A citation-based method for searching scientific literature

Alisa Pavel, Angela Serra, Luca Cattelani, Antonio Federico, Dario Greco. Methods Mol Biol 2022
Times Cited: 3







List of co-cited articles
16 articles co-cited >1



Times Cited
  Times     Co-cited
Similarity


INfORM: Inference of NetwOrk Response Modules.
Veer Singh Marwah, Pia Anneli Sofia Kinaret, Angela Serra, Giovanni Scala, Antti Lauerma, Vittorio Fortino, Dario Greco. Bioinformatics 2018
21
66

Volta: adVanced mOLecular neTwork Analysis.
Alisa Pavel, Antonio Federico, Giusy Del Giudice, Angela Serra, Dario Greco. Bioinformatics 2021
3
66

Integrated network analysis reveals new genes suggesting COVID-19 chronic effects and treatment.
Alisa Pavel, Giusy Del Giudice, Antonio Federico, Antonio Di Lieto, Pia A S Kinaret, Angela Serra, Dario Greco. Brief Bioinform 2021
15
66


Network Analysis Reveals Similar Transcriptomic Responses to Intrinsic Properties of Carbon Nanomaterials in Vitro and in Vivo.
Pia Kinaret, Veer Marwah, Vittorio Fortino, Marit Ilves, Henrik Wolff, Lasse Ruokolainen, Petri Auvinen, Kai Savolainen, Harri Alenius, Dario Greco. ACS Nano 2017
25
66

BMDx: a graphical Shiny application to perform Benchmark Dose analysis for transcriptomics data.
Angela Serra, Laura Aliisa Saarimäki, Michele Fratello, Veer Singh Marwah, Dario Greco. Bioinformatics 2020
10
66

The FAIR Guiding Principles for scientific data management and stewardship.
Mark D Wilkinson, Michel Dumontier, I Jsbrand Jan Aalbersberg, Gabrielle Appleton, Myles Axton, Arie Baak, Niklas Blomberg, Jan-Willem Boiten, Luiz Bonino da Silva Santos, Philip E Bourne,[...]. Sci Data 2016
66

Computationally prioritized drugs inhibit SARS-CoV-2 infection and syncytia formation.
Angela Serra, Michele Fratello, Antonio Federico, Ravi Ojha, Riccardo Provenzani, Ervin Tasnadi, Luca Cattelani, Giusy Del Giudice, Pia A S Kinaret, Laura A Saarimäki,[...]. Brief Bioinform 2022
8
66

INSIdE NANO: a systems biology framework to contextualize the mechanism-of-action of engineered nanomaterials.
Angela Serra, Ivica Letunic, Vittorio Fortino, Richard D Handy, Bengt Fadeel, Roberto Tagliaferri, Dario Greco. Sci Rep 2019
16
66

TinderMIX: Time-dose integrated modelling of toxicogenomics data.
Angela Serra, Michele Fratello, Giusy Del Giudice, Laura Aliisa Saarimäki, Michelangelo Paci, Antonio Federico, Dario Greco. Gigascience 2020
8
66

Transcriptomics in Toxicogenomics, Part II: Preprocessing and Differential Expression Analysis for High Quality Data.
Antonio Federico, Angela Serra, My Kieu Ha, Pekka Kohonen, Jang-Sik Choi, Irene Liampa, Penny Nymark, Natasha Sanabria, Luca Cattelani, Michele Fratello,[...]. Nanomaterials (Basel) 2020
18
66

Open TG-GATEs: a large-scale toxicogenomics database.
Yoshinobu Igarashi, Noriyuki Nakatsu, Tomoya Yamashita, Atsushi Ono, Yasuo Ohno, Tetsuro Urushidani, Hiroshi Yamada. Nucleic Acids Res 2015
223
66

Transcriptomics in Toxicogenomics, Part III: Data Modelling for Risk Assessment.
Angela Serra, Michele Fratello, Luca Cattelani, Irene Liampa, Georgia Melagraki, Pekka Kohonen, Penny Nymark, Antonio Federico, Pia Anneli Sofia Kinaret, Karolina Jagiello,[...]. Nanomaterials (Basel) 2020
21
66

