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 2022-08-01 to 2026-08-01.)

Article	Citations
Unifying duplication episode clustering and gene-species mapping inference	38
Mem-based pangenome indexing for k-mer queries	19
Improving spliced alignment by modeling splice sites with deep learning	18
Efficient gene orthology inference via large-scale rearrangements	17
On the complexity of non-binary tree reconciliation with endosymbiotic gene transfer	14
Fast, parallel, and cache-friendly suffix array construction	14
Pattern matching with Elastic-Degenerate strings and Elastic-Founder graphs	13
Correction: Heuristic shortest hyperpaths in cell signaling hypergraphs	10
Constructing phylogenetic networks via cherry picking and machine learning	9
AlfaPang: alignment free algorithm for pangenome graph construction	9
Quartets enable statistically consistent estimation of cell lineage trees under an unbiased error and missingness model	8
On a greedy approach for genome scaffolding	8
Swiftly identifying strongly unique k-mers	8
Faster computation of left-bounded shortest unique substrings	7
New algorithms for structure informed genome rearrangement	7
Extension of partial atom-to-atom maps: uniqueness and algorithms	7
Mutational signature refitting on sparse pan-cancer data	6
Estimating similarity and distance using FracMinHash	6
Unbiased anchors for reliable genome-wide synteny detection	6
Recombinations, chains and caps: resolving problems with the DCJ-indel model	5
Reconstructing rearrangement phylogenies of natural genomes	5
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
Fractional hitting sets for efficient multiset sketching	4
Computing double-pushout graph transformation rules and atom-to-atom maps from KEGG RCLASS data	4

Orientability of undirected phylogenetic networks to a desired class: practical algorithms and application to tree-child orientation	4
Constructing founder sets under allelic and non-allelic homologous recombination	4
Dolphyin: a combinatorial algorithm for identifying 1-Dollo phylogenies in cancer	4
Compression algorithm for colored de Bruijn graphs	4
ESKEMAP: exact sketch-based read mapping	4
Space-efficient computation of k-mer dictionaries for large values of k	3
Probing transcription factor subsets in gene regulatory networks	3
New generalized metric based on branch length distance to compare B cell lineage trees	3
Relative timing information and orthology in evolutionary scenarios	3
Metric multidimensional scaling for large single-cell datasets using neural networks	3
Investigating the complexity of the double distance problems	3
RNA triplet repeats: improved algorithms for structure prediction and interactions	3
Locality-sensitive bucketing functions for the edit distance	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
Predicting horizontal gene transfers with perfect transfer networks	2
Revisiting the complexity of and algorithms for the graph traversal edit distance and its variants	2
TINNiK: inference of the tree of blobs of a species network under the coalescent model	2
Eulertigs: minimum plain text representation of k-mer sets without repetitions in linear time	2