Christoph Ziegenhain

Publikationer
Forskningsbidrag
Populärvetenskap och samverkan

Artiklar

Article: CELL SYSTEMS. 2024;15(2):149-165.e10
Clonally heritable gene expression imparts a layer of diversity within cell types
Mold JE; Weissman MH; Ratz M; Hagemann-Jensen M; Hard J; Eriksson C-J; Toosi H; Berghenstrahle J; Ziegenhain C; von Berlin L; Martin M; Blom K; Lagergren J; Lundeberg J; Sandberg R; Michaeeurolsson J; Frisen J
Article: CANCER RESEARCH. 2024;84(2):211-225
Erythroid Differentiation Enhances RNA Mis-Splicing in SF3B1-Mutant Myelodysplastic Syndromes with Ring Sideroblasts
Moura PL; Mortera-Blanco T; Hofman IJ; Todisco G; Kretzschmar WW; Bjoerklund A-C; Creignou M; Hagemann-Jensen M; Ziegenhain C; Cabrerizo Granados D; Barbosa I; Walldin G; Jansson M; Ashley N; Mead AJ; Lundin V; Dimitriou M; Yoshizato T; Woll PS; Ogawa S; Sandberg R; Jacobsen SEW; Hellstrom-Lindberg E
Article: GENOME BIOLOGY. 2024;25(1):2
Tissue-specific RNA Polymerase II promoter-proximal pause release and burst kinetics in a Drosophila embryonic patterning network
Hunt G; Vaid R; Pirogov S; Pfab A; Ziegenhain C; Sandberg R; Reimegard J; Mannervik M
Article: NATURE AGING. 2023;3(11):1430-1445
Spatial and single-cell profiling of the metabolome, transcriptome and epigenome of the aging mouse liver
Nikopoulou C; Kleinenkuhnen N; Parekh S; Sandoval T; Ziegenhain C; Schneider F; Giavalisco P; Donahue K-F; Vesting AJ; Kirchner M; Bozukova M; Vossen C; Altmueller J; Wunderlich T; Sandberg R; Kondylis V; Tresch A; Tessarz P
Article: NATURE BIOTECHNOLOGY. 2022;40(10):1452-1457
Scalable single-cell RNA sequencing from full transcripts with Smart-seq3xpress
Hagemann-Jensen M; Ziegenhain C; Sandberg R
Article: LEUKEMIA. 2022;36(9):2281-2292
PARP14 is a novel target in STAT6 mutant follicular lymphoma
Mentz M; Keay W; Strobl CD; Antoniolli M; Adolph L; Heide M; Lechner A; Haebe S; Osterode E; Kridel R; Ziegenhain C; Wange LE; Hildebrand JA; Shree T; Silkenstedt E; Staiger AM; Ott G; Horn H; Szczepanowski M; Richter J; Levy R; Rosenwald A; Enard W; Zimber-Strobl U; Von Bergwelt-Baildon M; Hiddemann W; Klapper W; Schmidt-Supprian M; Rudelius M; Bararia D; Passerini V; Weigert O
Article: NATURE COMMUNICATIONS. 2022;13(1):3456
Ly6D⁺Siglec-H⁺ precursors contribute to conventional dendritic cells via a Zbtb46⁺Ly6D⁺ intermediary stage
Lutz K; Musumeci A; Sie C; Dursun E; Winheim E; Bagnoli J; Ziegenhain C; Rausch L; Bergen V; Luecken MD; Oostendorp RAJ; Schraml BU; Theis FJ; Enard W; Korn T; Krug AB
Article: NATURE METHODS. 2022;19(5):560-566
Molecular spikes: a gold standard for single-cell RNA counting
Ziegenhain C; Hendriks G-J; Hagemann-Jensen M; Sandberg R
Article: GENOME BIOLOGY. 2022;23(1):88
Prime-seq, efficient and powerful bulk RNA sequencing
Janjic A; Wange LE; Bagnoli JW; Geuder J; Nguyen P; Richter D; Vieth B; Vick B; Jeremias I; Ziegenhain C; Hellmann I; Enard W
Article: NATURE GENETICS. 2022;54(3):306-317
Transcriptional kinetics and molecular functions of long noncoding RNAs
Johnsson P; Ziegenhain C; Hartmanis L; Hendriks G-J; Hagemann-Jensen M; Reinius B; Sandberg R
Article: NATURE COMMUNICATIONS. 2021;12(1):6216
BAMboozle removes genetic variation from human sequence data for open data sharing
Ziegenhain C; Sandberg R
Article: PLOS COMPUTATIONAL BIOLOGY. 2021;17(3):e1008772
