RiNALMo: general-purpose RNA language models can generalize well on structure prediction tasks

A systematic benchmark of Nanopore long read RNA sequencing for transcript level analysis in human cell lines

The Applied genomics development strategy by the Croatian academy of sciences and arts paves the way for the future development of applied genomics in Croatia

RiNALMo: General-Purpose RNA Language Models Can Generalize Well on Structure Prediction Tasks

Geometric deep learning framework for de novo genome assembly

Detecting a wide range of epitranscriptomic modifications using a nanopore-sequencing-based computational approach with 1D score-clustering

Evaluating data requirements for high-quality haplotype-resolved genomes for creating robust pangenome references

Comparative Analysis of Nanopore-based Unsupervised Learning Methods in Epitranscriptomics

The Hitchhiker’s Guide to Sequencing Data Types and Volumes for Population-Scale Pangenome Construction

Telomere-to-telomere phased genome assembly using error-corrected Simplex nanopore reads

Rockfish: A transformer-based model for accurate 5-methylcytosine prediction from nanopore sequencing

Improving Metagenomic Classification Accuracy through Metagenome Assembly-driven Database Reduction

Facilitating genome structural variation analysis

Harnessing the Power of Language Models to Predict RNA Structure

Utilizing parental data in trio binning diploid de novo genome assembly

Reconstruction of short genomic sequences with graph convolutional networks

Reconstruction of short genomic sequences with graph convolutional networks

Removing chimeric reads improves metagenome assembly

Combining protein and RNA structures information in developing new scoring functions

Evaluation of RNA Atom Distance Prediction Models

Genome assembly and chemogenomic profiling of National Flower of Singapore Papilionanthe Miss Joaquim ‘Agnes’ reveals metabolic pathways regulating floral traits

Direct identification of A-to-I editing sites with nanopore native RNA sequencing

Asian Reference Genome Project

Time- and memory-efficient genome assembly with Raven

Detection of Modified Nucleotides Using Nanopore Sequencing and Deep Learning Methods

Rapid Microbe Detection Using Deep Learning

Whole genome comparison of Vibrio harveyi strains from the Mediterranean Sea

DNA Nanopore Sequencing Basecaller

Model dubokog učenja pore za sekvenciranje nanoporama

Efficacy of next-generation sequencing in bacterial zoonoses diagnostics

Deep learning model of nanopore sequencing pore

Deep Learning Model of Nanopore Sequencing Pore

Detection of Modified Nucleotide Clusters in Nanopore Sequenced RNA Reads

Detection of Modified Nucleotide Clusters in Nanopore Sequenced RNA Reads

Rapid alignment of high-fidelity seqeuncing data

Generalization of partial order alignment

Whole genome comparison of Vibrio harveyi strains from the Mediterranean Sea

Rapid overlapping of Single Molecule High-Fidelity Sequencing Data

Data Structure for Efficient Storage of Genome Sequencing Data

De Novo Diploid Assembly Using Third-Generation Sequencing Data

System For Monitoring a Subject During Google Search

A step towards neural genome assembly

Deep learning approach to determining the type of long reads

Benchmarking metagenomic classification tools for long read sequencing data

Microbe Detection Using Deep Learning

Genome Scaffolding Using Hi-C Sequencing

Pipeline for Detection Clusters of Modified Nucleotides in Nanopore Sequenced RNA Reads

De Novo Metagenome Assembly Using Third Generation Sequencing Dana

Microbe Detection Using Signal Processing and Locality Sensitive Hashing

Overlapping Single Molecule High-Fidelity Sequencing Data

Detecting Base Modifications in DNA Sequences

Statistical inference of exogenous and endogenous information propagation in social networks

Hybrid metagenomic assembly enables high- resolution analysis of resistance determinants and mobile elements in human microbiomes

