Students

W Aftab, S Lahiri, A Imhof: An open-source software for probabilistic identification of proteins in situ and visualization of proteomics data, MCPRO 100242

A. Lukacs, A. W. Thomae, P. Krueger, T. Schauer, A. V. Venkatasubramani, N. Y. Kochanova, W. Aftab, R. Choudhury, I. Forne & A. Imhof: The Integrity of the HMR complex is necessary for centromeric binding and reproductive isolation in Drosophila, https://doi.org/10.1371/journal.pgen.1009744

Lahiri S, Aftab W, Walenta L, Strauss L, Poutanen M, Mayerhofer A, Imhof A.; Life Sci Alliance. 2021 Jan 6;4(3):e202000672. doi: 10.26508/lsa.202000672. Print 2021 Mar. PMID: 33408244; MALDI-IMS combined with shotgun proteomics identify and localize new factors in male infertility.

Lahiri S, Aftab W, Walenta L, Strauss L, Poutanen M, Mayerhofer A, Imhof A. Life Sci Alliance. 2021 Jan 21;4(3):e202101015. doi: 10.26508/lsa.202101015. Print 2021 Mar. PMID: 33479050; Correction: MALDI-IMS combined with shotgun proteomics identify and localize new factors in male infertility.

Aftab W, Imhof A.; Adv Exp Med Biol. 2021;1336:105-128. doi: 10.1007/978-3-030-77252-9_6. PMID: 34628629; Discovery of Native Protein Complexes by Liquid Chromatography Followed by Quantitative Mass Spectrometry

Hayn M, Hirschenberger M, Koepke L, Nchioua R, Straub JH, Klute S, Hunszinger V, Zech F, Prelli Bozzo C, Aftab W, Christensen MH, Conzelmann C, Müller JA, Srinivasachar Badarinarayan S, Stürzel CM, Forne I, Stenger S, Conzelmann KK, Münch J, Schmidt FI, Sauter D, Imhof A, Kirchhoff F, Sparrer KMJ.; Cell Rep. 2021 May 18;35(7):109126. doi: 10.1016/j.celrep.2021.109126. Epub 2021 Apr 27. PMID: 33974846; Systematic functional analysis of SARS-CoV-2 proteins uncovers viral innate immune antagonists and remaining vulnerabilities

Singh AP, Salvatori R, Aftab W, Aufschnaiter A, Carlström A, Forne I, Imhof A, Ott M.; Mol Cell. 2020 Sep 17;79(6):1051-1065.e10. doi: 10.1016/j.molcel.2020.07.024. Epub 2020 Sep 1. PMID: 32877643; Molecular Connectivity of Mitochondrial Gene Expression and OXPHOS Biogenesis

Salvatori R, Kehrein K, Singh AP, Aftab W, Möller-Hergt BV, Forne I, Imhof A, Ott; M. Mol Cell. 2020 Feb 20;77(4):887-900.e5. doi: 10.1016/j.molcel.2019.11.019. Epub 2019 Dec 26. PMID: 31883951; Molecular Wiring of a Mitochondrial Translational Feedback Loop

Salvatori R, Aftab W, Forne I, Imhof A, Ott M, Singh AP. STAR Protoc. 2020 Dec 15;1(3):100219. doi: 10.1016/j.xpro.2020.100219. eCollection 2020 Dec 18. PMID: 33377112; Mapping protein networks in yeast mitochondria using proximity-dependent biotin identification coupled to proteomics

Basch M, Wagner M, Rolland S, Carbonell A, Zeng R, Khosravi S, Schmidt A, Aftab W, Imhof A, Wagener J, Conradt B, Wagener N.; Mol Biol Cell. 2020 Apr 1;31(8):753-767. doi: 10.1091/mbc.E19-06-0329. Epub 2020 Feb 12. PMID: 32049577; Msp1 cooperates with the proteasome for extraction of arrested mitochondrial import intermediates

Albig C, Tikhonova E, Krause S, Maksimenko O, Regnard C, Becker PB, Factor cooperation for chromosome discrimination in Drosophila, Nucleic Acids Res. 2019 Feb 28;47(4):1706-1724. doi: 10.1093/nar/gky1238.

Schauer, T., Ghavi-Helm, Y., Sexton, T., Albig, C., Regnard, C., Cavalli, G., Furlong, E.E.M., and Becker, P.B. (2017). The Drosophila Dosage Compensation Complex activates target genes by chromosome looping within the active compartment. bioRxiv.

Schauer, T., Ghavi‐Helm, Y., Sexton, T., Albig, C., Regnard, C., Cavalli, G., Furlong, E.E., and Becker, P.B. (2017). Chromosome topology guides the Drosophila Dosage Compensation Complex for target gene activation. EMBO reports 18, 1854-1868.

Kratzat H, Mackens-Kiani T, Ameismeier M, Potocnjak M, Cheng J, Dacheux E, Namane A, Berninghausen O, Herzog F, Fromont-Racine M, Becker T, Beckmann R: A structural inventory of native ribosomal ABCE1-43S pre-initiation complexes; EMBO J. 2021 Jan 4;40(1):e105179. doi: 10.15252/embj.2020105179. Epub 2020 Dec 8. PMID: 33289941; PMCID: PMC7780240.

Thoms, M., Buschauer, R., Ameismeier, M., Koepke, L., Denk, T., Hirschenberger, M., Kratzat, H., Hayn, M., Mackens-Kiani, T., Cheng, J., et al. (2020); Structural basis for translational shutdown and immune evasion by the Nsp1 protein of SARS-CoV-2. Science 369, 1249-1255.

Cheng, J., Lau, B., La Venuta, G., Ameismeier, M., Berninghausen, O., Hurt, E., and Beckmann, R. (2020). 90S pre-ribosome transformation into the primordial 40S subunit, Science 369, 1470-1476.

Ameismeier, M, Cheng, J, Berninghausen, O, and Beckmann, R, (2018); Visualizing late states of human 40S ribosomal subunit maturation. Nature 558, 49-253.

Ameismeier, M., Zemp, I., van den Heuvel, J., Berninghausen, O., Kutay, U., and Beckmann, R. (2020). Structural basis for the final steps of human 40S ribosome maturation. Nature

A-D Brunner, M Thielert, C G Vasilopoulou, C Ammar, F Coscia, A Mund, O B Hoerning, N Bache, A Apalategui, M Lubeck, S Richter, D S Fischer, O Raether, M A Park, F Meier, F J Theis, M Mann: Ultra-high sensitivity mass spectrometry quantifies single-cell proteome changes upon perturbation; BioRxiv, 2020.12. 22.423933

M T Strauss, I Bludau, W-F Zeng, E Voytik, C Ammar, J Schessner, R Ilango, M Gill, F Meier, S Willems, M Mann: AlphaPept, a modern and open framework for MS-based proteomics; doi: https://doi.org/10.1101/2021.07.23.453379

S J Schink, M Polk, E Athaide, A Mukherjee, C Ammar, X Liu, S Oh, Y-F Chang, M Basan: The energy requirements of ion homeostasis determine the lifespan of starving bacteria; doi: https://doi.org/10.1101/2021.11.22.469587

G Csaba, E Berchtold, A Hadziahmetovic, M Gruber, C Ammar, R Zimmer: Empires: Differential analysis of gene expression and alternative splicing; doi: https://doi.org/10.1101/2020.08.23.234237

C Ammar: Context-based analysis of mass spectrometry proteomics data; PhD Thesis, LMU Munich

S J Schink, E Biselli, C Ammar, U Gerland: Death rate of E. coli during starvation is set by maintenance cost and biomass recycling; Cell Systems, 9, ue 1, 2019, 64-73.e3, ISSN 2405-4712

C Ammar, M Gruber, G Csaba, R Zimmer: MS-EmpiRe Utilizes Peptide-level Noise Distributions for Ultra-sensitive Detection of Differentially Expressed Proteins [S]; Technological Innovation and Resources, Volume 18, ISSUE 9, P1880-1892, September 01, 2019

C Ammar, E Berchtold, G Csaba, A Schmidt, A Imhof, R Zimmer: Multi-reference spectral library yields almost complete coverage of heterogeneous LC-MS/MS data sets; J. Proteome Res. 2019, 18, 4, 1553–1566

S J Schink, E Biselli, C Ammar, U Gerland: Maintenance Cost and Biomass Recycling Determine Fitness of E. Coli During Starvation; September 26, 2018, SSRN: https://ssrn.com/abstract=3255561

Ammar, C., Berchtold, E., Csaba, G., Schmidt, A., Imhof, A., and Zimmer, R. (2017). Multi-reference spectral library yields almost complete coverage of heterogeneous LC-MS/MS data sets. bioRxiv, 180448.

C Ammar, K Frey, J Bauer, C Melzig, S Chiblak, M Hildebrandt, D Unholtz, C Kurz, S Brons, J Debus, A Abdollahi, K Parodi: Comparing the biological washout of β+-activity induced in mice brain after 12C-ion and proton irradiation; Phys. Med. Biol. 59 7229

A V Dass, S Wunnava, et al., F Gartner, S Angerpointner, E Frey, D Braun: RNA Oligomerisation without Added Catalyst from 2 ′ ,3 ′ ‑Cyclic Nucleotides by Drying at Air‑Water Interfaces; ChemSystemsChem e202200026 (2022)

J. Kranich, N.-K. Chlis, L. Rausch, A. Latha, M. Schifferer, T. Kurz, A. Foltyn-Arfa Kia, M. Simons, F. J. Theis & Th. Brocker; In vivo identification of apoptotic and extracellular vesicle-bound live cells using image-based deep learning; Journal of Extracellular Vesicles Volume 9, 2020 – Issue 1, Article: 1792683

A Auer, M T Strauss, S Strauss, R Jungmann; nanoTRON: a Picasso module for MLP-based classification of super-resolution data; btaa154, https://doi.org/10.1093/bioinformatics/btaa154

F Schueder, J Stein, F Stehr, A Auer, B Sperl, M T. Strauss, P Schwille & R Jungmann, An order of magnitude faster DNA-PAINT imaging by optimized sequence design and buffer conditions, Nature Methods, Oct 7th

Schlichthaerle T, Strauss MT, Schueder F, Auer A, Nijmeijer B, Kueblbeck M, Jimenez Sabinina V, Thevathasan JV, Ries J, Ellenberg J, Jungmann R; Angew Chem Int Ed Engl 58: 13004-13008 (2019); Direct Visualization of Single Nuclear Pore Complex Proteins Using Genetically-Encoded Probes for DNA-PAINT.

N. S. Deußner-Helfmann, A. Auer, M. T. Strauss, S. Malkusch, M. S. Dietz, H-D Barth, R. Jungmann, M. Heilemann, Nano letters, 18, 7, 4626-4630

Schlichthaerle T, Ganji M, Auer A, Wade O K, Jungmann R; Chembiochem (2018); Bacterial-derived antibody binders as small adapters for DNA-PAINT microscopy.

Auer A, Schlichthaerle T, Woehrstein J B, Schueder F, Strauss M T, Grabmayr H, Jungmann R; Chemphyschem 19: 3024-3034 (2018); Nanometer-scale Multiplexed Super-Resolution Imaging with an Economic 3D-DNA-PAINT Microscope.

Auer A, Strauss M T, Schlichthaerle T, Jungmann R ; Nano Lett 17: 6428-6434 (2017); Fast, Background-Free DNA-PAINT Imaging Using FRET-Based Probes.

G. Eraslan, Ž. Avsec, J. Gagneur, F. J. Theis, Deep learning: new computational modelling techniques for genomics, Nature Reviews Genetics, 20, 389–403 (2019)

Ž. Avsec, R. Kreuzhuber, J. Israeli, N. Xu, J. Cheng, A. Shrikumar, A. Banerjee, D. S Kim, T. Beier, L. Urban, A. Kundaje, O. Stegle, J. Gagneur, The Kipoi repository accelerates community exchange and reuse of predictive models for genomics, Nature biotechnology, 2019, PMID: 31138913

J. Cheng, M. H. Çelik, Y. D. Nguyen, Ž. Avsec, J. Gagneur, CAGI5 splicing challenge: Improved exon skipping and intron retention predictions with MMSplice, Human Mutation, 2019, PMID: 31070280

J. Cheng, T. Y. D. Nguyen, K. J. Cygan, M. H. Celik, W. Fairbrother, Ž. Avsec, J. Gagneur, MMSplice: modular modeling improves the predictions of genetic variant effects on splicing, Genome Biol. 2019, PMID: 30823901

F. Brechtmann, A. Matuseviciute, Ch. Mertes, V. A. Yepez, Z. Avsec, M. Herzog, D. M. Bader, H. Prokisch, J. Gagneur, OUTRIDER: A statistical method for detecting aberrantly expressed genes in RNA sequencing data, AJHG, 2018, PMID: 30503520

Avsec, Z., Barekatain, M., Cheng, J., Gagneur, J. (2017). Modeling positional effects of regulatory sequences with spline transformations increases prediction accuracy of deep neural networks. Bioinformatics doi.10.1093/bioinformatics/btx727

Cheng, J., Maier, K.C., Avsec, Z., Rus, P., and Gagneur, J. (2017). Cis-regulatory elements explain most of the mRNA stability variation across genes in yeast. Rna 23, 1648-1659.

