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JAMIA MILLIA ISLAMIA, CENTRAL UNIVERSITY, NEW DELHI, INDIA


About the Bioinformatics Centre
 

Welcome to BIF Center of the Department of Computer Science, Jamia Millia Islamia (A Central University), New Delhi, India. Bioinformatics has become a mission, critical to life science research and education across campuses. Here our faculty members work collaboratively to develop state-of-the-art computational techniques to extract knowledge from the burgeoning biological data, and to solve real-world problems mainly in human health.
Bioinformatics Infrastructure Facility (BIF) was established at Jamia during the year 2006, under BTISNet scheme, funded by the Department of Biotechnology (DBT), Government of India. Since its inception, the Centre as an additional offshoot of the Department has made significant progress through the support of DBT and the available infrastructure including human resources. The objective of the Centre is the promotion of Computational Biology ‘Teaching and Research’ through Bioinformatics scheme of BTISnet, and undertaking exhaustive steps for understanding the deeper structures of Biological data through computational techniques. The Department offers a M. Sc. Bioinformatics programme of two-years duration, in addition to other professional courses like MCA (3 years) and PGDCA (1 year).

 

Area of Specialization: Biological Data Mining, Bioinformatics, Systems Biology, Biological Databases, and Machine Learning.

 
Objectives

The objective of the Centre is to pursue cutting-edge research at the intersection of Computational Intelligence and Molecular Biology. The Centre is actively engaged in Computational research on gene and protein sequence analysis, protein structure prediction, molecular docking, and metabolic pathway analysis, in addition to applying Data Mining techniques for knowledge discovery from Biomedical literatures. The key areas of specialization of the faculty members include Biological Data Mining, Bioinformatics, Systems Biology, Biological Databases, and Machine Learning.

 
Current area of research

Biological Data Mining, Bioinformatics, Systems Biology, Computational Biology, Biological Databases, Machine Learning

 
Inter Institutional collaboration

At present the Center is collaborating with some faculty members from IIT Delhi, AIIMS, and JNU to teach some papers of M.Sc. Bioinformatics Programme. Renowned researchers from various institutions are also invited to deliver special lectures as a part of the departmental subject association.

Infrastructure facilities

The centre is well equipped with requisite hardware and software, partially acquired through the DBT support, is detailed as follows:

Computer and Communication Facility
High end-server - 01, Medium Server - 01, Monitor Workstations–TFT - 07, Desktop Work station - 05, Digital Camera - 01, Printer-HP-Laser - 03, Computer With DVD - 07; Setup of Network connectivity with 45 connecting nodes with Networking Switch 24-ports and Networking Switch 8-ports.
Scientific Software Packages
Software Solaris Sun NI Grid, IBM-SPSS PASW-18 Win-Based and Freeware: RasMol, PyMol, FoldX, Blast, Flasta, Clustaw, ClustalX, Arrayassist, Fylip, PDB, EBI, EXPSY, Natasa Server. Docking Software, GOLD Suite (GOLD, GoldMine and Hermes) 1 GOLD FlexLM licence server.
Achievements at a glance

The following research and development activities are undertaken at the Centre:

Research Projects
Principal Investigator: Khalid Raza; Title: Analysis of Microarray Data Using Artificial Intelligence Based Techniques. Duration: 2 Years (Ongoing w.e.f. April 1, 2013). Funding Agency: University Grants Commission, India (1.85 Lakhs)
 
Number of PhDs Awarded/Working
    • Sangeetha Subramaniam, “In Silico identification of potential inhibitors of drug targets in Plasmodium falciparum and design of target oriented virtual compound library”, 2012.
    • Ms. Meenakshi bhat, “In-Silico Phylogenetic Analysis of Protease Family”, 2013.
    • Shaurya Jauhari, Analysis of Gene Expression Data on Cancer Research: Challenges Ahead (status: working)
 
M. Sc. Bioinformatics Programme
Following are the notable progress with regard to the post graduate programme, M. Sc. Bioinformatics
 
  • Projects: Fourth Semester Students of M. Sc. Bioinformatics carried out their major projects in diverse areas of Bioinformatics, including Computational Biology, Drug Design, Micro Array Technology, Systems Biology, and Biological Databases.
  • Placements: Students got placed in esteemed companies like TCS, Cell Works, HCL etc. and some of them are pursuing research from abroad.
  • Curriculum: The curriculum of M. Sc. Bioinformatics is designed as per the envisioned requirements by the pioneers of the Bioinformatics including Prof. B. Jayaram (IITD), Dr. Punit Kaur (AIIMS Delhi), and Dr. Debasisa Mohanthy.
Faculty members

