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Anders Group: Publications
Publications and Preprints
2022 |
– | G H Putri, S Anders, P Th Pyl, J E Pimanda, F Zanini (2022): Analysing high-throughput sequencing data in Python with HTSeq 2.0, Bioinformatics, btac166. [Link] |
– | S A Herbst*, M Vesterlund*, ..., S Anders, ..., J Lehtiö*, S Dietrich* (2022): Proteogenomics refines the molecular classification of chronic lymphocytic leukemia, biorXiv preprint, [Link] |
– | D Carvajal Ibañez*, M Skabkin*, J Hooli*, S Cerrizuela, M Göpferich, A Jolly, M Zumwinkel, M Bertolini, Th Höfer, G Kramer, S Anders, A Telemann, A Marciniak-Czochra, A Martin-Villalba (2022): Interferon adjusts stem cell output in the young and old brain to meet demand independently of its antiviral function, biorXiv preprint, [Link]. |
2021 |
– | E Porcellato*, J C Gonzalez*, C Ahlmann-Eltze, M A Elsakka, I Shapira, J Fritsch, J A Navarro, S Anders, R B Russel, F T Wieland, C Metzendorf (2021): The S-palmitoylome and DHHC-PAT interactome of Drosophila melanogaster S2R+ cells indicate a high degree of conservation to mammalian palmitoylomes, biorXiv preprint, [Link]. |
– | S Witzel*, F Frauhammer*, P Steinacker, D Devos, PF Pradat, V Meininger, S Halbgebauer, P Oeckl, J Schuster, S Anders, J Dorst, M Otto*, AC Ludolph* (2021): Neurofilament light and heterogeneity of disease progression in amyotrophic lateral sclerosis: development and validation of a prediction model to improve interventional trials, Translational Neurodegeneration, 10: 31. [Link] |
– | LPM Kremer*, S Cerrizuela*, S Dehler, T Stiehl, J Weinmann, H Abendroth, S Kleber, A Laure, J El Andari, S Anders, A Marciniak-Czochra, D Grimm, A Martin-Villalba (2021): High-throughput screening of novel AAV capsids identifies variants for transduction of adult NSCs within the subventricular zone. Molecular Therapy – Methods & Clinical Development, 23: 33-50. [Link] |
– | A Deckert, S Anders, M de Allegri, H T Nguyen, A Soares, S McMahon, K Boerner, M Meurer, K Herbst, M Sand, L Koeppel, T Siems, L Brugnara, S Brenner, R Burk, D Lou, D Kirrmaier, Y Duan, S Ovchinnikova, M Marx, H G Kräusslich, M Knop, T Bärninghausen, C Denkinger (2021): Effectiveness and cost-effectiveness of four different strategies for SARS-CoV-2 surveillance in the general population (CoV-Surv Study): a structured summary of a study protocol for a cluster-randomised, two-factorial controlled trial. Trials 22:39. [Link] |
2020 |
– | N Kurzawa, I Becher, S Sridharan, H Franken, A Mateus, S Anders, M Bantscheff, W Huber, M M Savitski (2020): A computational method for detection of ligand-binding proteins from dose range thermal proteome profiles. Nature Communications, 11: 5783. [Link] |
– | S Klein*, TG Müller*, ..., S Anders, ..., K Börner*, P Chandla*: SARS-CoV-2 RNA extraction using magnetic beads for rapid large-scale testing by RT-qPCR and RT-LAMP. Viruses 12:863. [Link] |
– | M Winkler*, T Staniczek*, SW Kürschner*, CD Schmid*, H Schönhaber, J Cordero, L Kessler, A Mathes, C Sticht, M Neßling, A Uvarovskii, S Anders, X Zhang, G von Figura, D Hartmann, C Mogler, G Dobreva, K Schledzewski, C Géraud*, P-S Koch*, S Goerdt* (2020): Endothelial GATA4 controls liver fibrosis and regeneration by preventing a pathogenic switch in angiocrine signaling. Journal of Hepatology. [Link] |
– | M Göpferich*, N O George*, A Domingo Muelas, A Bizyn, R Pascual, D Fijalkowska, G Kalamakis, U Müller, J Krijgsveld, R Mendez, I Fariñas, W Huber, S Anders*, A Martin-Villalba* (2020): Single cell 3’UTR analysis identifies changes in alternative polyadenylation throughout neuronal differentiation and in autism. biorXiv preprint. [Link] |
