18. Computational Immunology: Models and Tools

Adria Carbo, Andrew Leber, Casandra Philipson, Josep Bassaganya-Riera, Kate Wendelsdorf, Keith Bisset, Madhav Marathe, Maksudul Alam, Monica Viladomiu, Pawel Michalak, Pinyi Lu, Raquel Hontecillas, Stefan Hoops, Stephen Eubank, Vida Abedi, and Xinwei Deng
Book #1 Elsevier, 2015.

BibTeX

@InBook{Alam2015g,
  chapter   = {Agent-Based Modeling and High Performance Computing},
  title     = {Computational Immunology: Models and Tools},
  publisher = {Elsevier},
  year      = {2015},
  author    = {Alam, Maksudul and Abedi, Vida and Bassaganya-Riera, Josep and Wendelsdorf, Katherine and Bisset, Keith and Deng, Xinwei and Eubank, Stephen and Hontecillas, Raquel and Hoops, Stefan and Marathe, Madhav},
  doi       = {10.1016/B978-0-12-803697-6.00006-0},
}

14. Parallel Graph Algorithms, chapter Distributed Memory Parallel Algorithms for Massive Graphs

Maksudul Alam, Shaikh Arifuzzaman, Hasanuzzaman Bhuiyan, Maleq Khan, V.S. Anil Kumar, and Madhav Marathe
Book #2 CRC Press / Taylor & Francis, 2015.

BibTeX

@inbook{Alam2015e,
	Author = {{\AAlam} and Arifuzzaman, Shaikh and Bhuiyan, Hasanuzzaman and Khan, Maleq and Vullikanti, Anil and Marathe, Madhav},
	Chapter = {Distributed Memory Parallel Algorithms for Massive Graphs},
	Publisher = {CRC Press/Taylor \& Francis},
	Title = {Parallel Graph Algorithms \emph{(Forthcoming)}},
	Year = {2019}}

17. Sensitivity Analysis of an ENteric Immunity SImulator (ENISI)-based Model of Immune Responses to Helicobacter pylori Infection

Maksudul Alam, Xinwei Deng, Casandra Philipson, Josep Bassaganya-Riera, Keith Bisset, Adria Carbo, Stephen Eubank, Raquel Hontecillas, Stefan Hoops, Yongguo Mei, Vida Abedi, and Madhav Marathe
Journal #1 PLoS ONE, 2015.

BibTeX

@Article{Alam2015a,
  Title                    = {Sensitivity Analysis of an ENteric Immunity SImulator (ENISI)-Based Model of Immune Responses to <italic>Helicobacter pylori</italic> Infection},
  Author                   = {Alam, Maksudul AND Deng, Xinwei AND Philipson, Casandra AND Bassaganya-Riera, Josep AND Bisset, Keith AND Carbo, Adria AND Eubank, Stephen AND Hontecillas, Raquel AND Hoops, Stefan AND Mei, Yongguo AND Abedi, Vida AND Marathe, Madhav},
  Journal                  = {PLoS ONE},
  Year                     = {2015},

  Month                    = {09},
  Number                   = {9},
  Pages                    = {e0136139},
  Volume                   = {10},

  Doi                      = {10.1371/journal.pone.0136139},
  Publisher                = {Public Library of Science},
  Url                      = {http://dx.doi.org/10.1371%2Fjournal.pone.0136139}
}

16. Parallel Algorithms for Generating Massive Random Networks with Given Degree Sequences

Maksudul Alam and Maleq Khan
Journal #2 International Journal of Parallel Programming, 2015.

BibTeX

@InProceedings{Alam2015,
  Title                    = {Parallel Algorithm for Generating Massive Random Networks with a Given Sequence of Expected Degrees},
  Author                   = {Maksudul Alam and Maleq Khan},
  Booktitle                = {The 12th Annual IFIP International Conference on Network and Parallel Computing},
  Year                     = {2015},
  Url                      = {http://arxiv.org/abs/1406.1215}
}

10. HMEC: A Heuristic Algorithm for Individual Haplotyping with Minimum Error Correction

Md. Shamsuzzoha Bayzid, Maksudul Alam, Abdullah Mueen, and Md. Saidur Rahman
Journal #3 ISRN Bioinformatics, 2013.

