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Present Affiliations 

* MRC-LMB
* Trinity College
* University of Cambridge

Past Affiliations 

* Molecular Biophysics Unit
* Indian Institute of Science
* Center for Biotechnology
* Anna University

M. Madan Babu, PhD 
Group Leader / Investigator 
MRC-Laboratory of Molecular Biology 
Hills Road, Cambridge CB2 2QH, United Kingdom 
University of Cambridge 
madanm@mrc-lmb.cam.ac.uk  


Invited book chapters

  • Introduction to microarray data analysis - M. Madan Babu* in Computational Genomics (Ed: R. Grant), Horizon Press, U.K. PDF, Pre-reprint & supplementary material
  • Contextual inference of protein function - Aswin S. N. Seshasayee & M. Madan Babu* in Encyclopaedia of Genetics, Genomics, Proteomics and Bioinformatics (Ed: S. Subramanian), John Wiley and Sons PDF, PDF of Pre-print
  • Gene Expression Studies in Arabidopsis thaliana - a network perspective - Aswin S. N. Seshasayee*, L. Aravind & M. Madan Babu* in Floriculture, Ornamental and Plant Biotechnology: advances and topical issues (Ed: Jaime A. Teixeira da Silva), PDF
  • Chemical Molecules that Regulate Transcription and Facilitate Cell-to-Cell Communication - Arthur Wuster* and M. Madan Babu* Wiley Encyclopaedia of Chemical Biology, PDF, Supplementary material
  • General trends in the evolution of prokaryotic transcriptional regulatory networks - M. Madan Babu*, S. Balaji, L. Aravind in Genome Dynamics PDF Supplementary website
  • Evolutionary systems biology: methods to reconstruct and compare transcriptional regulatory networks - M. Madan Babu*, Benjamin Lang, L. Aravind in Methods in Molecular Biology PDF Supplementary website

All publications (* indicates corresponding author; 1 indicates joint first authors)

2009

  • Dissecting the expression dynamics of RNA-binding proteins in post-transcriptional regulatory networks - Nitish Mittal, Nilanjan Roy, M. Madan Babu and Sarath Janga. PNAS, in press.
  • The efficiency of mitochondrial electron transport chain is increased in the long-lived mrg19 Saccharomyces cerevisiae - Nitish Mittal, M. Madan Babu, Nilanjan Roy. Aging Cell, PDF.
  • Xpf and Not the Fanconi Anaemia Proteins or Rev3 Accounts for the Extreme Resistance to Cisplatin in Dictyostelium discoideum - Xiao-Yin Zhang, Judith Langenick, David Traynor, M. Madan Babu, Rob Kay, Ketan Patel. PLoS Genetics, PDF.
  • Transcriptional control of the quorum sensing response in yeast - Arthur Wuster* and M. Madan Babu*. Molecular BioSystems, PDF.
  • Genomic analysis reveals a tight link between transcription factor dynamics and regulatory network architecture - Raja Jothi*,1, S. Balaji,1, Arthur Wuster, Joshua Grochow, Joerg Gsponer, Teresa Przytycka, L. Aravind and M. Madan Babu* Molecular Systems Biology, PDF.
  • Exploiting gene deletion fitness effects in yeast to understand the modular architecture of protein complexes under different growth conditions - R. Pache, M. Madan Babu* and P. Aloy*. BMC Systems Biology, PDF.
  • Investigating transcriptional regulation: From analysis of complex networks to discovery of cis-regulatory elements - Rekin's Janky, Jacques van Helden and M. Madan Babu. Methods, PDF
  • The rules of disorder or why disorder rules - Joerg Gsponer and M. Madan Babu. Prog Biophys Mol Biol, PDF
  • The impact of genomic neighborhood on the evolution of human and chimpanzee transcriptome - Subhajyoti De*, Sarah Teichmann and M. Madan Babu*. Genome Research, PDF, Cover image.
  • Transcript stability in the protein interaction network of Escherichia coli - Sarath Chandra Janga and M. Madan Babu. Molecular BioSystems, PDF, Cover image.

