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1. Discovery and classification of Twitter bots

Author

Shevtsov, Alexander Shevtsov Alexander, Oikonomidou, Maria, Antonakaki, Despoina, Pratikakis, Polyvios, Kanterakis, Alexandros, Ioannidis, Sotiris, and Fragopoulou, Paraskevi

Subjects
Computer Science - Social and Information Networks
Abstract

A very large number of people use Online Social Networks daily. Such platforms thus become attractive targets for agents that seek to gain access to the attention of large audiences, and influence perceptions or opinions. Botnets, collections of automated accounts controlled by a single agent, are a common mechanism for exerting maximum influence. Botnets may be used to better infiltrate the social graph over time and to create an illusion of community behavior, amplifying their message and increasing persuasion. This paper investigates Twitter botnets, their behavior, their interaction with user communities and their evolution over time. We analyzed a dense crawl of a subset of Twitter traffic, amounting to nearly all interactions by Greek-speaking Twitter users for a period of 36 months. We detected over a million events where seemingly unrelated accounts tweeted nearly identical content at nearly the same time. We filtered these concurrent content injection events and detected a set of 1,850 accounts that repeatedly exhibit this pattern of behavior, suggesting that they are fully or in part controlled and orchestrated by the same software. We found botnets that appear for brief intervals and disappear, as well as botnets that evolve and grow, spanning the duration of our dataset. We analyze statistical differences between bot accounts and human users, as well as botnet interaction with user communities and Twitter trending topics.

Published
2020
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2. Study of Alzheimer's disease- and frontotemporal dementia-associated genes in the Cretan Aging Cohort

Author

Mathioudakis, Lambros, Dimovasili, Christina, Bourbouli, Mara, Latsoudis, Helen, Kokosali, Evgenia, Gouna, Garyfallia, Vogiatzi, Emmanouella, Basta, Maria, Kapetanaki, Stefania, Panagiotakis, Simeon, Kanterakis, Alexandros, Boumpas, Dimitrios, Lionis, Christos, Plaitakis, Andreas, Simos, Panagiotis, Vgontzas, Alexandros, Kafetzopoulos, Dimitrios, and Zaganas, Ioannis

Published
2023
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3. A proxitome-RNA-capture approach reveals that processing bodies repress coregulated hub genes

Author

Carl Tryggers Foundation, Helge Ax:son Johnsons Stiftelse, Hellenic Foundation for Research & Innovation, European Commission, Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), Junta de Andalucía, Foundation for Research and Technology, Swedish Research Council for Sustainable Development, Kempestiftelserna, Liu, Chen [0000-0002-1604-0694], Mentzelopoulou, Andriani [0000-0003-4266-8714], Hatzianestis, Ioannis H [0009-0009-0213-775X], Tzagkarakis, Epameinondas [0009-0008-5615-2296], Skaltsogiannis, Vasileios [0000-0003-4155-9540], Ma, Xuemin [0000-0001-5690-7929], Michalopoulou, Vassiliki A [0000-0002-7663-2472], Romero-Campero, Francisco J. [0000-0001-9834-030X], Romero-Losada, Ana B [0000-0003-4073-3631], Sarris, Panagiotis F [0000-0001-7000-8997], Marhavy, Peter [0000-0002-0178-2230], Bölter, Bettina [0000-0002-7780-7289], Kanterakis, Alexandros [0000-0003-4276-0115], Gutierrez-Beltran, Emilio [0000-0001-7978-3164], Moschou, Panagiotis N [0000-0001-7212-0595], Liu, Chen, Mentzelopoulou, Andriani, Hatzianestis, Ioannis H, Tzagkarakis, Epameinondas, Skaltsogiannis, Vasileios, Ma, Xuemin, Michalopoulou, Vassiliki A, Romero-Campero, Francisco J., Romero-Losada, Ana B, Sarris, Panagiotis F, Marhavy, Peter, Bölter, Bettina, Kanterakis, Alexandros, Gutierrez-Beltran, Emilio, Moschou, Panagiotis N, Carl Tryggers Foundation, Helge Ax:son Johnsons Stiftelse, Hellenic Foundation for Research & Innovation, European Commission, Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), Junta de Andalucía, Foundation for Research and Technology, Swedish Research Council for Sustainable Development, Kempestiftelserna, Liu, Chen [0000-0002-1604-0694], Mentzelopoulou, Andriani [0000-0003-4266-8714], Hatzianestis, Ioannis H [0009-0009-0213-775X], Tzagkarakis, Epameinondas [0009-0008-5615-2296], Skaltsogiannis, Vasileios [0000-0003-4155-9540], Ma, Xuemin [0000-0001-5690-7929], Michalopoulou, Vassiliki A [0000-0002-7663-2472], Romero-Campero, Francisco J. [0000-0001-9834-030X], Romero-Losada, Ana B [0000-0003-4073-3631], Sarris, Panagiotis F [0000-0001-7000-8997], Marhavy, Peter [0000-0002-0178-2230], Bölter, Bettina [0000-0002-7780-7289], Kanterakis, Alexandros [0000-0003-4276-0115], Gutierrez-Beltran, Emilio [0000-0001-7978-3164], Moschou, Panagiotis N [0000-0001-7212-0595], Liu, Chen, Mentzelopoulou, Andriani, Hatzianestis, Ioannis H, Tzagkarakis, Epameinondas, Skaltsogiannis, Vasileios, Ma, Xuemin, Michalopoulou, Vassiliki A, Romero-Campero, Francisco J., Romero-Losada, Ana B, Sarris, Panagiotis F, Marhavy, Peter, Bölter, Bettina, Kanterakis, Alexandros, Gutierrez-Beltran, Emilio, and Moschou, Panagiotis N

Abstract

Cellular condensates are usually ribonucleoprotein assemblies with liquid- or solid-like properties. Because these subcellular structures lack a delineating membrane, determining their compositions is difficult. Here we describe a proximity-biotinylation approach for capturing the RNAs of the condensates known as processing bodies (PBs) in Arabidopsis (Arabidopsis thaliana). By combining this approach with RNA detection, in silico, and high-resolution imaging approaches, we studied PBs under normal conditions and heat stress. PBs showed a much more dynamic RNA composition than the total transcriptome. RNAs involved in cell wall development and regeneration, plant hormonal signaling, secondary metabolism/defense, and RNA metabolism were enriched in PBs. RNA-binding proteins and the liquidity of PBs modulated RNA recruitment, while RNAs were frequently recruited together with their encoded proteins. In PBs, RNAs follow distinct fates: in small liquid-like PBs, RNAs get degraded while in more solid-like larger ones, they are stored. PB properties can be regulated by the actin-polymerizing SCAR (suppressor of the cyclic AMP)-WAVE (WASP family verprolin homologous) complex. SCAR/WAVE modulates the shuttling of RNAs between PBs and the translational machinery, thereby adjusting ethylene signaling. In summary, we provide an approach to identify RNAs in condensates that allowed us to reveal a mechanism for regulating RNA fate.

