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Review: Tiling arrays (Jonhson et al., 2005)
Click
Review_Johnson_2005_dark_matter_rev.pdf
link to view the file.
◄ lezione 18 novembre - Genome level transcriptome analysis
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General informations....
podcast of the lectures (mp3)
Student's talk CALENDAR
Subjects for Student's talks, important
INFO: student's talk - AVVISO importante per presentazioni
read this article: Whitmarsh_jip_98
podcast of the lecture: Sept. 30, 2009
pdf lezioni
Task N.7: site-directed mutagenesis
Read the article: Verhey et al. 2001
Read the article: Blasius et al.
supplementary material: movies of Blasius et al
podcast of the lecture: october 05: part 1
podcast of the lecture: october 05: part 2
podcast of the lecture: october 07, part 1
podcast of the lecture: october 07, part 2
pdf_lezioni
Find and read the article: Parada et al. 2004
podcast of the lecture: october 09, part 1
podcast of the lecture: october 09, part 2
pdf_lezioni
Read the articles
podcast of the lecture: october 12: part 1
podcast of the lecture: october 12, part 2
podcast of the lecture: october 14, part 1
podcast of the lecture: october 14, part 2
pdf_lezioni
podcast of the lecture: october 16, part 1
podcast of the lecture: october 16, part 2
Read the article: Dikic et al 09, ubiquitin structure & function
pdf_lezioni
Read this article: Lum et al. Autophagy Cell 2005
Read the article (optional): Mol_Cell_2009_Kirkin.pdf
pdf delle lezioni
pdf of the lecture N.09
podcast 091021_01: stem cells
podcast 091021_02: stem cells
read this article: Takahashi et al, stem cells cell 2006
Read the article (optional): Pei et al. 2009, dedifferentiation review.pdf
Task 8: Where is the mistake....
Seminario "biosafety/biosecurity tools and policies", Malcom Dando and Giulio Mancini. Venerdì 23 ottobre 2009, 11-13
ppt_seminar
261009 lezione I parte
261009 lezione II parte
261009-articolo Zimmer
261009-movie1
261009-movie2
261009-movie3
261009-movie4
261009-MP3-1 parte
261009-MP3-2 parte
281009_read this article: Stein-Lavigne
281009 MP3 1 parte
281009 MP3 2 parte
lezione 281009
301009 - MP3- I parte
301009 - MP3- II parte
lezione 301009
021109 MP3 1 parte
021109 MP3 2 parte
lezione 021109 transgenici-knockout
041109 MP3 1 parte
lezione 021109 NRG1/ErbB4 alternative splicing
041109 MP3 2 parte
lezione 041109 NRG1/ErbB4 migrazione I parte
read this paper: Anton_NatNeuro_2004
paper Flames 2004 per "Stripe Choice Assay"
protocollo stripe choice assay
task "stripe choice assay"
061109 MP3 1 parte
061109 MP3 2 parte
lezione 061109 NRG1/ErbB4 migrazione II parte
lezione 06-091109 NRG1/ErbB4 ubiquitinazione
paper Sundvall 2008
091109 MP3 1 parte
091109 MP3 2 parte
paper Sardi 2006
lezione 091109 ErbB4 nucleare 1 parte
111109 MP3 1 parte
111109 MP3 2 parte
lezione 111109 ErbB4 nucleare 2 parte
materiale su Semaphorins-Plexin-Neuropilin
read this paper about RNA interference false positives and negatives
lecture: 13 Nov - The Organization of Genomes (slides)
Assignment BMG1: nucleotide sequence in database
Assignment BMG2 - Identificazione delle parti di una sequenza genica
lezione 16 novembre - Analysis of gene expression
Audio-Analysis of gene expression_MP3_stream
Article: Microarray of sporulating yeast (Chu et al, 1998)
Assignement BMG3 Choose a microarray for your experiment
Assignment BMG4 - Choose a beadarray for your experiment
lezione 18 novembre - Genome level transcriptome analysis
Review: What is a gene post-ENCODE? (Gernstein 2007)
Audio lezione 18-11-09
Lezione 20 novembre Pervasive genomic transcription (with happenings...)
Review: On RNA-Seq methods and outcome (Wang et al 2009)
Article: RNA-Seq on human poly(A)+ (Sultan et al. 2008)
Audio-lesson 4-Part 1
Audio-lesson 4-Part 2
Audio lesson 4 - Part 3
Lezione 23 novembre - Transcripts and promoters
Review: Mammalian promoters (Sandelin 2007)
Assignment BMG5: how to verify bioinformatic results
Lezione 25 novembre - Genome annotations
Audio lezione 25-11-09
Review: A very good review on small RNAs (Ghildiyal, 2009)
Article: Identification of human promoters (Kim et al 2005)
Assignment BMG6 - what can we conclude ?
