N. Hansen, N. Dwarshuis, H. Ji, A. Rhie, H. Loucks, G. Logsdon, M. Vollger, J. Storer, J. Kim, E. Adam, N. Altemose, D. Antipov, M. Asri, S. Barreira, S. Bohaczuk, A. Bzikadze, S. Carioscia, A. Carroll, K. Chao, Y. Chu, A. Das, P. Ebert, A. English, M. Fleharty, L. Fleming, G. Formenti, A. Guarracino, G. Hartley, K. Jenike, J. Kalleberg, Y. Kang, R. King, J. Lipovac, M. Mastoras, M. Mitchell, S. Negi, N. Olson, K. Oshima, L. Paulin, B. Pickett, D. Porubsky, J. Ranchalis, D. Ranjan, M. Rautiainen, H. Riethman, R. Schnabel, F. Sedlazeck, K. Shafin, M. Sikic, S. Solar, A. Sweeten, W. Timp, J. Wagner, D. Yoo, Y. Zhou, E. Garrison, E. Eichler, M. Schatz, A. Stergachis, R. O’Neill, K. Miga, S. Salzberg, S. Koren, J. Zook, A. Phillippy: "A complete diploid human genome benchmark for personalized genomics"

M. Schmitz, L. Vrček, K. Kawaguchi, M. Šikić: "DipGNNome: Diploid de novo genome assembly with geometric deep learning and beam-search"

L. Li, Y. Yao, I. Martinović, M. Kulkarni, Y. Pan, RG. Huber, M. Šikić: "HomRank: Homogeneous RNA Ranking for 3D Structure Evaluation"

M. Pintarić, RJ. Penić, M. Šikić: "RNA-xLSTM: Evaluating xLSTM as an Alternative Foundation to Transformers in RNA Modeling"

P. Sarashetti, J. Lipovac, Q. Jia, L. Wang, Z. Li, L. Vrcek, Y. Chen, F. Yao, Y. Sia, D. Lin, X. Zhang, D. Muliaditan, H. Low, S. Leong, C. Khor, E. Wong, W. Zheng, K. Krizanovic, J. Chambers, W. Hwang, P. Tan, J. Göke, M. Sikic, J. Liu: "A Complete Telomere-to-Telomere Diploid Reference Genome for South Asian Population"

S. Bakić, K. Friganović, B. Hooi, M. Šikić: "Campolina: A deep neural framework for accurate segmentation of nanopore signals"

RJ. Penić, T. Vlašić, RG. Huber, Y. Wan, M. Šikić: "Rinalmo: General-purpose RNA language models can generalize well on structure prediction tasks"

J. Lipovac, M. Šikić, R. Vicedomini, K. Križanović: "MADRe: Strain-Level Metagenomic Classification Through Assembly-Driven Database Reduction"

M. Šimunović, M. Šikić, A. Bankevich: "GnnDebugger: GNN based error correction in De Bruijn Graphs"

L. Vrček, X. Bresson, T. Laurent, M. Schmitz, K. Kawaguchi, M. Šikić: "Geometric deep learning framework for de novo genome assembly"

Y. Chen, N. Davidson, Y. Wan, F. Yao, Y. Su, H. Gamaarachchi, A. Sim, H. Patel, H. Low, C. Hendra, L. Wratten, C. Hakkaart, C. Sawyer, V. Iakovleva, P. Lee, L. Xin, H. Ng, J. Loo, X. Ong, H. Ng, J. Wang, W. Koh, S. Poon, D. Stanojevic, H. Tran, K. Lim, S. Toh, P. Ewels, H. Ng, N. Iyer, A. Thiery, W. Chng, L. Chen, R. DasGupta, M. Sikic, Y. Chan, B. Tan, Y. Wan, W. Tam, Q. Yu, C. Khor, T. Wüstefeld, A. Lezhava, P. Pratanwanich, M. Love, W. Goh, S. Ng, A. Oshlack, N. Iyer, Q. Yu, J. Göke: "A systematic benchmark of Nanopore long-read RNA sequencing for transcript-level analysis in human cell lines"

I. Vujaklija, S. Biđin, M. Volarić, S. Bakić, Z. Li, R. Foo, J. Liu, M. Šikić: "Detecting a wide range of epitranscriptomic modifications using a nanopore-sequencing-based computational approach with 1D score-clustering"

P. Sarashetti, J. Lipovac, F. Tomas, M. Šikić, J. Liu: "Evaluating data requirements for high-quality haplotype-resolved genomes for creating robust pangenome references"

I. Martinović, T. Vlašić, Y. Li, B. Hooi, Y. Zhang, M. Šikić: "A Comparative Review of Deep Learning Methods for RNA Tertiary Structure Prediction"