Published
2024

4. Interactive, Cloud-Native Workflows on HPC Using KNoC

Author

Maliaroudakis, Evangelos, Chazapis, Antony, Kanterakis, Alexandros, Marazakis, Manolis, Bilas, Angelos, 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, Anzt, Hartwig, editor, Bienz, Amanda, editor, Luszczek, Piotr, editor, and Baboulin, Marc, editor

Published
2022
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7. A proxitome-RNA-capture approach reveals that processing bodies repress coregulated hub genes

Author

Liu, Chen, primary, Mentzelopoulou, Andriani, additional, Hatzianestis, Ioannis H, additional, Tzagkarakis, Epameinondas, additional, Skaltsogiannis, Vasileios, additional, Ma, Xuemin, additional, Michalopoulou, Vassiliki A, additional, Romero-Campero, Francisco J, additional, Romero-Losada, Ana B, additional, Sarris, Panagiotis F, additional, Marhavy, Peter, additional, Bölter, Bettina, additional, Kanterakis, Alexandros, additional, Gutierrez-Beltran, Emilio, additional, and Moschou, Panagiotis N, additional

Published
2023
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8. Genome of The Netherlands population-specific imputations identify an ABCA6 variant associated with cholesterol levels.

Author

van Leeuwen, Elisabeth M, Karssen, Lennart C, Deelen, Joris, Isaacs, Aaron, Medina-Gomez, Carolina, Mbarek, Hamdi, Kanterakis, Alexandros, Trompet, Stella, Postmus, Iris, Verweij, Niek, van Enckevort, David J, Huffman, Jennifer E, White, Charles C, Feitosa, Mary F, Bartz, Traci M, Manichaikul, Ani, Joshi, Peter K, Peloso, Gina M, Deelen, Patrick, van Dijk, Freerk, Willemsen, Gonneke, de Geus, Eco J, Milaneschi, Yuri, Penninx, Brenda WJH, Francioli, Laurent C, Menelaou, Androniki, Pulit, Sara L, Rivadeneira, Fernando, Hofman, Albert, Oostra, Ben A, Franco, Oscar H, Mateo Leach, Irene, Beekman, Marian, de Craen, Anton JM, Uh, Hae-Won, Trochet, Holly, Hocking, Lynne J, Porteous, David J, Sattar, Naveed, Packard, Chris J, Buckley, Brendan M, Brody, Jennifer A, Bis, Joshua C, Rotter, Jerome I, Mychaleckyj, Josyf C, Campbell, Harry, Duan, Qing, Lange, Leslie A, Wilson, James F, Hayward, Caroline, Polasek, Ozren, Vitart, Veronique, Rudan, Igor, Wright, Alan F, Rich, Stephen S, Psaty, Bruce M, Borecki, Ingrid B, Kearney, Patricia M, Stott, David J, Adrienne Cupples, L, Genome of The Netherlands Consortium, Jukema, J Wouter, van der Harst, Pim, Sijbrands, Eric J, Hottenga, Jouke-Jan, Uitterlinden, Andre G, Swertz, Morris A, van Ommen, Gert-Jan B, de Bakker, Paul IW, Eline Slagboom, P, Boomsma, Dorret I, Wijmenga, Cisca, and van Duijn, Cornelia M

Subjects
Genome of The Netherlands Consortium, Humans, Cholesterol, ATP-Binding Cassette Transporters, Gene Frequency, Mutation, Missense, Netherlands, Genetic Association Studies, Mutation, Missense
Abstract

Variants associated with blood lipid levels may be population-specific. To identify low-frequency variants associated with this phenotype, population-specific reference panels may be used. Here we impute nine large Dutch biobanks (~35,000 samples) with the population-specific reference panel created by the Genome of The Netherlands Project and perform association testing with blood lipid levels. We report the discovery of five novel associations at four loci (P value

Published
2015

12. A Proxitome–RNA–capture Approach Reveals that Processing Bodies Repress Co–Regulated Hubs

Author

Liu, Chen, primary, Mentzelopoulou, Andriani, additional, Hatzianestis, Ioannis H., additional, Tzagkarakis, Epameinondas, additional, Scaltsoyiannes, Vassilis, additional, Ma, Xuemin, additional, Michalopoulou, Vassiliki A., additional, Romero–Campero, Francisco J., additional, Romero–Losada, Ana B., additional, Sarris, Panagiotis F., additional, Marhavy, Peter, additional, Bölter, Bettina, additional, Kanterakis, Alexandros, additional, Gutierrez–Beltran, Emilio, additional, and Moschou, Panagiotis N., additional

Published
2023
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13. Data-Driven Drug Repurposing in Diabetes Mellitus through an Enhanced Knowledge Graph †.

Author

Ouzounis, Sotiris, Kanterakis, Alexandros, Panagiotopoulos, Vasilis, Cavouras, Dionisis, Zoumpoulakis, Panagiotis, Matsoukas, Minos-Timotheos, Katsila, Theodora, and Kalatzis, Ioannis

Subjects
DRUG repositioning, DIABETES, KNOWLEDGE graphs, DISEASE incidence, HYPOGLYCEMIA
Abstract

Diabetes mellitus affects more than 400 million people worldwide, and the incidence of disease is rising. Current anti-hyperglycemic agents share major drawbacks, such as hypoglycemia and low potency due to a lack of target specificity. Drug repurposing accelerates drug research and development pipelines and empowers chemical space enrichment. Herein, we propose a data-driven approach towards drug repurposing in diabetes mellitus by integrating heterogeneous biomedical data in a unified knowledge graph. Through extensive data mining in public repositories, diabetes-related multimodal data have been retrieved. Several data analysis techniques were employed to extract information and define semantic associations, followed by data parsing and, next, descriptive statistics, regression, and cluster analysis. Biomedical entity recognition and negation detection were performed by natural language processing. Predefined biological ontologies served as reference endpoints for class definition upon data integration. Graph analytics were performed, and drug–drug, protein–protein, drug–protein, and drug–disease interactions were established. A majority vote-based machine learning framework for the prediction of human cytochrome P450 inhibitors was also integrated into the proposed enhanced knowledge graph analysis that facilitates data-driven ranking for drug repurposing candidates in diabetes mellitus. The presented method yields a ranked list of repurposing candidates. [ABSTRACT FROM AUTHOR]

