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Profile Publications(83)
XB-PERS-720

Publications By Aaron M. Zorn

Results 1 - 50 of 83 results

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Xenbase: deep integration of GEO & SRA RNA-seq and ChIP-seq data in a model organism database., Fortriede JD, Pells TJ, Chu S, Chaturvedi P, Wang D, Fisher ME, James-Zorn C, Wang Y, Nenni MJ, Burns KA, Lotay VS, Ponferrada VG, Karimi K, Zorn AM, Vize PD., Nucleic Acids Res. January 1, 2020; 48 (D1): D776-D782.      


Maximizing CRISPR/Cas9 phenotype penetrance applying predictive modeling of editing outcomes in Xenopus and zebrafish embryos., Naert T, Tulkens D, Edwards NA, Carron M, Shaidani NI, Wlizla M, Boel A, Demuynck S, Horb ME, Coucke P, Willaert A, Zorn AM, Vleminckx K., Sci Rep. January 1, 2020; 10 (1): 14662.                      


Sox17 and β-catenin co-occupy Wnt-responsive enhancers to govern the endoderm gene regulatory network., Mukherjee S, Chaturvedi P, Rankin SA, Fish MB, Wlizla M, Paraiso KD, MacDonald M, Chen X, Weirauch MT, Blitz IL, Cho KW, Zorn AM., Elife. January 1, 2020; 9                       


Xenbase: Facilitating the Use of Xenopus to Model Human Disease., Nenni MJ, Fisher ME, James-Zorn C, Pells TJ, Ponferrada V, Chu S, Fortriede JD, Burns KA, Wang Y, Lotay VS, Wang DZ, Segerdell E, Chaturvedi P, Karimi K, Vize PD, Zorn AM., Front Physiol. January 1, 2019; 10 154.          


Novel vectors for functional interrogation of Xenopus ORFeome coding sequences., Sterner ZR, Rankin SA, Wlizla M, Choi JA, Luedeke DM, Zorn AM, Buchholz DR., Genesis. January 1, 2019; 57 (10): e23329.        


Endosome-Mediated Epithelial Remodeling Downstream of Hedgehog-Gli Is Required for Tracheoesophageal Separation., Nasr T, Mancini P, Rankin SA, Edwards NA, Agricola ZN, Kenny AP, Kinney JL, Daniels K, Vardanyan J, Han L, Trisno SL, Cha SW, Wells JM, Kofron MJ, Zorn AM., Dev Cell. January 1, 2019; 51 (6): 665-674.e6.


Xenbase: a genomic, epigenomic and transcriptomic model organism database., 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., Nucleic Acids Res. January 1, 2018; 46 (D1): D861-D868.        


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


Navigating Xenbase: An Integrated Xenopus Genomics and Gene Expression Database., James-Zorn C, Ponferrada V, Fisher ME, Burns K, Fortriede J, Segerdell E, Karimi K, Lotay V, Wang DZ, Chu S, Pells T, Wang Y, Vize PD, Zorn A., Methods Mol Biol. January 1, 2018; 1757 251-305.


Evolutionarily conserved Tbx5-Wnt2/2b pathway orchestrates cardiopulmonary development., Steimle JD, Rankin SA, Slagle CE, Bekeny J, Rydeen AB, Chan SS, Kweon J, Yang XH, Ikegami K, Nadadur RD, Rowton M, Hoffmann AD, Lazarevic S, Thomas W, Boyle Anderson EAT, Horb ME, Luna-Zurita L, Ho RK, Kyba M, Jensen B, Zorn AM, Conlon FL, Moskowitz IP., Proc Natl Acad Sci U S A. January 1, 2018; 115 (45): E10615-E10624.                                  


Xenopus genomic data and browser resources., Vize PD, Zorn AM., Dev Biol. January 1, 2017; 426 (2): 194-199.  


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


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


Syndecan4 coordinates Wnt/JNK and BMP signaling to regulate foregut progenitor development., Zhang Z, Rankin SA, Zorn AM., Dev Biol. August 1, 2016; 416 (1): 187-199.                                  


