880 citations
- Lawrence Berkeley National LaboratoryUS8 papers
- University of California, BerkeleyUS6 papers
- University of California, DavisUS3 papers
- University of WashingtonUS3 papers
- Centre National de la Recherche ScientifiqueFR2 papers
- Cold Spring Harbor LaboratoryUS2 papers
- European Bioinformatics InstituteGB2 papers
- Howard Hughes Medical InstituteUS2 papers
- Indiana UniversityUS2 papers
- Indiana University BloomingtonUS2 papers
- QB3US2 papers
- University of California, San FranciscoUS2 papers
14 papers
CoverM: Read alignment statistics for metagenomics
Samuel T. N. Aroney, Rhys J. P. Newell, Jakob N. Nissen +3
Genome-centric analysis of metagenomic samples is a powerful method for understanding the function of microbial communities. Calculating read coverage is a central part of analysis…
Extracting Protein-Protein Interactions (PPIs) from Biomedical Literature using Attention-based Relational Context Information
Gilchan Park, Sean McCorkle, Carlos Soto +2
Because protein-protein interactions (PPIs) are crucial to understand living systems, harvesting these data is essential to probe disease development and discern gene/protein funct…
DNABERT-S: Pioneering Species Differentiation with Species-Aware DNA Embeddings
Zhihan Zhou, Weimin Wu, Harrison Ho +5
We introduce DNABERT-S, a tailored genome model that develops species-aware embeddings to naturally cluster and segregate DNA sequences of different species in the embedding space.…
Automated Annotation of Scientific Texts for ML-based Keyphrase Extraction and Validation
Oluwamayowa O. Amusat, Harshad Hegde, Christopher J. Mungall +5
Advanced omics technologies and facilities generate a wealth of valuable data daily; however, the data often lacks the essential metadata required for researchers to find and searc…
Distributed-Memory Parallel Contig Generation for De Novo Long-Read Genome Assembly
Giulia Guidi, Gabriel Raulet, Daniel Rokhsar +3
De novo genome assembly, i.e., rebuilding the sequence of an unknown genome from redundant and erroneous short sequences, is a key but computationally intensive step in many genomi…
The Parallelism Motifs of Genomic Data Analysis
Katherine Yelick, Aydin Buluc, Muaaz Awan +11
Genomic data sets are growing dramatically as the cost of sequencing continues to decline and small sequencing devices become available. Enormous community databases store and shar…