Predicting variant deleteriousness in non-human species: applying the CADD approach in mouse Autor Christian Groß, Dick de Ridder, Marcel Reinders

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Minimum error correction-based haplotype assembly: Considerations for long read data. Autor Sina Majidian, Mohammad Hossein Kahaei, Dick de Ridder

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Hap10: reconstructing accurate and long polyploid haplotypes using linked reads Autor Sina Majidian, Mohammad Hossein Kahaei, Dick de Ridder

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Hecaton: reliably detecting copy number variation in plant genomes using short read sequencing data Autor Raúl Y. Wijfjes, Sandra Smit, Dick de Ridder

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Beyond sequence: Structure-based machine learning Autor Janani Durairaj, Dick de Ridder, Aalt D.J. van Dijk

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Shifts in growth strategies reflect tradeoffs in cellular economics Autor Douwe Molenaar, Rogier van Berlo, Dick de Ridder, Bas Teusink

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Efficient inference of homologs in large eukaryotic pan-proteomes Autor Siavash Sheikhizadeh Anari, Dick de Ridder, M. Eric Schranz, Sandra Smit

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Unbiased Quantitative Models of Protein Translation Derived from Ribosome Profiling Data. Autor Alexey A Gritsenko, Marc Hulsman, Marcel J T Reinders, Dick de Ridder

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In silico assessment of a novel single-molecule protein fingerprinting method employing fragmentation and nanopore detection Autor Carlos de Lannoy, Florian Leonardus Rudolfus Lucas, Giovanni Maglia, Dick de Ridder

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Caretta – A multiple protein structure alignment and feature extraction suite Autor Mehmet Akdel, Janani Durairaj, Dick de Ridder, Aalt D.J. van Dijk

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Oomycete Metabolism Is Highly Dynamic and Reflects Lifestyle Adaptations Autor Sander Y. A. Rodenburg, Dick de Ridder, Francine Govers, Michael F. Seidl

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Family-Based Haplotype Estimation and Allele Dosage Correction for Polyploids Using Short Sequence Reads Autor Ehsan Motazedi, Ehsan Motazedi, Chris Maliepaard, Richard Finkers, Richard Visser, Dick de Ridder

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Evaluation of FRET X for single-molecule protein fingerprinting Autor Carlos Victor de Lannoy, Mike Filius, Raman van Wee, Chirlmin Joo, Dick de Ridder

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Editorial: Artificial Intelligence and Machine Learning Applications in Plant Genomics and Genetics Autor Aalt D. J. van Dijk, Shin-Han Shiu, Shin-Han Shiu, Dick de Ridder

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Genomic prediction in plants: opportunities for ensemble machine learning based approaches [version 2; peer review: 1 approved, 2 approved with reservations] Autor Aalt D.J. van Dijk, Shahid Mansoor, Muhammad Farooq, Dick de Ridder, Harm Nijveen

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Understanding regulation of metabolism through feasibility analysis. Autor Emrah Nikerel, Jan Berkhout, Fengyuan Hu, Bas Teusink, Marcel J T Reinders, Dick de Ridder

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Insight into neutral and disease-associated human genetic variants through interpretable predictors. Autor Bastiaan A van den Berg, Marcel J T Reinders, Dick de Ridder, Tjaart A P de Beer

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Sequence features of viral and human Internal Ribosome Entry Sites predictive of their activity. Autor Alexey A Gritsenko, Shira Weingarten-Gabbay, Shani Elias-Kirma, Ronit Nir, Dick de Ridder, Eran Segal

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Metabolic Model of the <italic toggle="yes">Phytophthora infestans</italic>-Tomato Interaction Reveals Metabolic Switches during Host Colonization Autor Sander Y. A. Rodenburg, Michael F. Seidl, Howard S. Judelson, Andrea L. Vu, Francine Govers, Dick de Ridder

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Comparative Assessment of Protein Large Language Models for Enzyme Commission Number Prediction Autor João Capela, Maria Zimmermann-Kogadeeva, Aalt D. J. van Dijk, Dick de Ridder, Oscar Dias, Miguel Rocha

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