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54,379 results

3. Power of Deep Learning Models in Bioinformatics

Author

Thareja, Preeti, Chhillar, Rajender Singh, Kacprzyk, Janusz, Series Editor, Pal, Nikhil R., Advisory Editor, Bello Perez, Rafael, Advisory Editor, Corchado, Emilio S., Advisory Editor, Hagras, Hani, Advisory Editor, Kóczy, László T., Advisory Editor, Kreinovich, Vladik, Advisory Editor, Lin, Chin-Teng, Advisory Editor, Lu, Jie, Advisory Editor, Melin, Patricia, Advisory Editor, Nedjah, Nadia, Advisory Editor, Nguyen, Ngoc Thanh, Advisory Editor, Wang, Jun, Advisory Editor, Bhattacharya, Abhishek, editor, Dutta, Soumi, editor, Dutta, Paramartha, editor, and Piuri, Vincenzo, editor

Published
2023
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4. Automated Segmentation of Patterned Cells in Micropatterning Microscopy Images

Author

Schurr, Jonas, Haghofer, Andreas, Lanzerstorfer, Peter, Winkler, Stephan, Filipe, Joaquim, Editorial Board Member, Ghosh, Ashish, Editorial Board Member, Prates, Raquel Oliveira, Editorial Board Member, Zhou, Lizhu, Editorial Board Member, Roque, Ana Cecília A., editor, Gracanin, Denis, editor, Lorenz, Ronny, editor, Tsanas, Athanasios, editor, Bier, Nathalie, editor, Fred, Ana, editor, and Gamboa, Hugo, editor

Published
2023
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5. Analysis of Extracellular Vesicle Data on Fluorescence and Atomic Force Microscopy Images

Author

Janout, Hannah, Schurr, Jonas, Haghofer, Andreas, Hauser, Fabian, Jacak, Jaroslaw, Winkler, Stephan, Filipe, Joaquim, Editorial Board Member, Ghosh, Ashish, Editorial Board Member, Prates, Raquel Oliveira, Editorial Board Member, Zhou, Lizhu, Editorial Board Member, Roque, Ana Cecília A., editor, Gracanin, Denis, editor, Lorenz, Ronny, editor, Tsanas, Athanasios, editor, Bier, Nathalie, editor, Fred, Ana, editor, and Gamboa, Hugo, editor

Published
2023
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6. Escherichia coli: Analysis of Features for Protein Localization Classification Employing Fusion Data

Author

Orjuela-Cañon, Alvaro David, Rodriguez, Diana C., Perdomo, Oscar, Filipe, Joaquim, Editorial Board Member, Ghosh, Ashish, Editorial Board Member, Prates, Raquel Oliveira, Editorial Board Member, Zhou, Lizhu, Editorial Board Member, Orjuela-Cañón, Alvaro David, editor, Lopez, Jesus, editor, Arias-Londoño, Julian David, editor, and Figueroa-García, Juan Carlos, editor

Published
2023
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8. A Machine Learning-Based Missing Data Imputation with FHIR Interoperability Approach in Sepsis Prediction

Author

Beltran, Cristian Fernando Toro, Ibañez, Erick Daniel Villarreal, Orejuela, Vivian Milen, García Henao, John Anderson, Filipe, Joaquim, Editorial Board Member, Ghosh, Ashish, Editorial Board Member, Prates, Raquel Oliveira, Editorial Board Member, Zhou, Lizhu, Editorial Board Member, Navaux, Philippe, editor, Barrios H., Carlos J., editor, Osthoff, Carla, editor, and Guerrero, Ginés, editor

Published
2022
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9. EGRE: Calculating Enrichment Between Genomic Regions

Author

Yu, Yang-En, Benton, Mary Lauren, Filipe, Joaquim, Editorial Board Member, Ghosh, Ashish, Editorial Board Member, Prates, Raquel Oliveira, Editorial Board Member, Zhou, Lizhu, Editorial Board Member, Han, Henry, editor, and Baker, Erich, editor

Published
2022
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10. Improving Bacterial sRNA Identification By Combining Genomic Context and Sequence-Derived Features

Author

Sorkhian, Mohammad, Nagari, Megha, Elsisy, Moustafa, Peña-Castillo, Lourdes, Goos, Gerhard, Founding Editor, Hartmanis, Juris, Founding Editor, Bertino, Elisa, Editorial Board Member, Gao, Wen, Editorial Board Member, Steffen, Bernhard, Editorial Board Member, Yung, Moti, Editorial Board Member, Chicco, Davide, editor, Facchiano, Angelo, editor, Tavazzi, Erica, editor, Longato, Enrico, editor, Vettoretti, Martina, editor, Bernasconi, Anna, editor, Avesani, Simone, editor, and Cazzaniga, Paolo, editor

Published
2022
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11. Metagenome Analysis of Two River Microbial Flora for Modeling River Microbial Diversity

Author

Ogawa, Jin Michel, Yairi, Ikuko Eguchi, Kacprzyk, Janusz, Series Editor, Pal, Nikhil R., Advisory Editor, Bello Perez, Rafael, Advisory Editor, Corchado, Emilio S., Advisory Editor, Hagras, Hani, Advisory Editor, Kóczy, László T., Advisory Editor, Kreinovich, Vladik, Advisory Editor, Lin, Chin-Teng, Advisory Editor, Lu, Jie, Advisory Editor, Melin, Patricia, Advisory Editor, Nedjah, Nadia, Advisory Editor, Nguyen, Ngoc Thanh, Advisory Editor, Wang, Jun, Advisory Editor, Takama, Yasufumi, editor, Matsumura, Naohiro, editor, Yada, Katsutoshi, editor, Matsushita, Mitsunori, editor, Katagami, Daisuke, editor, Abe, Akinori, editor, Kashima, Hisashi, editor, Hiraoka, Toshihiro, editor, Uchiya, Takahiro, editor, and Rzepka, Rafal, editor

Published
2022
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12. Cloud Based Exon Prediction Using Maximum Error Normalized Logarithmic Algorithms

Author

Rahman, Md. Zıa Ur, Haneesh, Annabathuni Chandra, Reddy, Bhimireddy Shanmukha Sai, Surekha, Sala, Srinivasareddy, Putluri, Filipe, Joaquim, Editorial Board Member, Ghosh, Ashish, Editorial Board Member, Prates, Raquel Oliveira, Editorial Board Member, Zhou, Lizhu, Editorial Board Member, Singh, Mayank, editor, Tyagi, Vipin, editor, Gupta, P. K., editor, Flusser, Jan, editor, Ören, Tuncer, editor, and Sonawane, V. R., editor