Early Screening for Preeclampsia

Supervised learning approach to long read classification

Discovering gene variants from sequencing data

Read classification using deep learning methods

Reference-Guided de novo Genome Assembly

Disentangling Sources of Influence in Online Social Networks

Upper bound in genome assembly

Polishing of a DNA sequence using deep learning methods

Using Reference Database for Plasmid Prediction

A Programming Library for Mapping Long RNA Reads

Short Reads Mapping

Long Reads Mapping

Sequence to graph mapping

Classification of 1D-Signal Types Using Deep Learning

Algorithms for de novo assembly of large genomes

A Benchmark of Tools for Metagenomic Species Identification

A Programming Library for Mapping Long RNA Reads

A Benchmark of Tools for Metagenomic Species Identification

Approaches to metagenomic classification and assembly

RNA Splice Aware Mapper

Yet another de novo genome assembler

Landau-Vishkin-Nussinov Algorithm for Pair-wise Sequence Alignment

Approximate Algorithm for Computing Alignment Between Two Long Sequences

De Novo Metagenome Assembly Using Read Clustering

Fast protein sequence similarity search

End-to-End Deep Learning Model for Base Calling of MinION Nanopore Reads

A service for DNA backup

Scaffolding Assembled Genomes with Long Reads

Learned index structures

Horizontal silicon nanowires for surface-enhanced Raman spectroscopy

Scaffolding Assembled Genomes with Long Reads

Hidden Markov Model for Base Calling of MinION Nanopore Reads

Protein Database Search Using Partial Order Alignment

Mobile application for collecting user activity data

The assessment of the expected genome assembly completeness from available reads

Evaluation of tools for long read RNA-seq splice- aware alignment

Silicon Nanowires Substrates Fabrication for Ultra-Sensitive Surface Enhanced Raman Spectroscopy Sensors

Fast and accurate de novo genome assembly from long uncorrected reads

Edlib: a C/C ++ library for fast, exact sequence alignment using edit distance

Analysis of a Metagenomic Sample Obtained by Third Generation Sequencing Technology

Identification of 1D-Signal Types Using Unsupervised Deep Learning

De Novo Assembly using Unsupervised Read Categorization

De Novo Assembly using Semi-Supervised Read Categorization

Algorithms for Layout Phase of De Novo Genome Assembly

Unsupervised Learning of Sequencing Read Types

Differentiating between Exogenous and Endogenous Information Propagation in Social Networks

Modeling Peer and External Influence in Online Social Networks: Case of 2013 Referendum in Croatia

Algorithm for the Alignment of Two Partial Order Alignment Graphs

Deep Learning Model for Base Calling of MinION Nanopore Reads

Classification of 1D-Signal Types Using Semi- Supervised Deep Learning

Computing the Error Profiles of Third Generation Sequencing Technologies

Inference of influence in social networks

Ra – Rapid de novo genome assembler

Informatics

RNA Transcriptome Mapping with GraphMap

Trade-offs in query and target indexing for the selection of candidates in protein homology searches

Read classification using semi-supervised deep learning

MinCall | MinION end2end convolutional deep learning basecaller

Rala - Rapid layout module for de novo genome assembly

Manual detection of false overlaps occurring during genome assembly

dna2vec: vector representation of variable length k-mers

Classification of Large-Scale Biological Annotations Using Word Embeddings Derived from Corpora of Biomedical Research Literature

Detectability of Patient Zero Depending on its Position in the Network

Real-Time Analysis of a Metagenomic Sample Obtained by Nanopore Based Sequencing Technology

Long RNA-Seq Alignment

RNA-seq Alignment Using Existing Gene Annotations

Tree of Bloom Filters

SWORD—a highly efficient protein database search

Evaluation of hybrid and non-hybrid methods for de novo assembly of nanopore reads

De novo assembly using long error-prone reads

TGTP-DB – a database for extracting genome, transcriptome and proteome data using taxonomy

Big data in the age of genomics

SWORD—a highly efficient protein database search

SIFT missense predictions for genomes

Fast and sensitive mapping of nanopore sequencing reads with GraphMap

Racon - Rapid consensus module for raw de novo genome assembly of long uncorrected reads

ALGORITHMS FOR DE NOVO GENOME ASSEMBLY FROM THIRD GENERATION SEQUENCING DATA

A reduced gene database for precision species detection

Identification of Patient Zero in Static and Temporal Networks : Robustness and Limitations

SW#db: GPU-Accelerated Exact Sequence Similarity Database Search

Scaffolding using long error-prone reads

Statistical inference algorithms for epidemic processes on complex networks

Enhanced suffix array

EAGLER - Eliminating Assembly Gaps by Long Extending Reads

Generating consensus sequence using partially ordered multiple sequence alignment graphs

Reconstruction of a phylogenetic tree using a neighbor-joining method

Suffix Tree

Some new results on assessment of Q-gram filter efficiency

Continuum model of gene expression

Phylogenetic tree reconstruction using maximum parsimony branch-and-bound algorithm

