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<h1 style="margin: 0.0px 0.0px 16.1px 0.0px; font: 24.0px Arial; -webkit-text-stroke: #000000"><span class="s1"><b>Fahad Saeed, Ph.D.<span class="Apple-converted-space"> </span></b></span></h1>
<p class="p2"><span class="s2"><a href="https://www.cis.fiu.edu/faculty-staff/saeed-fahad/">Associate Professor (Tenured), </a><a href="https://www.cis.fiu.edu/">Knight Foundation School of Computing and Information Sciences,<span class="Apple-converted-space"> </span></a></span></p>
<p class="p3"><span class="s3">Associate Professor,</span><span class="s4"> <a href="https://bsi.fiu.edu/about/index.html"><span class="s5">Biomolecular Sciences Institute (BSI),<span class="Apple-converted-space"> </span></span></a></span></p>
<p class="p3"><span class="s3">Associate Professor,</span><span class="s4"> <a href="https://medicine.fiu.edu/about/departments/human-and-molecular-genetics/index.html"><span class="s5">Herbert Wertheim School of Medicine,<span class="Apple-converted-space"> </span></span></a></span></p>
<p class="p4"><span class="s6"><a href="https://www.fiu.edu/">Florida International University (FIU)</a></span><span class="s1"> - The State University of Florida at Miami, FL USA</span></p>
<p class="p5"><span class="s7">Director: <a href="https://pcdslab.github.io/"><span class="s8"> Precision Computational Health and Biomedical Data Science Lab (Saeed Lab)</span></a></span></p>
<p class="p4"><span class="s1">Founder & CEO: <a href="https://neuromarkers.github.io/"><span class="s9">AI-NeoTech LLC</span></a></span></p>
<p class="p6"><span class="s1">Mailing Address: 11200 SW 8th St, Room CASE 261, Miami, FL 33199, USA<br>
E-mail: <a href="mailto:[email protected]"><span class="s9">[email protected]</span></a> Twitter: <a href="https://twitter.com/Prof_FahadSaeed"><span class="s9">@Prof_FahadSaeed</span></a> <br>
Phone: +1-305-348-3131 Office: CASE 261<br>
<a href="https://users.cs.fiu.edu/~fsaeed/CV/CV_Saeed.pdf"><span class="s9">Long CV (pdf)</span></a> <br>
<a href="https://scholar.google.com/citations?user=IPXv-GQAAAAJ&hl=en"><span class="s9">Google Scholar Profile</span></a><span class="Apple-converted-space"> </span></span></p>
<p class="p6"><span class="s1">I am co-chairing <a href="https://hpcbod.cs.fiu.edu/"><span class="s9">HPC-BOD workshop in conjunction with IEEE BigData 2024</span></a>. Consider contributing a paper (deadline: Oct 23rd, 2024)</span></p>
<h2 style="margin: 0.0px 0.0px 14.9px 0.0px; font: 18.0px Arial; -webkit-text-stroke: #000000; min-height: 21.0px"><span class="s1"></span><br></h2>
<h2 style="margin: 0.0px 0.0px 14.9px 0.0px; font: 18.0px Arial; -webkit-text-stroke: #000000"><span class="s1"><b>Biosketch</b></span></h2>
<p class="p4"><span class="s1">Fahad Saeed is an Award-winning Scientist, Entrepreneur, and Tenured Associate Professor in the <a href="https://www.cis.fiu.edu/"><span class="s10">School of Computing and Information Sciences</span></a> at <a href="https://www.fiu.edu/"><span class="s10">Florida International University (FIU)</span></a>, Miami FL and is the director of <a href="https://pcdslab.github.io/"><span class="s10"> Precision Computational Health and Biomedical Data Science Lab (Saeed Lab)</span></a></span><span class="s11"> </span><span class="s1">at FIU. Dr. Saeed's research interests are at the intersection of machine-learning, high performance computing and real-world applications, especially in computational biology.<span class="Apple-converted-space"> </span></span></p>
<p class="p4"><span class="s1">Dr. Saeed has published 90+ peer-reviewed research papers in leading proceedings, and journals, and 1 Book Chapter, edited 4 Conference Proceedings, 3 special issue journals, and 1 Book. His research is supported by highly competitive grants mainly from National Science Foundation (NSF) and National Institutes of Health (NIH). He has been awarded over <b>US$ 6.85 million</b> in external research funds - with more than <b>US$ 5.45 million</b> as a PI. He was awarded the NSF Research Initiation Initiative (CRII) Award bestowed to young and promising scientists in the first two years of their tenure-track position. Most recently he was awarded the <b>NSF Faculty Early Career Development (CAREER) Award</b> which is NSF's most prestigious award in support of early-career faculty who have the potential to serve as academic role models in research and education. His research has been supported by NVIDIA, Intel/Altera, Xilinx, National Science Foundation (NSF) and National Institutes of Health (NIH).</span></p>
<p class="p4"><span class="s1">Prior to joining FIU, Prof. Saeed was a tenure-track Assistant Professor in the <a href="https://wmich.edu/ece/"><span class="s10">Department of Electrical & Computer Engineering</span></a> and <a href="http://wmich.edu/cs/"><span class="s10">Department of Computer Science</span></a> at <a href="http://wmich.edu/"><span class="s10">Western Michigan University (WMU)</span></a>, Kalamazoo Michigan since Jan 2014. He was tenured and promoted to the rank of Associate Professor at WMU in August 2018. Dr. Saeed was a Post-Doctoral Fellow and then a Research Fellow in the <a href="https://esbl.nhlbi.nih.gov/"><span class="s10">Systems Biology Center</span></a> at <a href="https://www.nih.gov/"><span class="s10">National Institutes of Health (NIH)</span></a>, Bethesda MD from Aug 2010 to June 2011 and from June 2011 to January 2014 respectively. He received his PhD in the <a href="https://www.ece.uic.edu/"><span class="s10">Department of Electrical and Computer Engineering</span></a>, <a href="http://www.uic.edu/uic/"><span class="s10">University of Illinois at Chicago (UIC)</span></a> in 2010. He has served as a visiting scientist in world-renowned prestigious institutions such as <a href="http://www.bsse.ethz.ch/"><span class="s10">Department of Bio-Systems Science and Engineering (D-BSSE)</span></a>, <a href="http://www.ethz.ch/index_EN"><span class="s10">ETH Zurich</span></a>, <a href="http://www.isb-sib.ch/"><span class="s10">Swiss Institute of Bioinformatics (SIB)</span></a> and <a href="https://esbl.nhlbi.nih.gov/"><span class="s10">Epithelial Systems Biology Laboratory (ESBL)</span></a> at <a href="http://www.nih.gov/"><span class="s10">National Institutes of Health (NIH)</span></a> Bethesda, Maryland.<span class="Apple-converted-space"> </span></span></p>
<p class="p4"><span class="s1">Dr. Saeed has established a global profile as an Independent Researcher and leader in the field, and has been sought as panelist at the National and International funding agencies. These inlucde serving as panelist at various study sections at National Institutes of Health (NIH), National Science Foundation (NSF), NIH NIDDK, National Nuclear Security Administration (NNSA) Department of Energy (DOE), and as International expert and panelist for Croatian Science Foundation (CSF), University of Queensland Diamantina Institute in Australia, Belgium Fund for Scientific Research (F.R.S.- FNRS), and Natural Sciences & Engineering Research Council of Canada. He has served as the program co-chair of the Bioinformatics and Computational Biology (BICoB) Conference and IEEE International Conference on Bioinformatics and Biomedicine (IEEE BIBM). He is also a founding chair of IEEE Workshop on HPC solutions to Big Data Computational Biology (IEEE HPC-BCB). He also serves on the editorial board of Springer Journal of Network Modeling Analysis in Health Informatics and Bioinformatics, on the Editorial board of Journal of the American Society of Nephrology, and as Associate Editor for Frontiers of Digital Public Health (specialty section of Frontiers in Public Health, Frontiers in ICT and Frontiers in Computer Science). He has served on numerous IEEE/ACM program committees and is peer-reviewer for more than a two dozen journals.<span class="Apple-converted-space"> </span></span></p>
<p class="p4"><span class="s1">Dr. Saeed is a Senior Member of ACM and also a Senior Member of IEEE. His honors include <a href="http://thinkswiss.tumblr.com/"><span class="s10">ThinkSwiss Fellowship</span></a> (2007,2008), NIH Postdoctoral Fellowship Award (2010), <a href="https://www.training.nih.gov/felcom/fare"><span class="s10">Fellows Award for Research Excellence (FARE)</span></a> at NIH (2012), <a href="https://www.nsf.gov/funding/pgm_summ.jsp?pims_id=504952"><span class="s10">NSF CRII Award</span></a> (2015), <a href="https://wmich.edu/engineer/outstanding-past"><span class="s10">WMU Outstanding New Researcher Award</span><span class="s12"> </span></a>(2016), WMU Distinguished Research and Creative Scholarship Award (2018), , <a href="https://www.nsf.gov/funding/pgm_summ.jsp?pims_id=503214"><span class="s10">NSF CAREER Award</span></a> (2017), FIU KFSCIS Excellence in Applied Research Award (2020). More recently he was recognized as "Top Scholar” in "Research and Creative Activities" by FIU in 2022</span></p>
<p class="p9"><span class="s1"></span><br></p>
<h2 style="margin: 0.0px 0.0px 14.9px 0.0px; font: 18.0px Arial; -webkit-text-stroke: #000000"><span class="s1"><b>Recent Media Coverage</b></span></h2>
<ol class="ol1">
<li class="li4"><span class="s13"></span><span class="s1">"Wearable devices could help predict seizures", </span><span class="s14"><b>FIU News</b></span><span class="s1">, August 2022 <a href="https://news.fiu.edu/2022/seizure-prediction-fiu-researchers-work-to-improve-lives-for-epileptics"><span class="s10">Article Link</span></a></span></li>
<li class="li4"><span class="s13"></span><span class="s1">"NIH Awards FIU $1M to Develop Machine Learning Algorithms to Study Proteins", </span><span class="s14"><b>HPC Wire</b></span><span class="s1">, June 2020 <a href="https://www.hpcwire.com/off-the-wire/nih-awards-fiu-1m-to-develop-machine-learning-algorithms-to-study-proteins/"><span class="s10">Article Link</span></a></span></li>
<li class="li4"><span class="s13"></span><span class="s1">"FIU researchers think of a way to speed up a vaccine for COVID-19", </span><span class="s14"><b>Miami Herald</b></span><span class="s1">, June 2020 <a href="https://www.miamiherald.com/news/health-care/article243424276.html"><span class="s10">Article Link</span></a></span></li>
<li class="li4"><span class="s13"></span><span class="s1">"Research Grant Helps FIU Professor Reach One Step Closer To Coronavirus Vaccine", </span><span class="s14"><b>FIU PantherNow</b></span><span class="s1">, July 2020 <a href="http://panthernow.com/2020/07/06/research-grant-helps-fiu-professor-reach-one-step-closer-to-coronavirus-vaccine/"><span class="s10">Article Link</span></a></span></li>
<li class="li4"><span class="s13"></span><span class="s1">"NIH awards FIU $1M to develop machine-learning algorithms to study proteins - important for understanding, treating diseases", </span><span class="s14"><b>FIU News</b></span><span class="s1">, June 2020 <a href="https://news.fiu.edu/2020/nih-awards-fiu-1-million-to-develop-machine-learning-algorithms-to-study-proteins-important-for-understanding,-treating-diseases"><span class="s10">Article Link</span></a></span></li>
<li class="li4"><span class="s13"></span><span class="s1">"Dr. Saeed awarded prestigious $1 Million R01 grant from National Institute of Health", SCIS FIU News, May 2020 <a href="https://www.cis.fiu.edu/dr-saeed-awarded-prestigious-1-million-r01-grant-from-national-institute-of-health/"><span class="s10">Article Link</span></a></span></li>
