Developmental Biology
Publications

Publications

Aleksander, SA; Balhoff, J; Carbon, S; Cherry, JM; Drabkin, HJ; Ebert, D; Feuermann, M; Gaudet, P; Harris, NL; Hill, DP; Auchincloss, A; Argoud-Puy, G; Blatter, MC; Boutet, E. The Gene Ontology knowledgebase in 2023. Genetics: a periodical record of investigations bearing on heredity and variation. 2023; 224.

Bedard, MC; Chihanga, T; Carlile, A; Jackson, R; Brusadelli, MG; Lee, D; VonHandorf, A; Rochman, M; Dexheimer, PJ; Chalmers, J; Lambert, PF; Adam, M; Steven Potter, S; Wells, SI. Single cell transcriptomic analysis of HPV16-infected epithelium identifies a keratinocyte subpopulation implicated in cancer. Nature Communications. 2023; 14:1975.

Bouffi, C; Wikenheiser-Brokamp, KA; Chaturvedi, P; Sundaram, N; Goddard, GR; Wunderlich, M; Brown, NE; Staab, JF; Latanich, R; Zachos, NC; Mulloy, JC; Zorn, AM; Wells, JM; Helmrath, MA. In vivo development of immune tissue in human intestinal organoids transplanted into humanized mice. Nature Biotechnology. 2023; 41:824-831.

Brown, FN; Iwasawa, E; Shula, C; Fugate, EM; Lindquist, DM; Mangano, FT; Goto, J. Early postnatal microglial ablation in the Ccdc39 mouse model reveals adverse effects on brain development and in neonatal hydrocephalus. Fluids and Barriers of the CNS. 2023; 20:42.

Cai, H; Ao, Z; Tian, C; Wu, Z; Liu, H; Tchieu, J; Gu, M; Mackie, K; Guo, F. Brain Organoid Computing for Artificial Intelligence. 2023.

Cai, H; Ao, Z; Tian, C; Wu, Z; Liu, H; Tchieu, J; Gu, M; Mackie, K; Guo, F. Brain organoid reservoir computing for artificial intelligence. Nature Electronics. 2023; 6:1032-1039.

Cain, B; Webb, J; Yuan, Z; Cheung, D; Lim, HW; Kovall, RA; Weirauch, MT; Gebelein, B. Prediction of cooperative homeodomain DNA binding sites from high-throughput-SELEX data. Nucleic Acids Research (NAR). 2023; 51:6055-6072.

Chandel, AS; Stocker, M; Özbudak, EM. The Role of Fibroblast Growth Factor Signaling in Somitogenesis. DNA and Cell Biology. 2023; 42:580-584.

Chen, R; Qiu, K; Leong, DC Y; Kundu, BK; Zhang, C; Srivastava, P; White, KE; Li, G; Han, G; Guo, Z; Elles, CG; Diao, J; Sun, Y. A general design of pyridinium-based fluorescent probes for enhancing two-photon microscopy. Biosensors and Bioelectronics. 2023; 239:115604.

Dong, F; Amlal, H; Venkatakrishnan, J; Zhang, J; Fry, M; Yuan, Y; Cheng, YC; Hu, Y; Kao, WW-Y. The gene therapy for corneal pathology with novel nonsense cystinosis mouse lines created by CRISPR Gene Editing. The Ocular Surface. 2023; 29:432-443.

Edwards, NA; Kashyap, A; Warren, A; Agricola, ZN; Kenny, AP; Shen, Y; Chung, WK; Zorn, AM. Disrupted endosomal trafficking of the Vangl-Celsr polarity complex underlies congenital anomalies in trachea-esophageal morphogenesis. 2023.

Elliott, KH; Balchand, SK; Paese, CL B; Chang, CF; Yang, Y; Brown, KM; Rasicci, DT; He, H; Thorner, K; Chaturvedi, P; Murray, SA; Chen, J; Porollo, A; Peterson, KA; Brugmann, SA. Identification of a heterogeneous and dynamic ciliome during embryonic development and cell differentiation. Development (Cambridge). 2023; 150.