Ait-El-Mkadem, S., Dayem-Quere, M., Gusic, M., Chaussenot, A., Bannwarth, S., François, B., Genin, E.C., Fragaki, K., Volker-Touw, C.L.M., Vasnier, C., et al. Mutations in MDH2, Encoding a Krebs Cycle Enzyme, Cause Early-Onset Severe Encephalopathy. The American Journal of Human Genetics 100, 151-159.

Renner S, Martins AS, Streckel E, Braun-Reichhart C, Backman M, Prehn C, Klymiuk N, Bähr A, Blutke A, Landbrecht-Schessl C, Wünsch A, Kessler B, Kurome M, Hinrichs A, Koopmans SJ, Krebs S, Kemter E, Rathkolb B, Nagashima H, Blum H, Ritzmann M, Wanke R, Aigner B, Adamski J, Hrabě de Angelis M, Wolf E; Mild maternal hyperglycemia in INS C93S transgenic pigs causes impaired glucose tolerance and metabolic alterations in neonatal offspring; Dis Model Mech.

Blutke, A., Renner, S., Flenkenthaler, F., Backman, M., Haesner, S., Kemter, E., Landstrom, E., Braun-Reichhart, C., Albl, B., Streckel, E., et al. (2017). The Munich MIDY Pig Biobank – A unique resource for studying organ crosstalk in diabetes. Mol Metab 6, 931-940.

F. Brechtmann, A. Matuseviciute, Ch. Mertes, V. A. Yepez, Z. Avsec, M. Herzog, D. M. Bader, H. Prokisch, J. Gagneur, OUTRIDER: A statistical method for detecting aberrantly expressed genes in RNA sequencing data, AJHG, 2018, PMID: 30503520

Kremer, L.S., Bader, D.M., Mertes, C., Kopajtich, R., Pichler, G., Iuso, A., Haack, T.B., Graf, E., Schwarzmayr, T., Terrile, C., et al. (2017). Genetic diagnosis of Mendelian disorders via RNA sequencing. Nat Commun 8, 15824.

Bader, D.M., Wilkening, S., Lin, G., Tekkedil, M.M., Dietrich, K., Steinmetz, L.M., and Gagneur, J. (2015). Negative feedback buffers effects of regulatory variants. Molecular systems biology 11, 785.

Haack, T.B., Staufner, C., Kopke, M.G., Straub, B.K., Kolker, S., Thiel, C., Freisinger, P., Baric, I., McKiernan, P.J., Dikow, N., Harting, I., Beisse, F., Burgard, P., Kotzaeridou, U., Kühr, J., Himbert, U., Taylor, R.W., Distelmaier, F., Vockley, J., Ghaloul-Gonzalez, L., Zschocke, J., Kremer, L.S., Graf, E., Schwarzmayr, T., Bader, D.M., Gagneur, J., et al. (2015). Biallelic Mutations in NBAS Cause Recurrent Acute Liver Failure with Onset in Infancy. American journal of human genetics 97, 163-169.

Arloth, J., Bader, D.M., Röh, S., and Altmann, A. (2015). Re-Annotator: Annotation Pipeline for Microarray Probe Sequences. PloS one 10, e0139516.

M. Kober, S. Bergeler, E. Frey, Can a flux-based mechanism explain positioning of protein clusters in three-dimensional cell geometry? Biophysical Journal 117 (3), 420-428 (2019).

Bergeler, S., and Frey, E. (2018). Regulation of Pom cluster dynamics in Myxococcus xanthus, PLoS Comput Biol 14 (8), e1006358 (2018).

Schumacher, D., Bergeler, S., Harms, A., Vonck, J., Huneke-Vogt, S., Frey, E., and Søgaard-Andersen, L. (2017). The PomXYZ Proteins Self-Organize on the Bacterial Nucleoid to Stimulate Cell Division. Developmental Cell 41, 299-314. e213.

A Sandoval-Pérez, R M L Berger, A Garaizar, S E Farr, M A Brehm, G König, S W Schneider, R Collepardo-Guevara, V Huck, J O Rädler, C Aponte-Santamaría, DNA binds to a specific site of the adhesive blood-protein von Willebrand factor guided by electrostatic interactions, Nucleic Acids Research, gkaa466,

N K Sinha, A Ordureau, K Best, J A Saba, B Zinshteyn, E Sundaramoorthy, A Fulzele, D M Garshott, T Denk, M Thoms, J A Paulo, J W Harper, E J Bennett, R Beckmann, R Green; EDF1 coordinates cellular responses to ribosome collisions; eLife 2020;9:e58828

Wells JN, Buschauer R, Mackens-Kiani T, Best K, Kratzat H, Berninghausen O, Becker T, Gilbert W, Cheng J, Beckmann R.: Structure and function of yeast Lso2 and human CCDC124 bound to hibernating ribosomes; PLoS Biol. 2020 Jul 20;18(7):e3000780. doi: 10.1371/journal.pbio.3000780. PMID: 32687489; PMCID: PMC7392345.

S J Schink, E Biselli, C Ammar, U Gerland: Death rate of E. coli during starvation is set by maintenance cost and biomass recycling; Cell Systems, 9, ue 1, 2019, 64-73.e3, ISSN 2405-4712

S J Schink, E Biselli, C Ammar, U Gerland: Maintenance Cost and Biomass Recycling Determine Fitness of E. Coli During Starvation; September 26, 2018, SSRN: https://ssrn.com/abstract=3255561

Biselli, E., Agliari, E., Barra, A., Bertani, F.R., Gerardino, A., De Ninno, A., Mencattini, A., Di Giuseppe, D., Mattei, F., Schiavoni, G., et al. (2017). Organs on chip approach: a tool to evaluate cancer-immune cells interactions. Sci Rep-Uk 7, 12737.

M. Bojer, S. Kremser, and U. Gerland: Robust boundary formation in a morphogen gradient via cell-cell signaling; Physical Review E 105.6 (2022): 064405.

Bojer, M., Graf, I.R., and Frey, E. (2018). Self-organized system size oscillation of a stochastic lattice-gas model.; Phys. Rev. E 98, 012410

E. L. Kozak, J. R. Miranda-Rodríguez, A. Borges, K. Dierkes, A. Mineo, F. Pinto-Teixeira, O. Viader-Llargués, J. Solon, O. Chara, H. López-Schier; Quantitative videomicroscopy reveals latent control of cell-pair rotations in vivo. Development 1 May 2023; 150 (9): dev200975.

A S Ceccarelli, A Borges and O Chara: Size matters: tissue size as a marker for a transition between reaction–diffusion regimes in spatio-temporal distribution of morphogens; R. Soc. Open Sci. 9: 211112., 2022

Bozek M, Cortini R, Storti AE, Unnerstall U, Gaul U and Gompel N (2019) ATAC-seq reveals regional differences in enhancer accessibility during the establishment of spatial coordinates in the Drosophila blastoderm. Genome Research, 29(5): 771-783

Bozek M , Cortini R , Storti AE , Unnerstall U , Gaul U and Gompel N (2019) ATAC-seq reveals regional differences in enhancer accessibility during the establishment of spatial coordinates in the Drosophila blastoderm. Genome Research, 29(5): 771-783

D B Brückner, N Arlt, A Fink, P Ronceray, J O Rädler, and C P Broedersz; PNAS February 16, 2021 118 (7) e2016602118; Learning the dynamics of cell–cell interactions in confined cell migration

D. B. Brückner, A. Fink, J. O. Rädler, C. P. Broedersz: Disentangling the behavioural variability of confined cell migration, J. R. Soc. Interface (2020)

D. B. Brückner, P. Ronceray, C. P. Broedersz: Inferring the dynamics of underdamped stochastic systems, Phys. Rev. Lett. (2020)

Brückner, D., Fink, A., Schreiber, C., Röttgermann, P., Rädler, J., Broedersz, C.; Nature Physics (2019); Stochastic nonlinear dynamics of confined cell migration in two-state systems

A. Fink, D. B. Brückner, C. Schreiber, P. J. F. Röttgermann, C. P. Broedersz and J. O. Rädler, Area and geometry dependence of cell migration in asymmetric two-state micropatterns, Biophys. J. (2019)

Dietrich, M., Le Roy, H., Brückner, D.B., Engelke, H., Zantl, R., Rädler, J.O., and Broedersz, C.P. (2018). Guiding 3D cell migration in deformed synthetic hydrogel microstructures. Soft matter 14, 2816 -2826.

Burelbach, J., Brückner, D., Frenkel, D., Eiser, E. (2018). Thermophoretic forces on a mesoscopic scale. Soft Matter. 

M. Büttner, Z. Miao, F. A. Wolf, S. A. Teichmann, and F. J. Theis, A test metric for assessing single-cell RNA-seq batch correction. Nature Methods, 16, 43-49 (2019)

S. Tritschler, M. Büttner, D. S. Fischer, M. Lange, V. Bergen, H. Lickert, F. J. Theis, Concepts and limitations for learning developmental trajectories from single cell genomics, Development 2019 146: dev170506

Buttner, M., Miao, Z., Wolf, A., Teichmann, S.A., and Theis, F.J. (2017). Assessment of batch-correction methods for scRNA-seq data with a new test metric. bioRxiv, 200345.

Haghverdi, L., Büttner, M., Wolf, F.A., Buettner, F., and Theis, F.J. (2016). Diffusion pseudotime robustly reconstructs lineage branching. Nature methods 13, 845-848.

Angerer, P., Haghverdi, L., Büttner, M., Theis, F.J., Marr, C., and Buettner, F. (2015). destiny: diffusion maps for large-scale single-cell data in R. Bioinformatics.

M. Schnepf, C. Ludwig, P. Bandilla, S. Ceolin, U. Unnerstall, C. Jung, U. Gaul; Science (2020); Sensitive Automated Measurement of Histone-DNA Affinities in Nucleosomes;

Chakraborty S, Canzar S, Marschall T , Schulz MH, Chromatyping: Reconstructing Nucleosome Profiles from NOMe Sequencing Data; Research in Computational Molecular Biology. RECOMB 2018. Lecture Notes in Computer Science. 2018;10812:60-61. doi: 10.1007/978-3-319-16706-0_8

Chatzopoulou, E.I., Roskopf, C.C., Sekhavati, F., Braciak, T.A., Fenn, N.C., Hopfner, K.-P., Oduncu, F.S., Fey, G.H., and Rädler, J.O. (2016). Chip-based platform for dynamic analysis of NK cell cytolysis mediated by a triplebody. Analyst 141, 2284-2295.

Ž. Avsec, R. Kreuzhuber, J. Israeli, N. Xu, J. Cheng, A. Shrikumar, A. Banerjee, D. S Kim, T. Beier, L. Urban, A. Kundaje, O. Stegle, J. Gagneur, The Kipoi repository accelerates community exchange and reuse of predictive models for genomics, Nature biotechnology, 2019, PMID: 31138913

J. Cheng, M. H. Çelik, Y. D. Nguyen, Ž. Avsec, J. Gagneur, CAGI5 splicing challenge: Improved exon skipping and intron retention predictions with MMSplice, Human Mutation, 2019, PMID: 31070280

J. Cheng, T. Y. D. Nguyen, K. J. Cygan, M. H. Celik, W. Fairbrother, Ž. Avsec, J. Gagneur, MMSplice: modular modeling improves the predictions of genetic variant effects on splicing, Genome Biol. 2019, PMID: 30823901

Cheng, J., Nguyen, T.Y.D., Cygan, K.J., Celik, M.H., Fairbrother, W.G., Avsec, Z., Gagneur, J. (2018). Modular modeling improves the predictions of genetic variant effects on splicing. bioRxiv. doi.org/10.1101/438986

Avsec, Z., Barekatain, M., Cheng, J., Gagneur, J. (2017). Modeling positional effects of regulatory sequences with spline transformations increases prediction accuracy of deep neural networks. Bioinformatics doi.10.1093/bioinformatics/btx727

Cheng, J., Maier, K.C., Avsec, Z., Rus, P., and Gagneur, J. (2017). Cis-regulatory elements explain most of the mRNA stability variation across genes in yeast. Rna 23, 1648-1659.