Identification of genes expressed in the migrating primitive myeloid lineage of Xenopus laevis., Agricola ZN, Jagpal AK, Allbee AW, Prewitt AR, Shifley ET, Rankin SA, Zorn AM, Kenny AP., Dev Dyn. January 1, 2016; 245 (1): 47-55.                      


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


Genome evolution in the allotetraploid frog Xenopus laevis., Session AM, Uno Y, Kwon T, Chapman JA, Toyoda A, Takahashi S, Fukui A, Hikosaka A, Suzuki A, Kondo M, van Heeringen SJ, Quigley I, Heinz S, Ogino H, Ochi H, Hellsten U, Lyons JB, Simakov O, Putnam N, Stites J, Kuroki Y, Tanaka T, Michiue T, Watanabe M, Bogdanovic O, Lister R, Georgiou G, Paranjpe SS, van Kruijsbergen I, Shu S, Carlson J, Kinoshita T, Ohta Y, Mawaribuchi S, Jenkins J, Grimwood J, Schmutz J, Mitros T, Mozaffari SV, Suzuki Y, Haramoto Y, Yamamoto TS, Takagi C, Heald R, Miller K, Haudenschild C, Kitzman J, Nakayama T, Izutsu Y, Robert J, Fortriede J, Burns K, Lotay V, Karimi K, Yasuoka Y, Dichmann DS, Flajnik MF, Houston DW, Shendure J, DuPasquier L, Vize PD, Zorn AM, Ito M, Marcotte EM, Wallingford JB, Ito Y, Asashima M, Ueno N, Matsuda Y, Veenstra GJ, Fujiyama A, Harland RM, Taira M, Rokhsar DS., Nature. January 1, 2016; 538 (7625): 336-343.                              


Structure of Gremlin-2 in Complex with GDF5 Gives Insight into DAN-Family-Mediated BMP Antagonism., Nolan K, Kattamuri C, Rankin SA, Read RJ, Zorn AM, Thompson TB., Cell Rep. January 1, 2016; 16 (8): 2077-2086.          


The Xenopus ORFeome: A resource that enables functional genomics., Grant IM, Balcha D, Hao T, Shen Y, Trivedi P, Patrushev I, Fortriede JD, Karpinka JB, Liu L, Zorn AM, Stukenberg PT, Hill DE, Gilchrist MJ., Dev Biol. December 15, 2015; 408 (2): 345-57.          


Modeling human development and disease in Xenopus. Preface., LaBonne C, Zorn AM., Dev Biol. December 15, 2015; 408 (2): 179.


Regeneration of Thyroid Function by Transplantation of Differentiated Pluripotent Stem Cells., 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., Cell Stem Cell. November 5, 2015; 17 (5): 527-42.    


Xenbase: Core features, data acquisition, and data processing., James-Zorn C, Ponferrada VG, Burns KA, Fortriede JD, Lotay VS, Liu Y, Brad Karpinka J, Karimi K, Zorn AM, Vize PD., Genesis. August 1, 2015; 53 (8): 486-97.          


A Molecular atlas of Xenopus respiratory system development., Rankin SA, Thi Tran H, Wlizla M, Mancini P, Shifley ET, Bloor SD, Han L, Vleminckx K, Wert SE, Zorn AM., Dev Dyn. January 1, 2015; 244 (1): 69-85.                    


Xenbase, the Xenopus model organism database; new virtualized system, data types and genomes., Karpinka JB, Fortriede JD, Burns KA, James-Zorn C, Ponferrada VG, Lee J, Karimi K, Zorn AM, Vize PD., Nucleic Acids Res. January 1, 2015; 43 (Database issue): D756-63.    


