Publications

 2025:

Evaluating discrepancies in dimensionality reduction for time-series single-cell RNA-sequencing data.

Hackenberg M*, Canal Guitart L* (equal contribution), Backofen R, Binder H.  

bioRxiv, 2025. (Submitted.) https://doi.org/10.1101/2025.02.06.636822

Infusing structural assumptions into dimension reduction for single-cell RNA sequencing data to identify small gene sets. 

Hackenberg M*, Brunn N* (equal contribution), Vogel T, Binder H.

Nature Communications Biology, 2025. https://doi.org/10.1101/2024.02.15.580085

2024:

Interactors and effects of overexpressing YlxR/RnpM, a conserved RNA binding protein in cyanobacteria. 

Hemm L, Miucci A, Kraus A, Riediger M, Tholen S, Abdelaziz N, Georg J, Schilling O, Hess WR 

RNA Biology 21, 1-19. doi: 10.1080/15476286.2024.2429230.

Sparse dimensionality reduction for analyzing single-cell-resolved interactions. 

Brunn N, Hackenberg M, Vogel T, Binder H.  

bioRxiv, 2024.  https://doi.org/10.1101/2024.12.01.626228

Deciphering the molecular logic of WOX5 function in the root stem cell organizer. 

Zhang N, Bitterli P, Oluoch P, Hermann M, Aichinger E, Groot EP, Laux T.

EMBO J. 2024 Nov 18. doi: 10.1038/s44318-024-00302-2. 

Investigating a domain adaptation approach for integrating different measurement instruments in a longitudinal clinical registry.

Hackenberg M, Pfaffenlehner M, Behrens M, Pechmann A, Pechmann A, Kirschner J, Binder H.  

Biometrical Journal 67(1), 2024. https://doi.org/10.1002/bimj.70023

Cathepsin D inhibition during neuronal differentiation selectively affects individual proteins instead of overall protein turnover. 

Schneider J, Mitschke J, Bhat M, Vogele D, Schilling O, Reinheckel T, Heß L.

Biochimie. 2024 Nov;226:35-48. doi: 10.1016/j.biochi.2024.03.013. 

Proteomic analysis of non-muscle invasive and muscle invasive bladder cancer highlights distinct subgroups with metabolic, matrisomal, and immune hallmarks and emphasizes importance of the stromal compartment.

Dinh TJ, Rogg M, Cosenza-Contreras M, Li M, Zirngibl M, Pinter N, Kurowski K, Hause F, Pauli L, Imberg F, Huynh A, Schmid M, Glavinsky I, Braun L, Van Wymersch C, Bergmann L, Ungefug X, Kunz M, Werner T, Bernhard P, Espadas G, Brombacher E, Schueler J, Sabido E, Kreutz C, Gratzke C, Werner M, Grabbert M, Bronsert P, Schell C, Schilling O.  

J Pathol. doi: 10.1002/path.6367. 

Acute suppression of mitochondrial ATP production prevents apoptosis and provides an essential signal for NLRP3 inflammasome activation. 

Saller BS, Wöhrle S, Fischer L, Dufossez C, Ingerl IL, Kessler S, Mateo-Tortola M, Gorka O, Lange F, Cheng Y, Neuwirt E, Marada A, Koentges C, Urban C, Aktories P, Reuther P, Giese S, Kirschnek S, Mayer C, Pilic J, Falquez-Medina H, Oelgeklaus A, Deepagan VG, Shojaee F, Zimmermann JA, Weber D, Tai YH, Crois A, Ciminski K, Peyronnet R, Brandenburg KS, Wu G, Baumeister R, Heimbucher T, Rizzi M, Riedel D, Helmstädter M, Buescher J, Neumann K, Misgeld T, Kerschensteiner M, Walentek P, Kreutz C, Maurer U, Rambold AS, Vince JE, Edlich F, Malli R, Häcker G, Kierdorf K, Meisinger C, Köttgen A, Jakobs S, Weber ANR, Schwemmle M, Groß CJ, Groß O.

Immunity.  15:S1074-7613(24)00492-8. doi: 10.1016/j.immuni.2024.10.012. 

Size exclusion chromatography based proteomic and degradomic profiling of inflammasome-activated, murine bone marrow-derived dendritic cells highlights complex retention and release of cleavage products.

