Bilal Wajid

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In the realm of bioinformatics and computational biology, the most rudimentary data upon which all the analysis is built is the sequence data of genes, proteins and RNA. The sequence data of the entire genome is the solution to the genome assembly problem. The scope of this contribution is to provide an overview on the art of problem-solving applied within(More)
Genome sequences are the most basic, yet most essential pieces of data in all biological analysis. Genome sequence is the solution to the Genome Assembly problem which remakes the entire sequence from a set of reads which are unordered and very small in size. Genome Assembly problem is therefore, quite complex and is broadly divided into denovo and(More)
This paper introduces MiB, a comparative genome assembly pipeline that uses three key steps. The first step involves choosing the best reference sequence by using the Minimum Description Length (MDL) principle. The MDL principle not only chooses the best reference sequence (model) but also fine-tunes the model for a better assembly by rectifying all the(More)
: Reference assisted assembly requires the use of a reference sequence, as a model, to assist in the assembly of the novel genome. The standard method for identifying the best reference sequence for the assembly of a novel genome aims at counting the number of reads that align to the reference sequence, and then choosing the reference sequence which has the(More)
In systems biology, the regulation of gene expressions involves a complex network of regulators. Transcription factors (TFs) represent an important component of this network: they are proteins that control which genes are turned on or off in the genome by binding to specific DNA sequences. Transcription regulatory networks (TRNs) describe gene expressions(More)
A novel assembly pipeline, MiB, employs Minimum Description Length (MDL), de-Bruijn graphs and Bayesian estimation for reference assisted assembly of the novel genome. In a previous study MiB assembly was compared with nine other assembly algorithms showing significant improvement in results coupled with very large execution times. This correspondence(More)
stem5 is a STEM education initiative based at University of Engineering & Technology (UET) at Lahore, Pakistan. The initiative aims to rejuvenate STEM education in Pakistan by engaging university faculty and students in outreach activities targeted towards underprivileged students studying in the public school system. Volunteers include faculty,(More)
Bioinformatics skills required for genome sequencing often represent a significant hurdle for many researchers working in computational biology. This humble effort highlights the significance of genome assembly as a research area, focuses on its need to remain accurate, provides details about the characteristics of the raw data, examines some key metrics,(More)