Resume of Madan Babu Mohan

Name : Madan Babu (Forename)

Mohan (Surname/Family name)

Corresponding address : MRC-Laboratory of Molecular Biology

Hills Road, Cambridge – CB2 2QH, U.K.

Permanent address (in India): C5 Anand Bhavan

26 South Boag Road, T. Nagar, Chennai – 17, India.

Nationality : Indian

Date of Birth : 14th Nov 1979

Contact Phone : 44 - 01223 – 402041 (MRC-LMB)

Fax: 44 - 01223 – 213556 (MRC-LMB)

Contact Email :

Website:

Aim: Contribute to the advancement of mankind

by contributing to Science

Academic Background

<TBODY>Course / Authority / Year / Marks/Grade/Remarks
X standard / Board of Matriculation Education, TN / Mar 1995 / 1028/1100 (93.45%)
State 3rd Rank
XII Standard / Board of Secondary Education, TN / Mar 1997 / 1153/1200 (96.08%)
B. Tech (Industrial Biotechnology) / Anna University, Centre for Biotechnology / Aug 1997 to
May 2001 / CGPA: 9.8/10 (3.92/4.00)
University First / Gold Medallist
PhD (Computational Genomics) / University of Cambridge/
MRC-Laboratory of Molecular Biology / Oct 2001 to
Jul 2004 / LMB-Cambridge Fellowship
Trinity Honorary External Research Studentship
Max Perutz prize for outstanding research

Academic Awards (18)

  • Max Perutz prize for outstanding research carried out at the MRC Laboratory of Molecular Biology, UK (October 2004).
  • Visiting fellow at the National Center for Biotechnology Information (NCBI), National Institute of Health (NIH), USA. (2002, 2003).
  • European Science Foundation - Japanese Society for the Promotion of Sciences (ESF-JSPS) fellowship to participate in 'Bioinformatics workshop' in San Felix, Spain. (2003).
  • Runners up at the Young Bioinformaticians Forum held in Oxford University (2003).
  • European Science Foundation fellowship to participate in "Genome to Life" summer school in Corsica, France (2002).
  • DIMACS student travel award to attend DIMACS 2002 at Rutgers University, USA.
  • ISCB Student Award to attend RECOMB 2002, USA.
  • LMB-Cambridge Fellowship for the course of my PhD at MRC-LMB / University of Cambridge (from Oct 2001).
  • Honorary External Research Studentship for three years at Trinity College, Cambridge University (from Oct 2001).
  • Recipient of Cambridge Overseas Research Scholarship (ORS)
  • Gold Medal for securing the first position in the University (Industrial Biotechnology - CGPA - 9.8/10).
  • Indian Institute of Science - Young Fellow from 1997 till the duration of U.G. course (3 years).
  • Indian Academy of Sciences - Summer Research Fellowship during 1999 & 2000.
  • National Merit Scholarship based on XII std performance.
  • Association of Matriculation Schools – award for 3rd rank in the state in Matric Exam.
  • Nesarathnam Educational Trust - award for 3rd rank in the state in Matric Exam.
  • Shield from M.CT.M HSS for first in the school and for 3rd rank in the state in Matric Exam
  • Rotary club – award for 3rd rank in the state in Matric Exam

Presentations (27)