Published
2023
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14. A proxitome-RNA-capture approach reveals that processing bodies repress co-regulated hub genes

Author

Universidad de Sevilla. Departamento de Bioquímica Vegetal y Biología Molecular, Universidad de Sevilla. Departamento de Ciencias de la Computación e Inteligencia Artificial, Carl Tryggers Stiftelse foer Vetenskaplig Forskning, Svenska Forskningsradet Formas, European Union (UE), Helge Ax:son Johnsons stiftelse, Ministerio de Ciencia e Innovación (MICIN). España, Junta de Andalucía, Liu, Chen, Mentzelopoulou, Andriani, Hatzianestis, Ioannis H., Tzagkarakis, Epameinondas, Skaltsogiannis, Vasileios, Ma, Xuemin, Michalopoulou, Vassiliki A., Romero Campero, Francisco José, Romero Losada, Ana Belén, Sarris, Panagiotis F., Marhavy, Peter, Bolter, Bettina, Kanterakis, Alexandros, Gutiérrez Beltrán, Emilio, Moschou, Panagiotis N., Universidad de Sevilla. Departamento de Bioquímica Vegetal y Biología Molecular, Universidad de Sevilla. Departamento de Ciencias de la Computación e Inteligencia Artificial, Carl Tryggers Stiftelse foer Vetenskaplig Forskning, Svenska Forskningsradet Formas, European Union (UE), Helge Ax:son Johnsons stiftelse, Ministerio de Ciencia e Innovación (MICIN). España, Junta de Andalucía, Liu, Chen, Mentzelopoulou, Andriani, Hatzianestis, Ioannis H., Tzagkarakis, Epameinondas, Skaltsogiannis, Vasileios, Ma, Xuemin, Michalopoulou, Vassiliki A., Romero Campero, Francisco José, Romero Losada, Ana Belén, Sarris, Panagiotis F., Marhavy, Peter, Bolter, Bettina, Kanterakis, Alexandros, Gutiérrez Beltrán, Emilio, and Moschou, Panagiotis N.

Abstract

Cellular condensates are usually ribonucleoprotein assemblies with liquid- or solid-like properties. Because these subcellular structures lack a delineating membrane, determining their compositions is difficult. Here we describe a proximity-biotinylation approach for capturing the RNAs of the condensates known as processing bodies (PBs) in Arabidopsis (Arabidopsis thaliana). By combining this approach with RNA detection, in silico, and high-resolution imaging approaches, we studied PBs under normal conditions and heat stress. PBs showed a much more dynamic RNA composition than the total transcriptome. RNAs involved in cell wall development and regeneration, plant hormonal signaling, secondary metabolism/defense, and RNA metabolism were enriched in PBs. RNA-binding proteins and the liquidity of PBs modulated RNA recruitment, while RNAs were frequently recruited together with their encoded proteins. In PBs, RNAs follow distinct fates: in small liquid-like PBs, RNAs get degraded while in more solid-like larger ones, they are stored. PB properties can be regulated by the actin-polymerizing SCAR (suppressor of the cyclic AMP)-WAVE (WASP family verprolin homologous) complex. SCAR/WAVE modulates the shuttling of RNAs between PBs and the translational machinery, thereby adjusting ethylene signaling. In summary, we provide an approach to identify RNAs in condensates that allowed us to reveal a mechanism for regulating RNA fate.

Published
2023

16. Contributors

Author

Baker, Darrol J., primary, Bartsakoulia, Marina, additional, Chaouch, Melek, additional, Chimusa, Emile R., additional, Kanterakis, Alexandros, additional, Katsila, Theodora, additional, Komianou, Aggeliki, additional, Kumuthini, J., additional, Lambert, Christophe G., additional, Masimiremwa, Collen, additional, Patrinos, George P., additional, Potamias, George, additional, Sarris, Konstantinos, additional, Swertz, Morris A., additional, Tzimas, Giannis, additional, Viennas, Emmanouil, additional, and Zass, L., additional

Published
2018
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20. Towards the Discovery of Reliable Biomarkers from Gene-Expression Profiles: An Iterative Constraint Satisfaction Learning Approach

Author

Potamias, George, Koumakis, Lefteris, Kanterakis, Alexandros, Moustakis, Vassilis, Hutchison, David, editor, Kanade, Takeo, editor, Kittler, Josef, editor, Kleinberg, Jon M., editor, Mattern, Friedemann, editor, Mitchell, John C., editor, Naor, Moni, editor, Nierstrasz, Oscar, editor, Pandu Rangan, C., editor, Steffen, Bernhard, editor, Sudan, Madhu, editor, Terzopoulos, Demetri, editor, Tygar, Doug, editor, Vardi, Moshe Y., editor, Weikum, Gerhard, editor, Goebel, Randy, editor, Siekmann, Jörg, editor, Wahlster, Wolfgang, editor, Konstantopoulos, Stasinos, editor, Perantonis, Stavros, editor, Karkaletsis, Vangelis, editor, Spyropoulos, Constantine D., editor, and Vouros, George, editor

Published
2010
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23. Supporting Clinico-Genomic Knowledge Discovery: A Multi-strategy Data Mining Process

Author

Kanterakis, Alexandros, Potamias, George, 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, Nierstrasz, Oscar, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Sudan, Madhu, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Dough, Series editor, Vardi, Moshe Y., Series editor, Weikum, Gerhard, Series editor, Carbonell, Jaime G., editor, Siekmann, Jörg, editor, Antoniou, Grigoris, editor, Potamias, George, editor, Spyropoulos, Costas, editor, and Plexousakis, Dimitris, editor

Published
2006
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24. Biomedical Literature Mining for Text Classification and Construction of Gene Networks

Author

Antonakaki, Despoina, Kanterakis, Alexandros, Potamias, George, 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, Nierstrasz, Oscar, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Sudan, Madhu, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Dough, Series editor, Vardi, Moshe Y., Series editor, Weikum, Gerhard, Series editor, Carbonell, Jaime G., editor, Siekmann, Jörg, editor, Antoniou, Grigoris, editor, Potamias, George, editor, Spyropoulos, Costas, editor, and Plexousakis, Dimitris, editor

Published
2006
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25. Mining Time Series with Mine Time