Name

Designation

Dr. Muhammad Abulaish

Assoc. Professor & Head

Dr. Suraiya Jabin

Asst. Professor & Coordinator

Dr. Khurram Mustafa

Professor

Dr. Rafat Parveen

Assistant Professor

Dr. Syed Zeeshan Hussain

Assistant Professor

Dr. Mansaf Alam

Assistant Professor

Dr. Jahiruddin

Assistant Professor

Dr. Mohmmad Nazir

Assistant Professor

Mr. Khalid Raza

Assistant Professor


About the Institution
 

Jamia Millia Islamia derives its name from Urdu Language in which ‘Jamia’ means University and ‘Millia’ means National. The university, born off the Indian National movement and patriotic fervor, was founded in response to a call by Mahatma Gandhi in 1920 to boycott the Government-supported institutions. Today it has 9 faculties, 39 departments and 33 research centers with nearly 18000 students on rolls. The university has a distinction of offering education from nursery school to doctoral level. The story of Jamia is that of commitment and sacrifices by its founders. This continued to inspire commitment and sincerity of the teachers associated with this institution right from its inception to the present day.
The university includes separate Departments of Computer Science, Biosciences, and Biotechnology, in addition to a Centre for Interdisciplinary Research in Basic Sciences. These departments are well equipped with highly qualified/experienced staff members and research infrastructure, and engaged in heavy research/development activities. The achievements are visible from faculty publications, as posted under respective departments at the university website http://www.jmi.ac.in.
The Department of Computer Science has three modern air-conditioned Computing Labs, an air-conditioned Seminar Room, a Departmental Library, six Classrooms and offices for faculty and staff members. These are connected through a LAN to provide modern teaching and learning environment and fast access to the knowledge sources available worldwide. The computing labs are well equipped with Software like MATLAB, RapidMiner, Discovery Studio (DNA STAR, C),              GOLD Suite (GoldMine and Hermes), 1 GOLD FlexLM licence server, Servers for Database Applications, etc. The BIF Centre regularly organizes Trainings and Seminars/Workshops for Teachers/ Scientists/ Research Scholars/ Students to disseminate knowledge. The department has established linkages with other universities and research centers such as JNU, IIT, CDFD from where it draws most of the visiting faculties to teach additional specialized courses. M. Sc. Bioinformatics curriculum includes languages like C, C++, Java (J2EE, J2ME), XML, Perl, in addition to Data Structures, Databases, Data Mining, and Machine learning. Our labs provide strong foundation to our students in the field of Information Technology and Bioinformatics. .

 
 
Recent publications

 

Jahiruddin, Abulaish, M. & Dey, L.: A Concept-Driven Biomedical Knowledge Extraction and Visualization Framework for Conceptualization of Text Corpora, Journal of Biomedical Informatics, Vol. 43(6), Elsevier, ISSN: 1532-0464, pp. 1020-1035, 2010.

Abulaish, M. & Jahiruddin: Web Content Mining for Learning Generic Relations and Their Associations from Textual Biological Data, Biological Knowledge Discovery Handbook – Preprocessing, Mining, and Post-Processing of Biological Data, Mourad Elloumi and Albert Y. Zomaya (Eds.), John Wiley & Sons Inc., New Jersey, pp. 919-942, 2013.

Dey, L. and Abulaish, M.: A Fuzzy Ontology-Based Text Mining System for Knowledge Acquisition, Ontology Enhancement and Query Processing from Bio-Medical Texts, Computational Intelligence in Bioinformatics, Gary B. Fogel, David W. Corne and Yi Pan (Eds.), IEEE Press Series on Computational Intelligence, Wiley/ IEEE Inc., New Jersey, pp. 297-319, 2008.

Abulaish, M. & Dey, L.: Biological Relation Extraction and Query Answering from Medline Abstracts, Data and Knowledge Engineering, Vol. 61(2), Elsevier, pp. 228-262, 2007.
Khalid Raza and Atif N. Hasan, “A Comprehensive Evaluation of Machine Learning Techniques for Cancer Class Prediction Based on Microarray Data”, International Journal of Bioinformatics Research and Applications, Inderscience Publisher.

Sabahuddin Ahmad, Abuzar Hamza and Khalid Raza, "PREs-Clustered Motifs in Drosophila melanogaster", Res. J. Pharm., Biol. Chem. Sci., Vol. 4, Issue 4, pp. 1100-1110, 2013.

Khalid Raza and Rafat Parveen, “Reconstruction of gene regulatory network of colon cancer using information theoretic approach”, 4thInternational Conference (CONFLUENCE-2013): The Next Generation Information Technology Summit, 26-27 Sept., 2013. (IEEE Xplore)

Khalid Raza and Rajni Jaiswal, “Reconstruction and Analysis of Cancer-specific Gene Regulatory Networks from Gene Expression Profiles”, International Journal on Bioinformatics & Biosciences, Vol. 3, No. 2, pp. 25-34, 2013. ISSN 1839-9614, DOI: 10.5121/ijbb.2013.3103.

