User:PoojaJ

Personal data

Name

Pooja Jain

Country

India

Education

• M.S. in Bioinformatics from University Of Lisbon and Instituto Gulbenkian de Ciência, Portugal
• M.Sc. in Microbiology from Devi Ahilya University (DAVV), Indore, India (Specialisation: Industrial Microbiology)
• B.Sc. in Microbiology and Pharmaceutical Chemistry from MRSCPS, DAVV, Indore, India

Research interests

• Data Mining
• Structural Biology
• Biological Networks

E-mail

ku.ca.mahgnitton@1jpxcp

Website

Pooja Jain

Dissemination

Year 4 (Sep 2008 - Aug 2009)

Publication

• P. Jain, J.M. Garibaldi and J.D. Hirst, Supervised Machine Learning Algorithms for Protein Structure Classification, Computational Biology and Chemistry 33 (2009) 216–223.
• P. Jain and J.D. Hirst, Exploring protein structural dissimilarity to facilitate structure classification, BMC Structural Biology, 9:60,(2009).
• P. Jain and J. D. Hirst, A geometric approach to protein structural similarity and classification, Jornadas de Bioinformatica, Lisboa, Portugal, November 3-6, 2009.

Pending Publication

• P. Jain and J.D. Hirst, Automatic Protein Structure Classification using Random Forest, Submitted, Journal of Computational Biology.
• P. Jain, P. Frasconi and J.D. Hirst, Constrained Prediction of Protein Topology, In preparation.

Talks

• Constrained Protein Topology Prediction
  2008-09-15, Mini EURO Conference on Computational Biology, Bioinformatics and Medicine, Rome, Italy (20 min)
• Inferring Function Using Patterns of Native Disorder in Proteins, Lobley A et al. (2007), PLoS Comput Biol 3(8): e162
  2008-10-17, Computational Foundations of Nanoscience Journal Club (35 min)
• Exploring Protein Structural Dissimilarity to Ease Structure Classification
  2008-12-02, Computational Chemistry Group Seminar (45 min)
• Supervised Machine Learning Algorithms for Protein Structure Classification
  2009-02-10, IMA Group Seminar (25 min)

Posters

• Supervised Machine Learning Algorithms for Protein Structure Classification
  2009-01-26, Biochemical Society / Wellcome Trust Focused Meeting on "Protein evolution - sequences, structures and systems", Hinxton, Cambridge, United Kingdom

Year 3 (Sep 2007 - Aug 2008)

Talks

• The Pursuit of Predictive Guidance
  2008-03-10, Computational Chemistry Group Seminar (45 min)

Year 2 (Sep 2006 - Aug 2007)

Talks

• Protein Structure Prediction and Analysis
  2006-09-19, Computational Chemistry Group Seminar (45 min)
• Protein Structure: Prediction, Similarity and Classification
  2007-07-03, Computational Chemistry Group Seminar (45 min)
• Study of Protein Structural Descriptors: towards similarity and classification
  2007-07-11, EURO XXII, Prague, 2007 (25 min)

Posters

• Study of Protein Structural Descriptors: Towards Similarity and Classification Short Report
  CBSB2007,2007-05-02 - 2007-05-04, John von Neumann Institute for Computing, Julich, Germany

Networking, teaching and training activities

Year 4 (Sep 2008 - Aug 2009)

Writing Skills

• Academic Research Writing, Insessional 8 Weeks Module by CELE
• Getting going on your thesis, 2008-11-26, Graduate School
• Getting started with research design and statistics, 2008-11-24, 2008-12-01, 2008-12-10, Graduate School
• Finishing your thesis, 2008-11-24, Graduate School
• Virtual Statistical Tutor (an online referencing tool), Graduate School
• Statistical course. School of Computer Science, Nottingham, 2008-12-16
• Proofreading Workshop by CELE, Jubilee Campus,Nottingham, 2009-01-14 (2hrs) and 2009-01-21 (2hrs)

Conference

• Mini EURO-CBBM Conference, Rome, Italy, 2008-09-15 - 2008-09-17
• Biochemical Society/Wellcome Trust Focused Meeting, Hinxton, Cambridge, UK 2009-01-26 - 2009-02-27