BibTeX


                

8. Predictive Computational Modeling of the Mucosal Immune Responses during Helicobacter pylori Infection

Adria Carbo, Josep Bassaganya-Riera, Mireia Pedragosa, Monica Viladomiu, Madhav Marathe, Stephen Eubank, Katherine Wendelsdorf, Keith Bisset, Stefan Hoops, Xinwei Deng, Maksudul Alam, Barbara Kronsteiner, Yongguo Mei, Raquel Hontecillas
Journal #4 PLoS ONE, 2013.

BibTeX

@Article{Carbo2013,
  author    = {Carbo, Adria and Bassaganya-Riera, Josep and Pedragosa, Mireia and Viladomiu, Monica and Marathe, Madhav and Eubank, Stephen and Wendelsdorf, Katherine and Bisset, Keith and Hoops, Stefan and Deng, Xinwei and Alam, Maksudul and Kronsteiner, Barbara and Mei, Yongguo and Hontecillas, Raquel},
  title     = {Predictive Computational Modeling of the Mucosal Immune Responses during \textit{Helicobacter pylori} Infection},
  journal   = {PLoS ONE},
  year      = {2013},
  doi       = {10.1371/journal.pone.0073365},
  publisher = {Public Library of Science},
}

5. ENteric Immunity SImulator: A Tool for In Silico Study of Gastroenteric Infections

Katherine Wendelsdorf, Maksudul Alam, Josep Bassaganya-Riera, Keith Bisset, Stephen Eubank, Raquel Hontecillas, Stefan Hoops, and Madhav Marathe
Journal #5 IEEE Transactions on NanoBioscience, 2012.

BibTeX


                

24. Towards Native Execution of Deep Learning on a Leadership-Class HPC System

Srikanth B. Yoginath, Maksudul Alam, Arvind Ramanathan, Nouamane Laanait, and Kalyan S. Perumalla
Conference #1 Scalable Deep Learning over Parallel and Distributed Infrastructures, 2019.

BibTeX


                

23. GPU-based Parallel Algorithm for Generating Massive Scale-free Networks Using the Preferential Attachment Model

Maksudul Alam and Kalyan S. Perumalla
Conference #2 High Performance Big Graph Data Management, Analysis, and Mining, 2017.

BibTeX


                

20. Performance of Point and Range Queries using Radix Tree on GPUs

Maksudul Alam, Srikanth Yoginath, and Kalyan Perumalla
Conference #3 DSS, 2016.

BibTeX


                

19. An Efficient and Scalable Algorithmic Method for Generating Large-Scale Random Graphs

Maksudul Alam, Maleq Khan, Anil Vullikanti, and Madhav Marathe
Conference #4 Supercomputing, 2016.

BibTeX


                

15. Parallel Algorithm for Generating Massive Random Networks with a Given Sequence of Expected Degrees

Maksudul Alam and Maleq Khan
Conference #5 The 12th Annual IFIP International Conference on Network and Parallel Computing, 2015.

BibTeX


                

12. CINET 2.0: A CyberInfrastructure for Network Science

Sherif Abdelhamid, Maksudul Alam, Richard Alo, Shaikh Arifuzzaman, Pete Beckman, Tirtha Bhattacharjee, Hasanuzzaman Bhuiyan, Keith Bisset, Stephen Eubank, Albert Esterline, Edward Fox, Geoffrey Fox, S M Shamimul Hasan, Harshal Hayatnagarkar, Maleq Khan, Chris Kuhlman, Madhav Marathe, Natarajan Meghanathan, Henning S Mortveit, Judy Qiu, S S Ravi, Zalia Shams, Ongard Sirisaengtaksin, Samarth Swarup, V.S. Anil Kumar, and Tak-Lon Wu
Conference #6 The 10th IEEE International Conference on e-Science, 2014.

BibTeX


                

9. Distributed-memory parallel algorithms for generating massive scale-free networks using preferential attachment model

Maksudul Alam, Maleq Khan, and Madhav V. Marathe
Conference #7 International Conference for High Performance Computing, Networking, Storage and Analysis (Super Computing), 2013.

