Welcome, you are visiting at a not so recent home page of sarath (Sarath Chandra Janga). For an updated one, please click here. I am a Phd student in Molecular (Systems) Biology at MRC Laboratory of Molecular Biology , Darwin College, University of Cambridge, UK. I have previously worked at the Laboratory of Computational Genomics, Center for Genomic Sciences , UNAM, Cuernavaca, Mexico before starting my doctoral work at cambridge.

And this is me myself , some time back at niagara falls...

 

I did my Bachelors and Masters from Indian Institute of Technology(IIT) Delhi from 1998-2003 in Bio-chemical Engineering and Biotechnology focussing on Computational Genomics in my masters thesis.My current research can be put into Genomics and Gene regulation although now and then i keep trying other areas like Proteomics and Theoretical Biology. More precisely though not strictly limited I work in the following areas :

•  Understanding gene regulatory mechanisms in eukaryotic organisms at several distinct levels especially in the context of epigenetics and chromosomal organization.

•  Evolution, prediction and organization of operons and regulons in prokaryotes.

•  Understanding gene regulatory networks and their general topological properties in prokaryotes and eukaryotes.

•  Functional relationships between gene products to improve annotation strategies using genomic context.

•  Integrating diverse kinds of biological interaction datasets like protein-protein, regulatory and signal transduction pathways to understand systems level aspects of regulation.

My webpage is under continous construction :) so if you wish to know in more detail about me or my background then I suggest you have a look at my CURRICULUM VITAE in html or pdf format or drop a mail to (sarath AT mrc-lmb dot cam dot ac dot uk) if you have any particular question.

 

Peer reviewer for journals/conferences

•  Program chair for the Third International Student Council Symposium at ISMB (2007, Austria )

•  Program chair for the Second International Student Council Symposium at ISMB (2006, Brazil )

•  Organizing and Review committee member of Biosysbio (Bioinformatics, Synthetic and Systems Biology conference) (2007, U.K)

•  First Canadian Student Conference on Biomedical Computing (CSCBC) (2006, Canada )

•  IEEE Computational Systems Bioinformatics conference (2005, USA )

•  First International Students Symposium at ECCB, Madrid (2005, Spain )

•  Nucleic Acids Research

•  Bioinformatics

•  BMC Systems Biology

•  FEBS letters

•  Genome Biology

•  Journal of Biotechnology

•  Journal of Molecular Biology

•  Bioinformation

•  Reviewed grants for Czech Science Foundation.

 

Publications (published, in review and in preparation)

1) Janga, S.C., Moreno-Hagelsieb, G.(2004). Conservation of adjacency as evidence of paralogous operons. Nucleic Acids Res. 2004 Oct 11;32(18):5392-7 (PDF) (PUBMED)

2) Menchaca-Mendez, R.*, Janga, S.C.* & Collado-Vides, J. (2005).The Network of Transcriptional Interactions Imposes Linear Constrains in the Genome. OMICS: A Journal of Integrative Biology Jun 2005, Vol.9, No. 2: 139-145. (* Joint first authors) (PDF) (PUBMED )

3) Janga, S.C., Collado-Vides, J.,Moreno-Hagelsieb, G.(2005). Nebulon: a system for the inference of functional relationships of gene products from the rearrangement of predicted operons. Nucleic Acids Res. 2005 May 2;33(8):2521-30(PDF) (PUBMED) (Supplementary Material) (Web interface of Nebulon)

4) Martínez-Antonio, A., Janga, S.C., Salgado, H.,Collado-Vides, J .(2006). Internal sensing machinary directs the activity of the regulatory network in Escherichia coli. Trends in Microbiology, 2006 Vol.14, No. 1, 22-27 (appeared in the cover page of January Issue) (PDF) (PUBMED) (Supplementary Material)

5) González, V.,Santamaria, R.I.,Bustos P.,Hernández-González, I.,Medrano-Soto, A.,Moreno-Hagelsieb, G.,Janga, S.C.,Ramírez, M.A.,Jimenez-Jacinto, V.,Collado-Vides, J.,Dávila, G.,(2006) The partitioned Rhizobium etli genome: Genetic and metabolic redundancy in seven interacting replicons. Proc. Natl. Acad. Sci. U S A. 103(10): 3834-9, 2006 (PDF) (PUBMED) (Open Access article) (Web access to the Genome Sequence and RetliDB at Center for Genomic Sciences)

6) Moreno-Hagelsieb, G., Janga, S.C., (2007). Prokaryotic-wide gold standards and the effect of redundancy on the number of high-quality predictions using phylogenetic profiles. Proteins: Structure, Function, and Bioinformatics, 2007 (PDF) (PUBMED)

