Publications
Baker Institute Recent Publications
*For a full copy of those publications not publicly available, please contact us to request a copy.
June 2021
Schang Luis, Hu, Mi Yao, Flores Cortes Esteban, Sun Kairui. (2021). Chromatin-mediated epigenetic regulation of HSV-1 transcription as a potential target in antiviral therapy. Antiviral Res. 2021 May 31;105103.
Goetschius Daniel J, Hartmann Samantha R., Organtini Lindsey J, Callaway Heather, Huang Kai, Bator Carol M, Ashley Robert E, Makhov Alexander M, Conway James F, Parrish Colin R, Hafenstein Susan L. (2021). High-resolution asymmetric structure of a Fab–virus complex reveals overlap with the receptor binding site. PNAS. June 8, 2021 118 (23).
May 2021
Tomlinson Joy E, Wolfisberg Raphael, Fahnøe Ulrik, Patel Roosheel S, Trivedi Sheetal, Kumar Arvind, Sharma Himanshu, Nielsen Louise, McDonough Sean P, Bukh Jens, Tennant Bud C, Kapoor Amit, Rosenberg Brad R, Rice Charles M, Divers Thomas J, Van de Walle Gerlinde R, Scheel Troels K H (2021). Pathogenesis, miR-122 gene-regulation, and protective immune responses after acute equine hepacivirus infection. Hepatology. 2021 Mar 13.
Cummings Kevin J, Siler JD, Abou-Madi N, Goodman Laura B, Mitchell Patrick K, Tallmadge Rebecca M, Palena L, Childs-Sanford Sara Egst. (2021). Salmonella isolated from central New York wildlife admitted to a veterinary medical teaching hospital. In Press, Journal of Wildlife Diseases
March 2021
Wodarz Dominik, Komarova Natalia L, Schang Luis M. Role of high-dose exposure in transmission hot zones as a driver of SARS-CoV-2 dynamics. J R Soc Interface. 2021 Mar;18(176):20200916.
Tyson Gregory H, Ceric Olgica, Guag Jake, Nemser Sarah, Borenstein Stacey, Slavic Durda, Lippert Sarah, McDowell Rebecca, Krishnamurthy Aparna, Korosec Shannon, Friday Cheryl, Pople Neil, Saab Matthew E, Fairbrother Julie-Helene, Janelle Isabelle, McMillan Deanna, Bommineni Yugendar R, Simon David, Mohan Shipra, Sanchez Susan, Phillips Ashley, Bartlett Paula, Naikare Hemant, Watson Cynthia, Sahin Oorhan, Stinman Chloe, Wang Leyi, Maddox Carol, DeShambo Vanessa, Hendrix Kendrix, Lubelski Debra, Burklund Amy, Lubbers Brian, Reed Debbie, Jenkins Ttracie, Erol Erdal, Patel Mukeshbhai, Locke Stephan, Fortner Jordan, Peak Laura, Balasuriya Udeni, Mani Rinosh, Kettler Niesa, Olsen Karen, Zhang Shuping, Shen Zhenyu, Landinez Martha Pulido, Thornton Jay Kay, Thachil Anil, Byrd Melissa, Jacob Megan, Krogh Darlene, Webb Brett, Schaan Lynn, Patil Amar, Dasgupta Sarmila, Mann Shannon, Goodman Laura B, Franklin-Guild Rebecca June, Anderson Renee R, Mitchell Patrick K, Cronk Brittany D, Aprea Missy, Cui Jing, Jurkovic Dominika, Prarat Melanie, Zhang Yan, Shiplett Katherine, Campos Dubra D, Van Balen Rubio Joany, Ramanchandran Akhilesh, Talent Scott, Tewari Deepanker, Thirumalapura Nagaraja, Kelly Donna, Barnhart Denise, Hall Lacey, Rankin Sara D, Dietrich Jaclyn, Cole Sstephen, Scaria Joy, Antony Linto, Lawhon Sara D, Wu Jing, McCoy Christine, Dietz Kelly, Wolking Rebecca, Alexander Trevor, Burbick Claire, Reimschuessel Renate. (2021). Genomics accurately predicts antimicrobial resistance in Staphylococcus pseudintermedius collected as part of Vet-LIRN resistance monitoring. Vet Microbiol. 2021 Mar;254:109006.
