Mikhail Karasikov

ETH Zürich
0000-0001-6200-5972
karasikov.com
Publications22
h-index8
Citations189
Highly Influential Citations11
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Smooth orientation-dependent scoring function for coarse-grained protein quality assessment
TLDR
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. Expand
Sparse Binary Relation Representations for Genome Graph Annotation
TLDR
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. Expand
Dynamic compression schemes for graph coloring
TLDR
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. Expand
Blind prediction of homo‐ and hetero‐protein complexes: The CASP13‐CAPRI experiment
TLDR
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. Expand
Assessment of chemical‐crosslink‐assisted protein structure modeling in CASP13
TLDR
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. Expand
Communication-Efficient Jaccard similarity for High-Performance Distributed Genome Comparisons
TLDR
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. Expand
Global Genetic Cartography of Urban Metagenomes and Anti-Microbial Resistance
TLDR
This is the first systematic, worldwide study cataloging the urban microbial ecosystem, and identifies 4,424 species of urban microorganisms and a consistent “core” of 31 species found in nearly all samples that is largely distinct from any human commensal microbiome. Expand
MetaGraph: Indexing and Analysing Nucleotide Archives at Petabase-scale
TLDR
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. Expand
Cartography of opportunistic pathogens and antibiotic resistance genes in a tertiary hospital environment
TLDR
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. Expand
Metannot: A succinct data structure for compression of colors in dynamic de Bruijn graphs
TLDR
This work proposes a parallel construction method for and novel application of the wavelet trie as a dynamic data structure for compressing and indexing graph metadata, and finds that additionally encoding graph topology metadata improved compression ratios, particularly on data sets consisting of several mutually-exclusive reference genomes. Expand
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