Published
2021
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14. A First Glance into Reversing Senescence on Herbarium Sample Images Through Conditional Generative Adversarial Networks

Author

Villacis-Llobet, Juan, Lucio-Troya, Marco, Calvo-Navarro, Marvin, Calderon-Ramirez, Saul, Mata-Montero, Erick, Barbosa, Simone Diniz Junqueira, Editorial Board Member, Filipe, Joaquim, Editorial Board Member, Ghosh, Ashish, Editorial Board Member, Kotenko, Igor, Editorial Board Member, Zhou, Lizhu, Editorial Board Member, Crespo-Mariño, Juan Luis, editor, and Meneses-Rojas, Esteban, editor

Published
2020
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15. An Effective Protein Multiple Structure Alignment Using Parallel Computing

Author

Al-Neama, Mohammed W., Ali, Salwa M., Malallah, Fahad Layth, Saeed, Mustafa Ghanem, Barbosa, Simone Diniz Junqueira, Editorial Board Member, Filipe, Joaquim, Editorial Board Member, Ghosh, Ashish, Editorial Board Member, Kotenko, Igor, Editorial Board Member, Zhou, Lizhu, Editorial Board Member, Khalaf, Mohammed I., editor, Al-Jumeily, Dhiya, editor, and Lisitsa, Alexei, editor

Published
2020
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16. Jarvis: A Multimodal Visualization Tool for Bioinformatic Data

Author

Hutchens, Mark, Krishnaswamy, Nikhil, Cochran, Brent, Pustejovsky, James, Goos, Gerhard, Founding Editor, Hartmanis, Juris, Founding Editor, Bertino, Elisa, Editorial Board Member, Gao, Wen, Editorial Board Member, Steffen, Bernhard, Editorial Board Member, Woeginger, Gerhard, Editorial Board Member, Yung, Moti, Editorial Board Member, Stephanidis, Constantine, editor, Salvendy, Gavriel, editor, Wei, June, editor, Yamamoto, Sakae, editor, Mori, Hirohiko, editor, Meiselwitz, Gabriele, editor, Nah, Fiona Fui-Hoon, editor, and Siau, Keng, editor

Published
2020
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17. Portals for Interactive Steering of HPC Workflows

Author

Settlage, Robert, Rajamohan, Srijith, Lahmers, Kevin, Chalker, Alan, Franz, Eric, Gallo, Steve, Hudak, David, Barbosa, Simone Diniz Junqueira, Editorial Board Member, Filipe, Joaquim, Editorial Board Member, Ghosh, Ashish, Editorial Board Member, Kotenko, Igor, Editorial Board Member, Zhou, Lizhu, Editorial Board Member, Juckeland, Guido, editor, and Chandrasekaran, Sunita, editor

Published
2020
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19. BaaS - Bioinformatics as a Service

Author

Krishna, Ritesh, Elisseev, Vadim, Antao, Samuel, Hutchison, David, Series Editor, Kanade, Takeo, Series Editor, Kittler, Josef, Series Editor, Kleinberg, Jon M., Series Editor, Mattern, Friedemann, Series Editor, Mitchell, John C., Series Editor, Naor, Moni, Series Editor, Pandu Rangan, C., Series Editor, Steffen, Bernhard, Series Editor, Terzopoulos, Demetri, Series Editor, Tygar, Doug, Series Editor, Mencagli, Gabriele, editor, B. Heras, Dora, editor, Cardellini, Valeria, editor, Casalicchio, Emiliano, editor, Jeannot, Emmanuel, editor, Wolf, Felix, editor, Salis, Antonio, editor, Schifanella, Claudio, editor, Manumachu, Ravi Reddy, editor, Ricci, Laura, editor, Beccuti, Marco, editor, Antonelli, Laura, editor, Garcia Sanchez, José Daniel, editor, and Scott, Stephen L., editor

Published
2019
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20. High-Performance Hybrid Computing for Bioinformatic Analysis of Protein Superfamilies

Author

Suplatov, Dmitry, Sharapova, Yana, Shegay, Maxim, Popova, Nina, Fesko, Kateryna, Voevodin, Vladimir, Švedas, Vytas, Barbosa, Simone Diniz Junqueira, Editorial Board Member, Filipe, Joaquim, Editorial Board Member, Ghosh, Ashish, Editorial Board Member, Kotenko, Igor, Editorial Board Member, Zhou, Lizhu, Editorial Board Member, Voevodin, Vladimir, editor, and Sobolev, Sergey, editor

Published
2019
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21. A Parallel Algorithm for Eukaryotic Promoter Recognition

Author

Langroudi, Seyyed Mohammad Shaheri, Hamidi, Hamid Reza, Kermanshahani, Shokooh, Barbosa, Simone Diniz Junqueira, Editorial Board Member, Filipe, Joaquim, Editorial Board Member, Ghosh, Ashish, Editorial Board Member, Kotenko, Igor, Editorial Board Member, Zhou, Lizhu, Editorial Board Member, Grandinetti, Lucio, editor, Mirtaheri, Seyedeh Leili, editor, and Shahbazian, Reza, editor

Published
2019
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22. Peripheral blood RNA biomarkers for cardiovascular disease from bench to bedside: a position paper from the EU-CardioRNA COST action CA17129

Author

Stephanie Bezzina Wettinger, Maarten Vanhaverbeke, Costanza Emanueli, Johannes Grillari, Rosienne Farrugia, Monika Bartekova, Barbora Kalocayova, Soumaya Ben-Aicha, EU-CardioRNA Cost Action Ca, Markus Scholz, R. Attard, Yvan Devaux, Matthias Hackl, Fabio Martelli, David de Gonzalo-Calvo, Timo Brandenburger, and EU-CardioRNA COST Action (CA17129)

Subjects
Cardiovascular system -- Diseases, Physiology, business.industry, RNA, Genomics, Disease, Cardiovascular system -- Diseases -- Diagnosis, Bioinformatics, medicine.disease, Transcriptome, Physiology (medical), Heart failure, Cardiovascular system -- Diseases -- Treatment, Gene expression, medicine, Biomarker (medicine), Position paper, Cardiology and Cardiovascular Medicine, business
Abstract