<li class="li4"><span class="s13"></span><span class="s1">Distinguished Research and Creative Scholarship Award: Fahad Saeed",OVPR WMU, March 2018 <a href="https://wmich.edu/engineer/saeed-0"><span class="s10">Description</span></a> <a href="https://www.youtube.com/watch?v=UgGAtsuOyTA"><span class="s10">YouTube</span></a></span></li>
<li class="li4"><span class="s13"></span><span class="s1">Algorithms for Life, <a href="http://www.wmich.edu/research/algorithms-life"><span class="s10">WMU Annual Magazine</span></a>, Summer 2017</span></li>
<li class="li4"><span class="s13"></span><span class="s1">Rising Stars in Research, <a href="https://issuu.com/wmich/docs/wmu-magazine-summer-2017"><span class="s10">WMU Annual Magazine</span></a>, Summer 2017</span></li>
<li class="li4"><span class="s13"></span><span class="s1">Researchers Snag a prestigious National Prize, <a href="http://www.wmich.edu/news/2017/10/43181"><span class="s10">WMU News Link</span></a>, 2017</span></li>
<li class="li4"><span class="s13"></span><span class="s1">WMU Assistant Professor receives NSF CAREER Award, <a href="https://wmich.edu/engineer/fahad-saeed"><span class="s10">CEAS WMU Article Link</span></a></span></li>
<li class="li4"><span class="s13"></span><span class="s1">Surfing with Algorithms, <a href="https://sciencenode.org/feature/surfing-with-algorithms.php"><span class="s10">NSF Science Node</span></a>, March 2016</span></li>
<li class="li4"><span class="s13"></span><span class="s1">Working with Powerful Supercomputers, <a href="http://www.wmich.edu/sites/default/files/attachments/u593/2015/CEAS%20e%20news%20July15_0.pdf"><span class="s10">WMU CEAS News</span></a>, July 2015</span></li>
</ol>
<p class="p10"><span class="s1"></span><br></p>
<p class="p11"><span class="s1"></span><br></p>
<h2 style="margin: 0.0px 0.0px 14.9px 0.0px; font: 18.0px Arial; -webkit-text-stroke: #000000"><span class="s1"><b>Recent Honors</b></span></h2>
<ol class="ol1">
<li class="li4"><span class="s13"><b></b></span><span class="s1"><b>FIU Top Scholar</b>, <i>Research and Creative Activities </i>, Florida International University, Sept 2022 <a href="https://cec.fiu.edu/2022/09/congratulations-to-the-college-of-engineering-computing-cec-faculty-named-fiu-top-scholars"><span class="s9">CEC News Page</span></a><span class="Apple-converted-space"> </span></span></li>
<li class="li4"><span class="s13"></span><span class="s1">Associate Editor, <i>Experimental Results</i>, Cambirdge University Press, April 2022 <a href="https://www.cambridge.org/core/journals/experimental-results/information/editorial-board"><span class="s9">Editorial Board Page</span></a><span class="Apple-converted-space"> </span></span></li>
<li class="li4"><span class="s13"><b></b></span><span class="s1"><b>Keynote Speaker</b> at the 14th International Conference on Bioinformatics and Computational Biology (BICOB). More info here: <a href="https://sce.uhcl.edu/bicob22/"><span class="s9">BiCOB-2022</span></a> <a href="file:///Users/Prof.Saeed/Documents/GitHub/Prof-S.github.io/Keynote_2022.pdf"><span class="s9">KeyNote Certificate</span></a></span></li>
<li class="li4"><span class="s13"></span><span class="s1">Excellence in Applied Research Award, School of Computing and Information Science (SCIS), Florida International University (FIU), Dec 2020<span class="Apple-converted-space"> </span></span></li>
<li class="li4"><span class="s13"></span><span class="s1">Distinguished Research and Creative Scholarship Award, Office of Vice President of Research WMU, Feb 2018<span class="Apple-converted-space"> </span></span></li>
<li class="li4"><span class="s13"><b></b></span><span class="s1"><b>NSF CAREER Award</b>, 2017-2022</span></li>
<li class="li4"><span class="s13"></span><span class="s1">Highest Funding Award in a year for computer scientist, WMU 2017</span></li>
<li class="li4"><span class="s13"><b></b></span><span class="s1"><b>ACM Senior Member</b>, May 2017</span></li>
<li class="li4"><span class="s13"></span><span class="s1">Outstanding New Researcher Award, College of Engineering and Applied Science (CEAS), Western Michigan University, Jan 2016 (1 faculty member gets the award in a single year for the entire college consisting of 7 academic departments)</span></li>
<li class="li4"><span class="s13"><b></b></span><span class="s1"><b>IEEE Senior Member</b>, March 2015</span></li>
<li class="li4"><span class="s13"></span><span class="s1">NSF CISE Research Initiation Initiative (CRII) Award, Feb 2015 - Feb 2018</span></li>
<li class="li4"><span class="s13"></span><span class="s1">Fellows Award for Research Excellence (FARE), National Institutes of Health (NIH), June 2012 (Official award ceremony and US\$1000 travel grant)<span class="Apple-converted-space"> </span></span></li>
<li class="li4"><span class="s13"></span><span class="s1">Travel award from Swiss Institute of Bioinformatics (SIB), Summers 2009.<span class="Apple-converted-space"> </span></span></li>
<li class="li4"><span class="s13"></span><span class="s1">UIC Graduate Student Council (GSC) travel award for the BiCoB April 2009.<span class="Apple-converted-space"> </span></span></li>
<li class="li4"><span class="s13"></span><span class="s1">Recipient of Think Swiss Scholarship, by the Government of Switzerland for two years (2007 and 2008).<span class="Apple-converted-space"> </span></span></li>
<li class="li4"><span class="s13"></span><span class="s1">Travel award from D-BSSE ETH Zurich, Summers 2008.<span class="Apple-converted-space"> </span></span></li>
</ol>
<p class="p10"><span class="s1"></span><br></p>
<p class="p11"><span class="s1"></span><br></p>
<h2 style="margin: 0.0px 0.0px 14.9px 0.0px; font: 18.0px Arial; -webkit-text-stroke: #000000"><span class="s1"><b>Funding</b></span></h2>
<p class="p4"><span class="s1">Prof. Saeed has been awarded over <b>US$ 6.85 million</b> in external research funds - with more than <b>US$ 5.45 million</b> as a PI since 2014 (approx. US$ 700k per year) <br>
Most of the external research funds are competitively awarded from Federal Agencies such as National Science Foundation (NSF) and National Institutes of Health (NIH). Intramural funds and computing allocations are not included in this amount.<br>
</span><span class="s15"><br>
<br>
</span><span class="s2"><b>External Research Funds</b></span><span class="s1"> <br>
17. National Institutes of Health (NIH) R35GM153434 <b>[US$ 1.75 million]</b>, “Machine Learning Models for big data omics”, Fahad Saeed (PI), June 2024 - June 2029 (single PI grant: MIRA R35 Outstanding Investigator mechanism) | <a href="https://reporter.nih.gov/project-details/10842826"><span class="s16">NIH Reporter Award Page</span></a></span></p>
<p class="p4"><span class="s1">16. National Science Foundation (NSF) OAC-2312599 <b>[US$ 600,000]</b>, ``OAC Core: High Performance Computing Algorithms and Software for large-scale Mass Spectrometry based Omics", <b>Fahad Saeed (PI)</b>, Sept 2023 - Aug 2026 | <a href="https://www.nsf.gov/awardsearch/showAward?AWD_ID=2312599&HistoricalAwards=false"><span class="s10">NSF Award Page</span></a> <br>
15. National Science Foundation (NSF) TI-2322346 <b>[US$ 275,000]</b>, ``STTR Phase I: Patient-Specific System for Early Detection and Identification of Epileptic Seizures ", Saba Mehmood (PI), <b>Fahad Saeed (Co-PI)</b>, Oct 2023 - Sept 2024 | <a href="https://www.nsf.gov/awardsearch/showAward?AWD_ID=2322346&HistoricalAwards=false"><span class="s10">NSF Award Page</span></a> <br>
14. National Science Foundation (NSF) CHE-2304837 <b>[US$ 500,000]</b>, ``Development of Multidimensional Ion Mobility-Tandem Mass Spectrometry (IMSn-FT-ICR MSn) Tools for the Characterization of Complex Mixtures", Francisco Lima (PI), <b>Fahad Saeed (Co-PI)</b>, Sept 2023 - August 2026 | <a href="https://www.nsf.gov/awardsearch/showAward?AWD_ID=2304837&HistoricalAwards=false"><span class="s10">NSF Award Page</span></a> <br>
13. National Science Foundation (NSF) TI-2213951 <b>[US$ 250,000]</b>, ``PFI-TT: Artificial Intelligence-enabled Real-time System for Early Epileptic Seizure Detection and Prediction", <b>Fahad Saeed (PI)</b>, August 2022 - July 2024 | <a href="https://nsf.gov/awardsearch/showAward?AWD_ID=2213951&HistoricalAwards=false"><span class="s10">NSF Award Page</span></a> <br>
12. National Science Foundation (NSF) IIP-2143515 <b>[US$ 50,000]</b>, ``I-Corps: Utilizing Machine learning and Artificial Intelligence (AI) for Early Detection and Identification of Mental Disorders", <b>Fahad Saeed (PI)</b>, Sept 2021 - Sept 2022 | <a href="https://nsf.gov/awardsearch/showAward?AWD_ID=2143515&HistoricalAwards=false"><span class="s10">NSF Award Page</span></a> <br>
11. National Institutes of Health (NIH) Supplemental- 3R01GM134384-02S1<b>[US$ 100,000]</b>,"Compute-Cluster for Deep-Learning Models for Mass Spectrometry based Proteomics data" <b>Fahad Saeed (PI)</b>, August 2021 - May 2023 | <a href="https://reporter.nih.gov/search/JPw8nvBmvU6-k4cNICNDaA/project-details/10389445#details"><span class="s10">NIH Reporter Award Page</span></a> <br>
10. National Science Foundation (NSF) OAC-2126253 <b>[US$ 400,000]</b>, ``CC* Compute: RAPTOR - Reconfigurable Advanced Platform for Transdisciplinary Open Research", Jason Liu (PI), Jayantha Obeysekera (Co-PI), Keqi Zhang (Co-PI), Cassian D'Cunha (Co-PI), Mike Kirgan (SI), Yuepeng Li (SI), Vasilka Chergarova (SI), Yagya Joshi (SI), Jonathan Casco (SI), and <b>Fahad Saeed (Co-PI)</b>, Sept 2021 - Sept 2023 | <a href="https://nsf.gov/awardsearch/showAward?AWD_ID=2126253&HistoricalAwards=false"><span class="s10">NSF Award Page</span></a> <br>
9. National Institutes of Health (NIH) Supplemental- 3R01GM134384-01A1S1 <b>[US$ 205,291]</b>,"Multimodal Machine-Learning Algorithms for Early Detection, and Classification for Alzheimer Disorder and Related Dementia's" <b>Fahad Saeed (PI)</b>, May 2021 - May 2023 | <a href="https://reporter.nih.gov/search/DsVUa9EvRUaRq2hPFXrpVA/project-details/10163880#details"><span class="s10">NIH Reporter Award Page</span></a> <br>
8. National Institutes of Health (NIH), [R01GM134384] <b>[US$ 965,874]</b>, "Multimodal Machine-Learning and High Performance Computing Strategies for Big MS Proteomics Data", <b>Fahad Saeed (PI)</b> with Shu-Ching Chen (Co-Investigator), Jason Liu (Co-Investigator), Francisco Alberto Fernandez-Lima (Co-Investigator), and Sitharama Iyengar (Senior Personal), June 2020 - May 2023 | <a href="https://reporter.nih.gov/search/DsVUa9EvRUaRq2hPFXrpVA/project-details/9973317#details"><span class="s10">NIH Reporter Award Page</span></a> <br>
7. National Science Foundation (NSF) OAC-1925960 <b>[US$ 415,950]</b>, "CAREER: Towards Fast and Scalable Algorithms for Big Proteogenomics Data Analytics" <b>Fahad Saeed (PI)</b>, Sept 2018-April 2023 | <a href="https://nsf.gov/awardsearch/showAward?AWD_ID=1925960&HistoricalAwards=false"><span class="s10">NSF Award Page</span></a> <br>
6. National Science Foundation (NSF) CCF-1855441 <b>[US$ 7,708]</b>, "CRII: SHF: HPC Solutions to Big NGS Data Compression", <b>Fahad Saeed (PI)</b>, Sept 2018 - Jan 31, 2020 | <a href="https://nsf.gov/awardsearch/showAward?AWD_ID=1855441&HistoricalAwards=false"><span class="s10">NSF Award Page</span></a> <br>
5. National Science Foundation (NSF) ACI-1651724 <b>[US$ 499,999]</b>, "CAREER: Towards Fast and Scalable Algorithms for Big Proteogenomics Data Analytics" <b>Fahad Saeed (PI)</b>, April 2017-April 2019 | <a href="https://nsf.gov/awardsearch/showAward?AWD_ID=1651724&HistoricalAwards=false"><span class="s10">NSF Award Page</span></a> <br>
