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

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

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

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

Comparative Analysis of Nanopore-based Unsupervised Learning Methods in Epitranscriptomics

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

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

Reconstruction of short genomic sequences with graph convolutional networks

Utilizing parental data in trio binning diploid de novo genome assembly

Facilitating genome structural variation analysis

Reconstruction of short genomic sequences with graph convolutional networks

Improving Metagenomic Classification Accuracy through Metagenome Assembly-driven Database Reduction

Harnessing the Power of Language Models to Predict RNA Structure

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

Asian Reference Genome Project

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

Combining protein and RNA structures information in developing new scoring functions

Evaluation of RNA Atom Distance Prediction Models

Removing chimeric reads improves metagenome assembly

Detection of Modified Nucleotide Clusters in Nanopore Sequenced RNA Reads

Whole genome comparison of Vibrio harveyi strains from the Mediterranean Sea

Data Structure for Efficient Storage of Genome Sequencing Data

Generalization of partial order alignment

Rapid alignment of high-fidelity seqeuncing data

Time- and memory-efficient genome assembly with Raven

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

Efficacy of next-generation sequencing in bacterial zoonoses diagnostics

DNA Nanopore Sequencing Basecaller

Deep learning model of nanopore sequencing pore

Whole genome comparison of Vibrio harveyi strains from the Mediterranean Sea

Detection of Modified Nucleotide Clusters in Nanopore Sequenced RNA Reads

Rapid Microbe Detection Using Deep Learning

Detection of Modified Nucleotides Using Nanopore Sequencing and Deep Learning Methods

Deep Learning Model of Nanopore Sequencing Pore

Rapid overlapping of Single Molecule High-Fidelity Sequencing Data

Deep Learning Model of Nanopore Sequencing Pore

De Novo Diploid Assembly Using Third-Generation Sequencing Data

Microbe Detection Using Signal Processing and Locality Sensitive Hashing

System For Monitoring a Subject During Google Search

De Novo Metagenome Assembly Using Third Generation Sequencing Dana

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

Deep learning approach to determining the type of long reads

A step towards neural genome assembly

Overlapping Single Molecule High-Fidelity Sequencing Data

Microbe Detection Using Deep Learning

Benchmarking metagenomic classification tools for long read sequencing data

Genome Scaffolding Using Hi-C Sequencing

Detecting Base Modifications in DNA Sequences

Upper bound in genome assembly

Reference-Guided de novo Genome Assembly

Read classification using deep learning methods

Discovering gene variants from sequencing data

A Programming Library for Mapping Long RNA Reads

Short Reads Mapping

Long Reads Mapping

A Benchmark of Tools for Metagenomic Species Identification

Early Screening for Preeclampsia

Statistical inference of exogenous and endogenous information propagation in social networks

Algorithms for de novo assembly of large genomes

A Programming Library for Mapping Long RNA Reads

Classification of 1D-Signal Types Using Deep Learning

Sequence to graph mapping

Using Reference Database for Plasmid Prediction

A Benchmark of Tools for Metagenomic Species Identification

Approaches to metagenomic classification and assembly

Yet another de novo genome assembler

Supervised learning approach to long read classification

RNA Splice Aware Mapper

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

Disentangling Sources of Influence in Online Social Networks

Polishing of a DNA sequence using deep learning methods

Horizontal silicon nanowires for surface-enhanced Raman spectroscopy

Hidden Markov Model for Base Calling of MinION Nanopore Reads

Fast protein sequence similarity search

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

Approximate Algorithm for Computing Alignment Between Two Long Sequences

The assessment of the expected genome assembly completeness from available reads

A service for DNA backup

Learned index structures

Mobile application for collecting user activity data

Scaffolding Assembled Genomes with Long Reads

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

De Novo Metagenome Assembly Using Read Clustering

Scaffolding Assembled Genomes with Long Reads

Protein Database Search Using Partial Order Alignment

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

Read classification using semi-supervised deep learning

MinCall | MinION end2end convolutional deep learning basecaller

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

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

Fast and accurate de novo genome assembly from long uncorrected reads

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

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

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

Ra – Rapid de novo genome assembler

Rala - Rapid layout module for de novo genome assembly

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

Computing the Error Profiles of Third Generation Sequencing Technologies

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

Deep Learning Model for Base Calling of MinION Nanopore Reads

Identification of 1D-Signal Types Using Unsupervised Deep Learning

Informatics

De Novo Assembly using Unsupervised Read Categorization

Inference of influence in social networks

Algorithm for the Alignment of Two Partial Order Alignment Graphs

Manual detection of false overlaps occurring during genome assembly

dna2vec: vector representation of variable length k-mers

Analysis of a Metagenomic Sample Obtained by Third Generation Sequencing Technology