Despite significant advances in the diagnosis and treatment of cardiovascular diseases, recent calls have emphasized the unmet need to improve precision-based approaches in cardiovascular disease. Although some studies provide preliminary evidence of the diagnostic and prognostic potential of circulating coding and non-coding RNAs, the complex RNA biology and lack of standardization have hampered the translation of these markers into clinical practice. In this position paper of the CardioRNA COST action CA17129, we provide recommendations to standardize the RNA development process in order to catalyse efforts to investigate novel RNAs for clinical use. We list the unmet clinical needs in cardiovascular disease, such as the identification of high-risk patients with ischaemic heart disease or heart failure who require more intensive therapies. The advantages and pitfalls of the different sample types, including RNAs from plasma, extracellular vesicles, and whole blood, are discussed in the sample matrix, together with their respective analytical methods. The effect of patient demographics and highly prevalent comorbidities, such as metabolic disorders, on the expression of the candidate RNA is presented and should be reported in biomarker studies. We discuss the statistical and regulatory aspects to translate a candidate RNA from a research use only assay to an in-vitro diagnostic test for clinical use. Optimal planning of this development track is required, with input from the researcher, statistician, industry, and regulatory partners., peer-reviewed

Published
2021

23. Whole genome sequence of Vibrio cholerae directly from dried spotted filter paper.

Author

Bénard, Angèle H. M., Guenou, Etienne, Fookes, Maria, Ateudjieu, Jerome, Kasambara, Watipaso, Siever, Matthew, Rebaudet, Stanislas, Boncy, Jacques, Adrien, Paul, Piarroux, Renaud, Sack, David A., Thomson, Nicholas, and Debes, Amanda K.

Subjects
CHOLERA, TREPONEMA pallidum, FILTER paper, VIBRIO cholerae, NUCLEOTIDE sequencing, HEALTH facilities, CHOLERA toxin
Abstract

Background: Global estimates for cholera annually approximate 4 million cases worldwide with 95,000 deaths. Recent outbreaks, including Haiti and Yemen, are reminders that cholera is still a global health concern. Cholera outbreaks can rapidly induce high death tolls by overwhelming the capacity of health facilities, especially in remote areas or areas of civil unrest. Recent studies demonstrated that stool specimens preserved on filter paper facilitate molecular analysis of Vibrio cholerae in resource limited settings. Specimens preserved in a rapid, low-cost, safe and sustainable manner for sequencing provides previously unavailable data about circulating cholera strains. This may ultimately provide new information to shape public policy response on cholera control and elimination. Methodology/Principal findings: Whole genome sequencing (WGS) recovered close to a complete sequence of the V. cholerae O1 genome with satisfactory genome coverage from stool specimens enriched in alkaline peptone water (APW) and V. cholerae culture isolates, both spotted on filter paper. The minimum concentration of V. cholerae DNA sufficient to produce quality genomic information was 0.02 ng/μL. The genomic data confirmed the presence or absence of genes of epidemiological interest, including cholera toxin and pilus loci. WGS identified a variety of diarrheal pathogens from APW-enriched specimen spotted filter paper, highlighting the potential for this technique to explore the gut microbiome, potentially identifying co-infections, which may impact the severity of disease. WGS demonstrated that these specimens fit within the current global cholera phylogenetic tree, identifying the strains as the 7th pandemic El Tor. Conclusions: WGS results allowed for mapping of short reads from APW-enriched specimen and culture isolate spotted filter papers this provided valuable molecular epidemiological sequence information on V. cholerae strains from remote, low-resource settings. These results identified the presence of co-infecting pathogens while providing rare insight into the specific V. cholerae strains causing outbreaks in cholera-endemic areas. [ABSTRACT FROM AUTHOR]

Published
2019
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24. Deep Learning and GPU Based Approaches to Protein Secondary Structure Prediction

Author

Patel, Maulika S., Barbosa, Simone Diniz Junqueira, Series Editor, Filipe, Joaquim, Series Editor, Kotenko, Igor, Series Editor, Sivalingam, Krishna M., Series Editor, Washio, Takashi, Series Editor, Yuan, Junsong, Series Editor, Zhou, Lizhu, Series Editor, Ghosh, Ashish, Series Editor, Singh, Mayank, editor, Gupta, P. K., editor, Tyagi, Vipin, editor, Flusser, Jan, editor, and Ören, Tuncer, editor

Published
2018
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25. Parallelization of Protein Clustering Algorithm Using OpenMP

Author

Dhar, Dhruv, Hegde, Lakshana, Patil, Mahesh S., Chickerur, Satyadhyan, Barbosa, Simone Diniz Junqueira, Series Editor, Filipe, Joaquim, Series Editor, Kotenko, Igor, Series Editor, Sivalingam, Krishna M., Series Editor, Washio, Takashi, Series Editor, Yuan, Junsong, Series Editor, Zhou, Lizhu, Series Editor, Ghosh, Ashish, Series Editor, Singh, Mayank, editor, Gupta, P. K., editor, Tyagi, Vipin, editor, Flusser, Jan, editor, and Ören, Tuncer, editor

Published
2018
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26. An Introduction to the Computational Challenges in Next Generation Sequencing

Author

Szallasi, Zoltan, Barbosa, Simone Diniz Junqueira, Series Editor, Filipe, Joaquim, Series Editor, Kotenko, Igor, Series Editor, Sivalingam, Krishna M., Series Editor, Washio, Takashi, Series Editor, Yuan, Junsong, Series Editor, Zhou, Lizhu, Series Editor, Kalinichenko, Leonid, editor, Manolopoulos, Yannis, editor, Malkov, Oleg, editor, Skvortsov, Nikolay, editor, Stupnikov, Sergey, editor, and Sukhomlin, Vladimir, editor

Published
2018
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27. Community-Based Semantic Subgroup Discovery

Author

Škrlj, Blaž, Kralj, Jan, Vavpetič, Anže, Lavrač, Nada, Hutchison, David, Series Editor, Kanade, Takeo, Series Editor, Kittler, Josef, Series Editor, Kleinberg, Jon M., Series Editor, Mattern, Friedemann, Series Editor, Mitchell, John C., Series Editor, Naor, Moni, Series Editor, Pandu Rangan, C., Series Editor, Steffen, Bernhard, Series Editor, Terzopoulos, Demetri, Series Editor, Tygar, Doug, Series Editor, Weikum, Gerhard, Series Editor, Appice, Annalisa, editor, Loglisci, Corrado, editor, Manco, Giuseppe, editor, Masciari, Elio, editor, and Ras, Zbigniew W., editor