February 2021
Saikia Mridusmita, Holter Marlena, Donahue Leanna R, Lee Isaac S, Zheng Qiaonan C, Wise Journey L, Todero Jenna E, Phuong Daryl J, Garibay Darline, Coch Reilly, Sloop Kyle W, Garcia-Ocana Adolfo, Danko Charles G, Cummings Bethany P. (2021) GLP-1 receptor signaling increases PCSK1 and β cell features in human α cells.
Goodman Laura, Whittaker Gary (2021) Public health surveillance of infectious diseases: beyond point mutations. The Lancet Mircobe. Vol 2, Issue 2, E53-E54, 01 February 1, 2021.
Tufts Danielle M, Goodman Laura B, Benedict Meghan C, Davis April D, VanAcker Meredith C, Diuk-Wasser Maria. (2021). Association of the invasive Haemaphysalis longicornis tick with vertebrate hosts, other native tick vectors, and tick-borne pathogens in New York City, USA. Int J Parasitol. 2021 Feb;51(2-3):149-157.
January 2021
Patel Roosheel S, Tomlinson Joy E, Divers Thomas J, Van de Walle Gerlinde R, Rosenberg. (2021). Single-cell resolution landscape of equine peripheral blood mononuclear cells reveals diverse cell types including T-bet + B cells. BMC Biol. 2021 Jan 22;19(1):13.
Stout Alison E, Hofmar-Glennon Hayley G, André Nicole M, Goodman Laura B, Anderson Renee R, Mitchell Patrick K, Thompson Belinda S, Lejeune Manigandan, Whittaker Gary R, Goodrich Erin L (2021). Infectious disease surveillance of apparently healthy horses at a multi-day show using a novel nanoscale real-time PCR panel. J Vet Diagn Invest. 2021 Jan;33(1):80-86.
Mitchell Patrick K, Cronk Brittany D, Voorhees Ian EH, Rothenheber Derek, Anderson ReneeR, Chan Timothy H, Wasik Brian R, Dubovi EJ, Parrish Colin R, Goodman Laura B. Method comparison of targeted influenza A virus typing and whole-genome sequencing from respiratory specimens of companion animals. J Vet Diagn Invest. 2020 Nov 24;1040638720933875.
Gioia G, Addis MF, Goodman LB, Mitchell PK, Thompson B, Goodrich E, Moroni P. (2021). Draft Genome Sequence of Acholeplasma laidlawii Isolated from the Conjunctiva of a Heifer with Infectious Bovine Keratoconjunctivitis. Microbiol Resour Announc. 2021 Jan 28;10(4).
December 2020
Harman Rebecca M, Patel Roosheel S, Fan Jennifer C, Park Jee E, Rosenberg Brad R, Van de Walle Gerlinde R (2020) Single-cell RNA sequencing of equine mesenchymal stromal cells from primary donor-matched tissue sources reveals functional heterogeneity in immune modulation and cell motility. Stem Cell Res Ther. 2020 Dec 4; 11(1):524.
*This project was recognized by the Cornell Center for Vertebrate Genomics as a noteworthy publication.
Goetschius Daniel J, Hartmann Samantha R, Organtini Lindsey J, Callwaway Heather, Huang Kai, Bator Carol M, Ashley Robert E, Makhov Alexander M, Conway James F, Parrish Colin R, Hafenstein Susan. Mechanisms of antibody binding revealed by asymmetric Fab-virus complexes. bioRxiv : the preprint server for biology. 2020 December. Has not been formally peer-reviewed.