2008

  • Mechanistic Insight into Site-Restricted Monoubiquitination of FANCD2 by Ube2t, FANCL, and FANCI - Arno Alpi, Paul Pace, M. Madan Babu and Ketan Patel. Molecular Cell, PDF
  • Tight regulation of intrinsically unstructured proteins: from transcript synthesis to protein degradation - Joerg Gsponer*, Matthias Futschik, Sarah Teichmann and M. Madan Babu*. Science, PDF, Supplementary material, IUP values, Perspective
  • Gene regulation in three dimensions: Implications for genome evolution and disease - M. Madan Babu*, Sarath Chandra Janga, Ines de Santiago and Ana Pombo. Current Opinion in Genetics and Development, PDF, Cover image
  • Evidence for chromosomal preference, regional bias and positional clustering of binding in transcription factors - Sarath Chandra Janga*, Julio Collado-Vides and M. Madan Babu*. PNAS, PDF, Supplementary material
  • Principles of regulation of small molecule metabolism - Aswin SN Seshasayee, Gillian Fraser, M. Madan Babu and Nicholas Luscombe. Genome Research, PDF
  • Network based approaches for linking metabolism with environment: From organismal niches to ecological communities - Sarath Chandra Janga and M. Madan Babu. Genome Biology, PDF
  • Transcriptional Regulatory Networks - Sarath Chandra Janga* and M. Madan Babu*. Networks in Biology, Cambridge University Press, in press
  • Evolutionary and temporal dynamics of transcriptional networks - M. Madan Babu. Lecture Notes in Computer Science, PDF
  • Computational approaches to study transcriptional regulation - M. Madan Babu*. Biochemical Society Transactions, PDF
  • Comparison of transcription regulatory interactions inferred from high-throughput methods: what do they reveal - S. Balaji*, L. Iyer, M. Madan Babu* and L. Aravind. Trends in Genetics, PDF
  • Chemogenomics and Biotechnology - Arthur Wuster* and M. Madan Babu*. Trends in Biotechnology, PDF
  • Solitary and repetitive binding motifs for the AP2 complex alpha-appendage in amphiphysin and other accessory proteins - L. Olesen, M. Ford, E. Schmid, Y. Vallis, M. Madan Babu, P. Li, I. Mills, H. McMahon, and G. Praefcke. Journal of Biological Chemistry, PDF
  • Conservation and evolutionary dynamics of the agr cell-to-cell communication system across firmicutes - Arthur Wuster* and M. Madan Babu*. Journal of Bacteriology, PDF, Supplementary material

2007

  • High affinity DNA binding sites for H-NS provide a molecular basis for selective silencing within proteobacterial genomes - Benjamin Lang, N. Blot, E. Bouffartigues, M. Buckle, M. Geertz, C. Gualerzi, R. Mavathur, G. Muskhelishvili, C. Pon, S. Rimsky, S. Stella, M. Madan Babu* and Andrew Travers*. Nucleic Acids Research, PDF Supplementary material.
  • Functional and Transcriptional Coherency of Modules in the Human Protein Interaction Network - M.E. Futschik, G. Chaurasia, A. Tschaut, J. Russ, M. Madan Babu and H. Herzel. Journal of Integrative Bioinformatics, in press
  • Interplay Between Network Structures, Regulatory Modes and Sensing Mechanisms of Transcription Factors in the Transcriptional Regulatory Network of E. coli - S. Balaji1*, M. Madan Babu1* and L. Aravind, Journal of Molecular Biology, PDF Supplementary material
  • Chemical Molecules that Regulate Transcription and Facilitate Cell-to-Cell Communication - Arthur Wuster* and M. Madan Babu* Wiley Encyclopaedia of Chemical Biology, PDF, Supplementary material
  • General trends in the evolution of prokaryotic transcriptional regulatory networks - M. Madan Babu*, S. Balaji and L. Aravind, Genome Dynamics PDF Supplementary website
  • Evolutionary systems biology: methods to reconstruct and compare transcriptional regulatory networks - M. Madan Babu*, Benjamin Lang and L. Aravind, Methods in Molecular Biology PDF Supplementary website
  • Investigations on CH-Pi interactions in RNA binding proteins - A. Anbarasu, S. Anand, M. Madan Babu and R. Sethumadhavan International Journal of Biological Macromolecules PDF

