The Center for Computational and Integrative Biology (CCIB)
 

About the CCIB

Overview

What is computational and integrative biology? At a general level, computational biology is the study of biological systems using tools from traditional biomedical disciplines such as biology, chemistry and physics integrated with methods for analysis of interacting complex systems frommathematics and computer science. In particular, computational analysis is a prominent aspect of integrative biology, which analyzes a large number of interacting biological variables to obtain a fuller overall understanding of complex biological systems. The goal of integrative biology is to extract broad quantitative organizational principles that can relate interactions of component parts to macroscopic behaviors of the complex system. Examples of areas of investigation particularly amenable to an integrative approach include ecological and physiological systems. The Rutgers' Center for Computational and Integrative Biology (CCIB) emphasizes the development of mathematical models for these biological systems, application of the models to data from laboratory and field investigations, the adjustment of the model based on its fit to and predictive value for experimental results and the subsequent modification of the experimental design based on the predictions of the model.

Research Directions

The CCIB is comprise of over 40 nationally and internationally recognized scholars and researchers, many of whom have received prestigious awards and honors. The CCIB regularly receives research funding from the National Science Foundation (NSF) and the National Institutes of Health (NIH). Most recently, the CCIB has received a Major Research Instrumention (MRI) award from the NSF to construct a high-level computational cluster to support modeling projects. Some of the CCIB's current research directions include:

  • Biological Rhythms (circadian and ultradian)
  • Biofuels and sustainable energy
  • Predictive toxicology and pharmacology
  • Metagenomics
  • Movement of large groups and complex systems

The CCIB is always interested in exploring new research directions and is happy to lend its computational expertise to external collaborators. Please contact us if you are interested in discussing current or potential projects.

Scientific Working Groups

The CCIB faculty have been actively developing internal collaborative efforts, which have further expanded with the advent of the new Graduate Program. A number of focal points of these efforts have served as a basis for the formation of interdisciplinary Scientific Working Groups (SWGs). The SWGs provide further formal structure for the CCIB and its research directions. The CCIB Scientific Working Groups include:

Group 1 - Physiological
Group 2 - Metagenomic, ecological, biofuels
Group 3 - Biomedical
Group 4 - Mechanisms & pathways

The boundaries between the groups are not rigid; they define broad themes with possible overlaps. The SWGs represent the mechanism by which graduate students receive both peer and faculty mentorship and are exposed to multi-disciplinary research in biological signaling in different contextual/application areas. By combining faculty members from at least two different departments into thematic groups, the CCIB aims to foster research topics that will create linkages between diverse disciplines. This effort is reinforced through the graduate curriculum that serves to educate all CCIB graduate students with a basic understanding of the various topics related to biological signaling.

Collaborative Relationships

In addition to our core and contributing faculty, the CCIB has a number of external collabortive relationships locally, nationally, and internationally. Collaboration with the CCIB takes many forms. Many of our partners provide summer placements for our Graduate Program. Other partners collaborate with our faculty through research, both academic and within industry. Finally, the CCIB offers instructional collaboration in the form of the CCIB seminar series, professional development workshops for practising researchers, and visiting scholar positions. Some of our current collaborative partners include:

  • The Coriell Institute
  • Fox Chase Cancer Center
  • The University of Medicine and Dentistry of New Jersey
  • BioNJ
  • The Max Planck Institute
  • University College London
  • Cooper University Hospital
  • Rowan University Medical School
  • The Wistar Institute

 

 

 

 

 

 

 

 

 

 

 

 

Recent Publications

The table below includes a selection of some of our faculty's recent publications.

2012  
  The evolution of BMP signaling in Drosophila oogenesis: a receptor-based mechanism, M.G. Niepielko, K. Ip, J.S. Kanodia, D. Lun, and N. Yakoby, Biophysical Journal, 102:1722-1730, 2012.
 