November 2020
Ledet Melissa M, Harman Rebecca M, Fan Jennifer C, Schmitt-Matzen Emily, Diaz-Rubio Maria E, Zhang Sheng, Van de Walle Gerlinde (2020) Secreted sphingomyelins modulate low mammary cancer incidence observed in certain mammals. Sci Rep. 2020 Nov 25;10(1):20580
Vengust Modest, Jager Mason C, Zalig Valentina, Cociancich Vasilij, Laverack Melissa, Renshaw Randall W, Dubovi Edward, Tomlinson Joy E, Van de Walle Gerlinde R, Divers Thomas J. (2020). First report of equine parvovirus-hepatitis-associated Theiler's disease in Europe. Equine Vet J. 2020 Nov;52(6):841-847.
October 2020
Harman Rebecca M, Das Sanjna P, Bartlett Arianna P, Rauner Gat, Donahue Leanne R, Van de Walle Gerlinde R. (2020) Beyond tradition and convention: benefits of non-traditional model organisms in cancer research. Cancer Metastasis Rev. 2020 Oct 28.
September 2020
Komarova N Natalia, Schang Luis M, Wodarz Dominik L (2020) Patterns of the COVID19 pandemic spread around the world: exponential vs. power laws. Journal of the Royal Society Interface. 30 Sep 2020 – 01:10
Meliopoulos Victoria, Cherry Sean, Wohlgemuth Nicholas, Honce Rebekah, Barnard Karen, Gauger Phillip, Davis Todd, Shult Peter, Parrish Colin, Schultz-Cherry Stacey (2020)Primary swine respiratory epithelial cell lines for the efficient isolation and propagation of influenza A viruses. J Virol. 2020 Sep 23:JVI.01091-20
August 2020
Roebke Katherine E, Yingying Guo, Parker John SL, Danthi Pranav. Reovirus σ3 protein limits interferon expression and cell death induction. BioRxiv. 2020 August.
Tallmadge Rebecca L, Antczak Douglas F, Felippe Maria Julia Bevilaqua. Genetics of Immune Disease in the Horse Nucleic Acids Research. 2019 June 20;47(11). Vet Clin of North America, Equine Practice. Volume 36, Issue 2, August 2020, 273-288.
July 2020
Mukai Chinatsu, Nelson Jacquelyn L, Cheong Soon Hon, Diel de Amorim Mariana, Travis Alexander J. (2020). Impacts of oocyte/zygote timing for in vitro fertilization and gene editing in the dog. Theriogenology. 2020 Jul 1;150:347-352.
Blumberg Amit, Zhao Yixin, Huang Yi-Fei, Dukler Noah, Rice Edward J, Chivu Alexandra G, Krumholz Katie, Danko Charles G, Siepel Adam. (2020) Characterizing RNA stability genome-wide through combined analysis of PRO-seq and RNA-seq data. BioRxiv. 13 June 2020. Has not been formally peer-reviewed.
Tomlinson Joy E, Wolfisberg Raphael, Fahnøe Ulrik, Sharma Himanshu, Renshaw Randall W, Nielsen Louise, Nishiuchi Eiko, Holm Christina, Dubovi Edward, Rosenberg Brad R, Tennant Bud C, Bukh Jens, Kapoor Amit, Divers Thomas J, Rice Charles M, Van de Walle Gerlinde R, Scheel Troels K H. (2020) Equine pegiviruses cause persistent infection of bone marrow and are not associated with hepatitis. PLoS Pathog. 2020 Jul 10;16(7):e1008677.
Fortier Lisa Ann, Goodrich Laurie Ruth, Ribitsch Iris, Schnabel Lauren Virginia, Shepard David Owen, Van de Walle Gerlinde R, Watts Ashlee Elizabeth, Smith Roger Kenneth Whealands. One health in regenerative medicine: report on the second Havemeyer symposium on regenerative medicine in horses. Regen Med. 2020 Jun;15(6):1775-1787.