Vogele D, Wöhrle S, Saller BS, Fröhlich K, Barta BA, Cosenza-Contreras M, Groß O, Schilling O.  

Mol Omics. 28;20(9):595-610. doi: 10.1039/d4mo00163j. 

A coherent feed-forward loop in the Arabidopsis root stem cell organizer regulates auxin biosynthesis and columella stem cell maintenance. 

Sharma M, Friedrich T, Oluoch P, Zhang N, Peruzzo F, Jha V, Pi L, Groot EP, Kornet N, Follo M, Aichinger E, Fleck C, Laux T.

Epub 2024 Oct 11. PMID: 39394505.

TermineR: Extracting information on endogenous proteolytic processing from shotgun proteomics data.

Cosenza-Contreras M, Seredynska A, Vogele D, Pinter N, Brombacher E, Cueto RF, Dinh TJ, Bernhard P, Rogg M, Liu J, Willems P, Stael S, Huesgen PF, Kuehn EW, Kreutz C, Schell C, Schilling O.  

Proteomics. 24(19):e2300491. doi: 10.1002/pmic.202300491. 

PD-L1 blockade immunotherapy rewires cancer-induced emergency myelopoiesis. 

Boumpas A, Papaioannou AS, Bousounis P, Grigoriou M, Bergo V, Papafragkos I, Tasis A, Iskas M, Boon L, Makridakis M, Vlachou A, Gavriilaki E, Hatzioannou A, Mitroulis I, Trompouki E, Verginis P.

Front Immunol. 11;15:1386838. doi: 10.3389/fimmu.2024.1386838. 

Neoadjuvant chemo- or chemo-radiation-therapy of pancreatic ductal adenocarcinoma differentially shift ECM composition, complement activation, energy metabolism and ribosomal proteins of the residual tumor mass.

Stillger MN, Kurowski K, Bronsert P, Brombacher E, Kreutz C, Werner M, Tang L, Timme-Bronsert S, Schilling O.

Int J Cancer. 2024 Jun 15;154(12):2162-2175. doi: 10.1002/ijc.34867. 

The role of the 5’ sensing function of ribonuclease E in cyanobacteria

Hoffmann UA, Lichtenberg E, Rogh SN, Bilger R, Reimann V, Heyl F, Backofen R, Steglich C, Hess WR, Wilde A

RNA Biology, 21:1,1-18, doi: 10.1080/15476286.2024.2328438

Data-Independent Acquisition: A Milestone and Prospect in Clinical Mass Spectrometry-Based Proteomics. 

Fröhlich K, Fahrner M, Brombacher E, Seredynska A, Maldacker M, Kreutz C, Schmidt A, Schilling O.

Mol Cell Proteomics. 23(8):100800. doi: 10.1016/j.mcpro.2024.100800. 

Proteometabolomics of initial and recurrent glioblastoma highlights an increased immune cell signature with altered lipid metabolism.

Cosenza-Contreras M, Schäfer A, Sing J, Cook L, Stillger MN, Chen CY, Villacorta Hidalgo J, Pinter N, Meyer L, Werner T, Bug D, Haberl Z, Kübeck O, Zhao K, Stei S, Gafencu AV, Ionita R, Brehar FM, Ferrer-Lozano J, Ribas G, Cerdá-Alberich L, Martí-Bonmatí L, Nimsky C, Van Straaten A, Biniossek ML, Föll M, Cabezas-Wallscheid N, Büscher J, Röst H, Arnoux A, Bartsch JW, Schilling O.  

Neuro Oncol.  4;26(3):488-502. doi: 10.1093/neuonc/noad208. 

Multimodal profiling reveals site-specific adaptation and tissue residency hallmarks of γδ T cells across organs in mice

du Halgouet A, Bruder K, Peltokangas N, Darbois A, Obwegs D, Salou M, Thimme R, Hofmann M, Lantz O, Sagar

Nat Immunol  https://doi.org/10.1038/s41590-023-01710-y

The contribution of mRNA targeting to spatial protein localization in bacteria.

Shang W, Lichtenberg E, Mlesnita AM, Wilde A, Koch HG.  

FEBS J. 2024 Jan 16. doi: 10.1111/febs.17054. 

2023:

Heterogenous nuclear ribonucleoprotein D-like controls endothelial cell functions.

