Center for Stem Cell & Organoid Medicine (CuSTOM)
CuSTOM Publications


Riccetti, M; Gokey, JJ; Aronow, B; Perl, AT. The elephant in the lung: Integrating lineage-tracing, molecular markers, and single cell sequencing data to identify distinct fibroblast populations during lung development and regeneration. Matrix Biol. 2020 Sep;91-92:51-74.

Wilson, KD; Ameen, M; Guo, H; Abilez, OJ; Tian, L; Mumbach, MR; Diecke, S; Qin, X; Liu, Y; Yang, H; Ma, N; Gaddam, S; Cunningham, NJ; Gu, M; Neofytou, E; Prado, M; Hildebrandt, TB; Karakikes, I; Chang, HY; Wu, JC. Endogenous Retrovirus-Derived lncRNA BANCR Promotes Cardiomyocyte Migration in Humans and Non-human Primates. Dev Cell. 2020 Jul 28;S1534-5807(20)30580-3.

Cederquist, GY; Tchieu, J; Callahan, SJ; Ramnarine, K; Ryan, S; Zhang, C; Rittenhouse, C; Zeltner, N; Chung, SY; Zhou, T; Chen, S; Betel, D; White, RM; Tomishima, M; Studer, L. A Multiplex Human Pluripotent Stem Cell Platform Defines Molecular and Functional Subclasses of Autism-Related Genes. Cell Stem Cell. 2020 Jul 2;27(1):35-49.e6.

Bolte, C; Ustiyan, V; Ren, X; Dunn, AW; Pradhan, A; Wang, G; Kolesnichenko, OA; Deng, Z; Zhang, Y; Shi, D; Greenberg, JM; Jobe, AH; Kalin, TV; Kalinichenko, VV. Nanoparticle Delivery of Proangiogenic Transcription Factors into the Neonatal Circulation Inhibits Alveolar Simplification Caused by Hyperoxia. Am J Respir Crit Care Med. 2020 Jul 1;202(1):100-111.

Malara, MM; Blackstone, BN; Baumann, ME; Bailey, JK; Supp, DM; Powell, HM. Cultured Epithelial Autograft Combined with Micropatterned Dermal Template Forms Rete Ridges In Vivo. Tissue Eng Part A. 2020 Jun 29. [Epub ahead of print]

Black, M; Arumugam, P; Shukla, S; Pradhan, A; Ustiyan, V; Milewski, D; Kalinichenko, VV; Kalin, TV. FOXM1 nuclear transcription factor translocates into mitochondria and inhibits oxidative phosphorylation. Mol Biol Cell. 2020 Jun 15;31(13):1411-1424.

DeBruler, DM; Baumann, ME; Zbinden, JC; Blackstone, BN; Bailey, JK; Supp, DM; Powell, HM. Improved Scar Outcomes with Increased Daily Duration of Pressure Garment Therapy. Adv Wound Care (New Rochelle). 2020 Jun 2;9(8):453-461.

Venkatasubramanian, M; Chetal, K; Schnell, DJ; Atluri, G; Salomonis, N.Resolving single-cell heterogeneity from hundreds of thousands of cells through sequential hybrid clustering and NMF. Bioinformatics. 2020 Jun 1;36(12):3773-3780.

Althoff, M; Nayak, R;, Hegde, S; Wellendorf, A; Bohan, B; Filippi, MD; Xin, M; Lu, R; Geiger, H; Zheng, Y; Diaz-Meco, MT; Moscat, J; Cancelas, JA. Yap1-Scribble polarization is required for hematopoietic stem cell division and fate. Blood. 2020 Jun 1;blood.2019004113.

Muench, DE; Olsson, A; Ferchen, K; Pham, G; Serafin, RA; Chutipongtanate, S; Dwivedi, P; Song, B; Hay, S; Chetal, K; Trump-Durbin, LR; Mookerjee-Basu, J; Zhang, K; Yu, JC; Lutzko, C; Myers, KC; Nazor, KL; Greis, KD; Kappes, DJ; Way, SS; Salomonis, N; Grimes, HL. Mouse models of neutropenia reveal progenitor-stage-specific defects. Nature. 2020 Jun;582(7810):109-114.

