Degree Institution: University of Illinois
Degree: Ph.D. Biophysics and Computational Biology 1996
Dr. Cynthia Gibas received the Ph.D. in Biophysics and Computational Biology from University of Illinois at Urbana-Champaign in 1996. She subsequently worked as a bioinformatics analyst and programmer at the National Center for Supercomputing Applications. In 1999, she took a faculty position at Virginia Tech and was involved in the development of their Bioinformatics graduate programs and the initial formation of the Virginia Bioinformatics Institute. In 2005, she moved to UNC Charlotte. Her expertise is in genomic data analysis, visualization and integration with experience in analysis of next-gen sequencing data, genome assembly, comparative genomics, transcriptomics, molecular biophysics, and molecular modeling. Google Scholar Profile
Dr. Gibas’ current research is focused on development of automated methods for probe and target selection and microarray data analysis. Her research group is developing analytical methods that will take into account the biophysical properties of molecules involved in the array experiment. This work attempts to connect the real physical behavior of molecules to microarray experiment outcomes, and to eliminate confounding factors based on accurate models of molecular behavior. Microarrays are now so commonly used that providing new methods and standards for their use impacts broadly across many fields of molecular biology research. Long oligonucleotide microarrays the class of arrays that we are studying, are increasingly commonly used, and yet it is not known whether the parameters used to model hybridization reactions are valid in the microarray context. Complete hybridization of each target molecule to its intended probe is taken for granted, in a milieu where many competing binding scenarios may be equally valid. Dr. Gibas’ major funding is from the NIH; the project is titled “Biophysical Optimization of Oligonucleotide Microarrays”.
Dr. Gibas’ other research interests include development of devices for measuring hybridization in real time, application of visual analytics approaches to comparative genomics, and development of accurate molecular diagnostics.
DNA Microarray Analysis
DNA Microarray Experiment Design
A Harrison, H Binder, A Buhot, CJ Burden, E Carlon, C Gibas, LJ Gamble, A … Physico-chemical foundations underpinning microarray and next-generation sequencing experiments. Nucleic Acids Research. 2013.
A Price, R Kosara, C Gibas. Gene-RiViT: A visualization tool for comparative analysis of gene neighborhoods in prokaryotes. Biological Data Visualization (BioVis), 2012 IEEE Symposium on, 57-62. October 14, 2012.
AA Cain, R Kosara, CJ Gibas. GenoSets: Visual Analytic Methods for Comparative Genomics. PloS one 7 (10), e46401. October 3, 2012.
SS Morrison, T Williams, A Cain, B Froelich, C Taylor, C Baker-Austin, D… Pyrosequencing-based comparative genome analysis of Vibrio vulnificus environmental isolates. PloS one 7 (5), e37553. May 25, 2012.
C Gibas. Analytics approaches for the era of 10,000* genomes* and counting. Bioinformatics Research and Applications, 99-101, 2012.
C Gibas, SS Morrison, A Cain, C Baker-Austin, JD Oliver. Entire genome sequence of E-genotypes of Vibrio vulnificus biotype 1 strains.
RZ Gharaibeh, AA Fodor, CJ Gibas. Accurate estimates of microarray target concentration from a simple sequence-independent Langmuir model. PLoS One 5 (12), e14464. December 30, 2010.
LM Zahn, X Ma, NS Altman, Q Zhang, PK Wall, D Tian, CJ Gibas, R Gharaibeh … Comparative transcriptomics among floral organs of the basal eudicot Eschscholzia californica as reference for floral evolutionary developmental studies. Genome biology 11 (10), R101. October 15, 2010.
RZ Gharaibeh, JM Newton, JW Weller, CJ Gibas. Application of equilibrium models of solution hybridization to microarray design and analysis. PloS one 5 (6), e11048. June 10, 2010.
RZ Gharaibeh, AA Fodor, CJ Gibas. Background correction using dinucleotide affinities improves the performance of GCRMA. BMC bioinformatics 9 (1), 452. October 23, 2010.
