Demonstration venue · read-only. Every page can be browsed; the buttons that would change it are switched off. Create an account to run TaxoReview on your own data. A simulation from public publication records: the people listed were not invited and did not agree to review.
? Tutorial for this page

Baris Ekim

dblp:263/2524 · DBLP profile ↗
← Back
3ranked-venue papers
1as first author
2since 2021 · last 2025
0000-0002-4040-403XORCID · reported

Domains — the database's venue-derived domains; a paper can count in several

Applied, interdisciplinary, general and emerging computing · 3 · 1 first-author · 2 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
2 papers
Bioinformatics and computational biology · 100%
Theoretical computer science
1 paper
Algorithms and data structures · 100%

Topics — the 6 heaviest of 6, each with the papers that count most for it

TopicWeightPapersLastEvidence papers
Bioinformatics and computational biology › genomics
haplotype inference
0.912025
ralphi: A Deep Reinforcement Learning Framework for Haplotype Assembly · RECOMB 2025
Bioinformatics and computational biology › sequence analysis
seed design
0.812024
Designing efficient randstrobes for sequence similarity analyses · Bioinform. 2024
Bioinformatics and computational biology
sequence analysis
0.812024
Designing efficient randstrobes for sequence similarity analyses · Bioinform. 2024
Bioinformatics and computational biology › sequence analysis
sequence similarity
0.812024
Designing efficient randstrobes for sequence similarity analyses · Bioinform. 2024
Algorithms and data structures
randomized algorithms
0.412020
A Randomized Parallel Algorithm for Efficiently Finding Near-Optimal Universal Hitting Sets · RECOMB 2020
Algorithms and data structures › sequence algorithms
string algorithms
0.412020
A Randomized Parallel Algorithm for Efficiently Finding Near-Optimal Universal Hitting Sets · RECOMB 2020

Methods — techniques the papers use, named apart from their topics

deep reinforcement learning · 0.9entropy analysis · 0.8binary search tree · 0.8randomized algorithm · 0.4parallel algorithm · 0.4
YearPublicationVenuePosition
2025 ralphi: A Deep Reinforcement Learning Framework for Haplotype Assembly
Enzo Battistella, Anant Maheshwari, Baris Ekim, Bonnie Berger, Victoria Popic
RECOMB3
2024 Designing efficient randstrobes for sequence similarity analyses
abstract
MOTIVATION: 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.4
2020 A Randomized Parallel Algorithm for Efficiently Finding Near-Optimal Universal Hitting Sets
Baris Ekim, Bonnie Berger, Yaron Orenstein
RECOMB1