Transcriptional bursts explain autosomal random monoallelic expression and affect allelic imbalance
Larsson AJM; Ziegenhain C; Hagemann-Jensen M; Reinius B; Jacob T; Dalessandri T; Hendriks G-J; Kasper M; Sandberg R
Article: NATURE CELL BIOLOGY. 2021;23(1):23-31
Non-canonical Wnt/PCP signalling regulates intestinal stem cell lineage priming towards enteroendocrine and Paneth cell fates
Boettcher A; Buettner M; Tritschler S; Sterr M; Aliluev A; Oppenlaender L; Burtscher I; Sass S; Irmler M; Beckers J; Ziegenhain C; Enard W; Schamberger AC; Verhamme FM; Eickelberg O; Theis FJ; Lickert H
Article: NATURE COMMUNICATIONS. 2020;11(1):5972
Recent evolution of a TET-controlled and DPPA3/STELLA-driven pathway of passive DNA demethylation in mammals
Mulholland CB; Nishiyama A; Ryan J; Nakamura R; Yigit M; Glueck IM; Trummer C; Qin W; Bartoschek MD; Traube FR; Parsa E; Ugur E; Modic M; Acharya A; Stolz P; Ziegenhain C; Wierer M; Enard W; Carell T; Lamb DC; Takeda H; Nakanashi M; Bultmann S; Leonhardt H
Article: NATURE BIOTECHNOLOGY. 2020;38(6):708-714
Single-cell RNA counting at allele and isoform resolution using Smart-seq3
Hagemann-Jensen M; Ziegenhain C; Chen P; Ramskold D; Hendriks G-J; Larsson AJM; Faridani OR; Sandberg R
Article: NATURE BIOTECHNOLOGY. 2020;38(6):747-755
Benchmarking single-cell RNA-sequencing protocols for cell atlas projects
Mereu E; Lafzi A; Moutinho C; Ziegenhain C; McCarthy DJ; Alvarez-Varela A; Batlle E; Sagar; Gruen D; Lau JK; Boutet SC; Sanada C; Ooi A; Jones RC; Kaihara K; Brampton C; Talaga Y; Sasagawa Y; Tanaka K; Hayashi T; Braeuning C; Fischer C; Sauers S; Trefzer T; Conrad C; Adiconis X; Nguyen LT; Regev A; Levin JZ; Parekh S; Janjic A; Wange LE; Bagnoli JW; Enard W; Gut M; Sandberg R; Nikaido I; Gut I; Stegle O; Heyn H
Article: JOURNAL OF CLINICAL INVESTIGATION. 2020;130(6):3270-3286
c-Rel gain in B cells drives germinal center reactions and autoantibody production
Kober-Hasslacher M; Oh-Strauss H; Kumar D; Soberon V; Diehl C; Lech M; Engleitner T; Katab E; Fernandez-Saiz J; Piontek G; Li H; Menze B; Ziegenhain C; Enard W; Rad R; Boettcher JP; Anders H-J; Rudelius M; Schmidt-Supprian M
Article: NATURE COMMUNICATIONS. 2019;10(1):4667
A systematic evaluation of single cell RNA-seq analysis pipelines
Vieth B; Parekh S; Ziegenhain C; Enard W; Hellmann I
Article: JOURNAL OF NATURAL PRODUCTS. 2019;82(7):1961-1970
Chivosazole A Modulates Protein Protein Interactions of Actin
Wang S; Gegenfurtner FA; Crevenna AH; Ziegenhain C; Kliesmete Z; Enard W; Mueller R; Vollmar AM; Schneider S; Zahler S
Article: SCIENTIFIC REPORTS. 2019;9(1):9731
Actin stabilizing compounds show specific biological effects due to their binding mode
Wang S; Crevenna AH; Ugur I; Marion A; Antes I; Kazmaier U; Hoyer M; Lamb DC; Gegenfurtner F; Kliesmetes Z; Ziegenhain C; Enard W; Vollmar A; Zahler S
Article: HUMAN MOLECULAR GENETICS. 2019;28(5):701-717
Altered social behavior in mice carrying a cortical Foxp2 deletion
Medvedeva VP; Rieger MA; Vieth B; Mombereau C; Ziegenhain C; Ghosh T; Cressant A; Enard W; Granon S; Dougherty JD; Groszer M
Article: CELLULAR AND MOLECULAR LIFE SCIENCES. 2018;75(24):4539-4555
Transcriptional effects of actin-binding compounds: the cytoplasm sets the tone
Gegenfurtner FA; Zisis T; Al Danaf N; Schrimpf W; Kliesmete Z; Ziegenhain C; Enard W; Kazmaier U; Lamb DC; Vollmar AM; Zahler S