Published
2018
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28. CalciumCV: Computer Vision Software for Calcium Signaling in Astrocytes

Author

Kustikova, Valentina, Krivonosov, Mikhail, Pimashkin, Alexey, Denisov, Pavel, Zaikin, Alexey, Ivanchenko, Mikhail, Meyerov, Iosif, Semyanov, Alexey, Hutchison, David, Series Editor, Kanade, Takeo, Series Editor, Kittler, Josef, Series Editor, Kleinberg, Jon M., Series Editor, Mattern, Friedemann, Series Editor, Mitchell, John C., Series Editor, Naor, Moni, Series Editor, Pandu Rangan, C., Series Editor, Steffen, Bernhard, Series Editor, Terzopoulos, Demetri, Series Editor, Tygar, Doug, Series Editor, van der Aalst, Wil M. P., editor, Batagelj, Vladimir, editor, Glavaš, Goran, editor, Ignatov, Dmitry I., editor, Khachay, Michael, editor, Kuznetsov, Sergei O., editor, Koltsova, Olessia, editor, Lomazova, Irina A., editor, Loukachevitch, Natalia, editor, Napoli, Amedeo, editor, Panchenko, Alexander, editor, Pardalos, Panos M., editor, Pelillo, Marcello, editor, and Savchenko, Andrey V., editor

Published
2018
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29. The molecular basis of socially mediated phenotypic plasticity in a eusocial paper wasp

Author

Max Reuter, Benjamin A. Taylor, Seirian Sumner, Alessandro Cini, and Christopher D. R. Wyatt

Subjects
0106 biological sciences, 0301 basic medicine, Bioinformatics, Science, Wasps, education, Gene regulatory network, General Physics and Astronomy, Polistes dominula, 010603 evolutionary biology, 01 natural sciences, Article, General Biochemistry, Genetics and Molecular Biology, Machine Learning, 03 medical and health sciences, Gene expression, Animals, Humans, Gene Regulatory Networks, Social Behavior, Paper wasp, Phenotypic plasticity, Multidisciplinary, biology, Gene Expression Profiling, Computational Biology, General Chemistry, Animal behaviour, biology.organism_classification, Adaptation, Physiological, Phenotype, Eusociality, Gene Ontology, 030104 developmental biology, Evolutionary biology, Female, Adaptation, Transcriptome, Entomology, Algorithms
Abstract

Phenotypic plasticity, the ability to produce multiple phenotypes from a single genotype, represents an excellent model with which to examine the relationship between gene expression and phenotypes. Analyses of the molecular foundations of phenotypic plasticity are challenging, however, especially in the case of complex social phenotypes. Here we apply a machine learning approach to tackle this challenge by analyzing individual-level gene expression profiles of Polistes dominula paper wasps following the loss of a queen. We find that caste-associated gene expression profiles respond strongly to queen loss, and that this change is partly explained by attributes such as age but occurs even in individuals that appear phenotypically unaffected. These results demonstrate that large changes in gene expression may occur in the absence of outwardly detectable phenotypic changes, resulting here in a socially mediated de-differentiation of individuals at the transcriptomic level but not at the levels of ovarian development or behavior., Connecting genotypes to complex social behaviour is challenging. Taylor et al. use machine learning to show a strong response of caste-associated gene expression to queen loss, wherein individual wasp’s expression profiles become intermediate between queen and worker states, even in the absence of behavioural changes.

Published
2021

30. An Opposition Based Differential Evolution to Solve Multiple Sequence Alignment

Author

Pramanik, Sabari, Setua, S. K., Barbosa, Simone Diniz Junqueira, Series editor, Chen, Phoebe, Series editor, Filipe, Joaquim, Series editor, Kotenko, Igor, Series editor, Sivalingam, Krishna M., Series editor, Washio, Takashi, Series editor, Yuan, Junsong, Series editor, Zhou, Lizhu, Series editor, Mandal, J. K., editor, Dutta, Paramartha, editor, and Mukhopadhyay, Somnath, editor

Published
2017
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31. MapReduce in Computational Biology - A Synopsis

Author

Cattaneo, Giuseppe, Giancarlo, Raffaele, Piotto, Stefano, Ferraro Petrillo, Umberto, Roscigno, Gianluca, Di Biasi, Luigi, Chen, Phoebe, Series editor, Du, Xiaoyong, Series editor, Filipe, Joaquim, Series editor, Kara, Orhun, Series editor, Kotenko, Igor, Series editor, Liu, Ting, Series editor, Sivalingam, Krishna M., Series editor, Washio, Takashi, Series editor, Rossi, Federico, editor, Piotto, Stefano, editor, and Concilio, Simona, editor

Published
2017
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32. Improving Bioinformatics Analysis of Large Sequence Datasets Parallelizing Tools for Population Genomics

Author

Navarro, Javier, Vera, Gonzalo, Ramos-Onsins, Sebastián, Hernández, Porfidio, Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Weikum, Gerhard, Series editor, Desprez, Frédéric, editor, Dutot, Pierre-François, editor, Kaklamanis, Christos, editor, Marchal, Loris, editor, Molitorisz, Korbinian, editor, Ricci, Laura, editor, Scarano, Vittorio, editor, Vega-Rodríguez, Miguel A., editor, Varbanescu, Ana Lucia, editor, Hunold, Sascha, editor, Scott, Stephen L., editor, Lankes, Stefan, editor, and Weidendorfer, Josef, editor

Published
2017
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33. Performance Analysis and Optimization of SAMtools Sorting

Author

Weeks, Nathan T., Luecke, Glenn R., Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Weikum, Gerhard, Series editor, Desprez, Frédéric, editor, Dutot, Pierre-François, editor, Kaklamanis, Christos, editor, Marchal, Loris, editor, Molitorisz, Korbinian, editor, Ricci, Laura, editor, Scarano, Vittorio, editor, Vega-Rodríguez, Miguel A., editor, Varbanescu, Ana Lucia, editor, Hunold, Sascha, editor, Scott, Stephen L., editor, Lankes, Stefan, editor, and Weidendorfer, Josef, editor

