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 2022-01-01 to 2026-01-01.)

Article	Citations
Unifying duplication episode clustering and gene-species mapping inference	43
Mem-based pangenome indexing for k-mer queries	27
Fast, parallel, and cache-friendly suffix array construction	21
Efficient gene orthology inference via large-scale rearrangements	16
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	10
Constructing phylogenetic networks via cherry picking and machine learning	9
Correction: Heuristic shortest hyperpaths in cell signaling hypergraphs	9
Swiftly identifying strongly unique k-mers	8
New algorithms for structure informed genome rearrangement	8
Quartets enable statistically consistent estimation of cell lineage trees under an unbiased error and missingness model	8
AlfaPang: alignment free algorithm for pangenome graph construction	8
On a greedy approach for genome scaffolding	8
Estimating similarity and distance using FracMinHash	7
Faster computation of left-bounded shortest unique substrings	7
Unbiased anchors for reliable genome-wide synteny detection	7
Two metrics on rooted unordered trees with labels	6
Compression algorithm for colored de Bruijn graphs	6
Recombinations, chains and caps: resolving problems with the DCJ-indel model	6
Fractional hitting sets for efficient multiset sketching	6
Pfp-fm: an accelerated FM-index	6
Reconstructing rearrangement phylogenies of natural genomes	6
A new 1.375-approximation algorithm for sorting by transpositions	6
All galls are divided into three or more parts: recursive enumeration of labeled histories for galled trees	5

Constructing founder sets under allelic and non-allelic homologous recombination	5
ESKEMAP: exact sketch-based read mapping	5
Efficiently sparse listing of classes of optimal cophylogeny reconciliations	4
Rna triplet repeats: improved algorithms for structure prediction and interactions	4
Metric multidimensional scaling for large single-cell datasets using neural networks	4
Bi-alignments with affine gaps costs	4
New generalized metric based on branch length distance to compare B cell lineage trees	3
Relative timing information and orthology in evolutionary scenarios	3
Predicting horizontal gene transfers with perfect transfer networks	3
Space-efficient computation of k-mer dictionaries for large values of k	3
TINNiK: inference of the tree of blobs of a species network under the coalescent model	3
Perplexity: evaluating transcript abundance estimation in the absence of ground truth	3
Investigating the complexity of the double distance problems	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
Eulertigs: minimum plain text representation of k-mer sets without repetitions in linear time	2
Median quartet tree search algorithms using optimal subtree prune and regraft	2
Correction: Constructing founder sets under allelic and non-allelic homologous recombination	2