A5021585705- Genetic Mapping and Diversity in Plants and Animals
- Genetic and Clinical Aspects of Sex Determination and Chromosomal Abnormalities
- Animal Genetics and Reproduction
- RNA and protein synthesis mechanisms
- RNA modifications and cancer
- RNA Research and Splicing
- Genetic and phenotypic traits in livestock
- Genetic Associations and Epidemiology
- CRISPR and Genetic Engineering
- Cancer-related molecular mechanisms research
- Algorithms and Data Compression
- Bayesian Modeling and Causal Inference
- Animal Behavior and Reproduction
University of Milano-Bicocca
2022-2024
Abstract Alternative Splicing (AS) is a regulation mechanism that contributes to protein diversity and also associated many diseases tumors. splicing events quantification from RNA-Seq reads crucial step in understanding this complex biological mechanism. However, tools for AS detection show inconsistent results. This reduces their reliability fully capturing explaining alternative splicing. We introduce ESGq, novel approach the of across conditions based on read alignment against Event...
Pangenomes are becoming a powerful framework to perform many bioinformatics analyses taking into account the genetic variability of population, thus reducing bias introduced by single reference genome. With wider diffusion pangenomes, integrating with transcriptome diversity is natural extension that demands specific methods for its exploration. In this work, we extend notion spliced pangenomes annotated ; allows us introduce formal definition Alternative Splicing (AS) events on graph...
The somatic sex determination gene
The somatic sex determination gene transformer ( tra ) is required for the highly sexually dimorphic development of most cells, including those gonads. In addition, germline even though it not within germ cells. Germ cell autonomous expression also necessary their determination. To understand interplay between these signals, we compared phenotype and larval wild-type gonads sex-transformed XX ovaries transformed into testes were dramatically smaller than wild-type, with significant...
The somatic sex determination gene transformer ( tra ) is required for the highly sexually dimorphic development of most cells, including those gonads. In addition, germline even though it not within germ cells. Germ cell autonomous expression also necessary their determination. To understand interplay between these signals, we compared phenotype and larval wild-type gonads sex-transformed XX ovaries transformed into testes were dramatically smaller than wild-type, with significant...
Abstract Motivation The positional Burrows-Wheeler Transform ( PBWT ) has been introduced as a key data structure for indexing haplotype sequences with the main purpose of finding maximal matches in h containing w variation sites -time significant improvement over classical quadratic time approaches. However original does not allow queries modern biobank panels haplotypes consisting several millions haplotypes, they must be kept entirely memory. Results In this paper, we present method...
The Positional Burrows-Wheeler Transform (PBWT) is a data structure that indexes haplotype sequences in manner enables finding maximal matches h containing w variation sites O(hw) time. This represents significant improvement over classical quadratic-time approaches. However, the original PBWT does not allow for queries Biobank panels consist of several millions haplotypes, if an index haplotypes must be kept entirely memory.In this article, we leverage notion r-index proposed BWT to present...
Abstract Pangenomes are becoming a powerful framework to perform many bioinformatics analyses taking into account the genetic variability of population, thus reducing bias introduced by single reference genome. With wider diffusion pangenomes, integrating with transcriptome diversity is natural extension that demands specific methods for its exploration. In this work, we extend notion spliced pangenomes annotated ; allows us introduce formal definition Alternative Splicing (AS) events on...
A bstract The positional Burrows–Wheeler Transform (PBWT) was presented in 2014 by Durbin as a means to find all maximal haplotype matches h sequences containing w variation sites 𝒪( hw )-time. This time complexity of finding using the PBWT is significant improvement over naïve pattern-matching algorithm that requires 2 Compared more famous Burrows-Wheeler (BWT), however, relatively little amount attention has been paid PBWT. resulted less space-efficient data structures for building and...