Selected Publications

Below are listed selected publications tackling InfOmics' main reasearch topics. For a full and comprehensive list of publications of our lab, click here

Ryu J, Barkal S, Yu T, Jankowiak M, Zhou Y, et al.
Joint genotypic and phenotypic outcome modeling improves base editing variant effect quantification

Nature Genetics 2024; 56.

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Tognon M, Giugno R and Pinello L
A survey on algorithms to characterize transcription factor binding sites

Briefings in Bioinformatics 2023; bbad156.

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Heer M, Giudice L, Mengoni C, Giugno R and Rico D
Esearch3D: propagating gene expression in chromatin networks to illuminate active enhancers

Nucleic Acid Research 2023; gkad229.

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Cancellieri S, Zeng J, Yingqi Lin L, Tognon M, Anh Nguyen M, Jiecong L, Bombieri N, Maitland SA et al.
Human genetic diversity alters off-target outcomes of therapeutic gene editing

Nature Genetics 2023; 55(1): 34-43.

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Bonnici V, Giugno R
PANPROVA: pangenomic prokaryotic evolution of full assemblies

Bioinformatics 2022; 38(9): 2631-2632.

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Tognon M, Bonnici V, Garrison E, Giugno R and Pinello L
GRAFIMO: variant and haplotype aware motif scanning on pangenome graphs

PLOS Computational Biology 2021;17(9): e1009444

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Bonnici V, Maresi E and Giugno R
Challenges in gene-oriented approaches for pangenome content discovery

Briefings in Bioinformatics 2021;22(3): bbaa198.

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Cancellieri S, Canver MC, Bombieri N, Giugno R and Pinello L
CRISPRitz: rapid, high-throughput and variant-aware in silico off-target site identification for CRISPR genome editing

Bioinformatics 2020;36(7): 2001-2008.

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Bonnici V, Giugno R and Manca V
PanDelos: A dictionary-based method for pan-genome content discovery

BMC bioinformatics 2018;19(15): 47-59.

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Viesi E, Perricone U, Aloy P, Giugno R
APBIO: bioactive profiling of air pollutants through inferred bioactivity signatures and prediction of novel target interactions

Journal of Cheminformatics 2025, 17

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Aparo A, Avesani S, Parmigiani L, Napoli S, Bertoni F, Bonnici V, Cascione L, Giugno R
EasyCircR: Detection and reconstruction of circular RNAs post-transcriptional regulatory interaction networks

Computers in Biology and Medicine 2025, 188

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Mussalo L, Lampinen R, Avesani S, et al.
Traffic-related ultrafine particles impair mitochondrial functions in human olfactory mucosa cells – Implications for Alzheimer's disease

Redox Biology 2024, 75

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De Sanctis F, Dusi S, Caligola S, Anselmi C, et al.
Expression of the membrane tetraspanin claudin 18 on cancer cells promotes T lymphocyte infiltration and antitumor immunity in pancreatic cancer

Immunity 2024, 57

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Mussalo L, Avesani S, Shahbaz ML, Závodná T, Saveleva L, Järvinen A, Lampinen R, et al.
Emissions from modern engines induce distinct effects in human olfactory mucosa cells, depending on fuel and aftertreatment

Science of The Total Environment 2023, 905

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Viesi E, Sardina DS, Perricone U, Giugno R
APDB: a database on air pollutant characterization and similarity prediction

Database 2023; baad046.

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Avesani S, Viesi E, Alessandrí L, Motterle G, Bonnici V, Beccuti M, Calogero R, Giugno R
Stardust: improving spatial transcriptomics data analysis through space aware modularity optimization based clustering

GigaScience 2022; 11.

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De Sanctis F, Lamolinara A, Boschi F, Musiu C, Caligola S, Trovato R, Fiore A, Frusteri C et al.
Interrupting the nitrosative stress fuels tumor-specific cytotoxic T lymphocytes in pancreatic cancer

Journal for immunotherapy of cancer 2022, 10(1): e003549.

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Jäntti H, Sitnikova V, Ishchenko Y, Shakirzyanova A, Giudice L, Ugidos IF, Gómez-Budia M, Korvenlaita N et al.
Microglial amyloid beta clearance is driven by PIEZO1 channels

Journal of neuroinflammation 2022; 19(1): 1-22.

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Lampinen R, Górová V, Avesani S, Liddell JR, Penttilä E, Závodná T, Krejčík Z, Lehtola JM et al.
Biometal Dyshomeostasis in Olfactory Mucosa of Alzheimer's Disease Patients

International journal of molecular sciences 2022; 23(8): 4123.

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Lampinen R, Fazaludeen MF, Avesani S, Örd T, Penttilä E, Lehtola JM, Saari T, Hannonen S et al.
Single-Cell RNA-Seq Analysis of Olfactory Mucosal Cells of Alzheimer's Disease Patients

Cells 2022;11(4): 676.

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Sanna L, Kohronen P, Bouvy-Liivrand M, Caligola S, Turunen TA, Turunen MP, Hernandez de Sande A, Kolosowska N et al.
Peripheral inflammation preceeding ischemia impairs neuronal survival through mechanisms involving miR-127 in aged animals

Aging cell 2021;20(1): e13287.

