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Lab News Archive

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July 2016
Mohammed Aledhari has successfully defended his dissertation proposal. Congratulations !

Muaaz Awan has received Graduate Student Travel Award from CEAS WMU for attending ICPP conference in Philadelphia and present his paper. Congratulations !

June 2016
Muaaz Awan's paper "GPU-ArraySort: A parallel, in-place algorithm for sorting large number of arrays", has been accepted for Proceedings of International Conference on Parallel Processing (ICPP-2016), Philadelphia PA.

Mohamed Aledhari's paper "A Variable-Length Network Encoding Protocol for Big Genomic Data" has been accepted for Proceedings of  International Conference on Wired & Wireless Internet Communications (WWIC 2016), Greece.

April 2016
Sandino Vargas-Perez who is a PhD student in the lab represented WMU at the Midwestern Association of Graduate Schools conference in Chicago on April 8. He was selected on the basis of presentation at the regional Three-Minute Thesis (3MT) competition where he scored the highest among the competition. Here is a video of his talk.

Muaaz Awan who is a PhD student in PCDS has won the  Department-Level Graduate Research and Creative Scholars Award at WMU for 2015-2016. More details are available here. Congratulations Muaaz !

Lily Kitagawa, a K12 student in our lab has won the Intel Excellence in Computer Science Award. More details about her research and poster can be read here. Congratulations Lily !

March 2016
Our research was covered by Science Node entitled "Surfing with Algorithms". Science Node is a magazine that covers cutting edge research in big data & computing and is funded by NSF (in the US) and CERN (in the Europe).

Sandino Vargas-Pérez participated in "Grad Talks: Three-Minute Thesis competition" an event sponsored by WMU's Graduate College and the Graduate Student Association. He presented his research related to HPC compressive genomics and won one of the five $200 prizes. Congratulations Sandino !

February 2016
Prof. Saeed has been awarded US$ 16,000 from the National Science Foundation (NSF) as Research Experience for the Undergraduate (REU) supplement. The grant money will be used for introducing undergraduates to research in big data and high performance computing.

Prof. Fahad Saeed has been given "Outstanding New Researcher" award of the year 2015 from the College of Engineering and Science (CEAS) at WMU. More details about the award can be found at this link.

January 2016
Muaaz Awan and Fahad Saeed's paper entitled "MS-REDUCE: An ultrafast technique for reduction of Big Mass Spectrometry Data for high-throughput processing has been accepted in Oxford Bioinformatics

December 2015
Dr. Saeed gave a talk on "challenges and opportunities for HPC community in analyzing big data proteogenomics" at IEEE Global SIP 2015 that was held in Orlando Florida. 

November 2015
Congratulations to Dana Abdul-Qader for defending her MS Thesis titled "A High Performance Architecture for an Exact Match Short-Read Aligner Using Burrow-Wheeler Transform on FPGAs". We wish her all the best in her future endeavors.

Dr. Saeed just chaired a very successful and exciting IEEE workshop on HPC and big data computational biology in Washington DC. This workshop was held in conjunction with IEEE BIBM 2015.

October 2015
Lily Kitagawa from Kalamazoo Area Mathematics & Science Center (KAMSC) has joined the lab. She will be working on efficient algorithmic techniques for big genomic data.

September 2015
Dr. Saeed is a chair for new and exciting IEEE Workshop on High Performance Computing for Big Data Computational Biology (HPC-BCB 2015) which will be held in conjunction with IEEE BIBM 2015 in Washington DC. Invite your colleagues and students to submit high-quality research papers in the workshop. The paper submission deadline is extended till 19th Sept 2015

August 2015
Taban Eslami has joined Parallel Computing and Data Science Laboratory as a PhD Student. She will be working on HPC solutions to Big Genomics and Proteomics Data sets

Fahad Saeed's paper entitled "Big Data Proteogenomics and High Performance Computing: Challenges and Opportunities" has been accepted in the Symposium on Software defined Ecosystems and Green Computing, Proceedings of IEEE Global Conference on Signal and Information Processing (IEEE GlobalSIP ), Orlando Florida USA Dec 2015

June 2015
We have been allocated time (and space) on the NSF Extreme Science and Engineering Discovery Environment (XSEDE) super-computing infrastructure. Computing times on these machines are acquired via peer-review of the proposed projects. We will be conducting scalability studies for petascale genomics data using XSEDE computing machines. More can be read here.