N.-K. Chlis, L. Rausch, Th. Brocker, J. Kranich, F. J. Theis; Predicting single-cell gene expression profiles of imaging flow cytometry data with machine learning; Nucleic Acids Research, gkaa926, https://doi.org/10.1093/nar/gkaa926

N.-K. Chlis, A. Karlas, N.-A. Fasoul, M. Kallmayer, H.-H. Eckstein, F. J. Theis, V. Ntziachristos, C. Marr; A sparse deep learning approach for automatic segmentation of human vasculature in multispectral optoacoustic tomography, Photoacoustics Volume 20, December 2020, 100203

J. Kranich, N.-K. Chlis, L. Rausch, A. Latha, M. Schifferer, T. Kurz, A. Foltyn-Arfa Kia, M. Simons, F. J. Theis & Th. Brocker; In vivo identification of apoptotic and extracellular vesicle-bound live cells using image-based deep learning; Journal of Extracellular Vesicles Volume 9, 2020 – Issue 1, Article: 1792683

Chlis, N.K., Alexander Wolf, F., and Theis, F.J. (2017). Model-based branching point detection in single-cell data by K-Branches clustering. Bioinformatics.

Bozek M, Cortini R, Storti AE, Unnerstall U, Gaul U and Gompel N (2019) ATAC-seq reveals regional differences in enhancer accessibility during the establishment of spatial coordinates in the Drosophila blastoderm. Genome Research, 29(5): 771-783

Bozek M , Cortini R , Storti AE , Unnerstall U , Gaul U and Gompel N (2019) ATAC-seq reveals regional differences in enhancer accessibility during the establishment of spatial coordinates in the Drosophila blastoderm. Genome Research, 29(5): 771-783

Michel, M., Demel, C., Zacher, B., Schwalb, B., Krebs, S., Blum, H., Gagneur, J., and Cramer, P. (2017). TT-seq captures enhancer landscapes immediately after T-cell stimulation. Mol Syst Biol 13, 920.

Shetty, A., Kallgren, S.P., Demel, C., Maier, K.C., Spatt, D., Alver, B.H., Cramer, P., Park, P.J., and Winston, F. (2017). Spt5 Plays Vital Roles in the Control of Sense and Antisense Transcription Elongation. Molecular cell 66, 77-88 e75.

Eser, P., Wachutka, L., Maier, K.C., Demel, C., Boroni, M., Iyer, S., Cramer, P., and Gagneur, J. (2016). Determinants of RNA metabolism in the Schizosaccharomyces pombe genome. Mol Syst Biol 12, 857.

Schwalb, B., Michel, M., Zacher, B., Fruhauf, K., Demel, C., Tresch, A., Gagneur, J., and Cramer, P. (2016). TT-seq maps the human transient transcriptome. Science 352, 1225-1228.

M Narita, T Denk, Y Matsuo, T Sugiyama, C Kikuguchi, S Ito, N Sato, T Suzuki, S Hashimoto, I Machová, P Tesina, R Beckmann & T Inada; A distinct mammalian disome collision interface harbors K63-linked polyubiquitination of uS10 to trigger hRQT-mediated subunit dissociation, Nat Commun, 13, 6411 (2022)

Thoms, M., Buschauer, R., Ameismeier, M., Koepke, L., Denk, T., Hirschenberger, M., Kratzat, H., Hayn, M., Mackens-Kiani, T., Cheng, J., et al. (2020); Structural basis for translational shutdown and immune evasion by the Nsp1 protein of SARS-CoV-2. Science 369, 1249-1255.

N K Sinha, A Ordureau, K Best, J A Saba, B Zinshteyn, E Sundaramoorthy, A Fulzele, D M Garshott, T Denk, M Thoms, J A Paulo, J W Harper, E J Bennett, R Beckmann, R Green; EDF1 coordinates cellular responses to ribosome collisions; eLife 2020;9:e58828

Denk, J., Kretschmer, S., Halatek, J., Hartl, C., Schwille, P., and Frey, E. (2018). MinE conformational switching confers robustness on self-organized Min protein patterns. Proceedings of the National Academy of Sciences of the United States of America. DOI: 10.1073/pnas.1719801115

Denk, J., Huber, L., Reithmann, E., and Frey, E. (2016). Active Curved Polymers Form Vortex Patterns on Membranes. Phys Rev Lett 116.

D Yaneva, J L Sparks, M Donsbach, S Zhao, P Weickert, R Bezalel-Buch, J Stingele, J C Walter: The FANCJ helicase unfolds DNA-protein crosslinks to promote their repair, Mol Cell, 2023 Jan 5;83(1):43-56.e10.

E. Edeleva, A. Salditt, J. Stamp, P. Schwintek, J. Boekhoven and D. Braun, Continuous nonenzymatic cross-replication of DNA strands with in situ activated DNA oligonucleotides Chemical Science 10, 5807 – 5814, doi:10.1039/C9SC00770A (2019)

Dau, T., Edeleva, E.V., Seidel, S.A.I., Stockley, R.A., Braun, D., and Jenne, D.E. (2016). Quantitative analysis of protease recognition by inhibitors in plasma using microscale thermophoresis. Sci Rep-Uk 6, 35413.

B. Eraslan, D. Wang, M. Gusic, H. Prokisch, B. M. Hallstrom, M. Uhlen, A. Asplund, F. Ponten, Th. Wieland, Th. Hopf, H. Hahne, B. Kuster, J. Gagneur, Quantification and discovery of sequence determinants of protein per mRNA amount in 29 human tissues, Mol. Syst. Biol. 2019, PMID: 30777893

D. Wang, B. Eraslan, Th. Wieland, B. M. Hallstrom, Th. Hopf, D. P. Zolg, J. Zecha, A. Asplund, L-h. Li, Ch. Meng, M. Frejno, T. Schmidt, K. Schnatbaum, M. Wilhelm, F. Ponten, M. Uhlen, J. Gagneur, H. Hahne, B. Kuster, A deep proteome and transcriptome abundance atlas of 29 healthy human tissues, Mol. Syst. Biol. 2019, PMID: 30777892

G. Eraslan, Ž. Avsec, J. Gagneur, F. J. Theis, Deep learning: new computational modelling techniques for genomics, Nature Reviews Genetics, 20, 389–403 (2019)

Eraslan, G., Arloth, J., Martins, J., Iurato, S., Czamara, D., Binder, E.B., Theis, F.J., and Mueller, N.S. (2016). DeepWAS: Directly integrating regulatory information into GWAS using deep learning supports master regulator MEF2C as risk factor for major depressive disorder. bioRxiv.

M. Salfer, J. F. Collado, W. Baumeister, R. Fernández-Busnadiego, A. Martínez-Sánchez, Reliable estimation of membrane curvature for cryo-electron tomography, https://doi.org/10.1371/journal.pcbi.1007962

J Collado, M Kalemanov, F Campelo, C Bourgoint, F. Thomas, R Loewith, A Martínez-Sánchez, W Baumeister, Chr J Stefan, R Fernández-Busnadiego, Tricalbin-Mediated Contact Sites Control ER Curvature to Maintain Plasma Membrane Integrity, Developmental Cell, Vol 51, ISSUE 4, P476-487.e7, November 18, 2019

Collado, J., and Fernandez-Busnadiego, R. (2017). Deciphering the molecular architecture of membrane contact sites by cryo-electron tomography. Biochimica et biophysica acta.

G Palla, H Spitzer, M Klein, D Fischer, A Chr Schaar, L B Kuemmerle, S Rybakov, I L Ibarra, O Holmberg, I Virshup, M Lotfollahi, S Richter & F J Theis Squidpy: a scalable framework for spatial omics analysis, Nature Methods, 19,  171–178 (2022)

A-D Brunner, M Thielert, C G Vasilopoulou, C Ammar, F Coscia, A Mund, O B Hoerning, N Bache, A Apalategui, M Lubeck, S Richter, D S Fischer, O Raether, M A Park, F Meier, F J Theis, M Mann: Ultra-high sensitivity mass spectrometry quantifies single-cell proteome changes upon perturbation; BioRxiv, 2020.12. 22.423933

S. Tritschler, M. Büttner, D. S. Fischer, M. Lange, V. Bergen, H. Lickert, F. J. Theis, Concepts and limitations for learning developmental trajectories from single cell genomics, Development 2019 146: dev170506

D. S. Fischer, A. K. Fiedler, E. M. Kernfeld, R. M. J. Genga, A. Bastidas-Ponce,  M. Bakhti,  H. Lickert, J. Hasenauer, R. Maehr, F. J. Theis, Inferring population dynamics from single-cell RNA-sequencing time series data, Nature Biotechnology, 37, 461–468 (2019)

Fischer, D.S., Fiedler, A.K., Kernfeld, E., Genga, R.M., Hasenauer, J., Maehr, R., and Theis, F.J. (2017). Beyond pseudotime: Following T-cell maturation in single-cell RNAseq time series. bioRxiv, 219188.

Angerer, P., Simon, L., Tritschler, S., Wolf, F.A., Fischer, D., and Theis, F.J. (2017). Single cells make big data: New challenges and opportunities in transcriptomics. Current Opinion in Systems Biology 4, 85-91.

Barthels, C., Ogrinc, A., Steyer, V., Meier, S., Simon, F., Wimmer, M., Blutke, A., Straub, T., Zimber-Strobl, U., Lutgens, E., et al. (2017). CD40-signalling abrogates induction of RORγt(+) Treg cells by intestinal CD103(+) DCs and causes fatal colitis. Nature Communications 8, 14715.

Stapor, P., Froehlich, F., and Hasenauer, J. (2018). Optimization and uncertainty analysis of ODE models using second order adjoint sensitivity analysis. bioRxiv.

Villaverde, A.F., Froehlich, F., Weindl, D., Hasenauer, J., and Banga, J.R. (2018). Benchmarking optimization methods for parameter estimation in large kinetic models. bioRxiv.

Froehlich, F., Reiser, A., Fink, L., Woschee, D., Ligon, T., Theis, F., Raedler, J., and Hasenauer, J. (2018). Multi-Experiment Nonlinear Mixed Effect Modeling of Single-Cell Translation Kinetics after Transfection. bioRxiv.

Fröhlich, F., Reiser, A., Fink, L., Woschee, D., Ligon, T., Theis, F.J., Rädler, J.O., Hasenauer, J. (2018). Multi-experiment nonlinear mixed effect modeling of single-cell translation kinetics after transfection. npj Systems Biology and applications 4, Article number: 42

Fröhlich, F., Kaltenbacher, B, Theis, F.J., Hasenauer, J. (2017). Scalable parameter estimation for genome-scale biochemical reaction networks. Plos Comput Biol 13(1): e1005331.

Loos, C., Moeller, K., Fröhlich, F., Hucho, T., and Hasenauer, J. (2017). Mechanistic hierarchical population model identifies latent causes of cell-to-cell variability. bioRxiv, 171561.

Froehlich, F., Kessler, T., Weindl, D., Shadrin, A., Schmiester, L., Hache, H., Muradyan, A., Schuette, M., Lim, J.-H., Heinig, M., et al. (2017). Efficient parameterization of large-scale mechanistic models enables drug response prediction for cancer cell lines. bioRxiv, 174094.

Stapor, P., Weindl, D., Ballnus, B., Hug, S., Loos, C., Fiedler, A., Krause, S., Hroß, S., Fröhlich, F., and Hasenauer, J. (2017). PESTO: Parameter EStimation TOolbox. Bioinformatics.

Ligon, T.S., Fröhlich, F., Chi, O.T., Banga, J.R., Balsa-Canto, E., and Hasenauer, J. (2017). GenSSI 2.0: Multi-experiment structural identifiability analysis of SBML models. Bioinformatics.

Fröhlich, F., Loos, C., and Hasenauer, J. (2017). Scalable Inference of Ordinary Differential Equation Models of Biochemical Processes. arXiv preprint arXiv:171108079.

Fröhlich, F., Theis, F.J., Rädler, J.O., and Hasenauer, J. (2016). Parameter estimation for dynamical systems with discrete events and logical operations. Bioinformatics.

Fröhlich, F., Thomas, P., Kazeroonian, A., Theis, F.J., Grima, R., and Hasenauer, J. (2016). Inference for Stochastic Chemical Kinetics Using Moment Equations and System Size Expansion. Plos Comput Biol 12.

Kazeroonian, A., Fröhlich, F., Raue, A., Theis, F.J., and Hasenauer, J. (2016). CERENA: ChEmical REaction Network Analyzer-A Toolbox for the Simulation and Analysis of Stochastic Chemical Kinetics. PloS one 11, e0146732.

