25 papers · ranked by Valyu relevance
Alejandro Hernandez Wences, Michael C. Schatz
Genome assembly projects typically run multiple algorithms in an attempt to find the single best assembly, although those assemblies often have complementary, if untapped, strengths and weaknesses. We present our metassembler algorithm that merges multiple assemblies of a genome into a single superior sequence. We…
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…
Song Gao, Denis Bertrand, Niranjan Nagarajan
The assembly of large, repeat-rich eukaryotic genomes continues to represent a significant challenge in genomics. While long-read technologies have made the high-quality assembly of small, microbial genomes increasingly feasible, data generation can be prohibitively expensive for larger genomes. Fundamental advances in…
Juanjo Bermúdez
Genome assembly is a fundamental tool for biological research. Particularly, in microbiology, where budgets per sample are often scarce, it can make the difference between an inconclusive result and a fully valid conclusion. Identifying new strains or estimating the relative abundance of quasi-species in a sample are…
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…
Jing-Kai Fang, Yue-Feng Lin, Jun-Han Huang, Yibo Chen + 9 more
Computational biology holds immense promise as a domain that can leverage quantum advantages due to its involvement in a wide range of challenging computational tasks. Researchers have recently explored the applications of quantum computing in genome assembly implementation. However, the issue of repetitive sequences…
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…
Fabio F. de Oliveira, Leonardo A. Dias, Marcelo A. C. Fernandes
In bioinformatics, alignment is an essential technique for finding similarities between biological sequences. Usually, the alignment is performed with the Smith-Waterman (SW) algorithm, a well-known sequence alignment technique of high-level precision based on dynamic programming. However, given the massive data volume…
Caroline Rossi-Gendron, Farah El Fakih, Koyomi Nakazawa, Léa Chocron + 5 more
Self-assembly is both an advantageously spontaneous process to organize molecular or colloidal entities into synthetic functional superstructures and a key-feature of how life builds its components. However, compared to their living counterparts, synthetic materials made by self-assembly usually lack some of the…
Authors not listed
Synthetic DNA strands are programmable and biocompatible building blocks that can be combined through hybridization to form user-defined nanostructures, but their assembly traditionally requires cell-incompatible conditions, imposing a lengthy ex situ fabrication step before any application with living matter. Here we…
Nicholas Tjahjono, Evgeni Penev, Boris Yakobson
Programmable self-assembly provides a promising avenue to improve upon traditional synthesis and create multi-component materials with emergent properties and arbitrary nanoscale complexity. However, its most successful realizations utilizing DNA often use complicated arduous procedures that result in low yields. Here…
Max Doblas, Oscar Lostes-Cazorla, Quim Aguado-Puig, Cristian Iñiguez + 2 more
Pairwise sequence alignment is a core component of multiple sequencing-data analysis tools. Recent advancements in sequencing technologies have enabled the generation of longer sequences at a much lower price. Thus, long-read sequencing technologies have become increasingly popular in sequencing-based studies. However…
Yuan-Ping Pang
Cram’s supramolecular capsule Octacid4 can irreversibly and noncovalently self-assemble with small- molecule guests at room temperature, but how they self-assemble and what accelerates their assembly are open questions that hold the key to developing noncovalent irreversible complexes. This article reports 72 distinct…
Authors not listed
Artificial biomolecular nanotubes are a promising approach to build materials mimicking the capacity of the cellular cytoskeleton to grow and self-organize dynamically. Nucleic acid nanotechnology has demonstrated a variety of self-assembling nanotubes with programmable, robust features, and morphological similarities…
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…
Rituraj Borah, Karthick Raj AG, Antony Charles Minja, Sammy Verbruggen
The colloidal synthesis of functional nanoparticles have gained tremendous scientific attention in the last decades. In parallel to these advancements, another rapidly growing area is the self-assembly of these colloidal nanoparticles into greater periodic arrangements. Firstly, the organization of nanoparticles into…
Andrew Tarzia, Wentao Shan, Victor Posligua, Cameron Cox + 5 more
Heteroleptic (mixed-ligand) coordination cages are of interest as host systems with more structurally and functionally complex cavities than homoleptic architectures. The design of heteroleptic cages, however, is far from trivial. In this work, we experimentally probed the self-assembly of Pd(II) ions with binary…