List of publications

======================= In preparation =============================

A course-grained model of DNA for supercoil dynamics in single-molecule experiments , M. Öztürk, M. Sayar, and A. Kabakçıoğlu. In preperation.

======================= Submitted / Published =======================

NEUROD2 regulates Stim1 expression and store-operated calcium entry in cortical neurons, G. Guner, G. Guzelsoy, F.S. Isleyen, G.S. Sahin, C. Akkaya, E. Bayam, E.I. Kotan, A. Kabakcioglu and G. Ince-Dunn, eNeuro, 4(1), 0255 (2017).

Coherent organization in gene regulation: a study on six networks, Neşe Aral and A. Kabakçıoğlu, Physical Biology, 13, 026006 (2016).

Function changing mutations in glucocorticoid receptor evolution correlate with their relevance to mode coupling, B. Kav, M. Öztürk, and A. Kabakçıoğlu, Proteins: Structure, Function, and Bioinformatics, 84, 655-665 (2016).

Genome-wide target analysis of NeuroD2 reveals new insights into regulation of cortical projection neuron identity, E. Bayam, G.S. Şahin, G. Güzelsoy, G. Güner, A. Kabakçıoğlu, G. Ïnce-Dunn, BMC Genetics, 16, 681 (2015).

Coherent regulation in yeast's cell cycle network, N. Aral, A. Kabakçıoğlu, Physical Biology, 12, 036002 (2015).

Mode coupling points to functionally important residues in myosin II, O. Varol, D. Yuret, B. Erman, and A. Kabakçıoğlu, Proteins: Structure, Function, and Bioinformatics, 82(9), 1777 (2014).

Denaturation of circular DNA: supercoils and overtwist, A. Bar, A. Kabakçıoğlu, and D. Mukamel, Phys. Rev. E, 86(6), 061904 (2012).

Deep spin-glass hysteresis area collapse and scaling in the d=3 +/-J Ising model, O. Sarıyer, A. Kabakçıoğlu, and A. N. Berker, Phys. Rev. E, 86(4), 041107 (2012).

Constrained thermal denaturation of DNA under fixed linking number, A. Bar, A. Kabakçıoğlu, and D. Mukamel, CEJP, 10(3), 582 (2012).

Macroscopic loop formation in circular DNA denaturation, A. Kabakçıoğlu, A. Bar, and D. Mukamel, Phys. Rev. E, 85(5), 051919 (2012).

Denaturation of circular DNA: Supercoil mechanism , A. Bar, A. Kabakçıoğlu, and D. Mukamel, Phys. Rev. E, 84(4), 041935 (2011).

Anharmonicity and mode-coupling in a fluctuating protein, A. Kabakçıoğlu, M. Gur, D. Yuret, and B. Erman, Physical Biology, 7, 046005 (2010).

Twist/writhe partitioning in a coarse-grained DNA minicircle model , M. Sayar, B. Avşaroğlu, and A. Kabakçıoğlu, Phys. Rev. E, 81, 041916 (2010).
Also selected for the May 1, 2010 issue of Virtual Journal of Biological Physics Research

New results on the melting thermodynamics of a circular DNA chain , A. Kabakçıoğlu, E. Orlandini, and D. Mukamel, Physica A, 389 (15), 3002-3006 (2010).
MIT Symposium article dedicated to A. Nihat Berker on his 60th Birthday.

Anomalies in the transcriptional regulatory network of the yeast Saccharomyces Cerevisiae , M. Tuğrul and A. Kabakçıoğlu, Journal of Theoretical Biology, 263 (3), 328-336 (2010).

Robustness of Transcriptional Regulation in Yeast-like Model Boolean Networks , M. Tuğrul and A. Kabakçıoğlu, Int. J. Bifur. Chaos, 20 (3), 929-935 (2010).
"Modelling and Computation on Complex Networks", conference proceedings.

Supercoil formation in DNA denaturation , A. Kabakçıoğlu, E. Orlandini, and D. Mukamel, Phys. Rev. E 80 (1) Rapid Comm., 010903 (2009).
Also selected for publication in the July 15, 2009 issue of Virtual Journal of Biological Physics Research.

Transcriptional regulatory network topology from statistics of DNA binding sites , A. Kabakçıoğlu, Physica A 386, 764-769 (2007). Proceedings of the Pan American Scientific Institute (PASI) Conference on Disorder and Complexity.

Percolation transition in a dynamically clustered network , A. Zen, A. Kabakçıoğlu, and A.L. Stella, Phys. Rev. E 76, 026110 (2007).

The Information Coded in the Yeast Response Elements Accounts for Most of the Topological Properties of Its Transcriptional Regulation Network , D. Balcan, A. Kabakçıoğlu, M. Mungan, and A. Erzan, PLoS ONE 2(6): e501 (2007).

A scale free network hidden in the collapsing polymer , A. Kabakçıoğlu and A. L. Stella, Phys. Rev. E 72, 055102 (2005).

Analytical solution of a stochastic content-based network model , M. Mungan, A. Kabakçıoğlu, D. Balcan, and A. Erzan, J. Phys. A: Math. Gen. 38 9599 (2005).

Pseudoknots in a Homopolymer, A. Kabakçıoğlu and A. L. Stella, Phys. Rev. E 70, 011802 (2004).

Scaling Behavior of a Multiply Connected Fluctuating Interface in Two Dimensions, H. Kaya, A. Kabakçıoğlu, and A. Erzan, Fractals 11 227-232 (2003).

Connection-Length Optimization in Scale-Free Networks , S. S. Manna and A. Kabakçıoğlu, J. Phys. A: Math. Gen. 36, L279-L285 (2003).

Statistical Properties of Contact Vectors , A. Kabakçıoğlu, M. Vendruscolo, I. Kanter, and E. Domany, Phys. Rev. E 65, 41904 (2002).

Hard-Spin Mean-Field Theory: A Systematic Derivation and Exact Correlations in One Dimension , A. Kabakçıoğlu, Phys. Rev. E 61, 3366 (2000).

Delocalization Transition of a Rough Adsorption-Reaction Interface , H. Kaya, A. Kabakçıoğlu, and A. Erzan, Phys. Rev. E 61, 1102 (2000).

Strongly Asymmetric Tricriticality of Quenched Random-Field Systems , A. Kabakçıoğlu and A.N. Berker, Phys. Rev. Lett. 82, 2572 (1999).

Hard-Spin Mean-Field Theory, A.N. Berker, A. Kabakçıoğlu, R.R. Netz, and M.C. Yalabık, Tr. J. of Physics 18, 354 (1994).

Closed-Form Solutions and Free Energy of Hard-Spin Mean-Field Theory of a Fully Frustrated System , A. Kabakçıoğlu, A.N. Berker, and M.C. Yalabık, Phys. Rev. E 49, 2680 (1993).

Phase Transitions in Anisotropic Tetrahedral Ising Lattice, A. Kabakçıoğlu and M.C. Yalabık, Tr. J. of Physics 18, 404 (1994).