Topic outline

• 

  Advanced Molecular Biology 2019-2020

  
  

  • Announcements Forum
  • Course Forum
  • EXAM rules Page
  • Rules for online examination (year 2022) Page
  • Exam: starting question list, oral interview. Page
  • REMINDER

    Materials contained in these webpages are protected by copyright and should not be copied, printed or distributed outside the groups participating in this specific activity. 

  • Campusnet URL
  • Code of Ethical Conduct of the University Community Folder
  • Exams June 25 - Results File

  
  

  Topics index:
  

  • Student activities
  • Introduction to Regulatory Genomics
  • Chapter 1 - Genomes, Epigenomes and Nuclear organization
  • Chapter 2 - Establishment & maintenance of chromatin features
  • Chapter 3 - Transcriptional Regulation
  • Chapter 4 - Transcriptomes and post-transcriptional regulation
  • Chapter 5 - Applications in Medicine
  • Practice
  • Auxiliaries
  • EXAM TESTS

  
  
• 

  Student activities

  wikis, databases, background, methodology, Forum

  • Guide to Students Report Page
  • A guide to use collaborative Google Docs & Google Slides Page
  • Table for Report proposals Page
  • Student Wiki on methodology
  • How to use the Wiki File
  • Students Wiki on methodology: Group choice

    Select which subject you want to contribute to.

  • Evaluation of Students report: grades URL
  • Detailed report evaluation URL
  • Students Report - notes on evaluation Page
  • Internal Activities, Module 1 - Grades File
• 

  Introduction to Regulatory Genomics

  This section concerns a general introduction to the subjects of this course. Assessment of Students' background in this specific subject is planned. 

  • Welcome Book
  • Monday, March 2 Book
  • multimedia Folder
  • Lesson 0 (intro) pdf Folder
  • Textbook G Folder
  • Activity 1 - Ex. Levine Quiz
• 

  Chapter 1 - Genomes, Epigenomes and Nuclear organization

  Structure of Genomes and Epigenomes, i.e. the physical state of chromosomes and parts of them, the biochemical nature of different stetes and the topographical organization of mammalian nuclei. 

  • Ch.1 PDF Folder
  • Ch.1 lessons streaming Book
  • multimedia Folder
  • Chat on Ch 1, Lesson 2
  • Textbook_1 Folder
  • Research Paper_1 Folder
  • Activity 2 - Elements in Human Genome Quiz
  • Activity 3 - a tour on genome browser Lesson
  • Activity 4 - A database of proteins associated to the nuclear lamina
  • Activity 5 - Reddy et al. Quiz
• This topic
  

  Chapter 2 - Establishment & maintenance of chromatin features

  How epigenomic states of our genomes are established and modified during development and cell differentiation or reprogramming.

  • Ch. 2 pdf Folder
  • Ch 2 - Lessons streaming Book
  • Multimedia Folder
  • Textbook_2 Folder
  • Research_paper_2 Folder
  • On Research Paper 2 Wiki
  • Activity 6 - Few basic questions before proceeding Lesson
  • Monitoring Quiz
  • Activity 7 - An additional model of heterochromatin establishment and maintenance Lesson
• 

  Chapter 3 - Transcriptional Regulation

  The DNA sequences devoted to the regulation of gene transcription by transcription factors, coactivators and signal transduction pathways, as observed from a global point of view. 

  • Ch. 3 pdf Folder
  • Ch 3 - Lessons streaming Book
  • Textbooks - 3 Folder
  • Research Paper_3 Folder
  • Research Paper 3 - Discussion, questions and answers Wiki
• 

  Chapter 4 - Transcriptomes and post-transcriptional regulation

  What transcriptomes across different cell lines and tissues tell us. GO studies. Alternative transcripts and alternative splicing control. Small RNAs and RNA interference. Long-noncoding RNAs, miRNAs and Regulatory networks.

   

  • Chapter 4 - streamings Book
  • Ch.4 pdf Folder
  • Textbook - 4 Folder
  • Research Paper_4 Folder

    How HITS-CLIP can be modified for the accurate analysis of miRNA-mRNA pairs

  • Activity 8 - RNA types database
  • Activity 9: on RNA stability and localization Lesson
• 

  Chapter 5 - Applications in Medicine

  Prof. CUTRUPI lessons & activities 

  • Lesson Schedule Page
  • INTRODUCTION Book
  • Lesson1 Book
  • ClassAct_1 Quiz
  • Lesson 2 Book
  • ClassAct_2 Quiz
  • Lesson3 Book
  • ClassAct_3 Quiz
  • Lesson4 Book
  • ClassAct_4 Quiz
  • Lesson5 Book
  • ClassAct_5 Quiz
  • Lesson 6 Book
  • ClassAct_6 Quiz
  • Lesson7 Book
  • ClassAct7 Quiz
  • Lesson8 Book
  • ClassAct8 Quiz
  • Lesson pdf- 6 Folder
  • Bibliography - 6 Folder
  • LessonFeedback1 Book
  • LessonFeedback2 Book
  • LessonFeedback3 Book
• 

  Practice

  • NCBI browser Quiz
  • Exploring Ensemble_FirstPart Quiz
  • Exploring Ensembl_SecondPart Quiz
  • The Human Protein Atlas and EBI Expression Atlas Quiz
  • ENCODE and Roadmap Epigenomics data analysis with WashU Epigenome Browser Quiz
  • TCGA data analysis with CBioPortal Quiz
  • Gene set level analysis with Enrichr and GEO Quiz
  • Tutorial_online_resourse File
  • Bioinfo Part_Help Forum
  • OpenMeeting File
• 

  Auxiliaries

  • BACKGROUND: Human Genome Project + other basic tutorials Book
  • BACKGROUND: NGS sequencing technologies Book
  • BACKGROUND: DNA microarrays Book
  • Basic Mechanisms Book
  • The functional Genomics projects Book
• 

  EXAM TESTS

  • Oral interview complement sample Quiz