Related papers: DNA Sequence Alignment by Window based Optical Cor…
DNA read mapping is a computationally expensive bioinformatics task, required for genome assembly and consensus polishing. It requires to find the best-fitting location for each DNA read on a long reference sequence. A novel resistive…
Motivation: Illumina DNA sequencing is now the predominant source of raw genomic data, and data volumes are growing rapidly. Bioinformatic analysis pipelines are having trouble keeping pace. A common bottleneck in such pipelines is the…
Conjugated organic molecules represent an important area of materials chemistry for both fundamental scientific exploration and technological applications. Using a genetic algorithm to computationally screen up to ~25-50 million molecules…
Deep neural networks (DNNs) and, in particular, convolutional neural networks (CNNs) have brought significant advances in a wide range of modern computer application problems. However, the increasing availability of large amounts of…
Ancestral sequence reconstruction is a key task in computational biology. It consists in inferring a molecular sequence at an ancestral species of a known phylogeny, given descendant sequences at the tip of the tree. In addition to its many…
Rapid sequencing of individual human genome is prerequisite to genomic medicine, where diseases will be prevented by preemptive cures. Quantum-mechanical tunneling through single-stranded DNA in a solid-state nanopore has been proposed for…
We introduce an algorithm for the alignment of protein- coding sequences accounting for frameshifts. The main specificity of this algorithm as compared to previously published protein-coding sequence alignment methods is the introduction of…
Dot plots are a standard method for local comparison of biological sequences. In a dot plot, a substring to substring distance is computed for all pairs of fixed-size windows in the input strings. Commonly, the Hamming distance is used…
DNA-coated particles are promising as building blocks for functional and finite-sized assemblies because they can be programmed with orthogonal interactions owing to the sequence-specific hybridization of DNA strands. To fully exploit this…
The translation of comparative genomics into clinical decision support tools often depends on the quality of sequence alignments. However, currently used methods of multiple sequence alignments suffer from significant biases and problems…
Clustering multidimensional points is a fundamental data mining task, with applications in many fields, such as astronomy, neuroscience, bioinformatics, and computer vision. The goal of clustering algorithms is to group similar objects…
Motivation: Recent advances in sequencing technologies promise ultra-long reads of $\sim$100 kilo bases (kb) in average, full-length mRNA or cDNA reads in high throughput and genomic contigs over 100 mega bases (Mb) in length. Existing…
Frameshift mutations in protein-coding DNA sequences produce a drastic change in the resulting protein sequence, which prevents classic protein alignment methods from revealing the proteins' common origin. Moreover, when a large number of…
Approximate nearest-neighbor search (ANNS) algorithms are a key part of the modern deep learning stack due to enabling efficient similarity search over high-dimensional vector space representations (i.e., embeddings) of data. Among various…
We present a new approach for solving (minimum disagreement) correlation clustering that results in sublinear algorithms with highly efficient time and space complexity for this problem. In particular, we obtain the following algorithms for…
In Computer Vision, problem of identifying or classifying the objects present in an image is called Object Categorization. It is a challenging problem, especially when the images have clutter background, occlusions or different lighting…
In recent years significant attention has been attracted to proposals which utilize DNA for nanotechnological applications. Potential applications of these ideas range from the programmable self-assembly of colloidal crystals, to biosensors…
At the core of high throughput DNA sequencing platforms lies a bio-physical surface process that results in a random geometry of clusters of homogenous short DNA fragments typically hundreds of base pairs long - bridge amplification. The…
In the past several years, the problem of genome assembly has received considerable attention from both biologists and computer scientists. An important component of current assembly methods is the scaffolding process. This process involves…
Genomic signal processing has been used successfully in bioinformatics to analyze biomolecular sequences and gain varied insights into DNA structure, gene organization, protein binding, sequence evolution, etc. But challenges remain in…