Ranking of cell clusters in a single-cell RNA-sequencing analysis framework using prior knowledge von Oulas, Anastasis, Savva, Kyriaki, Karathanasis, Nestoras, Spyrou, George M

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Machine Learning Approaches Identify Genes Containing Spatial Information From Single-Cell Transcriptomics Data von Loher, Phillipe, Karathanasis, Nestoras

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Reproducibility efforts as a teaching tool: A pilot study von Karathanasis, Nestoras, Hwang, Daniel, Heng, Vibol, Abhimannyu, Rimal, Slogoff-Sevilla, Phillip, Buchel, Gina, Frisbie, Victoria, Li, Peiyao, Kryoneriti, Dafni, Rigoutsos, Isidore

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MiRduplexSVM: A High-Performing MiRNA-Duplex Prediction and Evaluation Methodology von Karathanasis, Nestoras, Tsamardinos, Ioannis, Poirazi, Panayiota

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omicsNPC: Applying the Non-Parametric Combination Methodology to the Integrative Analysis of Heterogeneous Omics Data von Karathanasis, Nestoras, Tsamardinos, Ioannis, Lagani, Vincenzo

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STATegra: Multi-Omics Data Integration - A Conceptual Scheme With a Bioinformatics Pipeline von Planell, Nuria, Lagani, Vincenzo, Sebastian-Leon, Patricia, van der Kloet, Frans, Ewing, Ewoud, Karathanasis, Nestoras, Urdangarin, Arantxa, Arozarena, Imanol, Jagodic, Maja, Tsamardinos, Ioannis, Tarazona, Sonia, Conesa, Ana, Tegner, Jesper, Gomez-Cabrero, David

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Non-parametric combination analysis of multiple data types enables detection of novel regulatory mechanisms in T cells of multiple sclerosis patients von Fernandes, Sunjay Jude, Morikawa, Hiromasa, Ewing, Ewoud, Ruhrmann, Sabrina, Joshi, Rubin Narayan, Lagani, Vincenzo, Karathanasis, Nestoras, Khademi, Mohsen, Planell, Nuria, Schmidt, Angelika, Tsamardinos, Ioannis, Olsson, Tomas, Piehl, Fredrik, Kockum, Ingrid, Jagodic, Maja, Tegnér, Jesper, Gomez-Cabrero, David

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FAIR+E pathogen data for surveillance and research: lessons from COVID-19 von Neves, Aitana, Cuesta, Isabel, Hjerde, Erik, Klemetsen, Terje, Salgado, David, van Helden, Jacques, Rahman, Nadim, Fatima, Nazeefa, Karathanasis, Nestoras, Zmora, Pawel, Åkerström, Wolmar Nyberg, Grellscheid, Sushma Nagaraja, Waheed, Zahra, Blomberg, Niklas

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A new microRNA target prediction tool identifies a novel interaction of a putative miRNA with CCND2 von Oulas, Anastasis, Karathanasis, Nestoras, Louloupi, Annita, Iliopoulos, Ioannis, Kalantidis, Kriton, Poirazi, Panayiota

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Gene selection for optimal prediction of cell position in tissues from single-cell transcriptomics data von Tanevski, Jovan, Nguyen, Thin, Truong, Buu, Karaiskos, Nikos, Ahsen, Mehmet Eren, Zhang, Xinyu, Shu, Chang, Xu, Ke, Liang, Xiaoyu, Hu, Ying, Pham, Hoang Vv, Xiaomei, Li, Le, Thuc D, Tarca, Adi L, Bhatti, Gaurav, Romero, Roberto, Karathanasis, Nestoras, Loher, Phillipe, Chen, Yang, Ouyang, Zhengqing, Mao, Disheng, Zhang, Yuping, Zand, Maryam, Ruan, Jianhua, Hafemeister, Christoph, Qiu, Peng, Tran, Duc, Nguyen, Tin, Gabor, Attila, Yu, Thomas, Guinney, Justin, Glaab, Enrico, Krause, Roland, Banda, Peter, Stolovitzky, Gustavo, Rajewsky, Nikolaus, Saez-Rodriguez, Julio, Meyer, Pablo

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Combining clinical and molecular data for personalized treatment in acute myeloid leukemia: A machine learning approach von Karathanasis, Nestoras, Papasavva, Panayiota L., Oulas, Anastasis, Spyrou, George M

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IsoMiRmap: fast, deterministic and exhaustive mining of isomiRs from short RNA-seq datasets von Loher, Phillipe, Karathanasis, Nestoras, Londin, Eric, F. Bray, Paul, Pliatsika, Venetia, Telonis, Aristeidis G., Rigoutsos, Isidore

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Don't use a cannon to kill the ... miRNA mosquito von Karathanasis, Nestoras, Tsamardinos, Ioannis, Poirazi, Panayiota

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Combining evidence from four immune cell types identifies DNA methylation patterns that implicate functionally distinct pathways during Multiple Sclerosis progression von Ewing, Ewoud, Kular, Lara, Fernandes, Sunjay J., Karathanasis, Nestoras, Lagani, Vincenzo, Ruhrmann, Sabrina, Tsamardinos, Ioannis, Tegner, Jesper, Piehl, Fredrik, Gomez-Cabrero, David, Jagodic, Maja

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GluA2 mRNA distribution and regulation by miR-124 in hippocampal neurons von Ho, Victoria M., Dallalzadeh, Liane O., Karathanasis, Nestoras, Keles, Mehmet F., Vangala, Sitaram, Grogan, Tristan, Poirazi, Panayiota, Martin, Kelsey C.

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FAIR+E pathogen data for surveillance and research: lessons from COVID-19 von Neves, Aitana, Cuesta, Isabel, Hjerde, Erik, Klemetsen, Terje, Salgado, David, van Helden, Jacques, Rahman, Nadim, Fatima, Nazeefa, Karathanasis, Nestoras, Zmora, Pawel, Åkerström, Wolmar Nyberg, Grellscheid, Sushma Nagaraja, Waheed, Zahra, Blomberg, Niklas

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Prediction of miRNA Targets von Oulas, Anastasis, Karathanasis, Nestoras, Louloupi, Annita, Pavlopoulos, Georgios A., Poirazi, Panayiota, Kalantidis, Kriton, Iliopoulos, Ioannis

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Finding Cancer-Associated miRNAs: Methods and Tools von Oulas, Anastasis, Karathanasis, Nestoras, Louloupi, Annita, Poirazi, Panayiota

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Combining evidence from four immune cell types identifies DNA methylation patterns that implicate functionally distinct pathways during Multiple Sclerosis progressionResearch in co... von Ewoud Ewing, Lara Kular, Sunjay J. Fernandes, Nestoras Karathanasis, Vincenzo Lagani, Sabrina Ruhrmann, Ioannis Tsamardinos, Jesper Tegner, Fredrik Piehl, David Gomez-Cabrero, Maja Jagodic

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Computational Identification of miRNAs Involved in Cancer von Oulas, Anastasis, Karathanasis, Nestoras, Poirazi, Panayiota

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