Fischer S, Lichtenthaeler C, Stepanenko A, Heyl F, Maticzka D, Kemmerer K, Klostermann M, Backofen R, Zarnack K, Weigand JE.  

Biol Chem. 10;405(4):229-239. doi: 10.1515/hsz-2023-0254. 

A statistical approach for latent dynamic modeling with differential equations.

Hackenberg M, Pechmann A, Kreutz C, Kirschner J, Binder H.  

arXiv, 2023. https://arxiv.org/abs/2311.16286

Systemic toxicity of snake venom metalloproteinases: Multi-omics analyses of kidney and blood plasma disturbances in a mouse model.

Trevisan-Silva D, Cosenza-Contreras M, Oliveira UC, da Rós N, Andrade-Silva D, Menezes MC, Oliveira AK, Rosa JG, Sachetto ATA, Biniossek ML, Pinter N, Santoro ML, Nishiyama-Jr MY, Schilling O, Serrano SMT.

Int J Biol Macromol. 2023 Dec 31;253(Pt 6):127279. doi: 10.1016/j.ijbiomac.2023.127279.

Proteometabolomics of initial and recurrent glioblastoma highlights an increased immune cell signature with altered lipid metabolism.

Cosenza-Contreras M, Schäfer A, Sing J, Cook L, Stillger MN, Chen CY, Hidalgo JV, Pinter N, Meyer L, Werner T, Bug D, Haberl Z, Kübeck O, Zhao K, Stei S, Gafencu AV, Ionita R, Brehar FM, Ferrer-Lozano J, Ribas G, Cerdá-Alberich L, Martí-Bonmatí L, Nimsky C, Van Straaten A, Biniossek ML, Föll M, Cabezas-Wallscheid N, Büscher J, Röst H, Arnoux A, Bartsch JW, Schilling O.

Neuro Oncol. 2023 Oct 26:noad208. doi: 10.1093/neuonc/noad208. 

Single Cell Sequencing - RDMkit data management guide

Rollin J, Tekman M, Videm P

https://rdmkit.elixir-europe.org/single_cell_sequencing

Unraveling the secrets of γδ T cells with single-cell biology

Nucleophosmin 1 cooperates with the methyltransferase DOT1L to preserve peri-nucleolar heterochromatin organization by regulating H3K27me3 levels and DNA repeats expression

Izzo A, Akol I, Villarreal A, Lebel S, Garcia-Miralles M, Cheffer A, Bovio P, Heidrich S, Vogel T

Epigenetics Chromatin.  28;16(1):36. doi: 10.1186/s13072-023-00511-9. 

The serum proteome of VA-ECMO patients changes over time and allows differentiation of survivors and non-survivors: an observational study.

Siegel PM, Barta BA, Orlean L, Steenbuck ID, Cosenza-Contreras M, Wengenmayer T, Trummer G, Wolf D, Westermann D, Schilling O, Diehl P  

J Transl Med. 2023 May 12;21(1):319. doi: 10.1186/s12967-023-04174-8. 

DOT1L activity affects neural stem cell division mode and reduces differentiation and ASNS expression

Appiah B, Fullio CL, Ossola C, Bertani I, Restelli E, Cheffer A, Polenghi M, Haffner C, Garcia-Miralles M, Zeis P, Treppner M, Bovio P, Schlichtholz L, Mas-Sanchez A, Zografidou L, Winter J, Binder H, Grün D, Kalebic N, Taverna E, Vogel T 

EMBO Rep. 29:e56233. doi: 10.15252/embr.202256233. 

Proteome alterations in human autopsy tissues in relation to time after death. 

Kocsmár É, Schmid M, Cosenza-Contreras M, Kocsmár I, Föll M, Krey L, Barta BA, Rácz G, Kiss A, Werner M, Schilling O, Lotz G, Bronsert P

Cell Mol Life Sci. 2023 Apr 5;80(5):117. 

Regulation of pSYSA defense plasmid copy number in Synechocystis through RNase E and a highly transcribed asRNA

Kaltenbrunner A, Reimann V, Hoffmann UA, Aoyagi T, Sakata M, Nimura-Matsune K, Watanabe S, Steglich C, Wilde A, Hess WR.

