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 2021-05-01 to 2025-05-01.)

Article	Citations
Natural family-free genomic distance	28
Unifying duplication episode clustering and gene-species mapping inference	20
Mem-based pangenome indexing for k-mer queries	16
Efficient gene orthology inference via large-scale rearrangements	14
Fast, parallel, and cache-friendly suffix array construction	12
A novel method for inference of acyclic chemical compounds with bounded branch-height based on artificial neural networks and integer programming	12
Bayesian optimization with evolutionary and structure-based regularization for directed protein evolution	11
On the complexity of non-binary tree reconciliation with endosymbiotic gene transfer	10
Constructing phylogenetic networks via cherry picking and machine learning	10
Binning long reads in metagenomics datasets using composition and coverage information	10
Embedding gene trees into phylogenetic networks by conflict resolution algorithms	10
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
New algorithms for structure informed genome rearrangement	7
On a greedy approach for genome scaffolding	7
Unbiased anchors for reliable genome-wide synteny detection	6
Compression algorithm for colored de Bruijn graphs	6
Approximation algorithm for rearrangement distances considering repeated genes and intergenic regions	6
Two metrics on rooted unordered trees with labels	6
Disk compression of k-mer sets	6
Recombinations, chains and caps: resolving problems with the DCJ-indel model	6
Fractional hitting sets for efficient multiset sketching	6
A new 1.375-approximation algorithm for sorting by transpositions	5
Heuristic algorithms for best match graph editing	5
Constructing founder sets under allelic and non-allelic homologous recombination	5

ESKEMAP: exact sketch-based read mapping	5
All galls are divided into three or more parts: recursive enumeration of labeled histories for galled trees	5
Pfp-fm: an accelerated FM-index	5
Efficiently sparse listing of classes of optimal cophylogeny reconciliations	4
Metric multidimensional scaling for large single-cell datasets using neural networks	4
Improving metagenomic binning results with overlapped bins using assembly graphs	4
An optimized FM-index library for nucleotide and amino acid search	4
Bi-alignments with affine gaps costs	4
New generalized metric based on branch length distance to compare B cell lineage trees	3
Space-efficient computation of k-mer dictionaries for large values of k	3
Predicting horizontal gene transfers with perfect transfer networks	3
Investigating the complexity of the double distance problems	3
Relative timing information and orthology in evolutionary scenarios	3
Perplexity: evaluating transcript abundance estimation in the absence of ground truth	3
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
The energy-spectrum of bicompatible sequences	2
Testing the agreement of trees with internal labels	2
Correction: Constructing founder sets under allelic and non-allelic homologous recombination	2
Eulertigs: minimum plain text representation of k-mer sets without repetitions in linear time	2
Exact transcript quantification over splice graphs	2
Locality-sensitive bucketing functions for the edit distance	2
Fulgor: a fast and compact k-mer index for large-scale matching and color queries	2