PhD in Engineering and Applied Science
Concentration: Computer Science
Specialization: Machine Learning and Bioinformatics
(Fall 2013 - July 2017)
New Orleans, LA 70148
Committee:
Md Tamjidul Hoque (chair), Christopher Summa,Shengru Tu, Wendy Schluchter, Huimin Chen
Dissertation: "Machine Learning based Protein Sequence to (un)Structure Mapping and Interaction Prediction"
Summary: Proteins are the fundamental macromolecules within a cell that carry out most of the biological functions. The computational study of protein structure and its functions, using machine learning and data analytics, is elemental in advancing the life-science research due to the fast-growing biological data and the extensive complexities involved in their analyses towards discovering meaningful insights. Mapping of protein’s primary sequence is not only limited to its structure, we extend that to its disordered component known as Intrinsically Disordered Proteins or Regions in proteins (IDPs/IDRs), and hence the involved dynamics, which help us explain complex interaction within a cell that is otherwise obscured. In this dissertation, we developed effective computational tools to predict disordered protein and its dynamics, model protein sequence information into distinguishing structural properties to recognize (un)structured residues, and identify potential peptide-recognition domain (PRD) residues that can induce disorder-to- order conformational change in short peptide-motifs to materialize transient interactions. We systematically mined and analyzed the large-scale biological data, and modeled the data using machine learning techniques, such as SVM, DNN, regression, reinforcement learning and boosting, and several ensemble learning methods.
Courses:
MSc (Engg.) in Computer Science and Engineering
(December 2009 - December 2012)
- Bangladesh University of Engineering and Technology (BUET)
Dhaka, Bangladesh
Thesis Title: "Vehicle Routing Problem with Soft Time Windows" [pdf]
Concentration: Evolutionary Computing Algorithms and Applications
Supervisor: M Sohel Rahman, PhD, Professor, Department of Computer Science and Engineering, Bangladesh University of Engineering and Technology, Dhaka - 1000, Bangladesh.
Courses:
BSc (Engg.) in Computer Science and Engineering
(December 2004 - October 2009)
- Bangladesh University of Engineering and Technology (BUET)
Dhaka, Bangladesh
Thesis Title: "Algorithms in Bioinformatics" [pdf]
Concentration: Stringology
Supervisor: Masud Hasan, PhD, Professor, Department of Computer Science and Engineering, Bangladesh University of Engineering and Technology, Dhaka - 1000, Bangladesh.
Courses:
Memberships
Programming/Scripting Language
Database/Data Analysis/Data Modeling
Software/Tools/Library