Transcriptomics in Toxicogenomics, Part I: Experimental Design, Technologies, Publicly Available Data, and Regulatory Aspects.
Pia Anneli Sofia Kinaret, Angela Serra, Antonio Federico, Pekka Kohonen, Penny Nymark, Irene Liampa, My Kieu Ha, Jang-Sik Choi, Karolina Jagiello, Natasha Sanabria,[...]. Nanomaterials (Basel) 2020
20
66

Gene ontology: tool for the unification of biology. The Gene Ontology Consortium.
M Ashburner, C A Ball, J A Blake, D Botstein, H Butler, J M Cherry, A P Davis, K Dolinski, S S Dwight, J T Eppig,[...]. Nat Genet 2000
66

Prospects and challenges for FAIR toxicogenomics data.
Laura A Saarimäki, Georgia Melagraki, Antreas Afantitis, Iseult Lynch, Dario Greco. Nat Nanotechnol 2022
3
66

BMDExpress 2: enhanced transcriptomic dose-response analysis workflow.
Jason R Phillips, Daniel L Svoboda, Arpit Tandon, Shyam Patel, Alex Sedykh, Deepak Mav, Byron Kuo, Carole L Yauk, Longlong Yang, Russell S Thomas,[...]. Bioinformatics 2019
66
33

Feature set optimization in biomarker discovery from genome-scale data.
V Fortino, G Scala, D Greco. Bioinformatics 2020
7
33

Molecular Signature of Asthma-Enhanced Sensitivity to CuO Nanoparticle Aerosols from 3D Cell Model.
Ingeborg Kooter, Marit Ilves, Mariska Gröllers-Mulderij, Evert Duistermaat, Peter C Tromp, Frieke Kuper, Pia Kinaret, Kai Savolainen, Dario Greco, Piia Karisola,[...]. ACS Nano 2019
14
33


A robust and accurate method for feature selection and prioritization from multi-class OMICs data.
Vittorio Fortino, Pia Kinaret, Nanna Fyhrquist, Harri Alenius, Dario Greco. PLoS One 2014
19
33

FastBMD: an online tool for rapid benchmark dose-response analysis of transcriptomics data.
Jessica Ewald, Othman Soufan, Jianguo Xia, Niladri Basu. Bioinformatics 2021
8
33

Manually curated transcriptomics data collection for toxicogenomic assessment of engineered nanomaterials.
Laura Aliisa Saarimäki, Antonio Federico, Iseult Lynch, Anastasios G Papadiamantis, Andreas Tsoumanis, Georgia Melagraki, Antreas Afantitis, Angela Serra, Dario Greco. Sci Data 2021
6
33


Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool.
Edward Y Chen, Christopher M Tan, Yan Kou, Qiaonan Duan, Zichen Wang, Gabriela Vaz Meirelles, Neil R Clark, Avi Ma'ayan. BMC Bioinformatics 2013
33

Patient similarity for precision medicine: A systematic review.
E Parimbelli, S Marini, L Sacchi, R Bellazzi. J Biomed Inform 2018
52
33

Grouping of nanomaterials to read-across hazard endpoints: a review.
L Lamon, K Aschberger, D Asturiol, A Richarz, A Worth. Nanotoxicology 2019
31
33

Multi-parametric and multi-regional histogram analysis of MRI: modality integration reveals imaging phenotypes of glioblastoma.
Chao Li, Shuo Wang, Angela Serra, Turid Torheim, Jiun-Lin Yan, Natalie R Boonzaier, Yuan Huang, Tomasz Matys, Mary A McLean, Florian Markowetz,[...]. Eur Radiol 2019
5
33

Manually curated and harmonised transcriptomics datasets of psoriasis and atopic dermatitis patients.
Antonio Federico, Veera Hautanen, Nils Christian, Andreas Kremer, Angela Serra, Dario Greco. Sci Data 2020
3
33

PathwAX: a web server for network crosstalk based pathway annotation.
Christoph Ogris, Thomas Helleday, Erik L L Sonnhammer. Nucleic Acids Res 2016
27
33

Cobalt nanoparticles trigger ferroptosis-like cell death (oxytosis) in neuronal cells: Potential implications for neurodegenerative disease.
Govind Gupta, Anda Gliga, Jonas Hedberg, Angela Serra, Dario Greco, Inger Odnevall Wallinder, Bengt Fadeel. FASEB J 2020
24
33