Sandino Perez and Fahad Saeed's paper entitled "A Parallel Algorithm for Compression of Big Next-Generation Sequencing (NGS) Datasetshas been accepted at the IEEE Workshop on Parallelism in Bioinformatics, Proceedings of Parallel and Distributed Processing with Applications (IEEE ISPA-15)Helsinki Finland

Melissa Basileo from the CS department (data science major) joined the PCDS Lab as an undergraduate student researcher. She will be working on chemical specific characterizations of mass spectrometry data for efficient compression and development of graphical user interfaces.

May 2015
Mohammed Aledhari and Fahad Saeed's paper entitled "Design and Implementation of Network Transfer Protocol for Big Genomic Data" has been accepted at the IEEE International Congress on Big Data (IEEE BigData Congress 2015), New York City, USA

March 2015
Prof. Saeed was selected to be elevated to the grade of IEEE Senior Member, which is bestowed on those who have made significant contributions to the profession. More details about senior membership can be found here.

High-school students, Binh Le and Adam Coles, from Kalamazoo Area Mathematics and Science Center (KAMSC) presented their research poster at Southwest Michigan Science and Engineering Fair held at WMU on 20th March. More details about their work can be read in our blog post.

February 2015
Prof. Fahad Saeed received Research Initiation Initiative Award (CRII) of US$ 171,341 from the National Science Foundation (NSF). The grant will support his research on high performance algorithms and architectures for Big Data. The research proposal entitled “HPC Solutions to Big NGS Data Compression” (Feb 2015 – Feb 2017) proposes to design and implement novel data-aware solutions for compression of large genomic data sets using high performance architectures and algorithms. Successful completion of this research will have significant impact on clinical as well as system biology labs and will move us one step closer to personal genomics era. This two-year pre-CAREER award was competitively awarded through NSF’s merit-review process and is supported by the NSF CCF Core program. Dr. Saeed is the sole PI on this grant.

January 2015
Dr. Fahad Saeed gave an invited seminar on Big Data Proteomics: High Performance Computing Methods & Applications at Lahore University of Management Sciences (LUMS) on 8th Jan.

Muaaz Awan and Fahad Saeed's paper entitled "On the sampling of Big Mass Spectrometry Data" has been accepted at the Bioinformatics and Computational Biology Conference, Hawaii USA 2015.

November 2014
Mohammed Aledhari from the CS department joined the PCDS Lab as a PhD student. He will be working on efficient networking solutions for Big Genomic Data.

October 2014
Prof. Saeed is now the founding co-director of the Center for High Performance Computing and Big Data (CHPCBD) at Western Michigan University (WMU). He will be heading this center along with Elise de Doncker and John Kapenga.

September 2014
High School students Binh Le and Adam Coles from Kalamazoo Area Mathematics and Science Center (KAMSC) have joined the lab as researchers. They will work on easy to use graphical user interfaces for domain scientists.

August 2014
Muaaz Awan joined the PCDS Laboratory as a Interdisciplinary CEAS PhD student with his home department as ECE. He will be working on High performance strategies for analysis of Big Mass Spectrometry data.

July 2014
Prof. Saeed has been invited as guest editor for special BICoB-2014 issue in the Journal of Bioinformatics and Computational Biology (JBCB)

June 2014
Mohammad Abu Shattal has joined the Parallel Computing and Data Science Laboratory as a PhD student. He will be working on high performance data transfer protocols for Big genomic Data

May 2014
Sandino Narciso Vargas Perez joined Parallel Computing and Data Science Laboratory as a PhD Student. He will be working on compression and data-reduction techniques for Big Next Generation Sequencing Data

April 2014
Dr. Fahad Saeed has received a hardware grant (2 DE5-NET-450 FPGA's) to continue our research in developing high performance solutions for Big Data Genomics using reconfiguarble computing architectures (US$ 16,000)

Saeed et. al's paper "Exploiting thread-level and instruction-level parallelism to cluster mass spectrometry data using multicore architectures" appeared in Springer Journal of Network Modeling Analysis in Health Informatics and Bioinformatics

March 2014
Prof. Fahad Saeed joined the editorial board of Springer Journal of Network Modeling Analysis in Health Informatics and Bioinformatics

Feb 2014
Dr. Fahad Saeed has received a hardware donation grant from NVIDIA: a K40 Tesla GPU to continue our research on high performance solutions to genome alignments (US$ 5,499)


Jan 2014
Saeed et. al's paper "CAMS-RS: Clustering Algorithm for Large-Scale Mass Spectrometry Data Using Restricted Search Space and Intelligent Random Sampling" appeared in IEEE/ACM Transactions on Computational Biology and Bioinformatics 
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