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

Struktura podataka za efikasno spremanje očitanja dobivenih sekvenciranjem genoma

Poopćenje algoritma za poravnanje parcijalnog uređaja

Brzo poravnanje visoko pouzdanih dugačkih očitanja

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

Model dubokog učenja pore za sekvenciranje nanoporama

De Novo Diploid Assembly Using Third-Generation Sequencing Data

Microbe Detection Using Signal Processing and Locality Sensitive Hashing

Sustav za praćenje ispitanika tijekom pretraživanja Google tražilicom

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

Popravljanje djelomično sastavljenoga genoma pomoći Hi-C očitanja

Detecting Base Modifications in DNA Sequences

Gornja granica u sastavljanju genoma

De novo sastavljanje genoma vođeno referencom

Klasifikacija očitanja koristeći metode dubokog učenja

Pronalaženje varijanti gena iz podataka dobivenih sekvenciranjem

Izgradnja biblioteke za poravnavanje parova dugačkih RNA o čitanja

Mapiranje kratkih očitanja

Mapiranje dugačkih očitanja

Ocjena alata za identifikaciju vrsta u metagenomskim uzorcima

Early Screening for Preeclampsia

Statistical inference of exogenous and endogenous information propagation in social networks

Algorithms for de novo assembly of large genomes

Izgradnja biblioteke za poravnavanje parova dugačkih RNA očitanja

Classification of 1D-Signal Types Using Deep Learning

Mapiranje slijeda na graf

Using Reference Database for Plasmid Prediction

Ocjena alata za identifikaciju vrsta u metagenomskim uzorcima

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

Poliranje DNA slijeda koristeći metode dubokog učenja

Horizontal silicon nanowires for surface-enhanced Raman spectroscopy

Hidden Markov Model for Base Calling of MinION Nanopore Reads

Brzo pretraživanje sličnih proteinskih sljedova

Landau-Vishkin-Nussinov algoritam za poravnanje dva niza

Približni algoritam za brzo računanje poravnanja dvaju dugačkih nizova

Procjena očekivanog stupnja potpunosti genoma iz dostupnih očitanja

Sustav za pohranu DNA

Naučene indeksne strukture

Mobilna aplikacija za prikupljanje podataka o korisničkoj aktivnosti

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

Informatika - materijali za predavanja na Vojnom studijskom programu

De Novo Assembly using Unsupervised Read Categorization

Inference of influence in social networks

Algoritam za određivanje ukupnog poravnanja dva grafa poravnanja parcijalnog uređaja

Ručno određivanje lažnih preklapanja koja nastaju pri sastavljanju genoma

dna2vec: vektorska reprezentacija k-torki različite duljine

Analiza metagenomskog uzorka dobivenog sekvenciranjem koristeći uređaje treće generacije

RNA Transcriptome Mapping with GraphMap

De novo assembly using long error-prone reads

Stablo Bloomovih filtara za spremanje sljedova

Poravnanje RNA očitanja na poznate gene

Poravnanje dugačkih RNA očitanja

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

Rekonstrukcija filogenetskog stabla metodom maksimalne uštede uz razgranaj-ograniči optimizaciju

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

Generiranje konsenzusnog slijeda iz grafova djelomicno uređenih višestrukih poravnanja

Alat za poravnanje dugackih očitanja

Global sequence alignment tool

REKONSTRUKCIJA FILOGENETSKOG STABLA KORISTEĆI METODU UDRUŽIVANJA SUSJEDA

Sufiksno stablo

Continuum model of gene expression

Statistical inference algorithms for epidemic processes on complex networks

Poboljšano sufiksno polje

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

Alat za poravnanje genoma

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

Alat za brzo pretraživanje baza bioloških sljedova

Identify pathogen organisms from a stream of RNA sequences

Otkrivanje preklapajućih DNA očitanja

Računalne metode za poboljšanje i validaciju sastavljenih genoma

Evaluacija aplikacija za pretraživanje baze proteinskih sljedova

Tool for aligning long DNA reads

SW#–GPU-enabled exact alignments on genome scale

Web sučelje za poravnanje sljedova

GPU implementacija vremenski i memorijski učinkovitoga paralelnog algoritma za poravnanje slijedova

