Publications, Presentations and Abstracts

Selected Publications
Selected Presentations / Abstracts

Selected Publications:

1. Bagga, P. (2008). Bioinformatics approaches for studying Untranslated Regions of mRNAs. In: Wilusz, J. ed. Methods in Molecular Biology Series: Post-Transcriptional Gene Regulation. The Humana Press Inc., Totowa New Jersey. pp. 1-21.

2. Kikin, O., Zappala, Z., D'Antonio, L., and Bagga, P. (2007-08). GRSDB2 and GRS_UTRdb: Databases of Quadruplex Forming G-rich Sequences in pre-mRNAs and mRNAs. Nucleic Acids Research. doi: 10.1093/nar/gkm982. (Special database issue). 36(suppl_1): D141-D148.

3. Kikin, O., D’Antonio, L., and Bagga, P.S. (2006). QGRS Mapper: A web-based server for predicting G-quadruplexes in nucleotide sequences. Nucleic Acids Research (Special Web Server Issue). 34: W676-W682.

4. Kostadinov, R., Malhotra, N., Viotti, M., Shine, R., D’Antonio, L., and Bagga, P.S. (2006) GRSDB: A database of quadruplex forming G-rich sequences in alternatively processed mammalian pre-mRNA sequences. Nucleic Acids Research (Special database issue). 34: D119-D124.

5. Bagga, P.S. (2005) Online Bioinformatics Laboratory. [online: web], Last updated April 2006, cited June 2006, URL: http://phobos.ramapo.edu/~pbagga/binf/binf_online_lab/frame_online_lab.htm

6. D’Antonio, L., and Bagga, P.S. (2004) Computational Methods for Predicting Intramolecular G-quadruplexes in Nucleotide Sequences. Computational Systems Bioinformatics, CSB 2004. Proceedings. 2004 IEEE , 16-19 Aug. 2004. Pages:561-562.

7. Arhin, G.K., Boots, M., Bagga, P.S., Milcarek, C., and Wilusz, J. (2002) Downstream Sequence Elements with Different Affinities for the hnRNP H/H’ Protein Influence the Processing Efficiency of Mammalian Polyadenylation Signals. Nucleic Acids Res. 30: 1842-1850.

8. Francis, M.A./Bagga*, P.S., Athwal, R.S. and Rainbow, A.J. (2001) Partial complementation of the DNA repair defects in cells from Xeroderma Pigmentosum groups A, C, D and F but not G by the denV gene from bacteriophage T4. Photochem. Photobiol. 72: 365-373.
   * First two authors contributed equally to this work.

9. Walter, J. and Bagga, P.S. (2000) Bioinformatics Resources on the Internet. [online: web], Last updated April 2005, cited 9 Dec. 2005, URL: http://phobos.ramapo.edu/~pbagga/binf/binf_res/binf_int_res.htm

10. Bagga, P.S. and Wilusz, J. (1999) Northwestern Screening of Expression Libraries. In: Haynes, S.R. ed. Methods in Molecular Biology Series : RNA-Protein Interaction Protocols,. The Humana Press Inc. Totowa New Jersey. pp. 245-256.

11. Bagga, P.S. , Arhin, G.K. and Wilusz, J. (1998) DSEF-1 is a member of the hnRNP H family of RNA binding proteins and stimulates pre-mRNA cleavage and polyadenylation. Nucleic Acids Research. 26: 5343-5350.

12. Francis, M.A. / Bagga*, P.S., Athwal, R.S. and Rainbow, A.J. (1997) Incomplete complementation of the DNA repair defect in Cockayne Syndrome cells by the denV gene from bacteriophage T4 suggests a deficiency in base excision repair. Mut. Res. 385: 59-74.
    * First two authors contributed equally to this work.

13. Ford, L.P., Bagga, P.S. and J. Wilusz (1997). The poly (A) tail inhibits the assembly of a 3' to 5' exonuclease in an in vitro RNA stability system. Mol. Cell. Biol. 17(1):398-406.

14. Bagga, P.S., Ford, L.C., Chen. F. and Wilusz, J. (1995). The G-Rich auxiliary downstream element has distinct sequence and position requirements and mediates efficient 3' end pre-mRNA processing through a trans-acting factor. Nucleic Acids Research. 23:1625-1631.

15. Ende, N., Ponzio, N.M., Giuliani, D., Ende, M., Bagga, P.S., Godyn, J. and Athwal, R.S. (1995) The effect of human cord blood on SJL/J mice after chemoablation and irradiation and its possible clinical significance. Immunol. Invest. 24:999-1012.