Zhang, J; He, Y; Yan, X; Chen, S; He, M; Lei, Y; Zhang, J; Gongol, B; Gu, M; Miao, Y; Bai, L; Cui, X; Wang, X; Zhang, Y; Fan, F; Li, Z; Shen, Y; Chou, CH; Huang, HD; Malhotra, A; Rabinovitch, M; Jing, ZC; Shyy, JY. MicroRNA-483 amelioration of experimental pulmonary hypertension. EMBO Mol Med. 2020 May 8;12(5):e11303.

Klein, A; Bayrau, B; Miao, Y; Gu, M. Isolation of Endocardial and Coronary Endothelial Cells from the Ventricular Free Wall of the Rat Heart. J Vis Exp. 2020 Apr 15;(158).

Goda, C; Balli, D; Black, M; Milewski, D; Le, T; Ustiyan, V; Ren, X; Kalinichenko, VV; Kalin, TV. Loss of FOXM1 in macrophages promotes pulmonary fibrosis by activating p38 MAPK signaling pathway. PLoS Genet. 2020 Apr 9;16(4):e1008692.

Reyes-Palomares, A; Gu, M; Grubert, F; Berest, I; Sa, S; Kasowski, M; Arnold, C; Shuai, M; Srivas, R; Miao, S; Li, D; Snyder, MP; Rabinovitch, M; Zaugg, JB. Remodeling of active endothelial enhancers is associated with aberrant gene-regulatory networks in pulmonary arterial hypertension. Nat Commun. 2020 Apr 3;11(1):1673.

Rubinstein, JD; Burns, K; Absalon, M; Lutzko, C; Leemhuis, T; Chandra, S; Hanley, PJ; Keller, MD; Davies, SM; Nelson, A; Grimley, M. EBV-directed viral-specific T-lymphocyte therapy for the treatment of EBV-driven lymphoma in two patients with primary immunodeficiency and DNA repair defects. Pediatr Blood Cancer. 2020 Mar;67(3):e28126.

Wu, Z; Parry, M; Hou, XY; Liu, MH; Wang, H; Cain, R; Pei, ZF; Chen, YC; Guo, ZY; Abhijeet, S; Chen, G. Gene therapy conversion of striatal astrocytes into GABAergic neurons in mouse models of Huntington's disease. Nat Commun. 2020 Feb 27;11(1):1105.

Sakabe, K; Takebe, T; Asai, A. Organoid Medicine in Hepatology. Clin Liver Dis (Hoboken). 2020 Feb 25;15(1):3-8.

Sunuwar, L; Yin, J; Kasendra, M; Karalis, K; Kaper, J; Fleckenstein, J;, Donowitz, M. Mechanical Stimuli Affect Escherichia coli Heat-Stable Enterotoxin-Cyclic GMP Signaling in a Human Enteroid Intestine-Chip Model. Infect Immun. 2020 Feb 20;88(3):e00866-19.

Singh, AK; Cancelas, JA. Gap Junctions in the Bone Marrow Lympho-Hematopoietic Stem Cell Niche, Leukemia Progression, and Chemoresistance. Int J Mol Sci. 2020 Jan 25;21(3):796.

Kasendra, M; Luc, R; Yin, J; Manatakis, DV; Kulkarni, G; Lucchesi, C; Sliz, J; Apostolou, A; Sunuwar, L; Obrigewitch, J; Jang, KJ; Hamilton, GA; Donowitz, M; Karalis, K. Duodenum Intestine-Chip for preclinical drug assessment in a human relevant model. Elife. 2020 Jan 14;9:e50135.

Sontheimer-Phelps, A; Chou, DB; Tovaglieri, A; Ferrante, TC; Duckworth, T; Fadel, C; Frismantas, V; Sutherland, AD; Jalili-Firoozinezhad, S; Kasendra, M; Stas, E; Weaver, JC; Richmond, CA; Levy, O; Prantil-Baun, R; Breault, DT; Ingber, DE. Human Colon-on-a-Chip Enables Continuous In Vitro Analysis of Colon Mucus Layer Accumulation and Physiology. Cell Mol Gastroenterol Hepatol. 2020;9(3):507-526.

Williams, SL; Tkach, JA; Rattan, MS; South, AP; Wessel, J; Kingma, PS. Feeding Tolerance, Intestinal Motility, and Superior Mesenteric Artery Blood Flow in Infants with Gastroschisis. Neonatology. 2020;117(1):95-101.