Fisher, M; James-Zorn, C; Ponferrada, V; Bell, AJ; Sundararaj, N; Segerdell, E; Chaturvedi, P; Bayyari, N; Chu, S; Pells, T; Foley, S; Karimi, K; Vize, PD; Zorn, AM. Xenbase: key features and resources of the Xenopus model organism knowledgebase. Genetics: a periodical record of investigations bearing on heredity and variation. 2023; 224.

Gipson, GR; Nolan, K; Kattamuri, C; Kenny, AP; Agricola, Z; Edwards, NA; Zinski, J; Czepnik, M; Mullins, MC; Zorn, AM; Thompson, TB. Formation and characterization of BMP2/GDF5 and BMP4/GDF5 heterodimers. BMC Biology. 2023; 21:16.

Halurkar, MS; Inoue, O; Mukherjee, R; Paese, CL B; Duszynski, M; Brugmann, SA; Lim, H; Sanchez-Gurmaches, J. The widely used Ucp1-CreEvdr transgene elicits complex developmental and metabolic phenotypes. 2023.

Iyyanar, PP R; Qin, C; Adhikari, N; Liu, H; Hu, YC; Jiang, R; Lan, Y. Developmental origin of the mammalian premaxilla. Developmental Biology. 2023; 503:1-9.

Keseroglu, K; Zinani, OQ H; Keskin, S; Seawall, H; Alpay, EE; Özbudak, EM. Stochastic gene expression and environmental stressors trigger variable somite segmentation phenotypes. Nature Communications. 2023; 14:6497.

Keseroglu, K; Zinani, OQ H; Özbudak, EM. Using single-molecule fluorescence in situ hybridization and immunohistochemistry to count RNA molecules in single cells in zebrafish embryos. Star Protocols. 2023; 4:102020.

Lampl, CD; Wikenheiser-Brokamp, KA; Woods, JC; Kofron, JM; McCormack, FX. Pulmonary Alveolar Microlithiasis. Orphan Lung Diseases. : Springer Nature; Springer Nature; 2023.

Lim, HW; Iwafuchi, M. Profiling Accessible Chromatin and Nucleosomes in the Mammalian Genome. . 2023.

Liu, L; Zhou, Y; Liu, Z; Li, J; Hu, L; He, L; Gao, G; Kidd, B; Walsh, A; Jiang, R; Wu, C; Zhang, K; Xie, L. Osr1 Regulates Macrophage-mediated Liver Inflammation in Nonalcoholic Fatty Liver Disease Progression. CMGH Cellular and Molecular Gastroenterology and Hepatology. 2023; 15:1117-1133.

Lofrano-Porto, A; Pereira, SA; Dauber, A; Bloom, JC B; Fontes, AN; Asimow, N; de Moraes, OL; Araujo, PA T; Abreu, AP; Guo, MH; Coelho, MS; Carroll, RS; Jiang, R; Kaiser, UB. OSR1 disruption contributes to uterine factor infertility via impaired Müllerian duct development and endometrial receptivity. The Journal of Clinical Investigation. 2023; 133.

Majd, H; Amin, S; Ghazizadeh, Z; Cesiulis, A; Arroyo, E; Lankford, K; Majd, A; Farahvashi, S; Chemel, AK; Okoye, M; Kocsis, JD; Chen, S; Studer, L; Fattahi, F. Deriving Schwann cells from hPSCs enables disease modeling and drug discovery for diabetic peripheral neuropathy. Cell Stem Cell. 2023; 30:632-647.e10.

Marek-Yagel, D; Stenke, E; Pode-Shakked, B; Dunne, C; Crushell, E; Bryce-Smith, A; McDermott, M; O’Sullivan, MJ; Veber, A; Krishnamurthy, M; Wells, JM; Anikster, Y; Bourke, B. Nonsense mutation in the novel PERCC1 gene as a genetic cause of congenital diarrhea and enteropathy. Human Genetics. 2023; 142:691-696.

