54 Publikationen
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2022 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2963686Luo, Xiao, Kang, Xiongbin, and Schönhuth, Alexander. “Enhancing Long-Read-Based Strain-Aware Metagenome Assembly”. Frontiers in Genetics 13 (2022): 868280.PUB | PDF | DOI | Download (ext.) | WoS | PubMed | Europe PMC
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2022 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2967245Ray, Sumanta, Lall, Snehalika, Mukhopadhyay, Anirban, Bandyopadhyay, Sanghamitra, and Schönhuth, Alexander. “Deep variational graph autoencoders for novel host-directed therapy options against COVID-19”. Artificial Intelligence in Medicine 134 (2022): 102418.PUB | DOI | WoS | PubMed | Europe PMC
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2021 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2952469Metselaar, Paula I, Mendoza-Maldonado, Lucero, Li Yim, Andrew Yung Fong, Abarkan, Ilias, Henneman, Peter, Te Velde, Anje A, Schönhuth, Alexander, Bosch, Jos A, Kraneveld, Aletta D, and Lopez-Rincon, Alejandro. “Recursive ensemble feature selection provides a robust mRNA expression signature for myalgic encephalomyelitis/chronic fatigue syndrome.”. Scientific reports 11.1 (2021): 4541.PUB | DOI | WoS | PubMed | Europe PMC
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2021 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2959624Lahnemann, David, Koster, Johannes, Fischer, Ute, Borkhardt, Arndt, McHardy, Alice C, and Schönhuth, Alexander. “Accurate and scalable variant calling from single cell DNA sequencing data with ProSolo”. Nature Communications 12.1 (2021): 6744.PUB | PDF | DOI | WoS | PubMed | Europe PMC
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2020 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2945617Lopez-Rincon, Alejandro, Mendoza-Maldonado, Lucero, Martinez-Archundia, Marlet, Schönhuth, Alexander, Kraneveld, Aletta D., Garssen, Johan, and Tonda, Alberto. “Machine Learning-Based Ensemble Recursive Feature Selection of Circulating miRNAs for Cancer Tumor Classification”. Cancers 12.7 (2020): 1785.PUB | DOI | WoS | PubMed | Europe PMC
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2020 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2943113Koster, Johannes, Dijkstra, Louis J, Marschall, Tobias, and Schönhuth, Alexander. “Varlociraptor: enhancing sensitivity and controlling false discovery rate in somatic indel discovery.”. Genome biology 21.1 (2020).PUB | DOI | WoS | PubMed | Europe PMC
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2019 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941754Baaijens, Jasmijn A, Van der Roest, Bastiaan, Köster, Johannes, Stougie, Leen, and Schönhuth, Alexander. “Full-length de novo viral quasispecies assembly through variation graph construction”. Bioinformatics 35.24 (2019): 5086-5094.PUB | DOI | WoS | PubMed | Europe PMC
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2019 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941756Yin, Bojian, Balvert, Marleen, van der Spek, Rick A A, Dutilh, Bas E, Bohté, Sander, Veldink, Jan, and Schönhuth, Alexander. “Using the structure of genome data in the design of deep neural networks for predicting amyotrophic lateral sclerosis from genotype”. Bioinformatics 35.14 (2019): i538-i547.PUB | DOI | WoS | PubMed | Europe PMC
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2019 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941760Lopez-Rincon, Alejandro, Martinez-Archundia, Marlet, Martinez-Ruiz, Gustavo U., Schönhuth, Alexander, and Tonda, Alberto. “Automatic discovery of 100-miRNA signature for cancer classification using ensemble feature selection”. BMC Bioinformatics 20.1 (2019): 480.PUB | DOI | WoS | PubMed | Europe PMC
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2019 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941677Denti, Luca, Previtali, Marco, Bernardini, Giulia, Schönhuth, Alexander, and Bonizzoni, Paola. “MALVA: Genotyping by Mapping-free ALlele Detection of Known VAriants”. iScience 18 (2019): 20-27.PUB | DOI | WoS | PubMed | Europe PMC