Fröhlich, F., Hross, S., Theis, F.J., and Hasenauer, J. (2014). Radial Basis Function Approximations of Bayesian Parameter Posterior Densities for Uncertainty Analysis. In: Mendes P., Dada J.O., Smallbone K. (eds) Computational Methods in Systems Biology. CMSB 2014. Lecture Notes in Computer Science, vol 8859. Springer, Cham

Fröhlich, F., Theis, F.J., and Hasenauer, J. (2014).  Uncertainty Analysis for Non-identifiable Dynamical Systems: Profile Likelihoods, Bootstrapping and More. In: Mendes P., Dada J.O., Smallbone K. (eds) Computational Methods in Systems Biology. CMSB 2014. Lecture Notes in Computer Science, vol 8859. Springer, Cham

P Schwille & B Frohn (2022), Hidden protein functions and what they may teach us; Trends Cell Biol. 32(2):102-109.

B. Frohn, T. Härtel, J. Cox, P. Schwille (2022): Tracing back variations in archaeal ESCRT-based cell division to protein domain architectures. PLoS One 17(3).

Ramirez, D., Garcia-Soriano, D.A., Raso, A., Feingold, M., Rivas, G., and Schwille, P. (2016). Chiral vortex dynamics on membranes is an intrinsic property of FtsZ, driven by GTP hydrolysis. bioRxiv.

A V Dass, S Wunnava, et al., F Gartner, S Angerpointner, E Frey, D Braun: RNA Oligomerisation without Added Catalyst from 2 ′ ,3 ′ ‑Cyclic Nucleotides by Drying at Air‑Water Interfaces; ChemSystemsChem e202200026 (2022)

F M Gartner, I R Graf and E Frey: The time complexity of self-assembly; PNAS, January 18, 2022, 119 (4) e2116373119

Gartner, F. M., Graf, I. R., Wilke, P., Geiger, P. M., & Frey, E. (2020), Stochastic yield catastrophes and robustness in self-assembly. ELife, 9, 1–37.

Geßele R., Halatek J., Würthner L. and Frey E; Geometric cues stabilise long- axis polarisation of PAR protein patterns in C. elegans., Nat. Commun. 11(1): 539, 2020. doi: 10.1038/s41467-020-14317-w

Pietrowski D., Gong Y., Mairhofer M., Gessele R. and Sator M.; Effects of Progesterone and its Metabolites on Human Granulosa Cells. Horm. Metab. Res. 46(2): 133-7. 2014. doi: 10.1055/s-0033-1357167

G. Giunta, H. Seyed-Allaei & U. Gerland, Cross-diffusion induced patterns for a single-step enzymatic reaction, Communications Physics volume 3, Article number: 167 (2020)

B Ramm, A Goychuk, A Khmelinskaia, P Blumhardt, K. Ganzinger, E Frey, P Schwille; Nature Physics 17, 850–858 (2021); A diffusiophoretic mechanism for ATP-driven transport without motor proteins

A Kosloff, A W Holle, J Young, M A George, O Heifler, A Goychuk, E Frey, J P Spatz, F Patolsky, R Elnathan, N H Voelcker; Journal of Nanobiotechnology 19, 51 (2021); Optically Transparent Vertical Silicon Nanowire Arrays for Live-Cell Imaging

D Rüdiger, K Kick, A Goychuk, A M Vollmar, E Frey, S Zahler; Cell Reports 32, 108015 (2020); Cell-Based Strain Remodeling of a Nonfibrous Matrix as an Organizing Principle for Vasculogenesis

F Zhou, S A Schaffer, Ch Schreiber, F J Segerer, A Goychuk, E Frey, J O Rädler; PLOS ONE 15, e0230679 (2020); Quasi-periodic migration of single cells on short microlanes

F Thüroff, A Goychuk, M Reiter, E Frey; eLife 6, e46842 (2019); Bridging the gap between single cell migration and collective dynamics

A Goychuk & E Frey, Physical Review Letters 123, 178101 (2019); Protein recruitment through indirect mechanochemical interactions

Gartner, F. M., Graf, I. R., Wilke, P., Geiger, P. M., & Frey, E. (2020), Stochastic yield catastrophes and robustness in self-assembly. ELife, 9, 1–37.

Striebel, M., Graf, I. R., & Frey, E. (2020). A mechanistic view of collective filament motion in active nematic networks. Biophysical Journal, 118(2), 313–324

Bojer, M., Graf, I.R., and Frey, E. (2018). Self-organized system size oscillation of a stochastic lattice-gas model.; Phys. Rev. E 98, 012410

Graf, I.R., and Frey, E. (2017). Generic transport mechanisms for molecular traffic in cellular protrusions. Phys Rev Lett 118, 128101.

Bauer, M., Graf, I.R., Ngampruetikorn, V., Stephens, G.J., and Frey, E. (2017). Exploiting ecology in drug pulse sequences in favour of population reduction. Plos Comput Biol 13, e1005747.

Vogel, S.K., Greiss, F., Khmelinskaia, A., and Schwille, P. (2017). Control of lipid domain organization by a biomimetic contractile actomyosin cortex. eLife 6.

Greiss, F., Kriegel, F., Braun, D. (2017). Probing the cooperativity of binding networks with high-throughput thermophoresis. Analytical Chemistry 89 (4), 2592-2597.

Greiss, F., Deligiannaki, M., Jung, C., Gaul, U., and Braun, D. (2016). Single-Molecule Imaging in Living Drosophila Embryos with Reflected Light-Sheet Microscopy. Biophys J 110, 939-946.

Reichl, M., Herzog, M., Greiss, F., Wolff, M., and Braun, D. (2015). Understanding the similarity in thermophoresis between single- and double-stranded DNA or RNA. Physical review E, Statistical, nonlinear, and soft matter physics 91, 062709.

Gropp, M.H.M., Klaips, C.L., Hartl, F.U. (2022): Formation of toxic oligomers of polyQ-expanded Huntingtin by prion-mediated cross-seeding; Mol Cell 82(22), 4290-4306, doi: 10.1016/j.molcel.2022.09.031.

Klaips, C.L., Gropp, M.H.M., Hipp, M.S., and Hartl, F.U. (2020): Sis1 potentiates the stress response to protein aggregation and elevated temperature. Nat Commun 11, 6271, doi: 10.1038/s41467-020-20000-x.

Graf, A., Krebs, S., Heininen-Brown, M., Zakhartchenko, V., Blum, H., and Wolf, E. (2014). Genome activation in bovine embryos: review of the literature and new insights from RNA sequencing experiments. Animal reproduction science 149, 46-58.

Hinzpeter, F., Gerland, U., Tostevin, F. (2017). Optimal compartmentalization strategies for metabolic microcompartments. Biophys J 112, 767 – 779

A. Ianeselli, D. Tetiker, J. Stein, A. Kühnlein, Ch B. Mast, D. Braun & T.-Y. D. Tang; Non-equilibrium conditions inside rock pores drive fission, maintenance and selection of coacervate protocells; Nature Chemistry volume 14, pages 32–39 (2022)

A Ianeselli, M Atienza, P W Kudella, U Gerland, Chr B Mast & D Braun: Water cycles in a Hadean CO₂ atmosphere drive the evolution of long DNA; Nat. Phys. (2022).

Ianeselli, A.; Mast, C. B.; Braun, D. Periodic Melting of Oligonucleotides by Oscillating Salt Concentrations Triggered by Microscale Water Cycles Inside Heated Rock Pores; Angew. Chemie Int. Ed., https://doi.org/10.1002/anie.201907909.

R. Imamoglu, D. Balchin, M. Hayer-Hartl & F. U. Hart; Nature Communications (2020); Bacterial Hsp70 resolves misfolded states and accelerates productive folding of a multi-domain protein

L Kater, N Wagener, O Berninghausen, Th Becker, W Neupert & R Beckmann; Structure of the Bcs1 AAA-ATPase suggests an airlock-like translocation mechanism for folded proteins; Nature Structural & Molecular Biology volume 27, pages142–149(2020)

L Kater, V Mitterer, M Thoms, J Cheng, O. Berninghausen, R Beckmann, E. Hurt; Construction of the Central Protuberance and L1 Stalk during 60S Subunit Biogenesis; Molecular Cell, Volume 79, Issue 4, 20 August 2020, Pages 615-628.e5

P Tesina, E Heckel, J Cheng, M Fromont-Racine, R Buschauer, L Kater, B Beatrix, O Berninghausen, A Jacquier, Th Becker & R Beckmann; Structure of the 80S ribosome–Xrn1 nuclease complex; Nature Structural & Molecular Biology volume 26, pages275–280(2019)

L Kater, B Frieg, O Berninghausen, H Gohlke, R Beckmann, A Kedrov; Partially inserted nascent chain unzips the lateral gate of the Sec translocon; EMBO Rep (2019)20:e48191https://doi.org/10.15252/embr.201948191

M Thoms, V Mitterer, L Kater, L Falquet, R Beckmann, D Kressler & E Hurt; Suppressor mutations in Rpf2–Rrs1 or Rpl5 bypass the Cgr1 function for pre-ribosomal 5S RNP-rotation; Nature Communications volume 9, Article number: 4094 (2018)

Kater, L., Thoms, M., Barrio-Garcia, C., Cheng, J., Ismail, S., Ahmed, Y.L., Bange, G., Kressler, D., Berninghausen, O., Sinning, I., et al. (2017). Visualizing the Assembly Pathway of Nucleolar Pre-60S Ribosomes. Cell 171, 1599-1610. e1514.

H. Eto, N. Soga, H. G. Franquelim, P. Glock, A. Khmelinskaia, L. Kai, M. Heymann, H. Noji and P. Schwille; Design of Sealable Custom-Shaped Cell Mimicries Based on Self- Assembled Monolayers on CYTOP Polymer, ACS Appl. Mater. Interfaces 2019, 11, 21372−21380

S. Kempter, A. Khmelinskaia, M. T. Strauss, P. Schwille, R. Jungmann, T. Liedl, W. Bae; Single Particle Tracking and Super-Resolution Imaging of Membrane-Assisted Stop-and-Go Diffusion and Lattice Assembly of DNA Origami; ACS Nano, 2019, 132, 996-1002

Franquelim, H.G., Khmelinskaia, A., Sobczak, J.P., Dietz, H., and Schwille, P. (2018). Membrane sculpting by curved DNA origami scaffolds. Nat Commun 9, 811.

A. Khmelinskaia, J. Mücksch, E. P. Petrov, H. G. Franquelim. P. Schwille; Control of Membrane Binding and Diffusion of Cholesteryl-Modified DNA Origami Nanostructures by DNA Spacers; Langmuir, 2018, 34, 49, 14921-14931

A. Khmelinskaia, J. Mücksch, F. Conci, G. Chwastek, P. Schwille; FCS Analysis of Protein Mobility on Lipid Monolayers, Open Archive Published: March 28, 2018 DOI:https://doi.org/10.1016/j.bpj.2018.02.031

W. Ye, S. Celiksoy, A. Jakab, A. Khmelinskaia, T. Heermann, A. Raso, S. V. Wegner, G. Rivas, P. Schwille, R. Ahijado-Guzmán, C. Sönnichsen; Plasmonic Nanosensors Reveal a Height Dependence of MinDE Protein Oscillations on Membrane Features, J. Am. Chem. Soc.2018, 140, 51

Vogel, S.K., Greiss, F., Khmelinskaia, A., and Schwille, P. (2017). Control of lipid domain organization by a biomimetic contractile actomyosin cortex. eLife 6.

Khmelinskaia, A., Franquelim, H.G., Petrov, E.P., and Schwille, P. (2016). Effect of anchor positioning on binding and diffusion of elongated 3D DNA nanostructures on lipid membranes. J Phys D Appl Phys 49.

Vera Kleene, Valentina Corvaglia, Erika Chacin, Ignasi Forne, David B Konrad, Pardis Khosravani, Céline Douat, Christoph F Kurat, Ivan Huc, Axel Imhof: DNA mimic foldamers affect chromatin composition and disturb cell cycle progression; Nucleic Acids Res., 2023 Aug 31; gkad681. doi: 10.1093/nar/gkad681,

A. G. Knorr, C. Schmidt, P. Tesina, O. Berninghausen, T. Becker, B. Beatrix & R. Beckmann, Ribosome–NatA architecture reveals that rRNA expansion segments coordinate N-terminal acetylation, Nature Structural & Molecular Biology 26, 35–39 (2019)

A G Knorr, Ch Schmidt, P Tesina, O Berninghausen, Th Becker, B Beatrix, R Beckmann; 4Ribosome-NatA architecture reveals that rRNA expansion segments coordinate N-terminal acetylation; Nat Struct Mol Biol; 2019 Jan;26(1):35-39.