⇒ | ZY Wang*, E Leushkin*, A Liechti, S Ovchinnikova, K Mößinger, T Brüning, C Rummel, F Grützner, M Cardoso-Moreira, P Janich, D Gatfield, B Diagouraga, B de Massy, ME Gill, AHFM Peters, S Anders, H Kaessmann* (2020): Transcriptome and translatome co-evolution in mammals. Nature, 588: 642-647. [Link] |
⇒ | V L Dao Thi*, K Herbst, K Boerner, M Meurer, LPM Kremer, D Kirrmaier, A Freistaedter, D Papagiannidis, C Galmozzi, S Klein, P Chandla, D Khalid, I Barreto Miranda, P Schnitzler, H-G Kraeusslich, M Knop*, S Anders* (2020): Screening for SARS-CoV-2 infections with colorimetric RT-LAMP and LAMP sequencing. Science Translational Medicine. [Link to paper] [Link to preprint] |
– | S Klein*, T G Müller*, ..., S Anders, ..., K Börner*, P Chandla* (2020): SARS-CoV-2 RNA extraction using magnetic beads for rapid large-scale testing by RT-qPCR and RT-LAMP. Viruses, 12:863. [Link to paper] [Link to preprint] |
– | E Segal, F Zhang, Z Lin, G King, ..., S Anders, ..., S Ovchinnikova, ... (Coronavirus Census Collective) (2020): Building an international consortium for tracking coronavirus health status. Nature Medicine, 26:1161. [Link to paper] [Link to preprint]
| ⇒ | T Roider, J Seufert, A Uvarovskii, F Frauhammer, …, S Anders*, S Dietrich* (2020): Dissecting intratumor heterogeneity of nodal B cell lymphomas on the transcriptional, genetic, and drug response level. Nature Cell Biology, 22:896. [Link to paper] [Link to preprint] |
⇒ | S Ovchinnikova, S Anders (2020): Exploring dimension-reduced embeddings with Sleepwalk. Genome Research 30:749 [Link]
| – | Y Zhu, L M Orre, Y Z Tran, G Mermelekas, H J Johansson, A Malyutina, S Anders, Janne Lehtiö (2020): DEqMS: a method for accurate variance estimation in differential protein expression analysis. Molecular & Cellular Proteomics, 19:1047. [Link]
| 2019 |
– | D Childs, K Bach, H Franken, S Anders, N Kurzawa, M Bantscheff, M Savitski, W Huber (2019): Non-parametric analysis of thermal proteome profiles reveals novel drug-binding proteins. Molecular & Cellular Proteomics, 18, 2506-2515 [Link] |
⇒ | C Ahlmann Eltze, S Anders (2019): proDA: Probabilistic dropout analysis for identifying differentially abundant proteins in label-free mass spectrometry. bioRxiv preprint 661496 [Link]
| ⇒ | M Cardoso-Moreira, J Halbert, D Valloton, B Velten, C Chen, Y Shao, A Liechti, K Ascenção, C Rummel, S Ovchinnikova, P V Mazin, I Xenarios, K Harshman, M Mort, D N Cooper, C Sandi, M J Soares, P G Ferreira, S Afonso, M Carneiro, J M Turner, J L VandeBerg, A Fallahshahroudi, P Jensen, R Behr, S Lisgo, S Lindsay, P Khaitovich, W Huber, J Baker, S Anders, Y W Zhang, H Kaessmann H. (2019): Gene expression across mammalian organ development. Nature 571, 505-509 [Link]
| – | S Bollepalli, T Korhonen, J Kaprio, S Anders*, M Ollikainen* (2019): EpiSmokEr: a robust classifier to determine smoking status from DNA methylation data. Epigenetics, 11: 13. [Link] |
– | I Lytvynenko, H Paternoga, A Thrun, A Balke, T A Müller, C H Chiang, K Nagler, G Tsaprailis, S Anders, I Bischofs, J A Maupin-Furlow, C M T Spahn, C A P Joazeiro (2019): Alanine tails signal proteolysis in bacterial ribosome-associated quality control. Cell 178:76-90 [Link]
| – | L Urpa, S Anders (2019): Focused multidimensional scaling: Interactive visualization for exploration of high-dimensional data. BMC Bioinformatics 10:221 [Link] |