Author

Koumakis, Lefteris, Moustakis, Vassilis, Kanterakis, Alexandros, Potamias, George, 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, Nierstrasz, Oscar, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Sudan, Madhu, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Dough, Series editor, Vardi, Moshe Y., Series editor, Weikum, Gerhard, Series editor, Carbonell, Jaime G., editor, Siekmann, Jörg, editor, Antoniou, Grigoris, editor, Potamias, George, editor, Spyropoulos, Costas, editor, and Plexousakis, Dimitris, editor

Published
2006
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26. Significance of regional population HLA immunogenetic datasets in the efficacy of umbilical cord blood banks and marrow donor registries: a study of Cretan HLA genetic diversity

Author

Latsoudis, Helen, primary, Stylianakis, Emmanouil, additional, Mavroudi, Irene, additional, Kanterakis, Alexandros, additional, Pavlidis, Pavlos, additional, Georgopoulou, Anthie, additional, Batsali, Aristea, additional, Gontika, Ioanna, additional, Fragiadaki, Irene, additional, Zamanakou, Maria, additional, Germenis, Anastasios E, additional, and Papadaki, Helen A., additional

Published
2022
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27. D6.2 - Preliminary conclusions about Federated Learning applied to clinical data

Author

Álvarez, Federico, Zazo, Santiago, Parras, Juan, Almodóvar, Alejandro, Alonso, Patricia, Giampieri, Enrico, Castellani, Gastone, Sani, Lorenzo, Rollo, Cesare, Sanavia, Tiziana, Krogh, Anders, Prada-Luengo, Íñigo, Kanterakis, Alexandros, Sfakianakis, Stelios, and Cremonesi, Francesco

Abstract

This report comprises the first contributions from different partners on Federated Learning (FL). Aftera preliminary introductory section where the fundamental procedures and limitations are described,we detail the well-known mathematical foundation of Federated Learning for convex problems. In thiscase, we present a key algorithm, Alternating Direction Multipliers Method (ADMM), which is ableto implement in a distributed way some fundamental problems such as regression (Ridge and LASSO)and classification (Logistic Regression and Support Vector Machines (SVM)). This procedure sharesthe fundamental approach of FL, which consists of performing some local processing, sharing someintermediate information and updating the local information with some global innovation. In a secondstep we introduce the extension of this approach to non-convexproblems using Bayesian Neural Networks(BNN) where the update is based on the cooperative construction of the posterior of weightsfrom different architectures. Several sections follow where different partners provide different contributionsdescribing our first initiatives on the topic. Some preliminary code from all partners hasbeen uploaded to a common repository to start creating a pool of methods and tools to foster incomingsynergies.

Published
2021
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29. Fine mapping of the celiac disease-associated LPP locus reveals a potential functional variant

Author

Almeida, Rodrigo, Ricaño-Ponce, Isis, Kumar, Vinod, Deelen, Patrick, Szperl, Agata, Trynka, Gosia, Gutierrez-Achury, Javier, Kanterakis, Alexandros, Westra, Harm-Jan, Franke, Lude, Swertz, Morris A., Platteel, Mathieu, Bilbao, Jose Ramon, Barisani, Donatella, Greco, Luigi, Mearin, Luisa, Wolters, Victorien M., Mulder, Chris, Mazzilli, Maria Cristina, Sood, Ajit, Cukrowska, Bozena, Núñez, Concepción, Pratesi, Riccardo, Withoff, Sebo, and Wijmenga, Cisca

Published
2014
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30. Integratie technieken voor moderne bio-informatica workflows

Author

Kanterakis, Alexandros, Kanterakis, Alexandros, Kanterakis, Alexandros, and Kanterakis, Alexandros

Abstract

Grote technologische vooruitgang maakt het nu mogelijk op grote schaal de genetica van mensen in kaart te brengen. De procedures zijn snel en relatief goedkoop, en genereren grote hoeveelheden data over de verschillende stadia van genetische regulatie. Interpretatie hiervan kan nieuw inzicht geven in menselijke fysiologie en zo bijdragen aan de verbetering van prognose en behandeling van ziekten. Echter, het omzetten van deze data in betekenisvolle kennis is een grote uitdaging. In dit proefschrift hebben we daarom gewerkt aan de synergie tussen verschillende wetenschappelijke vakgebieden, waaronder informatietechnologie (IT), biologie, geneeskunde en genetica, een relatief nieuw vakgebied: bio-informatica. Bio-informatica richt zich op het combineren van bestaande computationele oplossingen tot herbruikbare componenten, ook wel workflows genoemd, teneinde biologische data te analyseren. In deze thesis presenteer ik een collectie van nieuwe technieken die de kwaliteit van moderne bio-informatische workflows moeten verbeteren. Deze technieken gaan voorbij aan de klassieke doelstellingen van workflows: het efficiënt automatiseren van analyses en het optimaal gebruik maken van onderliggende computationele infrastructuren. Als uitbreiding op deze doelstellingen presenteer ik technieken die onervaren gebruikers helpen bij het inzetten van workflows; de connectiviteit van methoden verbeteren; moderne ‘social’ websystemen integreren; en de fouttolerantie verhogen. Ik laat ook zien hoe gebruikers aangemoedigd kunnen worden om deel te nemen aan community gebaseerde ondersteuningssystemen en kunnen leren om workflows te onderhouden door het concept van crowdsourcing. Samenvattend, deze technieken kunnen gebruikt worden om de reproduceerbaarheid van onderzoek te verhogen en genetica sneller dichterbij de klinische praktijk te brengen., Recent advances in technology have allowed the mass profiling of individual genetic profiles. Although this procedure is fast and relatively inexpensive, it generates huge amounts of data that describe many stages of the genetic regulation. Interpreting the data can shed light on human physiology and, most importantly, can help improve the prognosis and treatment of certain diseases. Transforming these data into meaningful information has been a major challenge in the life sciences. To achieve this transformation, we used the synergies between various scientific fields, including information technology (IT), biology, medicine and genetics. Efforts to build this synergy have given rise to a relatively new field of science called bioinformatics. Bioinformatics offers the scope to combine existing computational solutions into re-usable components, also called workflows. In this thesis, I present a collection of techniques to improve the quality of modern bioinformatic workflows. These techniques go beyond the classic objectives of workflows, which are to efficiently automate analyses and to make optimal use of the underlying computational infrastructure. As an extension to these objectives, I present techniques to help inexperienced users deploy such workflows, enhance their connectivity, exploit web technologies and increase their fault-tolerance. I also show how one can encourage users to engage in a community-based support system and learn to maintain workflows through the concept of crowdsourcing. Overall, these techniques can be used to increase the reproducibility of the conducted research and bring genetics closer to clinical practice.