2011  
  Mycorrhiza, J. Dighton. In: M. Schaechter (ed) Eukaryotic Microbes, Academic Press. Pp. 73-83. 2011.
  Analysis of complex metabolic behavior through pathway decomposition, K. Ip, C. Colijn, and D. S. Lun, BMC Syst. Biol., 5:91, June 2011.
  Control of multi-hop communication networks for inter-session network coding, A. Eryilmaz, D. S. Lun, and B. T. Swapna, IEEE Trans. Inform. Theory, 57(2):1092-1110, February 2011.
  Genetic and molecular characterization of a blue light photoreceptor MGWC-1 in Magnaporth oryzae, S. Kim, P. Singh, J. Park, S. Park, A. Friedman, T. Zheng, Y-H. Lee, K. Lee, .Fungal Genet. Biol. 48:400-407, 2011.
  The Thompson-Higman monoids Mk,i :  the J-order, the D-relation, and their complexity, J.C. Birget, International J. of Algebra and Computation 21(1-2) 1 - 34, March 2011.
  An IR Study of Poly-1,4-Phenylenevinylene (PPV), the 2,5-Dimethoxy Derivative [(MeO)2-PPV], and their Corresponding Xanthate Precursor Polymers and Monomers, D.Michael Byler, Y. Patel, G. A. Arbuckle-Keil, Spectrochimica Acta Part A, 79, 118-126, 2011.
 

A computational model for signaling pathways in bounded small-world networks corresponding to brain size. S. Man, D. Hong, M.A. Palis, J.V. Martin, Neurocomputing2011.

  Pattern formation by a moving morphogen source, J. J. Zartman, L. S. Cheung, M. G. Niepielko, C. Bonini, B. Haley, N. Yakoby, and S. Y. Shvartsman. Physical Biology, 2011.
  BMP signaling dynamics in the follicle cells of multiple Drosophila species, M. G. Niepielko, Y. Hernáiz-Hernández, and N. Yakoby. Developmental Biology, 354:151-159, 2011.
  Nematic Nonocomposites with Enhanced Optical Birefringence, K. K. Vardanyan, E. D. Palazzo, and R. D. Walton, Liq. Cryst. 38 (6) 709-715, 2011.
 

Time-evolving measures and macroscopic modeling of pedestrian flow, B. Piccoli, A. Tosin, Archive for Rational Mechanics and Analysis, 199 (2011), 707-738.

2010  
 

Multiple binding sites for the general anesthetic isoflurane identified in the nicotinic acetylcholine receptor transmembrane domain, G. Brannigan, D. N. LeBard, J. Hénin, R. G. Eckenhoff, M. L. Klein, Proc. Natl. Acad. Sci. USA 107(32), 14122-14127.

  An atomistic model for simulations of the general anesthetic isoflurane, J. Hénin, G. Brannigan, W. Dailey, R. Eckenhoff, M. L. Klein, Journal of Physical Chemistry B114, 604-612.
  Systems biology approaches to understanding mycobacterial survival mechanisms. H. I. M. Boshoff and D. S. Lun. Drug Discov. Today: Dis. Mech., 7(1):e75-e82, Spring 2010. Invited paper.
 

Sensitivity analysis of permeability parameters for flows on Barcelona networks, L. Rarita, C. D'Apice, B. Piccoli, D. Helbing, Journal of Differential Equations, 249 (2010), 3110-3131.

  Neurospora, a potential fungal organism for experimental and evolutionary ecology, Lee, K. & Dighton, J.Fungal Biology Reviews 2010.

 

Awards

NSF Grant Awards
MRI: Acquisition of a High-Performance Computing Cluster for the Interdisciplinary Research in Computational and Integrative Biology #1126052 Andrey Grigoriev (PI), Kwangwon Lee, Joe Martin, Michael Palis (Co-Principal Investigators)
Q-STEP: Community of Quantitative Scientists #0856435 Joe Martin (PI), Alex Roche; Daniel Bubb; Haydee Herrera (Co-Principal Investigators)
RUI: Evolution of clitellate cocoons: regulation, secretion and ultrastructure #0843419 Dan Shain (PI)
RUI: Energy Anabolism in Glacier Ice Worms: Evolution, Mechanisms and Contribution to Cold Adaptation #0820505 Dan Shain (PI)
RUI: Thyroid Hormone Physiology in Adult Rat Brain #0724962 Joe Martin (PI); Alex Roche (co-Principal Investigator)
NIH Grant Awards
ENERGY-BASED COLD TOLERANCE IN GENETICALLY TRACTABLE EUKARYOTIC SYSTEMS 115GM093685-01R Dan Shain (PI); Nir Yakoby (co-Principal Investigator)