OOIR: Observatory of International Research

Papers

(The TQCC of Algorithms for Molecular Biology is 5. 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 2021-06-01 to 2025-06-01.)

Article	Citations
Unifying duplication episode clustering and gene-species mapping inference	29
Mem-based pangenome indexing for k-mer queries	21
A novel method for inference of acyclic chemical compounds with bounded branch-height based on artificial neural networks and integer programming	16
Fast, parallel, and cache-friendly suffix array construction	12
Bayesian optimization with evolutionary and structure-based regularization for directed protein evolution	12
Efficient gene orthology inference via large-scale rearrangements	11
Embedding gene trees into phylogenetic networks by conflict resolution algorithms	10
On the complexity of non-binary tree reconciliation with endosymbiotic gene transfer	10
Constructing phylogenetic networks via cherry picking and machine learning	10
Binning long reads in metagenomics datasets using composition and coverage information	10
AlfaPang: alignment free algorithm for pangenome graph construction	8
Correction: Heuristic shortest hyperpaths in cell signaling hypergraphs	8
Quartets enable statistically consistent estimation of cell lineage trees under an unbiased error and missingness model	8
New algorithms for structure informed genome rearrangement	7
On a greedy approach for genome scaffolding	7
Disk compression of k-mer sets	7
Fractional hitting sets for efficient multiset sketching	6
Two metrics on rooted unordered trees with labels	6
Approximation algorithm for rearrangement distances considering repeated genes and intergenic regions	6
Recombinations, chains and caps: resolving problems with the DCJ-indel model	6
Estimating similarity and distance using FracMinHash	6
Unbiased anchors for reliable genome-wide synteny detection	6
A new 1.375-approximation algorithm for sorting by transpositions	5
Compression algorithm for colored de Bruijn graphs	5
Pfp-fm: an accelerated FM-index	5

All galls are divided into three or more parts: recursive enumeration of labeled histories for galled trees