Alkan Kabakçıoğlu

Koç University — Turkey

Biochemistry, Genetics and Molecular Biology · Life Sciences

10h-index349citations66works1.32yr avg
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Research Topics

DNA and Nucleic Acid Chemistry(12), Protein Structure and Dynamics(11), Theoretical and Computational Physics(11), Gene Regulatory Network Analysis(11), Bioinformatics and Genomic Networks(10)

Publications66 total

Two-Dimensional Latent Space Manifold of Brain Connectomes Across the Spectrum of Clinical Cognitive Decline
Bioengineering·2025Open Access
Neuromodulation via Krotov-Hopfield Improves Accuracy and Robustness of RBMs
arXiv (Cornell University)·2025Open Access
Hotter Is Not Faster for a Melting RNA Hairpin
Physical Review Letters·2025· 1 citedOpen Access
Hotter isn't faster for a melting RNA hairpin
arXiv (Cornell University)·2024Open Access
Reorganization of brain connectivity across the spectrum of clinical cognitive decline
Neurological Sciences·2024· 3 citedOpen Access
Siamese Graph Convolutional Network quantifies increasing structure-function discrepancy over the cognitive decline continuum
Computer Methods and Programs in Biomedicine·2024· 1 cited
Disentangled Attention Graph Neural Network for Alzheimer’s Disease Diagnosis
Lecture notes in computer science·2024· 4 cited
A quantum Otto engine with shortcuts to thermalization and adiabaticity
New Journal of Physics·2023· 14 citedOpen Access
A Quantum Otto Engine with Shortcuts to Thermalization and Adiabaticity
arXiv (Cornell University)·2023Open Access
Machine learning in and out of equilibrium
arXiv (Cornell University)·2023· 1 citedOpen Access
Proof for Minimum Sensitivity of Nested Canalizing Functions, a Fractal Bound, and Implications for Biology
Physical Review Letters·2022· 3 citedOpen Access
Critical dynamics in biological Boolean networks follows from symmetric response to input genes
TURKISH JOURNAL OF PHYSICS·2022Open Access
Nested canalizing functions minimize sensitivity and simultaneously promote criticality
arXiv (Cornell University)·2021· 1 citedOpen Access
Terminal neuron localization to the upper cortical plate is controlled by the transcription factor NEUROD2
Scientific Reports·2019· 19 citedOpen Access
Tension propagation during DNA hairpin folding
Journal of Statistical Mechanics Theory and Experiment·2019· 1 cited
Terminal neuron localization to the upper cortical plate is controlled by the transcription factor NEUROD2
2019Open Access
Zippering dynamics of an RNA hairpin: Role of helicity
Bulletin of the American Physical Society·2019
Role of Helicity in DNA Hairpin Folding Dynamics
Physical Review Letters·2018· 7 citedOpen Access
NEUROD2 Regulates<i>Stim1</i>Expression and Store-Operated Calcium Entry in Cortical Neurons
eNeuro·2017· 25 citedOpen Access
Coherent organization in gene regulation: a study on six networks
Physical Biology·2016· 3 citedOpen Access
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Frequent Co-authors

Gizem Guzelsoy(7), Gulayse Ince-Dunn(7), David Mukamel(7), Efil Bayam(6), Gulcan Semra Sahin(6), Gökhan Güner(6), Ayşe Erzan(4), Deniz Yüret(4), Amir Bar(4), Huaping Li(4), Burak Acar(4), Enzo Orlandini(3), Attilio L. Stella(3), Burak Erman(3), A. Nihat Berker(3), Demet Yüksel Dal(3), Hakan Gürvıt(3), Mehmet Sayar(2), Cansu Akkaya(2), Duygu Balcan(2)