2024
Protocol for optical, aqueous-based clearing of murine tissues using EZ Clear
STAR Protocols
Taeyong Ahn, Gabrielle E Largoza, Julia Younis; RE-JOIN Consortium; Mary E Dickinson, Chih-Wei Hsu, Joshua D Wythe
PMID: 38704833 / PMCID: PMC11089399 / DOI: 10.1016/j.xpro.2024.103053
2023
Three-dimensional microCT imaging of mouse heart development from early post-implantation to late fetal stages
Mammalian Genome
Nanbing Li-Villarreal, Tara L Rasmussen, Audrey E Christiansen, Mary E Dickinson, Chih-Wei Hsu
PMID: 36595063 / PMCID: PMC10290591 / DOI: 10.1007/s00335-022-09976-7
Comparative embryology of Delphinapterus leucas (beluga whale), Balaena mysticetus (bowhead whale), and Stenella attenuata (pan-tropical spotted dolphin) (Cetacea: Mammalia)
Journal of Morphology
Lia Gavazzi, Lisa N. Cooper, Sharon Usip, Robert Suydam, Raphaela Stimmelmayr, John C. George, Greg O'Corry-Crowe, Chih-Wei Hsu, Johannes Thewissen
PMID: 36538588 / PMCID: PMC10107513 / DOI: 10.1002/jmor.21543
Rewired m6A epitranscriptomic networks link mutant p53 to neoplastic transformation
Nature Communications
An Xu, Mo Liu, Mo-Fan Huang, Yang Zhang, Ruifeng Hu, Julian A. Gingold, Ying Liu, Dandan Zhu, Chian-Shiu Chien, Wei-Chen Wang, Zian Liao, Fei Yuan, Chih-Wei Hsu, Jian Tu, Yao Yu, Taylor Rosen, Feng Xiong, Peilin Jia, Yi-Ping Yang, Danielle A. Bazer, Ya-Wen Chen, Wenbo Li, Chad D. Huff, Jay-Jiguang Zhu, Francesca Aguilo, Shih-Hwa Chiou, Nathan C. Boles, Chien-Chen Lai, Mien-Chie Hung, Zhongming Zhao, Eric L. Van Nostrand, Ruiying Zhao, Dung-Fang Lee
PMID: 36973285 / PMCID: PMC10042811 / DOI: 10.1038/s41467-023-37398-9
2022
Mendelian gene identification through mouse embryo viability screening
Genome Medicine
Pilar Cacheiro, Carl Henrik Westerberg, Jesse Mager, Mary E Dickinson, Lauryl M J Nutter, Violeta Muñoz-Fuentes, Chih-Wei Hsu, Ignatia B Van den Veyver, Ann M Flenniken, Colin McKerlie, Stephen A Murray, Lydia Teboul, Jason D Heaney, K C Kent Lloyd, Louise Lanoue, Robert E Braun, Jacqueline K White, Amie K Creighton, Valerie Laurin, Ruolin Guo, Dawei Qu, Sara Wells, James Cleak, Rosie Bunton-Stasyshyn, Michelle Stewart, Jackie Harrisson, Jeremy Mason, Hamed Haseli Mashhadi, Helen Parkinson, Ann-Marie Mallon; International Mouse Phenotyping Consortium; Genomics England Research Consortium; Damian Smedley
PMID: 36229886 / PMCID: PMC9563108 / DOI: 10.1186/s13073-022-01118-7
EZ Clear for simple, rapid, and robust mouse whole organ clearing
eLife
Chih-Wei Hsu, Juan Cerda 3rd, Jason M Kirk, Williamson D Turner, Tara L Rasmussen, Carlos P Flores Suarez, Mary E Dickinson, Joshua D Wythe
PMID: 36218247 / PMCID: PMC9555867 / DOI: 10.7554/eLife.77419
Extensive identification of genes involved in congenital and structural heart disorders and cardiomyopathy
Nature Cardiovascular Research
