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 2021-11-01 to 2025-11-01.)

Article	Citations
Unifying duplication episode clustering and gene-species mapping inference	39
Mem-based pangenome indexing for k-mer queries	24
Fast, parallel, and cache-friendly suffix array construction	19
Efficient gene orthology inference via large-scale rearrangements	16
Binning long reads in metagenomics datasets using composition and coverage information	11
Embedding gene trees into phylogenetic networks by conflict resolution algorithms	9
On the complexity of non-binary tree reconciliation with endosymbiotic gene transfer	9
Constructing phylogenetic networks via cherry picking and machine learning	9
AlfaPang: alignment free algorithm for pangenome graph construction	8
Swiftly identifying strongly unique k-mers	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
On a greedy approach for genome scaffolding	7
New algorithms for structure informed genome rearrangement	7
Faster computation of left-bounded shortest unique substrings	6
Recombinations, chains and caps: resolving problems with the DCJ-indel model	6
Unbiased anchors for reliable genome-wide synteny detection	6
Reconstructing rearrangement phylogenies of natural genomes	6
Estimating similarity and distance using FracMinHash	6
Two metrics on rooted unordered trees with labels	6
A new 1.375-approximation algorithm for sorting by transpositions	5
Fractional hitting sets for efficient multiset sketching	5
Metric multidimensional scaling for large single-cell datasets using neural networks	4
Compression algorithm for colored de Bruijn graphs	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
An optimized FM-index library for nucleotide and amino acid search	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
Predicting horizontal gene transfers with perfect transfer networks	3
Space-efficient computation of k-mer dictionaries for large values of k	3
Perplexity: evaluating transcript abundance estimation in the absence of ground truth	3
Relative timing information and orthology in evolutionary scenarios	3
Investigating the complexity of the double distance problems	3
New generalized metric based on branch length distance to compare B cell lineage trees	2
Eulertigs: minimum plain text representation of k-mer sets without repetitions in linear time	2
Testing the agreement of trees with internal labels	2
Locality-sensitive bucketing functions for the edit distance	2
Correction: Constructing founder sets under allelic and non-allelic homologous recombination	2
TINNiK: inference of the tree of blobs of a species network under the coalescent model	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