4. National Institutes of Health (NIH) R15GM120820 <b>[US$ 418,533]</b>, "Parallel Algorithms for Big Data from Mass Spectrometry based Proteomics" <b>Fahad Saeed (PI)</b>, April 2017 - April 2020 | <a href="https://reporter.nih.gov/search/TK_E0DRy0UW3Nglbj-qBDA/project-details/9301702#similar-Projects"><span class="s10">NIH Reporter Award Page</span></a> (change of PI when Dr. Saeed changed institution to FIU) <br>
3. National Science Foundation (NSF) REU Supplement <b>[US$ 16,000]</b>, "CRII: SHF: HPC Solutions to Big NGS Data Compression" <b>Fahad Saeed (PI)</b>, Feb 2016 - Feb 2018 | <a href="https://nsf.gov/awardsearch/showAward?AWD_ID=1464268&HistoricalAwards=false"><span class="s10">NSF Award Page</span></a> <br>
2. National Science Foundation (NSF) CCF-1464268 <b>[US$ 171,341]</b>, "CRII: SHF: HPC Solutions to Big NGS Data Compression" <b>Fahad Saeed (PI)</b>, (Feb 2015 - Feb 2018 | <a href="https://nsf.gov/awardsearch/showAward?AWD_ID=1464268&HistoricalAwards=false"><span class="s10">NSF Award Page</span></a> <br>
1. National Science Foundation (NSF) CNS-1250264 <b>[US$ 200,000]</b>, "EAGER: High Performance Algorithms and Implementations for Biological Sequence Analysis and Genome Alignment" Ashfaq Khokhar, <b>Fahad Saeed (Co-PI)</b> (Sept 2012 - Aug 2015) | <a href="https://nsf.gov/awardsearch/showAward?AWD_ID=1250264&HistoricalAwards=false"><span class="s10">NSF Award Page</span></a> <br>
<br>
</span><span class="s2"><b>Equipment/Computing Allocations</b></span><span class="s1"> <br>
12. Xilinx [<b>US$ 13,195</b>]}, ``Design and development of FPGA based MS omics pipeline", <b>Fahad Saeed(PI)</b> (Equipment Grant, Versal AI Core EK-VCK190-G FPGA), March 2022 <br>
11. NSF XSEDE Extended Collaborative Support Service (ECSS) [<b>US$ 50,000,</b>], ``DeepSNAP: Scalable Machine Learning for Mass Spectrometry based Proteomics", Fahad Saeed (PI), (Jan 2021 - Dec 2021) 10. National Science Foundation XSEDE ASC200004 [125,000.0 Service Units (SU)/10,000.0 GB SDSC Medium-term disk storage (Data Oasis)/10,000.0 GPU Hours/75,000 Core hours on Clusters: <b>US$ 43,161.42</b>], ``DeepSNAP: Scalable Machine Learning for Mass Spectrometry based Proteomics", Fahad Saeed (PI), (Jan 2021 - Dec 2021)<br>
9. National Science Foundation XSEDE ASC200004 [100,000.0 Service Units (SU)/10,000.0 GB SDSC Medium-term disk storage (Data Oasis)/5,000.0 GPU Hours: <b>US$ 6,190]</b>, "DeepSNAP: Scalable Machine Learning for Mass Spectrometry based Proteomics", Fahad Saeed (PI), (March 2020 - Sept 2020)<br>
8. Intel Altera <b>[US$ 7,900]</b>, "MS proteomics analysis using reconfigurable hardware", Fahad Saeed(PI) (Equipment Grant, DE10-PRO-SX FPGA), Nov 2019<br>
7. National Science Foundation XSEDE supplemental grant TG-CCR150017 [30,000 Service Units (SU)/6TB SDSC Disk Storage/2500 GPU Hours: <b>US$ 450</b>], "Smart Index and Search for De Novo Proteogenomics", Fahad Saeed (PI), (March 2019 - June 2020)<br>
6. National Science Foundation XSEDE renewal grant TG-CCR150017 [30,000 Service Units (SU)/6TB SDSC Disk Storage/2500 GPU Hours: <b>US$ 3,159</b>], "Smart Index and Search for De Novo Proteogenomics", Fahad Saeed (PI), (March 2019 - March 2020)<br>
5. NVIDIA [<b>US$ 1149</b>], "High Performance Algorithms for Big Data Proteomics" Fahad Saeed (PI) (Equipment Grant for NVIDIA TITAN Xp GPU), August 2018<br>
4. National Science Foundation XSEDE renewal grant TG-CCR150017 [30,000 Service Units (SU)/6TB SDSC Disk Storage: <b>US$ 6564</b>], "A Distributed-Shared Memory Strategy to Speedup the Compression of Big Next-Generation Sequencing Datasets" Fahad Saeed (PI), (June 2016 - June 2018)<br>
3. National Science Foundation XSEDE startup grant TG-CCR150017 [30,000 Service Units (SU)], "Scalability study of compression algorithms for peta scale NGS data" Fahad Saeed (PI), (June 2015 - June 2016)<br>
2. Intel Altera <b>[US$ 16,000]</b>, "Short Reads mapping to the genome using reconfigurable hardware" Fahad Saeed(PI) (Equipment Grant, 2 DE5-NET-450 FPGA's), April 2014<br>
1. NVIDIA <b>[US$ 5499]</b>, "High Performance Algorithms for Genome Alignments" Fahad Saeed (PI) (Equipment Grant for Tesla K40 GPU), Feb 2014<br>
<br>
</span><span class="s2"><b>Intramural Grants</b></span><span class="s1"> <br>
2. Office of Vice President of Research,Western Michigan University (WMU) [<b>US$ 129,570</b>], "Scalable Algorithms for Big Proteogenomics Data Analytics" Fahad Saeed (PI), April 2017 - April 2020<br>
1. College and Engineering and Applied Science (CEAS), Western Michigan University (WMU) [<b>US$ 41,650</b>], "Developing HPC solutions to big fMRI data" Fahad Saeed (PI), April 2017 - June 2018</span></p>
<p class="p12"><span class="s1"></span><br></p>
<h2 style="margin: 0.0px 0.0px 0.0px 0.0px; font: 18.0px Arial; -webkit-text-stroke: #000000"><span class="s1"><b>Current Research Thrusts</b></span></h2>
<p class="p4"><span class="s1">The focus of my research is at the intersection of computational biology, big data, HPC and machine-learning. I am interested in developing machine-learning models for neuroscience and proteomics problems. I am also interested in designing and developing high-performance computing (HPC) algorithms for scientific problems. With my extensive experience working in interdisciplinary research I use novel ways to dealing with big data and domain specific knowledge and AI models including machine-learning and deep-learning algorithms.<span class="Apple-converted-space"> </span></span></p>
<p class="p4"><span class="s1">Machine-Learning Models for typical and a-typical brains using MRI/EEG data sets<span class="Apple-converted-space"> </span></span></p>
<p class="p4"><span class="s1">Machine-Learning Models for Mass Spectrometry based omics data sets<span class="Apple-converted-space"> </span></span></p>
<p class="p4"><span class="s1">High performance computing algorithms for big data from MS based omics<span class="Apple-converted-space"> </span></span></p>
<p class="p4"><span class="s1">Hardware/Software co-design for large scale omics<span class="Apple-converted-space"> </span></span></p>
<p class="p4"><span class="s1">Development of Network analysis methods for Scientific Data.</span></p>
<p class="p9"><span class="s1"></span><br></p>
<h2 style="margin: 0.0px 0.0px 14.9px 0.0px; font: 18.0px Arial; -webkit-text-stroke: #000000"><span class="s1"><b>Publications</b></span></h2>
<p class="p4"><span class="s1">All my publications are available on this page.<span class="Apple-converted-space"> </span></span></p>
<p class="p4"><span class="s1">In addition a similar list is also available on my lab webpage: <a href="https://pcdslab.github.io/papers/"><span class="s17">SaeedLab papers webpage</span></a>. Another way to get a list of my publications is via Google Scholar: <a href="https://scholar.google.com/citations?user=IPXv-GQAAAAJ&hl=en"><span class="s9">Google Scholar Profile</span></a> <br>
<br>
</span><span class="s18"><b>2024</b></span><span class="s15"><span class="Apple-converted-space"> </span></span></p>
<p class="p4"><span class="s1">108. Aghdam, Maryam Akhavan; Bozdag, Serdar; <b>Fahad Saeed</b>, <a href="https://pcdslab.github.io/papers/PVTAD-MRI"><span class="s19">PVTAD: Alzheimer’s Disease Diagnosis Using Pyramid Vision Transformer Applied to White Matter of T1-Weighted Structural MRI Data</span></a>, Proceedings of <i>IEEE International Symposium on Biomedical Imaging</i>, 2024<span class="Apple-converted-space"> </span></span></p>
<p class="p4"><span class="s1">107. Parani, Paras; Mohammad, Umair; <b>Fahad Saeed</b>, <a href="https://pcdslab.github.io/papers/seizure-prediction-llm-vit"><span class="s20">Utilizing Pretrained Vision Transfomers and Large Language Models for Epileptic Seizure Prediction</span></a>, Proceedings of the 8th International Conference on Data Science and Machine Learning (CDMA 2024) :1-8 (2024)</span></p>
<p class="p14"><span class="s21">106. Usman Tariq, and </span><span class="s22"><b>Fahad Saeed</b>, “ <a href="https://pcdslab.github.io/papers/ProteRift"><span class="s8">Predicting peptide properties from mass spectrometry data using deep attention-based multitask network and uncertainty quantification</span></a>, preprint bioRxiv 2024.08.21.609035, 2024</span></p>
<p class="p15"><span class="s3">105. </span><span class="s23">Umair Mohammad, <b>Fahad Saeed</b>, “<a href="https://www.biorxiv.org/content/10.1101/2024.07.17.604006.abstract"><span class="s24">MLSPred-Bench: ML-Ready Benchmark Leveraging Seizure Detection EEG data for Predictive Models</span></a>”, <i>Preprint bioRxiv</i>, July 2024</span></p>
<p class="p16"><span class="s3">104. </span><span class="s1">Umair Mohammad, <b>Fahad Saeed</b>, “<a href="https://link.springer.com/chapter/10.1007/978-3-031-57567-9_3"><span class="s25">Heterogeneity Aware Distributed Machine Learning at the Wireless Edge for Health IoT Applications: An EEG Data Case Study</span></a>”, pages 33 - 70, Book Chapter in <i>Springer Distributed Machine Learning and Computing: Theory and Applications</i>, March 2024</span></p>
<p class="p17"><span class="s3">103. </span><span class="s23">Abhishek Bhattarai, Umair Mohammad, <b>Fahad Saeed</b>, “<a href="https://ieeexplore.ieee.org/abstract/document/10500137/"><span class="s26">Communication Evaluation of a Wireless 4-Channel Wearable EEG for Brain-Computer Interface (BCI) and Healthcare Applications</span></a>”, <i>Proceedings of IEEE SoutheastCon,</i> March 2024</span></p>
<p class="p16"><span class="s3">102. </span><span class="s1">Muhammad Usman Tariq, Samuel Ebert, <b>Fahad Saeed</b>, “<a href="https://link.springer.com/protocol/10.1007/978-1-0716-4007-4_9"><span class="s25">Making MS Omics Data ML-Ready: SpeCollate Protocols</span></a>”, Book Chapter in <i>Springer Protein Bioinformatics</i>, pages 135-155, July 2024</span></p>
<p class="p18"><span class="s1"></span><br></p>
<p class="p4"><span class="s18"><b>2023</b></span><span class="s15"> <br>
</span><span class="s1">101. Oswaldo Artiles, Zeina Al Masry, <b>Fahad Saeed*</b>, "Confounding effects on the performance of machine learning analysis of static functional connectivity computed from rs-fMRI multi-site data", <i>Springer Neuroinformatics</i>, Pages 1-18, August 2023 <a href="https://link.springer.com/article/10.1007/s12021-023-09639-1"><span class="s9">Springer</span></a> <br>
100. Mohammad Al Olaimat, Jared Martinez, <b>Fahad Saeed</b>, Serdar Bozdag, "PPAD: A deep learning architecture to predict progression of Alzheimer's disease", <i>Oxford Bioinformatics </i>, Volume 39, Issue Supplement 1, June 2023, Pages i149-i157, July 2023 <a href="https://doi.org/10.1093/bioinformatics/btad249"><span class="s9">Oxford</span></a> <br>
99. Usman Tariq, and Fahad Saeed, "DeepAtles: Deep Attention-based Multitasking Network for Predicting Peptide Properties from Mass Spectrometry Data", submitted May 2023<br>
98. Muhammad Haseeb, and <b>Fahad Saeed*</b>, "GPU-Acceleration of the Distributed-Memory Database Peptide Search of Mass Spectrometry Data ", Submitted June 2023 <br>
97. Leyva, Dennys, Muhammad Usman Tariq, Jaffe Rudolf, <b>Fahad Saeed</b>, Francisco Fernández-Lima, "Description of Dissolved Organic Matter transformational networks at the molecular level", <i>ACS Journal of Environmental Science & Technology,</i>, Vol 57, No. 6, pages 2672-2681 Jan 2023<a href="https://pubs.acs.org/doi/full/10.1021/acs.est.2c04715"><span class="s9">American Chemical Society (ACS)</span></a> </span><span class="s15"><br>
<br>
</span><span class="s18"><b>2022</b></span><span class="s15"> <br>