Nadine Spielmann, Gregor Miller, Tudor I. Oprea, Chih-Wei Hsu, Gisela Fobo, Goar Frishman, Corinna Montrone, Hamed Haseli Mashhadi, Jeremy Mason, Violeta Munoz Fuentes, Stefanie Leuchtenberger, Andreas Ruepp, Matias Wagner, Dominik S. Westphal, Cordula Wolf, Agnes Görlach, Adrián Sanz-Moreno, Yi-Li Cho, Raffaele Teperino, Stefan Brandmaier, Sapna Sharma, Isabella Rikarda Galter, Manuela A. Östereicher, Lilly Zapf, Philipp Mayer-Kuckuk, Jan Rozman, Lydia Teboul, Rosie K. A. Bunton-Stasyshyn, Heather Cater, Michelle Stewart, Skevoulla Christou, Henrik Westerberg, Amelia M. Willett, Janine M. Wotton, Willson B. Roper, Audrey E. Christiansen, Christopher S. Ward, Jason D. Heaney, Corey L. Reynolds, Jan Prochazka, Lynette Bower, David Clary, Mohammed Selloum, Ghina Bou About, Olivia Wendling, Hugues Jacobs, Sophie Leblanc, Hamid Meziane, Tania Sorg, Enrique Audain, Arthur Gilly, Nigel W. Rayner, IMPC consortium, Genomics England Research Consortium, Marc-Phillip Hitz, Eleftheria Zeggini, Eckhard Wolf, Radislav Sedlacek, Steven A. Murray, Karen L. Svenson, Robert E. Braun, Jaqueline K. White, Lois Kelsey, Xiang Gao, Toshihiko Shiroishi, Ying Xu, Je Kyung Seong, Fabio Mammano, Glauco P. Tocchini-Valentini, Arthur L. Beaudet, Terrence F. Meehan, Helen Parkinson, Damian Smedley, Ann-Marie Mallon, Sara E. Wells, Harald Grallert, Wolfgang Wurst, Susan Marschall, Helmut Fuchs, Steve D. M. Brown, Ann M. Flenniken, Lauryl M. J. Nutter, Colin McKerlie, Yann Herault, K. C. Kent Lloyd, Mary E. Dickinson, Valerie Gailus-Durner, Martin Hrabe de Angelis
2020
Mouse models to study the pathophysiology of combined methylmalonic acidemia and homocystinuria, cblC type
Developmental Biology
Tiffany Chern, Annita Achilleos, Xuefei Tong, Chih-Wei Hsu, Leeyean Wong, Ross A. Poché
PMID: 32941884 \ PMCID: PMC7669717 \ DOI: 10.1016/j.ydbio.2020.09.005
A global Slc7a7 knockout mouse model demonstrates characteristic phenotypes of human lysinuric protein intolerance
Human Molecular Genetics
Bridget M Stroup, Ronit Marom, Xiaohui Li, Chih-Wei Hsu, Cheng-Yen Chang, Luan D Truong, Brian Dawson, Ingo Grafe, Yuqing Chen, Ming-Ming Jiang, Denise Lanza, Jennie Rose Green, Qin Sun, J P Barrish, Safa Ani, Audrey E Christiansen, John R Seavitt, Mary E Dickinson, Farrah Kheradmand, Jason D Heaney, Brendan Lee, Lindsay C Burrage
PMID: 32504080 \ PMCID: PMC7399531 \ DOI: 10.1093/hmg/ddaa107
Bioinformatics
Hamed Haselimashhadi, Jeremy C Mason, Violeta Munoz-Fuentes, Federico López-Gómez, Kolawole Babalola, Elif F Acar, Vivek Kumar, Jacqui White, Ann M Flenniken, Ruairidh King, Ewan Straiton, John Richard Seavitt, Angelina Gaspero, Arturo Garza, Audrey E Christianson, Chih-Wei Hsu, Corey L Reynolds, Denise G Lanza, Isabel Lorenzo, Jennie R Green, Juan J Gallegos, Ritu Bohat, Rodney C Samaco, Surabi Veeraragavan, Jong Kyoung Kim, Gregor Miller, Helmult Fuchs, Lillian Garrett, Lore Becker, Yeon Kyung Kang, David Clary, Soo Young Cho, Masaru Tamura, Nobuhiko Tanaka, Kyung Dong Soo, Alexandr Bezginov, Ghina Bou About, Marie-France Champy, Laurent Vasseur, Sophie Leblanc, Hamid Meziane, Mohammed Selloum, Patrick T Reilly, Nadine Spielmann, Holger Maier, Valerie Gailus-Durner, Tania Sorg, Masuya Hiroshi, Obata Yuichi, Jason D Heaney, Mary E Dickinson, Wurst Wolfgang, Glauco P Tocchini-Valentini, Kevin C Kent Lloyd, Colin McKerlie, Je Kyung Seong, Herault Yann, Martin Hrabé de Angelis, Steve D M Brown, Damian Smedley, Paul Flicek, Ann-Marie Mallon, Helen Parkinson, Terrence F Meehan