Published
2018

35. Documentation of clinically relevant genomic biomarker allele frequencies in the next‐generation FINDbase worldwide database

Author

Kounelis, Fotios, primary, Kanterakis, Alexandros, additional, Kanavos, Andreas, additional, Pandi, Maria‐Theodora, additional, Kordou, Zoe, additional, Manusama, Olivia, additional, Vonitsanos, Gerasimos, additional, Katsila, Theodora, additional, Tsermpini, Evangelia‐Eirini, additional, Lauschke, Volker M., additional, Koromina, Maria, additional, Spek, Peter J., additional, and Patrinos, George P., additional

Published
2020
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36. WGS-based telomere length analysis in Dutch family trios implicates stronger maternal inheritance and a role for RRM1 gene

Author

Nersisyan, Lilit, Nikoghosyan, Maria, Arakelyan, Arsen, Francioli, Laurent, Menelaou, A. (Androniki), Pulit, S.L. (Sara L.), Elbers, C.C. (Clara C.), Kloosterman, Wigard, van Setten, J. (Jessica), Nijman, Isaac, Renkens, Ivo, de Bakker, P.I.W. (Paul I. W.), Dijk, Freerk, Neerincx, Pieter, Deelen, Patrick, Kanterakis, Alexandros, Dijkstra, Martijn, Byelas, H. (Heorhiy), van der Velde, K.J. (K. Joeri), Platteel, Mathieu, Swertz, M.A. (Morris A.), Wijmenga, Cisca, Palamara, P.F. (Pier Francesco), Pe’er, I. (Itsik), Ye, K. (Kai), Lameijer, Eric-Wubbo, Moed, M.H. (Matthijs H.), Beekman, M. (Marian), Craen, Anton, Suchiman, H.E.D. (H. Eka D.), Slagboom, Eline, Guryev, Victor, Abdellaoui, Abdel, Jan Hottenga, J. (Jouke), Kattenberg, M. (Mathijs), Willemsen, Gonneke, Boomsma, Dorret, van Leeuwen, E.M. (Elisabeth M.), Karssen, Lennart, Amin, N. (Najaf), Rivadeneira, F. (Fernando), Isaacs, A. (Aaron), Hofman, A. (Albert), Uitterlinden, André, Duijn, Cornelia, van Oven, M. (Mannis), Kayser, M. (Manfred), Vermaat, Martijn, Laros, Jeroen, Dunnen, Johan, Enckevort, David, Mei, Hailiang, Li, M. (Mingkun), Stoneking, M. (Mark), Schaik, Barbera, Bot, Jan, Marschall, Tobias, Schönhuth, Alexander, Hehir-Kwa, Jayne, Handsaker, Robert, Polak, P. (Paz), Sohail, M. (Mashaal), Vuzman, D. (Dana), Estrada, Karol, McCarroll, S.A. (Steven A.), Sunyaev, S.R. (Shamil R.), Hormozdiari, Fereydoun, Koval, Vyacheslav, Medina-Gomez, C. (Carolina), Oostra, B. (Ben), Veldink, Jan, van den Berg, L.H. (Leonard H.), Pitts, S.J. (Steven J.), Potluri, S. (Shobha), Sundar, P. (Purnima), Cox, D.R. (David R.), Knijff, Peter, Li, Q. (Qibin), Li, Y. (Yingrui), Du, Yuanping, Chen, Ruoyan, Cao, H. (Hongzhi), Wang, J. (Jun), Li, N. (Ning), Cao, S. (Sujie), Bovenberg, Jasper, Ommen, Gert-Jan, The Genome of the Netherlands Consortium, Biological Psychology, APH - Health Behaviors & Chronic Diseases, APH - Personalized Medicine, Amsterdam Neuroscience - Mood, Anxiety, Psychosis, Stress & Sleep, APH - Mental Health, APH - Methodology, Groningen Institute for Gastro Intestinal Genetics and Immunology (3GI), Department of Health and Life Sciences, Groningen Research Institute for Asthma and COPD (GRIAC), Stem Cell Aging Leukemia and Lymphoma (SALL), Experimental Immunology, CCA - Cancer biology and immunology, Epidemiology and Data Science, Amsterdam Gastroenterology Endocrinology Metabolism, Epidemiology, Internal Medicine, Genetic Identification, Clinical Genetics, and Genome of the Netherlands Consortium

Subjects
Male, Telomere Homeostasis/genetics, Netherlands Twin Register (NTR), Non-Mendelian inheritance, lcsh:Medicine, Datasets as Topic, Ribonucleoside Diphosphate Reductase/genetics, Genome of the Netherlands consortium, Genome informatics, Genome, 0302 clinical medicine, Models, 80 and over, Inheritance Patterns, lcsh:Science, Child, Netherlands, Genetics, Aged, 80 and over, 0303 health sciences, Multidisciplinary, Age Factors, Functional genomics, Single Nucleotide, ASSOCIATION, Telomere, Middle Aged, 030220 oncology & carcinogenesis, Trait, Female, Maternal Inheritance, Biotechnology, Maternal Age, Adult, Ribonucleoside Diphosphate Reductase, Adolescent, Offspring, PROTEINS, Quantitative trait locus, Biology, Polymorphism, Single Nucleotide, Article, Paternal Age, 03 medical and health sciences, Young Adult, Sex Factors, LUNG-CANCER, Genetic, Humans, Polymorphism, Telomere/metabolism, General, Gene, METAANALYSIS, 030304 developmental biology, Aged, Whole genome sequencing, Models, Genetic, Whole Genome Sequencing, Human Genome, lcsh:R, Telomere Homeostasis, SIZE, SUBUNIT, CELLS, Linear Models, lcsh:Q, Genome-Wide Association Study
Abstract

Telomere length (TL) regulation is an important factor in ageing, reproduction and cancer development. Genetic, hereditary and environmental factors regulating TL are currently widely investigated, however, their relative contribution to TL variability is still understudied. We have used whole genome sequencing data of 250 family trios from the Genome of the Netherlands project to perform computational measurement of TL and a series of regression and genome-wide association analyses to reveal TL inheritance patterns and associated genetic factors. Our results confirm that TL is a largely heritable trait, primarily with mother’s, and, to a lesser extent, with father’s TL having the strongest influence on the offspring. In this cohort, mother’s, but not father’s age at conception was positively linked to offspring TL. Age-related TL attrition of 40 bp/year had relatively small influence on TL variability. Finally, we have identified TL-associated variations in ribonuclease reductase catalytic subunit M1 (RRM1 gene), which is known to regulate telomere maintenance in yeast. We also highlight the importance of multivariate approach and the limitations of existing tools for the analysis of TL as a polygenic heritable quantitative trait.

