Abstract – I will describe my work with the NCI TARGET Pediatric Acute Myeloid Leukemia consortium in which we are integrating data from 197 cancer whole genome sequences with mRNA and miRNA expression and DNA-methylation data, including verification of DNA variants via targeted re-sequencing, and frequency validation of confirmed variants in 650 additional patients.
Introduction to Next Generation Sequencing Data Analysis (May 2016)
Introduction to Next Generation Sequencing Data Analysis (May 2016) by the Core Facility for Bioinformatics
Noises and dynamics in cells: Mathematical modeling in systems biology
One important aspect in the systems biology is to gain understanding in the systems level with molecular basis. With molecular basis in the model, new treatment or genetic perturbation can be designed in order to change the systems behavior. In this talk, I’ll focus on the methodology and an application for simulating a biological system, particularly for systems with noises.
Genome Assembly, Annotation and Variant Calling Training And Workshop (May 2016)
Genome Assembly, Annotation and Variant Calling Training and Workshop (May 2016) by Core Facility for Bioinformatics
3rd Forensic Science Symposium Recognizes DNA as a Catalyst for Change
Now on its third year, the conference will focus on the theme “DNA as a Catalyst for Change”, highlighting the importance of forensics not only in securing public health and safety but also in its role in creating a meaningful change in society.
Deciphering how proteins engage the genome and direct cellular identities
All cells in our bodies encode the same genetic information yet different sets of genes are expressed in a given cell type to give it its particular identity. My laboratory studies how transcription factors (TFs) recognize genomic DNA to regulate when, where and to which level genes are expressed to direct cell fate decisions. We use structural modelling and quantitative biochemical assays to study TF dimerization on composite binding elements enriched in regulatory DNA sequences.
Systems Biology in the Philippines: Past, Present and Potential
Systems Biology activities in the Philippines began in early 2003 with courses on modeling biological networks at NIMBB and the Math Department, as well as the launch of the Mathematical Life Sciences Initiative (MLSI). The talk will present briefly the highlights of the First Decade of Systems Biology in the Philippines (2003-2013)-considered as the “Past”-which consisted largely of Filipino computational scientists collaborating with foreign experimental researchers.
Introduction to Genomics for Computational Scientists (April 2016)
Introduction to Genomics for Computational Scientists (April 2016) Workshop by the Core Facility for Bioinformatics
A Web-based Interactive Genome Library for Surveillance, Detection, Characterization and Drug-Resistance Monitoring of Influenza Virus Infection in the Philippines
Epidemiologic and genotypic information on influenza is difficult to obtain for developing countries, unless it is in the context of international programmes or collaborations. This data is important for tracking cases during pandemics like the 2009 A(H1N1) influenza outbreak. We sought to sequence novel A(H1N1); and design a prototype national web-based interactive genome library for surveillance, genotyping, and drug-resistance monitoring of influenza in the Philippines.
Kinetic Capillary Electrophoresis – a Swiss Army Knife for Studying Kinetics of Protein-DNA Interactions
Protein-DNA interactions play an important role in gene expression, DNA replication, DNA integrity control, and DNA damage repair. Understanding the mechanisms of these processes requires the knowledge of kinetics (rate constants) of reversible Protein-DNA binding. Electrophoresis has been the workhorse method for in vitro studies of such interactions.