asai, A; Enriquez, JR; Mccauley, HA; Kishimoto, K; Zorn, AM; Helmrath, MA; Denson, LA; Wells, JM. Deriving Human Intestinal Organoids with Functional Tissue-Resident Macrophages All From Pluripotent Stem Cells. Cellular and Molecular Gastroenterology and Hepatology (CMGH). 2025; 19(4):101444.

Tweedie, L; Riccetti, MR; Cain, B; Qin, S; Salomone, J; Webb, JA; Riesenberg, A; Ehrman, LA; Waclaw, RR; Kovall, RA; Gebelein, B; Campbell, K. Modelling a pathological GSX2 variant that selectively alters DNA binding reveals hypomorphic mouse brain defects. Disease Models & Mechanisms. 2025; 18(2).

Ushuhuda, EG; Nguyen, JT; Pfaltzgraff, NG; Wenner, SM; Kofron, M; Mikedis, MM. MEIOC prevents continued mitotic cycling and promotes meiotic entry during mouse oogenesis. Development. 2026; 153(1).

Ushuhuda, EG; Nguyen, JT; Pfaltzgraff, NG; Wenner, SM; Kofron, M; Mikedis, MM. MEIOC prevents continued mitotic cycling and promotes meiotic entry during mouse oogenesis. Development. 2026; 153(1).

Weinhaus, B; Homan, S; Kincaid, M; Tadwalkar, A; Gu, X; Kumar, S; Slaughter, A; Zhang, J; Wu, Q; Kofron, JM; Troutman, TD; Defalco, T; Lucas, D. Differential regulation of fetal bone marrow and liver hematopoiesis by yolk-sac-derived myeloid cells. Nature Communications. 2025; 16(1):4427.

Xiao, B; Mongan, M; Ko, CI; Hu, Y-C; Defalco, T; Greis, KD; Xia, Y. Generation and characterization of a Cre-Inducible MAP3K1 Gain-of-Function Model. Disease Models & Mechanisms. 2026.

Xue, X; Rahman, OM; Sun, S; Bok, J; Tang, A; Fu, J. Generation of spatially patterned human neural tube-like structures using microfluidic gradient devices. Nature Protocols. 2025.

Xue, X; Liu, Y; Fu, J. Bioengineering embryo models. Nature Reviews Bioengineering. 2025; 3(1):11-29.

Yoo, JJ; Serafin, EK; Kofron, JM; Baccei, ML. Early Life Injury Alters Spinal Astrocyte Development. Journal of Neuroscience. 2025; 45(42).

Zhang, J; Yang, C-Q; Liu, Z-Q; Wu, S-P; Li, Z-G; Zhang, L-M; Fan, H-W; Guo, Z-Y; Man, H-Y; Li, X; Lu, Y-M; Zhu, L-Q; Liu, D. Cpeb1 remodels cell type-specific translational program to promote fear extinction. Science Advances. 2025; 11(2):eadr8687.

Zhou, Y; Li, W-L; Liu, Z-Q; Ai, W-Q; Kou, J-X; Fan, H-W; Han, Z-T; Hu, Y-Z; Zhang, H-H; Jia, J-J; Man, H-Y; Lu, Y-M; Liu, D; Zhu, L-Q. Spinal cord Tau pathology induces tactile deficits and cognitive impairment in Alzheimer's disease via dysregulation of CCK neurons. Nature Neuroscience. 2025.