7) Janga, S.C., Huerta, A.M., Lamboy, W.F., Moreno-Hagelsieb, G.(2006). The distinctive signatures of DNA regions upstream both transcription unit boundaries and operon junctions. Nucleic Acids Res. 2006 August 12;34(14):3980-3987 (PDF) (PUBMED) (Supplementary Material)

8) Lozada-Chávez, I., Janga, S.C., Collado-Vides, J.(2006). Bacterial regulatory networks are extremely flexible in evolution. Nucleic Acids Res. 2006 July 13;34(12):3434-3445 (PDF) (PUBMED) (Supplementary Material)

9) Moreno-Campuzano,S., Janga, S.C., Perez-Rueda, E. (2006). Identification and analysis of DNA-binding Transcription Factors in Bacillus subtilis and other Firmicutes- A genomic approach. BMC Genomics . 2006 Jun 13;7(1):147 (PDF) (PUBMED) (Supplementary Material available online at BMC genomics)

10) Janga, S.C.,Salgado, H., Collado-Vides, J.,Martínez-Antonio, A. (2007). Internal versus external effector and transcription factor gene pairs differ in their relative chromosomal position in Escherichia coli. Journal of Molecular Biology, 2007 Vol. 368(1):263-72 (PDF) (PUBMED)

11) Janga, S.C., Perez-Rueda, E. (2007). Comparison of TF families in two model organisms reveals a lineage specific-expansion of transcriptional regulatory machinery (Submitted).

12) Janga, S.C. (2007). Prediction and evolution of transcription factors and their evolutionary families in prokaryotes BMC Systems Biology, 2007, 1(Suppl 1):P3 (tutorial presentation as part of the proceedings of the BioSysBio conference) (PDF)

13) Salgado, H., Martínez-Antonio, A.,Janga, S.C. (2007). Conservation of Transcriptional Sensing Systems in prokarya: A perspective from Escherichia coli. Febs letters, 2007 Vol. 581:3499-3506 (PDF) (PUBMED)

14) Janga, S.C., Collado-Vides, J. (2007). Structure and evolution of gene regulatory networks in microbial genomes. Research in Microbiology, 2007 (Featured on the cover page of the issue) (PDF) (PUBMED)

15) Janga, S.C., Salgado, H., Martínez-Antonio, A.,Collado-Vides, J. (2007). Co-ordination logic of sensing machinery in the transcriptional regulatory network of Escherichia coli. Nucleic Acids Research, 2007 (PDF) (PUBMED)

16) Gehlenborg, N., Corpas , M., Janga, S.C. (2007). Highlights from the Third International Society for Computational Biology Student Council Symposium BMC Bioinformatics, 2007 (PDF) (PUBMED)

17) Janga, S.C., Segura-Salazar, J., Moreno-Hagelsieb, G. (2008). OperomeDB: A comprehensive resource of predicted operon structures in complete prokaryotic genomes, (To be Submitted)

18) Hu, P., Janga, S.C., Butland, G. et. al (2008). Functional Atlas of the Uncharacterized Protein Repertoire of Escherichia coli. ( Submitted to Cell)

19) Janga, S.C., Collado-Vides, J., M. Madan Babu (2008). Evidence for the influence of nuclear organization in the organization of genes in eukaryotic chromosomes. (Submitted to Nature Genetics)

20) Janga, S.C., Salgado, H., Martínez-Antonio, A. (2007). Scale-free transcriptional regulatory network: is it encoded in the genome ? (Under review at Trends in Genetics)

21) Martínez-Antonio, A., Janga, S.C., Thieffry , D. (2008). Functional organization of E.coli transcriptional regulatory network ( Submitted to Journal of Molecular Biology )

22) Janga, S.C., Salgado, H., Martínez-Antonio, A. (2008). Combinatorial control and relative genome organization of transcription factors in bacterial regulatory networks. (To be Submitted)

23) Treviño-Quintanilla, L.,Salgado, H., Martinez-Flores, I., Collado-Vides, J., Janga, S.C. (2008). Regulation and interplay of sigma and anti-sigma factors in Escherichia coli. (to be submitted)

 

Poster Presentations (in reverse chronological order)

1) Plasticity of transcriptional regulatory machinery revealed from the comparison of the reportoires of regulators in two model organisms. (Poster as PNG image)
Sarath C Janga and Ernesto Perez-Rueda
ISMB(Intelligent systems for Molecular Biology), August 2006

2) Understanding operon recombinations in multi-replicon genomes: A perspective from Rhizobium etli . (Poster as PNG image)
Sarath C Janga, Julio Collado-Vides , and Gabriel Moreno-Hagelsieb
ICSB(International Conference on Systems Biology), October 2005

3) Internal Sensing Machinery directs the activity of the regulatory network in Escherichia coli . (Poster as PNG image)
Julio Collado-Vides, Sarath C Janga , Heladia Salgado and Agustino Martinez-Antonio
ICSB(International Conference on Systems Biology), October 2005

