Program of RECOMB-Seq 2026

May 24th, Sunday

Time Event Speaker/Details
8:30-9:30 Registration HELEXPO, Thessaloniki
9:25-9:30 Opening HELEXPO, Nikolaos Germanos conference center, Hall A
9:30-10:30 Keynote 1: Beyond reference sequences: algorithms for the next generation of sequence collections Camille Marchet, CNRS
10:30-11:00 Poster lightning talks (2 min each)
11:00-13:00 Poster session / Coffee break / Lunch
Session 1: Indexing and pangenome data structures Session chair: TBD
13:00-13:25 SuperBloom: Fast and precise filter for streaming queries [Proceedings] Etienne Conchon-Kerjan, Timothé Rouzé, Lucas Robidou, Florian Ingels and Antoine Limasset
13:25-13:50 Identifying all snarls and superbubbles in linear-time, via a unified SPQR-tree framework [Overlay] Francisco Sena, Aleksandr Politov, Corentin Moumard, Manuel Cáceres, Sebastian Schmidt, Juha Harviainen and Alexandru I. Tomescu
13:50-14:15 Pareto optimization of masked superstrings improves compression of pan-genome k-mer sets [Proceedings] Ján Plachý, Ondřej Sladký, Karel Břinda and Pavel Veselý
14:15-14:40 Hierarchical genomic feature annotation with variable-length queries [Overlay] Jarno N. Alanko, T. Rhyker Ranallo-Benavidez, Floris P. Barthel, Simon J. Puglisi and Camille Marchet
14:40-15:10 Coffee break
Session 2: Metagenomics and sequence classification Session chair: TBD
15:10-15:35 Interpolating and extrapolating node counts in colored compacted de Bruijn graphs for pangenome diversity [Proceedings] Luca Parmigiani and Pierre Peterlongo
15:35-16:00 Sensitive and scalable metagenomic classification using spaced metamers, reduced alphabets, and syncmers [Overlay] Jaebeom Kim and Martin Steinegger
16:00-16:25 Using mapping-profiles to refine strain-level metagenomic classification [Proceedings] Josipa Lipovac, Lune Angevin and Krešimir Križanović
16:25-16:37 FUSOR: Space efficient taxonomic classification using hybrid hierarchical interleaved binary fuse filters with a stash [Short talk] Tuna Okçu and Can Alkan
16:37-16:49 TDKC: Ultrafast and memory-efficient sequence classification for target pathogen diagnostics [Short talk] Seungmo Lee and Eleazar Eskin
16:49-17:01 A likelihood framework for estimating sequence distances and genome-wide (phylogenetic) pattern matching [Short talk] Ali Osman Berk Şapcı and Siavash Mirarab
17:01-17:13 A Bayesian framework for likelihood estimation of pathogenic reads in metagenomic data [Short talk] William O'Brien, Seungmo Lee, Vivek Agarwal and Eleazar Eskin
17:13-17:25 Blown out of proportion: Effect of PCR artifacts on wastewater surveillance [Short talk] Askar Gafurov, Kristína Boršová, Boris Klempa, Jozef Nosek, Brona Brejova and Tomas Vinar


May 25th, Monday

Time Event Speaker/Details
8:30-9:30 Registration HELEXPO, Thessaloniki
9:25-9:30 Opening HELEXPO, Nikolaos Germanos conference center, Hall A
9:30-10:30 Keynote 2: New scalable approaches to pangenome construction and repeat analysis in the era of diversity genomics
(incl. "A run-length-compressed skiplist data structure for dynamic GBWTs supports time and space efficient pangenome operations over syncmers" [Proceedings])		 Richard Durbin, University of Cambridge
Session 3: Single-cell transcriptomics and gene regulation Session chair: TBD
10:30-10:42 RANKOR: Direct drug prioritization from bulk and single-cell transcriptomic signatures [Short talk] Nikoletta Katsaouni and Marcel H. Schulz
10:42-10:54 BEACON: Bayesian contrastive learning for single-cell gene regulatory inference [Short talk] Yunwei Zhao, Ankit Bhardwaj, Preetha Balasubramanian and Lakshminarayanan Subramanian
10:54-11:06 Safe fusion for scRNA-seq trajectory recovery with uncertainty gating and CITE-seq validation [Short talk] Yunwei Zhao, Preetha Balasubramanian and Lakshminarayanan Subramanian
11:10-11:30 Coffee break
Session 4: RNA-seq, library design, and benchmarking Session chair: TBD
11:30-11:55 Unique molecular identifiers don't need to be unique: a collision-aware estimator for RNA-seq quantification [Proceedings] Dylan Agyemang, Rafael Irizarry and Tavor Baharav
11:55-12:20 PrimerDesigner: Designing efficient primers for synthesizing large protein libraries without cross-hybridization [Proceedings] Jonathan Mandl, Marcus Bluestone, Scott Longwell, Polly Fordyce and Yaron Orenstein
12:20-12:45 stPularity: Spatial domain identification via purity-constrained Louvain clustering on spatially-smoothed cell type proportions [Proceedings] Chandra Sekhar Reddy Edula, Yuxing Sun and Xiuwei Zhang
12:45-12:57 GenBenchQC: Automated quality control of genomic sequence benchmarks reveals widespread biases in deep learning datasets [Short talk] Stephanie Sammut, Eva Marsalkova, Panagiotis Alexiou and Katarina Gresova
13:00-14:05 Lunch
Session 5: Compression and string algorithms Session chair: TBD
14:05-14:17 Fast and optimal affine-gap sequence-to-graph alignment [Short talk] Albert Jiménez-Blanco, Lorién López-Villellas, Juan Carlos Moure, Miquel Moreto, and Santiago Marco-Sola
14:17-14:29 FASTR: A computation-native, lossless replacement for FASTQ [Short talk] Adrian Tkachenko, Sepehr Salem, Zulal Bingol, Nayeem Uddin Mohammed, Ayotomiwa Ezekiel Adeniyi, Akshat Prasanna, Alexander Zelikovsky, Serghei Mangul, Can Alkan and Mohammed Alser
14:30-14:55 Sassy: Fuzzy searching DNA sequences using SIMD [Overlay] Rick Beeloo and Ragnar Groot Koerkamp
14:55-15:20 Compressing suffix trees by path decompositions [Overlay] Ruben Becker, Davide Cenzato, Travis Gagie, Ragnar Groot Koerkamp, Sung-Hwan Kim, Giovanni Manzini and Nicola Prezza
15:20-15:45 Why phylogenies compress so well: combinatorial guarantees under the infinite sites model [Proceedings] Veronika Hendrychová and Karel Brinda
15:45-15:57 Somatic structural variations detection via tumor-specific strings [Short talk] Davide Cesare Monti, Paola Bonizzoni, Simone Ciccolella, Davide Cozzi, Gianluca Della Vedova, Luca Denti and Fereydoun Hormozdiari
16:00-16:30 Coffee break
16:30-17:30 Keynote 3: From Genomics to Therapeutics: Single-cell Circuitry and Rewiring in Alzheimer's, Schizophrenia, Obesity, Cancer. Manolis Kellis, MIT
17:30-19:00 Posters