⇒ | G Kalamakis, D Brüne, S Ravinchandran, …, S Anders*, A del Sol*, A Marciniak-Czochra*, A Martin-Villalba (2019): Quiescence modulates stem cell maintenance and regenerative capacity in the aging brain. Cell 176:1407 [Link] |
– | A C Foulkes, … S Anders … M R Barnes (2019): A Framework for Multi-Omic Prediction of Treatment Response to Biologic Therapy for Psoriasis. Journal of Investigative Dermatology 139:100 [Link] |
2018 |
– | K Närhi, …, S Anders, E Verschuren (2018): Spatial aspects of oncogenic signalling determine the response to combination therapy in slice explants from Kras‐driven lung tumours. Journal of Pathology 245:101. [Link] |
– | S Dietrich*, M Oleś*, J Lu*, L Sellner, S Anders, B Velten, …, W Huber, T Zenz (2018): Drug-perturbation-based stratification of blood cancer. Journal of Clinical Investigations 128:427. [Link] |
– | L Tessier, O Côté, M E Clark, L Viel, A Diaz-Méndez, S Anders, D Bienzle (2018): Gene set enrichment analysis of the bronchial epithelium implicates contribution of cell cycle and tissue repair processes in equine asthma. Scientific Reports 8:16408. [Link] |
2017 |
– | E I Andersson, …, S Anders, …, S Mustjoki (2017): Discovery of novel drug sensitivities in T-PLL by high-throughput ex vivo drug testing and mutation profiling. Leukemia 32:774. [Link] |
– | L Tessier, O Côté, M E Clark, L Viel, A Diaz-Méndez, S Anders, D Bienzle (2017): Impaired response of the bronchial epithelium to inflammation characterizes severe equine asthma. BMC Genomics 18:708. [Link] |
2016 |
– | A Zinkevičienė, D Kainov, I Girkontaitė, E Lastauskienė, V Kvedarienė, Y Fu Y, S Anders, V Velagapudi (2016): Activation of Tryptophan and Phenylalanine Catabolism in the Remission Phase of Allergic Contact Dermatitis: A Pilot Study. International Archives of Allergy and Immunology 170:262. [Link] |
– | S Söderholm, Y Fu, L Gaelings, …, S Anders, …, D Kainov (2016): Multi-omics studies towards novel modulators of influenza A virus-host interaction. Viruses 8:269. [Link] |
– | Y Fu, L Gaelings, S Söderholm, S Belanov, J Nandania, T A Nyman, S Matikainen, S Anders, V Velagapudi, D E Kainov (2016): JNJ872 inhibits influenza A virus replication without altering cellular antiviral responses. Antiviral Research 133:23. [Link] |
2015 |
⇒ | W Huber, V Carey, R Gentleman, S Anders, M Carlson, …, M Morgan (2015): Orchestrating high-throughput genomic analysis with Bioconductor. Nature Methods 12:115. [Link] |
⇒ | M Love, S Anders, V Kim, W Huber (2015): RNA-Seq workflow: gene-level exploratory analysis and differential expression [version 1; referees: 1 approved]. F1000 Research 4:1070. [Link] |
– | L Velten, S Anders, A Pękowska, A I Järvelin, W Huber, V J Pelechano, L M Steinmetz (2015): Single-cell polyadenylation-site mapping reveals variability in 3’ isoform choice. Molecular Systems Biology, 11:812. [Link] |
– | C Hauer, T Curk, S Anders, Th Schwarzl, …, M W Hentze, A E Kulozik (2015): Improved binding site assignment by high-resolution mapping of RNA-protein interactions using iCLIP. Nature Communications 6:7921. [Link] |
– | F A Klein, S Anders, T Pakozdi, Y Ghavi-Helm, E E M Furlong, W Huber (2015): FourCSeq: Analysis of 4C sequencing data. Bioinformatics 31: 3085–3091. [Link] |
⇒ | S Anders, P T Pyl, W Huber (2015): HTSeq – A Python framework to work with high-throughput sequencing data. Bioinformatics 31:166-169. [Link] |
2014 |
⇒ | M I Love, W Huber, S Anders (2014): Moderated estimation of fold change and dispersion for RNA-Seq data with DESeq2. Genome Biology 15:550. [Link] |