Moffatt, LT; Madrzykowski, D; Gibson, ALF; Powell, HM; Cancio, LC; Wade, CE; Choudhry, MA; Kovacs, EJ; Finnerty, CC; Majetschak, M; Shupp, JW; Standards in Biologic Lesions Working Group. Standards in Biologic Lesions: Cutaneous Thermal Injury and Inhalation Injury Working Group 2018 Meeting Proceedings. J Burn Care Res. 2020 May 2;41(3):604-611.

Oherle, K; Acker, E; Bonfield, M; Wang, T; Gray, J; Lang, I; Bridges, J; Lewkowich, I; Xu, Y; Ahlfeld, S; Zacharias, W; Alenghat, T; Deshmukh, H. Insulin-like Growth Factor 1 Supports a Pulmonary Niche that Promotes Type 3 Innate Lymphoid Cell Development in Newborn Lungs. Immunity. 2020 Apr 14;52(4):716-718.

Okabe, R; Chen-Yoshikawa, TF; Yoshizawa, A; Hirashima, T; Saito, M; Date, H; Takebe, T. Orthotopic foetal lung tissue direct injection into lung showed a preventive effect against paraquat-induced acute lung injury in mice. Eur J Cardiothorac Surg. 2020 Apr 7;ezaa091.

Basil, MC; Katzen, J; Engler, AE; Guo, M; Herriges, MJ; Kathiriya, JJ; Windmueller, R; Ysasi, AB; Zacharias, WJ; Chapman, HA; Kotton, DN; Rock, JR; Snoeck, HW; Vunjak-Novakovic, G; Whitsett, JA; Morrisey, EE. The Cellular and Physiological Basis for Lung Repair and Regeneration: Past, Present, and Future. Cell Stem Cell. 2020 Apr 2;26(4):482-502.

Satish, L; Evdokiou, A; Geletu, E; Hahn, JM; Supp, DM. Pirfenidone inhibits epithelial-mesenchymal transition in keloid keratinocytes. Burns Trauma. 2020 Feb 27;8:tkz007.

Boyce, ST; Supp, DM; Lloyd, CM. Exogenous Keratinocyte Growth Factor Is Not Required for Pigmentation of Skin Substitutes with Three Isogeneic Cell Types2020 Feb;26(3-4):214-224.

Nowrouzi, A; Sertorio, MG; Akbarpour, M; Knoll, M; Krunic, D; Kuhar, M; Schwager, C; Brons, S; Debus, J; Wells, SI; Wells, JM; Abdollahi, A. Personalized Assessment of Normal Tissue Radiosensitivity via Transcriptome Response to Photon, Proton and Carbon Irradiation in Patient-Derived Human Intestinal Organoids2020 Feb 18;12(2):469.

Blackstone, BN; Malara, MM; Baumann, ME; McFarland, K; Supp, DM; Powell, HM. Fractional CO 2 laser micropatterning of cell-seeded electrospun collagen scaffolds enables rete ridge formation in 3D engineered skin. Acta Biomater. 2020 Jan 15;102:287-297.

Khandelwal, P; Chaturvedi, V; Owsley, E; Lane, A; Heyenbruch, D; Lutzko, CM; Leemhuis, T; Grimley, MS; Nelson, AS; Davies, SM; Jordan, MB; Marsh, RA. CD38 bright CD8 + T Cells Associated with the Development of Acute GVHD Are Activated, Proliferating, and Cytotoxic Trafficking Cells. Biol Blood Marrow Transplant. 2020 Jan;26(1):1-6.

Thompson, WL; Takebe, T. Generation of multi-cellular human liver organoids from pluripotent stem cells. Methods Cell Biol. 2020;159:47-68.

Pradhan, S; Karve, SS; Weiss, AA; Hawkins, J; Poling, HM; Helmrath, MA; Wells, JM; McCauley, HA. Tissue Responses to Shiga Toxin in Human Intestinal Organoids. Cell Mol Gastroenterol Hepatol. 2020;10(1):171-190.

Shacham-Silverberg, V; Wells, JM. Generation of esophageal organoids and organotypic raft cultures from human pluripotent stem cells. Methods Cell Biol. 2020;159:1-22.

