TY - JOUR AU - Learn, C. A. PY - 2004 DA - 2004// TI - Resistance to tyrosine kinase inhibition by mutant epidermal growth factor receptor variant III contributes to the neoplastic phenotype of glioblastoma multiforme JO - Clin. Cancer Res VL - 10 UR - https://doi.org/10.1158/1078-0432.CCR-03-0521 DO - 10.1158/1078-0432.CCR-03-0521 ID - Learn2004 ER - TY - JOUR AU - Zhang, Z. -. M. PY - 2016 DA - 2016// TI - Pygo2 activates MDR1 expression and mediates chemoresistance in breast cancer via the Wnt/β-catenin pathway JO - Oncogene VL - 35 UR - https://doi.org/10.1038/onc.2016.10 DO - 10.1038/onc.2016.10 ID - Zhang2016 ER - TY - JOUR AU - Martín-Martín, N. PY - 2016 DA - 2016// TI - Stratification and therapeutic potential of PML in metastatic breast cancer JO - Nat Commun. VL - 7 UR - https://doi.org/10.1038/ncomms12595 DO - 10.1038/ncomms12595 ID - Martín-Martín2016 ER - TY - JOUR AU - Grossman, R. L. PY - 2016 DA - 2016// TI - Toward a shared vision for cancer genomic data JO - N. Engl. J. Med. VL - 375 UR - https://doi.org/10.1056/NEJMp1607591 DO - 10.1056/NEJMp1607591 ID - Grossman2016 ER - TY - JOUR AU - Audoux, J. PY - 2017 DA - 2017// TI - DE-kupl: exhaustive capture of biological variation in RNA-seq data through k-mer decomposition JO - Genome Biol. VL - 18 UR - https://doi.org/10.1186/s13059-017-1372-2 DO - 10.1186/s13059-017-1372-2 ID - Audoux2017 ER - TY - STD TI - Kirk, J. M. et al. Functional classification of long non-coding RNAs by k-mer content. Nat. Genet. 50, 1474–1482 (2018). ID - ref6 ER - TY - JOUR AU - Ounit, R. AU - Wanamaker, S. AU - Close, T. J. AU - Lonardi, S. PY - 2015 DA - 2015// TI - CLARK: fast and accurate classification of metagenomic and genomic sequences using discriminative k-mers JO - BMC Genomics VL - 16 UR - https://doi.org/10.1186/s12864-015-1419-2 DO - 10.1186/s12864-015-1419-2 ID - Ounit2015 ER - TY - JOUR AU - Breitwieser, F. P. AU - Baker, D. N. AU - Salzberg, S. L. PY - 2018 DA - 2018// TI - KrakenUniq: confident and fast metagenomics classification using unique k-mer counts JO - Genome Biol. VL - 19 UR - https://doi.org/10.1186/s13059-018-1568-0 DO - 10.1186/s13059-018-1568-0 ID - Breitwieser2018 ER - TY - JOUR AU - Thomas, A. PY - 2019 DA - 2019// TI - GECKO is a genetic algorithm to classify and explore high throughput sequencing data JO - Commun. Biol VL - 2 UR - https://doi.org/10.1038/s42003-019-0456-9 DO - 10.1038/s42003-019-0456-9 ID - Thomas2019 ER - TY - JOUR AU - Kokot, M. AU - Dlugosz, M. AU - Deorowicz, S. PY - 2017 DA - 2017// TI - KMC 3: counting and manipulating k-mer statistics JO - Bioinforma. Oxf. Engl. VL - 33 UR - https://doi.org/10.1093/bioinformatics/btx304 DO - 10.1093/bioinformatics/btx304 ID - Kokot2017 ER - TY - JOUR AU - Sacomoto, G. A. T. PY - 2012 DA - 2012// TI - KISSPLICE: de-novo calling alternative splicing events from RNA-seq data JO - BMC Bioinformatics VL - 13 UR - https://doi.org/10.1186/1471-2105-13-S6-S5 DO - 10.1186/1471-2105-13-S6-S5 