Frontiers in Microbiology 2023, doi: 10.3389/fmicb.2023.1112307 

Regulation of RNase E during the UV stress response in the cyanobacterium Synechocystis sp. PCC 6803.

Watanabe S, Stazic D, Georg J, Ohtake S, Sakamaki Y, Numakura M, Asayama M, Chibazakura T, Wilde A, Steglich C, Hess WR

mLife 2023 https://doi.org/10.1002/mlf2.12056

mRNA targeting eliminates the need for the signal recognition particle during membrane protein insertion in bacteria. 

Sarmah P, Shang W, Origi A, Licheva M, Kraft C, Ulbrich M, Lichtenberg E, Wilde A, Koch HG.

Cell Rep. 2023 Mar 28;42(3):112140. doi: 10.1016/j.celrep.2023.112140. 

Targeted and explorative profiling of kallikrein proteases and global proteome biology of pancreatic ductal adenocarcinoma, chronic pancreatitis, and normal pancreas highlights disease-specific proteome remodelling.

Werner J, Bernhard P, Cosenza-Contreras M, Pinter N, Fahrner M, Pallavi P, Eberhard J, Bronsert P, Rückert F, Schilling O

Neoplasia.  2023 Feb;36:100871. doi: 10.1016/j.neo.2022.100871. 

SPATA2 restricts OTULIN-dependent LUBAC activity independently of CYLD.

Griewahn L, Müller-Foxworth M, Peintner L, Wissler M, Weiss M, Brauns-Schubert P, Massoumi R, Borner C, Groß O, Yabal M, Charvet C, Maurer U 

Cell Rep. 2023 Jan 12;42(1):111961. doi: 10.1016/j.celrep.2022.111961. 

TGFβ1-Induced EMT in the MCF10A Mammary Epithelial Cell Line Model Is Executed Independently of SNAIL1 and ZEB1 but Relies on JUNB-Coordinated Transcriptional Regulation.

Antón-García P, Haghighi EB, Rose K, Vladimirov G, Boerries M, Hecht A

Cancers. 2023; 15(2):558. https://doi.org/10.3390/cancers15020558.

Transcriptional activity mediated by β-CATENIN and TCF/LEF family members is completely dispensable for survival and propagation of multiple human colorectal cancer cell lines.

Fröhlich J, Rose K, Hecht, A  

Sci Rep 2023 13, 287.

Multimodal epigenetic changes and altered NEUROD1 chromatin binding in the mouse hippocampus underlie FOXG1 syndrome.

Akol I, Izzo A, Gather F, Strack S, Heidrich S, Ó hAilín D, Villarreal A, Hacker C, Rauleac T, Bella C, Fischer A, Manke T, Vogel T

Proc Natl Acad Sci U S A. 2023 Jan 10;120(2):e2122467120. doi: 10.1073/pnas.2122467120. Epub 2023 Jan 4. 

The roles of proteases in prostate cancer

Koistinen H, Kovanen RM, Hollenberg MD, Dufour A, Radisky ES, Stenman UH, Batra J, Clements J, Hooper JD, Diamandis E, Schilling O, Rannikko A, Mirtti T.

IUBMB Life. 2023 Jan 4. doi: 10.1002/iub.2700. 

2022:

Proteome alterations during clonal isolation of established human pancreatic cancer cell lines.

Bernhard P, Feilen T, Rogg M, Fröhlich K, Cosenza-Contreras M, Hause F, Schell C, Schilling O.

Cell Mol Life Sci. 2022 Oct 22;79(11):561. doi: 10.1007/s00018-022-04584-9. 

TFEB induces mitochondrial itaconate synthesis to suppress bacterial growth in macrophages.

Schuster EM, Epple MW, Glaser KM, Mihlan M, Lucht K, Zimmermann JA, Bremser A, Polyzou A, Obier N, Cabezas-Wallscheid N, Trompouki E, Ballabio A, Vogel J, Buescher JM, Westermann AJ, Rambold AS

Nat Metab. 2022 4(7):856-866. doi: 10.1038/s42255-022-00605-w. Epub 2022 Jul 21. 

PI3K/AKT signaling allows for MAPK/ERK pathway independency mediating dedifferentiation-driven treatment resistance in melanoma.

Corrales E, Levit-Zerdoun E, Metzger P, Mertes R, Lehmann A, Münch J, Lemke S, Kowar S, Boerries M.