Published
2017
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34. Peptide hormone analysis in diagnosis and treatment of Differences of Sex Development: joint position paper of EU COST Action ‘DSDnet’ and European Reference Network on Rare Endocrine Conditions

Author

Johannsen, T.H., Andersson, A.M., Ahmed, S.F., Rijke, Y.B. de, Greaves, R.F., Hartmann, M.F., Hiort, O., Holterhus, P.M., Krone, N.P., Kulle, A., Ljubicic, M.L., Mastorakos, G., McNeilly, J., Pereira, A.M., Saba, A., Wudy, S.A., Main, K.M., Juul, A., Working Group 3 H, Work Package 5 Diag, and Clinical Chemistry

Subjects
Anti-Mullerian Hormone, Male, medicine.medical_specialty, Peptide Hormones, Endocrinology, Diabetes and Metabolism, Disorders of Sex Development, 030209 endocrinology & metabolism, Context (language use), Physical examination, Peptide hormone, Bioinformatics, 03 medical and health sciences, Rare Diseases, 0302 clinical medicine, Endocrinology, SDG 3 - Good Health and Well-being, Tandem Mass Spectrometry, Internal medicine, medicine, Humans, Endocrine system, Inhibins, Cost action, Immunoassay, medicine.diagnostic_test, business.industry, Network on, Disease Management, General Medicine, Luteinizing Hormone, Reference Standards, Europe, 030220 oncology & carcinogenesis, Practice Guidelines as Topic, Position paper, Female, Follicle Stimulating Hormone, business, Chromatography, Liquid, Hormone
Abstract

Differences of Sex Development (DSD) comprise a variety of congenital conditions characterized by atypical chromosomal, gonadal, or anatomical sex. Diagnosis and monitoring of treatment of patients suspected of DSD conditions include clinical examination, measurement of peptide and steroid hormones, and genetic analysis. This position paper on peptide hormone analyses in the diagnosis and control of patients with DSD was jointly prepared by specialists in the field of DSD and/or peptide hormone analysis from the European Cooperation in Science and Technology (COST) Action DSDnet (BM1303) and the European Reference Network on rare Endocrine Conditions (Endo-ERN). The goal of this position paper on peptide hormone analysis was to establish laboratory guidelines that may contribute to improve optimal diagnosis and treatment control of DSD. The essential peptide hormones used in the management of patients with DSD conditions are follicle-stimulating hormone, luteinising hormone, anti-Müllerian hormone, and Inhibin B. In this context, the following position statements have been proposed: serum and plasma are the preferred matrices; the peptide hormones can all be measured by immunoassay, while use of LC-MS/MS technology has yet to be implemented in a diagnostic setting; sex- and age-related reference values are mandatory in the evaluation of these hormones; and except for Inhibin B, external quality assurance programs are widely available.

Published
2020

35. Is <italic>PLOS ONE</italic> Attracting Highly Cited Papers in the Food Sciences? Comparing Authors' Most Cited Work to Their <italic>PLOS ONE</italic> Articles Published 2006-2016.

Author

Stankus, Tony

Subjects
INFORMATION sharing, FOOD safety, BIOINFORMATICS, IMMUNOINFORMATICS
Abstract

Since 2007, the Open Access journal PLOS ONE has published 194,622 expert-reviewed scientific papers, including 85 related to the human food sciences such as food safety, general food science, and nutrition. Seventy-five of their corresponding authors had previously published. Their most cited articles in other journals were identified and citation counts compared against those earned by their PLOS ONE papers. No PLOS ONE food sciences paper has yet been cited more than an author's best effort in the field in other journals. More than half (38) of the 75 PLOS ONE papers studied remain uncited even by their own authors. [ABSTRACT FROM AUTHOR]

Published
2018
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36. Comment on paper “Multi-strategy ensemble evolutionary algorithm for dynamic multi-objective optimization” by Wang and Li

Author

Vrugt, Jasper A., Robinson, Bruce A., and Hyman, James M.

Subjects
Engineering, Applications of Mathematics, Bioinformatics, Statistical Physics, Dynamical Systems and Complexity, Artificial Intelligence (incl. Robotics), Appl.Mathematics/Computational Methods of Engineering, Control , Robotics, Mechatronics, Multi-method optimization, Ensemble optimizer, AMALGAM
Abstract

This comment addresses the work of Wang and Li (DOI: 10.1007/s12293-009-0012-0, hereafter referred to as WL) published online on September 01, 2009 in a (special) issue of Memetic Computing. We respectfully beg to differ in opinion with WL and argue that the concept of multi-strategy evolutionary search used by WL is not particularly novel. Similar ideas have been presented elsewhere, and these publications date back to at least early 2007. For instance, in a series of papers published in PNAS (2007), SSSAJ (2008), WRR (2008), IEEE-TEVC (2009), JH (2010), Vrugt and coworkers have introduced AMALGAM, a multi-method (or ensemble) search approach to solve emerging single and multiple objective search and optimization problems. In the past few years, MATLAB, C++, Python, and R implementations of AMALGAM have been distributed extensively among researchers and practitioners in various fields of study.

Published
2010

37. Cardiovascular disease and COVID-19:a consensus paper from the ESC Working Group on Coronary Pathophysiology & Microcirculation, ESC Working Group on Thrombosis and the Association for Acute CardioVascular Care (ACVC), in collaboration with the European Heart Rhythm Association (EHRA)

Author

Maria Dorobantu, Dirk J. Duncker, Geneviève Derumeaux, Diana A. Gorog, Zorana Vasiljevic-Pokrajcic, Cor de Wit, Marija Vavlukis, Dimitris Tousoulis, Etto C. Eringa, Edina Cenko, Christian Hassager, Davor Miličić, Teresa Padró, Giuseppe De Luca, Gemma Vilahur, Marc J. Claeys, Lina Badimon, Danijela Trifunovic-Zamaklar, Raffaele Bugiardini, Frank R. Heinzel, Olivia Manfrini, Evangelos Oikonomou, Kurt Huber, RS: Carim - H08 Experimental atrial fibrillation, Fysiologie, Physiology, ACS - Diabetes & metabolism, Cenko E., Badimon L., Bugiardini R., Claeys M.J., De Luca G., de Wit C., Derumeaux G., Dorobantu M., Duncker D.J., Eringa E.C., Gorog D.A., Hassager C., Heinzel F.R., Huber K., Manfrini O., Milicic D., Oikonomou E., Padro T., Trifunovic-Zamaklar D., Vasiljevic-Pokrajcic Z., Vavlukis M., Vilahur G., and Tousoulis D.