Mayhew, CN; Singhania, R. A review of protocols for brain organoids and applications for disease modeling. Star Protocols. 2023; 4:101860.

McCauley, HA; Riedman, AM; Enriquez, JR; Zhang, X; Watanabe-Chailland, M; Sanchez, JG; Kechele, DO; Paul, EF; Riley, K; Burger, C; Lang, RA; Wells, JM. Enteroendocrine Cells Protect the Stem Cell Niche by Regulating Crypt Metabolism in Response to Nutrients. CMGH Cellular and Molecular Gastroenterology and Hepatology. 2023; 15:1293-1310.

Moritz, L; Schon, SB; Rabbani, M; Sheng, Y; Agrawal, R; Glass-Klaiber, J; Sultan, C; Camarillo, JM; Clements, J; Baldwin, MR; Li, JZ; Orwig, KE; Redding, S; Hammoud, SS. Sperm chromatin structure and reproductive fitness are altered by substitution of a single amino acid in mouse protamine 1. Nature Structural and Molecular Biology. 2023; 30:1077-1091.

Múnera, JO; Kechele, DO; Bouffi, C; Qu, N; Jing, R; Maity, P; Enriquez, JR; Han, L; Campbell, I; Mahe, MM; Hu, YC; Takebe, T; Helmrath, MA; Wells, JM. Development of functional resident macrophages in human pluripotent stem cell-derived colonic organoids and human fetal colon. Cell Stem Cell. 2023; 30:1434-1451.e9.

Ochi, H; Kato, T; Zorn, A; Hayashi, T; Inoue, T; Kondo, M; Taira, M; Michiue, T. Versatile utilities of amphibians (part 5). Development, Growth and Differentiation. 2023; 65:459-460.

Ochi, H; Michiue, T; Kato, T; Zorn, A; Hayashi, T; Inoue, T; Kondo, M; Taira, M. Versatile utilities of amphibians (part 4). Development, Growth and Differentiation. 2023; 65:4-5.

O'Donnell, A; Gonzalez, BA; Mukherjee, S; Wilson, R; Alfieri, CM; Swoboda, CO; Millay, DP; Zorn, AM; Yutzey, KE. Localized Prox1 Regulates Aortic Valve Endothelial Cell Diversity and Extracellular Matrix Stratification in Mice. Arteriosclerosis, Thrombosis, and Vascular Biology. 2023; 43:1478-1493.

Parkins, EV; Brager, DH; Rymer, JK; Burwinkel, JM; Rojas, D; Tiwari, D; Hu, YC; Gross, C. Mir324 knockout regulates the structure of dendritic spines and impairs hippocampal long-term potentiation. Scientific Reports. 2023; 13:21919.

Parkins, EV; Burwinkel, JM; Ranatunga, R; Yaser, S; Hu, YC; Tiwari, D; Gross, C. Age-Dependent Regulation of Dendritic Spine Density and Protein Expression in Mir324 KO Mice. Journal of Molecular Neuroscience. 2023; 73:818-830.

Peng, Y; Liou, B; Lin, Y; Mayhew, CN; Fleming, SM; Sun, Y. iPSC-derived neural precursor cells engineering GBA1 recovers acid β-glucosidase deficiency and diminishes α-synuclein and neuropathology. Molecular Therapy-Methods & Clinical Development. 2023; 29:185-201.

Rivron, NC; Martinez-Arias, A; Sermon, K; Mummery, C; Schöler, HR; Wells, J; Nichols, J; Hadjantonakis, AK; Lancaster, MA; Moris, N; Fu, J; Sturmey, RG; Niakan, K; Rossant, J; Kato, K. Changing the public perception of human embryology. Nature Cell Biology. 2023; 25:1717-1719.