Cell Commun Signal. 2022 20(1):187. doi: 10.1186/s12964-022-00989-y. 

The sRNA NsiR4 fine-tunes arginine synthesis in the cyanobacterium Synechocystis sp. PCC 6803 by post-transcriptional regulation of PirA.

Bolay P, Hemm L, Florencio FJ, Hess WR, Muro-Pastor MI, Klähn S.  

RNA Biol. 2022 Jan;19(1):811-818. doi: 10.1080/15476286.2022.2082147. 

Deep dynamic modeling with just two time points: Can we still allow for individual trajectories?

Hackenberg M, Harms P, Pfaffenlehner M, Pechmann A, Kirschner J, Schmidt T, Binder H  

Biom J. 2022 doi: 10.1002/bimj.202000366. Epub ahead of print. PMID: 35384018.

“Life is short, and art is long”: RNA degradation in cyanobacteria and model bacteria.

Zhang JY, Hess WR, Zhang CC

mLife 2022 1, 21–39. DOI: 10.1002/mlf2.12015.

The performance of deep generative models for learning joint embeddings of single-cell multi-omics data

Brombacher E, Hackenberg M,  Kreutz C, Binder H, Treppner M 

Front Mol Biosci 2022. doi: 10.3389/fmolb.2022.962644

Isolation of intact and active FoF1 ATP synthase using a FLAG-tagged subunit from the cyanobacterium Synechocystis sp. PCC 6803.

Song K, Tholen S, Schilling O, Hess WR

STAR Protocols 2022, 3, 101623. DOI: 10.1016/j.xpro.2022.101623.

Wnt/β-catenin signaling promotes neurogenesis in the diencephalospinal dopaminergic system of embryonic zebrafish.

Westphal M, Panza P, Kastenhuber E, Wehrle J, Driever W

Sci Rep. 2022 Jan 19;12(1):1030. doi: 10.1038/s41598-022-04833-8. 

AtpΘ is an inhibitor of F0F1 ATP synthase to arrest ATP hydrolysis during low-energy conditions in cyanobacteria.

Song K, Baumgartner D, Hagemann M, Muro-Pastor AM, Maaß S, Becher D, Hess WR

Current Biology 2022, 32, 136-148.e5. DOI: 10.1016/j.cub.2021.10.051.

Expression of the FoF1 ATP synthase inhibitor AtpΘ depends on small basic DNA-binding proteins and differential mRNA stability.

Song K, Hagemann M, Georg J, Maaß S, Becher D, Hess WR

Microbiology Spectrum 2022, 10.1128/spectrum.02562-21. DOI: 10.1128/spectrum.02562-21.

Acute, Chronic, and Treated Aortic Diseases Present Distinguishable Serum Proteome Fingerprints with Protein Profiles That Correlate with Disease Severity. 

Shahinian JH, Hauser-Stadler CB, Walter T, Discher P, Steenbuck ID, Schilling O, Czerny M.  

Biomedicines. 2022 Aug 28;10(9):2103. doi: 10.3390/biomedicines10092103. 

The transcriptional regulator RbcR controls ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) genes in the cyanobacterium Synechocystis sp. PCC 6803.

Bolay P, Schlüter S, Grimm S, Riediger M, Hess WR, Klähn S 

New Phytol 2022, 235, 432–445. DOI: 10.1111/nph.18139.

Interpretable generative deep learning: an illustration with single cell gene expression data.

Treppner M, Binder H, Hess M.

Hum Genet. 2022 Sep;141(9):1481-1498. doi: 10.1007/s00439-021-02417-6. Epub 2022 Jan 6. 

Krüppel-like factor 7 influences translation and pathways involved in ribosomal biogenesis in breast cancer.

Lüchtenborg AM, Metzger P, Cosenza Contreras M, Oria V, Biniossek ML, Lindner F, Fröhlich K, Malyi A, Erbes T, Gensch N, Maurer J, Thomsen A, Boerries M, Schilling O, Werner M, Bronsert P.

Breast Cancer Res. 2022 Oct 3;24(1):65. doi: 10.1186/s13058-022-01562-8. 

