Page 71 - scheppingen
P. 71
CODING AND SMALL NON-CODING TRANSCRIPTIONAL LANDSCAPE OF TSC
25. Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014 Aug 1;30(15):2114-20.
26. Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, Salzberg SL. TopHat2: accurate alignment of tran- scriptomes in the presence of insertions, deletions and gene fusions. Genome Biology. 2013;14(4).
27. Trapnell C, Roberts A, Goff L, et al. Differential gene and transcript expression analysis of RNA-seq
experiments with TopHat and Cufflinks. Nature Protocols. 2012 Mar;7(3):562-78.
28. Harrow J, Frankish A, Gonzalez JM, et al. GENCODE: The reference human genome annotation for
The ENCODE Project. Genome research. 2012 Sep;22(9):1760-74.
29. Smyth GK. In: G. R CV, W. H, I. RA, D. S, Eds. (Springer, 2005), editor. Bioinformatics and
Computational Biology Solutions using R and Bioconductor2005. p. 397-420.
30. Benjamini Y, Hochberg Y. Controlling the False Discovery Rate - a Practical and Powerful Approach to Multiple Testing. Journal of the Royal Statistical Society Series B-Methodological.
1995;57(1):289-300.
31. Shannon PT, Grimes M, Kutlu B, Bot JJ, Galas DJ. RCytoscape: tools for exploratory network anal-
ysis. Bmc Bioinformatics. 2013 Jul 9;14.
32. Scicluna BP, van Lieshout MH, Blok DC, Florquin S, van der Poll T. Modular Transcriptional
Networks of the Host Pulmonary Response during Early and Late Pneumococcal Pneumonia.
Molecular Medicine. 2015;21:430-41.
33. Bulgakov VP, Tsitsiashvili GS. Bioinformatics analysis of protein interaction networks: Statistics,
topologies, and meeting the standards of experimental biologists. Biochemistry-Moscow. 2013
Oct;78(10):1098-103.
34. Dong J, Horvath S. Understanding network concepts in modules. Bmc Systems Biology. 2007 Jun
4;1.
35. Song L, Langfelder P, Horvath S. Comparison of co-expression measures: mutual information,
correlation, and model based indices. Bmc Bioinformatics. 2012 Dec 9;13.
36. Dweep H, Sticht C, Pandey P, Gretz N. miRWalk - Database: Prediction of possible miRNA bind- ing sites by “walking” the genes of three genomes. Journal of Biomedical Informatics. 2011
Oct;44(5):839-47.
37. Darmanis S, Sloan SA, Zhang Y, et al. A survey of human brain transcriptome diversity at the single
cell level. Proceedings of the National Academy of Sciences of the United States of America. 2015
Jun 9;112(23):7285-90.
38. Liao Y, Smyth GK, Shi W. featureCounts: an efficient general purpose program for assigning
sequence reads to genomic features. Bioinformatics. 2014 Apr 01;30(7):923-30.
39. Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq
data with DESeq2. Genome Biology. 2014;15(12).
40. Hoogeveen-Westerveld M, Wentink M, van den Heuvel D, et al. Functional Assessment of Variants
in the TSC1 and TSC2 Genes Identified in Individuals with Tuberous Sclerosis Complex. Human
Mutation. 2011 Apr;32(4):424-35.
41. Prabowo AS, van Scheppingen J, Iyer AM, et al. Differential expression and clinical significance of
three inflammation-related microRNAs in gangliogliomas. J Neuroinflammation. 2015;12:97.
42. van Scheppingen J, Iyer AM, Prabowo A, et al. Expression of microRNAs miR21, miR146a and miR155 in tuberous sclerosis complex cortical tubers and their regulation in human astrocytes
and SEGA-derived cell cultures. Glia. 2016;in press.
43. Ramakers C, Ruijter JM, Deprez RH, Moorman AF. Assumption-free analysis of quantitative real-
time polymerase chain reaction (PCR) data. Neuroscience Letters. 2003;339(1):62-6.
44. Ruijter JM, Ramakers C, Hoogaars WM, et al. Amplification efficiency: linking baseline and bias in
the analysis of quantitative PCR data. Nucleic acids research. 2009 Apr;37(6):e45.
45. Darmanis S, Sloan SA, Zhang Y, et al. A survey of human brain transcriptome diversity at the single
cell level. Proc Natl Acad Sci U S A. 2015 Jun 9;112(23):7285-90.
46. Dombkowski AA, Batista CE, Cukovic D, et al. Cortical Tubers: Windows into Dysregulation of
Epilepsy Risk and Synaptic Signaling Genes by MicroRNAs. Cereb Cortex. 2016 Mar;26(3):1059-71.
47. Somel M, Liu X, Tang L, et al. MicroRNA-driven developmental remodeling in the brain distin-
guishes humans from other primates. PLoS Biol. 2011 Dec;9(12):e1001214.
48. Boon RA, Iekushi K, Lechner S, et al. MicroRNA-34a regulates cardiac ageing and function. Nature.
2013 Mar 07;495(7439):107-10.
69
three