Publications

  1. S. Müller and A. DiazSingle-Cell mRNA Sequencing in Cancer Research: Integrating the Genomic FingerprintFrontiers in Genetics. May, 2017.
  2. S. Müller, S. J. Liu, E. Di Lullo, M. Malatesta, A. Pollen, T. J. Nowakowski, G. Kohanbash, M. Aghi, A. Kriegstein, D. A. Lim, A. Diaz. Single-cell sequencing maps gene expression to mutational phylogenies in PDGF and EGF driven gliomas. Molecular Systems Biology. 12(11), 2016.
  3. A. Diaz*, S. J. Liu, C. Sandoval, A. Pollen, T. J. Nowakowski, D. A. Lim, A. Kriegstein. SCell: integrated analysis of single-cell RNA-seq data. Bioinformatics. 32(14), 2016. * corresponding author
  4. S. Liu, T. Nowakowski, A. Pollen, J. Lui, M. Horlbeck, F. Attenello, D. He, J. Weissman, A. Kriegstein, A. Diaz*, D. Lim*. Single cell analysis of long non-coding RNAs in the developing human neocortex. Genome Biology. 17(67), 2016. * corresponding author
  5. S. Müller, S. J. Liu, M. Malatesta, M. Aghi, A. Kriegstein, G. Kohanbash, D. A. Lim, A. DiazGENT-22. Single-cell profiling of glioblastoma biopsies identifies a family of activating PDGF-receptor deletions. Neuro-Oncology. 18(6), 2016. Adult Basic Research Award Soc Neuro-Onc 2016
  6. S. Müller, G. Kohanbash, S. J. Liu, D. Carrera, M. Aghi, D. Lim, H. Okada, A. Diaz. TMIC-29 Distinct molecular signatures of microglia and macrophages in the glioma perivascular niche. Neuro-Oncology. 18(6), 2016.
  7. J. Liu, E. Di Lullo, M. Malatesta, G. Kohanbash, B. Castro, H. Okada, A. Kriegstein, M. Aghi, D. Lim, A. Diaz. GENO-14.  Single-cell transcriptomics and genomics reveals a diversity of tumor and immune cell polarization signals in GBM.  Neuro-Oncology. 17(94), 2015.
  8. A. Pollen, T. Nowakowski, J. Chen, H. Retallack, C. Sandoval-Espinosa, C. Nicholas, J. Shuga, S. Liu, M. Oldham, A. Diaz, D. Lim, A. Leyrat, J. West, A. Kriegstein. Molecular Identity of Human Outer Radial Glia during Cortical Development. Cell, 163(1), 2015. PMCID: PMC4583716.
  9. A. Diaz, H. Qin, M. Ramalho-Santos, J. S. Song. HitSelect: A Comprehensive Tool for High-throughput Screening AnalysisNucleic Acids Research, 43(3), 2015. PMCID: PMC4330337.
  10. M. Suzawa, D. Miranda, K. Ramos, K. Ang, E. Faivre, C. Wilson, L. Caboni, M. Arkin, Y. Kim, R. Fletterick, A. Diaz, J. Schneekloth, H. Ingraham. A gene-expression screen identifies a non-toxic sumoylation inhibitor that Mimics SUMO-less human LRH-1 in liver. eLIFE, 2015.
  11. H. Qin*, A. Diaz*, L. Blouin, R. J. Lebbink, W. Patena, E. M. LeProust, M. T. McManus, J. S. Song, M. Ramalho-Santos, Systematic Identification of Barriers to Human iPS Cell Generation. Cell, 158(2), 2014. PMCID: PMC4130998. * co-first authors
  12. Nagarajan RP, Zhang B, Bell RJ, Johnson BE, Olshen AB, Sundaram V, Li D, Graham AE, Diaz A, Fouse SD, Smirnov I, Song J, Paris PL, Wang T, Costello JF. Recurrent epimutations activate gene body promoters in primary glioblastoma. Genome Research, 24:5, 2014. PMCID: PMC4009606.
  13. A. D. Ramos, A. Diaz, A. Nellore, R. N. Delgado, K. Y. Park, G. Gonzales-Roybal, M. C. Oldham, J. S. Song, D. A. Lim, Integration of Genome-wide Approaches Identifies lncRNAs of Adult Neural Stem Cells and Their Progeny in Vivo. Cell Stem Cell, 12(5), 2013. PMCID: PMC3662805.
  14. A. Nellore, K. Bobkov, E. Howe, A. Diaz, J. S. Song, NSeq: a multithreaded Java application for finding positioned nucleosomes from sequencing data. Front. Genet. Volume 11, January 2013. PMCID: PMC3542818.
  15. A. Diaz, A. Nellore, J. S. Song, CHANCE: comprehensive software for quality control and validation of ChIP-seq data. Genome Biology, 13(10), October 2012. PMCID: PMC4053734.
  16. A. Diaz, K. Park, D. Lim, J.S. Song, Normalization, bias correction, and peak calling for ChIP-seqStatistical Applications in Genetics and Molecular Biology. 11(3), March 2012. PMCID: PMC3342857.
  17. J. Hunkapiller, Y. Shen, A. Diaz, G. Cagney, D. McCleary, M. Ramalho-Santos, N. Krogan, B. Ren, J.S. Song, J.F. Reiter, Polycomb-Like 3 Promotes Polycomb Repressive Complex 2 Binding to CpG Islands and Embryonic Stem Cell Self-Renewal. PLoS Genetics. 8(3), March 2012. PMCID: PMC3305387.
  18. A. Diaz, An Error Analysis for Execution Traces of Hybrid Automata Using Jacobi's EquationNonlinear Analysis: Hybrid Systems. 2(1), March 2008, 74-80.
  19. P. -H. Maire, M. De Buhan, A. Diaz, C. Dobrzynski, G. Kluth, F. Lagoutiere, A Cell-Centered Arbitrary Lagrangian Eulerian (ALE) Method for Multimaterial Compressible FlowsEuropean Series in Applied and Industrial Mathematics: Proceedings Societe de Mathematiques Appliquees et Industrielles. Vol. 13 2008
  20. A. Diaz, Rezoning Techniques for ALE ComputationsProceedings of the 4th WSEAS/IASME Conference on Dynamical Systems and Control. October 2008
  21. A. Diaz, Extraction of Finite State Controllers, AD and DA maps, and Associated Small Topologies for Measure Valued Control LawsInternational Journal of Hybrid Systems, September 2003