Related papers: Anchor points for genome alignment based on Filter…

Multiple sequence alignment is a basic procedure in molecular biology, and it is often treated as being essentially a solved computational problem. However, this is not so, and here I review the evidence for this claim, and outline the…

In computational molecular biology, gene regulatory binding sites prediction in whole genome remains a challenge for the researchers. Now a days, the genome wide regulatory binding site prediction tools required either direct pattern…

We present new algorithms for the problem of multiple string matching of gapped patterns, where a gapped pattern is a sequence of strings such that there is a gap of fixed length between each two consecutive strings. The problem has…

Word alignment over parallel corpora has a wide variety of applications, including learning translation lexicons, cross-lingual transfer of language processing tools, and automatic evaluation or analysis of translation outputs. The great…

Genetic algorithms are a well-known method for tackling the problem of variable selection. As they are non-parametric and can use a large variety of fitness functions, they are well-suited as a variable selection wrapper that can be applied…

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…

A central problem in comparative genomics consists in computing a (dis-)similarity measure between two genomes, e.g. in order to construct a phylogeny. All the existing measures are defined on genomes without duplicates. However, we know…

In this paper we report on an algorithm for aligning multiple protein structures. The algorithm has been tested on a variety of inputs and it performs well in comparison to well-known algorithms for this problem.

Multiple genome alignment remains a challenging problem. Effects of recombination including rearrangement, segmental duplication, gain, and loss can create a mosaic pattern of homology even among closely related organisms. We describe a…

A recent approach for object detection and human pose estimation is to regress bounding boxes or human keypoints from a central point on the object or person. While this center-point regression is simple and efficient, we argue that the…

The anchor words algorithm performs provably efficient topic model inference by finding an approximate convex hull in a high-dimensional word co-occurrence space. However, the existing greedy algorithm often selects poor anchor words,…

Alignments, i.e., position-wise comparisons of two or more strings or ordered lists are of utmost practical importance in computational biology and a host of other fields, including historical linguistics and emerging areas of research in…

Precision oncology requires accurate molecular insights, yet obtaining these directly from genomics is costly and time-consuming for broad clinical use. Predicting complex molecular features and patient prognosis directly from routine…

Graded posets frequently arise throughout combinatorics, where it is natural to try to count the number of elements of a fixed rank. These counting problems are often $\#\textbf{P}$-complete, so we consider approximation algorithms for…

The alignment of biological sequences such as DNA, RNA, and proteins, is one of the basic tools that allow to detect evolutionary patterns, as well as functional/structural characterizations between homologous sequences in different…

Given a set of sequences, the distance between pairs of them helps us to find their similarity and derive structural relationship amongst them. For genomic sequences such measures make it possible to construct the evolution tree of…

We develop a family of techniques to align word embeddings which are derived from different source datasets or created using different mechanisms (e.g., GloVe or word2vec). Our methods are simple and have a closed form to optimally rotate,…

We propose a new compression scheme for genomic data given as sequence fragments called reads. The scheme uses a reference genome at the decoder side only, freeing the encoder from the burdens of storing references and performing…

Protein similarity searches are a routine job for molecular biologists where a query sequence of amino acids needs to be compared and ranked against an ever-growing database of proteins. All available algorithms in this field can be grouped…

Matched filters are widely used to localise signal patterns due to their high efficiency and interpretability. However, their effectiveness deteriorates for low signal-to-noise ratio (SNR) signals, such as those recorded on edge devices,…