Long read aligner

Global sequence alignment tool

Splice isoform identification from transcript graphs

De novo transcriptome assembly

Long Read RNA-seq Mapper

An SIMD dynamic programming C/C++ library

ExoLocator—an online view into genetic makeup of vertebrate proteins

Genome alignment tool

Tool for fast searching of protein sequences in databases

De novo metagenomic assembly using Bayesian model-based clustering

Identify pathogen organisms from a stream of RNA sequences

Computational approaches for refinement and validation of genome assemblies

RNA-seq mapper

Statistical Inference Framework for Source Detection of Contagion Processes on Arbitrary Network Structures

Simplification of the Overlap Graph

Finding overlapping DNA reads

Information propagation in online social networks

From Short to Long Reads: Benchmarking Assembly Tools

Approaches to DNA de novo Assembly

Proteini i nukleinske kiseline u vremenu i prostoru

Aspects of DNA Assembly Acceleration on Reconfigurable Platforms

GPU implementation of a space and time optimal parallel sequence alignment algorithm

The evaluation of protein database searching tools

Optical map assembly: graph correction module

Alternative splicing

Evaluation of a method for long read error correction

SW# - Sequence alignment library utilizing graphics processing units

Computing method for determing protein interactions

Protein database search optimization based on CUDA and MPI

Web interface for sequence alignment

Epidemic centrality — is there an underestimated epidemic impact of network peripheral nodes?

SW#–GPU-enabled exact alignments on genome scale

FastSIR algorithm : A fast algorithm for the simulation of the epidemic spread in large networks by using the susceptible–infected–recovered compartment model

Tool for aligning long DNA reads

GPU implementation of an efficient linear-memory algorithm for local sequence alignment

Web application for comparative analysis of protein paralogs

Implementation of compressed data structure for text searching based on FMindex

CUDA implementation of the algorithm for simulating the epidemic spreading over large networks

SWIG - Aligning structures using iterative application of Smith-Waterman algorithm

A tool for simulating sequence reads

Application for automatic analysis of protein coding genes

Large-Scale Functional Organization of Long-Range Chromatin Interaction Networks

BioMe : biologically relevant metals

Orhobalancer: web application for creation of taxonomically balanced sets of orthologous protein sequences

FM index implementation

Prediction of interacting protein residues using sequence and structure data.

BioMe - statistical analyzer for biologically relevant metals

Make Me Move – didactic computer game for learning structural molecular biology

GPU implementation of time efficient linear space local alignment algorithm

Adaptive wavelet transform implemented on CUDA platform

Electrostatic charge distribution calculation in CUDA

Protein docking tool: visualization module

Optimisation of firewall security rules

Smith-Waterman algorithm implementation using graphic cards with CUDA architecture

Prediction of solvent accessible surface area from protein sequence

Phase diagram of epidemic spreading — unimodal vs. bimodal probability distributions

Epidemic centrality – identifying “superspreaders” in complex networks

Implementation of algorithm for computing protein interactions

Detecting epistasis using ant colony optimization algorithm

Improved algorithm for selection and validation of best multivariate structure-property molecular models

Secondary structure prediction using only sequence data

Multiresolution analysis of macromolecular structures

Parallel Protein Docking Tool

Protein Docking tool: rotation and scoring modules

Protein Docking Tool: Steric Scan module

A solution for accessing to servers that are inside of mobile networks

Database of metals in proteins

Influence of quarantine on epidemic spread

Simulation of the impact organizing parties on propagation of viruses at spreading the infection

Representation of metals in proteins

Secondary protein structure analysis by the method of signal processing

Protein Docking Tool: Module For Interaction Detection

Prediction of protein-protein interactions using Random Forests

Analiza kodirajućih regija u genomu

Prediction of Protein-Protein Interaction Sites in Sequences and 3D Structures by Random Forests

Classification of coding regions in the genome

Comparison of the RADIUS and Diameter Protocols

Computational method for prediction of protein-protein interaction sites

Utjecaj zaraze na svojstva kompleksne mreže

Identification of key players in complex networks of blogs

Visualization of macromolecules

Metals in proteins: correlation between the metal- ion type, coordination number and the amino-acid residues involved in the coordination

PSAIA - Protein Structure and Interaction Analyzer

The automated construction of a testing set for predicting of protein interactions

Correlating protein surface shape and hydrophobicity using spherical harmonical expansions

Prediction of protein-protein hetero interaction sites from local sequence information using Random Forest

Protecting and controlling Virtual LANs by Linux router-firewall

Guidline to maintain an efficient email working environment

The content charging model in mobile packet networks

Mobile content efficiency and business model

WLAN securtiy

Content charging models in mobile packet networks