Nitin Bhardwaj's homepage

Nitin Bhardwaj

Ph.D.
266 Whitney Ave. BASS 426
Yale University
New Haven, CT 06511, USA
E-mail: nbhardwaj at gmail dot com

Research Interests Education Publications Traveling Photography Other interests

Research Interests

Biological networks and hierarchies
Protein structures and motions
Social networks and its effects

Education

Ph.D. in Computational Biology and Bioinformatics,

University of Illinois at Chicago, Chicago, Aug 2003 - December 2007
B. Tech in Chemical Engineering, Indian Institute of Technology, Bombay, India, July 1999 - July 2003

Publications

Journals

Shou C, Bhardwaj N , Lam HY, Yan KK, Kim PM, Snyder M, Gerstein MB. Measuring the evolutionary rewiring of biological networks. PLoS Comput Biol. 2011, Jan 6;7(1):e1001050.
Euskirchen GM, Auerbach RK, Davidov E, Gianoulis TA, Zhong G, Rozowsky J, Bhardwaj N , Gerstein MB, Snyder M. Diverse Roles and Interactions of the SWI/SNF Chromatin Remodeling Complex Revealed Using Global Approaches. PLoS Genet. 2011, Mar;7(3):e1002008. Epub 2011 Mar 3..
Bhardwaj N , Kim, P, Gerstein MB. Rewiring of Transcriptional Regulatory Networks: Hierarchy, Rather Than Connectivity, Better Reflects the Importance of Regulators. Science Signaling. 2010, 3, ra79 .
Bhardwaj N , Carson MB, Abyzov A, Yan KK, Lu H, Gerstein MB. Analysis of combinatorial regulation: scaling of partnerships between regulators with the number of governed targets. PLoS Comput Biol. 2010 May 27;6(5):e1000755.
Yan KK, Fang G, Bhardwaj N , Alexander RP, Gerstein M. Comparing genomes to computer operating systems in terms of the topology and evolution of their regulatory control networks. Proc Natl Acad Sci U S A. 2010 May 18;107(20):9186-91. Epub 2010 May 3.
Bhardwaj N , Yan KK, Gerstein MB. Analysis of diverse regulatory networks in a hierarchical context shows consistent tendencies for collaboration in the middle levels. Proc Natl Acad Sci U S A. 2010 Apr 13;107(15):6841-6.
Fang G, Bhardwaj N , Robilotto R, Gerstein MB. Getting started in gene orthology and functional analysis. PLoS Comput Biol. 2010 Mar 26;6(3):e1000703.
Bhardwaj N , Gerstein M, Lu H. Genome-wide sequence-based prediction of peripheral proteins using a novel semi-supervised learning technique. BMC Bioinformatics. 2010 Jan 18;11 Suppl 1:S6.
Yoon Y, Tong J, Lee PJ, Albanese A, Bhardwaj N , Källberg M, Digman MA, Lu H, Gratton E, Shin YK, Cho W. Molecular basis of the potent membrane-remodeling activity of the epsin 1 N-terminal homology domain. J Biol Chem. 2010 Jan 1;285(1):531-40. Epub 2009 Nov 1.
Meerschaert K, Tun MP, Remue E, De Ganck A, Boucherie C, Vanloo B, Degeest G, Vandekerckhove J, Zimmermann P, Bhardwaj N , Lu H, Cho W, Gettemans J. The PDZ2 domain of zonula occludens-1 and -2 is a phosphoinositide binding domain. Cell Mol Life Sci. 2009 Dec;66(24):3951-66. Epub 2009 Sep 22.
Cheng C, Bhardwaj N , Gerstein M. The relationship between the evolution of microRNA targets and the length of their UTRs. BMC Genomics. 2009 Sep 14;10:431.
Bhardwaj N , Gerstein M. Relating protein conformational changes to packing efficiency and disorder. Protein Sci. 2009 Jun;18(6):1230-40.
Bhardwaj N , Lu H. Co-expression among constituents of a motif in the protein-protein interaction network. J Bioinform Comput Biol. 2009 Feb;7(1):1-17.
Manna D, Bhardwaj N , Vora MS, Stahelin RV, Lu H, Cho W. Differential roles of phosphatidylserine, PtdIns(4,5)P2, and PtdIns(3,4,5)P3 in plasma membrane targeting of C2 domains. Molecular dynamics simulation, membrane binding, and cell translocation studies of the PKCalpha C2 domain. J Biol Chem. 2008 Sep 19;283(38):26047-58.
Bhardwaj N , Stahelin RV, Zhao G, Cho W, Lu H. MeTaDoR: a comprehensive resource for membrane targeting domains and their host proteins. Bioinformatics. 2007 Nov 15;23(22):3110-2.
Langlois RE, Carson MB, Bhardwaj N , Lu H. Learning to translate sequence and structure to function: identifying DNA binding and membrane binding proteins. Ann Biomed Eng. 2007 Jun;35(6):1043-52.
Bhardwaj N , Lu H. Residue-level prediction of DNA-binding sites and its application on DNA-binding protein predictions. FEBS Lett. 2007 Mar 6;581(5):1058-66.
Bhardwaj N , Stahelin RV, Langlois RE, Cho W, Lu H. Structural bioinformatics prediction of membrane-binding proteins. J Mol Biol. 2006 Jun 2;359(2):486-95.
Bhardwaj N , Langlois RE, Zhao G, Lu H. Kernel-based machine learning protocol for predicting DNA-binding proteins. Nucleic Acids Res. 2005 Nov 10;33(20):6486-93.
Chakrabarti S, Anand AP, Bhardwaj N , Pugalenthi G, Sowdhamini R. SCANMOT: searching for similar sequences using a simultaneous scan of multiple sequence motifs. Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W274-6.
Bhardwaj N , Lu H. Correlation between gene expression profiles and protein-protein interactions within and across genomes. Bioinformatics. 2005 Jun 1;21(11):2730-8.
Bhardwaj N , Langlois R, Zhao G, Lu H. Structure Based Prediction of Binding Residues on DNA-binding Proteins. Conf Proc IEEE Eng Med Biol Soc. 2005;3:2611-4.
Chakrabarti S, Bhardwaj N , Anand PA, Sowdhamini R. Improvement of alignment accuracy utilizing sequentially conserved motifs. BMC Bioinformatics. 2004 Oct 28;5:167.

Book Chapters

Bhardwaj, N, Källberg M, Cho W, Lu H. MeTaDoR: Online Resource and Prediction Server for Membrane Targeting Peripheral Proteins. In: Lipidomics. Armstrong D, ed. Totowa, New Jersey: The Humana Press Inc.; 2008.