RNA Transcriptome Mapping with GraphMap

De novo assembly using long error-prone reads

Tree of Bloom Filters

RNA-seq Alignment Using Existing Gene Annotations

Long RNA-Seq Alignment

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

Detectability of Patient Zero Depending on its Position in the Network

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

Fast and sensitive mapping of nanopore sequencing reads with GraphMap

SIFT missense predictions for genomes

SWORD—a highly efficient protein database search

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

ALGORITHMS FOR DE NOVO GENOME ASSEMBLY FROM THIRD GENERATION SEQUENCING DATA

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

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

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

A reduced gene database for precision species detection

Splice isoform identification from transcript graphs

EAGLER - Eliminating Assembly Gaps by Long Extending Reads

Generating consensus sequence using partially ordered multiple sequence alignment graphs

Long read aligner

Global sequence alignment tool

Reconstruction of a phylogenetic tree using a neighbor-joining method

Suffix Tree

Continuum model of gene expression

Statistical inference algorithms for epidemic processes on complex networks

Enhanced suffix array

Scaffolding using long error-prone reads

De novo transcriptome assembly

Long Read RNA-seq Mapper

Some new results on assessment of Q-gram filter efficiency

Simplification of the Overlap Graph

Information propagation in online social networks

Genome alignment tool

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

De novo metagenomic assembly using Bayesian model-based clustering

RNA-seq mapper

ExoLocator—an online view into genetic makeup of vertebrate proteins

An SIMD dynamic programming C/C++ library

Tool for fast searching of protein sequences in databases

Identify pathogen organisms from a stream of RNA sequences

Finding overlapping DNA reads

Computational approaches for refinement and validation of genome assemblies

The evaluation of protein database searching tools

Tool for aligning long DNA reads

SW#–GPU-enabled exact alignments on genome scale

Web interface for sequence alignment

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

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

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

Approaches to DNA de novo Assembly

From Short to Long Reads: Benchmarking Assembly Tools

Protein database search optimization based on CUDA and MPI

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

Proteins and Nucleic Acids in Space and Time

Aspects of DNA Assembly Acceleration on Reconfigurable Platforms

BioMe - statistical analyzer for biologically relevant metals

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

GPU implementation of time efficient linear space local alignment algorithm

Prediction of interacting protein residues using sequence and structure data.

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

BioMe : biologically relevant metals

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

FM index implementation

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

Application for automatic analysis of protein coding genes

Implementation of compressed data structure for text searching based on FMindex

A tool for simulating sequence reads

Web application for comparative analysis of protein paralogs

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

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

Epidemic centrality – identifying “superspreaders” in complex networks

Optimisation of firewall security rules

Adaptive wavelet transform implemented on CUDA platform

Protein docking tool: visualization module

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

Electrostatic charge distribution calculation in CUDA

Detecting epistasis using ant colony optimization algorithm

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

Smith-Waterman algorithm implementation using graphic cards with CUDA architecture

Implementation of algorithm for computing protein interactions

Prediction of solvent accessible surface area from protein sequence

Multiresolution analysis of macromolecular structures

Influence of quarantine on epidemic spread

Representation of metals in proteins

Parallel Protein Docking Tool

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

Protein Docking Tool: Steric Scan module

Secondary structure prediction using only sequence data

Secondary protein structure analysis by the method of signal processing

Protein Docking tool: rotation and scoring modules

Prediction of protein-protein interactions using Random Forests

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

Protein Docking Tool: Module For Interaction Detection

Database of metals in proteins

Classification of coding regions in the genome

Genome coding regions analysis

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

PSAIA - Protein Structure and Interaction Analyzer

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

Visualization of macromolecules

Computational method for prediction of protein-protein interaction sites

Influence of epidemic spread on network structure

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

Comparison of the RADIUS and Diameter Protocols

Identification of key players in complex networks of blogs

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

WLAN securtiy

Mobile content efficiency and business model

Content charging models in mobile packet networks