A. Lukacs, A. W. Thomae, P. Krueger, T. Schauer, A. V. Venkatasubramani, N. Y. Kochanova, W. Aftab, R. Choudhury, I. Forne & A. Imhof: The Integrity of the HMR complex is necessary for centromeric binding and reproductive isolation in Drosophila, https://doi.org/10.1371/journal.pgen.1009744

N. Kochanova, T. Schauer, G. P. Mathias, A. Lukacs, A. Schmidt, A. Flatley, A. Schepers A, A. W. Thomae, A. Imhof; Nucleic Acids Res. (2020); A multi-layered structure of the interphase chromocenter revealed by proximity-based biotinylation.

Kochanova, N., Schauer, T., Mathias, G.P., Lukacs, A., Schmidt, A., Flatley,  A., Schepers,A., Thomae, A.W., Imhof, A. (2018). Intricate structure of the interphase chromocenter revealed by the analysis of a factor involved in species formation. bioRxiv. doi.org/10.1101/441675

Saito K, Kratzat H, Campbell A, Buschauer R, Burroughs AM, Berninghausen O, Aravind L, Green R, Beckmann R, Buskirk AR: Ribosome collisions induce mRNA cleavage and ribosome rescue in bacteria; Nature. in press; doi: https://doi.org/10.1038/s41586-022-04416-7

Czech L, Mais CN, Kratzat H, Sarmah P, Giammarinaro P, Freibert SA, Esser HF, Musial J, Berninghausen O, Steinchen W, Beckmann R, Koch HG, Bange G: Inhibition of SRP-dependent protein secretion by the bacterial alarmone (p)ppGpp; Nat Commun. in press, doi:https://doi.org/10.1038/s41467-022-28675-0

Kratzat H, Mackens-Kiani T, Ameismeier M, Potocnjak M, Cheng J, Dacheux E, Namane A, Berninghausen O, Herzog F, Fromont-Racine M, Becker T, Beckmann R: A structural inventory of native ribosomal ABCE1-43S pre-initiation complexes; EMBO J. 2021 Jan 4;40(1):e105179. doi: 10.15252/embj.2020105179. Epub 2020 Dec 8. PMID: 33289941; PMCID: PMC7780240.

Thoms, M., Buschauer, R., Ameismeier, M., Koepke, L., Denk, T., Hirschenberger, M., Kratzat, H., Hayn, M., Mackens-Kiani, T., Cheng, J., et al. (2020); Structural basis for translational shutdown and immune evasion by the Nsp1 protein of SARS-CoV-2. Science 369, 1249-1255.

Nürenberg-Goloub E, Kratzat H, Heinemann H, Heuer A, Kötter P, Berninghausen O, Becker T, Tampé R, Beckmann R.: Molecular analysis of the ribosome recycling factor ABCE1 bound to the 30S post-splitting complex.; EMBO J. 2020 May 4;39(9):e103788. doi: 10.15252/embj.2019103788. Epub 2020 Feb 17. PMID: 32064661; PMCID: PMC7196836.

Wells JN, Buschauer R, Mackens-Kiani T, Best K, Kratzat H, Berninghausen O, Becker T, Gilbert W, Cheng J, Beckmann R.: Structure and function of yeast Lso2 and human CCDC124 bound to hibernating ribosomes; PLoS Biol. 2020 Jul 20;18(7):e3000780. doi: 10.1371/journal.pbio.3000780. PMID: 32687489; PMCID: PMC7392345.

Blagotinsek V, Schwan M, Steinchen W, Mrusek D, Hook JC, Rossmann F, Freibert SA, Kratzat H, Murat G, Kressler D, Beckmann R, Beeby M, Thormann KM, Bange G.: An ATP-dependent partner switch links flagellar C-ring assembly with gene expression: Proc Natl Acad Sci U S A. 2020 Aug 25;117(34):20826-20835. doi: 10.1073/pnas.2006470117. Epub 2020 Aug 11. PMID: 32788349; PMCID: PMC7456076.

Milger, K., Gotschke, J., Krause, L., Nathan, P., Alessandrini, F., Tufman, A., Fischer, R., Bartel, S., Theis, F.J., Behr, J., et al. (2017). Identification of a plasma miRNA biomarker signature for allergic asthma: A translational approach. Allergy 72, 1962-1971.

Garzorz-Stark, N., Lauffer, F., Krause, L., Thomas, J., Atenhan, A., Franz, R., Roenneberg, S., Boehner, A., Jargosch, M., Batra, R., et al. (2017). Toll-like receptor 7/8 agonists stimulate plasmacytoid dendritic cells to initiate TH17-deviated acute contact dermatitis in human subjects. Journal of Allergy and Clinical Immunology.

Glock P, Ramm B, Heermann T, Kretschmer S, Schweizer J, Mücksch J, Alagöz G, Schwille P (2019) Stationary patterns in a two-protein reaction-diffusion system, ACS Synth Biol 8(1):148-157

Denk, J., Kretschmer, S., Halatek, J., Hartl, C., Schwille, P., and Frey, E. (2018). MinE conformational switching confers robustness on self-organized Min protein patterns. Proceedings of the National Academy of Sciences of the United States of America. DOI: 10.1073/pnas.1719801115

Kretschmer, S., Harrington, L., and Schwille, P. (2018). Reverse and forward engineering of protein pattern formation. Philosophical Transactions of the Royal Society B: Biological Sciences 373.

Kretschmer, S., Zieske, K., and Schwille, P. (2017). Large-scale modulation of reconstituted Min protein patterns and gradients by defined mutations in MinE’s membrane targeting sequence. PloS one 12, e0179582.

Kretschmer, S., and Schwille, P. (2016). Pattern formation on membranes and its role in bacterial cell division. Current opinion in cell biology 38, 52-59.

Kretschmer, S., and Schwille, P. (2015). Rekonstitution biologischer Selbstorganisation in vitro. BIOspektrum 21, 148-150.

Kretschmer, S., and Schwille, P. (2014). Toward Spatially Regulated Division of Protocells: Insights into the E. coli Min System from in Vitro Studies. Life 4, 915-928.

Krzysztoń R, Woschée D, Reiser A, Schwake G, Strey HH, Rädler JO. Single-cell kinetics of siRNA-mediated mRNA degradation. Nanomedicine: Nanotechnology, Biology and Medicine. 2019;21:102077.

R. Krzysztoń, D. Woschée, A. Reiser, G. Schwake, H. H. Strey, J. O. Rädler; nano, 21, October 2019, 102077; Single-cell kinetics of siRNA-mediated mRNA degradation

Krzyszton, R., Salem, B., Lee, D.J., Schwake, G., Wagner, E., Rädler, J.O. (2017). Microfluidic self-assembly of folate-targeted monomolecular siRNA-lipid nanoparticles. Nanoscale 9, 7442-7453.

A. Ianeselli, D. Tetiker, J. Stein, A. Kühnlein, Ch B. Mast, D. Braun & T.-Y. D. Tang; Non-equilibrium conditions inside rock pores drive fission, maintenance and selection of coacervate protocells; Nature Chemistry volume 14, pages 32–39 (2022)

J. Kranich, N.-K. Chlis, L. Rausch, A. Latha, M. Schifferer, T. Kurz, A. Foltyn-Arfa Kia, M. Simons, F. J. Theis & Th. Brocker; In vivo identification of apoptotic and extracellular vesicle-bound live cells using image-based deep learning; Journal of Extracellular Vesicles Volume 9, 2020 – Issue 1, Article: 1792683

Blutke, A., Renner, S., Flenkenthaler, F., Backman, M., Haesner, S., Kemter, E., Landstrom, E., Braun-Reichhart, C., Albl, B., Streckel, E., et al. (2017). The Munich MIDY Pig Biobank – A unique resource for studying organ crosstalk in diabetes. Mol Metab 6, 931-940.

V. Bergen, M. Lange, S. Peidli, F. A. Wolf, F. J. Theis; Nature biotechnology 38 (12), 1408-1414; Generalizing RNA velocity to transient cell states through dynamical modeling

M Strunz, Lukas M Simon, M Ansari, J J Kathiriya, I Angelidis, Ch H Mayr, G Tsidiridis, M Lange, L F Mattner, M Yee, P Ogar, A Sengupta, I Kukhtevich, R Schneider, Z Zhao, C Voss, T Stoeger, J HL Neumann, A Hilgendorff, J Behr, M O’Reilly, M Lehmann, G Burgstaller, M Königshoff, H A Chapman, F J Theis, H B Schiller; Nature communications 11 (1), 1-20; Alveolar regeneration through a Krt8+ transitional stem cell state that persists in human lung fibrosis

M Lange, V Bergen, M Klein, M Setty, B Reuter, M Bakhti, H Lickert, M Ansari, J Schniering, H B Schiller, D Pe’er, F J Theis; doi: https://doi.org/10.1101/2020.10.19.345983; CellRank for directed single-cell fate mapping

S. Tritschler, M. Büttner, D. S. Fischer, M. Lange, V. Bergen, H. Lickert, F. J. Theis, Concepts and limitations for learning developmental trajectories from single cell genomics, Development 2019 146: dev170506

F. Erhard, MAP Baptista, T Krammer, T Hennig, M. Lange, P Arampatzi, C. S. Jürges, F. J. Theis, A.-E. Saliba, L. Dölken; Nature, 419–423, 19 (2019); scSLAM-seq reveals core features of transcription dynamics in single cells

C. Cartis, N. I. M. Gould, M. Lange; BIT Numerical Mathematics, 1-7, (2019); On monotonic estimates of the norm of the minimizers of regularized quadratic functions in Krylov spaces

Lavagi, I., Krebs, S., Simmet, K., Beck, A., Zakhartchenko, V., Wolf, E., and Blum, H. (2018). Single-cell RNA sequencing reveals developmental heterogeneity of blastomeres during major genome activation in bovine embryos. Sci Rep 8, 4071.

Leonaite, B., Han, Z., Basquin, J., Bonneau, F., Libri, D., Porrua, O., and Conti, E. (2017). Sen1 has unique structural features grafted on the architecture of the Upf1-like helicase family. The EMBO journal 36, 1590-1604.

M. C. Wigbers, F. Brauns, C. Y. Leung and E. Frey; Flow Induced Symmetry Breaking in a Conceptual Polarity Model, Cells 2020, 9(6), 1524;

O’Neill, L., Linder, G., van Buuren, M., & von Bayern, A.M.P. (2021). New Caledonian crows and hidden causal agents revisited; Animal Behavior and Cognition, 8(2), 166-189.

Ling, L., Mühling, B., Jaenichen, R., and Gompel, N.: Increased chromatin accessibility promotes the evolution of a transcriptional silencer in Drosophila., Sci. Adv. 9, (2023).

Xin, Y., Poul, Y. Le, Ling, L., Museridze, M., Mühling, B., Jaenichen, R., Osipova, E., and Gompel, N.: Enhancer evolutionary co-option through shared chromatin accessibility input, Proc. Natl. Acad. Sci. 117, 20636–20644 (2020).

Poul, Y. Le, Xin, Y., Ling, L., Mühling, B., Jaenichen, R., Hörl, D., Bunk, D., Harz, H., Leonhardt, H., Wang, Y., et al., & Museridze M, Gompel, N: Regulatory encoding of quantitative variation in spatial activity of a Drosophila enhancer. Sci. Adv. 6, eabe2955 (2020).

Lotfollahi, M., Rybakov, S., Hrovatin, K. et al., Theis, F. J., Biologically informed deep learning to query gene programs in single-cell atlases. Nat Cell Biol (2023). https://doi.org/10.1038/s41556-022-01072-x

M Lotfollahi, M Naghipourfar, M D Luecken, M Khajavi, M Büttner, M Wagenstetter, Ž Avsec, A Gayoso, N Yosef, M Interlandi, S Rybakov, A V Misharin & F J Theis, Mapping single-cell data to reference atlases by transfer learning, Nature Biotechnology, 40, 121–130 (2022)

G Palla, H Spitzer, M Klein, D Fischer, A Chr Schaar, L B Kuemmerle, S Rybakov, I L Ibarra, O Holmberg, I Virshup, M Lotfollahi, S Richter & F J Theis Squidpy: a scalable framework for spatial omics analysis, Nature Methods, 19,  171–178 (2022)

A. Gayoso, et al. M Lotfollahi & F J  Theis: A Python library for probabilistic analysis of single-cell omics data, Nature Biotechnology, 40,  163–166 (2022)

M Lotfollahi, F A Wolf, F J Theis: Machine learning for perturbational single-cell omics, Cell Systems, 12,  6, 16, 2021, 522-537

M Lotfollahi, M J Siavoshani, R S Hossein Zade & M Saberian, Deep packet: a novel approach for encrypted traffic classification using deep learning,  Soft Computing, 24, 1999–2012 (2020)

M Lotfollahi, M Naghipourfar, F J Theis, F A Wolf: Conditional out-of-distribution generation for unpaired data using transfer VAE, Bioinformatics, 36, Issue Supplement_2, 2020, i610–i617

M Lotfollahi, F A Wolf & F. J. Theis, scGen predicts single-cell perturbation responses, Nature Methods, 16, 715–721 (2019)

A. Lukacs, A. W. Thomae, P. Krueger, T. Schauer, A. V. Venkatasubramani, N. Y. Kochanova, W. Aftab, R. Choudhury, I. Forne & A. Imhof: The Integrity of the HMR complex is necessary for centromeric binding and reproductive isolation in Drosophila, https://doi.org/10.1371/journal.pgen.1009744

N. Kochanova, T. Schauer, G. P. Mathias, A. Lukacs, A. Schmidt, A. Flatley, A. Schepers A, A. W. Thomae, A. Imhof; Nucleic Acids Res. (2020); A multi-layered structure of the interphase chromocenter revealed by proximity-based biotinylation.