⇒ | P Brennecke*, S Anders*, J K Kim*, A A Kołodziejczyk, X Zhang, V Proserpio, B Baying, V Benes, S A Teichmann, J C Marioni, M G Heisler (2013): Accounting for technical noise in single-cell RNA-seq experiments. Nature Methods 10: 1093. [Link] |
– | S Wilkening*, G Lin*, E S Fritsch*, M M Tekkedil, S Anders, R Kuehn, ..., L M Steinmetz (2014): An evaluation of high-throughput approaches to QTL mapping in Saccharomyces cerevisiae. Genetics 196: 853. [Link] |
2013 |
⇒ | A Reyes*, S Anders*, R J Weatheritt, T J Gibson, L M Steinmetz, W Huber (2013): Drift and conservation of differential exon usage across tissues in primate species. PNAS 110: 15377. [Link] |
⇒ | S Anders, D J McCarthy, Y Chen, M Okoniewski, G K Smyth, W Huber, M D Robinson (2013): Count-based differential expression analysis of RNA sequencing data using R and Bioconductor. Nature Protocols 8: 1765. [Link] |
– | S Wilkening, V Pelechano, A I Järvelin, M M Tekkedil, S Anders, V Benes, L M Steinmetz (2013): An efficient method for genome-wide polyadenylation site mapping and RNA quantification. Nucleic Acids Research 41: e65. [Link] |
– | K Zarnack, J König, M Tajnik, I Martincorena, S Eustermann, I Stévant, A Reyes, S Anders, N M Luscombe, J Ule (2013): Direct competition between hnRNP C and U2AF65 protects the transcriptome from the exonization of Alu elements. Cell 152: 453-466. [Link] |
2012 |
⇒ | S Anders*, A Reyes*, W Huber (2012): Detecting differential usage of exons from RNA-seq data. Genome Research 22: 2008-2017. [Link] |
2011 |
⇒ | A Schlattl, S Anders, S M Waszak, W Huber, JO Korbel (2011): Relating CNVs to transcriptome data at fine resolution: assessment of the effect of variant size, type, and overlap with functional regions. Genome Research 21: 2004-2013. [Link] |
2010 |
⇒ | S Anders, W Huber (2010): Differential expression analysis for sequence count data. Genome Biology 11: R106. [Link] |
⇒ | S Thomsen, S Anders, S C Janga, W Huber, C R Alonso (2010): Genome-wide analysis of mRNA decay patterns during early Drosophila development. Genome Biology 11: R93. [Link] |
2009 |
– | M Morgan, S Anders, M Lawrence, P Aboyoun, H Pagès, R Gentleman (2009): ShortRead: a Bioconductor package for input, quality assessment and exploration of high-throughput sequence data. Bioinformatics 25: 2607. [Link] |
⇒ | S Anders (2009): Visualization of genomic data with the Hilbert curve. Bioinformatics 25: 1231-1235. [Link] |
2007 |
⇒ | S Anders, H J Briegel, W Dür (2007): A variational method based on weighted graph states. New Journal of Physics 9: 361. [Link] |
2006 |
– | C Kruszynska, S Anders, W Dür, H J Briegel (2006): Quantum communication cost of preparing multipartite entanglement. Physical Review A 73: 062328. [Link] |
⇒ | S Anders, M B Plenio, W Dür, F Verstraete, H J Briegel (2006): Ground-state approximation for strongly interacting spin systems in arbitrary spatial dimension. Physical Review Letters 97: 107206. [Link] |
⇒ | S Anders, H J Briegel (2006): Fast simulation of stabilizer circuits using a graph-state representation. Physical Review A 73: 022334. [Link] |
Software
DESeq2: R/Bioconductor package for comparative analysis of sequencing count data, successor to DESeq.
DEXSeq: R/Bioconductor package for comparative analysis of exon usage in RNA-Seq data.
DESeq: R/Bioconductor package for comparative analysis of sequencing count data.
HTSeq: Python package, programming framework to process high-throughput sequencing data.
HilbertVis: R/Bioconductor package for visualization of long genomic data sequences.
GraphSim: Python/C library for circuit simulation in quantum information theory. |