Computational pan-genomics: status, promises and challenges von Marschall, Tobias, Marz, Manja, Abeel, Thomas, Dijkstra, Louis, Dutilh, Bas E, Ghaffaari, Ali, Kersey, Paul, Kloosterman, Wigard P, Mäkinen, Veli, Novak, Adam M, Paten, Benedict, Porubsky, David, Rivals, Eric, Alkan, Can, Baaijens, Jasmijn A, Paul I W De Bakker, Boeva, Valentina, Bonnal, Raoul J P, Chiaromonte, Francesca, Chikhi, Rayan, Ciccarelli, Francesca D, Cijvat, Robin, Datema, Erwin, Van Duijn, Cornelia M, Eichler, Evan E, Ernst, Corinna, Eskin, Eleazar, Garrison, Erik, El-Kebir, Mohammed, Klau, Gunnar W, Korbel, Jan O, Eric-Wubbo Lameijer, Langmead, Benjamin, Martin, Marcel, Medvedev, Paul, Mu, John C, Neerincx, Pieter, Ouwens, Klaasjan, Peterlongo, Pierre, Pisanti, Nadia, Rahmann, Sven, Raphael, Ben, Reinert, Knut, de Ridder, Dick, de Ridder, Jeroen, Schlesner, Matthias, Schulz-Trieglaff, Ole, Sanders, Ashley D, Sheikhizadeh, Siavash, Shneider, Carl, Smit, Sandra, Valenzuela, Daniel, Wang, Jiayin, Wessels, Lodewyk, Zhang, Ying, Guryev, Victor, Vandin, Fabio, Ye, Kai, Schönhuth, Alexander

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Lung Cancer Prediction Using Neural Network Ensemble with Histogram of Oriented Gradient Genomic Features von Adetiba, Emmanuel, Olugbara, Oludayo

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WhatsHap: Weighted Haplotype Assembly for Future-Generation Sequencing Reads von Patterson, Murray, Marschall, Tobias, Pisanti, Nadia, van Iersel, Leo, Stougie, Leen, Klau, Gunnar W, Schönhuth, Alexander

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Overlap graph-based generation of haplotigs for diploids and polyploids von Baaijens, Jasmijn A, Schönhuth, Alexander

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Full-length de novo viral quasispecies assembly through variation graph construction von Baaijens, Jasmijn A, Van der Roest, Bastiaan, Köster, Johannes, Stougie, Leen, Schönhuth, Alexander

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OGRE: Overlap Graph-based metagenomic Read clustEring von Balvert, Marleen, Luo, Xiao, Hauptfeld, Ernestina, Schönhuth, Alexander, Dutilh, Bas E

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phasebook: haplotype-aware de novo assembly of diploid genomes from long reads von Luo, Xiao, Kang, Xiongbin, Schoenhuth, Alexander

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MATE-CLEVER: Mendelian-inheritance-aware discovery and genotyping of midsize and long indels von Marschall, Tobias, Hajirasouliha, Iman, Schönhuth, Alexander

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Strainline: full-length de novo viral haplotype reconstruction from noisy long reads von Luo, Xiao, Kang, Xiongbin, Schönhuth, Alexander

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Using the structure of genome data in the design of deep neural networks for predicting amyotrophic lateral sclerosis from genotype von Yin, Bojian, Balvert, Marleen, van der Spek, Rick A A, Dutilh, Bas E, Bohté, Sander, Veldink, Jan, Schönhuth, Alexander

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VeChat: correcting errors in long reads using variation graphs von Luo, Xiao, Kang, Xiongbin, Schönhuth, Alexander

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Viral quasispecies assembly via maximal clique enumeration von Töpfer, Armin, Marschall, Tobias, Bull, Rowena A, Luciani, Fabio, Schönhuth, Alexander, Beerenwinkel, Niko

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HyLight: Strain aware assembly of low coverage metagenomes von Kang, Xiongbin, Zhang, Wenhai, Li, Yichen, Luo, Xiao, Schönhuth, Alexander

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Hybrid-hybrid correction of errors in long reads with HERO von Kang, Xiongbin, Xu, Jialu, Luo, Xiao, Schönhuth, Alexander

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Accurate and scalable variant calling from single cell DNA sequencing data with ProSolo von Lähnemann, David, Köster, Johannes, Fischer, Ute, Borkhardt, Arndt, McHardy, Alice C., Schönhuth, Alexander

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Machine Learning-Based Ensemble Recursive Feature Selection of Circulating miRNAs for Cancer Tumor Classification von Lopez-Rincon, Alejandro, Mendoza-Maldonado, Lucero, Martinez-Archundia, Marlet, Schonhuth, Alexander, Kraneveld, Aletta D., Garssen, Johan, Tonda, Alberto

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Discovering motifs that induce sequencing errors von Allhoff, Manuel, Schönhuth, Alexander, Martin, Marcel, Costa, Ivan G, Rahmann, Sven, Marschall, Tobias

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CLEVER: clique-enumerating variant finder von MARSCHALL, Tobias, COSTA, IvanG, CANZAR, Stefan, BAUER, Markus, KLAU, Gunnar W, SCHLIEP, Alexander, SCHÖNHUTH, Alexander

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Computing linkage disequilibrium aware genome embeddings using autoencoders von Taş, Gizem, Westerdijk, Timo, Postma, Eric, Veldink, Jan H, Schonhuth, Alexander, Balvert, Marleen, Project MinE ALS GWAS Consortium

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Repeat- and error-aware comparison of deletions von Wittler, Roland, Marschall, Tobias, Schönhuth, Alexander, Mäkinen, Veli

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