Liu, T; Zhou, L; Yang, K; Iwasawa, K; Kadekaro, AL; Takebe, T; Andl, T; Zhang, Y. The β-catenin/YAP signaling axis is a key regulator of melanoma-associated fibroblasts. Signal Transduct Target Ther. 2019 Dec 24;4:63.

Fang, H; Yao, S; Chen, Q; Liu, C; Cai, Y; Geng, S; Bai, Y; Tian, Z; Zacharias, AL; Takebe, T; Chen, Y; Guo, Z; He, W; Diao, J. De Novo-Designed Near-Infrared Nanoaggregates for Super-Resolution Monitoring of Lysosomes in Cells, in Whole Organoids, and in Vivo. ACS Nano. 2019 Dec 24;13(12):14426-14436.

Hasegawa, T; Kikuta, J; Sudo, T; Matsuura, Y; Matsui, T; Simmons, S; Ebina, K; Hirao, M; Okuzaki, D; Yoshida, Y; Hirao, A; Kalinichenko, VV; Yamaoka, K; Takeuchi, T; Ishii, M. Identification of a novel arthritis-associated osteoclast precursor macrophage regulated by FoxM1. Nat Immunol. 2019 Dec;20(12):1631-1643.

Laskin, BL; Denburg, MR; Furth, SL; Moatz, T; Altrich, M; Kleiboeker, S; Lutzko, C; Zhu, X; Blackard, JT; Jodele, S; Lane, A; Wallace, G; Dandoy, CE; Lake, K; Duell, A; Litts, B; Seif, AE; Olson, T; Bunin, N; Davies, SM. The natural history of BK polyomavirus and the host immune response after stem cell transplantation. Clin Infect Dis. 2019 Dec 18;ciz1194.

Manabe, Y; Marchetti, R; Takakura, Y; Nagasaki, M; Nihei, W; Takebe, T; Tanaka, K; Kabayama, K; Chiodo, F; Hanashima, S; Kamada, Y; Miyoshi, E; Dulal, HP; Yamaguchi, Y; Adachi, Y; Ohno, N; Tanaka, H; Silipo, A; Fukase, K; Molinaro, A. The Core Fucose on an IgG Antibody is an Endogenous Ligand of Dectin-1. Angew Chem Int Ed Engl. 2019 Dec 16;58(51):18697-18702.

Nasr, T; Mancini, P; Rankin, SA; Edwards, NA; Agricola, ZN; Kenny, AP; Kinney, JL; Daniels, K; Vardanyan, J; Han, L; Trisno, S; Cha, SW; Wells, JM; Kofron, MJ; Zorn, AM. Endosome-Mediated Epithelial Remodeling Downstream of Hedgehog-Gli Is Required for Tracheoesophageal Separation. Dev Cell. 2019 Dec 16;51(6):665-674.e6.

Lau, ST; Li, Z; Pui-Ling, Lai F; Nga-Chum Lui K; Li, P; Munera, JO; Pan, G; Mahe, MM; Hui, CC; Wells, JM; Ngan, ES. Activation of Hedgehog Signaling Promotes Development of Mouse and Human Enteric Neural Crest Cells, Based on Single-Cell Transcriptome Analyses. Gastroenterology. 2019 Dec;157(6):1556-1571.e5.

Kechele, DO; Wells, JM. Recent advances in deriving human endodermal tissues from pluripotent stem cells. Curr Opin Cell Biol. 2019 Dec;61:92-100.

Shi, L; Kuhnell, D; Borra, VJ; Langevin, SM; Nakamura, T; Esfandiari, L. Rapid and label-free isolation of small extracellular vesicles from biofluids utilizing a novel insulator based dielectrophoretic device. Lab Chip. 2019 Nov 7;19(21):3726-3734.

Jang, KJ; Otieno, MA; Ronxhi, J; Lim, HK; Ewart, L; Kodella, KR; Petropolis, DB; Kulkarni, G; Rubins, JE; Conegliano, D; Nawroth, J; Simic, D; Lam, W; Singer, M; Barale, E; Singh, B; Sonee, M; Streeter, AJ; Manthey, C; Jones, B; Srivastava, A; Andersson, LC; Williams, D; Park, H; Barrile, R; Sliz, J; Herland, A; Haney, S; Karalis, K; Ingber, DE; Hamilton, GA. Reproducing human and cross-species drug toxicities using a Liver-Chip. Sci Transl Med. 2019 Nov 6;11(517):eaax5516.

