Baker Institute Recent Publications

*For a full copy of those publications not publicly available, please contact us to request a copy. 
 

April 2022

Arianna P. Bartlett, Rebecca M. Harman, Jennifer R. Weiss, Gerlinde R. Van de Walle. (2022). Establishment and characterization of equine mammary organoids using a method translatable to other non-traditional model species. In collection: Reproductive biology. Techniques and Resources. 12 April 2022

Malgorzata Rychlowska, Abigail Agyapong, Michael Weinfeld, Luis M Schang (2022). Zika Virus Induces Mitotic Catastrophe in Human Neural Progenitors by Triggering Unscheduled Mitotic Entry in the Presence of DNA Damage While Functionally Depleting Nuclear PNKP. J Virol.  2022 Apr 12;e0033322.

Tinyi Chu, Zhong Wang, Dana Pe’er, Charles G. Danko (2021). Bayesian cell-type deconvolution and gene expression inference reveals tumor-microenvironment interactions. Nature Cancer. 25 Apr 2022.

Jordan D Zehr, Sergei L. Kosakovsky Pond, Darren P Martin, Kristina Ceres, Gary R Whittaker, Jean K. Millet, Laura B Goodman, Michael J. Stanhope (2022). Recent zoonotic spillover and tropism shift of a Canine Coronavirus is associated with relaxed selection and putative loss of function in NTD subdomain of spike protein. Viruses. 21 April 2022. 14(5), 853.

March 2022

Sarah M Bell, Jacquelyn M Evans, Katy M Evans, Kate L Tsai, Rooksana E Noorai, Thomas R Famula, Dolores M Holle, Leigh Anne Clark (2022). Congenital idiopathic megaesophagus in the German shepherd dog is a sex-differentiated trait and is associated with an intronic variable number tandem repeat in Melanin-Concentrating Hormone Receptor 2. PLoS Genet. 2022 Mar 10;18(3):e1010044.

Roy Cohen, Chinatsu Mukai, Jacquelyn L. Nelson, Shoshana S. Zenilma, Danielle M. Sosnicki, Alexander J. Travis. (2022). A Genetically-targeted sensor reveals spatial and temporal dynamics of acrosomal calcium and sperm acrosome exocytosis. J Biol Chem. 2022 Mar 25;101868.

Zhong Wang, Alexandra G Chivu, Lauren A Choate, Edward J Rice, Donald C Miller, Tinyi Chu, Shao-Pei Chou, Nicole B Kingsley Jessica L Petersen, Carrie J Finno, Rebecca R Bellone, Douglas F Antczak, John T Lis, Charles G Danko (2022). Prediction of histone post-translational modification patterns based on nascent transcription data. Nat Genet. 2022 Mar;54(3):295-305.

Gilad Barshad, Lauren M Webb, Hung-An Ting, Oyebola O Oyesola, Oluomachi G Onyekwere, James J Lewis, Edward J Rice, Macy K Matheson, Xiao-Hong Sun, Jakob von Moltke, Charles G Danko, Elia D Tait Wojno (2022). E-Protein Inhibition in ILC2 Development Shapes the Function of Mature ILC2s during Allergic Airway Inflammation. J Immunol. 2022 Mar 1;208(5):1007-1020.

Tirosh Shapira, I Abrrey Monreal, Sébastien P Dion, David W Buchholz, Brian Imbiakha, Andrea D Olmstead, Mason Jager, Antoine Désilets, Guang Gao, Mathias Martins, Thierry Vandal, Connor A H Thompson, Aaleigha Chin, William D Rees, Theodore Steiner, Ivan Robert Nabi, Eric Marsault, Julie Sahler, Diego G Diel, Gerlinde R Van de Walle, Avery August, Gary R Whittaker, Pierre-Luc Boudreault, Richard Leduc, Hector C Aguilar, François Jean (2022). A TMPRSS2 inhibitor acts as a pan-SARS-CoV-2 prophylactic and therapeutic. Nature, 2022 Mar 28. Epub ahead of print.

Claire H Birkenheuer, Laura Dunn, Rachel Dufour, Joel D Baines (2022). ICP22 of Herpes Simplex Virus 1 Decreases RNA Polymerase Processivity. J Virol. 2022 Mar 9;96(5):e0219121.