Assignment BMG7: micro RNA specificity
Lezione 27 novembre - One gene more products
Audio lezione 27-11-09
Review: A review on Alternative Splicing in the pre-deep-sequencing era. (Matlin 2005).
Article: Alternative Splicing by RNA-Seq (Wang et al 2008)
Assignment BGM8: find the right protocol
Lezione 30 novembre - Chromatin
Review: Histone modifications and interacting proteins (Kouzarides 2007)
Audio lezione 30-11-09
Lezione 2 dicembre - Silencing & epigenetics
Review: Microarrays for chromatin status (Hoheisel 2006)
Review: Epigenetics and developent (Reik 2007)
Lezione 4 dicembre - Post-transcription & proteomics
Audio lezione 4-12-2009
Review: Proteome analysis using Mass Spectrometry (Gstaiger 2009)
Article: Comparative miRNA effect on mRNA and proteome (Selbach et al., 2008)
Programma svolto dal 13/1 al 4/12 (modulo per NU e BI)
Lezione 9 dicembre - Heterochromatin
Audio lezione 09-12-2009
Lezione 11 dicembre - Boundaries and territories
Audio lezione 11-12-2009
Review: Boundaries (Lunyak 2008)
Review: Active loops (Fraser 2007)
Lezione 14 dicembre - Methylomes
Audio lezione 14-12-2009 1° parte
Audio lezione 14-12-2009 2° parte
Article: genome-wide promoter CpG-methylation analysis (Weber 2007)
Assignment BMG8: problems with bisulfite conversion and deep-sequencing
Lezione 16 dicembre - Transcriptional activation
Audio lezione 16-12-2009
Article: interchromosomal interactions mediate Olfactory Receptor choice (Lomvardas 2006)
Lezione del 18 dicembre - transcription factor mapping
Article: ER mapping genome-wide (Carroll 2006) (Not mandatory)
Review: Transcription factor mapping genome-wide
Audio lezione 18-12-2009
Lezione 21 dicembre - coregulator dynamics
Article: Coactivator dynamics at a single gene after activation (Metivier 2003)
Review on coregulator cycling on nuclear receptors (Perissi 2006)
Audio lezione 21-12-2009
Lezione 8 gennaio 2010 - Signals and combinatorial transcriptional control
Audio lezione 08-01-2010
Résumé (Zhu et al., 2006)
Assignment BMG 9 - Differences between signal transduction pathways
Assignment BMG 10 - How to resolve an interaction dilemma?
Lezione 11 gennaio - Regulated Alternative Splicing
Audio lezione 11-01-2010
Review on the mechanisms of Alternative Splicing regulation - Chen & Manley, 2009.
Review on RNA processing regulation, with genome-wide methods. Licatalosi & Darnell, 2010.
Lezione del 13 gennaio - Processing to export
Audio lezione 13-01-2010
Review on "Cotranscriptionality" - Perales & Bentley, 2009.
Review on the biogenesis of RNA and export (Luna 2008)
Assignment BMG 11 - A method to study RNA-binding protein targets
Assignment BMG 12 - Hypothesis on Dscam mechanism.
Lezione del 15 gennaio - RNA localization
Audio lezione 15-01-2010
Review on RNA localization - Holt 2009
Article: RNA localization in yeast (Jambhekar 2005)
Lezione 18 gennaio - Control of RNA decay and translation
Article: miRNA targets (Grimsom et al., 2007)
Audio lezione 18-01-2010 1°parte
Audio lezione 18-01-2010 2°parte
Lezione supplementare 1 - 20/1/2010 - Clock genes (by Iachia-i- Blaca / Fava)
Lezione supplementare 2 - 20/1/2010 - Imprinted genes (by Bethaz-Ferrero)
Lezione supplementare 3 - 20/1/2010 "Methylome" by Macrì, Macrì, Raimo.
Audio lezione 20-01-2010
Article: Clock gene analysis (Zhang 2009)
Article: Imprinted gene by microarray (Steinhoff 2009)
Article: Methylome by deep-sequencing (Lister 2009)
Lezione del 22 gennaio - Alternative splicing in disease
Audio lezione 22-01-2010
Review: What is a gene post-ENCODE? (Gernstein 2007) ►
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