</span><span class="s1">96. Tianren Yang, Mai Al-Duailij, Serdar Bozdag, and <b>Fahad Saeed</b></span><span class="s27"><b><sup>* </sup></b></span><span class="s1">, "Classification of Autism Spectrum Disorder using Graph Convolutional Network and Graphlet Counting", 2nd International Workshop on Multi-Modal Medical Data Analysis, <i>Proceedings of IEEE International Conference on Big Data (IEEE BigData 2022)</i>, Osaka Japan, Dec 17-20 2022.<br>
95. <b>Fahad Saeed</b></span><span class="s27"><b><sup>* </sup></b></span><span class="s1">, and Muhammad Haseeb, "High-Performance Algorithms for Mass Spectrometry-Based Omics" ISBN-10: 3031019598, ISBN-13: 978-3031019593, <i>Springer Nature Switzerland AG</i>; 1st edition (September 3, 2022). <a href="https://link.springer.com/book/10.1007/978-3-031-01960-9#toc"><span class="s9"><b>Springer (Book: 10 Chapters, 156 pages)</b></span></a> <br>
94. Dennys Leyva, Rudolf Jaff, Jessica Courson, John S. Kominoski, Muhammad Usman Tariq, <b>Fahad Saeed</b> and Francisco Fernandez-Lima "</span><span class="s2">Molecular level characterization of DOM along a freshwater-to-estuarine coastal gradient in the Florida Everglades </span><span class="s1">", <i>Springer Aquatic Sciences</i>, volume 84, Article number: 63, Oct 2022 <a href="https://link.springer.com/article/10.1007/s00027-022-00887-y"><span class="s9"><b>Springer</b></span></a> <br>
93. Umair Muhammad, and <b>Fahad Saeed</b></span><span class="s27"><b><sup>* </sup></b></span><span class="s1">"</span><span class="s2">SPERTL: Epileptic Seizure Prediction using EEG with ResNets and Transfer Learning</span><span class="s1">", Proceedings of <i>IEEE International Conference on Biomedical and Health Informatics (BHI)</i>, Ioannina Greece, 27-30 September 2022.<br>
92. <b>Fahad Saeed</b></span><span class="s27"><b><sup>*</sup></b></span><span class="s1">, and Fahad Almuqhim, "</span><span class="s2">Systems And Methods For Diagnosing Autism Spectrum Disorder Using fMRI Data</span><span class="s1">", <i>U.S. Patent</i> US 11379981 B1, Issued July 5th 2022 <a href="https://users.cs.fiu.edu/~fsaeed/Patent_Fahad&Fahad.pdf"><span class="s10"><b>Local Copy</b></span></a> | US Patent<br>
91. <b>Fahad Saeed</b></span><span class="s27"><b><sup>*</sup></b></span><span class="s1">, and Muhammad Haseeb, "</span><span class="s2">Systems and methods for peptide identification</span><span class="s1">", <i>U.S. Patent</i> 11,309,061 B1, Issued April 19, 2022 <a href="https://users.cs.fiu.edu/~fsaeed/2T87777-US%2011309061.pdf"><span class="s10"><b>Local Copy</b></span></a> | US Patent<br>
90. Aledhari, Mohammed, Rehma Razzak, Basheer Qolomany, Ala Al-Fuqaha, and Fahad Saeed. "Biomedical IoT: Enabling Technologies, Architectural Elements, Challenges, and Future Directions." <i>IEEE Access</i>, vol. 10, pp. 31306-31339, 2022.<b> </b><a href="https://ieeexplore.ieee.org/abstract/document/9733908"><span class="s9"><b>IEEE</b></span></a> <br>
89. Leyva, Dennys, Muhammad Usman Tariq, Rudolf Jaff, <b>Fahad Saeed</b></span><span class="s27"><b><sup>*</sup></b></span><span class="s1">, and Francisco Fernandez Lima. "Unsupervised Structural Classification of Dissolved Organic Matter Based on Fragmentation Pathways." <i>Environmental science & technology, 56(2), 1458-1468</i> March 2022 <a href="https://pubs.acs.org/doi/full/10.1021/acs.est.1c04726?casa_token=oOObpRCOCTgAAAAA%3AjbteiUKU3lkq32vdhaT9poZUyuTMJ4BKUslVZHd5RS6rFWYn7U-M_kox7SiwBDevmeVB_W7wZIs8Ejdv&"><span class="s10"><b>ACS</b></span></a> <br>
88. <b>Fahad Saeed</b></span><span class="s27"><b><sup>*</sup></b></span><span class="s1">, and Muhammad Usman Tariq. "Systems and methods for measuring similarity between mass spectra and peptides." <i>U.S. Patent 11,251,031</i>, issued February 15, 2022. <a href="https://patentimages.storage.googleapis.com/e4/22/1b/ebeb82a5b991a1/US11251031.pdf"><span class="s10"><b>US Patent</b></span></a> <br>
87. <b>Fahad Saeed</b></span><span class="s27"><b><sup>*</sup></b></span><span class="s1">, Muhammad Haseeb, and SS Iyengar, "</span><span class="s2">Communication lower-bounds for distributed-memory computations for mass spectrometry-based omics data</span><span class="s1">" <i>Journal of Parallel and Distributed Computing (JPDC)</i>, Volume 161, Pages 37-47, March 2022 <a href="https://arxiv.org/pdf/2009.14123.pdf"><span class="s9"><b>arXiv</b></span></a> | <a href="https://www.sciencedirect.com/science/article/abs/pii/S0743731521002082"><span class="s9"><b>JPDC</b></span></a> <br>
<br>
</span><span class="s18"><b>2021</b></span><span class="s15"> <br>
</span><span class="s1">86. Oswaldo Artiles and <b>Fahad Saeed</b></span><span class="s27"><b><sup>*</sup></b></span><span class="s1">, "</span><span class="s2">A Multi-Factorial Assessment of Functional HumanAutistic Spectrum Brain Network Analysis</span><span class="s1">" International workshop on Reproducibility and Robustness in Biological Data Analysis (RROBIN), <i>Proceedings of IEEE InternationalConference on Bioinformatics and Biomedicine (BIBM)</i>, December 9-12, 2021 <a href="https://www.computer.org/csdl/proceedings-article/bibm/2021/09669679/1A9WbYkG9vG"><span class="s10"><b>IEEE</b></span></a> | <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9007171/"><span class="s10"><b>PubMed</b></span></a><br>
85. Khandaker Mamun Ahmed, Taban Eslami, <b>Fahad Saeed</b></span><span class="s27"><b><sup>*</sup></b></span><span class="s1">, and M. Hadi Amini, "</span><span class="s2">Deep-COVIDNet: Deep Convolutional Neural Network for COVID-19 Detection from Chest Ra-diographic Images</span><span class="s1">" International workshop on Machine Learning for Biological and MedicalImage Big Data, <i>Proceedings ofIEEE International Conference on Bioinformatics and Biomedicine(BIBM)</i>, December 9-12, 2021 <a href="https://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=9669767"><span class="s10"><b>IEEE Xplore</b></span></a> | <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9007173/#"><span class="s10"><b>PubMed</b></span></a><br>
84. Muhammad Usman Tariq, Dennys Leyva, Francisco Fernandez Lima, and <b>Fahad Saeed</b></span><span class="s27"><b><sup>*</sup></b></span><span class="s1">, "</span><span class="s2">Graph Theoretic Approach for the Analysis of Comprehensive Mass-Spectrometry (MS/MS) Data of Dissolved Organic Matter</span><span class="s1">", International Workshop on Biological Network Analysis and Integrative Graph-Based Approaches (IWBNA), <i>Proceedings of IEEE International Conference on Bioinformatics and Biomedicine (BIBM)</i>, December 9-12, 2021 <a href="https://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=9669289"><span class="s10"><b>IEEE Xplore</b></span></a> | <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9007174/"><span class="s10"><b>PubMed</b></span></a><br>
83. Usman Tariq, and <b>Fahad Saeed</b></span><span class="s27"><b><sup>*</sup></b></span><span class="s1"> , "</span><span class="s2">SpeCollate: Deep cross-modal similarity network for mass spectrometry data based peptide deductions</span><span class="s1">", </span><span class="s14"><b><i>PLoS ONE</i></b></span><span class="s1">, Vol. 16, Issue 10, Oct 2021 <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8555789/"><span class="s10"><b>PubMed</b></span></a> | <a href="https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0259349"><span class="s10"><b>PLoS</b></span></a><br>
82. Muhammad Haseeb, and <b>Fahad Saeed</b></span><span class="s27"><b><sup>*</sup></b></span><span class="s1"> , "</span><span class="s2">High performance computing framework for tera-scale database search of mass spectrometry data</span><span class="s1">", </span><span class="s14"><b><i>Nature Computational Science</i></b></span><span class="s1">, Vol. 1, 550-561, August 2021 <a href="https://arxiv.org/pdf/2102.02286.pdf"><span class="s10"><b>Arxiv</b></span></a> | <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8554525/"><span class="s10"><b>PubMed</b></span></a> | <a href="https://digitalcommons.fiu.edu/cgi/viewcontent.cgi?article=1027&context=cs_fac"><span class="s10"><b>Technical Report</b></span></a> | <a href="http://rdcu.be/cvFan"><span class="s10"><b>Nature</b></span></a><br>
81. Oswaldo Artiles, and <b>Fahad Saeed</b></span><span class="s27"><b><sup>*</sup></b></span><span class="s1">, "</span><span class="s2">TurboBC: A Memory Efficient and Scalable GPU Based Betweenness Centrality Algorithm in the Language of Linear Algebra</span><span class="s1">", International Workshop on Deployment and Use of Accelerators (DUAC), <i>Proceedings of 50th International Conference on Parallel Processing (ICPP)</i>, Chicago IL, August 2021 <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9015014/"><span class="s10"><b>PubMed</b></span></a> | <a href="https://dl.acm.org/doi/pdf/10.1145/3458744.3474047"><span class="s10"><b>ACM Digital Library</b></span></a><br>
80. Umair Muhammad, and <b>Fahad Saeed</b></span><span class="s27"><b><sup>*</sup></b></span><span class="s1">, "</span><span class="s2">Simulation Testbed for Evaluating Distributed Querying and Searching of Mass Spectrometry Big Data in a Network-based Infrastructure</span><span class="s1">", <i>Proceedings of 7th IEEE International Conference on Big Data Service and Applications (IEEE BIGDATASERVICE),</i> August 2021 <a href="https://ieeexplore.ieee.org/stamp/stamp.jsp?arnumber=9564313"><span class="s10"><b>IEEE Xplore</b></span></a><br>
79. Umair Muhammad, and <b>Fahad Saeed</b></span><span class="s27"><b><sup>*</sup></b></span><span class="s1">, "</span><span class="s2">Search Feasibility in Distributed MS-Proteomics Big Data</span><span class="s1">", Workshop on High Performance Computing, Big Data Analytics and Integration for Multi-Omics Biomedical Data (HPC-BOD), <i>Proceedings of 12th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM BCB)</i>, August 2021 (extended abstract) <a href="https://dl.acm.org/doi/10.1145/3459930.3470855"><span class="s10"><b>ACM Digital Library</b></span></a><br>
78. Sumesh Kumar, and <b>Fahad Saeed</b></span><span class="s27"><b><sup>*</sup></b></span><span class="s1">, "</span><span class="s2">Real-time peptide identification from high-throughput Mass-spectrometry data</span><span class="s1">", Workshop on High Performance Computing, Big Data Analytics and Integration for Multi-Omics Biomedical Data (HPC-BOD), <i>Proceedings of 12th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM BCB)</i>, August 2021 (extended abstract) <a href="https://dl.acm.org/doi/abs/10.1145/3459930.3470856"><span class="s10"><b>ACM Digital Library</b></span></a><br>
77. Sumesh Kumar, and <b>Fahad Saeed</b></span><span class="s27"><b><sup>*</sup></b></span><span class="s1">, "</span><span class="s2">Communication-optimized micro-architecture to compute Xcorr scores for peptide identification</span><span class="s1">", <i>Proceedings of International Conference on Field-Programmable Logic and Applications (FPL)</i>, May 2021<b> </b><a href="https://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=9556489"><span class="s10"><b>IEEE Xplore</b></span></a></span><span class="s11"><b> | </b><a href="https://pubmed.ncbi.nlm.nih.gov/35440952/"><span class="s28"><b>PubMed</b></span></a><b> | </b><a href="https://arxiv.org/pdf/2108.00147.pdf"><span class="s28"><b>Arxiv</b></span></a></span><span class="s1"><br>