BibTeX

@inproceedings{Alam2013,
 author = {Alam, Maksudul and Khan, Maleq and Marathe, Madhav V.},
 title = {Distributed-memory Parallel Algorithms for Generating Massive Scale-free Networks Using Preferential Attachment Model},
 booktitle = {Proceedings of the International Conference on High Performance Computing, Networking, Storage and Analysis},
 series = {SC '13},
 year = {2013},
 isbn = {978-1-4503-2378-9},
 location = {Denver, Colorado},
 pages = {91:1--91:12},
 articleno = {91},
 numpages = {12},
 url = {http://doi.acm.org/10.1145/2503210.2503291},
 doi = {10.1145/2503210.2503291},
 acmid = {2503291},
 publisher = {ACM},
 address = {New York, NY, USA},
 keywords = {big data, copy model, high performance computing, parallel algorithms, preferential attachment, random networks, scale-free networks},
} 

4. High-Performance Interaction-Based Simulation of Gut Immunopathologies with ENteric Immunity Simulator (ENISI)

Keith R. Bisset, Maksudul Alam, Josep Bassaganya-Riera, Adria Carbo, Stephen Eubank, Raquel Hontecillas, Stefan Hoops, Yongguo Mei, Katherine V. Wendelsdorf, Dawen Xie, Jae-Seung Yeom, and Madhav V. Marathe
Conference #8 The 26th IEEE International Parallel and Distributed Processing Symposium, 2012.

BibTeX


                

3. A Heuristic Algorithm for Minimum Conflict Individual Haplotyping

Md. Shamsuzzoha Bayzid, Maksudul Alam, and Md. Saidur Rahman
Conference #9 The conference on BioMedical Engineering and Informatics (BMEI), 2010.

BibTeX


                

2. A Heuristic Algorithm for Individual Haplotyping with Minimum Error Correction

Abdullah Al Mueen, Md. Shamsuzzoha Bayzid, Maksudul Alam, and Md. Saidur Rahman
Conference #10 The conference on BioMedical Engineering and Informatics (BMEI), 2008.

BibTeX


                

22. Generating Billion-Edge Scale-Free Networks in Seconds: Performance Study of a Novel GPU-based Preferential Attachment Model

Maksudul Alam and Kalyan S. Perumalla
Technical Report #1 Oak Ridge National Laboratory, 2017.

BibTeX


                

21. Computational Speed and Matching Quality using an Upper Bound on the Normalized Mutual Information

Maksudul Alam, Kalyan S. Perumalla, and Devin S. White
Technical Report #2 Oak Ridge National Laboratory, 2017.

BibTeX


                

7. Efficient algorithms for generating massive random networks

Maksudul Alam and Maleq Khan
Technical Report #3 Technical Report 13-064, NDSSL at Virginia Tech, 2013.

BibTeX


                

1001. A High-Performance Computing Based Modeling Environment to Study Mucosal Immunity

Maksudul Alam, Vida Abedi, Keith Bisset, Josep Bassaganya-Riera, Adria Carbo, Xinwei Deng, Stephen Eubank, Raquel Hontecillas, Stefan Hoops, Yongguo Mei, Casandra Philipson, Katherine Wendelsdorf, Jae-Seung Yeom, and Madhav Marathe
In-Preparation #1 N/A, 2011.

BibTeX


                

13. Parallel Algorithm for Generating Massive Random Networks with a Given Sequence of Expected Degrees

Maksudul Alam and Maleq Khan
Others #1 CoRR (Computing Research Repository), 2014.

BibTeX

@article{Alam2014,
  author    = {Maksudul Alam and Maleq Khan},
  title     = {Parallel Algorithm for Generating Massive Random Networks with a Given Sequence of Expected Degrees},
  journal   = {CoRR},
  volume    = {abs/1406.1215},
  year      = {2014},
  url       = {http://arxiv.org/abs/1406.1215}
}

11. Parallel algorithms for generating massive random networks

Maksudul Alam, Maleq Khan, and Madhav Marathe
Others #2 Poster presented at 2014 Google PhD Summit, February 25, Washington, D.C., 2014.

BibTeX


                

6. ENteric Immunity SImulator: A Tool for in silico Study of Mucosal Immune Responses

Maksudul Alam, Josep Bassaganya-Riera, Keith Bisset, Adria Carbo, Raquel Hontecillas, Stefan Hoops, Yongguo Mei, Katherine Wendelsdorf, Dawen Xie, Jae-Seung Yeom, and Madhav Marathe
Others #3 Poster presented at the Symposium on Modeling Immune Responses from Complex Data, University of Rochester, 2012.

BibTeX


                

1. Graph Modeling for Bioinformatics

Md. Shamsuzzoha Bayzid and Maksudul Alam
Others #4 Undergraduate Thesis, Bangladesh University of Engineering and Technology, 2007.

BibTeX