MaxQuant and MSstats in Galaxy Enable Reproducible Cloud-Based Analysis of Quantitative Proteomics Experiments for Everyone

Canonical TGFβ signaling induces collective invasion in colorectal carcinogenesis through a Snail1- and Zeb1-independent partial EMT

Flum M, Dicks S, Teng YH, Schrempp M, Nyström A, Börries M, Hecht A

Oncogene 2022,. https://doi.org/10.1038/s41388-022-02190-4

Phycobilisome breakdown effector NblD is required to maintain the cellular amino acid composition during nitrogen starvation.

Krauspe V, Timm S, Hagemann M, Hess WR

J Bacteriol. 2022  doi: 10.1128/JB.00158-21. 

2021:

Dynamic transcriptome analysis reveals signatures of paradoxical effect of vemurafenib on human dermal fibroblasts.

Corrales E, Levit-Zerdoun E, Metzger P, Kowar S, Ku M, Brummer T, Boerries M

Cell Commun Signal. 2021 19(1):123. doi: 10.1186/s12964-021-00801-3. 

Genome-wide identification and characterization of Fur-binding sites in the cyanobacteria Synechocystis sp. PCC 6803 and PCC 6714

Riediger M, Hernández-Prieto MA, Song K, Hess WR, Futschik ME

DNA Research 2021 dsab023, https://doi.org/10.1093/dnares/dsab023

Single-cell transcriptomic resolution of stem cells and their developmental trajectories in the hippocampus reveals epigenetic control of cell state perseverance.

Salas-Bastos A, Treppner M, Hermann JS, Koutsogiannis D, Binder H, Stadler MB, Grün D, Vogel T

bioRxiv 2021.07.21.452775; doi: https://doi.org/10.1101/2021.07.21.452775

Using Differentiable Programming for Flexible Statistical Modeling.

Hackenberg M, Grodd M, Kreutz C, Fischer M, Esins J, Grabenhenrich L, Karagiannidis C, Binder H 

The American Statistician 2021 (accepted) preprint: https://arxiv.org/abs/2012.05722 

Transcriptome-wide in vivo mapping of cleavage sites for the compact cyanobacterial ribonuclease E reveals insights into its function and substrate recognition. 

Hoffmann UA,  Heyl F,  Rogh SN,  Wallner T,  Backofen R,  Hess WR,  Steglich C,  Wilde A

Integrative analysis of the salt stress response in cyanobacteria.

Klähn S, Mikkat S, Riediger M, Georg J, Hess WR, Hagemann M

bioRxiv 2021.07.28.454097; https://doi.org/10.1101/2021.07.28.454097

Inflammation, Aging and Hematopoiesis: A Complex Relationship.

Bousounis P, Bergo V, Trompouki E

Cells. 2021 Jun 4;10(6):1386. doi: 10.3390/cells10061386. 

The temperature-regulated DEAD-box RNA helicase CrhR interactome: Autoregulation and photosynthesis-related transcripts.

Migur A, Heyl F, Fuss J, Srikumar A, Huettel B, Steglich C, Prakash JSS, Reinhardt R, Backofen R, Owttrim GW, Hess WR

J Exp Bot. 2021  doi: 10.1093/jxb/erab416. 

RNAProt: an efficient and feature-rich RNA binding protein binding site predictor 

Uhl M,  Tran VD,  Heyl F,  Backofen R

StoatyDive: Evaluation and classification of peak profiles for sequencing data.

Heyl F, Backofen R

Gigascience. 2021 10(6):giab045. doi: 10.1093/gigascience/giab045.

Chemotherapy-induced transposable elements activate MDA5 to enhance haematopoietic regeneration.

Clapes T, Polyzou A, Prater P, Sagar, Morales-Hernández A, Ferrarini MG, Kehrer N, Lefkopoulos S, Bergo V, Hummel B, Obier N, Maticzka D, Bridgeman A, Herman JS, Ilik I, Klaeylé L, Rehwinkel J, McKinney-Freeman S, Backofen R, Akhtar A, Cabezas-Wallscheid N, Sawarkar R, Rebollo R, Grün D, Trompouki E

Nat Cell Biol. 2021 Jul;23(7):704-717. doi: 10.1038/s41556-021-00707-9. Erratum in: Nat Cell Biol. 2021 Oct 5;: PMID: 34253898; PMCID: PMC8492473.