Article: THE ISME JOURNAL. 2018;12(12):2907-2918
Low spatial structure and selection against secreted virulence factors attenuates pathogenicity in Pseudomonas aeruginosa
Granato ET; Ziegenhain C; Marvig RL; Kummerli R
Article: NATURE COMMUNICATIONS. 2018;9(1):2937
Sensitive and powerful single-cell RNA sequencing using mcSCRB-seq
Bagnoli JW; Ziegenhain C; Janjic A; Wange LE; Vieth B; Parekh S; Geuder J; Hellmann I; Enard W
Article: BRIEFINGS IN FUNCTIONAL GENOMICS. 2018;17(4):220-232
Quantitative single-cell transcriptomics
Ziegenhain C; Vieth B; Parekh S; Hellmann I; Enard W
Article: GIGASCIENCE. 2018;7(6):giy059
zUMIs - A fast and flexible pipeline to process RNA sequencing data with UMIs
Parekh S; Ziegenhain C; Vieth B; Enard W; Hellmann I
Article: JOURNAL OF CELL SCIENCE. 2018;131(10):jcs212886
Micropatterning as a tool to identify regulatory triggers and kinetics of actin-mediated endothelial mechanosensing
Gegenfurtner FA; Jahn B; Wagner H; Ziegenhain C; Enard W; Geistlinger L; Raedler JO; Vollmar AM; Zahler S
Article: NATURE. 2018;554(7690):62-68
Evolutionary routes and KRAS dosage define pancreatic cancer phenotypes
Mueller S; Engleitner T; Maresch R; Zukowska M; Lange S; Kaltenbacher T; Konukiewitz B; Oellinger R; Zwiebel M; Strong A; Yen H-Y; Banerjee R; Louzada S; Fu B; Seidler B; Goetzfried J; Schuck K; Hassan Z; Arbeiter A; Schoenhuber N; Klein S; Veltkamp C; Friedrich M; Rad L; Barenboim M; Ziegenhain C; Hess J; Dovey OM; Eser S; Parekh S; Constantino-Casas F; de la Rosa J; Sierra MI; Fraga M; Mayerle J; Kloeppel G; Cadinanos J; Liu P; Vassiliou G; Weichert W; Steiger K; Enard W; Schmid RM; Yang F; Unger K; Schneider G; Varela I; Bradley A; Saur D; Rad R
Article: ONCOTARGET. 2017;8(65):108738-108759
Azacitidine combined with the selective FLT3 kinase inhibitor crenolanib disrupts stromal protection and inhibits expansion of residual leukemia-initiating cells in FLT3-ITD AML with concurrent epigenetic mutations
Garz A-K; Wolf S; Grath S; Gaidzik V; Habringer S; Vick B; Rudelius M; Ziegenhain C; Herold S; Weickert M-T; Smets M; Peschel C; Oostendorp RAJ; Bultmann S; Jeremias I; Thiede C; Doehner K; Keller U; Goetze KS
Article: PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. 2017;114(45):E9579-E9588
GATA2/3-TFAP2A/C transcription factor network couples human pluripotent stem cell differentiation to trophectoderm with repression of pluripotency
Krendl C; Shaposhnikov D; Rishko V; Ori C; Ziegenhain C; Sass S; Simon L; Mueller NS; Straub T; Brooks KE; Chavez SL; Enard W; Theis FJ; Drukker M
Article: BIOINFORMATICS. 2017;33(21):3486-3488
powsimR: power analysis for bulk and single cell RNA-seq experiments
Vieth B; Ziegenhain C; Parekh S; Enard W; Hellmann I
Journal article: EXPERIMENTAL HEMATOLOGY. 2017;53:s73
DECLINED PRESENTATION THE STANDARD TREATMENT OF ACUTE LYMPHOBLASTIC LEUKEMIA (ALL) IS BASED ON POLYCHEMOTHERAPY
Oezdemir EZ; Ebinger S; Ziegenhain C; Enard W; Jeremias I
Article: NATURE GENETICS. 2017;49(5):742-752
Chromatin-remodeling factor SMARCD2 regulates transcriptional networks controlling differentiation of neutrophil granulocytes
Witzel M; Petersheim D; Fan Y; Bahrami E; Racek T; Rohlfs M; Puchalka J; Mertes C; Gagneur J; Ziegenhain C; Enard W; Stray-Pedersen A; Arkwright PD; Abboud MR; Pazhakh V; Lieschke GJ; Krawitz PM; Dahlhoff M; Schneider MR; Wolf E; Horny H-P; Schmidt H; Schaffer AA; Klein C
