Biochemistry 158/258

Genomics, Bioinformatics & Medicine

Doug Brutlag

Yeast regulatory networks Lee et al. Science 298, 799-804 (2002)

Mattick (2004) Nature Reviews of Genetics 5, 316-323.

Pheasant & Mattick, Genome Res. 17: 1245-1253 (2007).

MicroRNA Biogenesis Annu. Rev. Cell Dev. Biol. 2007.23:175-205.

siRNA and miRNA Action Filipowicz, Curr. Op. Structural Biology 15: 331-341 (2005)

miRNA Action on Translation Filipowicz (2008) Nature Review Genetics 9:102-112.

Ribosome Drop Off mediated by mrRNA Petersen et al. (2006) Molecular Cell 21: 533-542.

miRNAs Mediate Temporal and Spatial Reciprocity during Differentiation Annu. Rev. Cell Dev. Biol. 2007.23:175-205

Genomic Organization of miRNA Genes Zhao Y, Srivastava D, TIBS 32:189,2007

Dicer Structure and Function Filipowicz, Curr. Op. Structural Biology 15: 331-341 (2005)

Argonaute Structure and Function Martin Jinek & Jennifer A. Doudna Nature 457, 405-412(22 January 2009)

Evolution of miRNAs Lim (2003) Genes & Dev. 17: 991-1008

miRNAs involved in Human Cancer Croce Nat Rev Genet. 2009 Oct;10(10):704-14.

miRNAs as Oncogenes and Tumor Supressors Zhang et al Dev Biol. 2007 Feb 1;302(1):1-12

The miR-17-92 Cluster is Activated by c-Myc O’Donnell et al. Nature 2005 435, 839-843

Role of miRNAs in Cancer and Apoptosis Lynan-Lennon Biol Rev Camb Philos Soc. 2009 Feb;84(1):55-71

Causes and consequences of microRNA dysregulation in cancer Croce Nat Rev Genet. 2009 Oct;10(10):704-14.

miRNAs as oncogenes and tumor suppressors. Zhang Dev Biol. 2007 Feb 1;302(1):1-1

Transcriptional regulatory networks in Saccharomyces cerevisiae. Lee Science. 2002 Oct 25;298(5594):799-804.

RNA regulation: a new genetics? Mattick Nat Rev Genet. 2004 Apr;5(4):316-23.

microRNA functions. BushatiAnnu Rev Cell Dev Biol. 2007;23:175-205.

Mechanisms of post-transcriptional regulation by microRNAs: are the answers in sight?Filiowicz Nat Rev Genet. 2008 Feb;9(2):102-14.

Post-transcriptional gene silencing by siRNAs and miRNAs. Filipowicz Curr Opin Struct Biol. 2005 Jun;15(3):331-41.

The microRNAs of Caenorhabditis elegans. Lim Genes Dev. 2003 Apr 15;17(8):991-1008.

A three-dimensional view of the molecular machinery of RNA interference. Jinek Nature. 2009 Jan 22;457(7228):405-12.

miRNAs and Cancer AAAI Science Webinars February 20 with George Calin, Brank Slack and Scott Hammond

Short RNAs repress translation after initiation in mammalian cells. Petersen Mol Cell. 2006 Feb 17;21(4):533-42.

Raising the estimate of functional human sequence. Pheasant Genome Res. 2007 Sep;17(9):1245-53.

A developmental view of microRNA function. Zhao Trends Biochem Sci. 2007 Apr;32(4):189-97.

c-Myc-regulated microRNAs modulate E2F1 expression O’Donnnell Nature. 2005 Jun 9;435(7043):839-43.

Nucleic Acid Research Database issue

mIrBase: miRBase: annotating high confidence microRNAs using deep sequencing data

miRNEST 2.0: a database of plant and animal microRNAs

miRTarBase update 2014: an information resource for experimentally validated miRNA-target interactions

PolymiRTS Database 3.0: linking polymorphisms in microRNAs and their target sites with human diseases and biological pathways

Affymetrix

Arrayit Corporation

Biocarta Cell Signaling Pathways

miRBASE

miRNA Target Database MicroCom

PathWork Diagnostics

miRBase: http://www.mirbase.org/

MicroCosm: http://www.ebi.ac.uk/enright-srv/microcosm/

miRNAminer: http://groups.csail.mit.edu/pag/mirnaminer

miRviewer: http://people.csail.mit.edu/akiezun/miRviewer

Patrocles: http://www.patrocles.org/

TargetRank: http://hollywood.mit.edu/targetrank

TargetScanS: http://www.targetscan.org