Matsui, Satoshi; Granitto, Marissa; Buckley, Morgan; Ludwig, Katie; Koigi, Sandra; Shiley, Joseph; Zacharias, William J; Mayhew, Christopher N; Lim, Hee-Woong; Iwafuchi, Makiko 2024. Pioneer and PRDM transcription factors coordinate bivalent epigenetic states to safeguard cell fate. Molecular cell, 84 3, 476-489.e10
Alarcon, Pablo C; Damen, Michelle S M A; Ulanowicz, Cassidy J; Sawada, Keisuke; Oates, Jarren R; Toth, Andrea; Wayland, Jennifer L; Chung, Hak; Stankiewicz, Traci E; Moreno-Fernandez, Maria E; Szabo, Sara; Zacharias, William J; Divanovic, Senad 2023. Obesity amplifies influenza virus-driven disease severity in male and female mice. Mucosal immunology, 16 6, 843-858
Guo, Minzhe; Wikenheiser-Brokamp, Kathryn A; Kitzmiller, Joseph A; Jiang, Cheng; Wang, Guolun; Wang, Allen; Preissl, Sebastian; Hou, Xiaomeng; Buchanan, Justin; Karolak, Justyna A; Miao, Yifei; Frank, David B; Zacharias, William J; Sun, Xin; Xu, Yan; Gu, Mingxia; Stankiewicz, Pawel; Kalinichenko, Vladimir V; Wambach, Jennifer A; Whitsett, Jeffrey A 2023. Single Cell Multiomics Identifies Cells and Genetic Networks Underlying Alveolar Capillary Dysplasia. American journal of respiratory and critical care medicine, 208 6, 709-725
He, Hua; Bell, Sheila M; Davis, Ashley Kuenzi; Zhao, Shuyang; Sridharan, Anusha; Na, Cheng-Lun; Guo, Minzhe; Xu, Yan; Snowball, John; Swarr, Daniel T; Zacharias, William J; Whitsett, Jeffrey A 2023. PRDM3/16 Regulate Chromatin Accessibility Required for NKX2-1 Mediated Alveolar Epithelial Differentiation and Function. bioRxiv : the preprint server for biology, ,
Reza, Abid A; Kohram, Fatemeh; Reza, Hasan A; Kalin, Timothy R; Kannan, Paranthaman S; Zacharias, William J; Kalinichenko, Vladimir V 2023. FOXF1 Regulates Alveolar Epithelial Morphogenesis through Transcriptional Activation of Mesenchymal WNT5A. American journal of respiratory cell and molecular biology, 68 4, 430-443
Toth, Andrea; Kannan, Paranthaman; Snowball, John; Kofron, Matthew; Wayman, Joseph A; Bridges, James P; Miraldi, Emily R; Swarr, Daniel; Zacharias, William J 2023. Alveolar epithelial progenitor cells require Nkx2-1 to maintain progenitor-specific epigenomic state during lung homeostasis and regeneration. Nature communications, 14 1, 8452
Wilburn, Adrienne N; McAlees, Jaclyn W; Haslam, David B; Graspeuntner, Simon; Schmudde, Inken; Laumonnier, Yves; Rupp, Jan; Chougnet, Claire A; Deshmukh, Hitesh; Zacharias, William J; König, Peter; Lewkowich, Ian P 2023. Delayed Microbial Maturation Durably Exacerbates Th17-driven Asthma in Mice. American journal of respiratory cell and molecular biology, 68 5, 498-510
Jackson, Courtney M; Demmert, Martin; Mukherjee, Shibabrata; Isaacs, Travis; Thompson, Ravyn; Chastain, Chase; Gray, Jerilyn; Senthamaraikannan, Paranth; Presicce, Pietro; Chetal, Kashish; Salomonis, Nathan; Miller, Lisa A; Jobe, Alan H; Kallapur, Suhas G; Zacharias, William J; Lewkowich, Ian P; Deshmukh, Hitesh; Chougnet, Claire A 2022. A potent myeloid response is rapidly activated in the lungs of premature Rhesus macaques exposed to intra-uterine inflammation. Mucosal immunology, 15 4, 730-744