June 2020
Cosgrove Elissa J, Sadeghi Raheleh, Schlamp Florencia, Holl Heather M. Moradi-Shahrbabak Mohammad, Miraei-Ashtiani Seyed Reza, Adballa Salma, Shykind Ben, Troedsson Mats, Stefaniuk-Szmukier Monika, Prabhu Anil, Bucca Stefania, Bugno-Poniewiersak Monika, Wallmer Barbara, Malek Joel, Miller Donald C., Clark Andrew G, Antczak Douglas F., Brooks, Samantha A. Genome Diversity and the Origin of the Arabian Horse. Scientific Reports.16 June 2020
May 2020
Mukai Chinatsu; Eunju Choi; Sams Kelly L; Klampen Elena Zu; Anguish Lynne; Marks Brooke A; Rice Edward J; Wang Zhong; Choate Lauren A; Chou Shao-Pei; Kato Yukinari; Miller Andrew; Danko Charles G; Coonrod Scott A. Chromatin run-on sequencing analysis finds that ECM remodeling plays an important role in canine hemangiosarcoma pathogenesis. BMC Veterinary Research. 28 May 2020.
April 2020
Sharara Fady, Seaman Eric, Morris Randy, Schinfeld Jay, Nichols Jennifer, Sobel Michael, Lee Annette, Somkuti Stephen, Hirshberg Steven, Budinetz Tara, Barmat Larry, Palermo Gianpiero, Rosenwaks Zev, Bar-Chama Natan, Bodie Joshua, Nicholas John, Payne John, McCoy Travis, Tarnawa Edward, Whitman-Elia Gail, Weissman Lauren, Doukakis Maria, Hurwitz Joshua, Leondires Mark, Murdock Cynthia, Ressler Ilana, Richlin Spencer, Williams Shaun, Wosnitzer Matthew, Butcher Michael, Kashanian James, Ahlering Peter, Aubuchon Mira, Ostemeir G. Charles, Travis Alexander J. Multicentric, prospective observational data show sperm capacitation predicts male fertility, and cohort comparison reveals a high prevalence of impaired capacitation in men questioning their fertility. Reproductive Biomedicine Online (RBMO). Vol. 41, Issue 1, p69-79, 1 July 2020.
Barnard Karen N, Alford-Lawrence Brynn K, Buchholz David W, Wasik Brian R, LaClair Justin R, Yu Hai, Honce Rebekah, Ruhl Stefan, Pajic Petar, Daugherity Erin K, Chen Xi, Schultz-Cherry Stacey L, Aguilar Hector C, Varki Ajit, Parrish Colin R. Modified sialic acids on mucus and erythrocytes inhibit influenza A HA and NA functions. J Virol. 2020 Apr 16; ;94(9):e01567-19.
March 2020
Harman Rebecca M, Theoret Christine L, Van de Walle Gerlinde R. The Horse as a Model for the Study of Cutaneous Wound Healing. Advances in Wound Care. 20 Mar 2019.
Marx Charlotte, Gardner Sophia, Harman Rebecca M, Van de Walle Gerlinde R. The c stromal cell (MSC) secretome impairs methicillin-resistant Staphylococcus aureus (MRSA) biofilms via cysteine protease activity in the equine model. Stem Cells Transl Med. 2020 Mar 26.
Vengust Modest, Jager Mason C, Zalig Valetina, Cociancich Vasilij, Laverack Melissa, Renshaw Randall W, Dubovi Edward, Tomlinson Joy E, Van de Walle Gerlinde R, Divers Thomas J. First report of Equine Parvovirus-Hepatitis-associated Theiler’s disease in Europe. Equine Vet. Journal BEVA. 2020 Mar 07.
Tomlinson Joy E, Jager Mason, Struzyna Alyssa, Lavrack Melissa, Fortier Lisa A, Dubovi Edward, Foil Lane D, Burbelo Peter D, Divers Thomas J, Van de Walle Gerlinde R. Tropism, pathology, and transmission of equine parvovirus-hepatitis. Emerging Microbes & Infections. 2020 Mar 20, 651-663.
