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 2021-06-01 to 2025-06-01.)

Article	Citations
Unifying duplication episode clustering and gene-species mapping inference	29
Mem-based pangenome indexing for k-mer queries	21
A novel method for inference of acyclic chemical compounds with bounded branch-height based on artificial neural networks and integer programming	16
Fast, parallel, and cache-friendly suffix array construction	12
Bayesian optimization with evolutionary and structure-based regularization for directed protein evolution	12
Efficient gene orthology inference via large-scale rearrangements	11
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
On the complexity of non-binary tree reconciliation with endosymbiotic gene transfer	10
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
Correction: Heuristic shortest hyperpaths in cell signaling hypergraphs	8
Disk compression of k-mer sets	7
New algorithms for structure informed genome rearrangement	7
On a greedy approach for genome scaffolding	7
Estimating similarity and distance using FracMinHash	6
Unbiased anchors for reliable genome-wide synteny detection	6
Fractional hitting sets for efficient multiset sketching	6
Two metrics on rooted unordered trees with labels	6
Approximation algorithm for rearrangement distances considering repeated genes and intergenic regions	6
Recombinations, chains and caps: resolving problems with the DCJ-indel model	6
All galls are divided into three or more parts: recursive enumeration of labeled histories for galled trees	5
A new 1.375-approximation algorithm for sorting by transpositions	5
Compression algorithm for colored de Bruijn graphs	5

Pfp-fm: an accelerated FM-index	5
Constructing founder sets under allelic and non-allelic homologous recombination	4
Metric multidimensional scaling for large single-cell datasets using neural networks	4
Heuristic algorithms for best match graph editing	4
Efficiently sparse listing of classes of optimal cophylogeny reconciliations	4
An optimized FM-index library for nucleotide and amino acid search	4
ESKEMAP: exact sketch-based read mapping	4
Perplexity: evaluating transcript abundance estimation in the absence of ground truth	3
Relative timing information and orthology in evolutionary scenarios	3
Investigating the complexity of the double distance problems	3
Bi-alignments with affine gaps costs	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	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
Locality-sensitive bucketing functions for the edit distance	2
Testing the agreement of trees with internal labels	2
The energy-spectrum of bicompatible sequences	2
New generalized metric based on branch length distance to compare B cell lineage trees	2
Median quartet tree search algorithms using optimal subtree prune and regraft	2
DeepGRP: engineering a software tool for predicting genomic repetitive elements using Recurrent Neural Networks with attention	2