Publications

Selected Publications from our Founders

  1. Cytokit: a single-cell analysis toolkit for high dimensional fluorescent microscopy imaging. Czech E, Aksoy BA, Aksoy P, Hammerbacher J. BMC Bioinformatics. 2019 Sep 2;20(1):448. doi: 10.1186/s12859-019-3055-3. PMID: 31477013
     

  2. MHCflurry: Open-Source Class I MHC Binding Affinity Prediction. O'Donnell TJ, Rubinsteyn A, Bonsack M, Riemer AB, Laserson U, Hammerbacher J. Cell Syst. 2018 Jul 25;7(1):129-132.e4. doi: 10.1016/j.cels.2018.05.014. Epub 2018 Jun 27. PMID: 29960884
     

  3. Computational Pipeline for the PGV-001 Neoantigen Vaccine Trial. Rubinsteyn A, Kodysh J, Hodes I, Mondet S, Aksoy BA, Finnigan JP, Bhardwaj N, Hammerbacher J. Front Immunol. 2018 Jan 18;8:1807. doi: 10.3389/fimmu.2017.01807. eCollection 2017. PMID: 29403468
     

  4. Chemotherapy weakly contributes to predicted neoantigen expression in ovarian cancer. O'Donnell T, Christie EL, Ahuja A, Buros J, Aksoy BA, Bowtell DDL, Snyder A, Hammerbacher J. BMC Cancer. 2018 Jan 22;18(1):87. doi: 10.1186/s12885-017-3825-0. PMID: 29357823
     

  5. Somatic Mutations and Neoepitope Homology in Melanomas Treated with CTLA-4 Blockade. Nathanson T, Ahuja A, Rubinsteyn A, Aksoy BA, Hellmann MD, Miao D, Van Allen E, Merghoub T, Wolchok JD, Snyder A, Hammerbacher J. Cancer Immunol Res. 2017 Jan;5(1):84-91. doi: 10.1158/2326-6066.CIR-16-0019. Epub 2016 Dec 12. PMID: 27956380
     

  6. pileup.js: a JavaScript library for interactive and in-browser visualization of genomic data. Vanderkam D, Aksoy BA, Hodes I, Perrone J, Hammerbacher J. Bioinformatics. 2016 Aug 1;32(15):2378-9. doi: 10.1093/bioinformatics/btw167. Epub 2016 Mar 29. PMID: 27153605
     

  7. Enriched protein screening of human bone marrow mesenchymal stromal cell secretions reveals MFAP5 and PENK as novel IL-10 modulators. Milwid JM, Elman JS, Li M, Shen K, Manrai A, Gabow A, Yarmush J, Jiao Y, Fletcher A, Lee J, Cima MJ, Yarmush ML, Parekkadan B. Mol Ther. 2014 May;22(5):999-1007. doi: 10.1038/mt.2014.17. Epub 2014 Feb 5. PMID: 24496384
     

  8. Secreted factors from bone marrow stromal cells upregulate IL-10 and reverse acute kidney injury. Milwid JM, Ichimura T, Li M, Jiao Y, Lee J, Yarmush JS, Parekkadan B, Tilles AW, Bonventre JV, Yarmush ML. Stem Cells Int. 2012;2012:392050. doi: 10.1155/2012/392050. Epub 2012 Dec 19. PMID: 23319959
     

  9. Mesenchymal stem cells as therapeutics. Parekkadan B, Milwid JM. Annu Rev Biomed Eng. 2010 Aug 15;12:87-117. doi: 10.1146/annurev-bioeng-070909-105309. Review. PMID: 20415588             

  10. Key Parameters of Tumor Epitope Immunogenicity Revealed Through a Consortium Approach Improve Neoantigen Prediction. Daniel K. Wells, Marit M. van Buuren, Kristen K. Dang, Vanessa M. Hubbard-Lucey, Kathleen C.F. Sheehan, Katie M. Campbell, Andrew Lamb, Jeffrey P. Ward, John Sidney, Ana B. Blazquez, Andrew J. Rech, Jesse M. Zaretsky, Begonya Comin-Anduix, Alphonsus H.C. Ng, William Chour, Thomas V. Yu, Hira Rizvi, Jia M. Chen, Patrice Manning, Gabriela M. Steiner, Xengie C. Doan, The Tumor Neoantigen Selection Alliance, Taha Merghoub, Justin Guinney, Adam Kolom, Cheryl Selinsky, Antoni Ribas, Matthew D. Hellmann, 
    Nir Hacohen, Alessandro Sette, James R. Heath, Nina Bhardwaj, Fred Ramsdell, Robert D. Schreiber, Ton N. Schumacher, Pia Kvistborg. Nadine A. Defranoux, 2020, Oct 09, doi:https://doi.org/10.1016/j.cell.2020.09.015

     

© 2020 Related Sciences. All Rights Reserved. 

RELATED SCIENCES is a registered trademark of Related Sciences LLC