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

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)

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.

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.

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

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 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

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.

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).

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.

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.

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).

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.

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).

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