RZ Gharaibeh, AA Fodor, CJ Gibas. Software note: using probe secondary structure information to enhance Affymetrix GeneChip background estimates. Computational Biology and Chemistry 31 (2), 92-98. April 30, 2007.
V Ratushna, D Sturgill, S Ramamoorthy, S Reichow, Y He, R Lathigra, N … Molecular targets for rapid identification of Brucella spp. BMC microbiology 6 (1), 13. February 22, 2006.
RK Karanam, A Ravindran, A Mukherjee, C Gibas, AB Wilkinson. Using fpga-based hybrid computers for bioinformatics applications. Xilinx Xcell Journal 58, 80-83, 2006.
VG Ratushna, JW Weller, CJ Gibas. Secondary structure in the target as a confounding factor in synthetic oligomer microarray design. BMC genomics 6 (1), 31. March 8, 2005.
VG Ratushna, JW Weller, CJ Gibas. Incorporation of Target RNA Secondary Structure Parameter into Synthetic Oligomer Probe Design.
A Kaluszka, C Gibas. Interactive gene-order comparison for multiple small genomes. Bioinformatics 20 (18), 3662-3664. December 12, 2004.
A Kaluszka, C Gibas. Genome Organization Analysis Tool. December 2004.
SM Halling, C Gibas, S Boyle, I López-Goñi, I Moriyón. Comparative genomics of Brucella melitensis, B. suis, and B. abortus. in: Frontier in the Molecular and Cellular Biology of Brucella (Ignacio Lopez-Goni et al., eds.), 85-102. Horizon Scientific Press, 2004.
C Gibas, D Sturgill, J Weller. GenoMosaic: on-demand multiple genome comparison and comparative annotation. Bioinformatics and Bioengineering, 2003. Proceedings. Third IEEE Symposium on Bioinformatics and Bioengineering. March 10, 2003, 158.
C Gibas, P Jambeck. Introduction à la bioinformatique (Concepts fondamentaux et outils logiciels). O’Reilly Editions. January 2002.
C Gibas, P Jambeck, H Mizushima, 水島洋. Jissen baio infomatikusu: genomu kenkyu no tameno konpyuta sukiru. Orairi Japan. 2002.
C Gibas, P Jambeck. Introduction à la bioinformatique. O’Reilly Editions. 2002.
C Gibas, P Jambeck, K Kumpf. Einfübrung in die Praktische Bioinformatik. O’Reilly Editions. 2002.
C Gibas, P Jambeck. Developing bioinformatics computer skills. Cambridge, MA: OReilly and Associates, April 23, 2001.
C Gibas, P Jambeck, C de Amorin Machado. Desenvolvendo Bioinformática: ferramentas de software para aplicações em biologia. Campus. 2001.
CJ Gibas, P Jambeck, S Subramaniam. Continuum electrostatic methods applied to pH-dependent properties of antibody–antigen association. Methods 20 (3), 292-309, March 31, 2000.
S Herrgård, CJ Gibas, S Subramaniam. Role of an electrostatic network of residues in the enzymatic action of the Rhizomucor miehei lipase family. Biochemistry 39 (11), 2921-2930, March 21, 2000.
CJ Gibas, S Subramaniam, JA McCammon, BC Braden, RJ Poljak. pH dependence of antibody/lysozyme complexation. Biochemistry 36 (50), 15599-15614, December 16, 1997.
C Gibas, S Subramaniam. Knowledge-based design of a soluble bacteriorhodopsin. Protein engineering 10 (10), 1175-1190, October 1, 1997.
CJ Gibas, S Subramaniam. Explicit solvent models in protein pKa calculations. Biophysical journal 71 (1), 138, July 1996.
M Blackwell, C Gibas, S Gygax, D Roman, B Wagner. The plastoquinone diffusion coefficient in chloroplasts and its mechanistic implications. Biochimica et Biophysica Acta (BBA)-Bioenergetics 1183 (3), 533-543, January 4, 1994.
L Nedbal, C Gibas, J Whitmarsh. Light saturation curves show competence of the water splitting complex in inactive photosystem II reaction centers. Photosynthesis research 30 (2), 85-94, December 1, 1991.