Ren, X; Ustiyan, V; Guo, M; Wang, G; Bolte, C; Zhang, Y; Xu, Y; Whitsett, JA; Kalin, TV; Kalinichenko, VV. Postnatal Alveologenesis Depends on FOXF1 Signaling in c-KIT + Endothelial Progenitor Cells. Am J Respir Crit Care Med. 2019 Nov 1;200(9):1164-1176.

Marks, KT; Landis, MW; Lim, FY; Haberman, B; Kingma, PS. Evaluation of Lung Injury in Infants with Congenital Diaphragmatic Hernia. J Pediatr Surg. 2019 Nov;54(11):2443-2447.

Ogawa-Ochiai, K; Yoshimura, K; Takebe, T; Iwahashi, M; Shirai, A; Tsuda, M; Ogawa, M; Ishikawa, H. The effect of contact needle therapy on fatigue in patients with cancer in palliative care: A study protocol for a randomized controlled trial. Medicine (Baltimore). 2019 Nov;98(44):e17809.

van Harten, AM; Poell, JB; Buijze, M; Brink, A; Wells, SI; René Leemans, C; Wolthuis, RMF; Brakenhoff, RH. Characterization of a head and neck cancer-derived cell line panel confirms the distinct TP53-proficient copy number-silent subclass. Oral Oncol. 2019 Nov;98:53-61.

Pradhan, A; Dunn, A; Ustiyan, V; Bolte, C; Wang, G; Whitsett, JA; Zhang, Y; Porollo, A; Hu, YC; Xiao, R; Szafranski, P; Shi, D; Stankiewicz, P; Kalin, TV; Kalinichenko, VV. The S52F FOXF1 Mutation Inhibits STAT3 Signaling and Causes Alveolar Capillary Dysplasia. Am J Respir Crit Care Med. 2019 Oct 15;200(8):1045-1056.

Peng, Y; Liou, B; Inskeep, V; Blackwood, R; Mayhew, CN; Grabowski, GA; Sun, Y. Intravenous infusion of iPSC-derived neural precursor cells increases acid β-glucosidase function in the brain and lessens the neuronopathic phenotype in a mouse model of Gaucher disease. Hum Mol Genet. 2019 Oct 15;28(20):3406-3421.

Koike, H; Iwasawa, K; Ouchi, R; Maezawa, M; Giesbrecht, K; Saiki, N; Ferguson, A; Kimura, M; Thompson, WL; Wells, JM; Zorn, AM; Takebe, T. Modelling human hepato-biliary-pancreatic organogenesis from the foregut-midgut boundary. Nature. 2019 Oct;574(7776):112-116.

Supp, DM; Hahn, JM; Combs, KA; McFarland, KL; Schwentker, A; Boissy, RE; Boyce, ST; Powell, HM; Lucky, AW. Collagen VII Expression Is Required in Both Keratinocytes and Fibroblasts for Anchoring Fibril Formation in Bilayer Engineered Skin Substitutes. Cell Transplant. Sep-Oct 2019;28(9-10):1242-1256.

Wang, X; Ye, F; Wen, Z; Guo, Z; Yu, C; Huang, WK; Rojas Ringeling, F; Su, Y; Zheng, W; Zhou, G; Christian, KM; Song, H; Zhang, M; Ming, GL. Structural interaction between DISC1 and ATF4 underlying transcriptional and synaptic dysregulation in an iPSC model of mental disorders. Mol Psychiatry. 2019 Aug 23. [Epub ahead of print]

Zhang, H; Tian, L; Shen, M; Tu, C; Wu, H; Gu, M; Paik, DT; Wu, JC. Generation of Quiescent Cardiac Fibroblasts From Human Induced Pluripotent Stem Cells for In Vitro Modeling of Cardiac Fibrosis. Circ Res. 2019 Aug 16;125(5):552-566.

Adelman, ER; Huang, HT; Roisman, A; Olsson, A; Colaprico, A; Qin, T; Lindsley, RC; Bejar, R; Salomonis, N; Grimes, HL; Figueroa, ME. Aging Human Hematopoietic Stem Cells Manifest Profound Epigenetic Reprogramming of Enhancers That May Predispose to Leukemia. Cancer Discov. 2019 Aug;9(8):1080-1101.

