L. Adleman, Q. Cheng, A. Goel, M. D. Huang, D. Kempe et al., Combinatorial optimization problems in self-assembly, Proceedings of the thiry-fourth annual ACM symposium on Theory of computing , STOC '02, pp.23-32, 2002.
DOI : 10.1145/509907.509913

URL : http://www-rcf.usc.edu/~dkempe/publications/selfassembly.pdf

L. M. Adleman, Molecular computation of solutions to combinatorial problems, Science, vol.266, issue.5187, 1994.
DOI : 10.1126/science.7973651

URL : http://www.usc.edu/dept/molecular-science/papers/fp-sci94.pdf

M. Amos and P. E. Dunne, DNA simulation of Boolean circuits, Proceedings of 3rd Annual Genetic Programming Conference, pp.679-683, 1997.

M. Amos, A. Gibbons, and P. E. Dunne, The complexity and viability of DNA. Biocomputing and emergent computation, p.97, 1997.

E. B. Baum and D. Boneh, Running dynamic programming algorithms on a DNA computer, DNA Based Computers II, vol.44, pp.77-80, 1999.
DOI : 10.1090/dimacs/044/05

URL : http://crypto.stanford.edu/~dabo/papers/biodynamic.ps.gz

R. Beigel and B. Fu, Solving intractable problems with DNA computing, Proceedings. Thirteenth Annual IEEE Conference on Computational Complexity (Formerly: Structure in Complexity Theory Conference) (Cat. No.98CB36247), p.154, 1998.
DOI : 10.1109/CCC.1998.694601

URL : http://1013seopc.eecs.uic.edu/papers/bf-dnasurvey-complexity98.PS.gz

R. Bijlani, Y. Cheng, D. A. Pearce, A. I. Brooks, and M. Ogihara, Prediction of biologically significant components from microarray data: Independently Consistent Expression Discriminator (ICED), Bioinformatics, vol.19, issue.1, pp.62-70, 2003.
DOI : 10.1093/bioinformatics/19.1.62

URL : https://academic.oup.com/bioinformatics/article-pdf/19/1/62/9732113/19062.pdf

D. Boneh, C. Dunworth, R. J. Lipton, and J. Sgall, Making DNA computers error resistant, DNA Based Computers II, vol.44, pp.163-170, 1996.
DOI : 10.1090/dimacs/044/13

URL : http://www.cs.princeton.edu/~dabo/papers/bioerror.ps.gz

D. Boneh, C. Dunworth, R. J. Lipton, and J. Sgall, On the computational power of DNA, Discrete Applied Mathematics, vol.71, issue.1-3, pp.1-3, 1996.
DOI : 10.1016/S0166-218X(96)00058-3

URL : https://doi.org/10.1016/s0166-218x(96)00058-3

S. Carroll, A complete programming environment for DNA computation, Workshop Non-Silicon Comp. NSC-1, pp.46-53, 2002.

J. Dassen, Molecular computation and splicing systems, 1996.

R. Deaton, R. C. Murphy, J. A. Rose, M. Garzon, D. R. Franceschetti et al., A DNA based implementation of an evolutionary search for good encodings for DNA computation, Proceedings of 1997 IEEE International Conference on Evolutionary Computation (ICEC '97), pp.267-271, 1997.
DOI : 10.1109/ICEC.1997.592311

S. Díaz, J. L. Esteban, and M. Ogihara, A DNA-based random walk method for solving k-SAT, pp.209-220
DOI : 10.1007/3-540-44992-2_14

G. Drakopoulos, Knowledge mining with tensor algebra. Tech. rep, 2017.

G. Drakopoulos, A. Kanavos, I. Karydis, S. Sioutas, and A. G. Vrahatis, Tensorbased semantically-aware topic clustering of biomedical documents, Computation, vol.5, issue.3, 2017.

G. Drakopoulos, A. Kanavos, and A. Tsakalidis, A Neo4j Implementation of Fuzzy Random Walkers, Proceedings of the 9th Hellenic Conference on Artificial Intelligence, SETN '16, p.SETN, 2016.
DOI : 10.1109/34.868688

G. Drakopoulos, A. Kanavos, and K. Tsakalidis, Fuzzy Random Walkers with Second Order Bounds: An Asymmetric Analysis, Algorithms, vol.11, issue.2, 2017.
DOI : 10.1137/S0895479897321362

P. E. Dunne, M. Amos, and A. Gibbons, Boolean transitive closure in DNA, 1998.

R. P. Feynman, There is plenty of room at the bottom, Engineering and science, vol.23, issue.5, pp.22-36, 1960.

B. Fu and R. Beigel, Length bounded molecular computing, Biosystems, vol.52, issue.1-3, pp.155-163, 1999.
DOI : 10.1016/S0303-2647(99)00042-8

A. Gehani and J. Reif, Micro flow bio-molecular computation, Biosystems, vol.52, issue.1-3, pp.197-216, 1999.
DOI : 10.1016/S0303-2647(99)00048-9

A. N. Gorban, K. O. Gorbunova, and D. C. Wunsch, Liquid Brain: The proof of algorithmic universality of quasichemical model of fine-grained parallelism, Neural Network World, vol.11, issue.4, pp.391-412, 2001.

D. Gusfield, Algorithms on strings, trees and sequences: Computer science and computational biology, 1997.
DOI : 10.1017/CBO9780511574931

A. Henaut and D. Contamine, Computation with DNA. Tech. rep., Rapport de recherche -Institut national de recherche en informatique et en automatique, 1996.

