Ashis Kumer Biswas

I am a Ph.D. student working with Professor Jean X. Gao in the BioMedical Computing and Intelligent Systems Lab at the Computer Science and Engineering Department, University of Texas at Arlington since Fall 2011. My research interests are in Bioinformatics, Data Mining and Machine Learning with focus on non-coding RNAs and their implication prediction.

I also am a Lecturer in the Computer Science and Engineering Department at the University of Dhaka since January 2010 and currently I am on a study leave.

I graduated with an MS in Computer Science and Engineering from University of Dhaka in 2009. Before that I completed my Bachelor of Science in Computer Science and Engineering from the same university in 2008. I also passed many sweet moments during my higher secondary level education at the Notre Dame College, Dhaka and secondary school level at the Rani Bilash Moni Government Boys' High School, Gazipur and elementary school level at Progati Primary School, BRRI, Gazipur.

For more information, please refer to my CV.

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News


Oct 15, 2016Our paper on the Robust Inductive Matrix Completion is accepted at the IEEE BIBM-2016
June 14, 2016"Multi-Block Bipartite Graph for Multimodal Genomic Data" - accepted at the IEEE TCBB
May 23, 2016At last, our PR2S2clust article is accepted at the Journal of Bioinformatics and Computational Biology (JBCB)!
April 10, 2016Big D Texas Marathon completed!
Sept 26, 2015CSPS 2015 notification of our paper: accepted!
Sept 06, 20152 papers get accepted at BIBM 2015
May 23, 2015NetMAHIB Journal article gets accepted.
April 8, 2015I am in the UTA Engineering news!!!
Nov 13, 2014Received best paper award at the BIBE 2014 conference!!

Coming up...


May 6, 2016Proposal defense! (DONE)
April 15, 2016Revision submission deadline! (DONE)
April 15, 2016PhD review. (DONE)
June 15, 2016IEEE BIBE submission deadline!
July 6, 2016ICMLA submission deadline!
August 14, 2016BIBM submission deadline!

 

Education

Ph.D. Candidate Computer Science and Engineering, University of Texas at Arlington, Arlington, TX, USA   (September 2011 - Now)
  Supervisor: Dr. Jean X. Gao  
MS Computer Science and Engineering, University of Dhaka, Dhaka, Bangladesh   (Session: 2005-2006, rank: 4th, marks: 77.38%)
  Supervisor: Dr. Nasimul Noman  
  Thesis: Machine Learning Approach to Predict Protein Phosphorylation Sites  
B.Sc. (Hons.) Computer Science and Engineering, University of Dhaka, Dhaka, Bangladesh   (Session: 2001-2005, rank: 1st, marks: 80.88%)
  4th Year thesis Supervisor: Dr. Hafiz Md. Hasan Babu  
  Thesis: Efficient Design of an N-bit Reversible Processor  

 

Publications

Journal Articles

Integrative approach for inference of gene regulatory networks using lasso-based random featuring and application to psychiatric disorders
Dongchul Kim, Mingon Kang, Ashis Kumer Biswas, Chunyu Liu and Jean X. Gao
BMC Medical Genomics, 2016.
DOI: [link] | Export: [bib]

 

Multi-Block Bipartite Graph for Multimodal Genomic Data
Mingon Kang, Juyoung Park, Dong-Chul Kim, Ashis Kumer Biswas, Chunyu Liu and Jean X. Gao
IEEE/ACM Transactions on Computational Biology and Bioinformatics (IEEE TCBB), 2016.
DOI: [link] | Export: [bib]

 

PR2S2Clust: Patched RNA-seq Read Segments' Structure-oriented Clustering
Ashis Kumer Biswas, and Jean X. Gao
Journal of Bioinformatics and Computational Biology, 2016.
DOI: [link] | Export: [bib] | Supplements: [link]

 

Inferring disease associations of the long non-coding RNAs through non-negative matrix factorization
Ashis Kumer Biswas, Mingon Kang, Dong-Chul Kim, Chris H. Q. Ding, Baoju Zhang, Xiaoyong Wu and Jean X. Gao
Network Modeling Analysis in Health Informatics and Bioinformatics (NetMAHIB) 4:1, 2015.
DOI: [link] | Export: [bib] | Supplements: [link]

 

CNCTDiscriminator: Coding and Non-coding Transcript Discriminator — An Excursion through Hypothesis Learning and Ensemble Learning Approaches
Ashis Kumer Biswas, Baoju Zhang, Xiaoyong Wu and Jean X. Gao
Journal of Bioinformatics and Computational Biology 11(5): 1342002, 2013.
DOI: [link] | Export: [bib] | Supplements: [link]

