Related papers: MOSGA: Modular Open-Source Genome Annotator
Single-cell RNA sequencing has transformed our ability to identify diverse cell types and their transcriptomic signatures. However, annotating these signatures-especially those involving poorly characterized genes-remains a major challenge.…
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,…
Gene Ontology (GO) is the most important resource for gene function annotation. It provides a way to unify biological knowledge across different species via a dynamic and controlled vocabulary. GO is now widely represented in the Semantic…
The biological significance of genomic features is often context-dependent. We present CruzDB, a fast and intuitive programmatic interface to the UCSC genome browser that facilitates integrative analyses of diverse local and remotely hosted…
Designing novel proteins with desired characteristics remains a significant challenge due to the large sequence space and the complexity of sequence-function relationships. Efficient exploration of this space to identify sequences that meet…
High-quality and large-scale data are key to success for AI systems. However, large-scale data annotation efforts are often confronted with a set of common challenges: (1) designing a user-friendly annotation interface; (2) training enough…
Motivation: The availability of thousands of invidual genomes of one species should boost rapid progress in personalized medicine or understanding of the interaction between genotype and phenotype, to name a few applications. A key…
Raw signal genome analysis (RSGA) has emerged as a promising approach to enable real-time genome analysis by directly analyzing raw electrical signals. However, rapid advancements in sequencing technologies make it increasingly difficult…
Gene studies are crucial for fields such as protein structure prediction, drug discovery, and cancer genomics, yet they face challenges in fully utilizing the vast and diverse information available. Gene studies require clean, factual…
Public repositories for genome and proteome annotations, such as the Gene Ontology (GO), rarely stores negative annotations, i.e. proteins not possessing a given function. This leaves undefined or ill defined the set of negative examples,…
With the boom in modern software development, open-source software has become an integral part of various industries, driving progress in computer science. However, the immense complexity and diversity of the open-source ecosystem also pose…
Bacteriophages are viruses that target bacteria, playing a crucial role in microbial ecology. Phage proteins are important in understanding phage biology, such as virus infection, replication, and evolution. Although a large number of new…
Image annotation and large annotated datasets are crucial parts within the Computer Vision and Artificial Intelligence fields.At the same time, it is well-known and acknowledged by the research community that the image annotation process is…
Data annotation is an essential component of the machine learning pipeline; it is also a costly and time-consuming process. With the introduction of transformer-based models, annotation at the document level is increasingly popular;…
Chromosome analysis is vital for diagnosing genetic disorders and guiding cancer therapy decisions through the identification of somatic clonal aberrations. However, developing an AI model are hindered by the overwhelming complexity and…
Next-generation sequencing technologies generate millions of short sequence reads, which are usually aligned to a reference genome. In many applications, the key information required for downstream analysis is the number of reads mapping to…
The Genome Warehouse (GWH), accessible at https://ngdc.cncb.ac.cn/gwh, is an extensively utilized public repository dedicated to the deposition, management and sharing of genome assembly sequences, annotations, and metadata. This paper…
We introduce Seshat, a new, simple and open-source software to efficiently manage annotations of speech corpora. The Seshat software allows users to easily customise and manage annotations of large audio corpora while ensuring compliance…
In recent years, the sequencing, assembling and annotation of prokaryotic genomes has become increasingly easy and cheap. Thus it becomes increasingly feasible and interesting to perform comparative genomics analyses of new genomes to those…
Microbes are essentially yet convolutedly linked with human lives on the earth. They critically interfere in different physiological processes and thus influence overall health status. Studying microbial species is used to be constrained to…