Tag: NetMHCpan
The impact of mutational clonality in predicting the response to immune checkpoint inhibitors in advanced urothelial cancer
Genomic analysis and cohort description We generated whole-exome sequencing (WES) and RNA sequencing (RNA-Seq) data from tumors and blood samples from 27 advanced urothelial cancer patients treated with anti-PD-1/PD-L1 ICIs at Hospital del Mar (Fig. 1a). WES data was obtained from the tumors before treatment as well as from blood samples,…
Geographically Biased Composition of NetMHCpan Training Datasets and Evaluation of MHC-Peptide Binding Prediction Accuracy on Novel Alleles
%PDF-1.5 % 363 0 obj <> endobj 551 0 obj <>stream application/pdf Geographically Biased Composition of NetMHCpan Training Datasets and Evaluation of MHC-Peptide Binding Prediction Accuracy on Novel Alleles 2023-09-03T15:23:34Z LaTeX with hyperref 2023-09-06T20:36:11-07:00 2023-09-06T20:36:11-07:00 pdfTeX-1.40.24 False This is pdfTeX, Version 3.141592653-2.6-1.40.24 (TeX Live 2022) kpathsea version 6.3.4 uuid:eeac1a1e-1dd1-11b2-0a00-b808276d7200 uuid:eeac1a20-1dd1-11b2-0a00-b80000000000 endstream…
Y chromosome loss in cancer drives growth by evasion of adaptive immunity
Caceres, A., Jene, A., Esko, T., Perez-Jurado, L. A. & Gonzalez, J. R. Extreme downregulation of chromosome Y and cancer risk in men. J. Natl Cancer Inst. 112, 913–920 (2020). Article PubMed PubMed Central Google Scholar Kido, T. & Lau, Y. F. Roles of the Y chromosome genes in human…
Kriptic Pharmaceuticals Limited hiring Bioinformatics Engineer in Dublin, County Dublin, Ireland
We are looking for a skilled bioinformatics engineer to develop and maintain the data analysis process of onco-genomics, especially of neoantigen prediction based Next Generation Sequencing data and IEDB/IGMT database. Responsibilities Responsible for algorithm research and process construction of tumor NGS related data analysis process; Responsible for neoantigens analysis and…
Protein code and shape used to predict peptide-protein interactions
Solving puzzles experimentally is enjoyable for many researchers. However, there are some puzzles that force even the best puzzlers to nominate modeling over experimental approaches to help decipher how the pieces fit together. Uncovering which proteins interact with which short peptide or protein fragment is an extremely complex puzzle. Yet,…
Efficient evolution of human antibodies from general protein language models
Acquiring amino acid substitutions via language model consensus We select amino acid substitutions recommended by a consensus of language models. We take as input a single wild-type sequence x = (x1,…,xN)∈ \(\mathcal{X}\)N, where \(\mathcal{X}\) is the set of amino acids, and N is the sequence length. We also require a set of…
Neoantigen-targeted CD8+ T cell responses with PD-1 blockade therapy
Schumacher, T. N. & Schreiber, R. D. Neoantigens in cancer immunotherapy. Science 348, 69–74 (2015). Article ADS CAS PubMed Google Scholar Tran, E., Robbins, P. F. & Rosenberg, S. A. Final common pathway’ of human cancer immunotherapy: targeting random somatic mutations. Nat. Immunol. 18, 255–262 (2017). Article CAS PubMed PubMed…
Automated Server Benchmarks
MHCI Weekly Benchmark results Overall scores Overall scores based on data sets submitted to the IEDB within a single week. The overall scores in the SRCC and AUC columns are calculated using performance values for only SRCC or AUC respectively. In the overall column, both evaluation types are used. Datasets…