Year 3 (Sep 2007 - Aug 2008)

Secondment

• Completed at Machine Learning and Neural Network Group, Università degli Studi di Firenze, Italy, 2008-03-20 - 2008-06-20

Fellowship meetings

Career Improvement Courses

• Proposal Writing for Scientists, 2008-01-08, Graduate School
• Introduction to writing successful fellowship applications, Online/Self Study course,Graduate School

Workshops

• HPC User Conference 2008, 2008-01-08 - 2008-01-08, University of Nottingham, UK

Year 2 (Sep 2006 - Aug 2007)

Fellowship meetings

• 2007-01-09, ASAP, School of Computer Science

Communication skills

• Presentation skills - building confidence (Science and Engineering), 2006-11-08, Graduate School
• How to prepare an effective poster presentation, 2006-11-14 and 2006-12-06, Graduate School
• Further presentation skills [GST2GP], 2006-01-26, Graduate School
• Getting going on your thesis and getting your work published, 2007-02-15, Graduate School

Workshops

• HPC User Conference 2007, 2007-01-16 - 2007-01-17, University of Nottingham, UK
• CBS Science Symposium 2007, 2007-02-23, University of Nottingham, UK
• MGMS Silver Jubilee Meeting 2007, 2007-03-13, The School of Oriental and African Studies (SOAS), London, UK
• Practical High Throughput Computing for Bioinformatics 2007,2007-03-26 - 2007-03-30, London E-Science Centre and Imperial College, London, UK
• From Computational Biophysics to Systems Biology 2007,2007-05-02 - 2007-05-04, John von Neumann Institute for Computing, Julich, Germany
• Workshop on OR in Computational Biology, Bioinformatics, and Medicine (EURO-CBBM) 2007,Prague, Czech Republic, 2007-07-08
• EURO XXII, Prague, 2007, 2007-07-08 - 2007-07-11

Year 1 (Sep 2005 - Aug 2006)

Fellowship meetings

• 2006-07-12, ASAP, School of Computer Science
• 2006-03-02, ASAP, School of Computer Science

Research skills

• Planning research and time management, 2006-06-23, Graduate School
• Introduction to quantitative research, 2006-05-15, Graduate School
• Nature of the PhD and the Supervision Process, 2006-03-13, Graduate School

Courses

• An introduction to Java programming, 2006-06-14 - 2006-09-10, Information Services
• C-Programming, 2006-03-30 - 2006-04-04, Information Services

Workshops

• CCPB Training Workshop on Analysis of Biomolecular Simulation Data 2006, 2006-07-07, University of Nottingham
• AMBER Basic and Advanced Training Workshop 2006, 2006-06-26 - 2006-06-30, Imperial College, London
• ISMB Symposium 2006, 2006-06-19 - 2006-06-20, University College, London

Ongoing activity

• Improving Topology Prediction with further constraints. 2008/6 - 2008/10
• Secondment at University of Florence. 2008/03 - 2008/05
• Analysis of Supervised Machine learning algorithm for structure classification. 2008/01 - 2008/02
• Prediction of structural descriptors and the results analysis. 2007/10
• Started preparing the manuscript and calculation of sequence only descriptors for SSEs. 2007/09
• Started the proposal for the work at Florence and needful bibliographic research. 2007/08
• Attended EURO - XXII, continued analysis for only homologous proteins, regression at the protein level with 10x regression. 2007/07
• Analysis of non-homologous protein datasets and preparation for EURO-XXII. 2007/06
• Organising the code and analysis of the BLAST results 2007/05
• Analysis of classification results and preparation for CBSB2007 workshop 2007/04
• Structural Classification of proteins using SVM 2007/03
• Classification of proteins based on geometric properties and comparison with SCOP classification 2007/02
• Extension of protein profile - Inclusion of SSE type and Surface Accessibility 2007/02
• Analysis of geometric arrangements of secondary structures in proteins 2007/01
• Finding Descriptors for Protein Structure, 2006/11