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Informações do Evento

Informações do Evento

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DATE: November, 18 - 22, 2019

LOCAL: Animal Science Department – Monogastrics Theater -  ESALQ/USP, at 11, Pádua Dias Avenue, Piracicaba, SP


COORDINATION

- Prof. Dr. Luiz Lehmann Coutinho (ESALQ/USP)

 

GUEST RESEARCHER

- Toni Reverter – CSIRO Agriculture and Food, Brisbane, Australia


PROGRAM

MONDAY 18 NOVEMBER 2019

1) 9:30 – 10:00: PREAMBLE:

i) Personal introductions: Fill out the Questionnaire ii) Course outline

 

2) 10:00 – 11:00: REVIEW OF MOLECULAR CELL BIOLOGY

i) Prokaryotes vs Eukaryotes ii) Sub-cellular components and organelles

iii) Basic cell functions: Replication, Transcription, and Translation iv) Organic compounds: Carbohydrates, Lipids, and Proteins v) The ABC of Metabolism

 

3) 11:30 – 13:00: REVIEW OF MOLECULAR ‘OMICS’ DATA

i) Genomics  ii) Epigenomics  iii) Transcriptomics iv) Proteomics  v) Metabolomics vi) Microbiomics

 

4) HOMEWORK

iv) Inner Life of the Cell: https://www.youtube.com/watch?v=FzcTgrxMzZk  v) Eric Lander (MIT): Transcription and Translation:

https://www.youtube.com/watch?v=tMr9XH64rtM 

 



TUESDAY 19 NOVEMBER 2019

1) 9:30 – 11:00: BRIEF OVERVIEW OF GENOTYPE DATA ANALYSIS

i) Essential Metrics: Minor allele frequency (MAF), Hardy-Weinberg equilibrium (HWE),

Heterozygosity, Runs of homozygosity (ROH), Linkage Disequilibrium (LD) ii) GRM: Genomic Relationship Matrix iii) GWAS: Genome-Wide Association Studies iv) GBLUP: Genomic Best Linear Unbiased Predictions

 

2) 11:30 – 13:00: INTRODUCTION TO TRANSCRIPTOMICS (RNA-SEQ) DATA ANALYSIS

i) Data Preparation, Edits, Transformation and Normalization ii) Differential expression and Functional categories of interest iii) Gene Ontology (GO) Enrichment and The GOrilla tool: http://cbl-gorilla.cs.technion.ac.il/  iv) Cluster analysis and the PermutMatrix software

 

3) HOMEWORK

i) PermutMatrix: http://www.atgc-montpellier.fr/permutmatrix/   ii) Data from Cánovas et al. (2014): https://www.ncbi.nlm.nih.gov/pubmed/25048735 



WEDNESDAY 20 NOVEMBER 2019

1) 9:30 – 11:00: BEYOND DIFFERENTIAL EXPRESSION

i)       The quest for causal mutations

ii)      eQTL – Expression Quantitative Trait Loci

2) 11:30 – 13:00: GENE CO-EXPRESSION NETWORKS

i) Basic network theory metrics: Motifs, connectivity degree and clustering coefficient ii) Algorithms for the inference of gene networks: Random vs Scale-Free networks iii) The Cytoscape software: https://cytoscape.org/ 

 

3) HOMEWORK

i) NetSimul F90 Program: Simulate random and scale-free networks   ii) Cytoscape: Co-Authorship Network 

 

 


THURSDAY 21 NOVEMBER 2019

1) 9:30 – 11:00:  THE PCIT ALGORITHM AND RIF METRICS

i) PCIT – Partial Correlation and Information Theory ii) RIF – Regulatory Impact Factors

 

2) 11:30 – 13:00: PRACTICE SESSION WITH PCIT AND RIF F90 CODES

i) Data from Cánovas et al. (2014): https://www.ncbi.nlm.nih.gov/pubmed/25048735

 

 


FRIDAY 22 NOVEMBER 2019

1) 9:30 – 11:00:  POST-GWAS ANALYSES

i)       Meta-analysis of GWAS results:

1.      Lin and Zeng, 2010. Genet Epidemiol. 34:10.1002/gepi.20435.

2.      Cantor, Lange and Sinsheimer, 2010. Am J Hum Genet 86:6-22.

3.      Bolormaa et al, 2014. PLoS Genet 10:e1004198.

ii)      Gene Co-Association Networks: The AWM (Association Weight Matrix) algorithm

1.      Fortes et al. 2010. Proc Natl Acad Sci USA 107:13642-13647.

2.      Reverter and Fortes. 2013. Methods Mol Biol. 1019:437-447. 

 

2) 11:30 – 13:00:  APPLICATIONS TO LIVESTOCK AND CONCLUDING REMARKS

i)       Beef cattle puberty: Cánovas et al. 2014. PLoS ONE 9:e102551. 

ii)      Porcine fatty acids: Ramayo-Caldas et al. 2014. BMC Genomics 15:232. 

iii)    Broiler feed efficiency:  Bottje et al. 2017. BMC Syst Biol. 11:29. 

iv)    Beef meat tenderness: Ramayo-Caldas et al. 2016. Genet Sel Evol 48:37.  v) Concluding Remarks 



TOTAL HOURS: 
40h


NUMBER OF VACANCIES: 
50


REGISTRATION


- Professional - R$ 200,00

- Student - R$ 200,00


INFORMATION

Luiz Lehman Coutinho

19 3429 4434

llcoutinho@usp.br

 

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