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2019 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941761Baaijens, Jasmijn A, and Schönhuth, Alexander. “Overlap graph-based generation of haplotigs for diploids and polyploids”. Bioinformatics 35.21 (2019): 4281-4289.PUB | DOI | WoS | PubMed | Europe PMC
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2019 | Preprint | Veröffentlicht | PUB-ID: 2941764Laehnemann, David, Köster, Johannes, Szczurek, Ewa, McCarthy, Davis J, Hicks, Stephanie C, Robinson, Mark D, Vallejos, Catalina A, Beerenwinkel, Niko, Campbell, Kieran R, Mahfouz, Ahmed, Pinello, Luca, Skums, Pavel, Stamatakis, Alexandros, Stephan-Otto Attolini, Camille, Aparicio, Samuel, Baaijens, Jasmijn, Balvert, Marleen, de Barbanson, Buys, Cappuccio, Antonio, Corleone, Giacomo, Dutilh, Bas E, Florescu, Maria, Guryev, Victor, Holmer, Rens, Jahn, Katharina, Jessurun Lobo, Thamar, Keizer, Emma M, Khatri, Indu, Kiełbasa, Szymon M, Korbel, Jan O, Kozlov, Alexey M, Kuo, Tzu-Hao, Lelieveldt, Boudewijn PF, Mandoiu, Ion I, Marioni, John C, Marschall, Tobias, Mölder, Felix, Niknejad, Amir, Rączkowski, Łukasz, Reinders, Marcel, de Ridder, Jeroen, Saliba, Antoine-Emmanuel, Somarakis, Antonios, Stegle, Oliver, Theis, Fabian J, Yang, Huan, Zelikovsky, Alex, McHardy, Alice C, Raphael, Benjamin J, Shah, Sohrab P, and Schönhuth, Alexander. “12 Grand Challenges in Single-Cell Data Science”. PeerJ (2019).PUB
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2018 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941769Ibrahim, Bashar, Arkhipova, Ksenia, Andeweg, Arno, Posada-Céspedes, Susana, Enault, François, Gruber, Arthur, Koonin, Eugene, Kupczok, Anne, Lemey, Philippe, McHardy, Alice, McMahon, Dino, Pickett, Brett, Robertson, David, Scheuermann, Richard, Zhernakova, Alexandra, Zwart, Mark, Schönhuth, Alexander, Dutilh, Bas, and Marz, Manja. “Bioinformatics Meets Virology: The European Virus Bioinformatics Center’s Second Annual Meeting”. Viruses 10.5 (2018): 256.PUB | DOI | WoS | PubMed | Europe PMC
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2017 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941784Baaijens, Jasmijn A., Aabidine, Amal Zine El, Rivals, Eric, and Schönhuth, Alexander. “De novo assembly of viral quasispecies using overlap graphs”. Genome Research 27.5 (2017): 835-848.PUB | DOI | WoS | PubMed | Europe PMC
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2017 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941786Ebler, Jana, Schönhuth, Alexander, and Marschall, Tobias. “Genotyping inversions and tandem duplications”. Bioinformatics 33.24 (2017): 4015-4023.PUB | DOI | WoS | PubMed | Europe PMC
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2016 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941788Francioli, Laurent C, Cretu-Stancu, Mircea, Garimella, Kiran V, Fromer, Menachem, Kloosterman, Wigard P, Samocha, Kaitlin E, Neale, Benjamin M, Daly, Mark J, Banks, Eric, DePristo, Mark A, de Bakker, Paul IW, and Schönhuth, Alexander. “A framework for the detection of de novo mutations in family-based sequencing data”. European Journal of Human Genetics 25.2 (2016): 227-233.PUB | DOI | WoS | PubMed | Europe PMC
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2016 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941793Gregor, I., Schönhuth, Alexander, and McHardy, A. C. “Snowball: strain aware gene assembly of metagenomes”. Bioinformatics 32.17 (2016): i649-i657.PUB | DOI | WoS | PubMed | Europe PMC
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2016 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941790Hehir-Kwa, Jayne Y., Marschall, Tobias, Kloosterman, Wigard P., Francioli, Laurent C., Baaijens, Jasmijn A., Dijkstra, Louis J., Abdellaoui, Abdel, Koval, Vyacheslav, Thung, Djie Tjwan, Wardenaar, René, Renkens, Ivo, Coe, Bradley P., Deelen, Patrick, de Ligt, Joep, Lameijer, Eric-Wubbo, van Dijk, Freerk, Hormozdiari, Fereydoun, Uitterlinden, André G., van Duijn, Cornelia M., Eichler, Evan E., de Bakker, Paul I. W., Swertz, Morris A., Wijmenga, Cisca, van Ommen, Gert-Jan B., Slagboom, P. Eline, Boomsma, Dorret I., Schönhuth, Alexander, Ye, Kai, and Guryev, Victor. “A high-quality human reference panel reveals the complexity and distribution of genomic structural variants”. Nature Communications 7.1 (2016): 12989.PUB | DOI | WoS | PubMed | Europe PMC
