457 citations · 613 across the 9 of their papers we have counts for
10 papers
LAFA: A Framework for Reproducible Longitudinal Assessment of Protein Function Annotation Models
An Phan, Yanli Wang, Frimpong Boadu +3
Motivation: Protein function prediction is a challenging task and an open problem in computational biology. The Critical Assessment of protein Function Annotation (CAFA) is a trien…
CAFA-evaluator: A Python Tool for Benchmarking Ontological Classification Methods
Damiano Piovesan, Davide Zago, Parnal Joshi +8
We present CAFA-evaluator, a powerful Python program designed to evaluate the performance of prediction methods on targets with hierarchical concept dependencies. It generalizes mu…
Reliable uncertainty estimate for antibiotic resistance classification with Stochastic Gradient Langevin Dynamics
Md-Nafiz Hamid, Iddo Friedberg
Antibiotic resistance monitoring is of paramount importance in the face of this on-going global epidemic. Deep learning models trained with traditional optimization algorithms (e.g…
Community-Wide Evaluation of Computational Function Prediction
Iddo Friedberg, Predrag Radivojac
A biological experiment is the most reliable way of assigning function to a protein. However, in the era of high-throughput sequencing, scientists are unable to carry out experimen…
An expanded evaluation of protein function prediction methods shows an improvement in accuracy
Yuxiang Jiang, Tal Ronnen Oron, Wyatt T Clark +144
Background: The increasing volume and variety of genotypic and phenotypic data is a major defining characteristic of modern biomedical sciences. At the same time, the limitations i…
A large scale prediction of bacteriocin gene blocks suggests a wide functional spectrum for bacteriocins
James T Morton, Stefan D Freed, Shaun W Lee +1
Bacteriocins are peptide-derived molecules produced by bacteria, whose recently-discovered functions include virulence factors and signalling molecules as well as their better know…
An Event-Driven Approach for Studying Gene Block Evolution in Bacteria
David C Ream, Asma R Bankapur, Iddo Friedberg
Motivation: Gene blocks are genes co-located on the chromosome. In many cases, genes blocks are conserved between bacterial species, sometimes as operons, when genes are co-transcr…
Sequence-Structure Relationship in Proteins: a Computational Analysis of Proteins that Differ in Sequence but Share the Same Fold
Iddo Friedberg
Mapping between sequence and structure is currently an open problem in structural biology. Despite many experimental and computational efforts it is not clear yet how the structure…
Biases in the Experimental Annotations of Protein Function and their Effect on Our Understanding of Protein Function Space
Alexandra M. Schnoes, David C. Ream, Alexander W. Thorman +2
The ongoing functional annotation of proteins relies upon the work of curators to capture experimental findings from scientific literature and apply them to protein sequence and st…
Biological Database of Images and Genomes: tools for community annotations linking image and genomic information
Andrew T. Oberlin, Dominika A. Jurkovic, Mitchell F. Balish +1
Genomic data and biomedical imaging data are undergoing exponential growth. However, our understanding of the phenotype-genotype connection linking the two types of data is lagging…