I am currently recruiting graduate and undergraduate students to work on projects in my lab. I currently have some research projects at all levels in genomics, transcriptomics, interactomics, machine learning, and cancer research. Some of the projects are listed below, though the list is not exclusive. If you have your own ideas, you are free to discuss them with me.
The main topics for theses and projects are in machine learning and applications in genomics, interactomics, and transcriptomics, mostly in cancer research. My lab projects involve mostly finding meaningful biomarkers in prostate cancer, breast cancer and bladder cancer. We mainly focus on stages of progression, location of tumours, survival/response to therapies, and others. The main tasks include classification, analysis, feature extraction and selection, pattern discovery, network/pathway analysis and visualization.
Problems in protein-protein interaction involve discovering new domains and short-linear motifs related to the interactions between proteins and other molecules, and also those interactions and motifs related to the dynamics of the interactome. Problems in transcriptomics involve analysis of next generation sequencing, ChIP-seq and RNA-seq data for discovering biomarkers in different types of cancer, and the role of alternative splicing, protein interactions and pathways.
At the PhD level, I am looking for students who are strong on algorithm design and analysis, lineal algebra and probability, and willingness to learn on quickly changing topics in fields of machine learning, interactomics and transcriptomics, including ChIP-seq, RNA-seq data analysis, big genomic data analysis, protein-protein interaction, dynamics of proteins, among others. Prospective students must demonstrate independence and creativity in conducting research. Knowledge of Perl, Python, Matlab and/or R is desirable. Knowledge in machine learning and bioinformatics is a requirement.
At the Master's level, I am looking for enthusiastic, self-motivated, research-oriented students to work within the areas of protein-protein interaction, ChIP-seq/RNA-seq data analysis, alternative splicing, applications on breast and prostate cancer, among others. The use of supervised and unsupervised machine learning techniques and/or visualization approaches is important.
Deep knowledge of Perl, Python, R and/or Matlab (or serious willingness to learn) is required. Knowledge or willingness to learn machine learning/bioinformatics/cryptography techniques is a requirement.
Note: At present, positions for Master's are not open for Master's students who want to take the Co-op stream.
Undergraduate Research Projects
I am looking for enthusiastic, self-motivated undergraduate students who have excellent analytical and programming skills, while being willing to accept challenges and engage in bioinformatics research problems in data analytics for genomics, proteomics and interactomics data, with applications to biomarker discovery. Feel free to contact me for more details about these projects.
Knowledge of Perl, Python, Script language, HTML, PhP, Joomla, R and/or Matlab (or serious willingness to learn) is required. Willingness to learn machine learning techniques and fundamental concepts in bioinformatics or computer security, while improving their algorithm design and analysis skills is also a requirement. I normally have several short-term and long-term projects in these fields. Feel free to contact me for more details or present your own ideas.