ID - Sacomoto2012 ER - TY - JOUR AU - Love, M. I. AU - Huber, W. AU - Anders, S. PY - 2014 DA - 2014// TI - Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 JO - Genome Biol. VL - 15 UR - https://doi.org/10.1186/s13059-014-0550-8 DO - 10.1186/s13059-014-0550-8 ID - Love2014 ER - TY - JOUR AU - Robinson, M. D. AU - McCarthy, D. J. AU - Smyth, G. K. PY - 2010 DA - 2010// TI - edgeR: a Bioconductor package for differential expression analysis of digital gene expression data JO - Bioinformatics VL - 26 UR - https://doi.org/10.1093/bioinformatics/btp616 DO - 10.1093/bioinformatics/btp616 ID - Robinson2010 ER - TY - JOUR AU - Ritchie, M. E. PY - 2015 DA - 2015// TI - limma powers differential expression analyses for RNA-sequencing and microarray studies JO - Nucleic Acids Res VL - 43 UR - https://doi.org/10.1093/nar/gkv007 DO - 10.1093/nar/gkv007 ID - Ritchie2015 ER - TY - JOUR AU - Sterne-Weiler, T. AU - Weatheritt, R. J. AU - Best, A. J. AU - Ha, K. C. H. AU - Blencowe, B. J. PY - 2018 DA - 2018// TI - Efficient and accurate quantitative profiling of alternative splicing patterns of any complexity on a laptop JO - Mol. Cell VL - 72 UR - https://doi.org/10.1016/j.molcel.2018.08.018 DO - 10.1016/j.molcel.2018.08.018 ID - Sterne-Weiler2018 ER - TY - STD TI - Rahman A, Hallgrímsdóttir I, Eisen M, Pachter L. Association mapping from sequencing reads using k-mers. eLife 2018;7:e32920. ID - ref16 ER - TY - JOUR AU - Drouin, A. PY - 2016 DA - 2016// TI - Predictive computational phenotyping and biomarker discovery using reference-free genome comparisons JO - BMC Genomics VL - 17 UR - https://doi.org/10.1186/s12864-016-2889-6 DO - 10.1186/s12864-016-2889-6 ID - Drouin2016 ER - TY - JOUR AU - Hastie, T. AU - The, T. PY - 2017 DA - 2017// TI - Elements of statistical learning second edition JO - Math Intell VL - 27 ID - Hastie2017 ER - TY - STD TI - Breiman, L. Out-of-bag estimation. in (1996). ID - ref19 ER - TY - JOUR AU - Bastien, R. R. L. PY - 2012 DA - 2012// TI - PAM50 breast cancer subtyping by RT-qPCR and concordance with standard clinical molecular markers JO - BMC Med Genomics VL - 5 UR - https://doi.org/10.1186/1755-8794-5-44 DO - 10.1186/1755-8794-5-44 ID - Bastien2012 ER - TY - JOUR AU - Hoadley, K. A. PY - 2018 DA - 2018// TI - Cell-of-origin patterns dominate the molecular classification of 10,000 tumors from 33 types of cancer JO - Cell VL - 173 UR - https://doi.org/10.1016/j.cell.2018.03.022 DO - 10.1016/j.cell.2018.03.022 ID - Hoadley2018 ER - TY - JOUR AU - Jeannot, E. PY - 2020 DA - 2020// TI - A single droplet digital PCR for ESR1 activating mutations detection in plasma JO - Oncogene VL - 39 UR - https://doi.org/10.1038/s41388-020-1174-y DO - 10.1038/s41388-020-1174-y ID - Jeannot2020 ER - TY - JOUR AU - Ciriello, G. PY - 2015 DA - 2015// TI - Comprehensive molecular portraits of invasive lobular breast cancer JO - Cell VL - 163 UR - https://doi.org/10.1016/j.cell.2015.09.033 DO - 