14 papers · ranked by Valyu relevance
Abhishek Agarwal, Piyush Agrawal, Aditi Sharma, Vinod Kumar + 2 more
IndiaBioDb (https://webs.iiitd.edu.in/raghava/indiabiodb/) is a manually curated comprehensive repository of bioinformatics resources developed and maintained by Indian researchers. This repository maintains information about more than 550 freely accessible functional resources that include around 263 biological…
Gilderlanio Santana de Araújo
Teaching computer programming is not a simple task and it is challenging to introduce the concepts of programming in graduate programs of other fields. Little efforts have been made on engaging students in computational development after programming trainings. An emerging need is to establish subjects of bioinformatics…
Fabrizio Pucci, Marianne Rooman
As an example of topic where biology and physics meet, we present the issue of protein folding and stability, and the development of thermodynamics-based bioinformatics tools that predict the stability and thermal resistance of proteins and the change of these quantities upon amino acid substitutions. These methods are…
Konstantinos F. Xylogiannopoulos
Pattern detection and string matching are fundamental problems in computer science and the accelerated expansion of bioinformatics and computational biology have made them a core topic for both disciplines. The SARS-CoV-2 pandemic has made such problems more demanding with hundreds or thousands of new genome variants…
Jerven Bolleman, Christopher J Mungall, Francesco Strozzi, Joachim Baran + 7 more
Nucleotide and protein sequence feature annotations are essential to understand biology on the genomic, transcriptomic, and proteomic level. Using Semantic Web technologies to query biological annotations, there was no standard that described this potentially complex location information as subject-predicate-object…
Yuka Yoshimura, Akifumi Hamada, Yohann Augey, Manato Akiyama + 1 more
Biological sequence classification is the most fundamental task in bioinformatics analysis. For example, in metagenome analysis, binning is a typical type of DNA sequence classification. In order to classify sequences, it is necessary to define sequence features. The k-mer frequency, base composition, and…
Diogo de Jesus Soares Machado, Camilla Reginatto De Pierri, Letícia Graziela Costa Santos, Leonardo Scapin + 4 more
The large amount of existing textual data justifies the development of new text mining tools. Bioinformatics tools can be brought to Text Mining, increasing the arsenal of resources. Here, we present BIOTEXT, a package of strategies for converting natural language text into biological-like information data, providing a…
Julia MI Barth, Scott Handley, Daniel Kintzl, Guy Leonard + 6 more
With the advent of high-throughput genome sequencing, bioinformatics training has become essential for research in evolutionary biology and related fields. However, individual research groups are often not in the position to teach students about the most up-to-date methodology in the field. To fill this gap, extended…
Serafima Dubnov, Zoe Piran, Hermona Soreq, Mor Nitzan
Rapid advancements in single-cell RNA-sequencing (scRNA-seq) technologies revealed the richness of myriad attributes encompassing cell identity, such as diversity of cell types, organ-of-origin, or developmental stage. However, due to the large scale of the data, obtaining an interpretable compressed representation of…
Michael C. Schatz
The last 20 years have been a remarkable era for biology and medicine. One of the most significant achievements has been the sequencing of the first human genomes, which has laid the foundation for profound insights into human genetics, the intricacies of regulation and development, and the forces of evolution.…
Sumaiya Nazeen, Bonnie Berger
Accurate assignment of metagenomic reads to their functional roles is an important first step towards gaining insights into the relationship between the human microbiomeincluding the collective genesand disease. Existing approaches focus on binning sequencing reads into known taxonomic classes or by genes, often…
Yunan Luo, Y. William Yu, Jianyang Zeng, Bonnie Berger + 1 more
Bacterial microbiomes of incredible complexity are found throughout the world, from exotic marine locations to the soil in our yards to within our very guts. With recent advances in Next-Generation Sequencing (NGS) technologies, we have vastly greater quantities of microbial genome data, but the nature of environmental…
Aaron Pomerantz, Nicolás Peñafiel, Alejandro Arteaga, Lucas Bustamante + 5 more
Advancements in portable scientific instruments provide promising avenues to expedite field work in order to understand the diverse array of organisms that inhabit our planet. Here we tested the feasibility for in situ molecular analyses of endemic fauna using a portable laboratory fitting within a single backpack, in…
Elaina Graham, John Heidelberg, Benjamin Tully
Metagenomics has become an integral part of defining microbial diversity in various environments. Many ecosystems have characteristically low biomass and few cultured representatives. Linking potential metabolisms to phylogeny in environmental microorganisms is important for interpreting microbial community functions…