Recursive splicing (RS) is a process in which an intron is removed from a nascent RNA molecule in two or more splicing events rather than one. We introduce a novel approach for detecting recursive spl...

Nature Methods - EviAnn surpasses existing genome annotation methods by leveraging gene expression and protein sequence homology evidence to achieve higher accuracy and efficiency.

Randomness is a powerful tool in the design and analysis of algorithms and data structures for nucleotide sequence data. Nucleotide sequences are not themselves random but are often randomized using hash functions. Despite their widespread use in genomics, there is no comprehensive review of the types of hash functions used and their various applications. In this survey intended for bioinformatic methods developers, we divide hash functions into four categories: scattering hash functions, permutations, minimum perfect hash functions, and locality-sensitive hash functions. For each category, we provide examples of both general-use hash functions that have been applied in nucleotide sequence analysis and hash functions that have been designed specifically for nucleotide sequence analysis. We highlight their salient properties, commonalities, differences, and application areas.

Alternative transcription initiation, splicing and polyadenylation generate extensive transcript diversity in eukaryotes, but its evolutionary significance has been disputed. This study analyses 166 t...

Matematiska institutionen består av cirka 120 forskare, lärare och administrativ personal och är organiserad i tre huvudsakliga avdelningar: Matematik, Matematisk statistik och Beräkningsmatematik

Long-read sequencing data is useful for detecting large and complex structural variations; however, technical artifacts can lead to false structural variant calls. In our analyses, we became aware of ...

Nature Reviews Genetics - In this Review, Ji et al. overview how rapidly advancing experimental and computational methods are enabling improved and automated annotation of gene structure and...

Analysis of data from pre-implantation genetic testing sheds light on the genetic basis of meiotic-origin aneuploidy, the leading cause of human pregnancy loss, identifying common genetic variants ass...

Workshop Data Structures in Bioinformatics

Competing theories seek to explain inconsistencies surrounding Alexander Fleming’s famed discovery.

Job Description Summary Organization's Summary Statement: The Department of Computer Science is top-ranked for research and teaching, with its undergraduate computer science program ranked 9th among p...

Job Description Summary Organization's Summary Statement: The postdoctoral research associate is responsible for developing novel computational methodology for high-throughput sequence genomics tasks,...

Videos on : (a) the Burrows-Wheeler Transform (BWT), (b) the FM Index, which uses the BWT to construct a full-text index, (c) Wheeler graphs, (d) r-index, an...

Human genome resequencing typically involves mapping reads to a reference genome to call variants; however, this approach suffers from both technical and reference biases, leaving many duplicated and ...

LexicMap uses a fixed set of probes to efficiently query gene sequences for fast and low-memory alignment.

An analysis of TCGA whole-genome sequencing samples yields a comprehensive resource for investigating the role of microbes in cancer.

Moving beyond the simplistic view of mitochondria as the power house of the cell, Roger et al. present the immense diversity of mitochondria and mitochondrial functions across eukaryotes, and bring th...

Things are about to get wild

Author summary Forward genetic mutagenesis screening is an unbiased approach for the identification of mutations linked to a phenotype of interest. While this approach can be a powerful tool for uncov...

For many years, machine learning-based ab initio gene finding approaches have been the central components of eukaryotic genome annotation pipelines, and they remain so today. The reliance on these app...