Subjects
Physiology, Disease, Review, CORONAVIRUS, 030204 cardiovascular system & hematology, Bioinformatics, endothelial dysfunction, 0302 clinical medicine, cytokine, Cardiometabolic Risk Factor, thrombosi, AcademicSubjects/MED00200, 030212 general & internal medicine, Endothelial dysfunction, CARDIOLOGY, Clinical Trials as Topic, Sex Characteristics, post-acute COVID-19, THROMBOEMBOLISM FOLLOWING HOSPITALIZATION, Inflammation/complications, Cardiovascular disease, Thrombosis, Pathophysiology, 3. Good health, Cardiovascular Diseases, Myocardial injury, Cardiovascular Diseases/enzymology, COVID-19/complications, Angiotensin-Converting Enzyme 2, medicine.symptom, Cardiology and Cardiovascular Medicine, Infection, Viral load, POSITION PAPER, Human, ANGIOTENSIN-CONVERTING ENZYME, EXPRESSION, SEX-DIFFERENCES, microcirculation, Inflammation, Angiotensin-Converting Enzyme 2/metabolism, 03 medical and health sciences, Post-Acute COVID-19 Syndrome, SDG 3 - Good Health and Well-being, Physiology (medical), medicine, Humans, thrombosis, business.industry, SARS-CoV-2, INFLAMMATORY RESPONSE, Cardiometabolic Risk Factors, COVID-19, medicine.disease, CARDIAC ARREST SYNDROME, cytokines, inflammation, Cardiovascular Injury, Myocardial fibrosis, Human medicine, business
Abstract

The cardiovascular system is significantly affected in coronavirus disease-19 (COVID-19). Microvascular injury, endothelial dysfunction, and thrombosis resulting from viral infection or indirectly related to the intense systemic inflammatory and immune responses are characteristic features of severe COVID-19. Pre-existing cardiovascular disease and viral load are linked to myocardial injury and worse outcomes. The vascular response to cytokine production and the interaction between severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) and angiotensin-converting enzyme 2 receptor may lead to a significant reduction in cardiac contractility and subsequent myocardial dysfunction. In addition, a considerable proportion of patients who have been infected with SARS-CoV-2 do not fully recover and continue to experience a large number of symptoms and post-acute complications in the absence of a detectable viral infection. This conditions often referred to as ‘post-acute COVID-19’ may have multiple causes. Viral reservoirs or lingering fragments of viral RNA or proteins contribute to the condition. Systemic inflammatory response to COVID-19 has the potential to increase myocardial fibrosis which in turn may impair cardiac remodelling. Here, we summarize the current knowledge of cardiovascular injury and post-acute sequelae of COVID-19. As the pandemic continues and new variants emerge, we can advance our knowledge of the underlying mechanisms only by integrating our understanding of the pathophysiology with the corresponding clinical findings. Identification of new biomarkers of cardiovascular complications, and development of effective treatments for COVID-19 infection are of crucial importance., Graphical Abstract Graphical Abstract

Published
2021

38. A Parallel Evolutionary Approach to the Molecular Docking Problem

Author

Espinosa-Galindo, Daniel, Fernández-Flores, Jesús A., Almanza-Román, Inés A., Palma-Orozco, Rosaura, Rosas-Trigueros, Jorge L., Diniz Junqueira Barbosa, Simone, Series editor, Chen, Phoebe, Series editor, Du, Xiaoyong, Series editor, Filipe, Joaquim, Series editor, Kara, Orhun, Series editor, Kotenko, Igor, Series editor, Liu, Ting, Series editor, Sivalingam, Krishna M., Series editor, Washio, Takashi, Series editor, Barrios Hernández, Carlos Jaime, editor, Gitler, Isidoro, editor, and Klapp, Jaime, editor

Published
2017
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39. Better Interpretable Models for Proteomics Data Analysis Using Rule-Based Mining

Author

Jayrannejad, Fahrnaz, Conrad, Tim O. F., Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Weikum, Gerhard, Series editor, Holzinger, Andreas, editor, Goebel, Randy, editor, Ferri, Massimo, editor, and Palade, Vasile, editor

Published
2017
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40. Ultra-Fast Detection of Higher-Order Epistatic Interactions on GPUs

Author

Jünger, Daniel, Hundt, Christian, González-Domínguez, Jorge, Schmidt, Bertil, Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Weikum, Gerhard, Series editor, Desprez, Frédéric, editor, Dutot, Pierre-François, editor, Kaklamanis, Christos, editor, Marchal, Loris, editor, Molitorisz, Korbinian, editor, Ricci, Laura, editor, Scarano, Vittorio, editor, Vega-Rodríguez, Miguel A., editor, Varbanescu, Ana Lucia, editor, Hunold, Sascha, editor, Scott, Stephen L., editor, Lankes, Stefan, editor, and Weidendorfer, Josef, editor

Published
2017
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41. Improving Multiobjective Phylogenetic Searches by Using a Parallel -Dominance Based Adaptation of the Firefly Algorithm

Author

Santander-Jiménez, Sergio, Vega-Rodríguez, Miguel A., Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Weikum, Gerhard, Series editor, Desprez, Frédéric, editor, Dutot, Pierre-François, editor, Kaklamanis, Christos, editor, Marchal, Loris, editor, Molitorisz, Korbinian, editor, Ricci, Laura, editor, Scarano, Vittorio, editor, Vega-Rodríguez, Miguel A., editor, Varbanescu, Ana Lucia, editor, Hunold, Sascha, editor, Scott, Stephen L., editor, Lankes, Stefan, editor, and Weidendorfer, Josef, editor

Published
2017
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42. An Enhancement of Privacy-Preserving Wildcards Pattern Matching

Author

Saha, Tushar Kanti, Koshiba, Takeshi, Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Weikum, Gerhard, Series editor, Cuppens, Frédéric, editor, Wang, Lingyu, editor, Cuppens-Boulahia, Nora, editor, Tawbi, Nadia, editor, and Garcia-Alfaro, Joaquin, editor

Published
2017
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44. Impact of nutraceuticals on markers of systemic inflammation: Potential relevance to cardiovascular diseases - A position paper from the International Lipid Expert Panel (ILEP)

