COVID-19 Research Publications

Avadhanula V, Creighton CJ, Ferlic-Stark L, Sucgang R, Zhang Y, Nagaraj D, Nicholson EG, Rajan A, Menon VKumar, Doddapaneni H, Muzny DM, Metcalf GA, Cregeen SJoan Javor, Hoffman KLouise, Gibbs RA, Petrosino J, Piedra PA. Longitudinal host transcriptional responses to SARS-CoV-2 infection in adults with extremely high viral load. bioRxiv. 2023;.
Nair M, Moss N, Bashir A, Garate D, Thomas D, Fu S, Phu D, Pham C. Mental health trends among medical students. Proc (Bayl Univ Med Cent). 2023;36(3):408-410.
Harris RA, Raveendran M, Lyfoung DT, Sedlazeck FJ, Mahmoud M, Prall TM, Karl JA, Doddapaneni H, Meng Q, Han Y, Muzny DM, Wiseman RW, O'Connor DH, Rogers J. Construction of a new chromosome-scale, long-read reference genome assembly for the Syrian hamster, Mesocricetus auratus. Gigascience. 2022;11.
Liu Y, Kearney J, Mahmoud M, Kille B, Sedlazeck FJ, Treangen TJ. Rescuing low frequency variants within intra-host viral populations directly from Oxford Nanopore sequencing data. Nat Commun. 2022;13(1):1321.
Dylus D, Altenhoff A, Majidian S, Sedlazeck FJ, Dessimoz C. Read2Tree: scalable and accurate phylogenetic trees from raw reads. bioRxiv. 2022;.
Walker K, Kalra D, Lowdon R, Chen G, Molik D, Soto DC, Dabbaghie F, Khleifat AAl, Mahmoud M, Paulin LF, Raza MSohail, Pfeifer SP, Agustinho DPaiva, Aliyev E, Avdeyev P, Barrozo ER, Behera S, Billingsley K, Chong LChuin, Choubey D, De Coster W, Fu Y, Gener AR, Hefferon T, Henke DMorgan, Höps W, Illarionova A, Jochum MD, Jose M, Kesharwani RK, Kolora SRohit Raj, Kubica J, Lakra P, Lattimer D, Liew C-S, Lo B-W, Lo C, Lötter A, Majidian S, Mendem SKumar, Mondal R, Ohmiya H, Parvin N, Peralta C, Poon C-L, Prabhakaran R, Saitou M, Sammi A, Sanio P, Sapoval N, Syed N, Treangen T, Wang G, Xu T, Yang J, Zhang S, Zhou W, Sedlazeck FJ, Busby B. The third international hackathon for applying insights into large-scale genomic composition to use cases in a wide range of organisms. F1000Res. 2022;11:530.
Liu Y, Kearney J, Mahmoud M, Kille B, Sedlazeck FJ, Treangen TJ. Rescuing Low Frequency Variants within Intra-Host Viral Populations directly from Oxford Nanopore sequencing data. bioRxiv. 2021;.
Farinholt T, Doddapaneni H, Qin X, Menon V, Meng Q, Metcalf GA, Chao H, Gingras M-C, Avadhanula V, Farinholt P, Agrawal C, Muzny DM, Piedra PA, Gibbs RA, Petrosino J. Transmission event of SARS-CoV-2 delta variant reveals multiple vaccine breakthrough infections. BMC Med. 2021;19(1):255.
Butler D, Mozsary C, Meydan C, Foox J, Rosiene J, Shaiber A, Danko D, Afshinnekoo E, MacKay M, Sedlazeck FJ, Ivanov NA, Sierra M, Pohle D, Zietz M, Gisladottir U, Ramlall V, Sholle ET, Schenck EJ, Westover CD, Hassan C, Ryon K, Young B, Bhattacharya C, Ng DL, Granados AC, Santos YA, Servellita V, Federman S, Ruggiero P, Fungtammasan A, Chin C-S, Pearson NM, Langhorst BW, Tanner NA, Kim Y, Reeves JW, Hether TD, Warren SE, Bailey M, Gawrys J, Meleshko D, Xu D, Couto-Rodriguez M, Nagy-Szakal D, Barrows J, Wells H, O'Hara NB, Rosenfeld JA, Chen Y, Steel PAD, Shemesh AJ, Xiang J, Thierry-Mieg J, Thierry-Mieg D, Iftner A, Bezdan D, Sanchez E, Campion TR, Sipley J, Cong L, Craney A, Velu P, Melnick AM, Shapira S, Hajirasouliha I, Borczuk A, Iftner T, Salvatore M, Loda M, Westblade LF, Cushing M, Wu S, Levy S, Chiu C, Schwartz RE, Tatonetti N, Rennert H, Imielinski M, Mason CE. Shotgun transcriptome, spatial omics, and isothermal profiling of SARS-CoV-2 infection reveals unique host responses, viral diversification, and drug interactions. Nat Commun. 2021;12(1):1660.
Melin AD, Orkin JD, Janiak MC, Valenzuela A, Kuderna L, Marrone F, Ramangason H, Horvath JE, Roos C, Kitchener AC, Khor CChuen, Lim WKhong, Lee JGH, Tan P, Umapathy G, Raveendran M, Harris RA, Gut I, Gut M, Lizano E, Nadler T, Zinner D, Le MD, Manu S, Rabarivola CJ, Zaramody A, Andriaholinirina N, Johnson SE, Jarvis ED, Fedrigo O, Wu D, Zhang G, Farh KKai-How, Rogers J, Marques-Bonet T, Navarro A, Juan D, Arora PS, Higham JP. Variation in predicted COVID-19 risk among lemurs and lorises. Am J Primatol. 2021;83(6):e23255.