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2015 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941807Palamara, Pier Francesco, Francioli, Laurent C., Wilton, Peter R., Genovese, Giulio, Gusev, Alexander, Finucane, Hilary K., Sankararaman, Sriram, Sunyaev, Shamil R., de Bakker, Paul I.W., Wakeley, John, Pe’er, Itsik, Price, Alkes L., and Schönhuth, Alexander. “Leveraging Distant Relatedness to Quantify Human Mutation and Gene-Conversion Rates”. The American Journal of Human Genetics 97.6 (2015): 775-789.PUB | DOI | WoS | PubMed | Europe PMC
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2015 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941797Kloosterman, Wigard P., Francioli, Laurent C., Hormozdiari, Fereydoun, Marschall, Tobias, Hehir-Kwa, Jayne Y., Abdellaoui, Abdel, Lameijer, Eric-Wubbo, Moed, Matthijs H., Koval, Vyacheslav, Renkens, Ivo, van Roosmalen, Markus J., Arp, Pascal, Karssen, Lennart C., Coe, Bradley P., Handsaker, Robert E., Suchiman, Eka D., Cuppen, Edwin, Thung, Djie Tjwan, McVey, Mitch, Wendl, Michael C., Uitterlinden, André, van Duijn, Cornelia M., Swertz, Morris A., Wijmenga, Cisca, van Ommen, GertJan B., Slagboom, P. Eline, Boomsma, Dorret I., Schönhuth, Alexander, Eichler, Evan E., de Bakker, Paul I.W., Ye, Kai, and Guryev, Victor. “Characteristics of de novo structural changes in the human genome”. Genome Research 25.6 (2015): 792-801.PUB | DOI | WoS | PubMed | Europe PMC
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2015 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941798Leung, Wai Yi, Marschall, Tobias, Paudel, Yogesh, Falquet, Laurent, Mei, Hailiang, Schönhuth, Alexander, and Maoz, Tiffanie Yael. “SV-AUTOPILOT: optimized, automated construction of structural variation discovery and benchmarking pipelines”. BMC Genomics 16.1 (2015): 238.PUB | DOI | WoS | PubMed | Europe PMC
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2015 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941804van 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 W.J.H., Francioli, Laurent C., Menelaou, Androniki, Pulit, Sara L., Rivadeneira, Fernando, Hofman, Albert, Oostra, Ben A., Franco, Oscar H., Leach, Irene Mateo, Beekman, Marian, de Craen, Anton J.M., 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., 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 I.W., Eline Slagboom, P., Boomsma, Dorret I., Wijmenga, Cisca, van Duijn, Cornelia M., and Schönhuth, Alexander. “Genome of the Netherlands population-specific imputations identify an ABCA6 variant associated with cholesterol levels”. Nature Communications 6.1 (2015): 6065.PUB | DOI | WoS | PubMed | Europe PMC
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2015 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941799Patterson, Murray, Marschall, Tobias, Pisanti, Nadia, van Iersel, Leo, Stougie, Leen, Klau, Gunnar W., and Schönhuth, Alexander. “WhatsHap: Weighted Haplotype Assembly for Future-Generation Sequencing Reads”. Journal of Computational Biology 22.6 (2015): 498-509.PUB | DOI | WoS | PubMed | Europe PMC
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2015 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941803van Leeuwen, Elisabeth M, Kanterakis, Alexandros, Deelen, Patrick, Kattenberg, Mathijs V, Slagboom, P Eline, de Bakker, Paul I W, Wijmenga, Cisca, Swertz, Morris A, Boomsma, Dorret I, van Duijn, Cornelia M, Karssen, Lennart C, Hottenga, Jouke Jan, and Schönhuth, Alexander. “Population-specific genotype imputations using minimac or IMPUTE2”. Nature Protocols 10.9 (2015): 1285-1296.PUB | DOI | WoS | PubMed | Europe PMC
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2015 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941805Francioli, Laurent C, Polak, Paz P, Koren, Amnon, Menelaou, Androniki, Chun, Sung, Renkens, Ivo, van Duijn, Cornelia M, Swertz, Morris, Wijmenga, Cisca, van Ommen, Gertjan, Slagboom, P Eline, Boomsma, Dorret I, Ye, Kai, Guryev, Victor, Arndt, Peter F, Kloosterman, Wigard P, de Bakker, Paul I W, Sunyaev, Shamil R, and Schönhuth, Alexander. “Genome-wide patterns and properties of de novo mutations in humans”. Nature Genetics 47.7 (2015): 822-826.PUB | DOI | WoS | PubMed | Europe PMC
