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 2021-12-01 to 2025-12-01.)

Article	Citations
Unifying duplication episode clustering and gene-species mapping inference	40
Mem-based pangenome indexing for k-mer queries	25
Fast, parallel, and cache-friendly suffix array construction	20
Efficient gene orthology inference via large-scale rearrangements	16
Binning long reads in metagenomics datasets using composition and coverage information	11
Correction: Heuristic shortest hyperpaths in cell signaling hypergraphs	9
On the complexity of non-binary tree reconciliation with endosymbiotic gene transfer	9
Constructing phylogenetic networks via cherry picking and machine learning	9
Embedding gene trees into phylogenetic networks by conflict resolution algorithms	9
AlfaPang: alignment free algorithm for pangenome graph construction	8
Quartets enable statistically consistent estimation of cell lineage trees under an unbiased error and missingness model	8
Swiftly identifying strongly unique k-mers	8
On a greedy approach for genome scaffolding	7
Faster computation of left-bounded shortest unique substrings	7
New algorithms for structure informed genome rearrangement	7
Reconstructing rearrangement phylogenies of natural genomes	6
Recombinations, chains and caps: resolving problems with the DCJ-indel model	6
Estimating similarity and distance using FracMinHash	6
Fractional hitting sets for efficient multiset sketching	6
Unbiased anchors for reliable genome-wide synteny detection	6
Two metrics on rooted unordered trees with labels	6
All galls are divided into three or more parts: recursive enumeration of labeled histories for galled trees	5
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

An optimized FM-index library for nucleotide and amino acid search	4
Metric multidimensional scaling for large single-cell datasets using neural networks	4
ESKEMAP: exact sketch-based read mapping	4
Bi-alignments with affine gaps costs	4
Constructing founder sets under allelic and non-allelic homologous recombination	4
Efficiently sparse listing of classes of optimal cophylogeny reconciliations	4
Space-efficient computation of k-mer dictionaries for large values of k	4
Predicting horizontal gene transfers with perfect transfer networks	3
Relative timing information and orthology in evolutionary scenarios	3
Testing the agreement of trees with internal labels	3
TINNiK: inference of the tree of blobs of a species network under the coalescent model	3
Investigating the complexity of the double distance problems	3
New generalized metric based on branch length distance to compare B cell lineage trees	3
Perplexity: evaluating transcript abundance estimation in the absence of ground truth	3
Locality-sensitive bucketing functions for the edit distance	2
Revisiting the complexity of and algorithms for the graph traversal edit distance and its variants	2
Median quartet tree search algorithms using optimal subtree prune and regraft	2
Fulgor: a fast and compact k-mer index for large-scale matching and color queries	2
Eulertigs: minimum plain text representation of k-mer sets without repetitions in linear time	2
Correction: Constructing founder sets under allelic and non-allelic homologous recombination	2
Heuristic shortest hyperpaths in cell signaling hypergraphs	2