Author

Massimiliano Ruscica, Peter E. Penson, Nicola Ferri, Cesare R. Sirtori, Matteo Pirro, G.B. John Mancini, Naveed Sattar, Peter P. Toth, Amirhossein Sahebkar, Carl J. Lavie, Nathan D. Wong, Maciej Banach, Julio Acosta, Mutaz Al-Khnifsawi, Fahad Alnouri, Fahma Amar, Atanas G. Atanasov, Gani Bajraktari, Sonu Bhaskar, Bojko Bjelakovic, Eric Bruckert, Richard Ceska, Arrigo F.G. Cicero, Xavier Collet, Olivier Descamps, Dragan Djuric, Ronen Durst, Marat V. Ezhov, Zlatko Fras, Dan Gaita, Adrian V. Hernandez, Steven R. Jones, Jacek Jozwiak, Nona Kakauridze, Amani Kallel, Niki Katsiki, Amit Khera, Karam Kostner, Raimondas Kubilius, Gustavs Latkovskis, A. David Marais, Seth S. Martin, Julio Acosta Martinez, Mohsen Mazidi, Dimitri P. Mikhailidis, Erkin Mirrakhimov, Andre R. Miserez, Olena Mitchenko, Natalya P. Mitkovskaya, Patrick M. Moriarty, Seyed Mohammad Nabavi, Devaki Nair, Demosthenes B. Panagiotakos, György Paragh, Daniel Pella, Zaneta Petrulioniene, Arman Postadzhiyan, Raman Puri, Ashraf Reda, Željko Reiner, Dina Radenkovic, Michał Rakowski, Jemaa Riadh, Dimitri Richter, Manfredi Rizzo, Maria-Corina Serban, Abdulla M.A. Shehab, Aleksandr B. Shek, Claudia Stefanutti, Tomasz Tomasik, Margus Viigimaa, Pedro Valdivielso, Dragos Vinereanu, Branislav Vohnout, Stephan von Haehling, Michal Vrablik, Hung-I Yeh, Jiang Zhisheng, Andreas Zirlik, Ruscica M, Penson PE, Ferri N, Sirtori CR, Pirro M, Mancini GBJ, Sattar N, Toth PP, Sahebkar A, Lavie CJ, Wong ND, Banach M, International Lipid Expert Panel (ILEP) and International Lipid Expert Panel Experts, Cicero AFG, Ruscica M., Penson P.E., Ferri N., Sirtori C.R., Pirro M., Mancini G.B.J., Sattar N., Toth P.P., Sahebkar A., Lavie C.J., Wong N.D., Banach M., Acosta J., Al-Khnifsawi M., Alnouri F., Amar F., Atanasov A.G., Bajraktari G., Bhaskar S., Bjelakovic B., Bruckert E., Ceska R., Cicero A.F.G., Collet X., Descamps O., Djuric D., Durst R., Ezhov M.V., Fras Z., Gaita D., Hernandez A.V., Jones S.R., Jozwiak J., Kakauridze N., Kallel A., Katsiki N., Khera A., Kostner K., Kubilius R., Latkovskis G., Marais A.D., Martin S.S., Martinez J.A., Mazidi M., Mikhailidis D.P., Mirrakhimov E., Miserez A.R., Mitchenko O., Mitkovskaya N.P., Moriarty P.M., Nabavi S.M., Nair D., Panagiotakos D.B., Paragh G., Pella D., Petrulioniene Z., Postadzhiyan A., Puri R., Reda A., Reiner Z., Radenkovic D., Rakowski M., Riadh J., Richter D., Rizzo M., Serban M.-C., Shehab A.M.A., Shek A.B., Stefanutti C., Tomasik T., Viigimaa M., Valdivielso P., Vinereanu D., Vohnout B., von Haehling S., Vrablik M., Yeh H.-I., Zhisheng J., Zirlik A., and UCL - (SLuc) Service de pathologie cardiovasculaire

Subjects
RM, Arterial disease, Anti-Inflammatory Agents, Inflammation, Disease, C-reactive protein, cardiovascular disease, inflammation, nutraceuticals, omega-3, position paper, red-yeast rice, 030204 cardiovascular system & hematology, Bioinformatics, Systemic inflammation, 03 medical and health sciences, 0302 clinical medicine, Nutraceutical, Medicine, Humans, Position paper, 030212 general & internal medicine, Uncategorized, Omega-3, biology, Cardiovascular disease, Nutraceuticals, Red-yeast rice, Biomarkers, Cardiovascular Diseases, Lipids, Dietary Supplements, Vascular inflammation, business.industry, C-reactive protein, Cardiovascular disease, Inflammation, Nutraceuticals, Omega-3, Position paper, Red-yeast rice, Anti-Inflammatory Agents, Biomarkers, Cardiovascular Diseases, Humans, Inflammation, Lipids, Dietary Supplements, biology.protein, medicine.symptom, Cardiology and Cardiovascular Medicine, business
Abstract

Inflammation is a marker of arterial disease stemming from cholesterol-dependent to -independent molecular mechanisms. In recent years, the role of inflammation in atherogenesis has been underpinned by pharmacological approaches targeting systemic inflammation that have led to a significant reduction in cardiovascular disease (CVD) risk. Although the use of nutraceuticals to prevent CVD has largely focused on lipid-lowering (e.g, red-yeast rice and omega-3 fatty acids), there is growing interest and need, especially now in the time of coronavirus pandemic, in the use of nutraceuticals to reduce inflammatory markers, and potentially the inflammatory CVD burden, however, there is still not enough evidence to confirm this. Indeed, diet is an important lifestyle determinant of health and can influence both systemic and vascular inflammation, to varying extents, according to the individual nutraceutical constituents. Thus, the aim of this Position Paper is to provide the first attempt at recommendations on the use of nutraceuticals with effective anti-inflammatory properties.