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2014 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941816Deelen, Patrick, Menelaou, Androniki, van Leeuwen, Elisabeth M, Kanterakis, Alexandros, van Dijk, Freerk, Medina-Gomez, Carolina, Francioli, Laurent C, Hottenga, Jouke Jan, Karssen, Lennart C, Estrada, Karol, Kreiner-Møller, Eskil, Rivadeneira, Fernando, van Setten, Jessica, Gutierrez-Achury, Javier, Westra, Harm-Jan, Franke, Lude, van Enckevort, David, Dijkstra, Martijn, Byelas, Heorhiy, van Duijn, Cornelia M, de Bakker, Paul I W, Wijmenga, Cisca, Swertz, Morris A, and Schönhuth, Alexander. “Improved imputation quality of low-frequency and rare variants in European samples using the ‘Genome of The Netherlands’”. European Journal of Human Genetics 22.11 (2014): 1321-1326.PUB | DOI | WoS | PubMed | Europe PMC
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2014 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941810Töpfer, Armin, Marschall, Tobias, Bull, Rowena A., Luciani, Fabio, Schönhuth, Alexander, and Beerenwinkel, Niko. “Viral Quasispecies Assembly via Maximal Clique Enumeration”. PLoS Computational Biology 10.3 (2014): e1003515.PUB | DOI | WoS | PubMed | Europe PMC
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2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941835El-Kebir, Mohammed, Marschall, Tobias, Wohlers, Inken, Patterson, Murray, Heringa, Jaap, Schönhuth, Alexander, and Klau, Gunnar W. “Mapping proteins in the presence of paralogs using units of coevolution”. BMC Bioinformatics 14.S15 (2013): S18.PUB | DOI | WoS | PubMed | Europe PMC
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2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941837Allhoff, Manuel, Schönhuth, Alexander, Martin, Marcel, Costa, Ivan G, Rahmann, Sven, and Marschall, Tobias. “Discovering motifs that induce sequencing errors”. BMC Bioinformatics 14.Suppl 5 (2013): S1.PUB | DOI | WoS | PubMed | Europe PMC
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2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941836Marschall, Tobias, Hajirasouliha, Iman, and Schönhuth, Alexander. “MATE-CLEVER: Mendelian-inheritance-aware discovery and genotyping of midsize and long indels”. Bioinformatics 29.24 (2013): 3143-3150.PUB | DOI | WoS | PubMed | Europe PMC
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2012 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941839Marschall, Tobias, Costa, Ivan G., Canzar, Stefan, Bauer, Markus, Klau, Gunnar W., Schliep, Alexander, and Schönhuth, Alexander. “CLEVER: clique-enumerating variant finder”. Bioinformatics 28.22 (2012): 2875-2882.PUB | DOI | WoS | PubMed | Europe PMC
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2012 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941840Hajirasouliha, Iman, Schönhuth, Alexander, de Juan, David, Valencia, Alfonso, and Sahinalp, S. Cenk. “Mirroring co-evolving trees in the light of their topologies”. Bioinformatics 28.9 (2012): 1202-1208.PUB | DOI | WoS | PubMed | Europe PMC
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2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941841Singer, Meromit, Engström, Alexander, Schönhuth, Alexander, and Pachter, Lior. “Determining Coding CpG Islands by Identifying Regions Significant for Pattern Statistics on Markov Chains”. Statistical Applications in Genetics and Molecular Biology 10.1 (2011): 759.PUB | DOI | WoS | PubMed | Europe PMC
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2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941842Hafemeister, Christoph, Costa, Ivan G., Schönhuth, Alexander, and Schliep, Alexander. “Classifying short gene expression time-courses with Bayesian estimation of piecewise constant functions”. Bioinformatics 27.7 (2011): 946-952.PUB | DOI | WoS | PubMed | Europe PMC
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2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941814Schönhuth, Alexander. “Generic identification of binary-valued hidden Markov processes”. Journal of Algebraic Statistics 5.1 (2011): 72-99.PUB
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