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Ramapo Success Story

“Teaching at Ramapo has been a fulfilling experience for me. The environment and opportunities provided at Ramapo have allowed me to develop a successful teaching philosophy and methodology. Along with a rewarding teaching experience at Ramapo, I have been able to engage in original scientific research and regularly publish in reputed peer reviewed journals, including the Oxford University Press. Much of my research at Ramapo College was performed with undergraduate students.

Ramapo College is unique in that it doesn’t have an academic department structure. This allows for highly interdisciplinary collaborations among faculty members from diverse disciplines. My scholarship has significantly benefited from collaborations with my peers from computer science and mathematics. Collaborative Bioinformatics research projects in my lab involve large scale genomic studies, particularly focusing on the regulation of human genes involved in cancer, apoptosis, and neurological abnormalities, including autism, dementia and Parkinson’s disease. Due to the very important pillar of experiential learning, Ramapo encourages faculty-student research, which is invaluable for learning and market placement. I have a passion to involve undergraduate students in my research projects. My research students have regularly co-authored publications with me and have made many award-winning presentations at national and international research conferences. The students I mentored have been accepted into doctoral programs at elite universities such as the University of Pennsylvania and Yale University, obtained jobs in international pharmaceuticals as scientists, and secured faculty positions in academic institutions.

Development of the career-oriented Bioinformatics major at Ramapo has been one of the largest and most important undertakings of my career as a faculty member so far and probably my biggest contribution to the college. In 2002, Ramapo became the first four-year college in the entire United States to have this highly desirable professional major. This achievement has helped Ramapo College stay ahead and gain reputation as a pioneer in Bioinformatics undergraduate education. I have served for 14 years as the convener of the Bioinformatics program since its inception.

Recognizing my contributions to the undergraduate education in Bioinformatics, Yale University invited me to write a manuscript at the time of the 10th anniversary of our program at Ramapo College. The manuscript was published in the Yale’s peer-reviewed journal. The article discussed the challenges of establishing such an important major and also highlighted several of our teaching methods and research initiatives, which have led to the success of this undergraduate program.”

– Paramjeet Bagga is a Professor of Biology and the Convener of Bioinformatics and first joined Ramapo in 1999. For more information, please visit Paramjeet’s Faculty Profile.

School:
School of Theoretical and Applied Science

Recent Publications

Selected Publications:
Frees, S., Menendez, C., Crum, M., and Bagga, P. (2014). QGRS-Conserve: a computational method for discovering evolutionarily conserved G-quadruplex motifs. Human Genomics. 8:8.

Bagga, P. (2012). Development of an undergraduate bioinformatics degree program at a liberal arts college. Yale J Biol Med. 85:309-21.

Menendez, C., Frees, S., and Bagga, P. (2012) QGRS-H Predictor: A Web Server for Predicting Homologous Quadruplex forming G-Rich Sequence Motifs in Nucleotide Sequences. Nucleic Acids Res. doi: 10.1093/nar/gks422. 40: W96-W103.

Bindra, R.S., Wang, J.T.L., and Bagga, P.S. (2010). Bioinformatics methods for studying microRNA and ARE mediated regulation of post-transcriptional gene expression. International Journal of Knowledge Discovery in Bioinformatics. 1: 97-112.

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.

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 Res. doi: 10.1093/nar/gkm982. (Special database issue). 36(suppl_1): D141-D148.

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.

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.

Selected Presentations/Abstracts:
Wight, H., Frees, S. and Bagga, P. (2015). Establishing a Relationship Between U-Rich Elements and G-quadruplexes Involved in Mammalian Polyadenylation. Scientista Symposium, New York, New York, USA.

Liu, M., Frees, S. and Bagga, P. (2015). A bioinformatic approach for mapping conserved regulatory U-Rich sequence motifs in the human transcriptome. TAS Student Research Symposium, Ramapo College of New Jersey, New Jersey, USA.

Wight, H., Frees, S. and Bagga, P. (2015). Relationship between cis-regulatory G-quadruplex and U-Rich sequence motifs involved in mammalian polyadenylation. TAS Student Research Symposium, Ramapo College of New Jersey, New Jersey, USA.

Mayberry, M., Frees, S., and Bagga, P.S. (2015). Using bioinformatics methods to correlate the prevalence of G-quadruplex motifs in the 5′-untranslated region with gene function. TAS Student Research Symposium, Ramapo College of New Jersey, New Jersey, USA.

Liu, M., Frees, S. and Bagga, P. (2014). Conservation of mammalian U-Rich elements involved in polyadenylation. Annual MACUB conference, Molloy College, New York, USA.

Wight, H., Frees, S. and Bagga, P. (2014). Bioinformatic approach to investigate a relationship between cis-regulatory elements involved in mammalian polyadenylation. Annual MACUB conference, Molloy College, New York, USA.

Mayberry, M., Frees, S., and Bagga, P.S. (2014). A bioinformatics method for cis-regulatory G-quadruplex motif density calculations in the 5′-untranslated regions of mammalian exomes. Annual MACUB conference, Molloy College, New York, USA.

Menendez, C., Crum, M., Frees, S., and Bagga, P.S. (2014). Exome Wide Identification of Evolutionary Conserved Cis-Regulatory G-quadruplexes Near PolyA Signals. International BAASANA (Business and Applied Science Academy) conference, Ramapo College of New Jersey, New Jersey, USA.
Note: This presentation won the First prize at the conference.

For a more complete list, please visit: http://pages.ramapo.edu/~pbagga/pub.html

Awards and Accomplishments


Fred and Florence Thomases Award for excellence in teaching and scholarship; outstanding contribution to the college/community and outstanding fulfillment of professional responsibility. Ramapo College of NJ, 2007-08.

More than 10 Faculty-Student Research awards within the last 15 years.

Education

Ph.D. School of Life Sciences, Guru Nanak Dev University, Amritsar, India. 1988
MS (Honors) School of Life Sciences, Guru Nanak Dev University, Amritsar, India. 1983
BS (Honors) School of Life Sciences, Guru Nanak Dev University, Amritsar, India. 1982

Classes Known For

Bioinformatics
Cell & Molecular Biology