10.1016/j.cell.2015.09.033 ID - Ciriello2015 ER - TY - JOUR AU - Han, B. PY - 2017 DA - 2017// TI - FOXC1: an emerging marker and therapeutic target for cancer JO - Oncogene VL - 36 UR - https://doi.org/10.1038/onc.2017.48 DO - 10.1038/onc.2017.48 ID - Han2017 ER - TY - JOUR AU - Yang, Y. PY - 2015 DA - 2015// TI - TPX2 promotes migration and invasion of human breast cancer cells JO - Asian Pac J. Trop. Med. VL - 8 UR - https://doi.org/10.1016/j.apjtm.2015.11.007 DO - 10.1016/j.apjtm.2015.11.007 ID - Yang2015 ER - TY - JOUR AU - Thakkar, A. PY - 2015 DA - 2015// TI - High expression of three-gene signature improves prediction of relapse-free survival in estrogen receptor-positive and node-positive breast tumors JO - Biomark. Insights VL - 10 UR - https://doi.org/10.4137/BMI.S30559 DO - 10.4137/BMI.S30559 ID - Thakkar2015 ER - TY - JOUR AU - Bjørklund, S. S. PY - 2017 DA - 2017// TI - Widespread alternative exon usage in clinically distinct subtypes of invasive ductal carcinoma JO - Sci. Rep. VL - 7 UR - https://doi.org/10.1038/s41598-017-05537-0 DO - 10.1038/s41598-017-05537-0 ID - Bjørklund2017 ER - TY - JOUR AU - Huang, D. W. AU - Sherman, B. T. AU - Lempicki, R. A. PY - 2009 DA - 2009// TI - Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources JO - Nat. Protoc. VL - 4 UR - https://doi.org/10.1038/nprot.2008.211 DO - 10.1038/nprot.2008.211 ID - Huang2009 ER - TY - JOUR PY - 2011 DA - 2011// TI - Integrated genomic analyses of ovarian carcinoma JO - Nature VL - 474 UR - https://doi.org/10.1038/nature10166 DO - 10.1038/nature10166 ID - ref29 ER - TY - JOUR AU - Villalobos, V. M. AU - Wang, Y. C. AU - Sikic, B. I. PY - 2018 DA - 2018// TI - Reannotation and analysis of clinical and chemotherapy outcomes in the ovarian data set from the Cancer Genome Atlas JO - JCO Clin. Cancer Inform. VL - 2 UR - https://doi.org/10.1200/CCI.17.00096 DO - 10.1200/CCI.17.00096 ID - Villalobos2018 ER - TY - STD TI - Goetz, M. P. et al. Tumor sequencing and patient-derived xenografts in the neoadjuvant treatment of breast cancer.  J Natl Cancer Inst. 2017;109(7):djw306. https://doi.org/10.1093/jnci/djw306. ID - ref31 ER - TY - JOUR AU - Yi, H. AU - Raman, A. T. AU - Zhang, H. AU - Allen, G. I. AU - Liu, Z. PY - 2018 DA - 2018// TI - Detecting hidden batch factors through data-adaptive adjustment for biological effects JO - Bioinforma. Oxf. Engl. VL - 34 UR - https://doi.org/10.1093/bioinformatics/btx635 DO - 10.1093/bioinformatics/btx635 ID - Yi2018 ER - TY - JOUR AU - Middleton, R. PY - 2017 DA - 2017// TI - IRFinder: assessing the impact of intron retention on mammalian gene expression JO - Genome Biol. VL - 18 UR - https://doi.org/10.1186/s13059-017-1184-4 DO - 10.1186/s13059-017-1184-4 ID - Middleton2017 ER - TY - JOUR AU - Shi, X. AU - Sun, X. PY - 2017 DA - 2017// TI - Regulation of paclitaxel activity by microtubule-associated proteins in cancer chemotherapy JO - Cancer Chemother. Pharmacol. VL - 80 UR - https://doi.org/10.1007/s00280-017-3398-2 