Cooper, J.C., Lukacs, A., Reich, S., Schauer, T., Imhof, A., Phadnis, N. (2018). Altered Localization of Hybrid Incompatibility Proteins in Drosophila,

Molecular Biology and Evolution, , msz105, https://doi.org/10.1093/molbev/msz105

Gerland, T.A., Sun, B., Smialowski, P., Lukacs, A., Thomae, A.W., and Imhof, A. (2017). The Drosophila speciation factor HMR localizes to genomic insulator sites. PloS one 12, e0171798.

J. J. B. Messelink, M. C. F. van Teeseling, J. Janssen, M. Thanbichler & C. P. Broedersz: Learning the distribution of single-cell chromosome conformations in bacteria reveals emergent order across genomic scales, Nature Communications, 12, 1963 (2021)

J. J. B. Messelink, F. Meyer, M. Bramkamp, C. P. Broedersz: Single-cell growth inference of Corynebacterium glutamicum reveals asymptotically linear growth, eLife 2021; 10:e70106

Luka Borozan, Francisca Rojas Ringeling, Shao-Yen Kao, Elena Nikonova, Pablo Monteagudo-Mesas, Domagoj Matijevic, Maria L. Spletter, Stefan Canzar, Counting pseudoalignments to novel splicing events. Bioinformatics (2023).

Pablo Monteagudo-Mesas, Cornelia Brönner, Parastou Kohvaei, Haris Amedi, Stefan Canzar, Mario Halic.
Ccr4–Not complex reduces transcription efficiency in heterochromatin. Nucleic Acids Research (2022).

Florian Eberhardt, Eric A. Bushong, Sébastien Phan, Steven Peltier, Pablo Monteagudo-Mesas, Tino Weinkauf, Andreas V. M. Herz, Martin Stemmler and Mark Ellisman, A Uniform and Isotropic Cytoskeletal Tiling Fills Dendritic Spines, eNeuro (2022).

Van Do H, Blažević M, Monteagudo P, Borozan L, Elbassioni K, Laue S, Rojas Ringeling F, Matijević D, Canzar C, Dynamic pseudo-time warping of complex single-cell trajectories; Research in Computational Molecular Biology. RECOMB 2019. Lecture Notes in Computer Science

F Mura, G Gradziuka and C. P. Broedersz, Soft Matter, Mesoscopic non-equilibrium measures can reveal intrinsic features of the active driving, Issue 40, 2019

G Gradziuk, F Mura, and C P Broedersz, Scaling behavior of nonequilibrium measures in internally driven elastic assemblies, Phys. Rev. E 99, 052406

Gnesotto, F., Mura, F., Gladrow, J., and Broedersz, C.P. Broken detailed balance and non-equilibrium dynamics in living systems. Rep Prog Phys. 2018 Jun;81(6):066601.

Mura, F., Gradziuk, G., and Broedersz, C. P. (2018). Non-equilibrium scaling behaviour in driven soft biological assemblies.,Phys. Rev. Lett. 121, 038002

Mura, F., Zaccone., A. (2016). Effects of shear flow on phase nucleation and crystallization. Physical Review E 93, 042803.

Xin, Y., Poul, Y. Le, Ling, L., Museridze, M., Mühling, B., Jaenichen, R., Osipova, E., and Gompel, N.: Enhancer evolutionary co-option through shared chromatin accessibility input, Proc. Natl. Acad. Sci. 117, 20636–20644 (2020).

Poul, Y. Le, Xin, Y., Ling, L., Mühling, B., Jaenichen, R., Hörl, D., Bunk, D., Harz, H., Leonhardt, H., Wang, Y., et al., & Museridze M, Gompel, N: Regulatory encoding of quantitative variation in spatial activity of a Drosophila enhancer. Sci. Adv. 6, eabe2955 (2020).

Knoll KR, Eustermann S, Niebauer V, Oberbeckmann E, Stoehr G, Schall K, Tosi A, Schwarz M, Buchfellner A, Korber P, Hopfner KP; The nuclear actin-containing Arp8 module is a linker DNA sensor driving INO80 chromatin remodeling. Nat Struct Mol Biol. 2018 Sep;25(9):823-832. doi: 10.1038/s41594-018-0115-8. Epub 2018 Sep 3. PMID: 30177756.

E. L. Kozak, S. Palit, J. R. Miranda-Rodríguez, A. Janjic, A. Böttcher, H. Lickert, W. Enard, F. J. Theis, H. López-Schier, Epithelial Planar Bipolarity Emerges from Notch-Mediated Asymmetric Inhibition of Emx2, CellPress, Volume 30, Issue 6, 23 March 2020, Pages 1142-1151.e6, https://doi.org/10.1016/j.cub.2020.01.027

S. Palit, Ch. Heuser, G. P. de Almeida, F. J. Theis and Ch. E. Zielinski, Meeting the Challenges of High-Dimensional Single-Cell Data Analysis in Immunology, Front. Immunol., 03 July 2019, https://doi.org/10.3389/fimmu.2019.01515

F. A. Vieira Braga, G. Kar, M. Berg, O. A. Carpaij, K. Polanski, L. M. Simon, S. Brouwer, T. Gomes, L. Hesse, J. Jiang, E. S. Fasouli, M. Efremova, R. Vento-Tormo, C. Talavera-López, M. R. Jonker, K. Affleck, S. Palit, P. M. Strzelecka, H. V. Firth, K. T. Mahbubani, A. Cvejic, K. B. Meyer, K. Saeb-Parsy, M. Luinge, C.-A. Brandsma, W. Timens, I. Angelidis, M. Strunz, G. H. Koppelman, A. J. van Oosterhout, H. B. Schiller, F. J. Theis, M. van den Berge, M. C. Nawijn & S. A. Teichmann, A cellular census of human lungs identifies novel cell states in health and in asthma, Nature Medicine volume 25, pages1153–1163(2019)

Ponce, L.P., Fenn, N.C., Moritz, N., Krupka, C., Kozik, J.H., Lauber, K., Subklewe, M., and Hopfner, K.P. (2017). SIRPalpha-antibody fusion proteins stimulate phagocytosis and promote elimination of acute myeloid leukemia cells. Oncotarget 8, 11284-11301.

Kratzat H, Mackens-Kiani T, Ameismeier M, Potocnjak M, Cheng J, Dacheux E, Namane A, Berninghausen O, Herzog F, Fromont-Racine M, Becker T, Beckmann R: A structural inventory of native ribosomal ABCE1-43S pre-initiation complexes; EMBO J. 2021 Jan 4;40(1):e105179. doi: 10.15252/embj.2020105179. Epub 2020 Dec 8. PMID: 33289941; PMCID: PMC7780240.

Ghodgaonkar-Steger M, Potocnjak M, Zimniak T, Fischböck-Halwachs J, Solis-Mezarino V, Singh S, Speljko T, Hagemann G, Drexler DJ, Witte G, Herzog F; C-Terminal Motifs of the MTW1 Complex Cooperatively Stabilize Outer Kinetochore Assembly in Budding Yeast. Cell Reports. 2020; 32, 108190.

Fischböck-Halwachs J., Singh S., Potocnjak M., Hagemann G., Solis-Mezarino V., Woike S., Ghodgaonkar-Steger M., Weissmann F., Gallego LD., Rojas J., Andreani J., Köhler A., Herzog F., The COMA complex interacts with Cse4 and positions Sli15/Ipl1 at the budding yeast inner kinetochore.; Elife. 2019 May 21;8. pii: e42879. doi: 10.7554/eLife.42879.

Ivic N., Potocnjak M., Solis-Mezarino V., Herzog F., Bilokapic S., Halic M.; Fuzzy Interactions Form and Shape the Histone Transport Complex.; Mol Cell. 2019 Mar 21;73(6):1191-1203.e6. doi: 10.1016/j.molcel.2019.01.032. Epub 2019 Feb 26.

K. Prayitno, T. Schauer, C. Regnard, P. B. Becker; Progressive dosage compensation during Drosophila embryogenesis is reflected by gene arrangement, EMBO reports (2019)e48138; https://doi.org/10.15252/embr.201948138

Ramirez, D., Garcia-Soriano, D.A., Raso, A., Feingold, M., Rivas, G., and Schwille, P. (2016). Chiral vortex dynamics on membranes is an intrinsic property of FtsZ, driven by GTP hydrolysis. bioRxiv.

Heermann T, Ramm B, Glaser S, Schwille P, Membrane-induced local self-enhancement of MinD membrane binding promotes Min protein pattern formation, J Mol Biol, 432(10):3191-3204

Ramm B, Heermann T, Schwille P (2019) The E. coli MinCDE system in the regulation of protein patterns and gradients, Cell Mol Life Sci

Glock P, Ramm B, Heermann T, Kretschmer S, Schweizer J, Mücksch J, Alagöz G, Schwille P (2019) Stationary patterns in a two-protein reaction-diffusion system, ACS Synth Biol 8(1):148-157

Ramm, B., Glock, P., Mücksch, J., Blumhardt, P., García-Soriano, D. A., Heymann, M., Schwille, P. (2018). The MinDE system is a generic spatial cue for membrane protein distribution in vitro.  Nat Commun. doi: 10.1038/s41467-018-06310-1.

Ramm, B., Glock, P., Schwille, P. (2018). In Vitro Reconstitution of Self-Organizing Protein Patterns on Supported Lipid Bilayers  J. Vis. Exp. (137). e58139, doi:10.3791/58139

Litschel T, Ramm B, Maas R, Heymann M, Schwille P (2018) Beating vesicles: Encapsulated protein oscillations cause dynamic membrane deformation, Angew Chemie Int Ed 57(50):16286–16290

Miyagi, A., Ramm, B., Schwille, P., and Scheuring, S. (2017). High-speed AFM reveals the inner workings of the MinDE protein oscillator. Nano letters.

Ramm B, Stigler J, Hinczewski M, Thirumalai D, Herrmann H, Woehlke G, Rief M, 2014, Sequence-resolved free energy profiles of stress bearing vimentin intermediate filaments. Proc Natl Acad Sci USA, 111(31):11359–11364.

Ramm B, Schwille P (2019) Crystal Ball: In vitro reconstitution of the bacterial cytoskeleton: Expected and unexpected new insights, Microb Biotechnol 12(1):74-76

Reiser, A., Woschee, D., Mehrotra, N., Krzyston, R., Strey, H.H., Rädler, O. (2019). Correlation of mRNA delivery timing and protein expression in lipid-based transfection. bioRxiv. doi: https://doi.org/10.1101/607986

Krzysztoń R, Woschée D, Reiser A, Schwake G, Strey HH, Rädler JO. Single-cell kinetics of siRNA-mediated mRNA degradation. Nanomedicine: Nanotechnology, Biology and Medicine. 2019;21:102077.

R. Krzysztoń, D. Woschée, A. Reiser, G. Schwake, H. H. Strey, J. O. Rädler; nano, 21, October 2019, 102077; Single-cell kinetics of siRNA-mediated mRNA degradation

Reiser, A., Zorn, M.L., Murschhauser, A., and Rädler, J.O. (2018). Single Cell Microarrays Fabricated by Microscale Plasma-Initiated Protein Patterning (μPIPP). In Cell-Based Microarrays (Springer), pp. 41-54.

Froehlich, F., Reiser, A., Fink, L., Woschee, D., Ligon, T., Theis, F., Raedler, J., and Hasenauer, J. (2018). Multi-Experiment Nonlinear Mixed Effect Modeling of Single-Cell Translation Kinetics after Transfection. bioRxiv.

