Publication Types:

The Evolution and Functional Impact of Human Deletion Variants Shared with Archaic Hominin Genomes

Journal
Yen-Lung Lin, Pavlos Pavlidis, Emre Karakoc, Jerry Ajay, Omer Gokcumen
Molecular Biology and Evolution, Volume 32, Issue 4, 1 April 2015, Pages 1008–1019

Allele sharing between modern and archaic hominin genomes has been variously interpreted to have originated from ancestral genetic structure or through non-African introgression from archaic hominins. However, evolution of polymorphic human deletions that are shared with archaic hominin genomes has yet to be studied. We identified 427 polymorphic human deletions that are shared with archaic hominin genomes, approximately 87% of which originated before the Human–Neandertal divergence (ancient) and only approximately 9% of which have been introgressed from Neandertals (introgressed). Recurrence, incomplete lineage sorting between human and chimp lineages, and hominid-specific insertions constitute the remaining approximately 4% of allele sharing between humans and archaic hominins. We observed that ancient deletions correspond to more than 13% of all common (>5% allele frequency) deletion variation among modern humans. Our analyses indicate that the genomic landscapes of both ancient and introgressed deletion variants were primarily shaped by purifying selection, eliminating large and exonic variants. We found 17 exonic deletions that are shared with archaic hominin genomes, including those leading to three fusion transcripts. The affected genes are involved in metabolism of external and internal compounds, growth and sperm formation, as well as susceptibility to psoriasis and Crohn’s disease. Our analyses suggest that these “exonic” deletion variants have evolved through different adaptive forces, including balancing and population-specific positive selection. Our findings reveal that genomic structural variants that are shared between humans and archaic hominin genomes are common among modern humans and can influence biomedically and evolutionarily important phenotypes.

Artifact | Datasets

A MLFQ Scheduling technique using M/M/c queues for grid computing

Journal
Dharamendra Chouhan, SM Dilip Kumar, Jerry Ajay
International Journal of Computer Science Issues, Vol. 10, Issue 2, No 1, March 2013

We model the objective function, that the jobs entering the scheduler have a Poisson’s distribution and the jobs that are sent out from the multilevel feedback scheduler are also distributed as a Poisson’s distribution. We also assume that the number of CPU’s in a processing element is not restricted to one, but rather many CPUs integrated into one PE. Therefore, we assume the M/M/c queue model for our calculations. In Kendall’s notation, we describes a system where arrivals form a single queue and are governed by a Poisson process, where there are c servers and job service times are exponentially distributed. Gridlets provided by the users are assigned to processing elements (PEs), and gridlets whose remaining service time is shifted between queues of the MLFQ scheduler to be completed. In MLFQ, the total architecture is divided into multiple prioritized queues. This approach provides gridlets which starve in the lower priority queue for long time to get resources. As a result, the response time of the starved gridlets decreases and overall turnaround time of the scheduling process decreases. This scheduling policy is simulated using Alea GridSim toolkit to test the performance. The proposed MLFQ scheduling algorithm works better in most of the scenarios when compared to FCFS and PBS_PRO algorithms.