Ruprecht-Karls-Universität Heidelberg

Anders Group: Publications

Publications and Preprints

2020
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, accepted.
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. [Link to paper] [Link to preprint]
N Kurzawa, I Becher, S Sridharan, H Franken, A Mateus, S Anders, M Bantscheff, W Huber, M M Savitski (2020): Computational analysis of ligand dose range thermal proteome profiles. bioRxiv preprint. [Link]
S Ovchinnikova, S Anders (2020): Exploring dimension-reduced embeddings with Sleepwalk. Genome Research, 30:749. [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. [Link to paper] [Link to preprint]
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]
S Ovchinnikova, S Anders (2019): Exploring dimension-reduced embeddings with Sleepwalk. BioRxiv preprint 603589    [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, doi:10.2217/epi-2019-0206
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 dataBioinformatics 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 experimentsNature 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 speciesPNAS 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 Bio­con­ductorNature 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 elementsCell 152: 453-466.   [Link]
2012
S Anders*, A Reyes*, W Huber (2012):  Detecting differential usage of exons from RNA-seq dataGenome 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 curveBioinformatics 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 entanglementPhysical 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. 

GraphSimPython/C library for circuit simulation in quantum information theory.