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Publications

list of RTG publications from 2017 to present

 

2024:

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

Hoffmann UALichtenberg ERogh SNBilger RReimann VHeyl FBackofen RSteglich CHess WR, Wilde A

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

 

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

du Halgouet A, Bruder KPeltokangas NDarbois A, Obwegs DSalou MThimme RHofmann MLantz 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:

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

Sagar

J Leuk Biol 00, 1-20. doi:10.1093/jleuko/qiad131.

 

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 SStazic DGeorg JOhtake SSakamaki YNumakura MAsayama MChibazakura TWilde ASteglich CHess 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

Pinter N, Glitzer D, Fahrner M, Fröhlich K, Johnson J, Grüning BA, Watschend B, Drepper F, Schilling O, Föll MC

J Proteome Res 2022, https://doi.org/10.1021/acs.jproteome.2c00051

 

Benchmarking of analysis strategies for data-independent acquisition proteomics using a large-scale dataset comprising inter-patient heterogeneity.

Fröhlich K, Brombacher E, Fahrner M, Vogele D, Kook L, Pinter N, Bronsert P, Timme-Bronsert S, Schmidt A, Bärenfaller K, Kreutz C, Schilling O.  

Nat Commun. 2022 13(1):2622. doi: 10.1038/s41467-022-30094-0. 

 

Paving Therapeutic Avenues for FOXG1 Syndrome: Untangling Genotypes and Phenotypes from a Molecular Perspective

Akol I, Gather F, Vogel T

Int J Mol Sci. 2022 23(2):954. doi: 10.3390/ijms23020954. 

 

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 MHecht 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 ATreppner MHermann 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

GigaScience. 2021 10(8):giab054. doi: 10.1093/gigascience/giab054

 

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

Nat Commun. 11(1):4111, 2020, doi: 10.1038/s41467-020-17873-3 

 

HRIBO - High-throughput analysis of bacterial ribosome profiling data

Gelhausen R, Svensson SL, Froschauer K, Heyl F, Hadjeras L, Sharma CM, Eggenhofer F, Backofen R

Bioinformatics btaa959., 2020, doi: 10.1093/bioinformatics/btaa959. 

 

Deciphering Cell Fate Decision by Integrated Single-Cell Sequencing Analysis

Sagar, Grün D

Annu Rev Biomed Data Sci. 3:1-22., 2020, doi: 10.1146/annurev-biodatasci-111419-091750. 

 

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

Westphal M, Sant P, Hauser AT, Jung M, Driever W 

Front Genet. 11:80, 2020 doi: 10.3389/fgene.2020.00080.

 

A single-cell RNA-sequencing training and analysis suite using the Galaxy framework

Tekman M, Batut B, Ostrovsky A, Antoniewski C, Clements D, Ramirez F, Etherington GJ, Hotz HR, Scholtalbers J, Mattning JR, Bellenger L, Doyle MA, Heydarian M, Huang N, Soranzo N, Moreno P, Mautner S, Paptheodorou I, Nekrutenko A, Taylor J, Blankenberg D, Backofen R, Grüning B

GigaScience 9:10,  2020, giaa102, doi: 10.1093/gigascience/giaa102

  

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

Ferrari F, Arrigoni L, Franz H, Izzo A, Butenko L, Trompouki E, Vogel T, Manke M

Nat Commun. 11:5200, 2020 doi:10.1038/s41467-020-19001-7

 

mRNA localization, reaction centre biogenesis and thylakoid membrane targeting in cyanobacteria

Mahbub M, Hemm L, Yang Y, Kaur R, Carmen H, Engl C, Huokko T, Riediger M, Watanabe S, Liu LN, Wilde A, Hess WR, Mullineaux CW

 

Stem cell ageing of the root apical meristem of Arabidopsis thaliana

Wein A, Le Gac AL, Laux T

Mech Ageing Dev. 111313, 2020; doi: 10.1016/j.mad.2020.111313.