Khattar, Divya; Fernandes, Sharlene; Snowball, John; Guo, Minzhe; Gillen, Matthew C; Jain, Suchi Singh; Sinner, Debora; Zacharias, William; Swarr, Daniel T 2022. PI3K signaling specifies proximal-distal fate by driving a developmental gene regulatory network in SOX9+ mouse lung progenitors. eLife, 11 ,
Stevens, Joseph; Steinmeyer, Shelby; Bonfield, Madeline; Peterson, Laura; Wang, Timothy; Gray, Jerilyn; Lewkowich, Ian; Xu, Yan; Du, Yina; Guo, Minzhe; Wynn, James L; Zacharias, William; Salomonis, Nathan; Miller, Lisa; Chougnet, Claire; O'Connor, Dennis Hartigan; Deshmukh, Hitesh 2022. The balance between protective and pathogenic immune responses to pneumonia in the neonatal lung is enforced by gut microbiota. Science translational medicine, 14 649, eabl3981
Sun, Xin; Perl, Anne-Karina; Li, Rongbo; Bell, Sheila M; Sajti, Eniko; Kalinichenko, Vladimir V; Kalin, Tanya V; Misra, Ravi S; Deshmukh, Hitesh; Clair, Geremy; Kyle, Jennifer; Crotty Alexander, Laura E; Masso-Silva, Jorge A; Kitzmiller, Joseph A; Wikenheiser-Brokamp, Kathryn A; Deutsch, Gail; Guo, Minzhe; Du, Yina; Morley, Michael P; Valdez, Michael J; Yu, Haoze V; Jin, Kang; Bardes, Eric E; Zepp, Jarod A; Neithamer, Terren; Basil, Maria C; Zacharias, William J; Verheyden, Jamie; Young, Randee; Bandyopadhyay, Gautam; Lin, Sara; Ansong, Charles; Adkins, Joshua; Salomonis, Nathan; Aronow, Bruce J; Xu, Yan; Pryhuber, Gloria; Whitsett, Jeff; Morrisey, Edward E 2022. A census of the lung: CellCards from LungMAP. Developmental cell, 57 1, 112-145.e2
Toth, Andrea; Steinmeyer, Shelby; Kannan, Paranthaman; Gray, Jerilyn; Jackson, Courtney M; Mukherjee, Shibabrata; Demmert, Martin; Sheak, Joshua R; Benson, Daniel; Kitzmiller, Joseph; Wayman, Joseph A; Presicce, Pietro; Cates, Christopher; Rubin, Rhea; Chetal, Kashish; Du, Yina; Miao, Yifei; Gu, Mingxia; Guo, Minzhe; Kalinichenko, Vladimir V; Kallapur, Suhas G; Miraldi, Emily R; Xu, Yan; Swarr, Daniel; Lewkowich, Ian; Salomonis, Nathan; Miller, Lisa; Sucre, Jennifer S; Whitsett, Jeffrey A; Chougnet, Claire A; Jobe, Alan H; Deshmukh, Hitesh; Zacharias, William J 2022. Inflammatory blockade prevents injury to the developing pulmonary gas exchange surface in preterm primates. Science translational medicine, 14 638, eabl8574
Cross, Gail; Ho, Jessica S Y; Zacharias, William; Jeyasekharan, Anand D; Marazzi, Ivan 2021. Emergency drug use in a pandemic: Harsh lessons from COVID-19. Cell, 184 22, 5497-5500
Hynds, Robert E; Zacharias, William J; Nikolić, Marko Z; Königshoff, Melanie; Eickelberg, Oliver; Gosens, Reinoud; de Coppi, Paolo; Janes, Sam M; Morrisey, Edward; Clevers, Hans; Ryan, Amy L; Stripp, Barry R; Sun, Xin; Kim, Carla F; Lin, Qing S 2021. National Heart, Lung, and Blood Institute and Building Respiratory Epithelium and Tissue for Health (BREATH) Consortium Workshop Report: Moving Forward in Lung Regeneration. American journal of respiratory cell and molecular biology, 65 1, 22-29