February 2022

Patrick K Mitchell, Leyi Wang, Bryce J Stanhope, Brittany D Cronk, Renee Anderson, Shipra Mohan, Lijuan Zhou, Susan Sanchez, Paula Bartlett, Carol Maddox, Vanessa DeShambo, Rinosh Mani, Lindsy M Hengesbach, Sarah Gresch, Katie Wright, Sunil Mor, Shuping Zhang, Zhenyu Shen, Lifang Yan, Rebecca Mackey, Rebecca Franklin-Guild, Yan Zhang, Melanie Prarat, Katherine Shiplett, Akhilesh Ramachandran, Sai Narayanan, Justin Sanders, Andree A Hunkapiller, Kevin Lahmers, Amanda A Carbonello, Nicole Aulik, Ailam Lim, Jennifer Cooper, Angelica Jones, Jake Guag, Sarah M Nemser, Gregory H Tyson, Ruth Timme, Errol Strain, Renate Reimschuessel, Olgica Ceric, Laura B Goodman . (2022). Multi-laboratory evaluation of the Illumina iSeq platform for whole genome sequencing of Salmonella, Escherichia coli and Listeria. Microb Genom. 2022 Feb;8(2):000717

Aitor Nogales, Kevin Chiem, Michael Breen, Marta L DeDiego, Colin R Parrish, Luis Martínez-Sobrido (2022). Generation and Characterization of Single-Cycle Infectious Canine Influenza A Virus (sciCIV) and Its Use as Vaccine Platform. Vaccine Technologies for Veterinary Viral Diseases pp 227-255.

January 2022

Taylorlyn Stephan, Shawn M Burgess , Hans Cheng , Charles G Danko , Clare A Gill, Erich D Jarvis, Klaus-Peter Koepfli, James E Koltes, Eric Lyons, Pamela Ronald, Oliver A Ryder, Lynn M Schriml, Pamela Soltis, Sue VandeWoude, Huaijun Zhou, Elaine A Ostrander, Elinor K Karlsson (2022). Darwinian genomics and diversity in the tree of life. Proc Natl Acad Sci U S A. 2022 Jan 25;119(4):e2115644119

Rolfe M Radcliffe, Lauren C Bookbinder, Sharon Y Liu, Joy E Tomlinson, Vanessa L Cook, Samuel D A Hurcombe, Thomas J Divers (2022). Collection and administration of blood products in horses: Transfusion indications, materials, methods, complications, donor selection, and blood testing. J Vet Emerg Crit Care (San Antonio). 2022 Jan;32(S1):108-122.

December 2021

Rebecca M Harman, Katherine A Churchill, Mason C Jager, Gerlinde R Van de Walle. (2021). The equine mesenchymal stromal cell secretome inhibits equid herpesvirus type 1 strain Ab4 in epithelial cells. Res Vet Sci.  2021 Dec;141:76-80.

Charlotte Marx, Sophia Gardner,  Rebecca M Harman, Bettina Wagner, Gerlinde R Van de Walle. (2021). Mesenchymal stromal cell-secreted CCL2 promotes antibacterial defense mechanisms through increased antimicrobial peptide expression in keratinocytes. Stem Cells Transl Med. 2021 Dec;10(12):1666-1679.

Madhav Mantri, Meleana M. Hinchman, David W. McKellar, Michael F. Z. Wang, Shaun T. Cross, John S. L. Parker, Iwijn De Vlaminck (2021). Spatiotemporal transcriptomics reveals pathogenesis of viral myocarditis. BioRxiv. 2021 Dec:9

November 2021

Lauren A Choate, Gilad Barshad, Pierce W McMahon, Iskander Said, Edward J Rice, Paul R Munn, James J Lewis, Charles G Danko. (2021). Multiple stages of evolutionary change in anthrax toxin receptor expression in humans. Nat Commun. 2021 Nov 15;12(1):6590.

Michael J Satlin, Jason Zucker, Benjamin R Baer, Mangala Rajan, Nathaniel Hupert, Luis M Schang, Laura C Pinheiro, Yanhan Shen, Magdalena E Sobieszczyk, Lars F Westblade, Parag Goyal, Martin T Wells, Jorge L Sepulveda, Monika M Safford (2021). Changes in SARS-CoV-2 viral load and mortality during the initial wave of the pandemic in New York City. PLoS One . 2021 Nov 19;16(11):e0257979.

October 2021

Barbara Delvescovo, Joy Tomlinson, Sally DeNottac, Elizabeth Hodged, Lauren Bookbinder, Hussni O. Mohammed, Thomas J.Diversa (2021). Bile Acids, Direct Bilirubin and Gamma-glutamyltransferase as Prognostic Indicators for Horses with Liver Disease in the Eastern United States: 82 Cases (1997-2019). Journal of Equine Vet Sci. Vol. 105, Oct 2021. 103729.

Kevin J Cummings, Julie D Siler, Noha Abou-Madi, Laura B Goodman, Patrick K Mitchell, Lauren Palena, Sara E Childs-Sanford. (2021). Salmonella Isolated from Central New York Wildlife Admitted to a Veterinary Medical Teaching Hospital.  J Wildl Dis. 2021 Oct 1;57(4):743-748.

