Algorithmic Designs for Biomolecular Nanostructures (ALBION)

Research Output

  • 6 Article
  • 2 Conference contribution
  • 1 Review Article
  • 1 Doctoral Thesis
2020

A comparison of deterministic and stochastic approaches for sensitivity analysis in computational systems biology

Simoni, G., Vo, H. T., Priami, C. & Marchetti, L., 23 Mar 2020, In : BRIEFINGS IN BIOINFORMATICS. 21, 2, p. 527-540 14 p.

Research output: Contribution to journalReview ArticleScientificpeer-review

Open Access
File
1 Citation (Scopus)
6 Downloads (Pure)

RuleDSD: A rule-based modelling and simulation tool for DNA strand displacement systems

Gautam, V., Long, S. & Orponen, P., 2020, Proceedings of the 13th International Joint Conference on Biomedical Engineering Systems and Technologies: Volume 3 BIOINFORMATICS. De Maria, E., Fred, A. & Gamboa, H. (eds.). p. 158-167 10 p.

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

Open Access
File
42 Downloads (Pure)
2019

A computational framework for DNA sequencing microscopy

Hoffecker, I. T., Yang, Y., Bernardinelli, G., Orponen, P. & Högberg, B., 4 Sep 2019, In : Proceedings of the National Academy of Sciences. 116, 39, p. 19282-19287 6 p., 1821178116.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
File
25 Downloads (Pure)

A Critical Comparison of Rejection-Based Algorithms for Simulation of Large Biochemical Reaction Networks

Thanh, V. H., 1 Aug 2019, In : Bulletin of Mathematical Biology. 81, 8, p. 3053-3073 21 p.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
File
4 Citations (Scopus)
99 Downloads (Pure)
2018

Algorithmic Design of Biomolecular Nanostructures

Mohammed, A., 2018, Aalto University. 168 p.

Research output: ThesisDoctoral ThesisCollection of Articles

Open Access

Algorithmic design of cotranscriptionally folding 2D RNA origami structures

Mohammed, A., Orponen, P. & Pai, S., 31 May 2018, Unconventional Computation and Natural Computation: 17th International Conference, UCNC 2018, Fontainebleau, France, June 25-29, 2018, Proceedings. Stepney, S. & Verlan, S. (eds.). p. 159-172 (Lecture Notes in Computer Science; vol. 10867).

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

Open Access
File
142 Downloads (Pure)

Design methods for 3D wireframe DNA nanostructures

Orponen, P., Mar 2018, In : Natural Computing. 17, 1, p. 147-160

Research output: Contribution to journalArticleScientificpeer-review

Open Access
File
6 Citations (Scopus)
115 Downloads (Pure)

Effects of design choices on the stiffness of wireframe DNA origami structures

Benson, E., Mohammed, A., Rayneau-Kirkhope, D., Gådin, A., Orponen, P. & Högberg, B., 25 Sep 2018, In : ACS Nano. 12, 9, p. 9291-9299 9 p.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
File
10 Citations (Scopus)
145 Downloads (Pure)

Efficient anticorrelated variance reduction for stochastic simulation of biochemical reactions

Vo, T., Sep 2018, In : IET SYSTEMS BIOLOGY.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
File
140 Downloads (Pure)

Efficient finite-difference method for computing sensitivities of biochemical reactions

Thanh, V. H., Zunino, R. & Priami, C., 1 Oct 2018, In : Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences. 474, 2218, p. 1-20

Research output: Contribution to journalArticleScientificpeer-review

File
1 Citation (Scopus)
10 Downloads (Pure)