2006

  • Estimating the prevalence and regulatory potential of the telomere looping effect in yeast transcription regulation - Madan Babu, M.*, Balaji, S, Iyer, L.M., Aravind, L* Cell Cycle, PDF Supplementary material.
  • The natural history of the WRKY-GCM1 zinc fingers and the relationship between transcription factors and transposons - Madan Babu, M.1,*, Iyer, L.M.1,* Balaji, S, Aravind, L* Nucleic Acids Research, PDF Supplementary material.
  • Uncovering distributed robustness in protein regulatory networks - Balaji, S, Iyer, L.M., Aravind, L* and Madan Babu, M.*, Journal of Molecular Biology, PDF, Supplementary material
  • Principles of combinatorial regulation in the transcriptional regulatory network of yeast - Balaji, S.1*, Madan Babu, M.1*, Iyer, L.M., Luscombe, N.M., Aravind, L., Journal of Molecular Biology, PDF
  • Gene Expression Studies in Arabidopsis thaliana - a network perspective - Aswin S. N. Seshasayee*, L. Aravind & M. Madan Babu* in Floriculture, Ornamental and Plant Biotechnology: advances and topical issues (Ed: Jaime A. Teixeira da Silva), PDF
  • Exploring the environmental preference of non-canonical interactions in (a/b)8 barrel proteins - Chakkaravarthi, S., Madan Babu, M., Gromiha, M., Jayaraman, G. and Sethumadhavan, R., Proteins Structure Function Genetics, PDF
  • Predicting the strongest domain-domain contact in interacting protein pairs - Nye, T., Berzuini, C., Gilks, W., Madan Babu, M., and Teichmann, S.A. Statistical Applications in Genetics and Molecular Biology, PDF.
  • The HIRAN Domain and Recruitment of Chromatin Remodeling and Repair Activities to Damaged DNA - Lakshminarayan M. Iyer, M. Madan Babu, L. Aravind, Cell Cycle, PDF.
  • Evolutionary dynamics of prokaryotic transcriptional regulatory networks - M. Madan Babu*, Sarah Teichmann, and Aravind, L.,*Journal of Molecular Biology, PDF, Supplementary material, Cover image.
  • A database of bacterial lipoproteins (DOLOP) with functional assignments to predicted lipoproteins - M. Madan Babu*,1, Leena Priya, M.1, Tamil Selvan, A., Madera, M., Gough, J., and Sankaran, K.*, Journal of Bacteriology, PDF.
  • Adaptive evolution by optimizing expression levels in different environments - M. Madan Babu*, and Aravind, L., Trends in Microbiology, PDF.

2005

  • The Transcriptional Landscape of the Mammalian Genome - Carninci, P et. al., Science, PDF.
  • Discovery of the principal specific transcription factors of Apicomplexa and their implication for the evolution of the AP2-integrase DNA binding domains - Balaji, S., M. Madan Babu,, Iyer, L.M., Aravind, L. Nucleic Acids Research, PDF
  • Contextual inference of protein function - Aswin S. N. Seshasayee & M. Madan Babu* in Wiley Encyclopaedia of Genetics, Genomics, Proteomics and Bioinformatics (Ed: S. Subramanian), John Wiley and Sons PDF, PDF of Pre-print
  • The genome of the social amoeba Dictyostelium discoideum - Eichinger, L. et. al., Nature, PDF
  • The many faces of Helix-Turn-Helix domain: transcription regulation and beyond - Aravind, L., Anantharaman, V., Balaji, S., M. Madan Babu, Iyer, L.M. FEMS Microbiology Reviews, PDF
  • Statistical analysis of domains in interacting protein pairs - Nye, T., Berzuini, C., Gilks, W., M. Madan Babu, and Teichmann, S.A. Bioinformatics, PDF


2004

  • Clathrin-coated pit assembly: The AP2 complex serves as an integration hub to order the dynamic network of accessory proteins - Praefcke, GJK., Ford, MGJ., Schmid, EM., Olesen, LE., Gallop, JL., Peak-Chew, S., Vallis, Y., M. Madan Babu, Mills, IG., and Harvey T. McMahon, EMBO Journal, PDF.
  • GenCompass: a universal system to analyse gene expression for any genome - N. Luscombe* and M. Madan Babu*, Trends in Biotechnology, PDF
  • Evolution of transcriptipnal regulatory networks - M. Madan Babu, PhD thesis submitted to the University of Cambridge. Thesis adviser: Sarah Teichmann.
  • Genome analysis of regulatory network dynamics - N. Luscombe*1, M. Madan Babu*1, H. Yu, M. Snyder, S. Teichmann* and M. Gerstein*, Nature, PDF.
  • Structure and evolution of gene regulatory networks - M. Madan Babu*1, N. Lucsombe1, M. Gerstein, S. Teichmann*, Curr. Opin. Struc. Biol, PDF PDF of the cover image.
  • Gene regulatory network growth by duplication - Sarah Teichmann* and M. Madan Babu*. Nature Genetics, PDF, Supplementary material
  • Introduction to microarray data analysis - M. Madan Babu* in Computational Genomics (Ed: R. Grant), Horizon Press, U.K. PDF, Pre-reprint & supplementary material