Synthetic single cell RNA sequencing data from small pilot studies using deep generative models

Treppner M, Salas-Bastos A, Hess M, Lenz S, Vogel T, Binder H

Sci Rep. 2021, 11: 9403, https://doi.org/10.1038/s41598-021-88875-4

Automation of peptide desalting for proteomic liquid chromatography - tandem mass spectrometry by centrifugal microfluidics.

Klatt JN, Dinh TJ, Schilling O, Zengerle R, Schmidt F, Hutzenlaub T, Paust N.

Lab Chip. 2021 Apr 28. doi: 10.1039/d1lc00137j. Epub ahead of print. 

Discovery of a small protein factor involved in the coordinated degradation of phycobilisomes in cyanobacteria.

Krauspe V, Fahrner M, Spät P, Macek B, Schilling O, Hess WR 

PNAS. 118: e2012277118, 2021, doi: 10.1073/pnas.2012277118.

Spatiotemporal sequence of mesoderm and endoderm lineage segregation during mouse gastrulation 

Probst S, Sagar, Tosic J, Schwan C, Grün D, Arnold SJ 

Development. 148(1):dev193789, 2021, doi: 10.1242/dev.193789.  

2020:

Analysis of a Photosynthetic Cyanobacterium Rich in Internal Membrane Systems via Gradient Profiling by Sequencing (Grad-seq)

Riediger M, Spät P, Bilger R, Voigt K, Maček B, Hess WR 

The Plant Cell koaa017, 2020, doi:10.1093/plcell/koaa017.

Galaxy CLIP- Explorer: a web server for CLIP-Seq data analysis

Heyl F, Maticzka D, Uhl M, Backofen R 

GigaScience 9(11):giaa108, 2020, doi: 10.1093/gigascience/giaa108.

Repetitive Elements Trigger RIG-I-like Receptor Signaling that Regulates the Emergence of Hematopoietic Stem and Progenitor Cells

Lefkopoulos S, Polyzou A, Derecka M, Bergo V, Clapes T, Cauchy P, Jerez-Longres C, Onishi-Seebacher M, Yin N, Martagon-Calderón NA, Potts KS, Klaeylé L, Liu F, Bowman TV, Jenuwein T, Mione MC, Trompouki E 

Immunity. 53(5):934-951, 2020, doi: 10.1016/j.immuni.2020.10.007. 

Deciphering the regulatory landscape of fetal and adult γδ T-cell development at single-cell resolution

Sagar, Pokrovskii M, Herman JS, Naik S, Sock E, Zeis P, Lausch U, Wegner M, Tanriver Y, Littman DR, Grün D

EMBO J. 39(13):e104159, 2020, doi: 10.15252/embj.2019104159.  

In Situ Maturation and Tissue Adaptation of Type 2 Innate Lymphoid Cell Progenitors

Zeis P, Lian M, Fan X, Herman JS, Hernandez DC, Gentek R, Elias S, Symowski C, Knöpper K, Peltokangas N, Friedrich C, Doucet-Ladeveze R, Kabat AM, Locksley RM, Voehringer D, Bajenoff M, Rudensky AY, Romagnani C, Grün D, Gasteiger G

Immunity. 53(4):775-792.e9, 2020, doi: 10.1016/j.immuni.2020.09.002. 

HIF-1α and HIF-2α differently regulate tumour development and inflammation of clear cell renal cell carcinoma in mice

Hoefflin R, Harlander S, Schäfer S, Metzger P, Kuo F, Schönenberger D, Adlesic M, Peighambari A, Seidel P, Chen CY, Consenza-Contreras M, Jud A, Lahrmann B, Grabe N, Heide D, Uhl FM, Chan TA, Duyster J, Zeiser R, Schell C, Heikenwalder M, Schilling O, Hakimi AA, Boerries M, Frew IJ

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Deciphering Cell Fate Decision by Integrated Single-Cell Sequencing Analysis

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Chemical Genetics Screen Identifies Epigenetic Mechanisms Involved in Dopaminergic and Noradrenergic Neurogenesis in Zebrafish

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DOT1L-mediated murine neuronal differentiation associates with H3K79me2 accumulation and preserves SOX2-enhancer accessibility

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A metabolic interplay coordinated by HLX regulates myeloid differentiation and AML through partly overlapping pathways.

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