12 papers · ranked by Valyu relevance
Mohammed Sahli, Tetsuo Shibuya
Background Genome assembly is considered to be a challenging problem in computational biology, and has been studied extensively by many researchers. It is extremely difficult to build a general assembler that is able to reconstruct the original sequence instead of many contigs. However, we believe that creating…
Chengxi Ye, Zhanshan Sam Ma, Charles H Cannon, Mihai Pop + 1 more
'Douglas W Yu'] Background The very large memory requirements for the construction of assembly graphs for de novo genome assembly limit current algorithms to super-computing environments. Methods In this paper, we demonstrate that constructing a sparse assembly graph which stores only a small fraction of the observed…
Pierre-Étienne Meunier
This model has been the center of several open problems and conjectures in the last fifteen years, and the first fully general results on its computational power were only proven recently (SODA 2014). These results, as well as ours, exemplify the intricate connections between computation and geometry that can occur in…
Lila Kari, Steffen Kopecki, Pierre-Étienne Meunier, Matthew J. Patitz + 1 more
'Matthew J. Patitz' 'Shinnosuke Seki'] In the field of algorithmic self-assembly, a long-standing unproven conjecture has been that of the NP-hardness of binary pattern tile set synthesis (2-Pats). The k-Pats problem is that of designing a tile assembly system with the smallest number of tile types which will…
Zeinab Taghavi
Background Acquiring genomes at single-cell resolution has many applications such as in the study of microbiota. However, deep sequencing and assembly of all of millions of cells in a sample is prohibitively costly. A property that can come to rescue is that deep sequencing of every cell should not be necessary to…
Abhishek Sharma, Dániel Czégel, Michael Lachmann, Christopher P. Kempes + 2 more
'Christopher P. Kempes' 'Sara I. Walker' 'Leroy Cronin'] Scientists have grappled with reconciling biological evolution1,2 with the immutable laws of the Universe defined by physics. These laws underpin life’s origin, evolution and the development of human culture and technology, yet they do not predict the emergence…
Tyler G. Moore, Max H. Garzon, Russell J. Deaton, Ming Dao
Inspired by biological systems, self-assembly aims to construct complex structures. It functions through piece-wise, local interactions among component parts and has the potential to produce novel materials and devices at the nanoscale. Algorithmic self-assembly models the product of self-assembly as the output of some…
Gage Siebert, Redwan Chowdhury, Louie Slocombe, Sara Walker
Assembly theory is an experimental and theoretical framework that introduces a metrological approach to detecting life, with potential applications across diverse substrates. Its two central observables are assembly index and copy number. The assembly index is the minimum number of joining operations required to…
Austin Luchsinger, Robert Schweller, Tim Wylie
The algorithmic self-assembly of shapes has been considered in several models of self-assembly. For the problem of shape construction, we consider an extended version of the Two-Handed Tile Assembly Model (2HAM), which contains positive (attractive) and negative (repulsive) interactions. As a result, portions of an…
Andrew Winslow
Previous work by Demaine et al. (2012) developed a strong connection between smallest context-free grammars and staged self-assembly systems for one-dimensional strings and assemblies. We extend this work to two-dimensional polyominoes and assemblies, comparing staged selfassembly systems to a natural generalization of…
Felipe A. Louza, Guilherme P. Telles, Steve Hoffmann, Cristina D. A. Ciferri
'Cristina D. A. Ciferri'] Background Suffix arrays, augmented by additional data structures, allow solving efficiently many string processing problems. The external memory construction of the generalized suffix array for a string collection is a fundamental task when the size of the input collection or the data…
Moya Chen, Doris Xin, Damien Woods
We study the computational complexity of the recently proposed nubot model of molecularscale self-assembly. The model generalises asynchronous cellular automata to have non-local movement where large assemblies of molecules can be pushed and pulled around, analogous to millions of molecular motors in animal muscle…