Shao, TY; Kinder, JM; Harper, G; Pham, G; Peng, Y; Liu, J; Gregory, EJ; Sherman, BE; Wu, Y; Iten, AE; Hu, YC; Russi, AE; Erickson, JJ; Miller-Handley, H; Way, SS. Reproductive outcomes after pregnancy-induced displacement of preexisting microchimeric cells. Science. 2023; 381:1324-1330.

Simsek, MF; Chandel, AS; Saparov, D; Zinani, OQ H; Clason, N; Özbudak, EM. Periodic inhibition of Erk activity drives sequential somite segmentation. Nature. 2023; 613:153-159.

Simsek, MF; Özbudak, EM. Human stem cell models unravel mechanisms of somite segmentation. Cell Stem Cell. 2023; 30:246-247.

Simsek, MF; Özbudak, EM. A design logic for sequential segmentation across organisms. The Federation of European Biochemical Societies (FEBS) Journal. 2023; 290:5086-5093.

Singh, A; Poling, HM; Chaturvedi, P; Thorner, K; Sundaram, N; Kechele, DO; Childs, CJ; McCauley, HA; Fisher, GW; Brown, NE; Spence, JR; Wells, JM; Helmrath, MA. Transplanted human intestinal organoids: a resource for modeling human intestinal development. Development (Cambridge). 2023; 150.

Soni, UK; Jenny, L; Hegde, RS. IGF-1R targeting in cancer - does sub-cellular localization matter?. Journal of Experimental and Clinical Cancer Research. 2023; 42:273.

Soni, UK; Wang, Y; Pandey, RN; Roberts, R; Pressey, JG; Hegde, RS. Molecularly Defined Subsets of Ewing Sarcoma Tumors Differ in Their Responses to IGF1R and WEE1 Inhibition. Clinical Cancer Research. 2023; 29:458-471.

Toth, A; Kannan, P; Snowball, J; Kofron, M; Wayman, JA; Bridges, JP; Miraldi, ER; Swarr, D; Zacharias, WJ. Alveolar epithelial progenitor cells require Nkx2-1 to maintain progenitor-specific epigenomic state during lung homeostasis and regeneration. Nature Communications. 2023; 14:8452.

Verma, R; Aggarwal, P; Bischoff, ME; Reigle, J; Secic, D; Wetzel, C; VandenHeuvel, K; Biesiada, J; Ehmer, B; Landero Figueroa, JA; Plas, DR; Medvedovic, M; Meller, J; Czyzyk-Krzeska, MF. Microtubule-associated protein MAP1LC3C regulates lysosomal exocytosis and induces zinc reprogramming in renal cancer cells. The Journal of biological chemistry. 2023; 299:104663.

Verrall, CE; Patel, S; Travitz, L; Tchieu, J; Dale, RC; Kasparian, NA; Winlaw, DS; Blue, GM. Biological and structural phenotypes associated with neurodevelopmental outcomes in congenital heart disease. Translational Pediatrics. 2023; 12:768-786.

Wang, T; Dao, L; Guo, Z; Li, T. (2023) A 3D Microfluidic Device with Vertical Channels toward In Vitro Reconstruction of Blood-Brain Barrier. 2023:1-4.

Wurmser, M; Madani, R; Chaverot, N; Backer, S; Borok, M; Dos Santos, M; Comai, G; Tajbakhsh, S; Relaix, F; Santolini, M; Sambasivan, R; Jiang, R; Maire, P. Overlapping functions of SIX homeoproteins during embryonic myogenesis. PLoS Genetics. 2023; 19:e1010781.

Xu, J; Iyyanar, PP R; Lan, Y; Jiang, R. Sonic hedgehog signaling in craniofacial development. Differentiation; Research in Biological Diversity. 2023; 133:60-76.

Zhou, LT; Liu, D; Kang, HC; Lu, L; Huang, HZ; Ai, WQ; Zhou, Y; Deng, MF; Li, H; Liu, ZQ; Bertram, L; Lu, Y; Guo, Z; Zhu, LQ. Tau pathology epigenetically remodels the neuron-glial cross-talk in Alzheimer's disease. Science Advances. 2023; 9:eabq7105.