Related papers: DEMETER: Efficient simultaneous curation of genome…
High quality gene models are necessary to expand the molecular and genetic tools available for a target organism, but these are available for only a handful of model organisms that have undergone extensive curation and experimental…
Motivation: Next-generation sequencing tools have enabled producing of huge amount of genomic information at low cost. Unfortunately, presence of sequencing errors in such data affects quality of downstream analyzes. Accuracy of them can be…
We introduce an improved version of RECKONER, an error corrector for Illumina whole genome sequencing data. By modifying its workflow we reduce the computation time even 10 times. We also propose a new method of determination of $k$-mer…
COnstraint-Based Reconstruction and Analysis (COBRA) provides a molecular mechanistic framework for integrative analysis of experimental data and quantitative prediction of physicochemically and biochemically feasible phenotypic states. The…
In this paper, we introduce CoRet, a dense retrieval model designed for code-editing tasks that integrates code semantics, repository structure, and call graph dependencies. The model focuses on retrieving relevant portions of a code…
De novo whole genome assembly reconstructs genomic sequence from short, overlapping, and potentially erroneous DNA segments and is one of the most important computations in modern genomics. This work presents HipMER, a high-quality…
Summary: With the rapid development of long-read sequencing technologies, the era of individual complete genomes is approaching. We have developed wgatools, a cross-platform, ultrafast toolkit that supports a range of whole genome alignment…
The way to infer well-supported phylogenetic trees that precisely reflect the evolutionary process is a challenging task that completely depends on the way the related core genes have been found. In previous computational biology studies,…
Metagenomics offers a way to analyze biotopes at the genomic level and to reach functional and taxonomical conclusions. The bio-analyzes of large metagenomic projects face critical limitations: complex metagenomes cannot be assembled and…
Referring image segmentation aims to segment an object referred to by natural language expression from an image. The primary challenge lies in the efficient propagation of fine-grained semantic information from textual features to visual…
Named-entity recognition (NER) is fundamental to extracting structured information from the >80% of healthcare data that resides in unstructured clinical notes and biomedical literature. Despite recent advances with large language models,…
The Transformer-based encoder-decoder architecture has recently made significant advances in recognizing handwritten mathematical expressions. However, the transformer model still suffers from the lack of coverage problem, making its…
The third-generation long reads sequencing technologies, such as PacBio and Nanopore, have great advantages over second-generation Illumina sequencing in de novo assembly studies. However, due to the inherent low base accuracy,…
A genome-scale reconstruction of human metabolism, Recon 2, is available but no interface exists to interactively visualise its content integrated with omics data and simulation results. We manually drew a comprehensive map, ReconMap 2.0,…
Genome sequencing is essential to decode genetic information, identify organisms, understand diseases and advance personalized medicine. A critical step in any genome sequencing technique is genome assembly. However, de novo genome…
Accurate lesion segmentation in whole-body PET/CT scans is crucial for cancer diagnosis and treatment planning, but limited datasets often hinder the performance of automated segmentation models. In this paper, we explore the potential of…
Detection Transformer (DETR) is a Transformer architecture based object detection model. In this paper, we demonstrate that it can also be used as a data augmenter. We term our approach as DETR assisted CutMix, or DeMix for short. DeMix…
Dense embedding models have become critical for modern information retrieval, particularly in RAG pipelines, but their performance often degrades when applied to specialized corpora outside their pre-training distribution. To address thi we…
Gene enhancers control when and where genes switch on, yet their sequence diversity and tissue specificity make them hard to pinpoint in colorectal cancer. We take a sequence-only route and fine-tune DNABERT-2, a transformer genomic…
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…