Fröhlich, F., Reiser, A., Fink, L., Woschee, D., Ligon, T., Theis, F.J., Rädler, J.O., Hasenauer, J. (2018). Multi-experiment nonlinear mixed effect modeling of single-cell translation kinetics after transfection. npj Systems Biology and applications 4, Article number: 42

M. Salfer, J. F. Collado, W. Baumeister, R. Fernández-Busnadiego, A. Martínez-Sánchez, Reliable estimation of membrane curvature for cryo-electron tomography, https://doi.org/10.1371/journal.pcbi.1007962

J Collado, M Kalemanov, F Campelo, C Bourgoint, F. Thomas, R Loewith, A Martínez-Sánchez, W Baumeister, Chr J Stefan, R Fernández-Busnadiego, Tricalbin-Mediated Contact Sites Control ER Curvature to Maintain Plasma Membrane Integrity, Developmental Cell, Vol 51, ISSUE 4, P476-487.e7, November 18, 2019

Bäuerlein, F.J.B., Saha, I., Mishra, A., Kalemanov, M., Martínez-Sánchez, A., Klein, R., Dudanova, I., Hipp, M.S., Hartl, F.U., Baumeister, W., Fernández-Busnadiego, R. (2017). In Situ Architecture and Cellular Interactions of PolyQ Inclusions. Cell 171, 179-187 e110.

Schwarz, M., Schall, K., Kallis, E., Eustermann, S., Guariento, M., Moldt, M., Hopfner, K.P., and Michaelis, J. (2018). Single-molecule nucleosome remodeling by INO80 and effects of histone tails. FEBS letters.

Eustermann, S., Schall, K., Kostrewa, D., Lakomek, K., Strauss, M., Moldt, M., and Hopfner, K.P. (2018). Structural basis for ATP-dependent chromatin remodelling by the INO80 complex. Nature.

Knoll KR, Eustermann S, Niebauer V, Oberbeckmann E, Stoehr G, Schall K, Tosi A, Schwarz M, Buchfellner A, Korber P, Hopfner KP; The nuclear actin-containing Arp8 module is a linker DNA sensor driving INO80 chromatin remodeling. Nat Struct Mol Biol. 2018 Sep;25(9):823-832. doi: 10.1038/s41594-018-0115-8. Epub 2018 Sep 3. PMID: 30177756.

Fischer L S, Klingner C, Schlichthaerle T, Strauss M T, Böttcher R, Fässler R, Jungmann R, Grashoff C; Nature Communications (2021); Quantitative single-protein imaging reveals molecular complex formation of integrin, talin, and kindlin during cell adhesion.

Hellmeier J, Platzer R, Eklund A S, Schlichthaerle T, Karner A, Motsch V, Schneider M C, Kurz E, Bamieh V, Brameshuber M, Preiner J, Jungmann R, Stockinger H, Schutz GJ, Huppa JB, Sevcsik E: Proc Natl Acad Sci U S A 118(4): e2016857118; (2021) DNA origami demonstrate the unique stimulatory power of single pMHCs as T cell antigens.

Curd A P, Leng J, Hughes R E, Cleasby A J, Rogers B, Trinh C H, Baird M A, Takagi Y, Tiede C, Sieben C, Manley S, Schlichthaerle T, Jungmann R, Ries J, Shroff H, Peckham M; Nano Letters, in press (2020); Nanoscale Pattern Extraction from Relative Positions of Sparse 3D Localizations.

Sograte-Idrissi S, Schlichthaerle T, Duque-Afonso C J, Alevra M, Strauss S, Moser T, Jungmann R, Rizzoli SO, Opazo F; Nanoscale 12: 10226-10239 (2020); Circumvention of common labelling artefacts using secondary nanobodies.

Schlichthaerle T, Strauss MT, Schueder F, Auer A, Nijmeijer B, Kueblbeck M, Jimenez Sabinina V, Thevathasan JV, Ries J, Ellenberg J, Jungmann R; Angew Chem Int Ed Engl 58: 13004-13008 (2019); Direct Visualization of Single Nuclear Pore Complex Proteins Using Genetically-Encoded Probes for DNA-PAINT.

Gotzke H, Kilisch M, Martinez-Carranza M, Sograte-Idrissi S, Rajavel A, Schlichthaerle T, Engels N, Jungmann R, Stenmark P, Opazo F, Frey S; Nat Commun 10: 4403 (2019); The ALFA-tag is a highly versatile tool for nanobody-based bioscience applications.

Boger C, Hafner A S, Schlichtharle T, Strauss M T, Malkusch S, Endesfelder U, Jungmann R, Schuman E M, Heilemann M; Neurophotonics 6: 035008 (2019); Super-resolution imaging and estimation of protein copy numbers at single synapses with DNA-point accumulation for imaging in nanoscale topography.

Frottin F, Schueder F, Tiwary S, Gupta R, Korner R, Schlichthaerle T, Cox J, Jungmann R, Hartl F U, Hipp MS; Science 365: 342-347 (2019) The nucleolus functions as a phase-separated protein quality control compartment.

Camargo Ortega G, Falk S, Johansson PA, Peyre E, Broix L, Sahu SK, Hirst W, Schlichthaerle T, …, Jungmann R, Bradke F, Borrell V, Geerlof A, Reber S, Tiwari VK, Huttner WB, Wilsch-Brauninger M, Nguyen L, Gotz M; Nature 567: 113-117 (2019); The centrosome protein AKNA regulates neurogenesis via microtubule organization.
Comment: GCO, SF and PAJ contributed equally to this work

Schlichthaerle T, Ganji M, Auer A, Wade O K, Jungmann R; Chembiochem (2018); Bacterial-derived antibody binders as small adapters for DNA-PAINT microscopy.

Basnet N, Nedozralova H, Crevenna AH, Bodakuntla S, Schlichthaerle T, Taschner M, Cardone G, Janke C, Jungmann R, Magiera MM, Biertumpfel C, Mizuno N; Nat Cell Biol 20: 1172-1180 (2018); Direct induction of microtubule branching by microtubule nucleation factor SSNA1.

Auer A, Schlichthaerle T, Woehrstein J B, Schueder F, Strauss M T, Grabmayr H, Jungmann R; Chemphyschem 19: 3024-3034 (2018); Nanometer-scale Multiplexed Super-Resolution Imaging with an Economic 3D-DNA-PAINT Microscope.

Schlichthaerle T, Eklund A S, Schueder F, Strauss M T, Tiede C, Curd A, Ries J, Peckham M, Tomlinson D C, Jungmann R; Angew Chem Int Ed Engl 57: 11060-11063 (2018); Site-Specific Labeling of Affimers for DNA-PAINT Microscopy.

Schueder, F., Strauss, M.T., Hoerl, D., Schnitzbauer, J., Schlichthaerle, T., Strauss, S., Yin, P., Harz, H., Leonhardt, H., and Jungmann, R. (2017). Universelles Superauflösungs-Multiplexing durch DNA-Austausch. Angewandte Chemie 129, 4111-4114.

Schnitzbauer, J., Strauss, M.T., Schlichthaerle, T., Schueder, F., and Jungmann, R. (2017). Super-resolution microscopy with DNA-PAINT. Nature protocols 12, 1198-1228.

Auer A, Strauss M T, Schlichthaerle T, Jungmann R ; Nano Lett 17: 6428-6434 (2017); Fast, Background-Free DNA-PAINT Imaging Using FRET-Based Probes.

Schueder F, Strauss M T, Hoerl D, Schnitzbauer J, Schlichthaerle T, Strauss S, Yin P, Harz H, Leonhardt H, Jungmann R; Angew Chem Int Ed Engl 56: 4052-4055 (2017); Universal Super-Resolution Multiplexing by DNA Exchange.

Schlichthaerle T, Strauss M T, Schueder F, Woehrstein J B, Jungmann R; Curr Opin Biotechnol 39: 41-47 (2016); DNA nanotechnology and fluorescence applications.

M. Schnepf, C. Ludwig, P. Bandilla, S. Ceolin, U. Unnerstall, C. Jung, U. Gaul; Science (2020); Sensitive Automated Measurement of Histone-DNA Affinities in Nucleosomes;

Jung C., Schnepf M., Bandilla P., Unnerstall U., Gaul U., High Sensitivity Measurement of Transcription Factor-DNA Binding Affinities by Competitive Titration Using Fluorescence Microscopy, J Vis Exp. 2019 Feb 7; (144). doi: 10.3791/58763.

Jung C., Bandilla P., von Reutern M., Schnepf M., Rieder S., Unnerstall U., Gaul U., True equilibrium measurement of transcription factor-DNA binding affinities using automated polarization microscopy, Nat Commun. 2018 Apr 23;9(1):1605. doi: 10.1038/s41467-018-03977-4. Erratum in: Nat Commun. 2019 Feb 5;10(1):689

Schwarz, M., Schall, K., Kallis, E., Eustermann, S., Guariento, M., Moldt, M., Hopfner, K.P., and Michaelis, J. (2018). Single-molecule nucleosome remodeling by INO80 and effects of histone tails. FEBS letters.

Stafford CA, Gassauer AM, de Oliveira Mann CC, Tanzer MC, Fessler E, Wefers B, Nagl D, Kuut G, Sulek K, Vasilopoulou C, Schwojer SJ, Wiest A, Pfautsch MK, Wurst W, Yabal M, Fröhlich T, Mann M, Gisch N, Jae LT, Hornung V.
Nature. 2022 Aug 24. doi: 10.1038/s41586-022-05125-x.

Shanmuganathan V., Schiller N., Magoulopoulou A., Cheng J., Braunger K., Cymer F., Berninghausen O., Beatrix B., Kohno K., Heijne GV., Beckmann R., Structural and mutational analysis of the ribosome-arresting human XBP1u, Elife. 2019 Jun 27; 8. pii: e46267. doi: 10.7554/eLife.46267.

Wild K., Juaire KD., Soni K., Shanmuganathan V., Hendricks A., Segnitz B., Beckmann R., Sinning I.; Reconstitution of the human SRP system and quantitative and systematic analysis of its ribosome interactions; Nucleic Acids Res. 2019 Apr 8;47(6):3184-3196. doi: 10.1093/nar/gky1324.

Schmidt, C., Becker, T., Heuer, A., Braunger, K., Shanmuganathan, V., Pech, M., Berninghausen, O., Wilson, D.N., and Beckmann, R. (2016). Structure of the hypusinylated eukaryotic translation factor eIF-5A bound to the ribosome. Nucleic acids research 44, 1944-1951.

Schmidt, C., Kowalinski, E., Shanmuganathan, V., Defenouillere, Q., Braunger, K., Heuer, A., Pech, M., Namane, A., Berninghausen, O., Fromont-Racine, M., Jacquier, A., Conti, E., Becker, T., Beckmann, R. (2016). The cryo-EM structure of a ribosome-Ski2-Ski3-Ski8 helicase complex. Science 354, 1431-1433.

Stirm, M., L. Fonteyne, B. Shashikadze, J. Stöckl, M. Kurome, B. Keßler, V. Zakhartchenko, E. Kemter, H. Blum, G. J. Arnold, K. Matiasek, R. Wanke, W. Wurst, H. Nagashima, F. Knieling, M. Walter, C. Kupatt, T. Fröhlich, N. Klymiuk and E. Wolf (2022). „Pig models for Duchenne muscular dystrophy – from disease mechanisms to validation of new diagnostic and therapeutic concepts.“ Neuromuscular Disorders. DOI:https://doi.org/10.1016/j.nmd.2022.04.005

Flenkenthaler, F., E. Ländström, B. Shashikadze, M. Backman, A. Blutke, J. Philippou-Massier, S. Renner, M. Hrabe de Angelis, R. Wanke, H. Blum, G. J. Arnold, E. Wolf and T. Fröhlich (2021): Differential Effects of Insulin-Deficient Diabetes Mellitus on Visceral vs. Subcutaneous Adipose Tissue-Multi-omics Insights From the Munich MIDY Pig Model, Frontiers in medicine 8: 751277-751277.

Shashikadze, B., F. Flenkenthaler, J. Stöckl, L. Valla, S. Renner, E. Kemter, E. Wolf and T. Fröhlich (2021): „Developmental Effects of (Pre-)Gestational Diabetes on Offspring: Systematic Screening Using Omics Approaches.“ Genes 12: 1991.

Stirm, M., L. M. Fonteyne, B. Shashikadze, M. Lindner, M. Chirivi, A. Lange, C. Kaufhold, C. Mayer, I. Medugorac, B. Kessler, M. Kurome, V. Zakhartchenko, A. Hinrichs, E. Kemter, S. Krause, R. Wanke, G. J. Arnold, G. Wess, H. Nagashima, M. Hrabĕ de Angelis, F. Flenkenthaler, L. A. Kobelke, C. Bearzi, R. Rizzi, A. Bähr, S. Reese, K. Matiasek, M. C. Walter, C. Kupatt, S. Ziegler, P. Bartenstein, T. Fröhlich, N. Klymiuk, A. Blutke and E. Wolf (2021). „A scalable, clinically severe pig model for Duchenne muscular dystrophy.“ Disease Models & Mechanisms 14(12).