 

Design of a Reversible Parallel Loading Shift Register
Ashis Kumer Biswas, Lafifa Jamal, M. A. Mottalib, Hafiz Md. Hasan Babu
Dhaka University Journal of Engineering & Technology. Vol. 1(2) 1-5, 2011.
File: [link] | Export: [bib]

 

Machine learning approach to predict protein phosphorylation sites by incorporating evolutionary information
Ashis Kumer Biswas, Nasimul Noman and Abdur Rahman Sikder
BMC Bioinformatics vol:11, number:1 pp: 273-289, 2010.
DOI: [link] | Export: [bib] | Supplements: [link]

 

Efficient Approaches for Designing Reversible Binary Coded Decimal Adders
Ashis Kumer Biswas, Md. Mahmudul Hasan, Ahsan Raja Chowdhury, Hafiz Md. Hasan Babu.
Microelectronics Journal vol:39, pp: 1693-1703, 2008.
DOI: [link] | Export: [bib]

 

Optimization of Reliability in a Real Time Security System Controlled by Embedded Internet Technology
Shah Mostafa Khaled , Rezaul Karim , Ashis Kumer Biswas, R.H. Rahman , Nusrat Nowsheen and Mohammad Abdul Qayum
Asian Journal of Information Technology, 6(10): 1050-1056, 2007.
Download: [link] | Export: [bib]

 

Conference Articles

Robust Inductive Matrix Completion Strategy to Explore Associations between LincRNAs and Human Disease Phenotypes
Ashis Kumer Biswas, Dongchul Kim, Mingon Kang, and Jean X. Gao
IEEE International Conference on Bioinformatics & Biomedicine, Shenzhen, China, Dec 15-18, 2016.
Paper acceptance rate: 19% as regular papers.
DOI: [#]

Improving Consensus Hierarchical Clustering Framework
Ashis Kumer Biswas, Baoju Zhang, Xiaoyong Wu and Jean X. Gao
The 4th International Conference on Communications, Signal Processing and Systems (CSPS 2015), Chengdu, Sichuan, China, Oct 23-24, 2015.
DOI: [link]

An Integrative Genomic Study for Multimodal Genomic Data Using Multi-Block Bipartite Graph
Mingon Kang, Juyoung Park, Dong-Chul Kim, Ashis Kumer Biswas, Chunyu Liu, and Jean Gao
Proceedings of IEEE International Conference on Bioinformatics & Biomedicine (IEEE BIBM 2015), Washington D.C., USA, Nov. 9-12, 2015.
DOI: [link]

 

Integrative approach for inference of gene regulatory networks using lasso-based random featuring and application to Psychiatric disorders
Dong-Chul Kim, Mingon Kang, Ashis Biswas, Chunyu Liu, and Jean Gao
Proceedings of IEEE International Conference on Bioinformatics & Biomedicine (IEEE BIBM 2015), Washington D.C., USA, Nov. 9-12, 2015.
DOI: [link]

 

NMF-based LncRNA-Disease Association Inference and Bi-clustering
Ashis Kumer Biswas, Jean X Gao, Baoju Zhang and Xiaoyong Wu
The 14th IEEE International Conference on BioInformatics and BioEngineering (BIBE-2014), held in Boca Raton, Florida, USA, November 10-12, 2014.
DOI: [link] Received the best paper award in the Bioinformatics category

 

A Multi-label Classification Framework to Predict Disease Associations of Long non-coding RNAs (lncRNAs)
Ashis Kumer Biswas, Baoju Zhang, Xiaoyong Wu and Jean X. Gao
The 3rd International Conference on Communications, Signal Processing, and Systems (CSPS) held in Hohhot, China, 14-15 July, 2014.
DOI: [link]

 

QLZCClust: Quaternary Lempel-Ziv Complexity based Clustering of the RNA-seq Read Block Segments
Ashis Kumer Biswas, Baoju Zhang, Xiaoyong Wu and Jean X. Gao
The 13th IEEE International Conference on Bioinformatics and Bioengineering (IEEE BIBE 2013) held in Chania, Greece, 10-13, November 2013.
DOI: [link]

 

An Information Integration Approach for classifying coding and non-coding genomic data
Ashis Kumer Biswas, Baoju Zhang, Xiaoyong Wu and Jean X. Gao
The International Conference on Communications Signal Processing and Systems, Sept 1-3, 2013, Tianjin, China.
DOI: [link]

 

Integrating RNA-seq transcript signals, Primary and Secondary Structure Information in Differentiating coding and non-coding RNA transcripts
Ashis Kumer Biswas, Jean Gao, Xiaoyong Wu and Baoju Zhang
The 5th International Conference on Bioinformatics and Computational Biology (BICoB) 2013, Honolulu, Hawaii.
Conference Program: [link]

