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 2020-11-01 to 2024-11-01.)

Article	Citations
Fast characterization of segmental duplication structure in multiple genome assemblies	18
Binning long reads in metagenomics datasets using composition and coverage information	15
Improving metagenomic binning results with overlapped bins using assembly graphs	14
Fulgor: a fast and compact k-mer index for large-scale matching and color queries	13
Fast lightweight accurate xenograft sorting	12
INGOT-DR: an interpretable classifier for predicting drug resistance in M. tuberculosis	10
Bayesian optimization with evolutionary and structure-based regularization for directed protein evolution	10
Disk compression of k-mer sets	9
Heuristic shortest hyperpaths in cell signaling hypergraphs	8
The Bourque distances for mutation trees of cancers	8
Parsimonious Clone Tree Integration in cancer	8
A new 1.375-approximation algorithm for sorting by transpositions	8
Approximation algorithm for rearrangement distances considering repeated genes and intergenic regions	7
On weighted k-mer dictionaries	6
Space-efficient representation of genomic k-mer count tables	6
An improved approximation algorithm for the reversal and transposition distance considering gene order and intergenic sizes	6
Treewidth-based algorithms for the small parsimony problem on networks	6
Distinguishing linear and branched evolution given single-cell DNA sequencing data of tumors	6
Embedding gene trees into phylogenetic networks by conflict resolution algorithms	5
A novel method for inference of acyclic chemical compounds with bounded branch-height based on artificial neural networks and integer programming	5
Pangenomic genotyping with the marker array	4
Mono-valent salt corrections for RNA secondary structures in the ViennaRNA package	4
Tree diet: reducing the treewidth to unlock FPT algorithms in RNA bioinformatics	4
Heuristic algorithms for best match graph editing	4
Natural family-free genomic distance	4

An optimized FM-index library for nucleotide and amino acid search	3
Adding hydrogen atoms to molecular models via fragment superimposition	3
Constructing phylogenetic networks via cherry picking and machine learning	3
LazyB: fast and cheap genome assembly	3
Exact transcript quantification over splice graphs	3
Quantifying steric hindrance and topological obstruction to protein structure superposition	3
Fast and accurate structure probability estimation for simultaneous alignment and folding of RNAs with Markov chains	3
Weighted ASTRID: fast and accurate species trees from weighted internode distances	3
Bi-alignments with affine gaps costs	3
Approximate search for known gene clusters in new genomes using PQ-trees	2
A topology-marginal composite likelihood via a generalized phylogenetic pruning algorithm	2
Fast and efficient Rmap assembly using the Bi-labelled de Bruijn graph	2
Using the longest run subsequence problem within homology-based scaffolding	2
All galls are divided into three or more parts: recursive enumeration of labeled histories for galled trees	2
Shape decomposition algorithms for laser capture microdissection	2
Efficient privacy-preserving variable-length substring match for genome sequence	2
A simpler linear-time algorithm for the common refinement of rooted phylogenetic trees on a common leaf set	2
Locality-sensitive bucketing functions for the edit distance	2