{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,3]],"date-time":"2026-03-03T15:17:11Z","timestamp":1772551031084,"version":"3.50.1"},"reference-count":9,"publisher":"Oxford University Press (OUP)","issue":"19","license":[{"start":{"date-parts":[[2017,6,15]],"date-time":"2017-06-15T00:00:00Z","timestamp":1497484800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100002428","name":"Austrian Science Fund","doi-asserted-by":"publisher","award":["W1101-B18"],"award-info":[{"award-number":["W1101-B18"]}],"id":[{"id":"10.13039\/501100002428","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004061","name":"Austrian National Bank","doi-asserted-by":"publisher","award":["16534"],"award-info":[{"award-number":["16534"]}],"id":[{"id":"10.13039\/501100004061","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2017,10,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>Recently, a number of powerful computational tools for dissecting tumor-immune cell interactions from next-generation sequencing data have been developed. However, the assembly of analytical pipelines and execution of multi-step workflows are laborious and involve a large number of intermediate steps with many dependencies and parameter settings. Here we present TIminer, an easy-to-use computational pipeline for mining tumor-immune cell interactions from next-generation sequencing data. TIminer enables integrative immunogenomic analyses, including: human leukocyte antigens typing, neoantigen prediction, characterization of immune infiltrates and quantification of tumor immunogenicity.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>TIminer is freely available at http:\/\/icbi.i-med.ac.at\/software\/timiner\/timiner.shtml.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btx377","type":"journal-article","created":{"date-parts":[[2017,6,8]],"date-time":"2017-06-08T11:09:22Z","timestamp":1496920162000},"page":"3140-3141","source":"Crossref","is-referenced-by-count":78,"title":["TIminer: NGS data mining pipeline for cancer immunology and immunotherapy"],"prefix":"10.1093","volume":"33","author":[{"given":"Elias","family":"Tappeiner","sequence":"first","affiliation":[{"name":"Division of Bioinformatics, Biocenter, Medical University of Innsbruck, Innsbruck, Austria"}]},{"given":"Francesca","family":"Finotello","sequence":"additional","affiliation":[{"name":"Division of Bioinformatics, Biocenter, Medical University of Innsbruck, Innsbruck, Austria"}]},{"given":"Pornpimol","family":"Charoentong","sequence":"additional","affiliation":[{"name":"Division of Bioinformatics, Biocenter, Medical University of Innsbruck, Innsbruck, Austria"}]},{"given":"Clemens","family":"Mayer","sequence":"additional","affiliation":[{"name":"Division of Bioinformatics, Biocenter, Medical University of Innsbruck, Innsbruck, Austria"}]},{"given":"Dietmar","family":"Rieder","sequence":"additional","affiliation":[{"name":"Division of Bioinformatics, Biocenter, Medical University of Innsbruck, Innsbruck, Austria"}]},{"given":"Zlatko","family":"Trajanoski","sequence":"additional","affiliation":[{"name":"Division of Bioinformatics, Biocenter, Medical University of Innsbruck, Innsbruck, Austria"}]}],"member":"286","published-online":{"date-parts":[[2017,6,15]]},"reference":[{"key":"2023020206464389700_btx377-B1","doi-asserted-by":"crossref","first-page":"64","DOI":"10.1186\/s13059-015-0620-6","article-title":"Characterization of the immunophenotypes and antigenomes of colorectal cancers reveals distinct tumor escape mechanisms and novel targets for immunotherapy","volume":"16","author":"Angelova","year":"2015","journal-title":"Genome Biol"},{"key":"2023020206464389700_btx377-B2","doi-asserted-by":"crossref","DOI":"10.1186\/s13059-017-1349-1","article-title":"xcell: digitally portraying the tissue cellular heterogeneity landscape","author":"Aran","year":"2017"},{"key":"2023020206464389700_btx377-B3","doi-asserted-by":"crossref","first-page":"525","DOI":"10.1038\/nbt.3519","article-title":"Near-optimal probabilistic RNA-seq quantification","volume":"34","author":"Bray","year":"2016","journal-title":"Nat. Biotechnol"},{"key":"2023020206464389700_btx377-B4","doi-asserted-by":"crossref","first-page":"248","DOI":"10.1016\/j.celrep.2016.12.019","article-title":"Pan-cancer immunogenomic analyses reveal genotype-immunophenotype relationships and predictors of response to checkpoint blockade","volume":"18","author":"Charoentong","year":"2017","journal-title":"Cell Rep"},{"key":"2023020206464389700_btx377-B5","doi-asserted-by":"crossref","first-page":"441","DOI":"10.1038\/nrg.2016.67","article-title":"Computational genomics tools for dissecting tumour-immune cell interactions","volume":"17","author":"Hackl","year":"2016","journal-title":"Nat. Rev. Genet"},{"key":"2023020206464389700_btx377-B6","doi-asserted-by":"crossref","first-page":"122.","DOI":"10.1186\/s13059-016-0974-4","article-title":"The Ensembl variant effect predictor","volume":"17","author":"McLaren","year":"2016","journal-title":"Genome Biol"},{"key":"2023020206464389700_btx377-B7","doi-asserted-by":"crossref","first-page":"33.","DOI":"10.1186\/s13073-016-0288-x","article-title":"NetMHCpan-3.0; improved prediction of binding to MHC class I molecules integrating information from multiple receptor and peptide length datasets","volume":"8","author":"Nielsen","year":"2016","journal-title":"Genome Med"},{"key":"2023020206464389700_btx377-B8","doi-asserted-by":"crossref","first-page":"15545","DOI":"10.1073\/pnas.0506580102","article-title":"Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles","volume":"102","author":"Subramanian","year":"2005","journal-title":"Proc. Natl. Acad. Sci. 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