DO - 10.1007/s00280-017-3398-2 ID - Shi2017 ER - TY - JOUR AU - Buljan, V. A. PY - 2018 DA - 2018// TI - Calcium-axonemal microtubuli interactions underlie mechanism(s) of primary cilia morphological changes JO - J. Biol. Phys. VL - 44 UR - https://doi.org/10.1007/s10867-017-9475-2 DO - 10.1007/s10867-017-9475-2 ID - Buljan2018 ER - TY - STD TI - Fornecker L-M, et al. Multi-omics dataset to decipher the complexity of drug resistance in diffuse large B-cell lymphoma. Sci. Rep. 2019;9. ID - ref36 ER - TY - JOUR AU - Agarwal, N. K. PY - 2013 DA - 2013// TI - Transcriptional regulation of serine/threonine protein kinase (AKT) genes by glioma-associated oncogene homolog 1 JO - J. Biol. Chem. VL - 288 UR - https://doi.org/10.1074/jbc.M112.425249 DO - 10.1074/jbc.M112.425249 ID - Agarwal2013 ER - TY - STD TI - Zhu C, Chen G, Zhao Y, Gao X-M, Wang J. Regulation of the development and function of B cells by ZBTB transcription factors. Front. Immunol. 2018;9. ID - ref38 ER - TY - STD TI - ncbi/sra-tools. (NCBI - National Center for Biotechnology Information/NLM/NIH, 2020) https://github.com/ncbi/sra-tools. UR - https://github.com/ncbi/sra-tools ID - ref39 ER - TY - STD TI - Li H, Handsaker B, Wysoker A, et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009;25(16):2078–9. https://doi.org/10.1093/bioinformatics/btp352. ID - ref40 ER - TY - STD TI - Shen W, Le S, Li Y, Hu F. SeqKit: A Cross-Platform and Ultrafast Toolkit for FASTA/Q File Manipulation. PLoS One. 2016;11(10):e0163962. Published 2016 Oct 5. https://doi.org/10.1371/journal.pone.0163962. ID - ref41 ER - TY - STD TI - FastQC: a quality control tool for high throughput sequence data – https://www.bioinformatics.babraham.ac.uk/projects/fastqc/. UR - https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ ID - ref42 ER - TY - JOUR AU - Park, G. AU - Hwang, H. -. K. AU - Nicodème, P. AU - Szpankowski, W. PY - 2009 DA - 2009// TI - Profiles of tries JO - SIAM J. Comput. VL - 38 UR - https://doi.org/10.1137/070685531 DO - 10.1137/070685531 ID - Park2009 ER - TY - STD TI - L. Dagum and R. Menon, "OpenMP: an industry standard API for shared-memory programming," in IEEE Computational Science and Engineering. 1998;5(1):46–55. https://doi.org/10.1109/99.660313. ID - ref44 ER - TY - JOUR AU - Curtin, R. PY - 2018 DA - 2018// TI - mlpack 3: a fast, flexible machine learning library JO - J. Open Source Softw VL - 3 UR - https://doi.org/10.21105/joss.00726 DO - 10.21105/joss.00726 ID - Curtin2018 ER - TY - STD TI - Dubitzky, W., Granzow, M. & Berrar, D. P. Fundamentals of data mining in genomics and proteomics. (Springer Science & Business Media, 2007). ID - ref46 ER - TY - STD TI - Shannon, C. E. The mathematical theory of communication. 1963. MD Comput. Comput. Med. Pract. 