Sastavljanje optičkih mapa: modul za korekciju grafa

Alternativno spajanje eksona

Evaluacija metode za ispravljanje pogrešaka kod dugačkih očitanja

SW# - Biblioteka za poravnanje sljedova korištenjem grafičkih procesora

Računalna metoda za računanje proteinskih interakcija

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

Proteini i nukleinske kiseline u vremenu i prostoru

Aspects of DNA Assembly Acceleration on Reconfigurable Platforms

BioMe - web sučelje baze biološki važnih metala

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

GPU implementacija vremenski efikasnog algoritma za lokalno poravnavanje s linearnom memorijskom složenosti

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 implementacija vremenski učinkovitog algoritma za lokalno poravnavanje s linearnom memorijskom složenosti

Implementacija FM indeksa

SWIG - Poravnanje struktura korištenjem iterativne primjene Smith-Waterman algoritma

Program za automatsku analizu protein kodirajućih gena

Implementacija komprimirane podatkovne strukture za pretraživanje teksta temeljene na FMindeksu

Program za simulaciju pročitanih nizova nukleotida

Web aplikacija za usporednu analizu proteinskih paraloga

Orthobalancer: aplikacija za kreiranje skupova bioloških vrsta usporedive taksonomske širine

Make Me Move - didaktička računalna igra za učenje strukturne molekularne biologije

Epidemic centrality – identifying “superspreaders” in complex networks

Optimiranje sigurnosnih pravila vatrozida

Adaptivna valićna transformacija ostvarena na CUDA arhitekturi

Alat za prianjanje proteina: modul za vizualizaciju

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

CUDA implementacija računanja elektrostatske raspodjele naboja

Pronalaženje epistatskih interakcija pomoću algoritma kolonije mrava

Poboljšani algoritam za izbor i provjeru kvalitete najboljih multivarijacijskih modela odnosa strukture i svojstava molekula

Implementacija Smith Waterman algoritma koristeći grafičke kartice s CUDA arhitekturom

Implementacija algoritma za računanje proteinskih interakcija

Predviđanje površine dostupne otapalu iz slijeda aminokiselinskih ostataka

Multiresolution analysis of macromolecular structures

Simulacija utjecaja karantena na smanjenje širenja epidemije

Baza zastupljenosti metala u proteinima

Parallel Protein Docking Tool

Sustav za pristup poslužiteljima u pokretnim mrežama

Alat za prianjanje proteina: modul za pripremu prianjanja

Predviđanje mjesta sekundarne strukture protein iz slijeda aminokiselinskih ostataka

Analiza sekundarne strukture proteina metodom obrade signala

Alat za prianjanje proteina: moduli za rotaciju i vrednovanje rezultata

Predviđanje mjesta proteinskih interakcija koristeći algoritam slučajnih šuma

Simulacija utjecaja okupljanja zaraženih gripom na širenje epidemije

Alat za prianjanje proteina: modul za utvrđivanje interakcija

Baza podataka metala u proteinima

Klasifikacija kodirajućih regija u genomu

Analiza kodirajućih regija u genomu

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

PSAIA - Protein Structure and Interaction Analyzer

Automatska izrada testnog skupa za predvidanje proteinskih interakcija

Vizualizacija makromolekula

Računalna metoda za predviđanje mjesta proteinskih interakcija

Utjecaj zaraze na svojstva kompleksne mreže

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

Identifikacija ključnih igrača u kompleksnim mrežama blogova

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

Efikasno upravljanje e-mailom

Model naplate sadržaja i usluga u mobilnim paketskim mrežama

Sigurnost bežičnih LAN-ova

Mobile content efficiency and business model

Modeli naplate sadržaja u mobilnim paketskim mrežama