4) Nebulon: a system for the inference of functional relationships of gene products from the rearrangement of predicted operons (Poster as PNG image)
Sarath C Janga, Julio Collado-Vides and Gabriel Moreno-Hagelsieb
ISMB, June 2005

5) No evidence for relation between co-regulation and transcriptional regulatory interactions in the evolution of regulatory networks. (Poster as PNG image)
Maribel Hernandez Rosales and Sarath C Janga
RECOMB, May 2005

6) The Complete Genome Sequence of Rhizobium etli. (Poster as PNG image)
Víctor González, Patricia Bustos, Rosa I. Santamaría, Ismael L. Hernández-González, Arturo Medrano -Soto, Sarath C Janga, Gabriel Moreno-Hagelsieb, Miguel A. Ramírez, Rosa E. Gómez, José L. Fernández, Julio Collado-Vides and Guillermo Dávila.
6 th European Nitrogen Fixation Conference, 25 th -28 th August 2004

7) Gene Ontology Network of Interactions among Operons in E.coli and B.subtilis. (Poster as PNG image)
Sarath C Janga, Ricardo Menchaca-Mendez, Cristhian Avila-Sanchez and Julio Collado-Vides
ISMB, August 2004

8) Finding modules using network motifs as building blocks. (Poster as PNG image)
Ricardo Menchaca-Mendez, Sarath C Janga, Cristhian Avila-Sanchez and Julio Collado-Vides
ISMB, August 2004

9) Inference of Biological Modules in the Escherichia coli. (Poster as PNG image)
Cristhian Avila-Sanchez, Sarath C Janga, Agustino Martínez-Antonio,Ricardo Menchaca-Mendez and Julio Collado-Vides.
ISMB, August 2004

10) A Study of Paralogous Operons. (Poster as PNG image)
Gabriel Moreno-Hagelsieb and Sarath C Janga
Poster Presented at HUGO Human Genome Meeting, Cancun , Mexico , April 27-30 2003

11) Gene Order Conservation in S.cerevisiae.
Sarath C Janga and G.P.Agarwal
Presented at Biohorizon 2003 and was adjudged the best poster

 

Contributed Book Chapters

•  Sarath Chandra Janga and M. Madan Babu ( Invited book chapter on transcriptional regulatory networks for Cambridge University Press (Ed: Michele Vendruscolo, Department of Chemistry, University of Cambridge )

 

Organizing committee member of conferences

1) Organizing committee member of the First Internal Student Council Symposium held at ECCB, Madrid 2005.

2) Program chair for the Second International Student Council Symposium (http://www.iscbsc.org/scs2.htm ) held at ISMB-06, Fortaleza.

3) Organizing committee member of BioSysBio conference (http://www.biosysbio.com) at Manchester, 2007.

4) Program chair for the Third International Student Council Symposium (http://www.iscbsc.org/scs3.htm ) held at ISMB-07, Vienna.

5) Program chair for the Fourth International Student Council Symposium (http://www.iscbsc.org/scs4.htm ) to be held at ISMB-08, Toronto.

 

Memberships

1) Member of All India Biotech. Association

2) Member of the International Society for computational Biology (ISCB) and ISCB-SC. Have been actively involved in the student council activities of the International Society for Computational Biology especially been leading the Events team to organise different events at the annual conference of the society, ISMB.Currently Vice-chair for the ISCB-SC.

3) Actively involved in the forum discussions of the bioinformatics association of india held online.

 

Photos (Outdated- coming up..)

When i am not working on this little machine i like visiting places. Here are some of the pics which i managed to collect and put them together though there are many which are still to be excavated from piles and piles.....:)

1) Lab..My place

2) Visit to Dagstuhl seminar , Germany (July 2004)

3) Some pics. from a backpacking trip with couple of friends in Germany, Switzerland, Italy, France, Belgium, Netherlands (July-August 2004)

4) ISMB-ECCB-04 at Glasgow, England and some places in england (August 2004)

5) My lab members and photos on different occasions can be seen here on Romualdo Zayas' home.

6) Trip to south of Mexico... (to appear)

7) Research stay in canada at WLU (July-August 2005) (to appear)

8) Visit to Brazil in August 2006

9) Misc. collection.

 

Misc. stuff & URLs

Some of my old friends from IIT do maintain blogs and you can browse them and post your comments.

http://almostastronaut.blogspot.com/

http://bewda.blogspot.com/

* I did teach part of an introductory bioinformatics course to students enrolled in Bachelors in Genomic Sciences and you can find the course content from the link below. Please feel free to let me know your comments if you happen to browse through the slides.

http://tikal.ccg.unam.mx/~sarath/bioinformatics/

 

Last updated: 10-03-08

 

  Visitors since August 2006

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