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 2020-04-01 to 2024-04-01.)

Article	Citations
Alignment- and reference-free phylogenomics with colored de Bruijn graphs	15
Improving metagenomic binning results with overlapped bins using assembly graphs	12
From pairs of most similar sequences to phylogenetic best matches	10
Binning long reads in metagenomics datasets using composition and coverage information	9
Fast lightweight accurate xenograft sorting	9
Evolution through segmental duplications and losses: a Super-Reconciliation approach	9
Fast characterization of segmental duplication structure in multiple genome assemblies	9
INGOT-DR: an interpretable classifier for predicting drug resistance in M. tuberculosis	9
Bayesian optimization with evolutionary and structure-based regularization for directed protein evolution	9
A new 1.375-approximation algorithm for sorting by transpositions	7
gsufsort: constructing suffix arrays, LCP arrays and BWTs for string collections	7
Disk compression of k-mer sets	7
An improved approximation algorithm for the reversal and transposition distance considering gene order and intergenic sizes	6
Space-efficient representation of genomic k-mer count tables	6
The Bourque distances for mutation trees of cancers	6
Distinguishing linear and branched evolution given single-cell DNA sequencing data of tumors	6
Approximation algorithm for rearrangement distances considering repeated genes and intergenic regions	6
Parsimonious Clone Tree Integration in cancer	5
The distance and median problems in the single-cut-or-join model with single-gene duplications	5
Reconstruction of time-consistent species trees	5
Heuristic shortest hyperpaths in cell signaling hypergraphs	5
Embedding gene trees into phylogenetic networks by conflict resolution algorithms	4
A novel method for inference of acyclic chemical compounds with bounded branch-height based on artificial neural networks and integer programming	4
Treewidth-based algorithms for the small parsimony problem on networks	3
Fulgor: a fast and compact k-mer index for large-scale matching and color queries	3

Pangenomic genotyping with the marker array	3
Detecting transcriptomic structural variants in heterogeneous contexts via the Multiple Compatible Arrangements Problem	3
A simpler linear-time algorithm for the common refinement of rooted phylogenetic trees on a common leaf set	3
Exact transcript quantification over splice graphs	3
LazyB: fast and cheap genome assembly	3
Context-aware seeds for read mapping	3
Bi-alignments with affine gaps costs	2
On weighted k-mer dictionaries	2
Efficient privacy-preserving variable-length substring match for genome sequence	2
On an enhancement of RNA probing data using information theory	2
Fast and accurate structure probability estimation for simultaneous alignment and folding of RNAs with Markov chains	2
Tree diet: reducing the treewidth to unlock FPT algorithms in RNA bioinformatics	2
Automated design of dynamic programming schemes for RNA folding with pseudoknots	2
Mono-valent salt corrections for RNA secondary structures in the ViennaRNA package	2
Precise parallel volumetric comparison of molecular surfaces and electrostatic isopotentials	2
All galls are divided into three or more parts: recursive enumeration of labeled histories for galled trees	2
Fast and efficient Rmap assembly using the Bi-labelled de Bruijn graph	2
Natural family-free genomic distance	2
Approximate search for known gene clusters in new genomes using PQ-trees	2
Quantifying steric hindrance and topological obstruction to protein structure superposition	2
Constructing phylogenetic networks via cherry picking and machine learning	2
Fast computation of genome-metagenome interaction effects	2
Heuristic algorithms for best match graph editing	2
Shape decomposition algorithms for laser capture microdissection	2
Adding hydrogen atoms to molecular models via fragment superimposition	2