Article: MOLECULAR CELL. 2017;65(4):631-643.e4
Comparative Analysis of Single-Cell RNA Sequencing Methods
Ziegenhain C; Vieth B; Parekh S; Reinius B; Guillaumet-Adkins A; Smets M; Leonhardt H; Heyn H; Hellmann I; Enard W
Article: JOURNAL OF EXPERIMENTAL MEDICINE (JEM). 2017;214(1):165-181
Niche WNT5A regulates the actin cytoskeleton during regeneration of hematopoietic stem cells
Schreck C; Istvanffy R; Ziegenhain C; Sippenauer T; Ruf F; Henkel L; Gaertner F; Vieth B; Florian MC; Mende N; Taubenberger A; Prendergast A; Wagner A; Pagel C; Grziwok S; Goetze KS; Guck J; Dean DC; Massberg S; Essers M; Waskow C; Geiger H; Schiemann M; Peschel C; Enard W; Oostendorp RAJ
Article: CANCER CELL. 2016;30(6):849-862
Characterization of Rare, Dormant, and Therapy-Resistant Cells in Acute Lymphoblastic Leukemia
Ebinger S; Oezdemir EZ; Ziegenhain C; Tiedt S; Alves CC; Grunert M; Dworzak M; Lutz C; Turati VA; Enver T; Horny H-P; Sotlar K; Parekh S; Spiekermann K; Hiddemann W; Schepers A; Polzer B; Kirsch S; Hoffmann M; Knapp B; Hasenauer J; Pfeifer H; Panzer-Gruemayer R; Enard W; Gires O; Jeremias I
Article: SCIENTIFIC REPORTS. 2016;6:25533
The impact of amplification on differential expression analyses by RNA-seq
Parekh S; Ziegenhain C; Vieth B; Enard W; Hellmann I
Article: AIDS. 2015;29(10):1147-1159
A new model for post-integration latency in macroglial cells to study HIV-1 reservoirs of the brain
Schneider M; Tigges B; Meggendorfer M; Helfer M; Ziegenhain C; Brack-Werner R
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Preprint: BIORXIV. 2024;BIORXIV
Compound models and Pearson residuals for single-cell RNA-seq data without UMIs.
Lause J; Ziegenhain C; Hartmanis L; Berens P; Kobak D
Letter: CELL RESEARCH. 2023;33(11):883-886
Platelet and myeloid lineage biases of transplanted single perinatal mouse hematopoietic stem cells
Stralin KB; Carrelha J; Winroth A; Ziegenhain C; Hagemann-Jensen M; Kettyle LM; Hillen A; Hogstrand K; Markljung E; Grasso F; Seki M; Mazzi S; Meng Y; Wu B; Chari E; Lehander M; Sandberg R; Woll PS; Jacobsen SEW
Editorial comment: NATURE METHODS. 2022;19(5):530-531
Novel spike-ins for single-cell sequencing enable ground-truth RNA counting
Ziegenhain C; Sandberg R
Corrigendum: NATURE CELL BIOLOGY. 2021;23(5):566-576
Non-canonical Wnt/PCP signalling regulates intestinal stem cell lineage priming towards enteroendocrine and Paneth cell fates (vol 23, pg 23, 2021)
Bottcher A; Buttner M; Tritschler S; Sterr M; Aliluev A; Oppenlander L; Burtscher I; Sass S; Irmler M; Beckers J; Ziegenhain C; Enard W; Schamberger AC; Verhamme FM; Eickelberg O; Theis FJ; Lickert H
Corrigendum: NATURE COMMUNICATIONS. 2020;11(1):6443
Recent evolution of a TET-controlled and DPPA3/STELLA-driven pathway of passive DNA demethylation in mammals (vol 11, pg 5972, 2020)
Mulholland CB; Nishiyama A; Ryan J; Nakamura R; Yigit M; Gluck IM; Trummer C; Qin W; Bartoschek MD; Traube FR; Parsa E; Ugur E; Modic M; Acharya A; Stolz P; Ziegenhain C; Wierer M; Enard W; Carell T; Lamb DC; Takeda H; Nakanishi M; Bultmann S; Leonhardt H

Forskningsbidrag

Decoding the interplay of regulation and stochasticity in alternative mRNA splicing
Swedish Research Council
1 January 2023 - 31 December 2026

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