Published
2019

37. Integrated clinical and omics approach to rare diseases : Novel genes and oligogenic inheritance in holoprosencephaly

Author

Kim, Artem, Savary, Clara, Dubourg, Christèle, Carré, Wilfrid, Mouden, Charlotte, Hamdi-Rozé, Houda, Guyodo, Hélène, Douce, Jerome Le, Génin, Emmanuelle, Campion, Dominique, Dartigues, Jean François, Deleuze, Jean François, Lambert, Jean Charles, Redon, Richard, Ludwig, Thomas, Grenier-Boley, Benjamin, Letort, Sébastien, Lindenbaum, Pierre, Meyer, Vincent, Quenez, Olivier, Dina, Christian, Bellenguez, Céline, Charbonnier-Le Clézio, Camille, Giemza, Joanna, Chatel, Stéphanie, Férec, Claude, Le Marec, Hervé, Letenneur, Luc, Nicolas, Gaël, Rouault, Karen, Bacq, Delphine, Boland, Anne, Lechner, Doris, Wijmenga, Cisca, Swertz, Morris A., Eline Slagboom, P., Van Ommen, Gert Jan B., Van Duijn, Cornelia M., Boomsma, Dorret I., De Bakker, Paul I.W., Bovenberg, Jasper A., De Craen, Anton J.M., Beekman, Marian, Hofman, Albert, Willemsen, Gonneke, Wolffenbuttel, Bruce, Platteel, Mathieu, Du, Yuanping, Chen, Ruoyan, Cao, Hongzhi, Cao, Rui, Sun, Yushen, Sujie Cao, Jeremy, Van Dijk, Freerk, Neerincx, Pieter B.T., Deelen, Patrick, Dijkstra, Martijn, Byelas, George, Kanterakis, Alexandros, Bot, Jan, Ye, Kai, Lameijer, Eric Wubbo, Vermaat, Martijn, Laros, Jeroen F.J., Den Dunnen, Johan T., De Knijff, Peter, Karssen, Lennart C., Van Leeuwen, Elisa M., Amin, Najaf, Koval, Vyacheslav, Rivadeneira, Fernando, Estrada, Karol, Hehir-Kwa, Jayne Y., De Ligt, Joep, Abdellaoui, Abdel, Hottenga, Jouke Jan, Mathijs Kattenberg, V., Van Enckevort, David, Mei, Hailiang, Santcroos, Mark, Van Schaik, Barbera D.C., Handsaker, Robert E., McCarroll, Steven A., Eichler, Evan E., Ko, Arthur, Sudmant, Peter, Francioli, Laurent C., Kloosterman, Wigard P., Nijman, Isaac J., Guryev, Victor, Pasquier, Laurent, Flori, Elisabeth, Gonzales, Marie, Bénéteau, Claire, Boute, Odile, Attié-Bitach, Tania, Roume, Joelle, Goujon, Louise, Akloul, Linda, Odent, Sylvie, Watrin, Erwan, Dupé, Valérie, De Tayrac, Marie, David, Véronique, Kim, Artem, Savary, Clara, Dubourg, Christèle, Carré, Wilfrid, Mouden, Charlotte, Hamdi-Rozé, Houda, Guyodo, Hélène, Douce, Jerome Le, Génin, Emmanuelle, Campion, Dominique, Dartigues, Jean François, Deleuze, Jean François, Lambert, Jean Charles, Redon, Richard, Ludwig, Thomas, Grenier-Boley, Benjamin, Letort, Sébastien, Lindenbaum, Pierre, Meyer, Vincent, Quenez, Olivier, Dina, Christian, Bellenguez, Céline, Charbonnier-Le Clézio, Camille, Giemza, Joanna, Chatel, Stéphanie, Férec, Claude, Le Marec, Hervé, Letenneur, Luc, Nicolas, Gaël, Rouault, Karen, Bacq, Delphine, Boland, Anne, Lechner, Doris, Wijmenga, Cisca, Swertz, Morris A., Eline Slagboom, P., Van Ommen, Gert Jan B., Van Duijn, Cornelia M., Boomsma, Dorret I., De Bakker, Paul I.W., Bovenberg, Jasper A., De Craen, Anton J.M., Beekman, Marian, Hofman, Albert, Willemsen, Gonneke, Wolffenbuttel, Bruce, Platteel, Mathieu, Du, Yuanping, Chen, Ruoyan, Cao, Hongzhi, Cao, Rui, Sun, Yushen, Sujie Cao, Jeremy, Van Dijk, Freerk, Neerincx, Pieter B.T., Deelen, Patrick, Dijkstra, Martijn, Byelas, George, Kanterakis, Alexandros, Bot, Jan, Ye, Kai, Lameijer, Eric Wubbo, Vermaat, Martijn, Laros, Jeroen F.J., Den Dunnen, Johan T., De Knijff, Peter, Karssen, Lennart C., Van Leeuwen, Elisa M., Amin, Najaf, Koval, Vyacheslav, Rivadeneira, Fernando, Estrada, Karol, Hehir-Kwa, Jayne Y., De Ligt, Joep, Abdellaoui, Abdel, Hottenga, Jouke Jan, Mathijs Kattenberg, V., Van Enckevort, David, Mei, Hailiang, Santcroos, Mark, Van Schaik, Barbera D.C., Handsaker, Robert E., McCarroll, Steven A., Eichler, Evan E., Ko, Arthur, Sudmant, Peter, Francioli, Laurent C., Kloosterman, Wigard P., Nijman, Isaac J., Guryev, Victor, Pasquier, Laurent, Flori, Elisabeth, Gonzales, Marie, Bénéteau, Claire, Boute, Odile, Attié-Bitach, Tania, Roume, Joelle, Goujon, Louise, Akloul, Linda, Odent, Sylvie, Watrin, Erwan, Dupé, Valérie, De Tayrac, Marie, and David, Véronique