Published
2021

45. Big-Data Approaches for Bioinformatics Workflows: A Comparative Assessment

Author

Nunes, Rickey T. P., Deshpande, Santosh L., Filipe, Joaquim, Editorial Board Member, Ghosh, Ashish, Editorial Board Member, Kotenko, Igor, Editorial Board Member, Prates, Raquel Oliveira, Editorial Board Member, Zhou, Lizhu, Editorial Board Member, Barbosa, Simone Diniz Junqueira, Editorial Board Member, Chen, Phoebe, Editorial Board Member, Du, Xiaoyong, Editorial Board Member, Kara, Orhun, Editorial Board Member, Liu, Ting, Editorial Board Member, Sivalingam, Krishna M., Editorial Board Member, Washio, Takashi, Editorial Board Member, Yuan, Junsong, Editorial Board Member, Unal, Aynur, editor, Nayak, Malaya, editor, Mishra, Durgesh Kumar, editor, Singh, Dharm, editor, and Joshi, Amit, editor

Published
2016
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46. Accelerating 3D Protein Structure Similarity Searching on Microsoft Azure Cloud with Local Replicas of Macromolecular Data

Author

Mrozek, Dariusz, Kutyła, Tomasz, Małysiak-Mrozek, Bożena, Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Weikum, Gerhard, Series editor, Wyrzykowski, Roman, editor, Deelman, Ewa, editor, Dongarra, Jack, editor, Karczewski, Konrad, editor, Kitowski, Jacek, editor, and Wiatr, Kazimierz, editor

Published
2016
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48. Peptide hormone analysis in diagnosis and treatment of Differences of Sex Development: joint position paper of EU COST Action ‘DSDnet’ and European Reference Network on Rare Endocrine Conditions

Author

Anders Juul, A Saba, Stefan A. Wudy, Alexandra Kulle, Michaela F. Hartmann, Marie Lindhardt Ljubicic, Jane McNeilly, Syed Faisal Ahmed, Ronda F. Greaves, George Mastorakos, de Rijke Yb, Olaf Hiort, Alberto M. Pereira, Andersson Am, Katharina M. Main, Trine Holm Johannsen, Nils Krone, and Paul Martin Holterhus

Subjects
business.industry, Network on, Medicine, Endocrine system, Position paper, Joint (building), Cost action, Peptide hormone, business, Bioinformatics
Published
2021

49. Classifying Human Blood Samples Using Characteristics of Single Molecules and Cell Structures on Microscopy Images

Author

Borgmann, Daniela, Mayr, Sandra, Polin, Helene, Obritzberger, Lisa, Schaller, Susanne, Dorfer, Viktoria, Jacak, Jaroslaw, Winkler, Stephan, Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Weikum, Gerhard, Series editor, Moreno-Díaz, Roberto, editor, Pichler, Franz, editor, and Quesada-Arencibia, Alexis, editor

Published
2015
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50. The molecular profiling of solid tumors by liquid biopsy: a position paper of the AIOM–SIAPEC-IAP–SIBioC–SIC–SIF Italian Scientific Societies

Author

A. Russo, Umberto Malapelle, Pierosandro Tagliaferri, Saverio Cinieri, Daniele Santini, M. Del Re, Nicola Silvestris, Antonio Marchetti, Carmine Pinto, Giuseppe Giuffrè, Ettore Capoluongo, Giancarlo Troncone, Romano Danesi, Giulio Rossi, Stefania Gori, Nicola Normanno, Matteo Fassan, Valerio Gristina, Andrea Sartore-Bianchi, Giordano D. Beretta, Lorena Incorvaia, Marta Castiglia, Russo A., Incorvaia L., Del Re M., Malapelle U., Capoluongo E., Gristina V., Castiglia M., Danesi R., Fassan M., Giuffre G., Gori S., Marchetti A., Normanno N., Pinto C., Rossi G., Santini D., Sartore-Bianchi A., Silvestris N., Tagliaferri P., Troncone G., Cinieri S., Beretta G.D., Russo, A., Incorvaia, L., Del Re, M., Malapelle, U., Capoluongo, E., Gristina, V., Castiglia, M., Danesi, R., Fassan, M., Giuffre, G., Gori, S., Marchetti, A., Normanno, N., Pinto, C., Rossi, G., Santini, D., Sartore-Bianchi, A., Silvestris, N., Tagliaferri, P., Troncone, G., Cinieri, S., and Beretta, G. D.

Subjects
Societies, Scientific, Cancer Research, Context (language use), Review, Neoplastic Cells, Bioinformatics, Circulating tumor cell, Circulating, Biomarkers, Tumor, Medicine, Humans, Digital polymerase chain reaction, Liquid biopsy, cfDNA, circulating tumor DNA, circulating cell-free DNA, ctDNA, digital PCR, liquid biopsy, next-generation sequencing, real-time PCR, Tumor, Circulating Neoplastic Cells, business.industry, Scientific, Neoplastic Cells, Circulating, Circulating Cell-Free DNA, Italy, Liquid Biopsy, Oncology, Circulating tumor DNA, Position paper, Societies, business, Biomarkers, Human
Abstract

The term liquid biopsy (LB) refers to the use of various biological fluids as a surrogate for neoplastic tissue to achieve information for diagnostic, prognostic and predictive purposes. In the current clinical practice, LB is used for the identification of driver mutations in circulating tumor DNA derived from both tumor tissue and circulating neoplastic cells. As suggested by a growing body of evidence, however, there are several clinical settings where biological samples other than tissue could be used in the routine practice to identify potentially predictive biomarkers of either response or resistance to targeted treatments. New applications are emerging as useful clinical tools, and other blood derivatives, such as circulating tumor cells, circulating tumor RNA, microRNAs, platelets, extracellular vesicles, as well as other biofluids such as urine and cerebrospinal fluid, may be adopted in the near future. Despite the evident advantages compared with tissue biopsy, LB still presents some limitations due to both biological and technological issues. In this context, the absence of harmonized procedures corresponds to an unmet clinical need, ultimately affecting the rapid implementation of LB in clinical practice. In this position paper, based on experts’ opinions, the AIOM–SIAPEC-IAP–SIBIOC–SIF Italian Scientific Societies critically discuss the most relevant technical issues of LB, the current and emerging evidences, with the aim to optimizing the applications of LB in the clinical setting., Highlights • In the current clinical practice LB is used for the identification of driver mutations in circulating tumor DNA (ctDNA). • New applications in tumors other than non-small-cell lung cancer (NSCLC) are emerging as useful clinical tools. • Other blood derivatives, together with other biofluids, are an active field of research and may be adopted in the near future. • Despite the evident advantages, liquid biopsy still presents limitations due to both biological and technological issues. • Standardization of the procedures needs to be addressed to ensure widespread implementation in clinical practice.

Published
2021