
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
Teaching
University undergraduate
- Algorithms and Data Structures (Lecturer in charge)
- Algorithms and Data Structures (Lecturer in charge)
- Bioinformatics 1 (Lecturer in charge, Lecturer in charge, Lecturer in charge)
- Bioinformatics 1 (Lecturer in charge, Lecturer in charge)
- BSc Thesis (Lecturers)
- Final BSc Thesis (Lecturers)
- Project C (Lecturers)
- Software Design Project (Lecturers)
- Software Design Project (Lecturers)
University graduate
- Bioinformatics 2 (Lecturer in charge)
- Bioinformatics 2 (Lecturer in charge)
- Complex Networks (Lecturer in charge)
- Complex Networks (Lecturer in charge)
- Creative Laboratory (Lecturer in charge)
- Introduction to Data Science (Lecturer in charge)
- Introduction to Data Science (Lecturer in charge)
- Graduation Thesis (Lecturers)
- Graduation Thesis (Lecturers)
- Graduation Thesis (Lecturers)
- Project (Lecturers)
- Project (Lecturers)
- Project (Lecturers)
- Project (Lecturers)
- Seminar (Lecturers)
- Seminar (Lecturers)
- Seminar 1 (Lecturers)
Postgraduate doctoral study programme
- Algorithms in bioinformatics (Lecturer in charge)
Competences
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Computational and artificial intelligence
Artificial intelligence Computation theory -
Computers and information processing
Network theory (graphs) DNA computing