16. Bagga, P.S., Sandhu, D.K. and Sharma, S. (1991). Effect of exogenous cyclic AMP on catabolite repression of cellulase formation in Aspergillus nidulans. Acta Biotechnologica. 11:395-402.

17. Sharma, S., Sandhu D.K. and Bagga, P.S. (1991). Physical characterization of isozymes of endo-beta-1,4- glucanase and beta-1,4-glucosidase from Aspergillus species. FEMS Microbiol. Lett. 79:99-104.

18. Bagga, P.S., Sandhu D.K. and Sharma S. (1990). Purification and characterization of cellulolytic enzymes produced by Aspergillus nidulans. J. Appl. Bacteriol. 68:61-68.

19. Sharma, S., Sandhu, D.K. and Bagga, P.S. (1990). Isozyme polymorphism of endo-beta-1,4-glucanase in Aspergillus nidulans. Biochem. Genet. 28: 21-29.

20. Sharma, S., Bagga, P.S. and Sandhu, D.K. (1990). Qualitative and quantitative changes in beta-1,4- glucosidase accompanying growth of Aspergillus nidulans. J. Basic Microbiol. 30: 363-370.

21. Bagga, P.S., Sandhu, D.K. and Sharma, S. (1989). Catabolite repression of cellulase production in Aspergillus nidulans. Proc. Biochem. 24:41-45.

22. Bagga, P.S., Sharma, S. and Sandhu, D.K. (1989). Development related changes in the production and expression of endo-beta-1,4-glucanase in Aspergillus nidulans. Genome 32:288-292.

23. Sandhu, D.K., Wadhwa, V. and Bagga, P.S. (1989). Use of lytic enzymes for protoplast production in Trichoderma reesei QM9414. Enzyme Microb. Technol. 11:21-25.

24. Sandhu, D.K., Bawa, S. and Bagga, P.S. (1989). Optimization of protoplast production from Trichoderma harzianum. Ind. J. Exp. Biol. 27: 180-181.

25. Sharma S., Sandhu, D.K. and Bagga, P.S. (1988). Isozyme polymorphism of beta-glucosidase in Aspergillus nidulans. Biochem. Genet. 26:331-342.

26. Sandhu, D.K., Bagga, P.S. and Sharma S. (1987). Cellulase production by catabolite repression resistant mutants of Aspergillus nidulans. Proceedings of the 4th European Congress of Biotechnology, Vol. 1, pp. 490-492, Amsterdam, Netherlands.

27. Sandhu, D.K., Sharma, S. and Bagga, P.S. (1987). Expression of endo-beta-1,4-glucanases in a developmental mutant of Aspergillus nidulans. Proceedings of the 4th European Congress of Biotechnology. Vol. 3, pp. 533-536, Amsterdam, Netherlands.

28. Bagga, P.S. and Sandhu D.K. (1987). Cellulase formation by Aspergillus nidulans. J. Ferment. Technol. 65:635-642.

29. Sandhu, D.K., Bagga, P.S. and Singh,S. (1985). Cellulolytic activity of thermophillous fungi isolated from soil. Kavaka. 13: 21-31.

Selected Presentations / Abstracts:

1. Lichay, J, and Bagga, P.S. (2008). Conserved G-Quadruplexes May Regulate The Expression of Mammalian MECP2 Gene Involved in Autism. Northern New Jersey JSHS: Junior Science and Humanities Symposium. Rutgers School of Engineering, New Brunswick, NJ.
   Note: This poster presentation won the First prize at the Symposium.

2. Zappala, Z., Kikin, O., D’Antonio, L., and Bagga, P.S. (2008). QGRS Mapper2: A suite of Computational tools for Comprehensive analysis of G-Quadruplexes in mRNAs and pre-mRNAs. TAS/SSHS Student Research Symposium, Ramapo College of New Jersey, New Jersey, USA.

3. Vasilev, V., Kikin, O., D’Antonio, L., and Bagga, P.S. (2007). Alternatively processed sites in apoptotic genes are associated With special G-quadruplex motifs. Annual MACUB conference. New York, USA.
   Note: This presentation won the First prize at the conference.

4. Melissa H.C., Higgs, G., Tolentino, A., D’Antonio, L., and Bagga, P.S. (2007). G-quadruplexes are conserved near rna processing sites of proto-oncogenes. Chemical and Biological Sciences Research Symposium, University of Maryland, Baltimore County, MD, USA.
   Note: This presentation won the First prize in its category at the symposium.