PMID: 31591642 / PMCID: PMC7115897 / DOI: 10.1093/bioinformatics/btz744
Soft windowing application to improve analysis of high-throughput phenotyping data
Human and mouse essentiality screens as a resource for disease gene discovery
Nature Communications
Pilar Cacheiro, Violeta Muñoz-Fuentes, Stephen A. Murray, Mary E. Dickinson, Maja Bucan, Lauryl M. J. Nutter, Kevin A. Peterson, Hamed Haselimashhadi, Ann M. Flenniken, Hugh Morgan, Henrik Westerberg, Tomasz Konopka, Chih-Wei Hsu, Audrey Christiansen, Denise G. Lanza, Arthur L. Beaudet, Jason D. Heaney, Helmut Fuchs, Valerie Gailus-Durner, Tania Sorg, Jan Prochazka, Vendula Novosadova, Christopher J. Lelliott, Hannah Wardle-Jones, Sara Wells, Lydia Teboul, Heather Cater, Michelle Stewart, Tertius Hough, Wolfgang Wurst, Radislav Sedlacek, David J. Adams, John R. Seavitt, Glauco Tocchini-Valentini, Fabio Mammano, Robert E. Braun, Colin McKerlie, Yann Herault, Martin Hrabě de Angelis, Ann-Marie Mallon, K. C. Kent Lloyd, Steve D. M. Brown, Helen Parkinson, Terrence F. Meehan, Damian Smedley, The Genomics England Research Consortium & The International Mouse Phenotyping Consortium
PMID: 32005800 / PMCID: PMC6994715 / DOI: 10.1038/s41467-020-14284-2
2019
High Resolution Imaging of Mouse Embryos and Neonates with X-Ray Micro-Computed Tomography
Current Protocols in Mouse Biology
Chih-Wei Hsu, Sowmya Kalaga, Uchechukwu Akoma, Tara L. Rasmussen, Audrey E. Christiansen, Mary E. Dickinson
PMID: 31195428 \ PMCID: PMC6594408 \ DOI: 10.1002/cpmo.63
New models for human disease from the International Mouse Phenotyping Consortium
Mammalian Genome
Pilar Cacheiro, Melissa A Haendel, Damian Smedley; International Mouse Phenotyping Consortium and the Monarch Initiative
PMID: 31127358 / PMCID: PMC6606664 / DOI: 10.1007/s00335-019-09804-5
2018
The effects of reduced hemodynamic loading on morphogenesis of the mouse embryonic heart
Developmental Biology
Tanner G. Hoog, Samantha J. Fredrickson, Chih-Wei Hsu, Steven M. Senger, Mary E. Dickinson, Ryan S. Udan
PMID: 30012423 / DOI: 10.1016/j.ydbio.2018.07.007
Rapid and Integrative Discovery of Retina Regulatory Molecules
Cell Reports
Nicholas E Albrecht, Jonathan Alevy, Danye Jiang, Courtney A Burger, Brian I Liu, Fenge Li, Julia Wang, Seon-Young Kim, Chih-Wei Hsu, Sowmya Kalaga, Uchechukwu Udensi, Chinwe Asomugha, Ritu Bohat, Angelina Gaspero, Monica J Justice, Peter D Westenskow, Shinya Yamamoto, John R Seavitt, Arthur L Beaudet, Mary E Dickinson, Melanie A Samuel
PMID: 30157441 / PMCID: PMC6170014 / DOI: 10.1016/j.celrep.2018.07.090
The role of FREM2 and FRAS1 in the development of congenital diaphragmatic hernia
Human Molecular Genetics
Valerie K Jordan, Tyler F Beck, Andres Hernandez-Garcia, Peter N Kundert, Bum-Jun Kim, Shalini N Jhangiani, Tomasz Gambin, Molly Starkovich, Jaya Punetha, Ingrid S Paine, Jennifer E Posey, Alexander H Li, Donna Muzny, Chih-Wei Hsu, Amber J Lashua, Xin Sun, Caraciolo J Fernandes, Mary E Dickinson, Kevin P Lally, Richard A Gibbs, Eric Boerwinkle, James R Lupski, Daryl A Scott
PMID: 29618029 / PMCID: PMC5985720 / DOI: 10.1093/hmg/ddy110
2017
