Demo Data from EDBT 2026 / reviewers in the wild / expert
Aryan Soltani Mohammadi
dblp:356/2283
· DBLP profile ↗
1ranked-venue papers
0as first author
1since 2021 · last 2024
—ORCID · none
Domains — the database's venue-derived domains; a paper can count in several
Applied, interdisciplinary, general and emerging computing · 1 · 1 since 2021
Expertise — from the expertise taxonomy: the topics of the expert's papers under the CCF categories. A weight counts papers with recency: 1 for a paper about the topic, 0.3 when the topic is its context, halved every five years.
| Interdisciplinary, comprehensive, and emerging computing
1 paper |
Bioinformatics and computational biology · 100% |
Topics — the 3 heaviest of 3, each with the papers that count most for it
| Topic | Weight | Papers | Last | Evidence papers |
|---|---|---|---|---|
Bioinformatics and computational biology › sequence analysis
seed design |
0.8 | 1 | 2024 | Designing efficient randstrobes for sequence similarity analyses · Bioinform. 2024 |
Bioinformatics and computational biology
sequence analysis |
0.8 | 1 | 2024 | Designing efficient randstrobes for sequence similarity analyses · Bioinform. 2024 |
Bioinformatics and computational biology › sequence analysis
sequence similarity |
0.8 | 1 | 2024 | Designing efficient randstrobes for sequence similarity analyses · Bioinform. 2024 |
Methods — techniques the papers use, named apart from their topics
entropy analysis · 0.8binary search tree · 0.8
| Year | Publication | Venue | Position |
|---|---|---|---|
| 2024 | Designing efficient randstrobes for sequence similarity analysesabstractMOTIVATION: Substrings of length k, commonly referred to as k-mers, play a vital role in sequence analysis. However, k-mers are limited to exact matches between sequences leading to alternative constructs. We recently introduced a class of new constructs, strobemers, that can match across substitutions and smaller insertions and deletions. Randstrobes, the most sensitive strobemer proposed in Sahlin (Effective sequence similarity detection with strobemers. Genome Res 2021a;31:2080-94. https://doi.org/10.1101/gr.275648.121), has been used in several bioinformatics applications such as read classification, short-read mapping, and read overlap detection. Recently, we showed that the more pseudo-random the behavior of the construction (measured in entropy), the more efficient the seeds for sequence similarity analysis. The level of pseudo-randomness depends on the construction operators, but no study has investigated the efficacy. RESULTS: In this study, we introduce novel construction methods, including a Binary Search Tree-based approach that improves time complexity over previous methods. To our knowledge, we are also the first to address biases in construction and design three metrics for measuring bias. Our evaluation shows that our methods have favorable speed and sampling uniformity compared to existing approaches. Lastly, guided by our results, we change the seed construction in strobealign, a short-read mapper, and find that the results change substantially. We suggest combining the two results to improve strobealign's accuracy for the shortest reads in our evaluated datasets. Our evaluation highlights sampling biases that can occur and provides guidance on which operators to use when implementing randstrobes. AVAILABILITY AND IMPLEMENTATION: All methods and evaluation benchmarks are available in a public Github repository at https://github.com/Moein-Karami/RandStrobes. The scripts for running the strobealign analysis are found at https://github.com/NBISweden/strobealign-evaluation. Moein Karami, Aryan Soltani Mohammadi, Marcel Martin, Baris Ekim, Lidong Guo, Giulio Ermanno Pibiri, Rob Patro, Kristoffer Sahlin |
Bioinform. | 2 |