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Sajia Akhter

Sajia Akhter space

Location: GMCS 429

Phone: +1 619 594-3137

Email: sakhter@sciences.sdsu.edu

Sajia’s lab blog

Bio
I am a Ph.D. student in Computational Science Research Center (CSRC) at SDSU. I joined the lab in Fall, 2007.
Research
Currently, I am working on identifying prophages. Based on different properties of phages, I am developing an algorithm, which can determine known and unknown prophages in a bacterial genome.
I also conduct my research on the assembly problem – especially designing efficient assembler for very short sequences (SOLiD/Solexa). 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.
Education
  • 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, 2006. I have achieved the Vice Chancellor Award for the Best Thesis in Computer Science.
Publications
  • 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, Accepted in BMC Bioinformatics 2010.
  • 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, Journal of Computer Science 3(3): 130-133, 2007, Science Publication, New York, USA.

Posters
  • 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

Rob Edwards

Lab members

Principal Investigator
Rob Edwards

 

 Postgraduate Researchers
Jeremy Frank
Dave Matthews

 

PhD Students
Rob S

 

Master Students
Adam

Katelyn McNair

Steven Williams

Sheridan

Undergraduate Students
Palla
Heqiao

Blaire Robinson

Visiting Researchers

 

Lab Alumni

Brian Hudson

Ramy Aziz
Andres
nick
carny

bas
stephanie
Matthew
brad
ben
Huy
Amanda Trindade
Thiago Bruce
Promita Bose
Vasken Kamiksisian
Vasken Kamiksisian
Joakim
Matt Seitz
Matt Seitz
Rima Soury

 

Master students

Nick Celms

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Nick Celms has been part of the Edwards lab since the Summer of 2008, and works on visualizations of BLAST comparisons. He spent his first two years as an undergraduate at the University of Washington before transferring to San Diego State’s computer science department. Nick is one of SDSU’s first wave of cross-trained students participating in the BioMath program, an emerging NSF priority. Outside the lab, Nick is the Vice President of a student organization called Compassion for African Villages that sends aide to the village of Rundongo, Zimbabwe.

 

Carny Cheng

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Carny is a Computational Science Masters student. His research focuses mainly on web services providing middleware for scientists to access cyberinfrastructure resources. Carny holds two Bachelors degrees from University of California, San Diego in Computer Engineering and economics. He has spent sometime working in the software industry at Websense, Inc. where he bounced from project to project eventually settling in text classification.

Carny also serves as the lab system administrator. It is advisable to stay on Carny’s good-side if you want your access to the lab’s computing resources.

 

Kate McNair

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Kate is a …

 

Undergraduates

Matt Hagen

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???

 

Josh Hoffman

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Josh is a Computer Science student pursuing a Bachelor of Science degree at San Diego State. He is currently writing utilities which extract various information from Blast outputs. His most recent project involves finding Bidirectional Best Hits in a given Blast output.

 

Vasken Kamiksisian

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Vasken Kamiksisian is an SDSU Computer Science student working to create OpenSocial applications and gadgets relating to the lab research. Users of these applications will be able to pull information from servers all over the globe. In addition to quickly retrieving information, users will be able to use the tools located on these remote servers. All users need to do is add the gadgets to their respective account (i.e. iGoogle, Orkut, Facebook, etc.).

Here is a google gadget that searches information on the lab’s servers. Bioinformatics Search

 

Matt Seitz

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Matt is a Computer Science undergraduate who is currently in his final semester at SDSU. He started working with the lab in the Spring ’09 semester.

His current work is to develop Open Social applications that can help the lab quickly pull data or use tools located on remote servers. By integrating the Open Social framework, these applications will be portable. This allows them to be easily integrated across many different platforms.

See Vasken’s bio for a link to a text search that can be added to your Google, MySpace, Orkut, or other valid Open Social supporting account.

PhD Students

Sajia Akhter

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Sajia is a Ph.D. student in the computational science research center (CSRC) at SDSU. She joined Edwards Lab in Fall, 2007. Before coming to SDSU, she completed her B.Sc. in American International University-Bangladesh.

Sajia conducts her research on assembly of short-read sequencing data. Especially she looks for more time and memory efficient variations of existing assembly algorithms. Apart from that she also worked on applying information theory on metagenomes and microbial genomes. She found that information theory can be effectively applied on finding informative sequences.

 

Robert Schmieder

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bla bla blub

 

Victor Seguritan

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I am Victor ….