76. Fahad Almuqhim, and <b>Fahad Saeed</b></span><span class="s27"><b><sup>*</sup></b></span><span class="s1">, "</span><span class="s2">ASD-SAENet: Sparse Autoencoder for detecting Autism Spectrum Disorder (ASD) using fMRI data</span><span class="s1">", <i>Frontiers in Computational Neuroscience</i>, Vol. 15, p. 27, March 2021 <a href="https://www.frontiersin.org/articles/10.3389/fncom.2021.654315/full"><span class="s10"><b>Frontiers</b></span></a></span><span class="s11"><b> </b></span><span class="s1"><br>
75. Muaaz Awan, Abdullah Awan, and <b>Fahad Saeed</b></span><span class="s27"><b><sup>*</sup></b></span><span class="s1">, "</span><span class="s2">Benchmarking Mass Spectrometry based Proteomics Algorithms using a Simulated Database</span><span class="s1">", <i>Springer Network Modeling Analysis in Health Informatics and Bioinformatics</i>, Vol. 10, Article 23, March 2021 <a href="https://link.springer.com/article/10.1007/s13721-021-00298-3"><span class="s10"><b>Springer</b></span></a><br>
74. Oswaldo Artiles, and <b>Fahad Saeed</b></span><span class="s27"><b><sup>*</sup></b></span><span class="s1">, ``</span><span class="s2">TurboBFS: GPU Based Breadth-First Search (BFS) Algorithms in the Language of Linear Algebra</span><span class="s1">", 11th IEEE Workshop Parallel/ Distributed Combinatorics and Optimization (PDCO 2021), Proceedings of <i>IEEE International Parallel and Distributed Processing Symposium Workshops (IEEE IPDPSW)</i>, May 2021<br>
73. Taban Eslami, Fahad Almuqhim, Joseph S. Raiker, <b>Fahad Saeed</b></span><span class="s27"><b><sup>*</sup></b></span><span class="s1">, "</span><span class="s2">Machine Learning Methods for Diagnosing Autism Spectrum Disorder and Attention- Deficit/Hyperactivity Disorder Using Functional and Structural MRI: A Survey</span><span class="s1">", <i>Frontiers of Neuroinformatics</i>, Vol. 14, pp 62, 2021</span><span class="s11"> <a href="https://www.frontiersin.org/articles/10.3389/fninf.2020.575999/full"><span class="s28"><b>Frontiers</b></span></a></span><span class="s1"><br>
72. Muhammad Usman Tariq, Muhammad Haseeb, Mohammed Aledhari, Rehma Razzak, Reza M Parizi, and <b>Fahad Saeed</b></span><span class="s27"><b><sup>*</sup></b></span><span class="s1">, "</span><span class="s2">Methods for Proteogenomics Data Analysis, Challenges, and Scalability Bottlenecks: A Survey</span><span class="s1">",<i> IEEE Access</i>, vol. 9, pp. 5497-5516, 2021 <a href="https://ieeexplore.ieee.org/abstract/document/9309010"><span class="s10"><b>IEEE Access</b></span></a></span><span class="s15"><br>
<br>
</span><span class="s18"><b>2020</b></span><span class="s15"> <br>
</span><span class="s1">71. Taban Eslami, Joseph S Raiker, <b>Fahad Saeed</b>, "</span><span class="s2">Explainable and Scalable Machine-Learning Algorithms for Detection of Autism Spectrum Disorder using fMRI Data</span><span class="s1">" Book Chapter arXiv preprint arXiv:2003.01541, 2020 <a href="https://arxiv.org/ftp/arxiv/papers/2003/2003.01541.pdf"><span class="s10"><b>arXiv</b></span></a><br>
70. Bronte Wen, Hyun Jun Jung, Lihe Chen, <b>Fahad Saeed</b>, and Mark Knepper, "</span><span class="s2">NGS-Integrator: An efficient tool for combining multiple NGS data tracks using minimum Bayes" factors</span><span class="s1">", <i>BMC Genomics</i>, Nov 2020 </span><span class="s11"><b>BMC</b></span><span class="s1"> <br>
69. Mohammed Aledhari, Rehma Razzak, Reza Parizi, and <b>Fahad Saeed</b></span><span class="s27"><b><sup>*</sup></b></span><span class="s1">, "</span><span class="s2">Federated Learning: A Survey on Enabling Technologies, Protocols, and Applications</span><span class="s1">", <b><i>IEEE Access</i></b>, Vol. 8, pp. 140699--140725, July 2020 <a href="https://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=9153560"><span class="s10"><b>IEEE Access</b></span></a><br>
</span><span class="s15"><br>
</span><span class="s18"><b>2019</b></span><span class="s15"> <br>
</span><span class="s1">68. Taban Eslami, Vahid Mirjalili, Alvis Fong, Angela R. Laird, and <b>Fahad Saeed</b></span><span class="s27"><b><sup>*</sup></b></span><span class="s1">, "</span><span class="s2">ASD-DiagNet: A Hybrid Learning Approach for Detection of Autism Spectrum Disorder Using fMRI Data</span><span class="s1">" <i>Frontiers of Neuroinformatics</i>, vol. 13, pages 70, Nov 2019</span><span class="s11"> <a href="https://arxiv.org/pdf/1904.07577.pdf"><span class="s28"><b>arXiv</b></span></a> | <a href="https://www.frontiersin.org/articles/10.3389/fninf.2019.00070/full"><span class="s28"><b>Frontiers</b></span></a></span><span class="s1"><br>
67. Oswaldo Artiles, and <b>Fahad Saeed*</b>, "</span><span class="s2">GPU-SFFT: A GPU based parallel algorithm for computing the Sparse Fast Fourier Transform (SFFT) of k-sparse signals</span><span class="s1">" Workshop on Performance Engineering with Advances in Software and Hardware for Big Data Sciences (PEASH), <i>Proceedings of IEEE Conference on Big Data (IEEE BigData 2019)</i>, Los Angeles, CA, USA, Dec. 09-12, 2019 <a href="https://users.cs.fiu.edu/~fsaeed/Reports/GPU-SFFT.pdf"><span class="s10"><b>Tech Report</b></span></a></span><span class="s11"> | <a href="https://ieeexplore.ieee.org/abstract/document/9006579"><span class="s28"><b>IEEE Xplore</b></span></a></span><span class="s1"><br>
66. Muhammad Haseeb, and <b>Fahad Saeed*</b>, "</span><span class="s2">Efficient Shared Peak Counting in Database Peptide Search Using Compact Data Structure for Fragment-Ion Index</span><span class="s1">" <i>Proceedings of IEEE International Conference on Bioinformatics and Biomedicine (IEEE BIBM)</i>, San Diego, CA, Nov 2019 (Acceptance Rate: 100/543=18%) <a href="https://users.cs.fiu.edu/~fsaeed/Reports/PID6229257.pdf"><span class="s10"><b>Tech Report</b></span></a></span><span class="s11"> | <a href="https://ieeexplore.ieee.org/document/8983114"><span class="s28"><b>IEEE Xplore</b></span></a></span><span class="s1"><br>
65. Mohammed Aledhari, Shelby Joji, Mohamed Hefeida, and <b>Fahad Saeed*</b>, "</span><span class="s2">Optimized CNNbased Diagnosis System to Detect the Pneumonia from Chest Radiographs</span><span class="s1">" Workshop on Computational Aspects for Clinical Diagnostics and Decision Making in Healthcare using Biomedical Signal and Image, <i>Proceedings of IEEE International Conference on Bioinformatics and Biomedicine (IEEE BIBM),</i> San Diego, CA, Nov 2019 <a href="https://users.cs.fiu.edu/~fsaeed/Reports/PID6229257.pdf"><span class="s10"><b>Tech Report</b></span></a></span><span class="s11"> | <a href="https://ieeexplore.ieee.org/document/8983114"><span class="s28"><b>IEEE Xplore</b></span></a></span><span class="s1"><br>
64. Taban Eslami, and <b>Fahad Saeed*</b>, "</span><span class="s2">Auto-ASD-Network: A technique based on Deep Learning and Support Vector Machines for diagnosing Autism Spectrum Disorder using fMRI data</span><span class="s1">" Workshop on Machine Learning Models for Multi-omics Data Integration, in <i>Proceedings of 10th ACM Conference on Bioinformatics, Computational Biology (ACM BCB)</i>, Niagara Falls, New York, September 7-10, 2019. <a href="https://dl.acm.org/citation.cfm?doid=3307339.3343482"><span class="s10"><b>ACM</b></span></a></span><span class="s11"> | <a href="https://digitalcommons.fiu.edu/cgi/viewcontent.cgi?article=1017&context=cs_fac"><span class="s28"><b>Tech Report</b></span></a></span><span class="s1"><br>
63. Muhammad Haseeb, Fatima Afzali, and <b>Fahad Saeed*</b>, "</span><span class="s2">LBE: A Computational Load Balancing Algorithm for Speeding up Parallel Peptide Search in Mass-Spectrometry based Proteomics</span><span class="s1"> ", <i>Proceedings of IEEE International Parallel & Distributed Processing Symposium Workshops (IPDPSW)</i>, Brazil, May 20, 2019 <a href="https://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=8778342"><span class="s10"><b>IEEE Xplore</b></span></a></span><span class="s11"><b> </b>| <a href="https://digitalcommons.fiu.edu/cgi/viewcontent.cgi?article=1014&context=cs_fac"><span class="s28"><b>Tech Report</b></span></a></span><span class="s1"><br>
62. Taban Eslami, and <b>Fahad Saeed</b></span><span class="s27"><b><sup>*</sup></b></span><span class="s1">, "</span><span class="s2">GPU-DFC: A GPU-based parallel algorithm for computing dynamic-functional connectivity of big fMRI data</span><span class="s1">",Proceedings of<i>IEEE International Conference On Big Data Service And Applications (IEEE Big Data Service 2019)</i>,San Francisco East Bay, California, USA, April 4 - 9, 2019 <a href="https://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=8848251"><span class="s10"><b>IEEE Xplore</b></span></a></span><span class="s11"> | <a href="https://digitalcommons.fiu.edu/cgi/viewcontent.cgi?article=1015&context=cs_fac"><span class="s28"><b>Tech Report</b></span></a></span><span class="s1"> </span><span class="s15"><br>
<br>
</span><span class="s18"><b>2018</b></span><span class="s15"> <br>
</span><span class="s1">61. Muaaz Awan, and <b>Fahad Saeed</b></span><span class="s27"><b><sup>*</sup></b></span><span class="s1">,"</span><span class="s2">MaSSâ€Simulator: A Highly Configurable Simulator for Generating MS/MS Datasets for Benchmarking of Proteomics Algorithms</span><span class="s1">",<i>Wiley Proteomics,</i>Oct 2018<a href="https://doi.org/10.1002/pmic.201800206"><span class="s10"><b>Wiley</b></span></a></span><span class="s11"><b>|</b><a href="https://www.ncbi.nlm.nih.gov/pubmed/30216669"><span class="s28"><b>PubMed</b></span></a></span><span class="s1"><br>
60. Muaaz Awan, Taban Eslami, and <b>Fahad Saeed</b></span><span class="s27"><b><sup>*</sup></b></span><span class="s1">, "</span><span class="s2">GPU-DAEMON: GPU Algorithm Design,Data Management & Optimization template for array based big omics data</span><span class="s1">" <i>Elsevier Computersin Biology and Medicine</i>, Aug 2018 <a href="https://www.sciencedirect.com/science/article/pii/S001048251830235X"><span class="s10"><b>Elsevier</b></span></a></span><span class="s11"> <b>| </b><a href="https://www.ncbi.nlm.nih.gov/pubmed/30145436"><span class="s28"><b>PubMed</b></span></a></span><span class="s1"><br>
59.<b> Fahad Saeed</b></span><span class="s27"><b><sup>*</sup></b></span><span class="s1">, "</span><span class="s2">Towards quantifying psychiatric diagnosis using machine learning algorithms and big fMRI data</span><span class="s1">" <i>BMC Big Data Analytics</i>, Vol. 3, No. 1, pp. 1-7, May 2018 <a href="https://link.springer.com/article/10.1186/s41044-018-0033-0"><span class="s10"><b>Springer</b></span></a></span><span class="s11"><b> </b>| <a href="https://bdataanalytics.biomedcentral.com/articles/10.1186/s41044-018-0033-0"><span class="s28"><b>BMC</b></span></a></span><span class="s1"><br>
58. Taban Eslami, and <b>Fahad Saeed</b></span><span class="s27"><b><sup>*</sup></b></span><span class="s1">, "</span><span class="s2">Fast-GPU-PCC: A GPU-Based Technique to Compute Pairwise Pearson's Correlation Coefficients for Time Series Data - An fMRI Study</span><span class="s1">",<i>MDPI High-Throughput</i>,April 2018<a href="http://www.mdpi.com/2571-5135/7/2/11/htm"><span class="s10"><b>MDPI</b></span></a></span><span class="s11"><b>|</b><a href="https://www.ncbi.nlm.nih.gov/pubmed/29677161"><span class="s28"><b>PubMed</b></span></a></span><span class="s1"><br>
57. Mohammed Aledhari, Marianne Di Pierro, Mohamed Hefeida, and <b>Fahad Saeed*</b>, "</span><span class="s2">A Deep Learning-Based Data Minimization Algorithm for Fast and Secure Transfer of Big Genomic Datasets</span><span class="s1">",<i>IEEE Transactions on Big Data</i>, Feb 2018 <a href="http://ieeexplore.ieee.org/document/8290833/"><span class="s10"><b>IEEE Xplore</b></span></a><br>