D. Stanojević, Z. Li, S. Bakić, R. Foo, M. Šikić: "Rockfish: A transformer-based model for accurate 5-methylcytosine prediction from nanopore sequencing"

F. Sedlic, J. Sertić, A. Markotić, D. Primorac, A. Slavica, L. Zibar, K. Vlahoviček, V. Kušec, I. Barić, V. Paar, F. Borovečki, L. Žmak, I. Kurolt, N. Canki-Klain, S. Roksandić, I. Rinčić, H. Jurić, V. Škaro, D. Marjanović, P. Projić, D. Primorac, A. Starčević, D. Vujaklija, M. Šikić, K. Križanović, S. Gamulin: "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"

D. Stanojević, D. Lin, S. Nurk, P. Florez de Sessions, M. Šikić: "Telomere-to-telomere phased genome assembly using HERRO-corrected simplex Nanopore reads"

I. Vujaklija, S. Biđin, M. Šikić: "Comparative Analysis of Nanopore-based Unsupervised Learning Methods in Epitranscriptomics"

J. Marić, K. Križanović, S. Riondet, N. Nagarajan, M. Šikić: "Comparative analysis of metagenomic classifiers for long-read sequencing datasets"

M. Simunovic, L. Vrcek, M. Sikic: "Graph neural network meets de Bruijn genome assembly"

F. Bosnić, M. Šikić: "Finding Hamiltonian cycles with graph neural networks"

L. Vrček, X. Bresson, T. Laurent, M. Schmitz, M. Šikić: "Reconstruction of short genomic sequences with graph convolutional networks"

M. Šikić: "Facilitating genome structural variation analysis"

A.H. Lim, Z.J. Low, P.N. Shingate, J.H. Hong, S.C. Chong, C.C.Y. Ng, W. Liu, R. Vaser, M. Šikić, W.K.K. Sung, N. Nagarajan, P. Tan, B.T. Teh: "Genome assembly and chemogenomic profiling of National Flower of Singapore Papilionanthe Miss Joaquim ‘Agnes’ reveals metabolic pathways regulating floral …"

T.A. Nguyen, J.W.J. Heng, P. Kaewsapsak, E.P.L. Kok, D. Stanojević, H. Liu, A. Cardilla, A. Praditya, Z. Yi, M. Lin, J.G.A. Aw, Y.Y. Ho, K.L.E. Peh, Y. Wang, Q. Zhong, J. Heraud-Farlow, S. Xue, B. Reversade, C. Walkley, Y.S. Ho, M. Šikić, Y. Wan, M.H. Tan: "Direct identification of A-to-I editing sites with nanopore native RNA sequencing"

L. Vrček, X. Bresson, T. Laurent, M. Schmitz, M. Šikić: "Learning to Untangle Genome Assembly with Graph Convolutional Networks"

D. Stanojevic, Z. Li, R. Foo, M. Sikic: "Rockfish, A Transformer-based Model for Accurate 5-Methylcytosine Prediction from Nanopore Sequencing"

S. Duvnjak, Ž. Pavlinec, R. Vaser, K. Križanović, M. Šikić, M. Zdelar-Tuk, I. Reil, S. Špičić: "Efficacy of next-generation sequencing in bacterial zoonoses diagnostics"

R Vaser, M Šikić: "Time-and memory-efficient genome assembly with Raven"

Y Chen, N Davidson, YK Wan, H Patel, F Yao, HM Low, C Hendra et al.: "A systematic benchmark of Nanopore long read RNA sequencing for transcript level analysis in human cell lines"

L Vrček, P Veličković, M Šikić: "A step towards neural genome assembly"

J Maric, K Krizanovic, S Riondet, N Nagarajan, M Šikić: "Benchmarking metagenomic classification tools for long-read sequencing data"

R Vaser, M Šikić: "Yet another de novo genome assembler"

M Piškorec, T Šmuc, M Šikić: "Disentangling sources of influence in online social networks"

D Bertrand, J Shaw, M Kalathiyappan, AHQ Ng, MS Kumar, C Li et al.: "Hybrid metagenomic assembly enables high-resolution analysis of resistance determinants and mobile elements in human microbiomes"

J Marić, M Šikić: "Approaches to metagenomic classification and assembly"

T Šebrek, J Tomljanović, J Krapac, M Šikić: "Read classification using semi-supervised deep learning"

N Miculinić, M Ratković, M Šikić: "MinCall-MinION end2end convolutional deep learning basecaller"

J Marić, I Sović, K Križanović, N Nagarajan, M Šikić: "Graphmap2-splice-aware RNA-seq mapper for long reads"

K Križanović, A Echchiki, J Roux, M Šikić: "Evaluation of tools for long read RNA-seq splice-aware alignment"

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