Sajia Akhter

Sajia Akhter

Sajia Akhter space

Location: GMCS 429

Phone: +1 619 594-3137


Sajia’s lab blog

I am a Ph.D. student in Computational Science Research Center (CSRC) at SDSU. I have joined the lab in Fall, 2007.
Currently, I am working on sequence alignment. The goal of this project is to develop a local sequence alignment tool for both DNA and protein sequences, which will work faster than contemporary tools but will give the same or better accuracy.

I have also designed a phage detection algorithm (PhiSpy) for identifying known and undefined prophages in microbial genomes. In PhiSpy, seven distinctive characteristics of prophages are used to predict prophages. These characteristics are protein length, transcription strand directionality, customized AT and GC skew, the abundance of unique phage words, phage insertion points and the similarity of phage proteins.

In the past I worked on applying the information theory on metagenomics and microbial community. I have found that the information theory can be effectively applied on finding informative sequences.
  • PhD Student, Computational Science Research Center, SDSU, (started in Fall 07)
  • Bachelor of Science in Computer Science – Summa Cum Laude, American International university-Bangladesh (AIUB), Bangladesh, 2007. I have achieved the Vice Chancellor Award for the Best Thesis in Computer Science.
  • Sajia Akhter; Ramy K. Aziz; Robert A. Edwards. PhiSpy: a novel algorithm for finding prophages in bacterial genomes that combines similarity- and composition-based strategies, 2012 Nucleic Acids Research doi: 10.1093/nar/gks406
  • Hedin M, Starrett J, Akhter S, Schönhofer AL, Shultz JW. Phylogenomic Resolution of Paleozoic Divergences in Harvestmen (Arachnida, Opiliones) via Analysis of Next-Generation Transcriptome Data, 2012 PLoS ONE 7(8): e42888. doi:10.1371/journal.pone.0042888
  • Noriko Cassman, Alejandra Prieto-Davó, Kevin Walsh, Genivaldo G. Z. Silva, Florent Angly, Sajia Akhter, Katie Barott, Julia Busch, Tracey McDole, J. Matthew Haggerty, Dana Willner, Gadiel Alarcón, Osvaldo Ulloa, Edward F. DeLong, Bas Dulith, Forest Rohwer, Elizabeth A. Dinsdale. Oxygen minimum zones harbor novel viral communities with low diversity. Environmental Microbiology 2012 [Accepted]
  • Terry Disz, Sajia Akhter, Daniel Cuevas, Robert Olson, Ross Overbeek, Veronika Vonstein, Rick Stevens and Robert Edwards, Accessing the SEED Genome Databases via Web Services API: Tools for Programmers 2010 BMC Bioinformatics 11:319 doi:10.1186/1471-2105-11-319.
  • Sajia Akhter, Ipshita Sarkar, Kazi Golam Rabbany, Nahid Akter, Shamim Akhter, Yann Chemin and Honda Kiyoshi, Adapting the LMF Temporal Splining Procedure From Serial to MPI/Linux Clusters, 2007 Journal of Computer Science 3(3): 130-133, Science Publication, New York, USA.

  • Sajia Akhter, Robert Edwards, Tools fot fast sequence alignment, Student Research Symposium, SRS, San diego State University, San Diego, CA, 2012
  • Sajia Akhter, Anca Segall, Molly Schmid, Robert Edwards, Investigating Quinolone Resistance Sequences in Environmental Samples, General meeting of the American Society for Microbiology (ASM), San Diego, CA, 2010
  • Sajia Akhter, Robert Edwards, Assembler for SoLiD data: Improving the memory management of Velvet assembler, 7th Rocky Mountain Bioinformatics Conference, Aspen, Colorado, 2009
  • Sajia Akhter, Barbara Bailey, Peter Salamon, and Robert Edwards, Shannon’s Uncertainty and Kullback-Leibler Divergence in Microbial Genome and Metagenome Sequences, Poster Session, 1st International Conference on Bioinformatics and Computational Biology (BICoB), 2009