Ouchi, R; Togo, S; Kimura, M; Shinozawa, T; Koido, M; Koike, H; Thompson, W; Karns, RA; Mayhew, CN; McGrath, PS; McCauley, HA; Zhang, RR; Lewis, K; Hakozaki, S; Ferguson, A; Saiki, N; Yoneyama, Y; Takeuchi, I; Mabuchi, Y; Akazawa, C; Yoshikawa, HY; Wells, JM; Takebe, T. Modeling Steatohepatitis in Humans with Pluripotent Stem Cell-Derived Organoids. Cell Metab. 2019 Aug 6;30(2):374-384.e6.

Zhang, X; McGrath, PS; Salomone, J; Rahal, M; McCauley, HA; Schweitzer, J; Kovall, R; Gebelein, B; Wells, JM. A Comprehensive Structure-Function Study of Neurogenin3 Disease-Causing Alleles during Human Pancreas and Intestinal Organoid Development. Dev Cell. 2019 Aug 5;50(3):367-380.e7.

Yoder, LM; Higano, NS; Schapiro, AH; Fleck, RJ; Hysinger, EB; Bates, AJ; Kingma, PS; Merhar, SL; Fain, SB; Woods, JC. Elevated lung volumes in neonates with bronchopulmonary dysplasia measured via MRI. Pediatr Pulmonol. 2019 Aug;54(8):1311-1318.

Cornacchia, D; Zhang, C; Zimmer, B; Chung, SY; Fan, Y; Soliman, MA; Tchieu, J; Chambers, SM; Shah, H; Paull, D; Konrad, C; Vincendeau, M; Noggle, SA; Manfredi, G; Finley, LWS; Cross, JR; Betel, D; Studer, L. Lipid Deprivation Induces a Stable, Naive-to-Primed Intermediate State of Pluripotency in Human PSCs. Cell Stem Cell. 2019 Jul 3;25(1):120-136.e10.

Vatine, GD; Barrile, R; Workman, MJ; Sances, S; Barriga, BK; Rahnama, M; Barthakur, S; Kasendra, M; Lucchesi, C; Kerns, J; Wen, N; Spivia, WR; Chen, Z; Van Eyk, J; Svendsen, CN. Human iPSC-Derived Blood-Brain Barrier Chips Enable Disease Modeling and Personalized Medicine Applications. Cell Stem Cell. 2019 Jun 6;24(6):995-1005.e6.

Baumann, ME; Blackstone, BN; Malara, MM; Clairmonte, IA; Supp, DM; Bailey, JK; Powell, HM. Fractional CO 2 laser ablation of porcine burn scars after grafting: Is deeper better? Burns. 2020 Jun;46(4):937-948.

Bolte, C; Kalin, TV; Kalinichenko, VV. Molecular, cellular, and bioengineering approaches to stimulate lung regeneration after injury. Semin Cell Dev Biol. 2020 Apr;100:101-108.

Boyce, ST; Supp, DM; Lloyd, CM. Exogenous Keratinocyte Growth Factor Is Not Required for Pigmentation of Skin Substitutes with Three Isogeneic Cell Types. Tissue Eng Part A. 2020 Feb;26(3-4):214-224.

Blackstone, BN; Malara, MM; Baumann, ME; McFarland, K; Supp, DM; Powell, HM. Fractional CO 2 laser micropatterning of cell-seeded electrospun collagen scaffolds enables rete ridge formation in 3D engineered skin. Acta Biomater. 2020 Jan 15;102:287-297.

Zhang RR, Koido M, Tadokoro T, Ouchi R, Matsuno T, Ueno Y, Sekine K, Takebe T, Taniguchi H. Human iPSC-Derived Posterior Gut Progenitors Are Expandable and Capable of Forming Gut and Liver OrganoidsStem Cell Reports. 2018 Mar 13;10(3):780-793. 

Rankin SA, McCracken KW, Luedeke DM, Han L, Wells JM, Shannon JM, Zorn AM. Timing is everything: Reiterative Wnt, BMP and RA signaling regulate developmental competence during endoderm organogenesis. Dev Biol. 2018 Feb 1;434(1):121-132.