Published
2019

38. Integrated clinical and omics approach to rare diseases: Novel genes and oligogenic inheritance in holoprosencephaly

Author

CMM Groep Kaaij, Genetica Klinische Genetica, Cancer, CMM Groep De Ridder, Child Health, CMM Groep Kloosterman, CMM USEQ Facility, Hubrecht Institute with UMC, Kim, Artem, Savary, Clara, Dubourg, Christèle, Carré, Wilfrid, Mouden, Charlotte, Hamdi-Rozé, Houda, Guyodo, Hélène, Douce, Jerome Le, Génin, Emmanuelle, Campion, Dominique, Dartigues, Jean François, Deleuze, Jean François, Lambert, Jean Charles, Redon, Richard, Ludwig, Thomas, Grenier-Boley, Benjamin, Letort, Sébastien, Lindenbaum, Pierre, Meyer, Vincent, Quenez, Olivier, Dina, Christian, Bellenguez, Céline, Charbonnier-Le Clézio, Camille, Giemza, Joanna, Chatel, Stéphanie, Férec, Claude, Le Marec, Hervé, Letenneur, Luc, Nicolas, Gaël, Rouault, Karen, Bacq, Delphine, Boland, Anne, Lechner, Doris, Wijmenga, Cisca, Swertz, Morris A., Eline Slagboom, P., Van Ommen, Gert Jan B., Van Duijn, Cornelia M., Boomsma, Dorret I., De Bakker, Paul I.W., Bovenberg, Jasper A., De Craen, Anton J.M., Beekman, Marian, Hofman, Albert, Willemsen, Gonneke, Wolffenbuttel, Bruce, Platteel, Mathieu, Du, Yuanping, Chen, Ruoyan, Cao, Hongzhi, Cao, Rui, Sun, Yushen, Sujie Cao, Jeremy, Van Dijk, Freerk, Neerincx, Pieter B.T., Deelen, Patrick, Dijkstra, Martijn, Byelas, George, Kanterakis, Alexandros, Bot, Jan, Ye, Kai, Lameijer, Eric Wubbo, Vermaat, Martijn, Laros, Jeroen F.J., Den Dunnen, Johan T., De Knijff, Peter, Karssen, Lennart C., Van Leeuwen, Elisa M., Amin, Najaf, Koval, Vyacheslav, Rivadeneira, Fernando, Estrada, Karol, Hehir-Kwa, Jayne Y., De Ligt, Joep, Abdellaoui, Abdel, Hottenga, Jouke Jan, Mathijs Kattenberg, V., Van Enckevort, David, Mei, Hailiang, Santcroos, Mark, Van Schaik, Barbera D.C., Handsaker, Robert E., McCarroll, Steven A., Eichler, Evan E., Ko, Arthur, Sudmant, Peter, Francioli, Laurent C., Kloosterman, Wigard P., Nijman, Isaac J., Guryev, Victor, Pasquier, Laurent, Flori, Elisabeth, Gonzales, Marie, Bénéteau, Claire, Boute, Odile, Attié-Bitach, Tania, Roume, Joelle, Goujon, Louise, Akloul, Linda, Odent, Sylvie, Watrin, Erwan, Dupé, Valérie, De Tayrac, Marie, David, Véronique, CMM Groep Kaaij, Genetica Klinische Genetica, Cancer, CMM Groep De Ridder, Child Health, CMM Groep Kloosterman, CMM USEQ Facility, Hubrecht Institute with UMC, Kim, Artem, Savary, Clara, Dubourg, Christèle, Carré, Wilfrid, Mouden, Charlotte, Hamdi-Rozé, Houda, Guyodo, Hélène, Douce, Jerome Le, Génin, Emmanuelle, Campion, Dominique, Dartigues, Jean François, Deleuze, Jean François, Lambert, Jean Charles, Redon, Richard, Ludwig, Thomas, Grenier-Boley, Benjamin, Letort, Sébastien, Lindenbaum, Pierre, Meyer, Vincent, Quenez, Olivier, Dina, Christian, Bellenguez, Céline, Charbonnier-Le Clézio, Camille, Giemza, Joanna, Chatel, Stéphanie, Férec, Claude, Le Marec, Hervé, Letenneur, Luc, Nicolas, Gaël, Rouault, Karen, Bacq, Delphine, Boland, Anne, Lechner, Doris, Wijmenga, Cisca, Swertz, Morris A., Eline Slagboom, P., Van Ommen, Gert Jan B., Van Duijn, Cornelia M., Boomsma, Dorret I., De Bakker, Paul I.W., Bovenberg, Jasper A., De Craen, Anton J.M., Beekman, Marian, Hofman, Albert, Willemsen, Gonneke, Wolffenbuttel, Bruce, Platteel, Mathieu, Du, Yuanping, Chen, Ruoyan, Cao, Hongzhi, Cao, Rui, Sun, Yushen, Sujie Cao, Jeremy, Van Dijk, Freerk, Neerincx, Pieter B.T., Deelen, Patrick, Dijkstra, Martijn, Byelas, George, Kanterakis, Alexandros, Bot, Jan, Ye, Kai, Lameijer, Eric Wubbo, Vermaat, Martijn, Laros, Jeroen F.J., Den Dunnen, Johan T., De Knijff, Peter, Karssen, Lennart C., Van Leeuwen, Elisa M., Amin, Najaf, Koval, Vyacheslav, Rivadeneira, Fernando, Estrada, Karol, Hehir-Kwa, Jayne Y., De Ligt, Joep, Abdellaoui, Abdel, Hottenga, Jouke Jan, Mathijs Kattenberg, V., Van Enckevort, David, Mei, Hailiang, Santcroos, Mark, Van Schaik, Barbera D.C., Handsaker, Robert E., McCarroll, Steven A., Eichler, Evan E., Ko, Arthur, Sudmant, Peter, Francioli, Laurent C., Kloosterman, Wigard P., Nijman, Isaac J., Guryev, Victor, Pasquier, Laurent, Flori, Elisabeth, Gonzales, Marie, Bénéteau, Claire, Boute, Odile, Attié-Bitach, Tania, Roume, Joelle, Goujon, Louise, Akloul, Linda, Odent, Sylvie, Watrin, Erwan, Dupé, Valérie, De Tayrac, Marie, and David, Véronique

Published
2019

43. Transmission of human mtDNA heteroplasmy in the Genome of the Netherlands families: support for a variable-size bottleneck