Finding Our Way through Phenotypes., Deans AR, Lewis SE, Huala E, Anzaldo SS, Ashburner M, Balhoff JP, Blackburn DC, Blake JA, Burleigh JG, Chanet B, Cooper LD, Courtot M, Csösz S, Cui H, Dahdul W, Das S, Dececchi TA, Dettai A, Diogo R, Druzinsky RE, Dumontier M, Franz NM, Friedrich F, Gkoutos GV, Haendel M, Harmon LJ, Hayamizu TF, He Y, Hines HM, Ibrahim N, Jackson LM, Jaiswal P, James-Zorn C, Köhler S, Lecointre G, Lapp H, Lawrence CJ, Le Novère N, Lundberg JG, Macklin J, Mast AR, Midford PE, Mikó I, Mungall CJ, Oellrich A, Osumi-Sutherland D, Parkinson H, Ramírez MJ, Richter S, Robinson PN, Ruttenberg A, Schulz KS, Segerdell E, Seltmann KC, Sharkey MJ, Smith AD, Smith B, Specht CD, Squires RB, Thacker RW, Thessen A, Fernandez-Triana J, Vihinen M, Vize PD, Vogt L, Wall CE, Walls RL, Westerfeld M, Wharton RA, Wirkner CS, Woolley JB, Yoder MJ, Zorn AM, Mabee P., PLoS Biol. January 1, 2015; 13 (1): e1002033.    


A New Nomenclature of Xenopus laevis Chromosomes Based on the Phylogenetic Relationship to Silurana/Xenopus tropicalis., Matsuda Y, Uno Y, Kondo M, Gilchrist MJ, Zorn AM, Rokhsar DS, Schmid M, Taira M., Cytogenet Genome Res. January 1, 2015; 145 (3-4): 187-91.


Gene regulatory networks governing lung specification., Rankin SA, Zorn AM., J Cell Biochem. August 1, 2014; 115 (8): 1343-50.


Enhanced XAO: the ontology of Xenopus anatomy and development underpins more accurate annotation of gene expression and queries on Xenbase., Segerdell E, Ponferrada VG, James-Zorn C, Burns KA, Fortriede JD, Dahdul WM, Vize PD, Zorn AM., J Biomed Semantics. October 18, 2013; 4 (1): 31.      


Structure of protein related to Dan and Cerberus: insights into the mechanism of bone morphogenetic protein antagonism., Nolan K, Kattamuri C, Luedeke DM, Deng X, Jagpal A, Zhang F, Linhardt RJ, Kenny AP, Zorn AM, Thompson TB., Structure. August 6, 2013; 21 (8): 1417-29.


Different thresholds of Wnt-Frizzled 7 signaling coordinate proliferation, morphogenesis and fate of endoderm progenitor cells., Zhang Z, Rankin SA, Zorn AM., Dev Biol. June 1, 2013; 378 (1): 1-12.                              


Xenbase: expansion and updates of the Xenopus model organism database., James-Zorn C, Ponferrada VG, Jarabek CJ, Burns KA, Segerdell EJ, Lee J, Snyder K, Bhattacharyya B, Karpinka JB, Fortriede J, Bowes JB, Zorn AM, Vize PD., Nucleic Acids Res. January 1, 2013; 41 (Database issue): D865-70.    


The Xenbase literature curation process., Bowes JB, Snyder KA, James-Zorn C, Ponferrada VG, Jarabek CJ, Burns KA, Bhattacharyya B, Zorn AM, Vize PD., Database (Oxford). January 1, 2013; 2013 bas046.    


Par6b regulates the dynamics of apicobasal polarity during development of the stratified Xenopus epidermis., Wang S, Cha SW, Zorn AM, Wylie C., PLoS One. January 1, 2013; 8 (10): e76854.                      


Prolonged FGF signaling is necessary for lung and liver induction in Xenopus., Shifley ET, Kenny AP, Rankin SA, Zorn AM., BMC Dev Biol. December 17, 2012; 12 27.                      


Sizzled-tolloid interactions maintain foregut progenitors by regulating fibronectin-dependent BMP signaling., Kenny AP, Rankin SA, Allbee AW, Prewitt AR, Zhang Z, Tabangin ME, Shifley ET, Louza MP, Zorn AM., Dev Cell. August 14, 2012; 23 (2): 292-304.                                


Suppression of Bmp4 signaling by the zinc-finger repressors Osr1 and Osr2 is required for Wnt/β-catenin-mediated lung specification in Xenopus., Rankin SA, Gallas AL, Neto A, Gómez-Skarmeta JL, Zorn AM., Development. August 1, 2012; 139 (16): 3010-20.                                                                                


CRIM1 complexes with ß-catenin and cadherins, stabilizes cell-cell junctions and is critical for neural morphogenesis., Ponferrada VG, Fan J, Vallance JE, Hu S, Mamedova A, Rankin SA, Kofron M, Zorn AM, Hegde RS, Lang RA., PLoS One. January 1, 2012; 7 (3): e32635.                        