56. Usman Tariq, and <b>Fahad Saeed</b></span><span class="s27"><b><sup>*</sup></b></span><span class="s1">, "</span><span class="s2">Parallel Sampling-Pipeline for Indefinite Stream of Heterogeneous Graphs using OpenCL for FPGAs</span><span class="s1">" Workshop on Energy-Efficient Big Data Analytics,Proceedings of <i>IEEE International Conference on Big Data (IEEE BigData)</i>, pp. 1-10, Seattle, WA Dec 10-13, 2018 <a href="https://ieeexplore.ieee.org/abstract/document/8621979"><span class="s10"><b>IEEE Xplore</b></span></a><br>
55. Mohammed Aledhari, Marianne Di Pierro, and <b>Fahad Saeed</b></span><span class="s27"><b><sup>*</sup></b></span><span class="s1">, "</span><span class="s2">A Fourier-Based Data Minimization Algorithm for Fast and Secure Transfer of Big Genomic Datasets</span><span class="s1">" Proceedings of<i>IEEE Big Data Congress</i>, San Francisco CA USA, July 2-7, 2018 <a href="https://ieeexplore.ieee.org/document/8457740"><span class="s10"><b>IEEE Xplore</b></span></a><br>
54. Taban Eslami, and <b>Fahad Saeed</b></span><span class="s27"><b><sup>*</sup></b></span><span class="s1">, "</span><span class="s2">Similarity based classification of ADHD using Singular Value Decomposition</span><span class="s1">",Proceedings of<i>ACM Conference on Computing Frontiers (ACM-CF)</i>, Ischia, Italy, May 2018 <a href="https://dl.acm.org/citation.cfm?id=3203239"><span class="s10"><b>ACM</b></span></a></span><span class="s11"> | <a href="https://scholarworks.wmich.edu/cgi/viewcontent.cgi?article=1013&context=pcds_reports"><span class="s28"><b>Tech Report</b></span></a><b>|</b><a href="https://www.youtube.com/watch?v=HHosXrnijbw"><span class="s28"><b>Presentation (YouTube)</b></span></a></span><span class="s1"><br>
</span><span class="s15"><br>
</span><span class="s18"><b>2017</b></span><span class="s15"><br>
</span><span class="s1">53. Sandino Vargas-Prez and <b>Fahad Saeed*</b>, "</span><span class="s2">A Hybrid MPI-OpenMP Strategy to Speedup the Compression of Big Next-Generation Sequencing Datasets</span><span class="s1">",<i>IEEE Transactions on Parallel and Distributed Systems,</i>March 2017 <a href="http://scholarworks.wmich.edu/cgi/viewcontent.cgi?article=1006&context=pcds_reports"><span class="s10"><b>Tech Report</b></span></a></span><span class="s11"><b>|</b><a href="http://ieeexplore.ieee.org/document/7895161/"><span class="s28"><b>IEEE Xplore</b></span></a></span><span class="s1"><br>
52. Usman Tariq, Umer Cheema and <b>Fahad Saeed</b></span><span class="s27"><b><sup>*</sup></b></span><span class="s1">,</span><span class="s2">"Power-Efficient and Highly Scalable Parallel Graph Sampling using FPGAs"</span><span class="s1">, Proceedings of<i>International Conference on Reconfigurable Computing and FPGAs (ReConFig)</i>, Cancun, Mexico, December 4-6, 2017<a href="http://scholarworks.wmich.edu/cgi/viewcontent.cgi?article=1012&context=pcds_reports"><span class="s10"><b>Tech Report</b></span></a></span><span class="s11"><b>|</b><a href="http://ieeexplore.ieee.org/document/8279806/"><span class="s28"><b>IEEE Xplore</b></span></a></span><span class="s1"><br>
51. Sandino Vargas-P'erez and <b>Fahad Saeed</b></span><span class="s27"><b><sup>*</sup></b></span><span class="s1">, "</span><span class="s2">Scalable Data Structure to Compress Next-Generation Sequencing Files and its Application to Compressive Genomics</span><span class="s1">", Proceedings of<i>IEEE International Conference on Bioinformatics and Biomedicine (IEEE BIBM),</i>Kansas City, MO, USA, Nov 13-16, 2017<a href="http://scholarworks.wmich.edu/cgi/viewcontent.cgi?article=1009&context=pcds_reports"><span class="s10"><b>Tech Report</b></span></a></span><span class="s11"><b>|</b><a href="http://ieeexplore.ieee.org/document/8217953/"><span class="s28"><b>IEEE Xplore</b></span></a></span><span class="s1"><br>
50. Muaaz Gul Awan and <b>Fahad Saeed</b></span><span class="s27"><b><sup>*</sup></b></span><span class="s1">, "</span><span class="s2">An Out-of-Core GPU based dimensionality reduction algorithm for Big Mass Spectrometry Data and its application in bottom-up Proteomics</span><span class="s1">", Proceedings of<i>ACM Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM BCB)</i>,Boston MA, August 2017<a href="http://scholarworks.wmich.edu/cgi/viewcontent.cgi?article=1007&context=pcds_reports"><span class="s10"><b>Tech Report</b></span></a></span><span class="s11"><b>|</b><a href="https://dl.acm.org/citation.cfm?id=3107466"><span class="s28"><b>ACM</b></span></a><b>|</b><a href="https://www.ncbi.nlm.nih.gov/pubmed/28868521"><span class="s28"><b>PubMed</b></span></a></span><span class="s1"><br>
49. Taban Eslami, Muaaz Gul Awan and <b>Fahad Saeed</b></span><span class="s27"><b><sup>*</sup></b></span><span class="s1">, "</span><span class="s2">GPU-PCC: A GPU based technique to compute pairwise Pearson's Correlation Coefficients for big fMRI data</span><span class="s1">",Workshop on Parallel and Cloud-based Bioinformatics and Biomedicine (ParBio),Proceedings of<i>ACM Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM BCB)</i>,Boston MA, August 2017<a href="http://scholarworks.wmich.edu/cgi/viewcontent.cgi?article=1008&context=pcds_reports"><span class="s10"><b>Tech Report</b></span></a></span><span class="s11"><b>|</b><a href="https://dl.acm.org/citation.cfm?doid=3107411.3108173"><span class="s28"><b>ACM</b></span></a></span><span class="s1"><br>
48. Mohammed Aledhari, Ali Marhoon, Ali Al-Qaabi, and <b>Fahad Saeed</b></span><span class="s27"><b><sup>*</sup></b></span><span class="s1"><b>,</b>"</span><span class="s2">A New Cryptography Algorithm to Protect Cloud-based Healthcare Services</span><span class="s1">",Proceedings of<i>Workshop on Safe, Energy-Aware, & Reliable Connected Health, IEEE/ACM Conference on Connected Health: Applications, Systems and Engineering Technologies (IEEE/ACM CHASE-SEARCH)</i>,Philadelphia PA, July 2017 <a href="http://ieeexplore.ieee.org/abstract/document/8010572/"><span class="s10"><b>IEEE Xplore</b></span></a><br>
</span><span class="s15"><br>
</span><span class="s18"><b>2016</b></span><span class="s15"><br>
</span><span class="s1">47. Pablo C. Sandoval, J'Neka S. Claxton, Jae Wook Lee, <b>Fahad Saeed</b>, Jason D. Hoffert and Mark A. Knepper, "</span><span class="s2">Systems-level analysis reveals selective regulation of Aqp2 gene expression by vasopressin</span><span class="s1">",<i>Nature Scientific Reports</i>, Vol. 6, article number 34863, October 2016 <a href="http://www.nature.com/articles/srep34863"><span class="s10"><b>Nature</b></span></a></span><span class="s11"><b>|</b><a href="https://www.ncbi.nlm.nih.gov/pubmed/27725713"><span class="s28"><b>PubMed</b></span></a></span><span class="s1"><br>
46. Muaaz Awan and <b>Fahad Saeed*</b>,</span><span class="s2">"MS-REDUCE: An ultrafast technique for reduction of Big Mass Spectrometry Data for high-throughput processing"</span><span class="s1">, accepted in<i>Oxford Bioinformatics</i>, Jan 2016<a href="http://scholarworks.wmich.edu/pcds_reports/4/"><span class="s10"><b>Tech Report</b></span></a></span><span class="s11"><b>|</b><a href="http://www.ncbi.nlm.nih.gov/pubmed/26801958"><span class="s28"><b>PubMed</b></span></a><b>|</b><a href="https://bioinformatics.oxfordjournals.org/content/early/2016/01/21/bioinformatics.btw023.abstract"><span class="s28"><b>Oxford</b></span></a></span><span class="s1"><br>
45. Muaaz Gul Awan and <b>Fahad Saeed</b></span><span class="s27"><b><sup>*</sup></b></span><span class="s1">, "</span><span class="s2">GPU-ArraySort: A parallel, in-place algorithm forsorting large number of arrays</span><span class="s1">", Proceedings of<i>Workshop on High Performance Computingfor Big Data, International Conference on Parallel Processing (ICPP-2016)</i>, Philadelphia PA,August 2016<a href="http://scholarworks.wmich.edu/cgi/viewcontent.cgi?article=1004&context=pcds_reports"><span class="s10"><b>Tech Report</b></span></a></span><span class="s11"><b>|</b><a href="http://ieeexplore.ieee.org/abstract/document/7576456/"><span class="s28"><b>IEEE Xplore</b></span></a></span><span class="s1"><br>
44. Majdi Maabreh, Ajay Gupta and <b>Fahad Saeed</b></span><span class="s27"><b><sup>*</sup></b></span><span class="s1">, "</span><span class="s2">A Parallel Peptide Indexer and DecoyGenerator for Crux Tide using OpenMP</span><span class="s1">", Proceedings of<i>Workshop on High PerformanceComputing Systems for Biomedical, Bioinformatics and Life Sciences, International Conference on High Performance Computing & Simulation (HPCS 2016)</i>, Innsbruck, Austria, July2016 <a href="http://ieeexplore.ieee.org/stamp/stamp.jsp?arnumber=7568364"><span class="s10"><b>IEEE Xplore</b></span></a><br>
43. Mohammed Aledhari, Mohamed S Hefeida and <b>Fahad Saeed</b></span><span class="s27"><b><sup>*</sup></b></span><span class="s1">, "</span><span class="s2">A Variable-Length Network Encoding Protocol for Big Genomic Data</span><span class="s1">", Proceedings of<i>International Conference on Wired & Wireless Internet Communications (WWIC 2016)</i>, Thessaloniki, Greece May 2016 <a href="http://link.springer.com/chapter/10.1007/978-3-319-33936-8_17"><span class="s10"><b>Springer</b></span></a><br>
42. Mohamed S Hefeida and <b>FahadSaeed</b></span><span class="s27"><b><sup>*</sup></b></span><span class="s1">, "</span><span class="s2">Data Aware Communication for Energy Harvesting Sensor Networks</span><span class="s1">", Proceedings of<i>InternationalConference on Wired & Wireless Internet Communications (WWIC 2016)</i>, Thessaloniki, Greece May 2016 <a href="http://link.springer.com/chapter/10.1007/978-3-319-33936-8_10"><span class="s10"><b>Springer</b></span></a><br>
</span><span class="s15"><br>
</span><span class="s18"><b>2015</b></span><span class="s15"><br>
</span><span class="s1">41. Sookkasem Khositseth, Panapat Uawithya, Poorichaya Somparn, Komgrid Charngkaew, Nattakan Thippamom, Jason D. Hoffert, <b>Fahad Saeed</b>, D. Michael Payne, Shu Hui Chen, Robert A. Fenton and Trairak Pisitkun, "</span><span class="s2">Autophagic degradation of aquaporin-2 is an early event in hypokalemia-induced nephrogenic diabetes insipidus</span><span class="s1">",<i>Nature Scientific Reports</i>, Dec 2015<a href="http://www.nature.com/articles/srep18311"><span class="s10"><b>Nature</b></span></a></span><span class="s11"><b>|</b><a href="http://www.ncbi.nlm.nih.gov/pubmed/26674602"><span class="s28"><b>PubMed</b></span></a></span><span class="s1"><br>
40.<b> Fahad Saeed</b></span><span class="s27"><b><sup>*</sup></b></span><span class="s1">, "</span><span class="s2">Big Data Proteogenomics and High Performance Computing: Challenges andOpportunities</span><span class="s1">",<i>Symposium on Signal and Information Processing for Software-Defined Ecosystems, and Green Computing, Proceedings of IEEE Global Conference on Signal and Information Processing (IEEE GlobalSIP),</i>Orlando Florida, Dec 2015<a href="http://scholarworks.wmich.edu/pcds_reports/3/"><span class="s10"><b>Tech Report</b></span></a></span><span class="s11"><b>|</b><a href="http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=7418173"><span class="s28"><b>IEEE Xplore</b></span></a></span><span class="s1"><br>
39. Proceedings of 7th International Conference on Bioinformatics and Computational Biology (BICoB), with Hisham Al-Mubaid and Nurit Haspel, March 2015.<br>