T. Hinze and M. Sturm, Towards an in-vitro implementation of a universal distributed splicing model for DNA computation, Proc. Theorietag pp, pp.185-189, 2000.

J. D. Hoheisel and M. Vingron, DNA chip technology. Biospektrum, vol.4, pp.17-20, 1998.

A. Kanavos, G. Drakopoulos, and A. Tsakalidis, Graph Community Discovery Algorithms in Neo4j with a Regularization-based Evaluation Metric, Proceedings of the 13th International Conference on Web Information Systems and Technologies, p.WEBIST, 2017.
DOI : 10.5220/0006382104030410

M. Y. Kao and V. Ramachandran, DNA self-assembly for constructing 3D boxes, pp.429-440, 2001.

R. M. Karp, C. Kenyon, and O. Waarts, Error-resilient DNA computation, Random Structures and Algorithms, vol.131, issue.1, pp.458-467, 1996.
DOI : 10.1006/inco.1996.0094

URL : https://hal.archives-ouvertes.fr/hal-02101766

S. Kontopoulos and G. Drakopoulos, A space efficient scheme for graph representation, 2014.

T. H. Labean, H. Yan, J. Kopatsch, F. Liu, E. Winfree et al., Construction, Analysis, Ligation, and Self-Assembly of DNA Triple Crossover Complexes, Journal of the American Chemical Society, vol.122, issue.9, pp.1848-1860, 2000.
DOI : 10.1021/ja993393e

R. J. Lipton, Speeding up computations via molecular biology, DNA Based Computers, vol.27, pp.67-74, 1995.
DOI : 10.1090/dimacs/027/05

A. Narayanan and S. Zorbalas, DNA algorithms for computing shortest paths, Proceedings of genetic programming, p.723, 1998.

M. Ogihara, Relating the minimum model for DNA computation and Boolean circuits, Proceedings of the 1st Annual Conference on Genetic and Evolutionary Computation, pp.1817-1821, 1999.

M. Ogihara and A. Ray, Circuit evaluation: Thoughts on a killer application in DNA computing Computing with Bio-Molecules. Theory and Experiments pp, pp.111-126, 1998.

M. Ogihara and A. Ray, DNA-based self-propagating algorithm for solving boundedfan-in Boolean circuits, Genetic Programming, vol.98, pp.725-730, 1998.

M. Ogihara and A. Ray, The minimum DNA computation model and its computational power. Unconventional Models of Computation pp, pp.309-322, 1998.

M. Ogihara and A. Ray, Executing parallel logical operations with DNA, Proceedings of the 1999 Congress on Evolutionary Computation-CEC99 (Cat. No. 99TH8406), pp.972-979, 1999.
DOI : 10.1109/CEC.1999.782528

URL : http://www.cs.rochester.edu/u/ogihara/research/DNA/cec.ps.gz

M. Ogihara and A. Ray, Simulating Boolean Circuits on a DNA Computer, Algorithmica, vol.25, issue.2-3, pp.239-250, 1999.
DOI : 10.1007/PL00008276

URL : http://bi.snu.ac.kr/Courses/g-ai04_2/p226-ogihara.pdf

N. Pisanti, DNA computing: A survey, Bulletin of the EATCS, vol.64, pp.188-216, 1998.

Z. F. Qiu and M. Lu, Take Advantage of the Computing Power of DNA Computers, International Parallel and Distributed Processing Symposium, pp.570-577, 2000.
DOI : 10.1007/3-540-45591-4_78

J. H. Reif, Paradigms for biomolecular computation, First International Conference on Unconventional Models of Computation, pp.72-93, 1998.

J. H. Reif, Parallel Biomolecular Computation: Models and Simulations, Algorithmica, vol.25, issue.2-3, pp.142-175, 1999.
DOI : 10.1007/PL00008272

URL : http://www.cs.duke.edu/~reif/paper/Molecular.pdf

J. H. Reif, COMPUTING: Successes and Challenges, Science, vol.296, issue.5567, pp.478-479, 2002.
DOI : 10.1126/science.1070978

J. H. Reif, The emergence of the discipline of biomolecular computation in the US, 2002.

J. H. Reif, The design of autonomous DNA nanomechanical devices: Walking and rolling DNA. Lecture notes in computer science pp, pp.22-37, 2003.
DOI : 10.1007/3-540-36440-4_3

URL : http://www.cs.duke.edu/~reif/paper/DNAmotor/DNAmotor.pub.pdf

D. Rooß, Recent developments in DNA-computing, Proceedings 1997 27th International Symposium on Multiple- Valued Logic, pp.3-9, 1997.
DOI : 10.1109/ISMVL.1997.601366

P. W. Rothemund and E. Winfree, The program-size complexity of self-assembled squares, pp.459-468, 2000.
DOI : 10.1145/335305.335358

URL : http://www.dna.caltech.edu/Papers/squares_STOC.pdf

B. Wang, Implementation of a dynamic programming algorithm for DNA Sequence alignment on the Cell Matrix architecture, 2002.

P. Wasiewicz, P. Borsuk, J. J. Mulawka, and P. Wegle´nskiwegle´nski, Implementation of data flow logical operations via self-assembly of DNA, International Parallel Processing Symposium, pp.174-182, 1999.
DOI : 10.1007/BFb0097898

H. Yan, T. H. Labean, L. Feng, and J. H. Reif, Directed nucleation assembly of DNA tile complexes for barcode-patterned lattices, Proceedings of the National Academy of Sciences, vol.8, issue.14, pp.8103-8108, 2003.
DOI : 10.1073/pnas.91.22.10747

URL : http://www.pnas.org/content/100/14/8103.full.pdf