Loss of Apela Peptide in Mice Causes Low Penetrance Embryonic Lethality and Defects in Early Mesodermal Derivatives
Cell Reports
Laina Freyer, Chih-Wei Hsu, Sonja Nowotschin, Andrea Pauli, Junji Ishida, Keiji Kuba, Akiyoshi Fukamizu, Alexander F Schier, Pamela A Hoodless, Mary E Dickinson, Anna-Katerina Hadjantonakis
PMID: 28854362 / PMCID: PMC5580402 / DOI: 10.1016/j.celrep.2017.08.014
Tubulogenesis of co-cultured human iPS-derived endothelial cells and human mesenchymal stem cells in fibrin and gelatin methacrylate gels
Biomaterial Science
Gisele A Calderon, Patricia Thai, Chih-Wei Hsu, Bagrat Grigoryan, Sydney M Gibson, Mary E Dickinson, Jordan S Miller
PMID: 28661522 / DOI: 10.1039/c7bm00223h
2016
Three-dimensional microCT imaging of mouse development from early post-implantation to early postnatal stages
Developmental Biology
Chih-Wei Hsu, Leeyean Wong, Tara L Rasmussen, Sowmya Kalaga, Melissa L McElwee, Lance C Keith, Ritu Bohat, John R Seavitt, Arthur L Beaudet, Mary E Dickinson
PMID: 27671873 / PMCID: PMC5405732 / DOI: 10.1016/j.ydbio.2016.09.011
High-throughput discovery of novel developmental phenotypes
Nature
Mary E Dickinson, Ann M Flenniken, Xiao Ji, Lydia Teboul, Michael D Wong, Jacqueline K White, Terrence F Meehan, Wolfgang J Weninger, Henrik Westerberg, Hibret Adissu, Candice N Baker, Lynette Bower, James M Brown, L Brianna Caddle, Francesco Chiani, Dave Clary, James Cleak, Mark J Daly, James M Denegre, Brendan Doe, Mary E Dolan, Sarah M Edie, Helmut Fuchs, Valerie Gailus-Durner, Antonella Galli, Alessia Gambadoro, Juan Gallegos, Shiying Guo, Neil R Horner, Chih-Wei Hsu, Sara J Johnson, Sowmya Kalaga, Lance C Keith, Louise Lanoue, Thomas N Lawson, Monkol Lek, Manuel Mark, Susan Marschall, Jeremy Mason, Melissa L McElwee, Susan Newbigging, Lauryl M J Nutter, Kevin A Peterson, Ramiro Ramirez-Solis, Douglas J Rowland, Edward Ryder, Kaitlin E Samocha, John R Seavitt, Mohammed Selloum, Zsombor Szoke-Kovacs, Masaru Tamura, Amanda G Trainor, Ilinca Tudose, Shigeharu Wakana, Jonathan Warren, Olivia Wendling, David B West, Leeyean Wong, Atsushi Yoshiki; International Mouse Phenotyping Consortium; Jackson Laboratory; Infrastructure Nationale PHENOMIN, Institut Clinique de la Souris (ICS); Charles River Laboratories; MRC Harwell; Toronto Centre for Phenogenomics; Wellcome Trust Sanger Institute; RIKEN BioResource Center; Daniel G MacArthur, Glauco P Tocchini-Valentini, Xiang Gao, Paul Flicek, Allan Bradley, William C Skarnes, Monica J Justice, Helen E Parkinson, Mark Moore, Sara Wells, Robert E Braun, Karen L Svenson, Martin Hrabe de Angelis, Yann Herault, Tim Mohun, Ann-Marie Mallon, R Mark Henkelman, Steve D M Brown, David J Adams, K C Kent Lloyd, Colin McKerlie, Arthur L Beaudet, Maja Bućan, Stephen A Murray
PMID: 27626380 / PMCID: PMC5295821 / DOI: 10.1038/nature19356
Lineage tracing of Sox2-expressing progenitor cells in the mouse inner ear reveals a broad contribution to non-sensory tissues and insights into the origin of the organ of Corti
Developmental Biology
Rende Gu, Rogers M Brown 2nd, Chih-Wei Hsu, Tiantian Cai, Alyssa L Crowder, Victor G Piazza, Tegy J Vadakkan, Mary E Dickinson, Andrew K Groves