38. Sandino N. V. Perez and <b>Fahad Saeed</b></span><span class="s27"><b><sup>*</sup></b></span><span class="s1">, "</span><span class="s2">A Parallel Algorithm for Compression of Big Next-Generation Sequencing (NGS) Datasets</span><span class="s1">",<i>Proceedings of Paralleland Distributed Processing with Applications (IEEE ISPA-15)</i>, Vol.3. pp. 196-201 Helsinki Finland, Aug 2015<a href="http://scholarworks.wmich.edu/pcds_reports/2/"><span class="s10"><b>Tech Report</b></span></a></span><span class="s11"><b>|</b><a href="http://ieeexplore.ieee.org/xpl/articleDetails.jsp?arnumber=7345648"><span class="s28"><b>IEEE Xplore</b></span></a></span><span class="s1"><br>
37. Mohammed Aledhari and <b>Fahad Saeed</b></span><span class="s27"><b><sup>*</sup></b></span><span class="s1">,</span><span class="s2">"Design and Implementation of Network Transfer Protocol for BigGenomic Data"</span><span class="s1">,<i>Proceedings ofIEEE International Congress on Big Data (IEEE BigData Congress)</i>, pp. 281-288, New York City, USA, June 2015 (18% acceptance rate)<a href="http://scholarworks.wmich.edu/pcds_reports/1/"><span class="s10"><b>Tech Report</b></span></a></span><span class="s11"><b>|</b><a href="http://ieeexplore.ieee.org/xpl/articleDetails.jsp?arnumber=7207231"><span class="s28"><b>IEEE Xplore</b></span></a></span><span class="s1"><br>
36. Muaaz Awan and <b>Fahad Saeed</b></span><span class="s27"><b><sup>*</sup></b></span><span class="s1">,</span><span class="s2">"On the sampling of Big Mass Spectrometry Data"</span><span class="s1">, Proceedings of<i>Bioinformatics and Computational Biology (BICoB)</i>Conference, Honolulu Hawaii, March 2015<a href="https://docs.google.com/viewer?a=v&pid=sites&srcid=ZGVmYXVsdGRvbWFpbnxkcmZhaGFkc2FlZWR8Z3g6NTdjOWUwYTIyYjFjOTA0NA"><span class="s10"><b>Tech Report</b></span></a><br>
<br>
</span><span class="s18"><b>2014</b></span><span class="s15"><br>
</span><span class="s1">35. Akshay Sanghi, Matthew Zaringhalam, Callan Corcoran, <b>Fahad Saeed</b>, Jason D. Hoffert, Pablo C Sandoval, Trairak Pisitkun, and Mark A. Knepper, "</span><span class="s2">A Knowledge Base of Vasopressin Actions in Kidney</span><span class="s1">",<i>American Journal of Physiology</i>, July 2014<a href="http://ajprenal.physiology.org/content/early/2014/07/15/ajprenal.00012.2014"><span class="s9"><b>AJP</b></span></a><b>|</b><a href="http://www.ncbi.nlm.nih.gov/pubmed/25056354"><span class="s9"><b>PubMed</b></span></a><br>
34.<b> Fahad Saeed*</b>, Jason Hoffert, Trairak Pisitkun, Mark Knepper,</span><span class="s2">"Exploiting thread-level and instruction-level parallelism to cluster mass spectrometry data using multicore architectures"</span><span class="s1">,<i>Network Modeling Analysis in Health Informatics and Bioinformatics,</i> 3, No. 1, pp 1-19, Feb. 2014 <a href="http://link.springer.com/article/10.1007/s13721-014-0054-1"><span class="s10"><b>Springer</b></span></a></span><span class="s11"><b>|</b><a href="http://www.ncbi.nlm.nih.gov/pubmed/25045604"><span class="s28"><b>PubMed</b></span></a></span><span class="s1"><br>
33. Jason D. Hoffert, Trairak Pisitkun, Fahad Saeed, Justin L. Wilson and, Mark A. Knepper, "</span><span class="s2">Global analysis of the effects of the V2 receptor antagonist satavaptan on protein phosphorylation in collecting duct</span><span class="s1">",<i>American Journal of Physiology</i>, Vol. 306, No. 410-421,Feb. 2014<a href="http://ajprenal.physiology.org/content/306/4/410"><span class="s10"><b>AJP</b></span></a></span><span class="s11"><b>|</b><a href="http://www.ncbi.nlm.nih.gov/pubmed/24259510"><span class="s28"><b>PubMed</b></span></a></span><span class="s1"><br>
32. Proceedings of 6th International Conference on Bioinformatics and Computational Biology (BICoB), with Bhaskar Dasgupta, Hisham Al-Mubaid and Nurit Haspel, March 2014.<br>
31.<b> Fahad Saeed*</b>, Jason Hoffert and Mark Knepper, "</span><span class="s2">CAMS-RS: Clustering Algorithm for Large-Scale Mass Spectrometry Data using Restricted Search Space and Intelligent Random-Sampling</span><span class="s1">",<i>IEEE/ACM Transactions onComputational Biology and Bioinformatics,</i>11, No.1, pp.128,141, Jan. 2014<a href="https://sites.google.com/site/drfahadsaeed/Tech_Report_CAMS_RS.pdf?attredirects=0"><span class="s10"><b>Tech Report</b></span></a></span><span class="s11"><b>|</b><a href="http://www.ncbi.nlm.nih.gov/pubmed/24277952"><span class="s28"><b>PubMed</b></span></a><b>|</b><a href="http://ieeexplore.ieee.org/xpl/articleDetails.jsp?arnumber=6674297"><span class="s28"><b>IEEE Xplore</b></span></a></span><span class="s1"><br>
</span><span class="s15"><br>
</span><span class="s18"><b>2013</b></span><span class="s15"><br>
</span><span class="s1">30.<b> Fahad Saeed</b></span><span class="s27"><b><sup>*</sup></b></span><span class="s1">, Trairak Pisitkun, Jason D. Hoffert, Sara Rashidian, Guanghui Wang, Marjan Gucek, and Mark A. Knepper,</span><span class="s2">"PhosSA: Fast and Accurate Phosphorylation Site Assignment Algorithm for Mass Spectrometry Data"</span><span class="s1">,<i>Proteome Science</i>Volume 11, Supplement 1, November 2013 <a href="http://www.proteomesci.com/content/11/S1/S14/abstract"><span class="s10"><b>Proteome Science</b></span></a></span><span class="s11"><b>| PubMed</b></span><span class="s1"><br>
29. Pablo C. Sandoval, Dane H. Slentz, Trairak Pisitkun, <b>Fahad Saeed</b>, Jason D. Hoffert and Mark A. Knepper, "</span><span class="s2">Proteome-wide measurement of protein half-lives and translation rates in vasopressin-sensitive collecting duct cells</span><span class="s1">",<i>Journal of the American Society of Nephrology (JASN)</i>, March 2013 <a href="http://jasn.asnjournals.org/content/early/2013/09/11/ASN.2013030279.abstract"><span class="s10"><b>JASN</b></span></a></span><span class="s11"><b>|</b><a href="http://www.ncbi.nlm.nih.gov/pubmed/24029424"><span class="s28"><b>PubMed</b></span></a></span><span class="s1"><br>
28. <b>Fahad Saeed</b></span><span class="s27"><b><sup>*</sup></b></span><span class="s1">, Jason D. Hoffert, and Mark A. Knepper, "</span><span class="s2">A High Performance Algorithm for Clustering of Large-Scale Protein Mass Spectrometry Data using Multi-Core Architectures</span><span class="s1">", proceedings of<i>IEEE/ACM International Symposium on Network Enabled Health Informatics, Biomedicine and Bioinformatics (HI-BI-BI)</i>, August 2013 (25% acceptance ratefor full papers)<a href="http://www.saeedfahad.com/Tech_report_HI-BI-BI_2013.pdf"><span class="s10"><b>Tech Report</b></span></a></span><span class="s11"><b>|</b><a href="http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=6785810"><span class="s28"><b>IEEE Xplore</b></span></a></span><span class="s1"><br>
27. Steven J Bolger, Patricia A Gonzales, Jason D Hoffert, <b>Fahad Saeed</b>, Trairak Pisitkun and Mark A Knepper,"</span><span class="s2">Quantitative phosphoproteomics implicates clusters of proteins involved in cell-cell adhesion and transcriptional regulation in the vasopressin signalingnetwork</span><span class="s1">."<i>FASEB JOURNAL</i>. Vol. 27. 9650 ROCKVILLE PIKE, BETHESDA, MD 20814-3998 USA: FEDERATION AMER SOC EXP BIOL, 2013.<br>
26. Special issue on selected papers from the 5th international conference on bioinformatics and computational biology (BICoB 2013) with Bhaskar Dasgupta and Hisham Al-Mubaid, Journal of Bioinformatics and Computational Biology (JBCB) Volume 11, Issue 05, October 2013<br>
25. Proceedings of 5th International Conference on Bioinformatics and Computational Biology (BICoB), with Bhaskar Dasgupta, and Hisham Al-Mubaid (ISBN: 978-1-880843-89-5), March 2013<br>
</span><span class="s15"><br>
</span><span class="s18"><b>2012</b></span><span class="s15"><br>
</span><span class="s1">24. Steven Bolger, Patricia Gonzales Hurtado, Jason Hoffert, <b>Fahad Saeed</b>, Trairak Pisitkun, and Mark Knepper, "</span><span class="s2">Quantitative Phosphoproteomics in Nuclei of Vasopressin-Sensitive Renal Collecting Duct Cells</span><span class="s1">",<i>American Journal of Physiology (AJP)</i>, September 2012 <a href="http://ajpcell.physiology.org/content/early/2012/09/12/ajpcell.00260.2012.abstract"><span class="s10"><b>AJP</b></span></a></span><span class="s11"><b>|</b><a href="http://www.ncbi.nlm.nih.gov/pubmed/22992673"><span class="s28"><b>PubMed</b></span></a></span><span class="s1"><br>
23. Boyang Zhao, Trairak Pisitkun, Jason D. Hoffert, Mark A. Knepper, and <b>Fahad Saeed</b></span><span class="s27"><b><sup>*</sup></b></span><span class="s1">, "</span><span class="s2">CPhos: A Programto Calculate and Visualize Evolutionarily Conserved Functional Phosphorylation Sites</span><span class="s1">", Wiley<i>PROTEOMICS,</i>August 2012<a href="http://onlinelibrary.wiley.com/doi/10.1002/pmic.201200189/abstract"><span class="s10"><b>Wiley</b></span></a></span><span class="s11"><b>|</b><a href="http://www.ncbi.nlm.nih.gov/pubmed/23001821"><span class="s28"><b>PubMed</b></span></a></span><span class="s1"><br>
22. Jacqueline Douglass, Ruwan Gunaratne, Davis Bradford, <b>Fahad Saeed</b>, Jason D. Hoffert, Peter J. Steinbach,Mark A. Knepper, and Trairak Pisitkun, "</span><span class="s2">Identifying Protein Kinase Target Preferences Using MassSpectrometry</span><span class="s1">",<i>American Journal of Physiology (AJP)</i>, June 2012<a href="http://ajpcell.physiology.org/content/early/2012/06/20/ajpcell.00166.2012.abstract"><span class="s10"><b>AJP</b></span></a></span><span class="s11"><b>|</b><a href="http://www.ncbi.nlm.nih.gov/pubmed/22723110"><span class="s28"><b>PubMed</b></span></a></span><span class="s1"><br>
21.<b> Fahad Saeed</b>, Alan Perez-Rathke, Jaroslaw Gwarnicki, Tanya Berger-Wolf, Ashfaq Khokhar, "</span><span class="s2">A High Performance Multiple Sequence Alignment System for Pyrosequencing Reads from Multiple Reference Genomes</span><span class="s1">",<i>Journal of Parallel and Distributed Computing (JPDC)</i>, Volume 72, Issue 1, Pages 83-93,January 2012<a href="http://www.sciencedirect.com/science/article/pii/S0743731511001584"><span class="s10"><b>JPDC</b></span></a></span><span class="s11"><b>|</b><a href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3486434/"><span class="s28"><b>PubMed</b></span></a></span><span class="s1"><br>
20. Jason D. Hoffert, Trairak Pisitkun, <b>Fahad Saeed</b>, Jae H. Song, Chung-Lin Chou, and Mark A. Knepper, "</span><span class="s2">Dynamics of the G protein-coupled vasopressin V2 receptor Signaling Network revealed by Quantitative Phosphoproteomics</span><span class="s1">"<i>Mol Cell Proteomics (MCP),</i>Feb 2012<a href="http://www.mcponline.org/content/early/2011/12/05/mcp.M111.014613.abstract"><span class="s10"><b>MCP</b></span></a></span><span class="s11"><b>|</b><a href="http://www.ncbi.nlm.nih.gov/pubmed/22108457"><span class="s28"><b>PubMed</b></span></a></span><span class="s1"> <br>
19. Trairak Pisitkun, Jason D. Hoffert, <b>Fahad Saeed</b>and Mark Knepper, "</span><span class="s2">NHLBI-AbDesigner: An online tool for design of peptide-directed antibodies</span><span class="s1">",<i>American Journal of Physiology (AJP)</i>, Jan 2012<a href="http://ajpcell.physiology.org/content/early/2011/09/22/ajpcell.00325.2011.abstract"><span class="s10"><b>AJP</b></span></a></span><span class="s11"><b>|</b><a href="http://www.ncbi.nlm.nih.gov/pubmed/21956165"><span class="s28"><b>PubMed</b></span></a></span><span class="s1"> <br>
