### 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).