Karimi K, Fortriede JD, Lotay VS, Burns KA, Wang DZ, Fisher ME, Pells TJ, James-Zorn C, Wang Y, Ponferrada VG, Chu S, Chaturvedi P, Zorn AM, Vize PD. Xenbase: a genomic, epigenomic and transcriptomic model organism databaseNucleic Acids Res. 2018 Jan 4;46(D1):D861-D868.
Múnera JO, Sundaram N, Rankin SA, Hill D, Watson C, Mahe M, Vallance JE, Shroyer NF, Sinagoga KL, Zarzoso-Lacoste A, Hudson JR, Howell JC, Chatuvedi P,Spence JR, Shannon JM, Zorn AM, Helmrath MA, Wells JM. Differentiation of Human Pluripotent Stem Cells into Colonic Organoids via Transient Activation of BMP Signaling. Cell Stem Cell. 2017 Jul 6;21(1):51-64.e6.

Camp JG, Sekine K, Gerber T, Loeffler-Wirth H, Binder H, Gac M, Kanton S, Kageyama J, Damm G, Seehofer D, Belicova L, Bickle M, Barsacchi R, Okuda R, Yoshizawa E, Kimura M, Ayabe H, Taniguchi H, Takebe T, Treutlein B. Multilineage communication regulates human liver bud development from pluripotency. Nature.2017 Jun 22;546(7659):533-538.

Aslan Y, Tadjuidje E, Zorn AM, Cha SW. High-efficiency non-mosaic CRISPR-mediated knock-in and indel mutation in F0 Xenopus. Development. 2017 Aug 1;144(15):2852-2858.

Zorn AM. Development of the digestive system. Semin Cell Dev Biol. 2017 Jun;66:1-2.

Han L, Xu J, Grigg E, Slack M, Chaturvedi P, Jiang R, Zorn AM. Osr1 functions downstream of Hedgehog pathway to regulate foregut development. Dev Biol. 2017 Jul 1;427(1):72-83.

Sekine K, Takebe T, Taniguchi H. Liver Regeneration Using Cultured Liver BudMethods Mol Biol. 2017;1597:207-216.

Stevens ML, Chaturvedi P, Rankin SA, Macdonald M, Jagannathan S, Yukawa M, Barski A, Zorn AM. Genomic integration of Wnt/β-catenin and BMP/Smad1 signaling coordinates foregut and hindgut transcriptional programs. Development. 2017 Apr 1;144(7):1283-1295.

Asai A, Aihara E, Watson C, Mourya R, Mizuochi T, Shivakumar P, Phelan K, Mayhew C, Helmrath M, Takebe T, Wells J, Bezerra JA. Paracrine signals regulate human liver organoid maturation from induced pluripotent stem cells. Development. 2017 Mar 15;144(6):1056-1064.

Mahe MM, Brown NE, Poling HM, Helmrath MA. In Vivo Model of Small Intestine. Methods Mol Biol. 2017;1597:229-245.

Sinagoga KL, Stone WJ, Schiesser JV, Schweitzer JI, Sampson L, Zheng Y, Wells JM. Distinct roles for the mTOR pathway in postnatal morphogenesis, maturation and function of pancreatic islets. Development. 2017 Jul1;144(13):2402-2414.

Múnera JO, Wells JM. Generation of Gastrointestinal Organoids from Human Pluripotent Stem Cells. Methods Mol Biol. 2017;1597:167-177.

McCauley HA, Wells JM. Pluripotent stem cell-derived organoids: using principles of developmental biology to grow human tissues in a dish. Development. 2017 Mar 15;144(6):958-962.

McCracken KW, Wells JM. Mechanisms of embryonic stomach development. Semin Cell Dev Biol. 2017 Jun;66:36-42.

Arora N, Imran Alsous J, Guggenheim JW, Mak M, Munera J, Wells JM, Kamm RD,Asada HH, Shvartsman SY, Griffith LG. A process engineering approach to increase organoid yield. Development. 2017 Mar 15;144(6):1128-1136.

McCracken KW, Aihara E, Martin B, Crawford CM, Broda T, Treguier J, Zhang X,Shannon JM, Montrose MH, Wells JM. Wnt/β-catenin promotes gastric fundus specification in mice and humans. Nature. 2017 Jan 12;541(7636):182-187.