Rindler, Tara N; Brown, Kari M; Stockman, Courtney A; van Lieshout, Laura P; Martin, Emily P; Weaver, Timothy E; Zacharias, William J; Wootton, Sarah K; Whitsett, Jeffrey A; Bridges, James P 2021. Efficient Transduction of Alveolar Type 2 Cells with Adeno-associated Virus for the Study of Lung Regeneration. American journal of respiratory cell and molecular biology, 65 1, 118-121
Zacharias, William 2021. Detecting oxygen changes in the lungs. Science (New York, N.Y.), 371 6524, 32-33
Basil, Maria C; Katzen, Jeremy; Engler, Anna E; Guo, Minzhe; Herriges, Michael J; Kathiriya, Jaymin J; Windmueller, Rebecca; Ysasi, Alexandra B; Zacharias, William J; Chapman, Hal A; Kotton, Darrell N; Rock, Jason R; Snoeck, Hans-Willem; Vunjak-Novakovic, Gordana; Whitsett, Jeffrey A; Morrisey, Edward E 2020. The Cellular and Physiological Basis for Lung Repair and Regeneration: Past, Present, and Future. Cell stem cell, 26 4, 482-502
Jackson, Courtney M; Mukherjee, Shibabrata; Wilburn, Adrienne N; Cates, Chris; Lewkowich, Ian P; Deshmukh, Hitesh; Zacharias, William J; Chougnet, Claire A 2020. Pulmonary Consequences of Prenatal Inflammatory Exposures: Clinical Perspective and Review of Basic Immunological Mechanisms. Frontiers in immunology, 11 , 1285
Oherle, Katherine; Acker, Elizabeth; Bonfield, Madeline; Wang, Timothy; Gray, Jerilyn; Lang, Ian; Bridges, James; Lewkowich, Ian; Xu, Yan; Ahlfeld, Shawn; Zacharias, William; Alenghat, Theresa; Deshmukh, Hitesh 2020. Insulin-like Growth Factor 1 Supports a Pulmonary Niche that Promotes Type 3 Innate Lymphoid Cell Development in Newborn Lungs. Immunity, 52 4, 716-718
Oherle, Katherine; Acker, Elizabeth; Bonfield, Madeline; Wang, Timothy; Gray, Jerilyn; Lang, Ian; Bridges, James; Lewkowich, Ian; Xu, Yan; Ahlfeld, Shawn; Zacharias, William; Alenghat, Theresa; Deshmukh, Hitesh 2020. Insulin-like Growth Factor 1 Supports a Pulmonary Niche that Promotes Type 3 Innate Lymphoid Cell Development in Newborn Lungs. Immunity, 52 2, 275-294.e9
Paris, Andrew J; Hayer, Katharina E; Oved, Joseph H; Avgousti, Daphne C; Toulmin, Sushila A; Zepp, Jarod A; Zacharias, William J; Katzen, Jeremy B; Basil, Maria C; Kremp, Madison M; Slamowitz, April R; Jayachandran, Sowmya; Sivakumar, Aravind; Dai, Ning; Wang, Ping; Frank, David B; Eisenlohr, Laurence C; Cantu, Edward; Beers, Michael F; Weitzman, Matthew D; Morrisey, Edward E; Worthen, G Scott 2020. STAT3-BDNF-TrkB signalling promotes alveolar epithelial regeneration after lung injury. Nature cell biology, 22 10, 1197-1210
Rajaram, Sanjeeth; Canaday, Laura M; Ochayon, David E; Rangel, Kelly M; Ali, Ayad; Gyurova, Ivayla E; Krishnamurthy, Durga; Fletcher, Jonathan S; Reighard, Seth D; Cox, Andrew; Weirauch, Matthew T; Kottyan, Leah C; Deshmukh, Hitesh; Zacharias, William J; Borchers, Michael T; Waggoner, Stephen N 2020. The Promise and Peril of Natural Killer Cell Therapies in Pulmonary Infection. Immunity, 52 6, 887-889
