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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: cowell lg. BMC Bioinformatics. 2016 Oct 6;17(Suppl 13):333. doi: 10.1186/s12859-016-1214-3. BMC Bioinformatics. 2016. PMID: 27766961 Free PMC article.
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: cowell lg. BMC Bioinformatics. 2017 Oct 11;18(1):448. doi: 10.1186/s12859-017-1853-z. BMC Bioinformatics. 2017. PMID: 29020925 Free PMC article.
Adaptive Immune Receptor Repertoire Community recommendations for sharing immune-repertoire sequencing data.
Rubelt F, Busse CE, Bukhari SAC, Bürckert JP, Mariotti-Ferrandiz E, Cowell LG, Watson CT, Marthandan N, Faison WJ, Hershberg U, Laserson U, Corrie BD, Davis MM, Peters B, Lefranc MP, Scott JK, Breden F; AIRR Community; Luning Prak ET, Kleinstein SH. Rubelt F, et al. Among authors: cowell lg. Nat Immunol. 2017 Nov 16;18(12):1274-1278. doi: 10.1038/ni.3873. Nat Immunol. 2017. PMID: 29144493 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: cowell lg. Front Immunol. 2018 May 8;9:976. doi: 10.3389/fimmu.2018.00976. eCollection 2018. Front Immunol. 2018. PMID: 29867956 Free PMC article.
Reproducibility and Reuse of Adaptive Immune Receptor Repertoire Data.
Breden F, Luning Prak ET, Peters B, Rubelt F, Schramm CA, Busse CE, Vander Heiden JA, Christley S, Bukhari SAC, Thorogood A, Matsen Iv FA, Wine Y, Laserson U, Klatzmann D, Douek DC, Lefranc MP, Collins AM, Bubela T, Kleinstein SH, Watson CT, Cowell LG, Scott JK, Kepler TB. Breden F, et al. Among authors: cowell lg. Front Immunol. 2017 Nov 1;8:1418. doi: 10.3389/fimmu.2017.01418. eCollection 2017. Front Immunol. 2017. PMID: 29163494 Free PMC article.
Data Sharing and Reuse: A Method by the AIRR Community.
Corrie BD, Christley S, Busse CE, Cowell LG, Neller KCM, Rubelt F, Schwab N; AIRR Community. Corrie BD, et al. Among authors: cowell lg. Methods Mol Biol. 2022;2453:447-476. doi: 10.1007/978-1-0716-2115-8_23. Methods Mol Biol. 2022. PMID: 35622339 Free PMC article.
owlcpp: a C++ library for working with OWL ontologies.
Levin MK, Cowell LG. Levin MK, et al. Among authors: cowell lg. J Biomed Semantics. 2015 Sep 16;6:35. doi: 10.1186/s13326-015-0035-z. eCollection 2015. J Biomed Semantics. 2015. PMID: 26388983 Free PMC article.
78 results