OOIR: Observatory of International Research

Papers

(The TQCC of Algorithms for Molecular Biology is 4. The table below lists those papers that are above that threshold based on CrossRef citation counts [max. 250 papers]. The publications cover those that have been published in the past four years, i.e., from 2022-08-01 to 2026-08-01.)

Article	Citations
Unifying duplication episode clustering and gene-species mapping inference	38
Mem-based pangenome indexing for k-mer queries	19
Improving spliced alignment by modeling splice sites with deep learning	18
Efficient gene orthology inference via large-scale rearrangements	17
On the complexity of non-binary tree reconciliation with endosymbiotic gene transfer	14
Fast, parallel, and cache-friendly suffix array construction	14
Pattern matching with Elastic-Degenerate strings and Elastic-Founder graphs	13
Correction: Heuristic shortest hyperpaths in cell signaling hypergraphs	10
AlfaPang: alignment free algorithm for pangenome graph construction	9
Constructing phylogenetic networks via cherry picking and machine learning	9
Swiftly identifying strongly unique k-mers	8
Quartets enable statistically consistent estimation of cell lineage trees under an unbiased error and missingness model	8
On a greedy approach for genome scaffolding	8
Faster computation of left-bounded shortest unique substrings	7
New algorithms for structure informed genome rearrangement	7
Extension of partial atom-to-atom maps: uniqueness and algorithms	7
Mutational signature refitting on sparse pan-cancer data	6
Estimating similarity and distance using FracMinHash	6
Unbiased anchors for reliable genome-wide synteny detection	6
Recombinations, chains and caps: resolving problems with the DCJ-indel model	5
Reconstructing rearrangement phylogenies of natural genomes	5
Dolphyin: a combinatorial algorithm for identifying 1-Dollo phylogenies in cancer	4
Compression algorithm for colored de Bruijn graphs	4
ESKEMAP: exact sketch-based read mapping	4
Pfp-fm: an accelerated FM-index	4

All galls are divided into three or more parts: recursive enumeration of labeled histories for galled trees	4
Fractional hitting sets for efficient multiset sketching	4
Computing double-pushout graph transformation rules and atom-to-atom maps from KEGG RCLASS data	4
Orientability of undirected phylogenetic networks to a desired class: practical algorithms and application to tree-child orientation	4
Constructing founder sets under allelic and non-allelic homologous recombination	4