  • (Invited) Transcriptional regulatory networks, 31st annual conference of the Indian Immunological Society – 17th Dec 2004.
  • (Invited) Special lecture on systems biology, structure and dynamics of transcriptional regulatory networks, Alpha College of Arts and Sciences – 7th Dec 2004.
  • (Invited) Guest lecture on genomics, proteomics and systems biology, National programme in bioinformatics and information technology. TNVC – 26th Nov 2004.
  • (Invited) Structure, evolution and dynamics of the yeast transcriptional regulatory network, G.N. Ramachandran Hall, Madras University – 24th Nov 2004.
  • (Invited) Structure, evolution and dynamics of the yeast transcriptional regulatory network, PSI - University of Zurich, Switzerland – 20th Oct 2004.
  • (Invited) Structure and evolution of transcriptional regulatory networks in prokaryotes, MRC Laboratory of Molecular Biology, Cambridge - 15th Oct 2004.
  • (Invited) Non-canonical interactions in protein structures, British Crystallographic Association spring meeting, Univ. of Manchester - 8th Apr 2004.
  • (Invited) General mechanisms for the evolution of gene regulatory networks, 2nd Trilateral Symposium in Structural Biology, Yokohama City University, Japan - 24th Mar 2004.
  • (Invited) Structure, Evolution and Dynamics of the gene regulatory network in yeast, RIKEN Institute, Yokohama, Japan - 23rd Mar 2004.
  • (Invited) Evolution and dynamics of the gene regulatory network in yeast at Trinity College, University of Cambridge - 12th Feb 2004.
  • (Invited) Dynamic nature of the gene regulatory network in yeast at the European Bioinformatics Institute workshop - Dec 2003.
  • (Invited) General mechanisms for the evolution of gene regulatory networks at Oxford University - Oct 2003.
  • (Seminar series) Mechanisms for the evolution of regulatory networks at the EBI, Hinxton, Cambridge - Sep 2003.
  • (Seminar series) Protein families and the evolution of the gene regulatory network in E. coli at MRC-LMB - Mar 2003.
  • (Invited) Evolution of the gene regulatory network in E. coli at Darwin College, University of Cambridge - Jan 2003.
  • (Invited) Guest lecture on Biological Databases, Training programme on Bioinformatics & Information Technology at Bioinformatics Centre & ARIS Cell, Madras Veterinary College, India - Nov 2002.
  • (Invited) Evolution of transcription factors and the gene regulatory network in prokaryotes at the University of California, Berkeley - 20th Sep 2002.
  • (Seminar series) Evolution of transcription factors and the gene regulatory network in E. coli at Stanford University - 19th Sep 2002.
  • (Seminar series) Protein Families and Regulatory Patterns in the Transcription Factors of E. coli at MRC-LMB - 1st May 2002
  • (Seminar series) Regulatory Patterns in the Transcription Factors of E. coli at NCBI, NIH, Bethesda, Maryland, USA - 23rd Apr 2002
  • (Seminar series) Protein Families in the Transcription Factors of E. coli at Cornell University, Ithaca, USA - 12th Apr 2002
  • (General) Unix for Beginners at MRC-Laboratory of Molecular Biology during Nov 2001
  • (General) Telnet, FTP for Beginners at MRC-Laboratory of Molecular Biology during Nov 2001
  • (Invited) Protein Sequence Analysis and Biological Databases - National workshop on Bioinformatics in TNVC, Chennai, India during May 2001
  • (Invited) PERL for Biologists - Invited lecture for 3 days at DSQ Biotech, Bangalore, India during Apr 2001
  • (Invited) Introduction to Biological Databases - National workshop on Bioinformatics held in TNVC, Chennai, India during Dec 2000
  • (Invited) Co-ordinator and Instructor for the hands on session in the 3 day national workshop on Bioinformatics organized by the Bioinformatics Center at CBT, Anna University, Chennai, India during Nov 24-26, 2000

Refereed manuscript(s) for (9)

Nature Genetics, Trends in Genetics, Gene, Nucleic Acids Research, PEDs letters, FEBS letters, Biological and Medicinal Chemistry, Genome Biology and Bioinformatics.

Posters Presented (6)

  • Mechanisms for the evolution of regulatory networks – 13th March, Trinity College Science Symposium, Cambridge.
  • Gene regulatory network growth by duplication - 25th - 30th Oct, San Felix, Spain
  • Evolution of the gene regulatory network in E. coli by duplication - 11th - 14th June, Stockholm, Sweden
  • Protein Families and Regulatory Patterns in the Transcription Factors of E. coli at RECOMB 2002 - 18th - 21st April 2002, Washington DC, USA
  • Protein Families and Regulatory Patterns in the Transcription Factors of E. coli at DIMACs - Complexity in Biosystems conference - 8th - 10th April 2002, Rutgers University, USA
  • A Novel C-H..O hydrogen bond stabilized polypeptide chain reversal motif at the C-terminus of helices in proteins - 19th October 2001, MRC-LMB

Publications in Conference Proceedings (2)

  • Protein Families and Regulatory Patterns in the Transcription Factors of E. coli at RECOMB 2002 - 18th - 21st April 2002, Washington DC, USA – poster abstract
  • Integrating Bioinformatics, Medical Sciences and Drug Discovery - M. Madan Babu - accepted for presentation at the National Conference on Medical Informatics at Vijayawada, held during 24-25 Nov 2000

Undergraduate (B. Tech) Thesis

  • Analysis of C-H...O hydrogen bonding in helix terminus
  • DATE - Database of TIM barrel enzymes
  • Target selection for structural genomics and the structural status for the completed microbial genomes
  • Computational identification of Chorismate mutase in the M. leprae genome

Invited Book chapters (3)

1. Madan Babu, M. (2004) Introduction to Microarray Data Analysis, book chapter in Computational Genomics, Horizon press (Grant, R. Editor).

2. Aswin Sai Narain, S. and Madan Babu, M*. (2005) Contextual inference of protein function, chapter in Encyclopaedia of Genomics, Proteomics and Bioinformatics, John Wiley & Sons, (Subramanian, S. Editor).

3. Madan Babu, M (2005) Evolution and dynamics of transcriptional regulatory networks, book chapter in Introduction to Systems Biology, in preparation.

Publications in Journals (* indicates corresponding author & 1 indicates joint first author)

Transcriptional regulatory systems

1. Teichmann, S. A.* and Madan Babu, M.* (2004). Gene regulatory network growth by duplication, Nature Genetics, 36(5):492-6.

2. Luscombe, N.1*, Madan Babu, M.1*, Yu, H., Snyder, M., Teichmann, S. A.* and Gerstein, M.* (2004). Genomic analysis of regulatory network dynamics reveals large topological changes, Nature, 431:308-12.