New doxycycline-inducible transgenic lines in Xenopus., Rankin SA, Zorn AM, Buchholz DR., Dev Dyn. June 1, 2011; 240 (6): 1467-74.        


A gene regulatory network controlling hhex transcription in the anterior endoderm of the organizer., Rankin SA, Kormish J, Kofron M, Jegga A, Zorn AM., Dev Biol. March 15, 2011; 351 (2): 297-310.                            


Directed differentiation of human pluripotent stem cells into intestinal tissue in vitro., Spence JR, Mayhew CN, Rankin SA, Kuhar MF, Vallance JE, Tolle K, Hoskins EE, Kalinichenko VV, Wells SI, Zorn AM, Shroyer NF, Wells JM., Nature. February 3, 2011; 470 (7332): 105-9.      


The genome of the Western clawed frog Xenopus tropicalis., Hellsten U, Harland RM, Gilchrist MJ, Hendrix D, Jurka J, Kapitonov V, Ovcharenko I, Putnam NH, Shu S, Taher L, Blitz IL, Blumberg B, Dichmann DS, Dubchak I, Amaya E, Detter JC, Fletcher R, Gerhard DS, Goodstein D, Graves T, Grigoriev IV, Grimwood J, Kawashima T, Lindquist E, Lucas SM, Mead PE, Mitros T, Ogino H, Ohta Y, Poliakov AV, Pollet N, Robert J, Salamov A, Sater AK, Schmutz J, Terry A, Vize PD, Warren WC, Wells D, Wills A, Wilson RK, Zimmerman LB, Zorn AM, Grainger R, Grammer T, Khokha MK, Richardson PM, Rokhsar DS., Science. April 30, 2010; 328 (5978): 633-6.


Xenbase: gene expression and improved integration., Bowes JB, Snyder KA, Segerdell E, Jarabek CJ, Azam K, Zorn AM, Vize PD., Nucleic Acids Res. January 1, 2010; 38 (Database issue): D607-12.      


Improved cre reporter transgenic Xenopus., Rankin SA, Hasebe T, Zorn AM, Buchholz DR., Dev Dyn. September 1, 2009; 238 (9): 2401-8.          


Rasip1 is required for endothelial cell motility, angiogenesis and vessel formation., Xu K, Chong DC, Rankin SA, Zorn AM, Cleaver O., Dev Biol. May 15, 2009; 329 (2): 269-79.      


Vertebrate endoderm development and organ formation., Zorn AM, Wells JM., Annu Rev Cell Dev Biol. January 1, 2009; 25 221-51.


Sfrp5 coordinates foregut specification and morphogenesis by antagonizing both canonical and noncanonical Wnt11 signaling., Li Y, Rankin SA, Sinner D, Kenny AP, Krieg PA, Zorn AM., Genes Dev. November 1, 2008; 22 (21): 3050-63.                        


spib is required for primitive myeloid development in Xenopus., Costa RM, Soto X, Chen Y, Zorn AM, Amaya E., Blood. September 15, 2008; 112 (6): 2287-96.                                      


The efficiency of Xenopus primordial germ cell migration depends on the germplasm mRNA encoding the PDZ domain protein Grip2., Kirilenko P, Weierud FK, Zorn AM, Woodland HR., Differentiation. April 1, 2008; 76 (4): 392-403.                    


Sox17 and Sox4 differentially regulate beta-catenin/T-cell factor activity and proliferation of colon carcinoma cells., Sinner D, Kordich JJ, Spence JR, Opoka R, Rankin S, Lin SC, Jonatan D, Zorn AM, Wells JM., Mol Cell Biol. November 1, 2007; 27 (22): 7802-15.                


Repression of Wnt/beta-catenin signaling in the anterior endoderm is essential for liver and pancreas development., McLin VA, Rankin SA, Zorn AM., Development. June 1, 2007; 134 (12): 2207-17.            

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