PMID: 27090805 / PMCID: PMC4875846 / DOI: 10.1016/j.ydbio.2016.03.027
RONIN Is an Essential Transcriptional Regulator of Genes Required for Mitochondrial Function in the Developing Retina
Cell Reports
Ross A Poché, Min Zhang, Elda M Rueda, Xuefei Tong, Melissa L McElwee, Leeyean Wong, Chih-Wei Hsu, Marion Dejosez, Alan R Burns, Donald A Fox, James F Martin, Thomas P Zwaka, Mary E Dickinson
PMID: 26876175 / PMCID: PMC4767647 / DOI: 10.1016/j.celrep.2016.01.039
Yap and Taz play a crucial role in neural crest-derived craniofacial development
Development
Jun Wang, Yang Xiao, Chih-Wei Hsu, Idaliz M Martinez-Traverso, Min Zhang, Yan Bai, Mamoru Ishii, Robert E Maxson, Eric N Olson, Mary E Dickinson, Joshua D Wythe, James F Martin
PMID: 26718006 / PMCID: PMC4760309 / DOI: 10.1242/dev.126920
2015
Improved Angiogenesis in Response to Localized Delivery of Macrophage-Recruiting Molecules
PLoS One
Chih-Wei Hsu, Ross A Poché, Jennifer E Saik, Saniya Ali, Shang Wang, Nejla Yosef, Gisele A Calderon, Larry Scott Jr, Tegy J Vadakkan, Irina V Larina, Jennifer L West, Mary E Dickinson
PMID: 26132702 / PMCID: PMC4489184 / DOI: 10.1371/journal.pone.0131643
Macrophages engulf endothelial cell membrane particles preceding pupillary membrane capillary regression
Developmental Biology
Ross A Poché, Chih-Wei Hsu, Melissa L McElwee, Alan R Burns, Mary E Dickinson
PMID: 25912686 / PMCID: PMC4469537 / DOI: 10.1016/j.ydbio.2015.03.017
2014
Quantitative imaging of cell dynamics in mouse embryos using light-sheet microscopy
Development
Ryan S Udan, Victor G Piazza, Chih-Wei Hsu, Anna-Katerina Hadjantonakis, Mary E Dickinson
PMID: 25344073 / PMCID: PMC4302910 / DOI: 10.1242/dev.111021
2011
Visible light photoinitiation of mesenchymal stem cell-laden bioresponsive hydrogels
European Cells & Materials
Chelsea S Bahney, T.J. Lujan, Chih-Wei Hsu, M Bottling, Jennifer L West, Brian Johnstone
PMID: 21761391 / PMCID: PMC5050040 / DOI: 10.22203/ecm.v022a04
Cathepsin K-sensitive poly(ethylene glycol) hydrogels for degradation in response to bone resorption
Journal of Biomedical Materials Research, PART A
Chih-Wei Hsu, Ronke M Olabisi, Elizabeth A Olmsted-Davis, Alan R Davis, Jennifer L West
PMID: 21523904 / DOI: 10.1002/jbm.a.33076
A bioresponsive hydrogel tuned to chondrogenesis of human mesenchymal stem cells
FASEB Journal
Chelsea S Bahney, Chih-Wei Hsu, Jung U Yoo, Jennifer L West, Brian Johnstone
PMID: 21282205 / PMCID: PMC6188228 / DOI: 10.1096/fj.10-165514
2004 - 2007
Increased expression of extracellular matrix proteins in rapid atrial pacing-induced atrial fibrillation
Heart Rhythm
Chih-Sheng Lin, Ling-Ping Lai, Jiunn-Lee Lin, Yu-Ling Sun, Chih-Wei Hsu, Chien-Lung Chen, Simon J T Mao, Shoei K Stephen Huang
PMID: 17599682 / DOI: 10.1016/j.hrthm.2007.03.034
Differentially transcribed genes in skeletal muscle of Duroc and Taoyuan pigs
Gene transfections with p53 and p21 inhibit cell proliferation, collagen type I, leukemia inhibitory factor, and tumor necrosis factor-alpha expression in leiomyoma cells
FASEB Journal
Yao-Yuan Hsieh, Chi-Chen Chang, Chih-Wei Hsu, Chich-Sheng Lin
PMID: 15193492 / DOI: 10.1016/j.fertnstert.2004.02.062