3. Madan Babu, M.1*, Luscombe, N.1, Aravind, L., Gerstein, M., Teichmann, S.A.* (2004). Structure and evolution of gene regulatory networks. Current Opinion in Structural Biology, 14(3):283-91.

4. Luscombe, N.* and Madan Babu, M* (2004) Gene expression analysis using the hexamer-based universal microarray (research update), Trends in Biotechnology.

5. Madan Babu, M.* and Teichmann, S. A. (2003). Evolution of transcription factors and the gene regulatory network in Escherichia coli, Nucleic Acids Research, 31(4):1234-1244.

6. Madan Babu, M.* and Teichmann, S. A. (2003). Functional determinants of transcription factors in Escherichia coli: protein families and binding sites, Trends in Genetics, 19(2):75-79.

7. Madan Babu, M.* (2003) Did the loss of sigma factors initiate pseudogene accumulation in M. leprae?, Trends in Microbiology, 11(2):59-61.

8. Teichmann, S. A. and Madan Babu, M. (2002). Conservation of gene co-regulation in prokaryotes and eukaryotes, Trends in Biotechnology, 20(10):407-410.

Protein structure & non-canonical interactions

9. Madan Babu, M.* (2003) NCI: a server to identify non canonical interactions in protein structures, Nucleic Acids Research, 31(13), 3345-8.

10. Madan Babu, M., Singh, S.K. and Balaram, P. (2002). A C-H...O hydrogen bond stabilized polypeptide chain reversal motif at the C terminus of helices in proteins, Journal of Molecular Biology, 322(4):871-880.

11. Singh, S.K., Madan Babu, M. and Balaram, P. (2002) Registering alpha-helices and beta-strands using backbone C-H...O interactions, Proteins: structure function and genetics, 51(2):167-171.

12. Nye, T., Berzuini, C., Gilks, W., Madan Babu, M., and Teichmann, S.A. (2004) Statistical analysis of domains in interacting protein pairs, Bioinformatics.

13. Praefcke, G.J.K., Ford, M.G.J., Schmid, E.M., Olesen, L.E., Gallop, J., Chew, S.Y., Vallis, Y., Madan Babu, M., Mills, G. and McMahon, H.T. (2004). Clathrin-coated pit assembly: The AP2 complex serves as an integration hub to order the dynamic network of accessory proteins, EMBO Journal, 23(22):4371-83

Microbial genome analysis

14. Madan Babu, M. and Sankaran, K. (2002). DOLOP - a database of bacterial lipoproteins, Bioinformatics, 18(4):641-643.

15. Madan Babu, M., Kamalakkannan, S., Subrahmanyam, Y.V.B.K. and Sankaran, K. (2002) Shigella apyrase - a novel variant of bacterial acid phosphatases? - FEBS Letters, 512(1-3):8-12.

16. Madan Babu, M.*, Bhargavi, J., Singh, R. S. and Singh, S. K. (2001) Virulence factors of Bordetella pertussis, Current Science, 80(12):1512-1522.

Research manuscripts in preparation or submitted:

17. Madan Babu, M.*, Teichmann, S. A. and Aravind, L. (2004). Evolution and reconstruction of the gene regulatory network in prokaryotes, submitted.

18. Madan Babu, M., Teichmann, S.A., and Berloff, N.G. (2004) Inferring regulatory networks from gene expression data.

19. Madan Babu, M*. (2004). Classification and the role of non-canonical interactions in proteins and at the protein-protein interface.

20. Berzuini, C., Nye, T., Madan Babu, M., Teichmann, S.A., Gilks, W. (2004) Statistical prediction of protein-protein contacts.

21. Sukumaran, S.K., Madan Babu, M. and Prasadarao, N. V. (2004). Interaction of the E. coli protein OmpA with human receptors.

22. Madan Babu, M*., and Rajkumar, S*. (2004) Computational identification of a new Acyl-Homoserine Lactone synthase gene in P. aeruginosa

23. Madan Babu, M.*, Leena Priya, M., Tamil Selvan, A., Madera, M., Gough, J. and Sankaran, K.* (2004). An updated version of DOLOP with functional assignments to predicted lipoproteins.

24. Anantharaman, V., Madan Babu, M., and Aravind, L. (2004) Database of proteins involved in RNA metabolism.

Referees

  1. Dr. Sarah Teichmann – PhD supervisor
MRC-Laboratory of Molecular Biology
Hills Road, Cambridge CB2 2QH, UK
Email: /
  1. Dr. Cyrus Chothia – Second PhD supervisor
MRC-Laboratory of Molecular Biology
Hills Road, Cambridge CB2 2QH, UK
Email:
  1. Prof. P. Balaram
Molecular Biophysics Unit
Indian Institute of Science (IISc)
Bangalore 560012, INDIA
Email: /
  1. Dr. K. Sankaran
Assistant Professor
Centre for Biotechnology
Anna University, Chennai 600025, INDIA
Email: