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 2022-05-01 to 2026-05-01.)

Article	Citations
Improving spliced alignment by modeling splice sites with deep learning	35
Unifying duplication episode clustering and gene-species mapping inference	24
Mem-based pangenome indexing for k-mer queries	18
Fast, parallel, and cache-friendly suffix array construction	13
Binning long reads in metagenomics datasets using composition and coverage information	12
Efficient gene orthology inference via large-scale rearrangements	12
On the complexity of non-binary tree reconciliation with endosymbiotic gene transfer	11
Embedding gene trees into phylogenetic networks by conflict resolution algorithms	11
Pattern matching with Elastic-Degenerate strings and Elastic-Founder graphs	9
Correction: Heuristic shortest hyperpaths in cell signaling hypergraphs	9
Constructing phylogenetic networks via cherry picking and machine learning	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	7
Swiftly identifying strongly unique k-mers	7
New algorithms for structure informed genome rearrangement	7
Estimating similarity and distance using FracMinHash	6
Faster computation of left-bounded shortest unique substrings	6
Unbiased anchors for reliable genome-wide synteny detection	6
Reconstructing rearrangement phylogenies of natural genomes	5
Recombinations, chains and caps: resolving problems with the DCJ-indel model	5
Constructing founder sets under allelic and non-allelic homologous recombination	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
Computing double-pushout graph transformation rules and atom-to-atom maps from KEGG RCLASS data	4

Two metrics on rooted unordered trees with labels	4
Compression algorithm for colored de Bruijn graphs	4
Fractional hitting sets for efficient multiset sketching	4
Bi-alignments with affine gaps costs	3
Relative timing information and orthology in evolutionary scenarios	3
Metric multidimensional scaling for large single-cell datasets using neural networks	3
ESKEMAP: exact sketch-based read mapping	3
Space-efficient computation of k-mer dictionaries for large values of k	3
RNA triplet repeats: improved algorithms for structure prediction and interactions	3
Investigating the complexity of the double distance problems	3
Orientability of undirected phylogenetic networks to a desired class: practical algorithms and application to tree-child orientation	3
Predicting horizontal gene transfers with perfect transfer networks	2
Locality-sensitive bucketing functions for the edit distance	2
Correction: Constructing founder sets under allelic and non-allelic homologous recombination	2
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
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
Median quartet tree search algorithms using optimal subtree prune and regraft	2