Swarr, Daniel; Putcha, Nirupama; Zacharias, William 2020. "PIK"ing Out New Epigenetic Markers in Lung Disease. American journal of respiratory and critical care medicine, 201 9, 1029-1030
Xiao, Deyi; Li, Xiaohong; Rouchka, Eric C; Waigel, Sabine; Zacharias, Wolfgang; McMasters, Kelly M; Hao, Hongying 2020. Comparative gene expression analysis in melanocytes driven by tumor cell-derived exosomes. Experimental cell research, 386 1, 111690
Alapati, Deepthi; Zacharias, William J; Hartman, Heather A; Rossidis, Avery C; Stratigis, John D; Ahn, Nicholas J; Coons, Barbara; Zhou, Su; Li, Hiaying; Singh, Kshitiz; Katzen, Jeremy; Tomer, Yaniv; Chadwick, Alexandra C; Musunuru, Kiran; Beers, Michael F; Morrisey, Edward E; Peranteau, William H 2019. In utero gene editing for monogenic lung disease. Science translational medicine, 11 488,
Frank, David B; Penkala, Ian J; Zepp, Jarod A; Sivakumar, Aravind; Linares-Saldana, Ricardo; Zacharias, William J; Stolz, Katharine G; Pankin, Josh; Lu, MinQi; Wang, Qiaohong; Babu, Apoorva; Li, Li; Zhou, Su; Morley, Michael P; Jain, Rajan; Morrisey, Edward E 2019. Early lineage specification defines alveolar epithelial ontogeny in the murine lung. Proceedings of the National Academy of Sciences of the United States of America, 116 10, 4362-4371
Tighe, Robert M; Redente, Elizabeth F; Yu, Yen-Rei; Herold, Susanne; Sperling, Anne I; Curtis, Jeffrey L; Duggan, Ryan; Swaminathan, Suchitra; Nakano, Hideki; Zacharias, William J; Janssen, William J; Freeman, Christine M; Brinkman, Ryan R; Singer, Benjamin D; Jakubzick, Claudia V; Misharin, Alexander V 2019. Improving the Quality and Reproducibility of Flow Cytometry in the Lung. An Official American Thoracic Society Workshop Report. American journal of respiratory cell and molecular biology, 61 2, 150-161
Dolinay, Tamás; Aonbangkhen, Chanat; Zacharias, William; Cantu, Edward; Pogoriler, Jennifer; Stablow, Alec; Lawrence, Gladys G; Suzuki, Yoshikazu; Chenoweth, David M; Morrisey, Edward; Christie, Jason D; Beers, Michael F; Margulies, Susan S 2018. Protein kinase R-like endoplasmatic reticulum kinase is a mediator of stretch in ventilator-induced lung injury. Respiratory research, 19 1, 157
Rossidis, Avery C; Stratigis, John D; Chadwick, Alexandra C; Hartman, Heather A; Ahn, Nicholas J; Li, Haiying; Singh, Kshitiz; Coons, Barbara E; Li, Li; Lv, Wenjian; Zoltick, Philip W; Alapati, Deepthi; Zacharias, William; Jain, Rajan; Morrisey, Edward E; Musunuru, Kiran; Peranteau, William H 2018. In utero CRISPR-mediated therapeutic editing of metabolic genes. Nature medicine, 24 10, 1513-1518
Zacharias, William J; Frank, David B; Zepp, Jarod A; Morley, Michael P; Alkhaleel, Farrah A; Kong, Jun; Zhou, Su; Cantu, Edward; Morrisey, Edward E 2018. Regeneration of the lung alveolus by an evolutionarily conserved epithelial progenitor. Nature, 555 7695, 251-255