 

AutoRELACS: automated generation and analysis of ultra-parallel ChIP-seq.

Arrigoni L, Ferrari F, Weller J, Bella C, Boehnisch U, Manke, T

Sci Rep. 10(1):12400, 2020. doi: 10.1038/s41598-020-69443-8. 

 

Gray de Cristoforis A, Ferrari F, Clotman F, Vogel T

Mol Brain. 13(1):85, 2020,   doi: 10.1186/s13041-020-00623-3.

 

Loss of the nuclear Wnt pathway effector TCF7L2 promotes migration and invasion of human colorectal cancer cells.

Wenzel J, Rose K, Haghighi EB, Lamprecht C, Rauen G, Freihen V, Kesselring R, Boerries M, Hecht A.

Oncogene. 2020, doi: 10.1038/s41388-020-1259-7. 

 

EBF1-deficient bone marrow stroma elicits persistent changes in HSC potential. 

Derecka M, Herman JS, Cauchy P, Ramamoorthy S, Lupar E, Grün D, Grosschedl R

Nat. Immunol. 21:261–273, 2020, doi: 10.1038/s41590-020-0595-7.


2019:

Revealing dynamics of gene expression variability in cell state space.

Grün D.

Nat Methods. 2019, doi: 10.1038/s41592-019-0632-3.

 

Biocomputational Analyses and Experimental Validation Identify the Regulon Controlled by the Redox-Responsive Transcription Factor RpaB.

Riediger M, Kadowaki T, Nagayama R, Georg J, Hihara Y, Hess WR.

iScience, 15:316-331, 2019, doi: 10.1016/j.isci.2019.04.033. 

 

Genome-wide mapping of DNA-binding sites identifies stemnessrelated genes as directly repressed targets of SNAIL1 in colorectal cancer cells.

Beyes S, Andrieux J, Schrempp M, Aicher D, Wenzel JAntón-García P, Boerries M, Hecht A.

Oncogene. 2019, doi: 10.1038/s41388-019-0905-4.

 

A human liver cell atlas reveals heterogeneity and epithelial progenitors.

Aizarani N, Saviano A, Sagar, Mailly L, Durand S, Herman JS, Pessaux P, Baumert TF, Grün D.

 

Mapping microglia states in the human brain through the integration of high-dimensional techniques.

Sankowski R, Böttcher C, Masuda T, Geirsdottir L, Sagar, Sindram E, Seredenina T, Muhs A, Scheiwe C, Shah MJ, Heiland DH, Schnell O, Grün D, Priller J, Prinz M.

Nat Neurosci. 22(12):2098-2110, 2019, doi: 10.1038/s41593-019-0532-y

 

Lineage Inference and Stem Cell Identity Prediction Using Single-Cell RNA-Sequencing Data.

Sagar, Grün D 

Methods Mol Biol 1975:277-301, 2019, doi: 10.1007/978-1-4939-9224-9_13. 


2018:

FOXG1 Regulates PRKAR2B Transcriptionally and Posttranscriptionally via miR200 in the Adult Hippocampus.

Weise SC, Arumugam G, Villarreal A, Videm P, Heidrich S, Nebel N, Dumit VI, Sananbenesi F, Reimann V, Craske M, Schilling O, Hess WR, Fischer A, Backofen R, Vogel T.

Mol Neurobiol. 2018, doi: 10.1007/s12035-018-1444-7. 

 

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

Piragyte I, Clapes T, Polyzou A, Klein Geltink RI, Lefkopoulos S, Yin N, Cauchy P, Curtis JD, Klaeylé L, Langa X, Beckmann CCA, Wlodarski MW, Müller P, Van Essen D, Rambold A, Kapp FG, Mione M, Buescher JM, Pearce EL, Polyzos A, Trompouki E.

Nat Commun. 9(1):3090, 2018 doi: 10.1038/s41467-018-05311-4.

 

GraphDDP: a graph-embedding approach to detect differentiation pathways in single-cell-data using prior class knowledge.

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