5. Zappala, Z., D’Antonio, L., and Bagga, P.S. (2007). QGRS-UTR Mapper: A Web based program for prediction of G-quadruplexes in mRNA untranslated regions. The 15th annual international conference on Intelligent Systems for Molecular Biology (ISMB), International Society for Computational Biology (ISCB), Vienna, Austria.

6. Tolentino, A., Melissa H.C., Kikin, O., D’Antonio, L., and Bagga, P.S. (2007) Phylogenetics of G-quadruplexes mapped near RNA processing sites of mammalian genes. Student Research Symposium, Ramapo College of New Jersey, NJ, USA.

7. Zappala, Z., D’Antonio, L., and Bagga, P.S. (2007). A Bioinformatics tool for analyzing G-quadruplexes in the mRNA untranslated regions.The Annual ECSC Student Symposium, Saint Mount Vincent College, NY, USA.

8. Kikin, O, Kostadinov, R., Malhotra, N., Viotti, M., D’Antonio, L., and Bagga, P.S. (2006). Web-Based computational tools for predicting G-quadruplexes in mammalian genes. The 14th annual international conference on Intelligent Systems for Molecular Biology (ISMB), International Society for Computational Biology (ISCB), Fortaleza, Brazil.

9. Malhotra N, Viotti M, Kostadinov R, Shine R, D’Antonio L., and Bagga P.S. (2006). Development of GRSDB, a database of quadruplex forming G-rich sequences in alternatively processed mammalian pre-mRNA sequences. The 17th Annual SJU Sigma Xi/60th Annual ECSC Student Symposium, Saint Joseph's University, Philadelphia, PA, USA.

10. Kikin, O, D’Antonio, L., and Bagga, P.S. (2006). A Web-based software suite for predicting G-quadruplex structures in genomic sequences, The 17th Annual SJU Sigma Xi/60th Annual ECSC Student Symposium, Saint Joseph's University, Philadelphia, PA, USA.

11. Malhotra, N., Kostadinov, R., Viotti, M., Shine, R., D’Antonio, L., and Bagga, P.S. (2005). Development of GRSDB, a database of quadruplex forming G-Rich sequences in alternatively processed mammalian pre-mRNA sequences. Chemical and Biological Sciences Research Symposium, University of Maryland, Baltimore County, MD, USA.

12. Kostadinov, R., Iqbal, F., Votti, M., D’Antonio, L., and Bagga, P.S. (2005) Distribution of G-Quadruplex Forming Sequences Near RNA Processing Sites of Alternatively Processed Mouse Transcripts. RNA Processing Meeting of the RNA Society, Banff, Canada.

13. Kostadinov, R., D’Antonio, L., and Bagga, P.S. (2005) Development of Bioinformatics Tools for Data-mining and Analysis of G-quadruplex Forming Sequences in Mammalian Transcripts. Student Research Symposium, Ramapo College of New Jersey, NJ, USA.

14. Kostadinov, R., D’Antonio, L., and Bagga, P.S. (2004) Development Of Computational Tools For Predicting G-Quadruplex Forming Motifs In Mammalian Transcripts. Chemical and Biological Sciences Research Symposium, University of Maryland, Baltimore County, MD, USA.
    Note: This presentation won the First prize at the symposium.

15. D’Antonio, L., and Bagga, P.S. (2004) Computational Methods for Predicting Intramolecular G-quadruplexes in Nucleotide Sequences. IEEE Computational Systems Bioinformatics Conference, Stanford University, Stanford, CA, USA.

16. Cabral, C., Kazmi, M., Bhatia, S., Kostadinov, R. and Bagga, P.S. (2004). Analysis of Differentially Processed Mouse Transcripts Associated With Conserved ‘G’-Rich Elements. Student Mini Symposium, Ramapo College of New Jersey, NJ, USA.

17. Kostadinov, R., Dancik, G., Shine, R., D’Antonio, L. and Bagga, P.S. (2004). Development Of A Software Tool And A Database For Analysis Of G-Quadruplex Forming Sequences In Mammalian Genome. Student Mini Symposium, Ramapo College of New Jersey, NJ, USA.

18. Cabral, C., Kazmi, M., Bhatia, S., Kostadinov, R. and Bagga, P.S. (2003). Bioinformatics Analysis Of ‘G’-Rich Elements In Differentially Processed Mouse Transcripts. Chemical and Biological Sciences Research Symposium, University of Maryland, Baltimore County, MD, USA.