Ghodgaonkar-Steger M, Potocnjak M, Zimniak T, Fischböck-Halwachs J, Solis-Mezarino V, Singh S, Speljko T, Hagemann G, Drexler DJ, Witte G, Herzog F; C-Terminal Motifs of the MTW1 Complex Cooperatively Stabilize Outer Kinetochore Assembly in Budding Yeast. Cell Reports. 2020; 32, 108190.

Fischböck-Halwachs J., Singh S., Potocnjak M., Hagemann G., Solis-Mezarino V., Woike S., Ghodgaonkar-Steger M., Weissmann F., Gallego LD., Rojas J., Andreani J., Köhler A., Herzog F., The COMA complex interacts with Cse4 and positions Sli15/Ipl1 at the budding yeast inner kinetochore.; Elife. 2019 May 21;8. pii: e42879. doi: 10.7554/eLife.42879.

Ivic N., Potocnjak M., Solis-Mezarino V., Herzog F., Bilokapic S., Halic M.; Fuzzy Interactions Form and Shape the Histone Transport Complex.; Mol Cell. 2019 Mar 21;73(6):1191-1203.e6. doi: 10.1016/j.molcel.2019.01.032. Epub 2019 Feb 26.

Solis-Mezarino, V., and Herzog, F. (2017). compleXView: a server for the interpretation of protein abundance and connectivity information to identify protein complexes. Nucleic acids research.

F. Stehr, J. Stein, F. Schueder, P. Schwille, R. Jungmann; Flat-top TIRF illumination boosts DNA-PAINT imaging and quantification, Nature Communications, (2019). 10: 1268

O. K. Wade, J. B. Woehrstein, P. C. Nickels, S. Strauss, F. Stehr, J. Stein, F. Schueder, M.T. Strauss, M. Ganji, J. Schnitzbauer, H. Grabmayr, P. Yin, P. Schwille, R. Jungmann; 124-color super-resolution imaging by engineering DNA-PAINT blinking kinetics; Nano Letters (2019). 19(4): 2641-2646

J Stein, F Stehr, P Schueler, P Blumhardt, F Schueder, J Mücksch, R  Jungmann, P Schwille, Toward Absolute Molecular Numbers in DNA-PAINT, Nano Lett.2019, September 19, 2019,

F Schueder, J Stein, F Stehr, A Auer, B Sperl, M T. Strauss, P Schwille & R Jungmann, An order of magnitude faster DNA-PAINT imaging by optimized sequence design and buffer conditions, Nature Methods, Oct 7th

P. Blumhardt, J. Stein, J. Mücksch, F. Stehr, J. Bauer, R. Jungmann, P. Schwille; Photo-Induced Depletion of Binding Sites in DNA-PAINT Microscopy; Molecules (2018);  23(12): 3165

A Auer, M T Strauss, S Strauss, R Jungmann; nanoTRON: a Picasso module for MLP-based classification of super-resolution data; btaa154, https://doi.org/10.1093/bioinformatics/btaa154

S. Strauss, R. Jungmann; Up to 100-fold speed-up and multiplexing in optimized DNA-PAINT; Nature Methods (2020); DOI: 10.1038/s41592-020-0869-x

M.I.E. Harwardt, M.S. Schröder, Y. Li, S. Malkusch, P. Freund, S. Gupta, N. Janjic, S. Strauss, R. Jungmann, M.S. Dietz, M. Heilemann; Single-Molecule Super-Resolution Microscopy Reveals Heteromeric Complexes of MET and EGFR upon Ligand Activation; International Journal of Molecular Sciences (2020); DOI: 10.3390/ijms21082803

Sograte-Idrissi S, Schlichthaerle T, Duque-Afonso C J, Alevra M, Strauss S, Moser T, Jungmann R, Rizzoli SO, Opazo F; Nanoscale 12: 10226-10239 (2020); Circumvention of common labelling artefacts using secondary nanobodies.

O. K. Wade, J. B. Woehrstein, P. C. Nickels, S. Strauss, F. Stehr, J. Stein, F. Schueder, M.T. Strauss, M. Ganji, J. Schnitzbauer, H. Grabmayr, P. Yin, P. Schwille, R. Jungmann; 124-color super-resolution imaging by engineering DNA-PAINT blinking kinetics; Nano Letters (2019). 19(4): 2641-2646

S. Strauss, P.C. Nickels, M.T. Strauss, V.J. Sabinina, J. Ellenberg, J.D. Carter, S. Gupta, N. Janjic, R. Jungmann; Modified aptamers enable quantitative sub-10-nm cellular DNA-PAINT imaging; Nature Methods (2018).15: 1172-1180; DOI: 10.1038/s41592-018-0105-0

Schueder F, Strauss M T, Hoerl D, Schnitzbauer J, Schlichthaerle T, Strauss S, Yin P, Harz H, Leonhardt H, Jungmann R; Angew Chem Int Ed Engl 56: 4052-4055 (2017); Universal Super-Resolution Multiplexing by DNA Exchange.

T. Su, T. Izawa, M. Thoms, Y. Yamashita, J. Cheng, O. Berninghausen, F. U. Hartl, T. Inada, W. Neupert & R. Beckmann, Structure and function of Vms1 and Arb1 in RQC and mitochondrial proteome homeostasis, Nature, 570, 538–542 (2019)

Tian, P., Steward, A., Kudva, R., Su, T., Shilling, P.J., Nickson, A.A., Hollins, J.J., Beckmann, R., Von Heijne, G., Best, R., et al. (2018). The Folding Pathway of an Ig Domain is Conserved On and Off the Ribosome. bioRxiv.

Su, T., Cheng, J., Sohmen, D., Hedman, R., Berninghausen, O., von Heijne, G., Wilson, D.N., and Beckmann, R. (2017). The force-sensing peptide VemP employs extreme compaction and secondary structure formation to induce ribosomal stalling. eLife 6.

S. Tritschler, M. Büttner, D. S. Fischer, M. Lange, V. Bergen, H. Lickert, F. J. Theis, Concepts and limitations for learning developmental trajectories from single cell genomics, Development 2019 146: dev170506

Tritschler, S., Theis, F.J., Lickert, H., and Böttcher, A. (2017). Systematic single-cell analysis provides new insights into heterogeneity and plasticity of the pancreas. Molecular metabolism 6, 974-990.

Angerer, P., Simon, L., Tritschler, S., Wolf, F.A., Fischer, D., and Theis, F.J. (2017). Single cells make big data: New challenges and opportunities in transcriptomics. Current Opinion in Systems Biology 4, 85-91.

Anuroop Venkateswaran Venkatasubramani, Toshiharu Ichinose, Mai Kanno, Ignasi Forne, Hiromu Tanimoto, Shahaf Peleg, Axel Imhof: The fruit fly acetyltransferase chameau promotes starvation resilience at the expense of longevity, EMBO Rep., 2023 Sep 19;e57023. doi: 10.15252/embr.202357023

Tim Wartewig, Jay Daniels, Miriam Schulz, Erik Hameister, Abhinav Joshi, Joonhee Park, Emma Morrish, Anuroop V. Venkatasubramani, Filippo M. Cernilogar, Frits H. A. van Heijster, Christian Hundshammer, Heike Schneider, Filippos Konstantinidis, Judith V. Gabler, Christine Klement, Henry Kurniawan, Calvin Law, Yujin Lee, Sara Choi, Joan Guitart, Ignasi Forne, Jérôme Giustinani, Markus Müschen, Salvia Jain, David M. Weinstock, Roland Rad, Nicolas Ortonne, Franz Schilling, Gunnar Schotta, Axel Imhof, Dirk Brenner, Jaehyuk Choi & Jürgen Ruland: PD-1 instructs a tumor-suppressive metabolic program that restricts glycolysis and restrains AP-1 activity in T cell lymphoma, Nat Cancer (2023). https://doi.org/10.1038/s43018-023-00635-7

A Müller-Eigner, A Sanz-Moreno, I de-Diego, A Venkateswaran Venkatasubramani, M Langhammer, R Gerlini, B Rathkolb, A Aguilar-Pimentel, T Klein-Rodewald, J Calzada-Wack, L Becker, S Palma-Vera, B Gille, I Forne, A Imhof et al.: Dietary intervention improves health metrics and life expectancy of the geneticeally obese Titan mouse, Communications Biology, 5, 408 (2022)

A. Lukacs, A. W. Thomae, P. Krueger, T. Schauer, A. V. Venkatasubramani, N. Y. Kochanova, W. Aftab, R. Choudhury, I. Forne & A. Imhof: The Integrity of the HMR complex is necessary for centromeric binding and reproductive isolation in Drosophila, https://doi.org/10.1371/journal.pgen.1009744

L. J. Dietz, A. Venkateswaran Venkatasubramani, A. Müller-Eigner, M. Hrabe de Angelis, A. Imhof, L. Becker, S. Peleg; Measuring and Interpreting Oxygen Consumption Rates in Whole Fly Head Segments; doi: 10.3791/58601

Magdalini Serefidou, A V Venkatasubramani and A Imhof, The Impact of One Carbon Metabolism on Histone Methylation, Front. Genet., 28 August 2019, https://doi.org/10.3389/fgene.2019.00764

von Bronk, B., Götz, A. and Opitz, M., (2018), Complex microbial systems across different levels of description, Physical Biology, 15, 5

B. von Bronk, A. Götz and M. Opitz; Locality of interactions in three-strain bacterial competition in E. coli; Physical Biology, Volume 16, Number 1

A. Stöcker, S. Brockhaus, S. Schaffer, B. von Bronk, M. Opitz, S. Greven; Boosting Functional Response Models for Location, Scale and Shape with an Application to Bacterial Competition; arXiv:1809.09881

von Bronk, B., Schaffer, S.A., Gotz, A., and Opitz, M. (2017). Effects of stochasticity and division of labor in toxin production on two-strain bacterial competition in Escherichia coli. PLoS biology 15, e2001457.

Kesel, S., von Bronk, B., Falcon Garcia, C., Gotz, A., Lieleg, O., and Opitz, M. (2017). Matrix composition determines the dimensions of Bacillus subtilis NCIB 3610 biofilm colonies grown on LB agar. RSC Advances 7, 31886-31898.

O. K. Wade, J. B. Woehrstein, P. C. Nickels, S. Strauss, F. Stehr, J. Stein, F. Schueder, M.T. Strauss, M. Ganji, J. Schnitzbauer, H. Grabmayr, P. Yin, P. Schwille, R. Jungmann; 124-color super-resolution imaging by engineering DNA-PAINT blinking kinetics; Nano Letters (2019). 19(4): 2641-2646

Schlichthaerle T, Ganji M, Auer A, Wade O K, Jungmann R; Chembiochem (2018); Bacterial-derived antibody binders as small adapters for DNA-PAINT microscopy.

M C Wigbers, T H Tan, F Brauns, J Liu, S Z Swartz, E Frey & N Fakhri; Nature Physics (2021); A hierarchy of protein patterns robustly decodes cell shape information

M. C. Wigbers, F. Brauns, C. Y. Leung and E. Frey; Flow Induced Symmetry Breaking in a Conceptual Polarity Model, Cells 2020, 9(6), 1524;

M R Wolff, A Schmid, P Korber, U Gerland; Effective dynamics of nucleosome configurations at the yeast PHO5 promoter; eLife 2021;10:e58394

E. Oberbeckmann, M. Wolff, N. Krietenstein, M. Heron, J. L. Ellins, A. Schmid, S. Krebs, H. Blum, U. Gerland and Ph. Korber, Absolute nucleosome occupancy map for the Saccharomyces cerevisiae genome, Genome Res. December 2019 29:

Yepez M, V.A., Kremer, L.S., Iuso, A., Gusic, M., Kopajtich, R., Konarikova, E., Nadel, A., Wachutka, L., Prokisch, H., and Gagneur, J. (2018). OCR-Stats: Robust estimation and statistical testing of mitochondrial respiration activities using Seahorse XF Analyzer. doi: https://doi.org/10.1101/231522

F. Brechtmann, A. Matuseviciute, Ch. Mertes, V. A. Yepez, Z. Avsec, M. Herzog, D. M. Bader, H. Prokisch, J. Gagneur, OUTRIDER: A statistical method for detecting aberrantly expressed genes in RNA sequencing data, AJHG, 2018, PMID: 30503520

Nakamoto, M., Tao, J., & Yu, J. Ageas: Automated machine learning based genetic regulatory element extraction system. bioRxiv.2022