OOIR: Observatory of International Research

Papers

(The median citation count of Algorithms for Molecular Biology is 2. 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 2021-08-01 to 2025-08-01.)

Article	Citations
Unifying duplication episode clustering and gene-species mapping inference	31
Mem-based pangenome indexing for k-mer queries	24
Efficient gene orthology inference via large-scale rearrangements	17
A novel method for inference of acyclic chemical compounds with bounded branch-height based on artificial neural networks and integer programming	13
Fast, parallel, and cache-friendly suffix array construction	11
Binning long reads in metagenomics datasets using composition and coverage information	10
On the complexity of non-binary tree reconciliation with endosymbiotic gene transfer	10
Embedding gene trees into phylogenetic networks by conflict resolution algorithms	9
AlfaPang: alignment free algorithm for pangenome graph construction	8
Constructing phylogenetic networks via cherry picking and machine learning	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	7
On a greedy approach for genome scaffolding	7
Swiftly identifying strongly unique k-mers	7
Approximation algorithm for rearrangement distances considering repeated genes and intergenic regions	6
New algorithms for structure informed genome rearrangement	6
Faster computation of left-bounded shortest unique substrings	6
Estimating similarity and distance using FracMinHash	6
Reconstructing rearrangement phylogenies of natural genomes	5
Unbiased anchors for reliable genome-wide synteny detection	5
Compression algorithm for colored de Bruijn graphs	5
Two metrics on rooted unordered trees with labels	5
Fractional hitting sets for efficient multiset sketching	5
Recombinations, chains and caps: resolving problems with the DCJ-indel model	5
A new 1.375-approximation algorithm for sorting by transpositions	4

Constructing founder sets under allelic and non-allelic homologous recombination	4
Efficiently sparse listing of classes of optimal cophylogeny reconciliations	4
Pfp-fm: an accelerated FM-index	4
ESKEMAP: exact sketch-based read mapping	4
An optimized FM-index library for nucleotide and amino acid search	4
All galls are divided into three or more parts: recursive enumeration of labeled histories for galled trees	4
Heuristic algorithms for best match graph editing	4
Relative timing information and orthology in evolutionary scenarios	3
Bi-alignments with affine gaps costs	3
Space-efficient computation of k-mer dictionaries for large values of k	3
Metric multidimensional scaling for large single-cell datasets using neural networks	3
Predicting horizontal gene transfers with perfect transfer networks	2
New generalized metric based on branch length distance to compare B cell lineage trees	2
TINNiK: inference of the tree of blobs of a species network under the coalescent model	2
Investigating the complexity of the double distance problems	2
Locality-sensitive bucketing functions for the edit distance	2
Median quartet tree search algorithms using optimal subtree prune and regraft	2
Perplexity: evaluating transcript abundance estimation in the absence of ground truth	2
Testing the agreement of trees with internal labels	2