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Software bits 

Papers (statistics)

  • Rossell D. A framework for posterior consistency in model selection. 2018. arxiv 1806.04071
  • Fúquene J., Steel M.F.J., Rossell D. On choosing mixture components via non-local priors (2018). arxiv 1604.00314
  • Papaspiliopoulos O., Rossell D. Bayesian block-diagonal variable selection and model averaging. (2017). Biometrika, 104, 343-359. Technical report, Biometrika version
  • Rossell D, Rubio FJ. Tractable Bayesian variable selection: beyond normality (2017). Journal of the American Statistical Association (DOI 10.1080/01621459.2017.1371025). JASA version. Technical report
  • Rossell D., Steel M.F.J. Continuous mixtures with skewness and heavy tails. In Handbook of mixture analysis, Chapter 10, CRC press 2017.
  • Stephan-Otto Attolini C., Peña V., Rossell D. (2015) Designing alternative splicing RNA-seq studies. Beyond generic guidelines. Bioinformatics, btv436, 1-7, doi: 10.1093/bioinformatics/btv436.
  • Rossell D. Big Data and Statistics. A statistician's perspective (2014). Mètode Science Studies Journal - Annual Review, 5, 143-149. DOI: 10.7203/metode.83.3590. pdf 
  • Rossell D., Stephan-Otto Attolini C., Kroiss M., Stöcker A. (2014) Quantifying alternative splicing from paired-end RNA-seq data. Annals of Applied Statistics, 8:1, 309-330. Paper. Supplementary material. Corrigendum. See Bioconductor package casper
  • Font-Burgada J, Reina O, Rossell D, Azorin F. (2014) chroGPS, a global chromatin positioning system for the functional analysis and visualization of the epigenome. Nucleid Acids Research, 42(4):2126-37. See Bioconductor package chroGPS 
  • Rossell D., Telesca D., Johnson V.E. (2013) High-Dimensional Bayesian Classifiers using Non-Local Priors. In Statistical Models for Data Analysis, XV: 305-314. Eds. P. Giudici, S. Ingrassia, M. Vichy. Springer, ISBN 978-3-319-00032-9. Paper. See R package mombf
  • Rossell D., Müller P. (2013) Sequential Stopping for High-Throughput Experiments. Biostatistics, 14(1): 75-86. doi:10.1093/biostatistics/kxs026. Technical report. See Bioconductor package gaga
  • Johnson V.E., Rossell D. (2012) Bayesian model selection in High-dimensional settings. Journal of the American Statistical Association, 107, 498, 649-660ErrataSee R package mombf
  • Planet E., Stephan-Otto Attolini C., Reina O., Flores O., Rossell D. (2012) htSeqTools: High-Throughput Sequencing Quality Control, Processing and Visualization in R. Bioinformatics; Vol. 28(4): 589-590. See Bioconductor package htSeqTools
  • Johnson V.E., Rossell D. (2010) Non-Local Prior Densities for Default Bayesian Hypothesis Tests. Journal of the Royal Statistical Society B, 72, 143-170. technical report (see R package mombf)
  • Rossell D., Scott C., Guerra R. (2008) Semi-parametric Differential Expression Analysis via Partial Mixture Estimation. Statistical Applications in Genetics and Molecular Biology, Vol.7, 1, 15. (Published paper , technical report) ( (see software section)
  • Rossell D., Baladandayuthapani, V., Johnson, V.E. (2008) Bayes Factors Based on Test Statistics under Order Restrictions. In Hoijtink H., Klugkist I. , Boelen P. Bayesian evaluation of informative hypotheses in psychology. Springer, pp. 111-129. (see R library isoregbf in software section).   
  • Rossell D., Mueller P., Rosner G. (2006) Screening designs for drug development. Biostatistics, 8:595-608 (technical report) (see software section)

Papers (cross-disciplinary)