Farinholt T, Doddapaneni H, Qin X, Menon V, Meng Q, Metcalf GA, Chao H, Gingras M-C, Farinholt P, Agrawal C, Muzny DM, Piedra PA, Gibbs RA, Petrosino J. Transmission event of SARS-CoV-2 Delta variant reveals multiple vaccine breakthrough infections. medRxiv. 2021;.
Chen F, Zhang Y, Sucgang R, Ramani S, Corry D, Kheradmand F, Creighton CJ. Meta-analysis of host transcriptional responses to SARS-CoV-2 infection reveals their manifestation in human tumors. Sci Rep. 2021;11(1):2459.
Cheng J, Zhou J, Fu S, Fu J, Zhou B, Chen H, Fu J, Wei C. Prostate adenocarcinoma and COVID-19: The possible impacts of TMPRSS2 expressions in susceptibility to SARS-CoV-2. J Cell Mol Med. 2021;25(8):4157-4165.
Sapoval N, Mahmoud M, Jochum MD, Liu Y, Elworth RALeo, Wang Q, Albin D, Ogilvie HA, Lee MD, Villapol S, Hernandez KM, Berry IMaljkovic, Foox J, Beheshti A, Ternus K, Aagaard KM, Posada D, Mason CE, Sedlazeck FJ, Treangen TJ. SARS-CoV-2 genomic diversity and the implications for qRT-PCR diagnostics and transmission. Genome Res. 2021;31(4):635-644.
Li D, Liu X, Zhang L, He J, Chen X, Liu S, Fu J, Fu S, Chen H, Fu J, Cheng J. COVID-19 disease and malignant cancers: The impact for the gene expression in susceptibility to SARS-CoV-2. Int J Biol Sci. 2021;17(14):3954-3967.
Doddapaneni H, Cregeen SJavornik, Sucgang R, Meng Q, Qin X, Avadhanula V, Chao H, Menon V, Nicholson E, Henke D, Piedra F-A, Rajan A, Momin Z, Kottapalli K, Hoffman KL, Sedlazeck FJ, Metcalf GA, Piedra PA, Muzny DM, Petrosino JF, Gibbs RA. Oligonucleotide capture sequencing of the SARS-CoV-2 genome and subgenomic fragments from COVID-19 individuals. PLoS One. 2021;16(8):e0244468.
Butler DJ, Mozsary C, Meydan C, Danko D, Foox J, Rosiene J, Shaiber A, Afshinnekoo E, MacKay M, Sedlazeck FJ, Ivanov NA, Sierra M, Pohle D, Zietz M, Gisladottir U, Ramlall V, Westover CD, Ryon K, Young B, Bhattacharya C, Ruggiero P, Langhorst BW, Tanner N, Gawrys J, Meleshko D, Xu D, Steel PAD, Shemesh AJ, Xiang J, Thierry-Mieg J, Thierry-Mieg D, Schwartz RE, Iftner A, Bezdan D, Sipley J, Cong L, Craney A, Velu P, Melnick AM, Hajirasouliha I, Horner SM, Iftner T, Salvatore M, Loda M, Westblade LF, Cushing M, Levy S, Wu S, Tatonetti N, Imielinski M, Rennert H, Mason CE. Shotgun Transcriptome and Isothermal Profiling of SARS-CoV-2 Infection Reveals Unique Host Responses, Viral Diversification, and Drug Interactions. bioRxiv. 2020;.
Doddapaneni H, Cregeen SJavornik, Sucgang R, Meng Q, Qin X, Avadhanula V, Chao H, Menon V, Nicholson E, Henke D, Piedra F-A, Rajan A, Momin Z, Kottapalli K, Hoffman KL, Sedlazeck FJ, Metcalf GA, Piedra PA, Muzny DM, Petrosino JF, Gibbs RA. Oligonucleotide capture sequencing of the SARS-CoV-2 genome and subgenomic fragments from COVID-19 individuals. bioRxiv. 2020;.
Sapoval N, Mahmoud M, Jochum MD, Liu Y, Elworth RALeo, Wang Q, Albin D, Ogilvie H, Lee MD, Villapol S, Hernandez KM, Berry IMaljkovic, Foox J, Beheshti A, Ternus K, Aagaard KM, Posada D, Mason CE, Sedlazeck FJ, Treangen TJ. Hidden genomic diversity of SARS-CoV-2: implications for qRT-PCR diagnostics and transmission. bioRxiv. 2020;.
Doddapaneni H, Cregeen SJavornik, Sucgang R, Meng Q, Qin X, Avadhanula V, Chao H, Menon V, Nicholson E, Henke D, Piedra F-A, Rajan A, Momin Z, Kottapalli K, Hoffman KL, Sedlazeck FJ, Metcalf GA, Piedra PA, Muzny DM, Petrosino JF, Gibbs RA. Oligonucleotide Capture Sequencing of the SARS-CoV-2 Genome and Subgenomic Fragments from COVID-19 Individuals. bioRxiv. 2020;.