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Page 1
CyVerse: Cyberinfrastructure for open science.
Swetnam TL, Antin PB, Bartelme R, Bucksch A, Camhy D, Chism G, Choi I, Cooksey AM, Cosi M, Cowen C, Culshaw-Maurer M, Davey R, Davey S, Devisetty U, Edgin T, Edmonds A, Fedorov D, Frady J, Fonner J, Gillan JK, Hossain I, Joyce B, Lang K, Lee T, Littin S, McEwen I, Merchant N, Micklos D, Nelson A, Ramsey A, Roberts S, Sarando P, Skidmore E, Song J, Sprinkle MM, Srinivasan S, Stanzione D, Strootman JD, Stryeck S, Tuteja R, Vaughn M, Wali M, Wall M, Walls R, Wang L, Wickizer T, Williams J, Wregglesworth J, Lyons E. Swetnam TL, et al. Among authors: fonner j. PLoS Comput Biol. 2024 Feb 7;20(2):e1011270. doi: 10.1371/journal.pcbi.1011270. eCollection 2024 Feb. PLoS Comput Biol. 2024. PMID: 38324613 Free PMC article.
Leveraging the national cyberinfrastructure for biomedical research.
LeDuc R, Vaughn M, Fonner JM, Sullivan M, Williams JG, Blood PD, Taylor J, Barnett W. LeDuc R, et al. Among authors: fonner jm. J Am Med Inform Assoc. 2014 Mar-Apr;21(2):195-9. doi: 10.1136/amiajnl-2013-002059. Epub 2013 Aug 20. J Am Med Inform Assoc. 2014. PMID: 23964072 Free PMC article.
VDJServer: A Cloud-Based Analysis Portal and Data Commons for Immune Repertoire Sequences and Rearrangements.
Christley S, Scarborough W, Salinas E, Rounds WH, Toby IT, Fonner JM, Levin MK, Kim M, Mock SA, Jordan C, Ostmeyer J, Buntzman A, Rubelt F, Davila ML, Monson NL, Scheuermann RH, Cowell LG. Christley S, et al. Among authors: fonner jm. Front Immunol. 2018 May 8;9:976. doi: 10.3389/fimmu.2018.00976. eCollection 2018. Front Immunol. 2018. PMID: 29867956 Free PMC article.
Prediction of whole-cell transcriptional response with machine learning.
Eslami M, Borujeni AE, Eramian H, Weston M, Zheng G, Urrutia J, Corbet C, Becker D, Maschhoff P, Clowers K, Cristofaro A, Hosseini HD, Gordon DB, Dorfan Y, Singer J, Vaughn M, Gaffney N, Fonner J, Stubbs J, Voigt CA, Yeung E. Eslami M, et al. Among authors: fonner j. Bioinformatics. 2022 Jan 3;38(2):404-409. doi: 10.1093/bioinformatics/btab676. Bioinformatics. 2022. PMID: 34570169
VDJPipe: a pipelined tool for pre-processing immune repertoire sequencing data.
Christley S, Levin MK, Toby IT, Fonner JM, Monson NL, Rounds WH, Rubelt F, Scarborough W, Scheuermann RH, Cowell LG. Christley S, et al. Among authors: fonner jm. BMC Bioinformatics. 2017 Oct 11;18(1):448. doi: 10.1186/s12859-017-1853-z. BMC Bioinformatics. 2017. PMID: 29020925 Free PMC article.
VDJML: a file format with tools for capturing the results of inferring immune receptor rearrangements.
Toby IT, Levin MK, Salinas EA, Christley S, Bhattacharya S, Breden F, Buntzman A, Corrie B, Fonner J, Gupta NT, Hershberg U, Marthandan N, Rosenfeld A, Rounds W, Rubelt F, Scarborough W, Scott JK, Uduman M, Vander Heiden JA, Scheuermann RH, Monson N, Kleinstein SH, Cowell LG. Toby IT, et al. Among authors: fonner j. BMC Bioinformatics. 2016 Oct 6;17(Suppl 13):333. doi: 10.1186/s12859-016-1214-3. BMC Bioinformatics. 2016. PMID: 27766961 Free PMC article.
Biocompatibility implications of polypyrrole synthesis techniques.
Fonner JM, Forciniti L, Nguyen H, Byrne JD, Kou YF, Syeda-Nawaz J, Schmidt CE. Fonner JM, et al. Biomed Mater. 2008 Sep;3(3):034124. doi: 10.1088/1748-6041/3/3/034124. Epub 2008 Sep 3. Biomed Mater. 2008. PMID: 18765899 Free PMC article.