19. Kostadinov, R., Dancik, G., Shine, R., D’Antonio, L. and Bagga, P.S. (2003). Development of Bioinformatics Tools for Analysis of Conserved Regulatory Sequences in Mammalian Pre-mRNAs. Chemical and Biological Sciences Research Symposium, University of Maryland, Baltimore County, MD, USA.
    Note: This presentation won the Second prize at the symposium.

20. Dancik, G., Pieris, H., Bandaranayake, R. and Bagga, P.S. (2003). Prediction of Potential ‘G’-Rich elements near Processing Sites in Human pre-mRNAs. RNA Processing Meeting of the RNA Society, Vienna, Austria.

21. Dancik, G. and Bagga, P.S. (2002). Development of a Prototype Bioinformatics Program for Mapping Conserved Elements in Genomic Sequences. Chemical and Biological Sciences Research Symposium, University of Maryland, Baltimore County, MD, USA.
    Note: This presentation won the Second prize at the symposium.

22. Pieris, H., Weise-Riccardi, S., Bandaranayake, R. and Bagga, P.S. (2002). Genomic Distribution of a Conserved ‘G’-Rich Element That May Be Involved In RNA-Processing Site Selection. Chemical and Biological Sciences Research Symposium, University of Maryland, Baltimore County, MD, USA.

23. Dancik, G. and Bagga, P.S. (2002). Development of Bioinformatics Software Tool for Mapping Conserved GRS Elements in human pre-mRNAs. Annual MACUB conference. New York, USA.

24. Pieris, H., Weise-Riccardi, S., Bandaranayake, R. and Bagga, P.S. (2002). A ‘G’ rich Element Conserved In Human Pre-mRNA’s May be Involved In RNA Processing Site Selection. Annual MACUB conference. New York, USA.
    Note: This presentation won the First prize at the conference.

25. Pieris, H., Moharita, A., Mimaryan, G., Johnson, M., Touleughian, M., and Bagga, P. (2002). A ‘G’-rich sequence is conserved near RNA processing sites in human pre-mRNAs. Beyond Genome: Bioinformatics and Genome Research, San Diego, CA, USA.

26. Pieris, H., Moharita, A., Mimaryan, G., Johnson, M., Touleughian, M., and Bagga, P. (2002) Distribution of A Conserved Sequence near RNA Processing Sites of Human Pre-mRNAs. Annual Meeting of "American Association for Advancement of Science" (AAAS), Boston, MA, USA.

27. Moharita, A., Mimaryan, G., Pieris, H., Degirmen, A., Touleughian, M. and Bagga, P.S. (2001). Bioinformatics analysis of Human Genes for a 'G-Rich Sequence' found near splice sites. Annual MACUB conference. New Jersey, USA.

28. Mimaryan, G., Moharita, A., Pieris, H., Degirmen, A., Touleughian, M. and Bagga, P.S. (2001). Bioinformatics analysis of a conserved sequence found in 5' Cap and poly(A) regions of human pre-mRNAs. Annual MACUB conference. New Jersey, USA.
    Judged the First Prize Winning Presentation

29. Walter, J. and Bagga, P.S. (2000). A rich, annotated collection of bioinformatics related resource links on the world wide web. Annual MACUB conference. New York, USA.

30. Barnes, K., Peiris, T., Yalamanchilli, R., Walter, J. and Bagga, P. S. (2000). A strategy for Site-specific mutagenesis of a human recombinant protein, DSEF-1, an auxiliary cleavage-polyadenylation factor. Annual MACUB conference. New York, USA.

31. Boots, M., Arhin, G.K., Lutz, C.S., Bagga, P.S., Milcarek, C., and Wilusz, J. (2000). HnRNPH.H' and F may be antagonistic factors that affect the processing of numerous mammalian polyadenylation signals. RNA Processing Meeting of The RNA Society. Wisconsin, USA.

32. Francis, M.A. / Bagga, P.S*., Athwal, R.S. and Rainbow, A.J. (1998). Partial complementation of DNA repair deficiency by endonuclease V in Xeroderma Pigmentosum groups A, C and D but reduced in F and G. 26th Annual meeting of American Society for Photobiology. Snowbird, Utah, USA.
    * First two authors contributed equally to this work.

33. Bagga, P.S. Arhin, G. and Wilusz, J. (1997). DSEF-1 Stimulates cleavage and polyadenylation of mammalian pre-mRNAs. RNA Processing Meeting of The RNA Society. Banff, Canada. Eukaryotic mRNA Processing meeting. Cold Spring Harbor Laboratory, New York, USA. Aug. 1997.

