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Publications

2021:

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

Heyl F, Backofen R.

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

 

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.

Costa F, Grün D, Backofen R.

Nat Commun  9(1):3685, 2018, doi: 10.1038/s41467-018-05988-7.

 

From cyanobacteria and algae to land plants: The RpaB/Ycf27 regulatory network in transition

Riediger M, Hihara Y, Hess, WR.

Perspectives in Phycology, Vol. 5 No. 1 (2018), p. 13 - 25

 

Protection from UV light is an evolutionarily conserved feature of the haematopoietic niche.

Kapp FG, Perlin JR, Hagedorn EJ, Gansner JM, Schwarz DE, O'Connell LA, Johnson NS, Amemiya C, Fisher DE, Wölfle U, Trompouki E, Niemeyer CM, Driever W, Zon LI.

Nature. 2018 Jun;558(7710):445-448. doi: 10.1038/s41586-018-0213-0. Epub 2018 Jun 13.

 

Bloody Zebrafish: Novel Methods in Normal and Malignant Hematopoiesis.

de Pater E, Trompouki E.

Front Cell Dev Biol. 2018 Oct 15;6:124. doi: 10.3389/fcell.2018.00124. eCollection 2018.

PMID: 30374440 

 

FateID infers cell fate bias in multipotent progenitors from single-cell RNA-seq data.

Herman JS, Sagar, Grün D.

Nat Methods. 2018 May;15(5):379-386. doi: 10.1038/nmeth.4662. Epub 2018 Apr 9.

PMID:29630061

 

High-Throughput Single-Cell RNA Sequencing and Data Analysis.

SagarHerman JS, Pospisilik JA, Grün D.

Methods Mol Biol. 2018;1766:257-283. doi: 10.1007/978-1-4939-7768-0_15.

PMID:29605858

 

The primary transcriptome of the fast-growing cyanobacterium Synechococcus elongatus UTEX 2973.

Tan X, Hou S, Song K, Georg J, Klähn S, Lu X, Hess WR.

Biotechnol Biofuels. 2018 Aug 4;11:218. doi: 10.1186/s13068-018-1215-8. eCollection 2018.

PMID:30127850