Author

Li, Mingkun, Rothwell, Rebecca, Vermaat, Martijn, Wachsmuth, Manja, Schröder, Roland, Laros, Jeroen F J, Van Oven, Mannis, De Bakker, Paul I W, Bovenberg, Jasper A., Van Duijn, Cornelia M., Van Ommen, Gert Jan B, Slagboom, P. Eline, Swertz, Morris A., Wijmenga, Cisca, Kayser, Manfred, Boomsma, Dorret I., Zöllner, Sebastian, De Knijff, Peter, Stoneking, Mark, De Craen, Anton J M, Beekman, Marian, Hofman, Albert, Willemsen, Gonneke, Wolffenbuttel, Bruce, Platteel, Mathieu, Du, Yuanping, Chen, Ruoyan, Cao, Hongzhi, Cao, Rui, Sun, Yushen, Cao, Jeremy Sujie, Van Dijk, Freerk, Neerincx, Pieter B T, Deelen, Patrick, Dijkstra, Martijn, Byelas, George, Kanterakis, Alexandros, Bot, Jan, Ye, Kai, Lameijer, Eric Wubbo, Den Dunnen, Johan T., Karssen, Lennart C., Van Leeuwen, Elisa M., Amin, Najaf, Koval, Vyacheslav, Rivadeneira, Fernando, Estrada, Karol, Hehir-Kwa, Jayne Y., De Ligt, Joep, Abdellaoui, Abdel, Hottenga, Jouke Jan, Kattenberg, V. Mathijs, Van Enckevort, David, Mei, Hailiang, Santcroos, Mark, Van Schaik, Barbera D C, Handsaker, Robert E., McCarroll, Steven A., Eichler, Evan E., Ko, Arthur, Sudmant, Peter, Francioli, Laurent C., Kloosterman, Wigard P., Nijman, Isaac J., Guryev, Victor, Genetic Identification, Epidemiology, Groningen Institute for Gastro Intestinal Genetics and Immunology (3GI), Biological Psychology, EMGO+ - Quality of Care, and Amsterdam Neuroscience - Mood, Anxiety, Psychosis, Stress & Sleep

Subjects
Male, Netherlands Twin Register (NTR), 0301 basic medicine, LEVEL, Inheritance Patterns, Twins, Twin Study, POINT MUTATIONS, Genome, Gene Frequency, Paternal mtDNA transmission, Genetics(clinical), Non-U.S. Gov't, Genetics (clinical), Netherlands, Genetics, Research Support, Non-U.S. Gov't, PURIFYING SELECTION, MITOCHONDRIAL-DNA MUTATIONS, RANDOM GENETIC DRIFT, HUMAN-DISEASE, Heteroplasmy, Female, Mitochondrial DNA, TISSUES, OOCYTES, Biology, Research Support, INHERITANCE, DNA, Mitochondrial, White People, Genetic Heterogeneity, 03 medical and health sciences, SDG 3 - Good Health and Well-being, Journal Article, Humans, Family, Selection, Genetic, Allele, Allele frequency, Alleles, Models, Statistical, Polymorphism, Genetic, Models, Genetic, Research, Twin study, Minor allele frequency, 030104 developmental biology, Mutation, MELAS SYNDROME
Abstract

Although previous studies have documented a bottleneck in the transmission of mtDNA genomes from mothers to offspring, several aspects remain unclear, including the size and nature of the bottleneck. Here, we analyze the dynamics of mtDNA heteroplasmy transmission in the Genomes of the Netherlands (GoNL) data, which consists of complete mtDNA genome sequences from 228 trios, eight dizygotic (DZ) twin quartets, and 10 monozygotic (MZ) twin quartets. Using a minor allele frequency (MAF) threshold of 2%, we identified 189 heteroplasmies in the trio mothers, of which 59% were transmitted to offspring, and 159 heteroplasmies in the trio offspring, of which 70% were inherited from the mothers. MZ twin pairs exhibited greater similarity in MAF at heteroplasmic sites than DZ twin pairs, suggesting that the heteroplasmy MAF in the oocyte is the major determinant of the heteroplasmy MAF in the offspring. We used a likelihood method to estimate the effective number of mtDNA genomes transmitted to offspring under different bottleneck models; a variable bottleneck size model provided the best fit to the data, with an estimated mean of nine individual mtDNA genomes transmitted. We also found evidence for negative selection during transmission against novel heteroplasmies (in which the minor allele has never been observed in polymorphism data). These novel heteroplasmies are enhanced for tRNA and rRNA genes, and mutations associated with mtDNA diseases frequently occur in these genes. Our results thus suggest that the female germ line is able to recognize and select against deleterious heteroplasmies.

Published
2016

44. Integration techniques for modern bioinformatics workflows

Author

Kanterakis, Alexandros, Swertz, Morris, and Wijmenga, Cisca

Abstract

Grote technologische vooruitgang maakt het nu mogelijk op grote schaal de genetica van mensen in kaart te brengen. De procedures zijn snel en relatief goedkoop, en genereren grote hoeveelheden data over de verschillende stadia van genetische regulatie. Interpretatie hiervan kan nieuw inzicht geven in menselijke fysiologie en zo bijdragen aan de verbetering van prognose en behandeling van ziekten. Echter, het omzetten van deze data in betekenisvolle kennis is een grote uitdaging. In dit proefschrift hebben we daarom gewerkt aan de synergie tussen verschillende wetenschappelijke vakgebieden, waaronder informatietechnologie (IT), biologie, geneeskunde en genetica, een relatief nieuw vakgebied: bio-informatica. Bio-informatica richt zich op het combineren van bestaande computationele oplossingen tot herbruikbare componenten, ook wel workflows genoemd, teneinde biologische data te analyseren. In deze thesis presenteer ik een collectie van nieuwe technieken die de kwaliteit van moderne bio-informatische workflows moeten verbeteren. Deze technieken gaan voorbij aan de klassieke doelstellingen van workflows: het efficiënt automatiseren van analyses en het optimaal gebruik maken van onderliggende computationele infrastructuren. Als uitbreiding op deze doelstellingen presenteer ik technieken die onervaren gebruikers helpen bij het inzetten van workflows; de connectiviteit van methoden verbeteren; moderne ‘social’ websystemen integreren; en de fouttolerantie verhogen. Ik laat ook zien hoe gebruikers aangemoedigd kunnen worden om deel te nemen aan community gebaseerde ondersteuningssystemen en kunnen leren om workflows te onderhouden door het concept van crowdsourcing. Samenvattend, deze technieken kunnen gebruikt worden om de reproduceerbaarheid van onderzoek te verhogen en genetica sneller dichterbij de klinische praktijk te brengen.

Published
2018

48. Scanning of Genetic Variants and Genetic Mapping of Phenotypic Traits in Gilthead Sea Bream Through ddRAD Sequencing

Author

Kyriakis, Dimitrios, primary, Kanterakis, Alexandros, additional, Manousaki, Tereza, additional, Tsakogiannis, Alexandros, additional, Tsagris, Michalis, additional, Tsamardinos, Ioannis, additional, Papaharisis, Leonidas, additional, Chatziplis, Dimitris, additional, Potamias, George, additional, and Tsigenopoulos, Costas S., additional

Published
2019
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