34. Ford, L.P., Bagga, P.S. and Wilusz, J. (1996). The mechanism of RNA stabilization by the poly(A) tail. RNA Processing Meeting of The RNA Society. Wisconsin, USA.

35. Chen, F., Bagga, P.S., and Wilusz, J. (1996). Analysis of downstream core and auxiliary elements of the mammalian polyadenylation signal. RNA Processing Meeting of The RNA Society. Wisconsin, USA.

36. Ford, L.P., Bagga, P.S. and Wilusz, J. (1996). Identification of the mechanism of poly(A) tail stabilization of mRNA using a novel in vitro system. Annual meeting of New Jersey Commission on Cancer Research, New Jersey, USA.

37. Bagga, P.S. and Wilusz, J. (1995). A conserved G-rich sequence is recognized by a novel site specific ribonuclease activity. Annual meeting of New Jersey Commission on Cancer Research, New Jersey, USA.

38. Bagga, P.S., Qian, Z. and Wilusz,J. (1994). Site specific cleavage mediated by a common G-Rich element. RNA Processing Meeting of The RNA Society. Madison, Wisconsin, USA.

39. Qian , Z., Bagga, P.S., Chen, F. and Wilusz, J. (1994). The role of G-Rich and U-Rich sequences in efficient polyadenylation. RNA Processing Meeting of The RNA Society. Madison, Wisconsin, USA.

40. Bagga, P.S. and Athwal, R.S. (1992). Complementation of the DNA repair defect in Xeroderma Pigmentosum and Cockayne Syndrome cells by bacteriophage T4 gene denV. 42nd Annual meeting of The American Society of Human Genetics. San Francisco, California, USA.

41. Bagga, P.S., Singh, I. and Athwal, R.S. (1991). Introduction of bacteriophage T4 endonuclease V gene (denV) into Cockayne Syndrome cells can complement UV induced DNA damage. AACR Conference on "Cellular Responses to Environmental DNA damage". Banff, Alberta, Canada.

42. Kaur, G.P., Bagga, P.S., Rinaldy, A., Lloyd, R.S. and Athwal, R.S. (1991). Two gene hypothesis for DNA repair defect in XP-A: Identification of second gene on human chromosome 8. Proceedings of the 8th International Congress of Human Genetics, Vol. 49(4), p. 409, Washington D.C., USA.

43. Kaur, G.P., Bagga,P.S. and Athwal R.S. (1990). Relationship of gene dosage and DNA repair in XP cells. 41st Annual Meeting of The American Society of Human Genetics, Cincinnati, Ohio, USA.

44. Bagga, P.S., Sandhu, D.K. and Sharma, S. (1988). Role of cyclic AMP in catabolite repression of cellulase biosynthesis in Aspergillus nidulans. Genome 30(suppl.):51.

45. Sandhu, D.K., Bagga, P.S. and Sharma, S. (1988). Regulation of cellulase formation in Aspergillus nidulans and its catabolite repression resistant mutants. 8th International Conference on Global Impacts of Applied Microbiol. and International Conference on Applied Biology and Biotechnology, Hong Kong.

46. Sharma, S., Sandhu, D.K. and Bagga, P.S. (1988). Isozyme polymorphism of endo-beta 1,4-glucanase in natural populations of Aspergillus nidulans. Genome. 30(Suppl.):357.

47. Sandhu, D.K., Bagga P.S. and Sharma, S. (1988). Proteases may be involved in catabolite repression of cellulase formation: Evidence from derepressed mutants of Aspergillus nidulans. 8th International Biotechnology Symposium, Paris, France.

48. Sandhu, D.K., Sharma, S. and Bagga, P.S. (1986). Genetic variation of isozymes of endo-beta-1,4-glucanases in natural populations of Aspergillus nidulans. 27th AMI Conference, Nagpur, India.

49. Sandhu, D.K. and Bagga, P.S. (1986). Role of proteases during catabolite repression of cellulase biosynthesis in Aspergillus nidulans. XIVth International Congress of Microbiology, Manchester, U.K.

50. Sandhu, D.K., Sharma, S. Bagga P.S. and Gohalwar C.S. (1985). Developmental expression and genetic variability of isozymes of endo-glucanases of Aspergillus nidulans Advances in Fermentation, UK.

51. Sandhu, D.K. and Bagga P.S. (1984). Localization and induction of cellulases of Aspergillus nidulans. 25th AMI Conference, G.B.P.U.T., Pantnagar, India.