Basic biology and role of interleukin-17 in immunity and inflammation.
Camille Zenobia, George Hajishengallis. Periodontol 2000 2015
172
33

Wisdom of crowds for robust gene network inference.
Daniel Marbach, James C Costello, Robert Küffner, Nicole M Vega, Robert J Prill, Diogo M Camacho, Kyle R Allison, Manolis Kellis, James J Collins, Gustavo Stolovitzky. Nat Methods 2012
850
33


WebGestalt 2019: gene set analysis toolkit with revamped UIs and APIs.
Yuxing Liao, Jing Wang, Eric J Jaehnig, Zhiao Shi, Bing Zhang. Nucleic Acids Res 2019
33

Machine-learning-driven biomarker discovery for the discrimination between allergic and irritant contact dermatitis.
Vittorio Fortino, Lukas Wisgrill, Paulina Werner, Sari Suomela, Nina Linder, Erja Jalonen, Alina Suomalainen, Veer Marwah, Mia Kero, Maria Pesonen,[...]. Proc Natl Acad Sci U S A 2020
16
33


The Reactome pathway Knowledgebase.
Antonio Fabregat, Konstantinos Sidiropoulos, Phani Garapati, Marc Gillespie, Kerstin Hausmann, Robin Haw, Bijay Jassal, Steven Jupe, Florian Korninger, Sheldon McKay,[...]. Nucleic Acids Res 2016
838
33


Cytoscape: a software environment for integrated models of biomolecular interaction networks.
Paul Shannon, Andrew Markiel, Owen Ozier, Nitin S Baliga, Jonathan T Wang, Daniel Ramage, Nada Amin, Benno Schwikowski, Trey Ideker. Genome Res 2003
33

Bioinformatics-assisted, integrated omics studies on medicinal plants.
Xiaoxia Ma, Yijun Meng, Pu Wang, Zhonghai Tang, Huizhong Wang, Tian Xie. Brief Bioinform 2020
14
33

Multi-objective optimization methods in novel drug design.
George Lambrinidis, Anna Tsantili-Kakoulidou. Expert Opin Drug Discov 2021
5
33

NanoSolveIT Project: Driving nanoinformatics research to develop innovative and integrated tools for in silico nanosafety assessment.
Antreas Afantitis, Georgia Melagraki, Panagiotis Isigonis, Andreas Tsoumanis, Dimitra Danai Varsou, Eugenia Valsami-Jones, Anastasios Papadiamantis, Laura-Jayne A Ellis, Haralambos Sarimveis, Philip Doganis,[...]. Comput Struct Biotechnol J 2020
40
33

Multi-class computational evolution: development, benchmark evaluation and application to RNA-Seq biomarker discovery.
Nathaniel M Crabtree, Jason H Moore, John F Bowyer, Nysia I George. BioData Min 2017
4
33


Integrating toxicogenomics into human health risk assessment: lessons learned from the benzo[a]pyrene case study.
Nikolai L Chepelev, Ivy D Moffat, Sarah Labib, Julie Bourdon-Lacombe, Byron Kuo, Julie K Buick, France Lemieux, Amal I Malik, Sabina Halappanavar, Andrew Williams,[...]. Crit Rev Toxicol 2015
37
33

MVDA: a multi-view genomic data integration methodology.
Angela Serra, Michele Fratello, Vittorio Fortino, Giancarlo Raiconi, Roberto Tagliaferri, Dario Greco. BMC Bioinformatics 2015
31
33

Map and model-moving from observation to prediction in toxicogenomics.
Andreas Schüttler, Rolf Altenburger, Madeleine Ammar, Marcella Bader-Blukott, Gianina Jakobs, Johanna Knapp, Janet Krüger, Kristin Reiche, Gi-Mick Wu, Wibke Busch. Gigascience 2019
12
33


Integration of genome-wide mRNA and miRNA expression, and DNA methylation data of three cell lines exposed to ten carbon nanomaterials.
Giovanni Scala, Veer Marwah, Pia Kinaret, Jukka Sund, Vittorio Fortino, Dario Greco. Data Brief 2018
5
33


Co-cited is the co-citation frequency, indicating how many articles cite the article together with the query article. Similarity is the co-citation as percentage of the times cited of the query article or the article in the search results, whichever is the lowest. These numbers are calculated for the last 100 citations when articles are cited more than 100 times.