 

Infobox Suggestion for Wikipedia Entities
Afroza Sultana, Quazi M. Hasan, Ashis Kumer Biswas, Soumyava Das, Habibur Rahman, Chris Ding and Chengkai Li
The 21st ACM international conference on Information and knowledge management (CIKM 2012); Pages 2307-2310.
DOI: [link]

 

Incorporating Evolutionary Information in Protein Phosphorylation Site Predictions
Ashis Kumer Biswas, Abdur Rahman Sikder and Nasimul Noman
The 8th Asia Pacific Bioinformatics Conference (APBC 2010), held on 18-21 January 2010 in Bengalore, India.

 

A Novel Approach to Design BCD Adder and Carry Skip BCD Adder
Ashis Kumer Biswas, Md. Mahmudul Hasan, Moshaddek Hasan, Ahsan Raja Chowdhury and Hafiz Md. Hasan Babu
The 21st International Conference on VLSI Design, 4-8 January 2008, pp: 566-571 (IEEE Computer Society 2008).
DOI: [link]

 

Present status of Telecommunication in Bangladesh and its impact on ICT
Shah Mostafa Khaled, Ashis Kumer Biswas, Mohammad Abdul Qayuum and M Lutfar Rahman
The 9th International Conference on Computer and Information Technology (ICCIT), 2006, pp: 221-226

 

An Analysis on Human Resource Development in the ICT Sector of Bangladesh
Shah Mostafa Khaled, Ashis Kumer Biswas, M. Lutfar Rahman, Suraiya Pervin
The 8th International Conference on Computer and Information Technology (ICCIT), 2005; pp:507-512.

 

 

Employments


September 2011 - Now University of Texas at Arlington, Arlington, TX, USA
  Graduate Teaching Assistant, Department of Computer Science and Engineering.
January 2010 - Now University of Dhaka, Dhaka, Bangladesh
  Lecturer, Department of Computer Science and Engineering. (on study leave since Aug 1, 2011)
April 2009 - January 2010 University of Asia Pacific, Dhaka, Bangladesh
  Lecturer, Department of Computer Science and Engineering.
February 2008 - December 2008 State University of Bangladesh, Dhaka, Bangladesh
  Lecturer, Department of Computer Science and Engineering.

 

Honors and Awards / Achievements

Education

Best Paper Award in the Bioinformatics category
Received at the 14th IEEE International Conference on BioInformatics and BioEngineering (BIBE-2014) conference for the paper "NMF-based LncRNA-Disease Association Inference and Bi-clustering"

Enhanced Graduate Teaching Assistantship
From the University of Texas at Arlington, September 2011 - Now

Attorney Alamgir Gold Medal 2005
From the University of Dhaka for achieving the highest score in the B.Sc. (Hons.) among all the students in the faculty of Science (session: 2005).

Kudrat-E-Khuda Scholarship 2005
From the University of Dhaka for securing the 1st position in the B.Sc. (Hons.) (session: 2005).

 

Programming Competitions

6th Position as team "DU Apocalypse"
ACM International Collegiate Programming Contest (ACM ICPC) 2006, Dhaka site

10th Position as team "DU Apocalypse"
EWUIPC (an Inter-University Programming Contest at East West University, Dhaka, Bangladesh), 2006

13th Position as team "DU Apocalypse"
AIPC (an Inter-university programming contest at American International University, Dhaka, Bangladesh, 2006.

40th Position as team "DU Knights"
ACM International Collegiate Programming Contest (ACM ICPC) 2004, Dhaka site.

 

Professional Certifications

CCNA (Cisco Certified Network Associate)
My certificate verification number: 393854170255GPXM. The certificate can be verified at http://www.ciscocertificates.com/verify.cfm

 

Athletics

Marathon Finisher
Completed the USATF certified 26.2 miles of the Big D Texas Marathon presented by Mellew Productions, Dallas, TX (April 10, 2016). I took 4:50:26 to finish. My Bib no. 641. [ Finisher Certificate ]

Half Marathon Finisher
Completed the USATF certified 13.1 miles of the Austin Half Marathon presented by Freescale, Austin, TX (February 16, 2014). I took 2:35:42 to finish. My Bib No. 6688. [ Finisher Certificate ]

 

Services


Paper Reviewer BIBM-2015,2014,2013
  BMC Bioinformatics-2016
  CBM-2014
  ETRI-2015
  MEJ-2015
  NetMAHIB-2015

 

Hobbies

Running        
Hiking      
Biking      
Traveling
Photography