Related papers: Motif Caller: Sequence Reconstruction for Motif-Ba…
Image-based sequencing of mRNA makes it possible to see where in a tissue sample a given gene is active, and thus discern large numbers of different cell types in parallel. This is crucial for gaining a better understanding of tissue…
Current genomic foundation models (GFMs) rely on extensive neural computation to implicitly approximate conserved biological motifs from single-nucleotide inputs. We propose Gengram, a conditional memory module that introduces an explicit…
This work considers the task of representation learning on the attributed relational graph (ARG). Both the nodes and edges in an ARG are associated with attributes/features allowing ARGs to encode rich structural information widely observed…
MotifbreakR is a software tool that scans genetic variants against position weight matrices of transcription factors (TF) to determine the potential for the disruption of TF binding at the site of the variant. It leverages the Bioconductor…
Recent genomic foundation models largely adopt large language model architectures that treat DNA as a one-dimensional token sequence. However, exhaustive sequential reading is structurally misaligned with sparse and discontinuous genomic…
The search for patterns or motifs in data represents a problem area of key interest to finance and economic researchers. In this paper we introduce the Motif Tracking Algorithm, a novel immune inspired pattern identification tool that is…
Predicting molecular properties with data-driven methods has drawn much attention in recent years. Particularly, Graph Neural Networks (GNNs) have demonstrated remarkable success in various molecular generation and prediction tasks. In…
Motivation: Genome and Proteome Alignments, represented by the Multiple Alignment File (MAF) format, have become a standard approach in the field of comparative genomics and proteomics. However, current approaches lack a direct method for…
Most DNA sequencing technologies are based on the shotgun paradigm: many short reads are obtained from random unknown locations in the DNA sequence. A fundamental question, studied in arXiv:1203.6233, is what read length and coverage depth…
Foundation models have made significant strides in understanding the genomic language of DNA sequences. However, previous models typically adopt the tokenization methods designed for natural language, which are unsuitable for DNA sequences…
Synthetic DNA approaches 227.5 exabytes per gram of storage density with stability over millennial timescales. Realising this capacity requires error-correction codes that recover data from substantial synthesis and sequencing errors.…
Methods for reducing and directly controlling the speed of DNA through a nanopore are needed to enhance sensing performance for direct strand sequencing and detection/mapping of sequence-specific features. We have created a method for…
A hypercomplex representation of DNA is proposed to facilitate comparison of DNA sequences with fuzzy composition. Using hypercomplex number representation, conventional sequence analysis method, such as, dot matrix analysis, dynamic…
A method for encoding information in DNA sequences is described. The method is based on the precision-resolution framework, and is aimed to work in conjunction with a recently suggested terminator-free template independent DNA synthesis…
Ensembl's human non-coding and protein coding genes are used to automatically find DNA pattern motifs. The Backus-Naur form (BNF) grammar for regular expressions (RE) is used by genetic programming to ensure the generated strings are legal.…
Motivation Protein fold recognition is an important problem in structural bioinformatics. Almost all traditional fold recognition methods use sequence (homology) comparison to indirectly predict the fold of a tar get protein based on the…
Error-correcting codes over sets, with applications to DNA storage, are studied. The DNA-storage channel receives a set of sequences, and produces a corrupted version of the set, including sequence loss, symbol substitution, symbol…
DNA has many valuable characteristics that make it suitable for a long-term storage medium, in particular its durability and high information density. DNA can be stored safely for hundreds of years with virtually no degradation, in contrast…
RNA design aims to identify RNA sequences that fold into a target secondary structure. This task is challenging in terms of computational efficiency. Most existing methods focus on either minimum free energy (MFE)-based or ensemble-based…
This paper studies the problem of encoding messages into sequences which can be uniquely recovered from some noisy observations about their substrings. The observed reads comprise consecutive substrings with some given minimum overlap. This…