Workman MJ, Mahe MM, Trisno S, Poling HM, Watson CL, Sundaram N, Chang CF,Schiesser J, Aubert P, Stanley EG, Elefanty AG, Miyaoka Y, Mandegar MA, Conklin BR, Neunlist M, Brugmann SA, Helmrath MA, Wells JM. Engineered human pluripotent-stem-cell-derived intestinal tissues with a functional enteric nervous system. Nature Medicine. 2017 Jan;23(1):49-59.
Shinozawa T, Yoshikawa HY, Takebe T. Reverse engineering liver buds through self-driven condensation and organization towards medical application. Dev Biol. 2016 Dec 15;420(2):221-229.

Rankin SA, Han L, McCracken KW, Kenny AP, Anglin CT, Grigg EA, Crawford CM, Wells JM, Shannon JM, Zorn AM. A Retinoic Acid-Hedgehog Cascade Coordinates Mesoderm-Inducing Signals and Endoderm Competence during Lung Specification. Cell Rep. 2016 Jun 28;16(1):66-78.

Zhang Z, Rankin SA, Zorn AM. Syndecan4 coordinates Wnt/JNK and BMP signaling to regulate foregut progenitor development. Dev Biol. 2016 Aug 1;416(1):187-99.

McCauley HA, Wells JM. Sweet Relief: Reprogramming Gastric Endocrine Cells to Make Insulin. Cell Stem Cell. 2016 Mar 3;18(3):295-7.

Chlon TM, Ruiz-Torres S, Maag L, Mayhew CN, Wikenheiser-Brokamp KA, Davies SM, Mehta P, Myers KC, Wells JM, Wells SI. Overcoming Pluripotent Stem Cell Dependence on the Repair of Endogenous DNA Damage. Stem Cell Reports. 2016 Jan 12;6(1):44-54.

Wells JM. Regenerative medicine in 2015: Generating and regenerating the digestive system. Nat Rev Gastroenterol Hepatol. 2016 Feb;13(2):65-6.

Kurmann AA, Serra M, Hawkins F, Rankin SA, Mori M, Astapova I, Ullas S, Lin S, Bilodeau M, Rossant J, Jean JC, Ikonomou L, Deterding RR, Shannon JM, Zorn AM, Hollenberg AN, Kotton DN. Regeneration of Thyroid Function by Transplantation of Differentiated Pluripotent Stem Cells. Cell Stem Cell. 2015 Nov 5;17(5):527-42.

McGrath PS, Watson CL, Ingram C, Helmrath MA, Wells JM. The Basic Helix-Loop-Helix Transcription Factor NEUROG3 Is Required for Development of the Human Endocrine Pancreas. Diabetes. 2015 Jul;64(7):2497-505.

McGrath PS, Wells JM. SnapShot: GI tract development. Cell. 2015 Mar 26;161(1):176-176.e1.

Sinagoga KL, Wells JM. Generating human intestinal tissues from pluripotent stem cells to study development and disease. EMBO J. 2015 May 5;34(9):1149-63.

Dye BR, Hill DR, Ferguson MA, Tsai YH, Nagy MS, Dyal R, Wells JM, Mayhew CN, Nattiv R, Klein OD, White ES, Deutsch GH, Spence JR. In vitro generation of human pluripotent stem cell derived lung organoids. Elife. 2015 Mar 24;4.

Mahe MM, Sundaram N, Watson CL, Shroyer NF, Helmrath MA. Establishment of human epithelial enteroids and colonoids from whole tissue and biopsy. J Vis Exp. 2015 Mar 6;(97).

Wells JM. Developmental biology. Regional identity of gut stem cells--one gene to rule them all. Nat Rev Gastroenterol Hepatol. 2015 Mar;12(3):125-6.

McCracken KW, Catá EM, Crawford CM, Sinagoga KL, Schumacher M, Rockich BE,Tsai YH, Mayhew CN, Spence JR, Zavros Y, Wells JM. Modelling human development and disease in pluripotent stem-cell-derived gastric organoids. Nature. 2014 Dec 8;516(7531):400-4.

Watson CL, Mahe MM, Múnera J, Howell JC, Sundaram N, Poling HM, Schweitzer JI,Vallance JE, Mayhew CN, Sun Y, Grabowski G, Finkbeiner SR, Spence JR, Shroyer NF,Wells JM, Helmrath MA. An in vivo model of human small intestine using pluripotent stem cells. Nat Med. 2014 Nov;20(11):1310-4.