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Smooth orientation-dependent scoring function for coarse-grained protein quality assessment
A novel single-model QA method called SBROD (Smooth Backbone-Reliant Orientation-Dependent) method, which uses only the backbone protein conformation, and hence it can be applied to scoring coarse-grained protein models, which is potentially applicable to continuous gradient-based optimization of protein conformations.
A global metagenomic map of urban microbiomes and antimicrobial resistance
Sparse Binary Relation Representations for Genome Graph Annotation
- Mikhail Karasikov, Harun Mustafa, Amir Joudaki, Sara Javadzadeh No, G. Rätsch, A. Kahles
- Computer SciencebioRxiv
- 12 November 2018
This work presents a systematic analysis of five different state-of-the-art annotation compression schemes that evaluates key metrics on both artificial and real-world data and discusses how different data characteristics influence the compression performance.
Blind prediction of homo‐ and hetero‐protein complexes: The CASP13‐CAPRI experiment
CAPRI Round 46 indicates that residues in binding interfaces were less well predicted in this set of targets than in previous Rounds, providing useful insights for directions of future improvements.
Dynamic compression schemes for graph coloring
- Harun Mustafa, I. Schilken, Mikhail Karasikov, Carsten Eickhoff, G. Rätsch, A. Kahles
- Computer SciencebioRxiv
- 17 March 2018
Two new approaches for a compressed representation of a graph coloring are presented: a lossless compression scheme based on a novel application of wavelet tries as well as a highly accurate lossy compressionbased on a set of Bloom filters.
Cartography of opportunistic pathogens and antibiotic resistance genes in a tertiary hospital environment
Spatiotemporal characterization of microbial diversity and antibiotic resistance in a tertiary-care hospital reveals broad distribution and persistence of antibiotic-resistant organisms that could cause opportunistic infections in a healthcare setting.
Assessment of chemical‐crosslink‐assisted protein structure modeling in CASP13
This largest‐to‐date blind assessment reveals benefits of using data assistance in difficult to model protein structure prediction cases, but suggests that with the unprecedented advance in accuracy to predict contacts in recent years, experimental crosslinks will be useful only if their specificity and accuracy further improved and they are better integrated into computational workflows.
Communication-Efficient Jaccard similarity for High-Performance Distributed Genome Comparisons
- Maciej Besta, Raghavendra Kanakagiri, Edgar Solomonik
- Computer ScienceIEEE International Parallel and Distributed…
- 11 November 2019
The design and implementation of SimilarityAtScale is designed and implemented, the first communication-efficient distributed algorithm for computing the Jaccard similarity among pairs of large datasets, and the resulting scheme is the first to enable accurateJaccard distance derivations for massive datasets, using large-scale distributed-memory systems.
Global Genetic Cartography of Urban Metagenomes and Anti-Microbial Resistance
A global metagenomic and antimicrobial resistance atlas of urban mass transit systems from 58 cities, spanning 3,741 samples and 4,424 taxonomically-defined microorganisms collected for from 2015-2017, provides an essential first draft of the global AMR burden of the world’s cities.
MetaGraph: Indexing and Analysing Nucleotide Archives at Petabase-scale
This work presents MetaGraph, a versatile framework for the scalable analysis of extensive sequence repositories, and introduces the concept of differential assembly, which allows for the extraction of sequences present in a foreground set of samples but absent in a given background set.