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 2021-09-01 to 2025-09-01.)

Article	Citations
Mem-based pangenome indexing for k-mer queries	33
Unifying duplication episode clustering and gene-species mapping inference	24
Efficient gene orthology inference via large-scale rearrangements	17
Fast, parallel, and cache-friendly suffix array construction	13
Binning long reads in metagenomics datasets using composition and coverage information	11
On the complexity of non-binary tree reconciliation with endosymbiotic gene transfer	10
Embedding gene trees into phylogenetic networks by conflict resolution algorithms	9
Constructing phylogenetic networks via cherry picking and machine learning	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
Correction: Heuristic shortest hyperpaths in cell signaling hypergraphs	8
Swiftly identifying strongly unique k-mers	8
On a greedy approach for genome scaffolding	7
New algorithms for structure informed genome rearrangement	6
Reconstructing rearrangement phylogenies of natural genomes	6
Estimating similarity and distance using FracMinHash	6
Approximation algorithm for rearrangement distances considering repeated genes and intergenic regions	6
Faster computation of left-bounded shortest unique substrings	6
Unbiased anchors for reliable genome-wide synteny detection	6
Fractional hitting sets for efficient multiset sketching	5
Two metrics on rooted unordered trees with labels	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
Pfp-fm: an accelerated FM-index	4

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