2003

  • NCI: a server to identify non canonical interactions in protein structures - M. Madan Babu*. Nucleic Acids Research, PDF
  • Loss of sigma factors could have initiated pseudogene accumulation in the Mycobacterium leprae genome - M. Madan Babu*. Trends in Microbiology, PDF, Supplementary material.
  • Evolution of Transcription Factors and the Gene Regulatory Network in E. coli - M. Madan Babu* and Sarah A. Teichmann. Nucleic Acids Research, PDF, Supplementary material
  • Functional Determinants of Transcription Factors: Protein Families and Binding Sites - M. Madan Babu* and Sarah. A. Teichmann. Trends in Genetics PDF, Supplementary material.

2002

  • Conservation of coregulation in prokaryotes and eukaryotes - Sarah Teichmann and M. Madan Babu Trends in Biotechnonology PDF
  • DOLOP - Database of Bacterial Lipoproteins - M. Madan Babu and Krishnan Sankaran. Bioinformatics PDF
  • Shigella apyrase - a novel variant of bacterial acid phosphatases? - M. Madan Babu, S. Kamalakkannan, Y.V.B.K. Subrahmanyam and Krishnan Sankaran. FEBS Letters PDF
  • A C-H..O hydrogen bond stabilized polypeptide chain reversal motif at the C-terminus of helices in proteins - M. Madan Babu, S. Kumar Singh and P. Balaram. Journal of Molecular Biology PDF
  • Inventing polypeptide folds. Registering a helices and b strands using backbone C-H..O interactions - S. Kumar Singh, M. Madan Babu and P. Balaram. Proteins: Structure Function and Genetics, PDF.
  • Virulence factors of Bordetella pertussis - M. Madan Babu*, J. Bhargavi, S. Ranajeet Singh and S. Kumar Singh. Current Science, PDF


General Articles
  • New Strains of V. cholerae - M. Madan Babu and K. Sankaran -7th Sep 2000, The Hindu, Science and Technology Section of the Indian National Newspaper. HTML    At the site
  • Bioinformatics - Aid for Genetic Data Management and Drug Discovery - M. Madan Babu - Nov 2000, CSI Communications of Computer Society of India. HTML
  • Computer applications in new drug discovery - M. Madan Babu and J. Bhargavi - manuscript in preparation.
  • Errors in Genome Annotation - M. Madan Babu Verve 2002 (Proceedings of Biotechcellence 2002, National Level Students Symposium in Biotechnology) HTML
  • Proteomics - M. Madan Babu. Verve 2001 (Proceedings of Biotechcellence 2001, National Level Students Symposium in Biotechnology)
  • Antifreeze Proteins - M. Madan Babu. Verve 2001 (Proceedings of Biotechcellence 2001, National Level Students Symposium in Biotechnology)
  • Bioinformatics - M. Madan Babu. Verve 2000 (Proceedings of Biotechcellence 2000, National Level Students Symposium in Biotechnology) HTML

Posters Presented
  • 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 - PDF
  • Protein Families and Regulatory Patterns in the Transcription Factors of E. coli at RECOMB 2002 - 18th - 21st April 2002, Washington DC, USA PDFs
  • 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 PDFs
  • 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 PDF

Publications in Conference Proceedings
  • Protein Families and Regulatory Patterns in the Transcription Factors of E. coli at RECOMB 2002 - 18th - 21st April 2002, Washington DC, USA PDFs - 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. PDF

Undergraduate (B. Tech) Thesis
  • Analysis of C-H...O hydrogen bonding in helix terminus - Chapter I PDF
  • DATE - Database of TIM barrel enzymes - Chapter II PDF
  • Target selection for structural genomics and the structural status for the completed microbial genomes - Chapter III PDF
  • Computational identification of Chorismate mutase in the M. leprae genome - Chapter IV PDF

Summer Project Reports and Other Projects