February 2020
Nguyen Tri., Lee, Sohyoung, Yang Yi-An, Ahn Changwan, Sim Ji Hyun, Kei Tiffany G., Barnard Karnard N, Yu Hai, Millano Shawn K, Chen Xi, Parrish, Colin R, Song, Jeongmin. The role of 9-O-acetylated glycan receptor moieties in the typhoid toxin binding and intoxication. PLoS Pathog. 2020 Feb 21;16(2).
December 2019
Wasik Brian R, Voorhees Ian EH, Barnard Karen N, Alford-Lawrence Brynn K, Weichert Wendy S, Hood Grace, Nogales Aitor, Martínez-Sobrido Luis, Holmes Edward C, Parrish Colin R. Influenza Viruses in Mice: Deep Sequencing Analysis of Serial Passage and Effects of Sialic Acid Structural Variation. J Virol. 2019 Dec 1;93(23).
Barnard Karen N, Wasik Brian R, LaClair JR, Buchholz DW, Weichert Wendy S, Alford-Lawrence Brynn K, Aguilar Hector C, Parrish Colin R. Expression of 9-O- and 7,9-O-Acetyl Modified Sialic Acid in Cells and Their Effects on Influenza Viruses. mBio. 2019 Dec 3;10(6).
Wasik Brian R, Voorhees Ian EH, Parrish Colin R. Canine and Feline Influenza. Cold Spring Harb Perspect Med. 2019 Dec 30;
Voorhees Ian EH, Lee Hyunwook, Allison Andrew B, Lopez-Astacio Robert, Goodman Laura B, Oyesola Oyebola O, Omobowale Omobowale, Fagbohun Olusegun, Dubovi Edward J, Hafenstein Susan L, Holmes Edward C, Parrish Colin R. Limited Intrahost Diversity and Background Evolution Accompany 40 Years of Canine Parvovirus Host Adaptation and Spread. J Virol. 2019 Dec 12;94(1).
Kshitiz, Afzal Junaid, Maziarz Jamie D, Hamidzadeh Archer, Liang Cong, Erkenbrack Eric M, Kim Hong Nam, Haeger Jan-Dirk, Pfarrer Christiane, Hoang Thomas, Ott Troy, Spencer Thomas, Pavličev Mihaela, Antczak Douglas F, Levchenko Andrea, Wagner Günter P. Evolution of placental invasion and cancer metastasis are causally linked. Nat Ecol Evol. 2019 Dec;3(12):1743-1753.
November 2019
McGregor Douglas D, Fraser David R, Parker John SL. Tracking Veterinary Students Who Aspire to Careers in Science. J Vet Med Educ. 2019 Mar 28;1-6.
Hu MiYao, Depledge Daniel P, Cortes Esteban F, Breuer Judith, Schang Luis M. Chromatin dynamics and the transcriptional competence of HSV-1 genomes during lytic infections. PLOS Pathogens. 2019 Nov 14;15(11).
Holmes Camille M, Violette Nathaniel, Miller Donald, Wagner Bettina, Svansson Vihjalmur, Antczak Douglas F. MHC haplotype diversity in Icelandic horses determined by polymorphic microsatellites. Genes Immun. 2019 Nov;20(8):660-670.
October 2019
Lu Yen-Chu, Chu Tinyi, Hall Matthew S, Fu Dah-Jiun, Shi Qquanming, Chiu Alan, An Duo, Wang Long-Hai, Pardo Yehudah, Southard Teresa, Danko Charles G, Liphardt Jan, Nikitin Alexander Y, Wu Mingming, Fischbach Claudia, Coonrod Scott, Ma Minglin. (2019). Physical confinement induces malignant transformation in mammary epithelial cells. Biomaterials. 2019 Oct;217:119307.
Lee Hyunhook, Callaway Heather M, Cifuente Javier O, Bator Carol M, Parrish Colin R, Hafenstein Susan L. Transferrin receptor binds virus capsid with dynamic motion. Proc Natl Acad Sci U S A. 2019 Oct 8;116(41):20462-20471.