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Kolosowska N, Gotkiewicz M, Dhungana H, Giudice L, Giugno R, Box D, Huuskonen MT, Korhonen P et al.
Intracerebral overexpression of miR-669c is protective in mouse ischemic stroke model by targeting MyD88 and inducing alternative microglial/macrophage activation

Journal of neuroinflammation 2020;17(1): 1-21.

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Giannuzzi D, Giudice L, Marconato L, Ferraresso S, Giugno R, Bertoni F and Aresu L
Integrated analysis of transcriptome, methylome and copy number aberrations data of marginal zone lymphoma and follicular lymphoma in dog

Veterinary and comparative oncology 2020;18(4): 645-655.

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Bister N, Pistono C, Huremagic B, Jolkkonen J, Giugno R and Malm T
Hypoxia and extracellular vesicles: A review on methods, vesicular cargo and functions

Journal of extracellular vesicles 2020;10(1): e12002.

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Trovato R, Fiore A, Sartori S, Canè S, Giugno R, Cascione L, Paiella S, Salvia R et al.
Immunosuppression by monocytic myeloid-derived suppressor cells in patients with pancreatic ductal carcinoma is orchestrated by STAT3

Journal for immunotherapy of cancer 2019;7(1): 1-16.

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Konttinen H, Castro Cabral-da-Silva M, Ohtonen S, Wojciechowski S, Shakirzyanova A, Caligola S, Giugno R, Ishchenko Y et al.
PSEN1ΔE9, APPswe, and APOE4 Confer Disparate Phenotypes in Human iPSC-Derived Microglia

Stem cell reports 2019;13(4): 669-683.

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Ruggeri L, Viesi E, Betti A, Giugno R
Unveiling Novel Gene-Drug-Disease Interactions with GDD-BERT

IEEE 13th International Conference on Healthcare Informatics (ICHI) 2025

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Aparo A, Sala P, Bonnici V and Giugno R
TEDAR: Temporal dynamic signal detection of adverse reactions

Artificial Intelligence in Medicine 2021;122: 102212.

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Licheri N, Bonnici V, Beccuti M and Giugno R
GRAPES-DD: exploiting decision diagrams for index-driven search in biological graph databases

BMC bioinformatics 2021;22(1): 1-24.

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Micale G, Pulvirenti A, Ferro A, Giugno R and Sasha D
Fast methods for finding significant motifs on labelled multi-relational networks

Journal of Complex Networks 2019;7(6): 817-837.

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Bombieri N, Bonnici V and Giugno R
Parallel Searching on Biological Networks

In 2019 27th Euromicro International Conference on Parallel, Distributed and Network-Based Processing (PDP) pp. 307-314. IEEE.

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Aparo A, Bonnici V, Micale G, Ferro A, Shasha, Pulvirenti A and Giugno R
Fast Subgraph Matching Strategies Based on Pattern-Only Heuristics

Interdisciplinary Sciences: Computational Life Sciences 2019;11(1): 21-32.

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Bonnici V, De Caro G, Constantino G, Liuni S, D'Elia D, Bombieri N, Licciulli F and Giugno R
Arena-Idb: a platform to build human non-coding RNA interaction networks

BMC bioinformatics 2018;19(10): 25-38.

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Bonnici V, Busato F, Aldegheri S, Akhmedov M, Cascione L, Arribas Carmena A, Bertoni F, Bombieri N et al.
cuRnet: an R package for graph traversing on GPU

BMC bioinformatics, 19(10) 2018, 15-24.

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Sardina DS, Micale G, Ferro A, Pulvirenti A and Giugno R
INBIA: a boosting methodology for proteomic network inference

BMC bioinformatics 2018;19(7): 77-88.

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Bonnici V and Giugno R
On the Variable Ordering in Subgraph Isomorphism Algorithms

IEEE/ACM transactions on computational biology and bioinformatics 2016;14(1): 193-203.

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Alaimo S, Bonnici V, Cancemi D, Ferro A, Giugno R and Pulvirenti A
DT-Web: a web-based application for drug-target interaction and drug combination prediction through domain-tuned network-based inference

BMC systems biology 2015;9(3): 1-11.

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Privitera AP, Distefano R, Wefer HA, Ferro A, Pulvirenti A and Giugno R
OCDB: a database collecting genes, miRNAs and drugs for obsessive-compulsive disorder

Database 2015.

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Rinnone F, Micale G, Bonnici V, Bader GD, Shasha D, Ferro A, Pulvirenti A and Giugno R
NetMatchStar: an enhanced Cytoscape network querying app

F1000Research 2015;4.

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Alaimo S, Pulvirenti A, Giugno R and Ferro A
Drug–target interaction prediction through domain-tuned network-based inference

Bioinformatics 2013;29(16): 2004-2008.

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Bonnici V, Giugno R, Pulvirenti A, Shasha D and Ferro A
A subgraph isomorphism algorithm and its application to biochemical data

BMC bioinformatics 2013;14(7): 1-13.

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Shasha D, Wang JTL and Giugno R
Algorithmics and applications of tree and graph searching

In Proceedings of the twenty-first ACM SIGMOD-SIGACT-SIGART symposium on Principles of database systems (pp. 39-52) 2002.

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Giugno R and Shasha D
GraphGrep: A fast and universal method for querying graphs

In Object recognition supported by user interaction for service robots (Vol. 2, pp. 112-115). IEEE. 2002.

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