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Agnieszka Danek
Researcher at Silesian University of Technology
Publications - 23
Citations - 284
Agnieszka Danek is an academic researcher from Silesian University of Technology. The author has contributed to research in topics: Genomics & Computer science. The author has an hindex of 8, co-authored 21 publications receiving 242 citations. Previous affiliations of Agnieszka Danek include Faculdade de Engenharia da Universidade do Porto.
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Genome compression: a novel approach for large collections.
TL;DR: A novel Ziv-Lempel-style compression algorithm squeezes a single human genome to ∼400 KB, showing how to obtain several times higher compression ratio than of the best reported results, on two large genome collections.
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GDC 2: Compression of large collections of genomes
TL;DR: This paper proposes an algorithm that is able to compress the collection of 1092 human diploid genomes about 9,500 times, which is about 4 times better than what is offered by the other existing compressors.
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Indexes of large genome collections on a PC.
TL;DR: MuGI, Multiple Genome Index, is presented, which reports all occurrences of a given pattern, in exact and approximate matching model, against a collection of thousand(s) genomes, which fits in a standard computer with 16–32 GB, or even 8 GB, of RAM, and is fast.
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Kmer-db: instant evolutionary distance estimation.
TL;DR: Kmer‐db is a new tool for estimating evolutionary relationship on the basis of k‐mers extracted from genomes or sequencing reads that estimates distances between pathogens in <7 min (on a modern workstation), 26 times faster than Mash.
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Evaluation and integration of functional annotation pipelines for newly sequenced organisms: the potato genome as a test case.
David Amar,Itziar Frades,Agnieszka Danek,Tatyana Goldberg,Sanjeev Kumar Sharma,Pete E. Hedley,Estelle Proux-Wéra,Estelle Proux-Wéra,Erik Andreasson,Ron Shamir,Oren Tzfadia,Erik Alexandersson +11 more
TL;DR: An improved functional annotation of both PGSC and ITAG potato gene models is offered, as well as tools that can be applied to additional pipelines and improve annotation in other organisms, and a simple GO structure-based algorithm that reconciles the predictions of the different pipelines.