18.<b> Fahad Saeed</b></span><span class="s27"><b><sup>*</sup></b></span><span class="s1">, Trairak Pisitkun, Jason Hoffert, Guanghui Wang, Marjan Gucek, and Mark Knepper, "</span><span class="s2">An Efficient Dynamic Programming Algorithm for Phosphorylation Site Assignment of Large-Scale Mass Spectrometry Data</span><span class="s1">",<i>International Workshop on Computational Proteomics, proceedings of IEEE International Conference on Bioinformatics and Biomedicine (BIBM)</i>, Philadelphia USA, Oct 2012 (20% acceptance rate) <a href="http://ieeexplore.ieee.org/xpl/articleDetails.jsp?arnumber=6470210"><span class="s10"><b>IEEE Xplore</b></span></a></span><span class="s11">|<a href="http://www.ncbi.nlm.nih.gov/pubmed/23471519"><span class="s28"><b>PubMed</b></span></a></span><span class="s1"> <br>
17.<b> Fahad Saeed</b></span><span class="s27"><b><sup>*</sup></b></span><span class="s1">, Trairak Pisitkun, Jason Hoffert, and Mark A. Knepper, "</span><span class="s2">High Performance PhosphorylationSite Assignment Algorithm for Mass Spectrometry Data using Multicore Systems</span><span class="s1">", accepted in<i>International Workshop on Parallel and Cloud-based Bioinformatics and Biomedicine (ParBio),ACM Conference on Bioinformatics,Computational Biology and Biomedicine (ACM-BCB)</i>, Orlando Florida USA, Oct 2012(33 papers accepted out of 159 papers submitted: 21% acceptance rate)<a href="http://dl.acm.org/citation.cfm?id=2383056"><span class="s10"><b>ACM</b></span></a></span><span class="s11"><b>|</b><a href="http://www.saeedfahad.com/Tech_Report_ACM_BCB_2012.pdf"><span class="s28"><b>Tech Report</b></span></a></span><span class="s1"> <br>
16.<b> Fahad Saeed</b></span><span class="s27"><b><sup>*</sup></b></span><span class="s1">, Trairak Pisitkun, Mark Knepper, and Jason Hoffert, "</span><span class="s2">An Efficient Algorithm for Clustering of Large-Scale Mass Spectrometry Data</span><span class="s1">", accepted in<i>IEEE International Conference on Bioinformatics and Biomedicine (BIBM)</i>, Philidelphia USA, Oct 2012. (62 short paper accepted out of 299 paperssubmitted: 20.7 % acceptance rate)<a href="http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=6392738&tag=1"><span class="s10"><b>IEEE Xplore</b></span></a></span><span class="s11"><b>|</b><a href="http://arxiv.org/abs/1301.0834"><span class="s28"><b>arXiv:1301.0834</b></span></a><b>|</b><a href="http://www.ncbi.nlm.nih.gov/pubmed/23471471"><span class="s28"><b>PubMed</b></span></a></span><span class="s1"> <br>
15.<b> Fahad Saeed</b></span><span class="s27"><b><sup>*</sup></b></span><span class="s1">and Ashfaq Khokhar, "</span><span class="s2">Parallel Algorithm for Center-Star Sequence Alignments with applications to Short Reads</span><span class="s1">" accepted in 4th International<i>Conference on Bioinformatics and Computational Biology (BICoB)</i>, Las Vegas, Nevada, USA, March 12 - 14, 2012 <br>
14. Boyang Zhao, Trairak Pisitkun, Jason D. Hoffert, Mark A. Knepper, and <b>Fahad Saeed</b>, "</span><span class="s2">An Information Theory-Based Approach to Assess the Functional Significance of Phosphorylation Sites in Proteomes of Renal Tubule Epithelia</span><span class="s1">", poster at<i>International Society of Nephrology (ISN) Symposium</i>, Ann Arbor Michigan, USA, June 2012 <br>
13. Proceedings of 4th International Conference on Bioinformatics and Computational Biology (BICoB), with Hisham Al-Mubaid and Ashfaq Khokhar (ISBN: 978-1-880843-85-7), March 2012 <br>
</span><span class="s15"><br>
</span><span class="s18"><b>2011</b></span><span class="s15"> <br>
</span><span class="s1">12. <b>Fahad Saeed</b></span><span class="s27"><b><sup>*</sup></b></span><span class="s1">, Trairak Pisitkun, Mark A. Knepper, and Jason D. Hoffert, "</span><span class="s2">Mining Temporal Patterns from iTRAQ Mass Spectrometry(LC-MS/MS) Data</span><span class="s1">" In proceedings of<i>Bioinformatics and Computational Biology Conference (BICoB)</i>pp 152-159, New Orleans USA, March 23-25, 2011<a href="http://arxiv.org/abs/1104.5510"><span class="s10"><b>arXiv:1104.5510v1</b></span></a> <br>
11. <b>Fahad Saeed</b>, J. Hoffert, P. Pisitkun, M. Knepper, "</span><span class="s2">Mapping-based temporal pattern mining algorithm identifies unique clusters of phosphopeptides regulated by vasopressin in collecting duct</span><span class="s1">", meeting abstracts<i>Experimental Biology (EB),</i> Washington DC, USA April 2011 <br>
10. Hoffert, T. Pisitkun, <b>Fahad Saeed</b>, J. Song, M. Knepper, "</span><span class="s2">Large-scale iTRAQ-based quantification of phosphorylation changes during vasopressin signaling</span><span class="s1">", Featured Topic and abstract<i>Experimental Biology (EB)</i>, Washington DC USA April 2011 </span><span class="s15"><br>
<br>
</span><span class="s18"><b>2010</b></span><span class="s15"> <br>
</span><span class="s1">9. <b>Fahad Saeed,</b> "</span><span class="s2">High performance computational biology algorithms</span><span class="s1">", (Doctoral dissertation). Retrieved from<i>ProQuest Dissertations and Theses</i>(Accession Order No. AAT 3431281, ISBN: 9781124308067)<a href="http://gradworks.umi.com/34/31/3431281.html"><span class="s10"><b>ProQuest</b></span></a> <br>
8.<b> Fahad Saeed</b>and Ashfaq Khokhar<b>, "</b></span><span class="s2">Parallel Algorithm for Center Star Sequence and Alignments with applications to short reads</span><span class="s1"><b>"</b>International<i>conference on bioinformatics and computational biology (ACM-BCB)</i>Poster Session, in August 2010 <br>
7. <b>Fahad Saeed</b>, Lukas Burger, Ashfaq Khokhar, and Mihaela Zavolan, "</span><span class="s2">A graph-theoretic framework for efficient computation of HMM based motif finder</span><span class="s1">",<i>Technical Report, University of Illinois at Chicago</i>, Jan 2010 <br>
</span><span class="s15"><br>
</span><span class="s18"><b>2009</b></span><span class="s15"> <br>
</span><span class="s1">6.<b> Fahad Saeed</b>, Ashfaq Khokhar, "</span><span class="s2">A Domain Decomposition Strategy for Alignment of Multiple Biological Sequences on Multiprocessor Platforms</span><span class="s1">",<i>Journal of Parallel and Distributed Computing (JPDC)</i>Vol 69, Issue 7, July 2009<a href="http://arxiv.org/abs/0905.1744v1"><span class="s10"><b>arXiv:0905.1744v1</b></span></a></span><span class="s11"><b>|</b><a href="http://portal.acm.org/citation.cfm?id=1551190"><span class="s28"><b>JPDC</b></span></a></span><span class="s1"> <br>
5.<b> Fahad Saeed</b>and Lukas Burger "</span><span class="s2">High Performance Graph Theoretic model for finding Regulatory Elements and motifs</span><span class="s1">",<i>Technical Report, Zavolan Group, Swiss Institute of Bioinformatics (SIB)</i>, University of Basel Switzerland, August 2009 <br>
4. <b>Fahad Saeed</b>, Ashfaq Khokhar, Osvaldo Zagordi and Niko Beerenwinkel. "</span><span class="s2">Multiple Sequence Alignment System for Pyrosequencing Reads</span><span class="s1">"<i>Lecture Notes in Computer Science (LNCS)</i>, Volume 5462/2009, 2009<a href="http://arxiv.org/abs/0901.2753"><span class="s10"><b>arXiv:0901.2753</b></span></a></span><span class="s11"><b>|</b><a href="http://www.springerlink.com/content/x14j0w4l20268010/"><span class="s28"><b>Springer</b></span></a></span><span class="s1"> </span><span class="s15"><br>
<br>
</span><span class="s18"><b>2008 and earlier</b></span><span class="s15"> <br>
</span><span class="s1">3.<b> Fahad Saeed</b>and Ashfaq Khokhar, "</span><span class="s2">Sample-Align-D: A High Performance Multiple Sequence Alignment System using Phylogenetic Sampling and Domain Decomposition</span><span class="s1">", in Proc.<i>IEEE International Workshop on High Performance Computational Biology (HiCOMB 2008), IPDPS,</i>Monday, April 14, 2008.<a href="http://arxiv.org/abs/0901.2742"><span class="s10"><b>arXiv:0901.2742</b></span></a></span><span class="s11"><b>|</b><a href="http://ieeexplore.ieee.org/xpl/freeabs_all.jsp?arnumber=4536174"><span class="s28"><b>IEEE Xplore</b></span></a></span><span class="s1"> <br>
2.<b> Fahad Saeed</b>,</span><span class="s2">"Pyro-Align: Sample-Align based Multiple Alignment system for Pyrosequencing Reads of Large Number</span><span class="s1">",<i>Technical Report, Beerenwinkel Group Computational Biology, Department of Biosystems Science and Engineering, Eth Zurich</i>Switzerland, August 2008.<a href="http://arxiv.org/abs/0901.2751"><span class="s10"><b>arXiv:0901.2751</b></span></a> <br>
1. <b>Fahad Saeed</b>and Ashfaq Khokhar, "</span><span class="s2">An overview of multiple sequence alignments and their limitations</span><span class="s1">",<i>Technical Report, Multimedia System Laboratory, University of Illinois at Chicago</i>, May 2007<a href="http://arxiv.org/abs/0901.2747"><span class="s10"><b>arXiv:0901.2747</b></span></a><span class="Apple-converted-space"> </span></span></p>
<h2 style="margin: 0.0px 0.0px 0.0px 0.0px; font: 18.0px Arial; -webkit-text-stroke: #000000"><span class="s1"><b>Software and Code</b></span></h2>
<p class="p4"><span class="s1">Most of the code that we develop can be found listed at our <a href="https://saeedlab.cis.fiu.edu/software/"><span class="s9">Lab Software Page</span></a><span class="Apple-converted-space"> </span></span></p>
<p class="p4"><span class="s1">We also maintain a very healthy GitHub page at <a href="https://github.com/pcdslab/"><span class="s9">Github Page</span></a><span class="Apple-converted-space"> </span></span></p>
<p class="p11"><span class="s1"></span><br></p>
<h2 style="margin: 0.0px 0.0px 0.0px 0.0px; font: 18.0px Arial; -webkit-text-stroke: #000000"><span class="s1"><b>Information for Prospective Students/Postdocs/VisitingScholars</b></span></h2>
<p class="p4"><span class="s1">We are always seeking creative people with solid analytical capabilities, versatile computational skills applicable to parallel computing, machine learning, and computational biology. Our group is committed to conducting research in computational, data, and engineering sciences in the context of biomedical, clinical, and public health disciplines and applying this knowledge to support the nation’s leading health initiatives. I am always looking for bright, hardworking students and trainees to join my group. If you are seeking a research career in machine learning, data mining, high-performance computing, bioinformatics and related areas, and you have a strong background in mathematics and programming, do reach out. The current opening are below:</span></p>
<p class="p19"><span class="s1"></span><br></p>
<p class="p20"><span class="s29">If you are a <b>prospective PhD student</b> please read and fill out the details <a href="https://forms.gle/vwzi6fVkr1rHoxj96"><span class="s30">here</span></a>.</span><span class="s1"><br>
</span><span class="s29">If you are a <b>prospective Post-Doctoral Fellow</b>, please read and fill out the details <a href="https://forms.gle/vxJ3HMiydeV8scPo7"><span class="s31">here</span></a></span><span class="s32">.</span></p>
<p class="p11"><span class="s1"></span><br></p>
<h2 style="margin: 0.0px 0.0px 0.0px 0.0px; font: 18.0px Arial; -webkit-text-stroke: #000000"><span class="s1"><b>Current and Former Students and Staff</b></span></h2>
<p class="p4"><span class="s1">We have a track record of mentoring students in attaining high impact positions including but not limited to Staff Scientists positions at UC Berkeley, Tenure-track position in Kennesaw State University and Kalamazoo College, as well as data scientists in industrial research positions. A list of current and former students in my group can be found at this link: <a href="https://saeedlab.cis.fiu.edu/people/"><span class="s9">Current and Former Group Members</span></a><span class="Apple-converted-space"> </span></span></p>
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