September 2019
Ray Judhajeet*, Munn Paul R*, Vihervaara Anniina, Lewis James J, Ozer Abdullah¥, Danko Charles G¥, Lis JT¥ (2019). Chromatin conformation remains stable upon extensive transcriptional changes driven by heat shock. Proc Natl Acad Sci U S A. 2019 Sep 10. pii: 201901244.
Tramontano Enzo, Tarbet Bart, Spengler Jessica R, Seley-Radtke Katherine, Meier Chris, Jordan Robert, Janeba Zlatko, Gowen Brian, Gentry Brian, Esté Jose A, Bray Mike, Andrei Graciela, Schang Luis M; on behalf of the International Society for Antiviral Research – ISAR. Meeting report: 32nd International conference on antiviral research. Antiviral Res. 2019 Sep;169:104550.
Wasik Brian R, de Wit Emmie, Munster Vincent, Lloyd-Smith James O, Martinez-Sobrido Luis, Parrish Colin R. Onward transmission of viruses: how do viruses emerge to cause epidemics after spillover?. Philos Trans R Soc Lond B Biol Sci. 2019 Sep 30;374(1782):20190017.
Wasik Brian R, Voorhees Ian EH, Barnard Karen N, Alford-Lawrence Brynn K, Weichert Wendy S, Hood Grace, Nogales Aitor, Martínez-Sobrido Luis, Holmes Edward C, Parrish Colin R, Influenza Viruses in Mice: Deep Sequencing Analysis of Serial Passage and Effects of Sialic Acid Structural Variation. Journal of Virology. 11 Sep 2019
Pepin, Kim M, Hopken Matthew W, Shriner Susan A, Spackman Erica, Abdo, Zaid, Parrish Colin, Riley, Steven, Lloyd-Smith, James O, Piaggio Antoinette J. Improving risk assessment of the emergence of novel influenza A viruses by incorporating environmental surveillance. Philos Trans R Soc Lond B Biol Sci. 2019 Sep 30;374(1782):20180346
August 2019
Tomlinson Joy E, Van de Walle Gerlinde R, Divers Thomas J. What do we know about hepatitis viruses in horses? Vet Clin North Am Equine Pract. 2019 Aug; 35(2):351-362.
Mishra Neha, Schwerdtner Lidja, Sams Kelly, Mondal Santanu, Ahmad Fareed, Schmidt Reinhold E, Coonrod Scott A, Thompson Paul R, Lerch Markus M, Bossaller Lukas. Cutting Edge: Protein Arginine Deiminase 2 and 4 Regulate NLRP3 Inflammasome-Dependent IL-1β Maturation and ASC Speck Formation in Macrophages. J Immunol. 2019 Aug 15;203(4):795-800.
July 2019
Chou Shao-Pei, Danko Charles G¥ (2019). AlleleHMM: a data-driven method to identify allele-specific differences in distributed functional genomic marks. Nucleic Acids Research. 2019 June 20;47(11)
Bensing Barbara A, Li Liang, Yakovenko Olga, Wong Maurice, Barnard Karen N, Iverson Tina M, Lebrilla Carlito B, Parrish Colin R, Thomas Wendy E, Xiong Yan, Sullam Paul M. Recognition of specific sialoglycan structures by oral streptococci impacts the severity of endocardial infection. PLoS Pathog. 2019 Jun;15(6):e1007896.
Goetschius Daniel J, Parrish Colin R, Hafenstein Susan. Asymmetry in icosahedral viruses. Curr Opin Virol. 2019 Jun 27;36:67-73.
Parrish Colin R, Voorhees Ian EH. H3N8 and H3N2 Canine Influenza Viruses: Understanding These New Viruses in Dogs. Vet Clin North Am Small Anim Pract. 2019 Jul;49(4):643-649.
Fiscal Year 2019 Publications
Fiscal Year 2018 Publications
Fiscal Year 2017 Publications
