For a full up-to-date list on all publications click here.
Featured Publications:
An omic and multidimensional spatial atlas from serial biopsies of an evolving metastatic breast cancer
Citation:
Johnson BE, Creason AL, Stommel JM, Keck JM, Parmar S, Betts CB, Blucher A, Boniface C, Bucher E, Burlingame E, Camp T, Chin K, Eng J, Estabrook J, Feiler HS, Heskett MB, Hu Z, Kolodzie A, Kong BL, Labrie M, Lee J, Leyshock P, Mitri S, Patterson J, Riesterer JL, Sivagnanam S, Somers J, Sudar D, Thibault G, Weeder BR, Zheng C, Nan X, Thompson RF, Heiser LM, Spellman PT, Thomas G, Demir E, Chang YH, Coussens LM, Guimaraes AR, Corless C, Goecks J, Bergan R, Mitri Z, Mills GB, Gray JW. An omic and multidimensional spatial atlas from serial biopsies of an evolving metastatic breast cancer. Cell Rep Med. 2022 Feb 15;3(2):100525. doi: 10.1016/j.xcrm.2022.100525. PMID: 35243422; PMCID: PMC8861971.
Associated websites and highlights:
- SMMART Clinical Trial Program
- Story of the first SMMART clinical trial patient (featured in the scientific article above)
Pepsickle rapidly and accurately predicts proteasomal cleavage sites for improved neoantigen identification
Citation:
Weeder BR, Wood MA, Li E, Nellore A, Thompson RF. pepsickle rapidly and accurately predicts proteasomal cleavage sites for improved neoantigen identification. Bioinformatics. 2021 Nov 5;37(21):3723-3733. doi: 10.1093/bioinformatics/btab628. PMID: 34478497.
Associated software and repositories:
Chronological List of Publications:
Carratt SA, Kong GL, Coblentz C, Schonrock Z, Maloney L, Weeder B, Yashar W, Callahan R, Blaylock H, Coleman C, Coleman D, Braun TP, Maxson JE. RUNX1::ETO translocations must precede CSF3R mutations to promote acute myeloid leukemia development. Leukemia. 2023 Mar 9. doi: 10.1038/s41375-023-01862-8. Epub ahead of print. PMID: 36894620.
Johnson BE, Creason AL, Stommel JM, Keck JM, Parmar S, Betts CB, Blucher A, Boniface C, Bucher E, Burlingame E, Camp T, Chin K, Eng J, Estabrook J, Feiler HS, Heskett MB, Hu Z, Kolodzie A, Kong BL, Labrie M, Lee J, Leyshock P, Mitri S, Patterson J, Riesterer JL, Sivagnanam S, Somers J, Sudar D, Thibault G, Weeder BR, Zheng C, Nan X, Thompson RF, Heiser LM, Spellman PT, Thomas G, Demir E, Chang YH, Coussens LM, Guimaraes AR, Corless C, Goecks J, Bergan R, Mitri Z, Mills GB, Gray JW. An omic and multidimensional spatial atlas from serial biopsies of an evolving metastatic breast cancer. Cell Rep Med. 2022 Feb 15;3(2):100525. doi: 10.1016/j.xcrm.2022.100525. PMID: 35243422; PMCID: PMC8861971.
Weeder BR, Wood MA, Li E, Nellore A, Thompson RF. pepsickle rapidly and accurately predicts proteasomal cleavage sites for improved neoantigen identification. Bioinformatics. 2021 Nov 5;37(21):3723-3733. doi: 10.1093/bioinformatics/btab628. PMID: 34478497.
Nguyen A, David JK, Maden SK, Wood MA, Weeder BR, Nellore A, Thompson RF. Human Leukocyte Antigen Susceptibility Map for Severe Acute Respiratory Syndrome Coronavirus 2. J Virol. 2020 Jun 16;94(13):e00510-20. doi: 10.1128/JVI.00510-20. PMID: 32303592; PMCID: PMC7307149.
Wood MA, Weeder BR, David JK, Nellore A, Thompson RF. Burden of tumor mutations, neoepitopes, and other variants are weak predictors of cancer immunotherapy response and overall survival. Genome Med. 2020 Mar 30;12(1):33. doi: 10.1186/s13073-020-00729-2. PMID: 32228719; PMCID: PMC7106909.
David JK, Maden SK, Weeder BR, Thompson RF, Nellore A. Putatively cancer-specific exon-exon junctions are shared across patients and present in developmental and other non-cancer cells. NAR Cancer. 2020 Jan 29;2(1):zcaa001. doi: 10.1093/narcan/zcaa001. PMID: 34316681; PMCID: PMC8209686.
Braun TP, Okhovat M, Coblentz C, Carratt SA, Foley A, Schonrock Z, Curtiss BM, Nevonen K, Davis B, Garcia B, LaTocha D, Weeder BR, Grzadkowski MR, Estabrook JC, Manning HG, Watanabe-Smith K, Jeng S, Smith JL, Leonti AR, Ries RE, McWeeney S, Di Genua C, Drissen R, Nerlov C, Meshinchi S, Carbone L, Druker BJ, Maxson JE. Myeloid lineage enhancers drive oncogene synergy in CEBPA/CSF3R mutant acute myeloid leukemia. Nat Commun. 2019 Nov 29;10(1):5455. doi: 10.1038/s41467-019-13364-2. Erratum in: Nat Commun. 2022 Jun 16;13(1):3471. PMID: 31784538; PMCID: PMC6884457.