Aankita Kaur, Mansaf Alam, Role of Knowledge Engineering in the Development of a Hybrid Knowledge Based Medical Information System for Atrial Fibrillation, American Journal of Industrial and Business Management, Vol.3 No.1, page 36-41, DOI: 10.4236/ajibm.2013.31005, January 17 2013, Scientific Research, USA.

Khalid Raza and Akhilesh Mishra, “A Novel Anticlustering Filtering Algorithm for the Prediction of Genes as a Drug Target”, American Journal of Biomedical Engineering, Vol. 2, No. 5, pp. 206-2011, 2012. DOI: 10.5923/j.ajbe.20120205.03

Khalid Raza and Rafat Parveen, “Soft Computing Approach for Modeling Genetic Regulatory Networks”, Advances in Intelligent Systems and Computing, Vol. 178, pp 1-11, Springer-Verlag Berlin Heidelberg, ISBN 978-3-642-31599-2, 2012.

Khalid Raza and Rafat Parveen, “Evolutionary Algorithms in Genetic Regulatory Network Model”, Journal of Advanced Bioinformatics Applications and Research, Vol. 1, No.3, pp. 271-280, 2012, ISSN 0976-2604.

Rafat Parveen and Sami M Halawani, “Modeling of Gene Regulatory Networks for the Development of Endomesoderm in Sea Urchins Embryo and E. Coli”, International Journal of Research and Reviews in Computer Science, Vol 3, No 3, 2012.

Sangeetha Subramanium, Monica Mehrotra and Dinesh Gupta, ‘Virtual High Throughput Screening (vHTS) – A perspective’, in Bioinformation Journal (Online ISSN 0973-2063; Print ISSN 0973-8894), a scientific journal publishing research articles in biological knowledge discovery after full peer review. pp. 14-17. (Impact Factor – 1.15)

Subramaniam, S.; Mehrotra, M.; Gupta, D., ’Support Vector Machine Based Classification Model for Screening Plasmodium falciparum Proliferation Inhibitors and Non-Inhibitors’. Biomedical Engineering and Computational Biology 2011.

Subramaniam, S.; Mehrotra, M.; Gupta, D., Support Vector Machine based prediction of P. falciparum proteasome inhibitors and development of focused library by molecular docking. Combinatorial Chemistry & High Throughput Screening 2011,14 (10).898-907. (Impact factor -  2.573 ).

Abulaish, M., Jahiruddin & Dey, L.: Mining Biological Interactions from Biomedical Texts for Efficient Query Answering, Jake Y. Chen & Stefano Lonardi (eds.), Biological Data Mining, Chapman & Hall/CRC Data Mining and Knowledge Discovery Series, Taylor and Francis Group Publisher, ISBN: 9781420086843, pp. 485-527, 2009. (Book Chapter)

Dey, L., Abulaish, M., Goyel, R. & Jahiruddin: Semantic Integration of Information through Relation Mining – Application to Bio-Medical Text Processing, in: Proceedings of the 2nd International Conference on Pattern Recognition and Machine Intelligence (PReMI'07), Kolkata, India; Lecture Notes in Computer Science, Springer, December 18-22, pp. 365-372, 2007.

Dey, L., Abulaish, M. & Jahiruddin: Relation Extraction from Texts for Efficient Access to Information – Application to Bio-Medical Text Processing, in: Proceedings of the 3rd Indian International Conference on Artificial Intelligence (IICAI’07), Pune, India ISBN: 978-0-9727412-2-4, December 17-19, pp. 1719-1737, 2007.

Dey, L., Abulaish, M., Sharma, G. & Jahiruddin: Text Mining through Entity-Relationship Based Information Extraction, in: Proceedings of the IEEE/WIC/ACM International Conference on Web Intelligence - Workshop on Biomedical Applications of Web Technologies, Silican Valley, USA, November 2-5, pp. 177-180, 2007.
 

Contacts

Head, D/o Computer Science
Jamia Millia Islamia (A Central University)
Jamia Nagar, New Delhi – 110025, India.
E-mail: mabulaish@jmi.ac.in
Phone: +91 (11) 26980014 (direct), EPABX: +91 (11) 26981717-3450
 

Dr. Suraiya Jabin
Coordinator, BIF
Asst. Professor, D/o Computer Science
Jamia Millia Islamia (A Central University)
Jamia Nagar, New Delhi – 110025, India.
E-mail: jmiuniv.btisnet@nic.in, sjabin@jmi.ac.in

 

 

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