  • Marty R, Kaabinejadian S, van de Haar J, Rossell D, Ideker T, Hildebrand W, Engin HB, Font-Burgada J, Carter H. MHC-I genotype restricts the oncogenic mutational landscape. Cell, 171, 1272-1283 (2017)
  • Gavard R, Rossell D; Spencer S, Barrow M. Themis: Batch Pre-processing for Ultrahigh Resolution Mass Spectra of Complex Mixtures. Analytical Chemistry, 89, 11383-11390 (2017).
  • Font-Burgada J, Shalapour S, Ramaswamy S, Hsueh B, Rossell D, Umemura A, Taniguchi K, Nakagawa H, Valasek MA, Ye L, Kopp JL, Sander M, Carter H, Deisseroth K, Verma IM, Karin M. (2015) Hybrid Periportal Hepatocytes Regenerate the Injured Liver without Giving Rise to Cancer. Cell, 162(4):766-79.
  • Calon A, Lonardo E, Berenguer A, Espinet E, Hernando-Momblona X, Iglesias M, Sevillano M, Palomo-Ponce S, Tauriello DVF, Byrom D, Cortina C, Morral C, Barceló C, Tosi S, Riera A, Stephan-Otto Attolini C, Rossell D, Sancho E, Batlle E. (2015) Stromal gene expression defines poor prognosis subtypes in colorectal cancer. Nature Genetics, 47, 320-329. doi:10.1038/ng.3225
  • Duran-Frigola M, Rossell D, Aloy P. (2014) A chemo-centric view of human health and disease. Nature Communications 01/2014; 5:5676. DOI:10.1038/ncomms6.
  • Kalari KR; Necela BM; Tang X; Lau M; Passow JEE; Kachergus JM; Anderson SK; Sun Z; Baheti S; Carr JM; Baker TR; Thompson KJ; Radisky DC; Joseph RW; McLaughlin SA; Chai H-S; Stephan-Otto Attolini C; Rossell D; Asmann YW; Thompson EA; Perez EA (2013). An integrated model of the transcriptome of HER2-positive breast cancer. PLOS ONE, 8(11), 1-21, e79298.
  • Kalari, K. R., Chai, H. S., Asmann, Y. W., Tang, X., Rossell, D., Baheti, S. et al. (2012). Modeling the transcriptome landscape of HER2+ breast cancer. Cancer Research, 72(8 Supplement), 4926-4926.
  • Calon A, Espinet E, Palomo-Ponce S, Tauriello DVF, Iglesias M, Céspedes MV, Sevillano M, Nadal C, Jung P, Zhang XH-F, Byrom D, Riera A, Rossell D, Mangues R, Massague J, Sancho E, Batlle E. (2012) Dependency of colorectal cancer on a TGF-beta-driven programme in stromal cells for metastasis initiation. Cancer Cell, 22(5), 571-584.
  • Lloret-Llinares M, Perez-Lluch S, Rossell D, Morán T, Ponsà J, Auer H, Corominas M, Azorin F. dKDM5/LID regulates H3K4me3 dynamics at the transcription-start site (TSS) of actively transcribed developmental genes (2012). Nucleic Acids Research, 40(19):9493-505
  • Kalari KR, Rossell D, Necela BM, Asmann YW, Nair A, Baheti S, Kachergus JM, Younkin CS, Baker TR, Carr JM, Xiaojia T, Walsh M, Chai HS, Sun Z, Hart SN, Leontovich AA, Hossain A, Kocher JP, Perez EA, Reisman DN, Fields AP, Thompson A. (2012) Deep sequence analysis of non-small cell lung cancer: Integrated analysis of gene expression, alternative splicing, and single nucleotide variations in lung adenocarcinomas with and without oncogenic KRAS mutations. Frontiers in Cancer Genetics, 2:12. doi: 10.3389/fonc.2012.00012
  • Jung P., Sato T., Merlos-Suárez A., Barriga F.M., Iglesias M., Rossell D., Gallardo M.M., Blasco M.A., Sancho E., Clevers H., Batlle E. (2011) Isolation and in vitro expansion of human colonic stem cells. Nature Medicine, 17, 1225-1227 (doi: 10.1038/nm.2470)
  • Merlos-Suarez A., Barriga F.M., Jung P., Iglesias M., Céspedes M.V., Rossell D., Sevillano M., Hernando-Momblona X., da Silva-Diz V., Muñoz P., Clevers H., Sancho E., Mangues R., Battle E. (2011) The Intestinal Stem Cell Signature Identifies Colorectal Cancer Stem Cells and Predicts Disease Relapse. Cell Stem Cell, 8, 511-524
  • Janic A., Mendizabal L., Llamazares S., Rossell D., Gonzalez C. (2010) Ectopic expression of germline genes drives malignant brain tumor growth in Drosophila. Science, 330 (3012), 1824-1827.
  • Geslain R., Cubells L., Bori-Sanz T., Álvarez-Medina,R., Rossell D., Martí E., Ribas de Pouplana L. (2009) Chimeric tRNAs as tools to induce proteome damage and identify components of stress responses. Nucleic Acids Research, 2009, 38, 5, e30.
  • Font-Burgada J., Rossell D., Auer H., Azorín F (2008). Drosophila HP1c isoform interacts with the zinc-finger proteins WOC and Relative-of-WOC to regulate gene expression. Genes Dev, 2008, 22 (21), 3007-3023.