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 2021-04-01 to 2025-04-01.)

Article	Citations
Space-efficient representation of genomic k-mer count tables	27
Mem-based pangenome indexing for k-mer queries	20
Locality-sensitive bucketing functions for the edit distance	16
Compression algorithm for colored de Bruijn graphs	14
Unifying duplication episode clustering and gene-species mapping inference	12
Global exact optimisations for chloroplast structural haplotype scaffolding	12
Natural family-free genomic distance	11
Weighted ASTRID: fast and accurate species trees from weighted internode distances	10
Testing the agreement of trees with internal labels	10
Fast lightweight accurate xenograft sorting	10
Distinguishing linear and branched evolution given single-cell DNA sequencing data of tumors	10
phyBWT2: phylogeny reconstruction via eBWT positional clustering	9
Pfp-fm: an accelerated FM-index	8
Quartets enable statistically consistent estimation of cell lineage trees under an unbiased error and missingness model	8
Fast characterization of segmental duplication structure in multiple genome assemblies	7
New algorithms for structure informed genome rearrangement	6
Disk compression of k-mer sets	6
Adding hydrogen atoms to molecular models via fragment superimposition	6
Tree diet: reducing the treewidth to unlock FPT algorithms in RNA bioinformatics	6
A new 1.375-approximation algorithm for sorting by transpositions	6
Eulertigs: minimum plain text representation of k-mer sets without repetitions in linear time	5
On a greedy approach for genome scaffolding	5
Pangenomic genotyping with the marker array	5
Bayesian optimization with evolutionary and structure-based regularization for directed protein evolution	5
Fast, parallel, and cache-friendly suffix array construction	5

Exact transcript quantification over splice graphs	5
Using Robinson-Foulds supertrees in divide-and-conquer phylogeny estimation	5
Median quartet tree search algorithms using optimal subtree prune and regraft	5
Dollo-CDP: a polynomial-time algorithm for the clade-constrained large Dollo parsimony problem	4
Efficient gene orthology inference via large-scale rearrangements	4
A novel method for inference of acyclic chemical compounds with bounded branch-height based on artificial neural networks and integer programming	4
DeepGRP: engineering a software tool for predicting genomic repetitive elements using Recurrent Neural Networks with attention	3
The energy-spectrum of bicompatible sequences	3
Heuristic algorithms for best match graph editing	3
Fast and efficient Rmap assembly using the Bi-labelled de Bruijn graph	3
Approximation algorithm for rearrangement distances considering repeated genes and intergenic regions	3
ESKEMAP: exact sketch-based read mapping	2
An optimized FM-index library for nucleotide and amino acid search	2
Shape decomposition algorithms for laser capture microdissection	2
Correction: Constructing founder sets under allelic and non-allelic homologous recombination	2
Revisiting the complexity of and algorithms for the graph traversal edit distance and its variants	2
All galls are divided into three or more parts: recursive enumeration of labeled histories for galled trees	2
A simpler linear-time algorithm for the common refinement of rooted phylogenetic trees on a common leaf set	2
Constructing founder sets under allelic and non-allelic homologous recombination	2
Fulgor: a fast and compact k-mer index for large-scale matching and color queries	2
A classification algorithm based on dynamic ensemble selection to predict mutational patterns of the envelope protein in HIV-infected patients	2
EMMA: a new method for computing multiple sequence alignments given a constraint subset alignment	2