Jacob, Anjali; Morley, Michael; Hawkins, Finn; McCauley, Katherine B; Jean, J C; Heins, Hillary; Na, Cheng-Lun; Weaver, Timothy E; Vedaie, Marall; Hurley, Killian; Hinds, Anne; Russo, Scott J; Kook, Seunghyi; Zacharias, William; Ochs, Matthias; Traber, Katrina; Quinton, Lee J; Crane, Ana; Davis, Brian R; White, Frances V; Wambach, Jennifer; Whitsett, Jeffrey A; Cole, F Sessions; Morrisey, Edward E; Guttentag, Susan H; Beers, Michael F; Kotton, Darrell N 2017. Differentiation of Human Pluripotent Stem Cells into Functional Lung Alveolar Epithelial Cells. Cell stem cell, 21 4, 472-488.e10
Zepp, Jarod A; Zacharias, William J; Frank, David B; Cavanaugh, Christina A; Zhou, Su; Morley, Michael P; Morrisey, Edward E 2017. Distinct Mesenchymal Lineages and Niches Promote Epithelial Self-Renewal and Myofibrogenesis in the Lung. Cell, 170 6, 1134-1148.e10
Paris, Andrew J; Liu, Yuhong; Mei, Junjie; Dai, Ning; Guo, Lei; Spruce, Lynn A; Hudock, Kristin M; Brenner, Jacob S; Zacharias, William J; Mei, Hankun D; Slamowitz, April R; Bhamidipati, Kartik; Beers, Michael F; Seeholzer, Steven H; Morrisey, Edward E; Worthen, G Scott 2016. Neutrophils promote alveolar epithelial regeneration by enhancing type II pneumocyte proliferation in a model of acid-induced acute lung injury. American journal of physiology. Lung cellular and molecular physiology, 311 6, L1062-L1075
Zacharias, William J; Madison, Blair B; Kretovich, Katherine E; Walton, Katherine D; Richards, Neil; Udager, Aaron M; Li, Xing; Gumucio, Deborah L 2011. Hedgehog signaling controls homeostasis of adult intestinal smooth muscle. Developmental biology, 355 1, 152-62
Zacharias, William J; Li, Xing; Madison, Blair B; Kretovich, Katherine; Kao, John Y; Merchant, Juanita L; Gumucio, Deborah L 2010. Hedgehog is an anti-inflammatory epithelial signal for the intestinal lamina propria. Gastroenterology, 138 7, 2368-77, 2377.e1-4
Kolterud, Asa; Grosse, Ann S; Zacharias, William J; Walton, Katherine D; Kretovich, Katherine E; Madison, Blair B; Waghray, Meghna; Ferris, Jennifer E; Hu, Chunbo; Merchant, Juanita L; Dlugosz, Andrzej A; Kottmann, Andreas H; Gumucio, Deborah L 2009. Paracrine Hedgehog signaling in stomach and intestine: new roles for hedgehog in gastrointestinal patterning. Gastroenterology, 137 2, 618-28
Lees, Charlie W; Zacharias, William J; Tremelling, Mark; Noble, Colin L; Nimmo, Elaine R; Tenesa, Albert; Cornelius, Jennine; Torkvist, Leif; Kao, John; Farrington, Susan; Drummond, Hazel E; Ho, Gwo-Tzer; Arnott, Ian D R; Appelman, Henry D; Diehl, Lauri; Campbell, Harry; Dunlop, Malcolm G; Parkes, Miles; Howie, Sarah E M; Gumucio, Deborah L; Satsangi, Jack 2008. Analysis of germline GLI1 variation implicates hedgehog signalling in the regulation of intestinal inflammatory pathways. PLoS medicine, 5 12, e239
Krause, Ange; Zacharias, William; Camarata, Troy; Linkhart, Barbara; Law, Evelyn; Lischke, Antje; Miljan, Erik; Simon, Hans-Georg 2004. Tbx5 and Tbx4 transcription factors interact with a new chicken PDZ-LIM protein in limb and heart development. Developmental biology, 273 1, 106-20