14, 306–317 (1997). ID - ref47 ER - TY - JOUR AU - Sanderson, C. AU - Curtin, R. PY - 2016 DA - 2016// TI - Armadillo: a template-based C++ library for linear algebra JO - J. Open Source Softw. VL - 1 UR - https://doi.org/10.21105/joss.00026 DO - 10.21105/joss.00026 ID - Sanderson2016 ER - TY - STD TI - CEPHES Mathematical function library. http://www.netlib.org/cephes/. UR - http://www.netlib.org/cephes/ ID - ref49 ER - TY - STD TI - Lightweight C++ command line option parser. jarro2783/cxxopts. 2020. https://github.com/jarro2783/cxxopts. UR - https://github.com/jarro2783/cxxopts ID - ref50 ER - TY - STD TI - JSON for Modern C++, N. nlohmann/json. 2020. https://github.com/nlohmann/json. UR - https://github.com/nlohmann/json ID - ref51 ER - TY - STD TI - van der Walt S, Colbert SC, Varoquaux G. The NumPy array: a structure for efficient numerical computation. Comput. Sci. Eng. 2011. https://doi.org/10.1109/MCSE.2011.37. ID - ref52 ER - TY - STD TI - Mckinney, W. Data structures for statistical computing in Python. Proc. 9th Python Sci. Conf. (2010). ID - ref53 ER - TY - JOUR AU - Pedregosa, F. PY - 2011 DA - 2011// TI - Scikit-learn: machine learning in Python JO - J. Mach. Learn. Res. VL - 12 ID - Pedregosa2011 ER - TY - STD TI - Federico Comitani. fcomitani/SimpSOM: v1.3.4. (Zenodo, 2019). https://doi.org/10.5281/zenodo.2621560. ID - ref55 ER - TY - JOUR AU - Kurtzer, G. M. AU - Sochat, V. AU - Bauer, M. W. PY - 2017 DA - 2017// TI - Singularity: scientific containers for mobility of compute JO - PLOS ONE VL - 12 UR - https://doi.org/10.1371/journal.pone.0177459 DO - 10.1371/journal.pone.0177459 ID - Kurtzer2017 ER - TY - JOUR AU - Patro, R. AU - Duggal, G. AU - Love, M. I. AU - Irizarry, R. A. AU - Kingsford, C. PY - 2017 DA - 2017// TI - Salmon provides fast and bias-aware quantification of transcript expression JO - Nat. Methods VL - 14 UR - https://doi.org/10.1038/nmeth.4197 DO - 10.1038/nmeth.4197 ID - Patro2017 ER - TY - JOUR AU - Williams, C. R. AU - Baccarella, A. AU - Parrish, J. Z. AU - Kim, C. C. PY - 2017 DA - 2017// TI - Empirical assessment of analysis workflows for differential expression analysis of human samples using RNA-Seq JO - BMC Bioinformatics VL - 18 UR - https://doi.org/10.1186/s12859-016-1457-z DO - 10.1186/s12859-016-1457-z ID - Williams2017 ER - TY - STD TI - dbGaP/database of genotypes and phenotypes/ National Center for Biotechnology Information, National Library of Medicine (NCBI/NLM) https://www.ncbi.nlm.nih.gov/gap. UR - https://www.ncbi.nlm.nih.gov/gap ID - ref59 ER - TY - STD TI - Athar A. et al., 2019. ArrayExpress update - from bulk to single-cell expression data. Nucleic Acids Res, https://doi.org/10.1093/nar/gky964, Pubmed ID 30357387. ID - ref60 ER - TY - STD TI - Lorenzi, C. et al. iMOKA: k-mer based software to analyze large collections of sequencing data. (GitHub, 2020). https://github.com/RitchieLabIGH/iMOKA. UR - https://github.com/RitchieLabIGH/iMOKA ID - ref61 ER - TY - STD TI - Lorenzi, C. et al. iMOKA: k-mer based software to analyze large collections of sequencing data. (Zenodo, 2020). https://doi.org/10.5281/zenodo.4008947. ID - ref62 ER -