César Arenas-Mena, Sofija Miljovska, Edward J Rice, Justin Gurges, Tanvi Shashikant, Zihe Wang, Sevinç Ercan, Charles G Danko (2021). Identification and prediction of developmental enhancers in sea urchin embryos. BMC Genomics. 2021 Oct 19;22(1):751.

Mason C Jager, Joy E Tomlinson, Robert A Lopez-Astacio, Colin R Parrish, Gerlinde R Van de Walle (2021). Small but mighty: old and new parvoviruses of veterinary significance. Virol J. 2021 Oct 24;18(1):210.

September 2021

Francesco Cicconardi, James J Lewis, Simon H Martin, Robert D Reed, Charles G Danko, Stephen H Montgomery (2021). Chromosome Fusion Affects Genetic Diversity and Evolutionary Turnover of Functional Loci but Consistently Depends on Chromosome Size. Mol Biol Evol. 2021 Sep 27;38(10):4449-4462.

Joy E Tomlinson, Raphael Wolfisberg, Ulrik Fahnøe, Roosheel S Patel, Sheetal Trivedi, Arvind Kumar, Himanshu Sharma, Louise Nielsen, Sean P McDonough, Jens Bukh, Bud C Tennant, Amit Kapoor, Brad R Rosenberg, Charles M Rice, Thomas J Divers, Gerlinde R Van de Walle, Troels K H Scheel (2021). Pathogenesis, MicroRNA-122 Gene-Regulation, and Protective Immune Responses After Acute Equine Hepacivirus Infection. Hepatology. 2021 Sep;74(3):1148-1163

August 2021

Yixin Zhao, Noah Dukler, Gilad Barshad, Shushan Toneyan, Charles G Danko, Adam Siepel (2021). Deconvolution of Expression for Nascent RNA sequencing data (DENR) highlights pre-RNA isoform diversity in human cells. Bioinformatics. 2021 Aug 11;37(24):4727-4736.

Christopher H Lee, Krishnan Raghunathan, Gwen M Taylor, Andrea J French, Raquel Tenorio, Isabel Fernández de Castro, Cristina Risco, John S L Parker, Terence S Dermody (2021). Reovirus Nonstructural Protein σNS Recruits Viral RNA to Replication Organelles. mBio. 2021 Aug 31;12(4):e0140821.

Luis M Schang, MiYao Hu, Esteban Flores Cortes, Kairui Sun (2021). Chromatin-mediated epigenetic regulation of HSV-1 transcription as a potential target in antiviral therapy. Antiviral Res. 2021 Aug;192:105103.

July 2021

Yingying Guo, Meleana M Hinchman, Mercedes Lewandrowsk, Shaun T Cross, Danica M Sutherland, Olivia L Welsh, Terence S Dermody  John S L Parker. (2021). The multi-functional reovirus σ3 protein is a virulence factor that suppresses stress granule formation and is associated with myocardial injury. PLoS Pathog. 2021 Jul 8;17(7):e1009494.

Kaiping Deng, Steffen Uhlig, Hon S Ip, Mary Lea Killian, Laura B Goodman, Sarah Nemser, Jodie Ulaszek, Shannon Pickens, Robert Newkirk, Matthew Kmet, Kirstin Frost, Karina Hettwer, Bertrand Colson, Kapil Nichani, Anja Schlierf, Andriy Tkachenko, Ravinder Reddy, Renate Reimschuessel. (2022). Interlaboratory comparison of SARS-CoV2 molecular detection assays in use by U.S. veterinary diagnostic laboratories. J Vet Diagn Invest. 2021 Nov;33(6):1039-1051.

James J Lewis, Francesco Cicconard, Simon H Martin, Robert D Reed, Charles G Danko, Stephen H Montgomery (2021). The Dryas iulia Genome Supports Multiple Gains of a W Chromosome from a B Chromosome in Butterflies. Genome Biol Evol. 2021 Jul 6;13(7):evab128.

Rebecca M Harman, Christine L Theoret, Gerlinde R Van de Walle (2021). The Horse as a Model for the Study of Cutaneous Wound Healing. Adv Wound Care (New Rochelle). 2021 Jul;10(7):381-399.

Dermody Terence S., Parker John S.L., & B. Sherry. Orthoreoviruses. (2021) In Fields Virology, 7th Edition (In Press). Eds. Damania, Knipe, Whelan, and Howley.

 

Fiscal Year 2021 Publications
Fiscal Year 2020 Publications
Fiscal Year 2019 Publications
Fiscal Year 2018 Publications
Fiscal Year 2017 Publications