ACCELERATED RNA SPLICING DYNAMICS DURING ERYTHROID DIFFERENTIATION AMPLIFY MIS-SPLICING IN SF3B1-MUTANT MDS-RS von Moura, P., Mortera-Blanco, T., Hofman, I., Todisco, G., Kretzschmar, W., Björklund, A.-C., Creignou, M., Hagemann-Jensen, M., Ziegenhain, C., Granados, D., Barbosa, I., Walldin, G., Jansson, M., Mead, A., Lundin, V., Dimitriou, M., Yoshizato, T., Woll, P., Ogawa, S., Sandberg, R., Jacobsen, S.E., Hellstrom-Lindberg, E.

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Single-cell RNA counting at allele and isoform resolution using Smart-seq3 von Hagemann-Jensen, Michael, Ziegenhain, Christoph, Chen, Ping, Ramsköld, Daniel, Hendriks, Gert-Jan, Larsson, Anton J. M., Faridani, Omid R., Sandberg, Rickard

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BAMboozle removes genetic variation from human sequence data for open data sharing von Ziegenhain, Christoph, Sandberg, Rickard

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Scalable single-cell RNA sequencing from full transcripts with Smart-seq3xpress von Hagemann-Jensen, Michael, Ziegenhain, Christoph, Sandberg, Rickard

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A systematic evaluation of single cell RNA-seq analysis pipelines von Vieth, Beate, Parekh, Swati, Ziegenhain, Christoph, Enard, Wolfgang, Hellmann, Ines

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Comparative Analysis of Single-Cell RNA Sequencing Methods von Ziegenhain, Christoph, Vieth, Beate, Parekh, Swati, Reinius, Björn, Guillaumet-Adkins, Amy, Smets, Martha, Leonhardt, Heinrich, Heyn, Holger, Hellmann, Ines, Enard, Wolfgang

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Characterization of a novel dormant, drug resistant, stem cell subpopulation in acute lymphoblastic leukemia von Ebinger, S, Ozdemir, E, Tiedt, S, Ziegenhain, C, Castro-Alves, C, Enard, W, Jeremias, I

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zUMIs - A fast and flexible pipeline to process RNA sequencing data with UMIs von Parekh, Swati, Ziegenhain, Christoph, Vieth, Beate, Enard, Wolfgang, Hellmann, Ines

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Novel spike-ins for single-cell sequencing enable ground-truth RNA counting von Ziegenhain, C, Sandberg, R

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Sensitive and powerful single-cell RNA sequencing using mcSCRB-seq von Bagnoli, Johannes W., Ziegenhain, Christoph, Janjic, Aleksandar, Wange, Lucas E., Vieth, Beate, Parekh, Swati, Geuder, Johanna, Hellmann, Ines, Enard, Wolfgang

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Molecular spikes: a gold standard for single-cell RNA counting von Ziegenhain, Christoph, Hendriks, Gert-Jan, Hagemann-Jensen, Michael, Sandberg, Rickard

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Transcriptional kinetics and molecular functions of long noncoding RNAs von Johnsson, Per, Ziegenhain, Christoph, Hartmanis, Leonard, Hendriks, Gert-Jan, Hagemann-Jensen, Michael, Reinius, Björn, Sandberg, Rickard

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Prime-seq, efficient and powerful bulk RNA sequencing von Janjic, Aleksandar, Wange, Lucas E, Bagnoli, Johannes W, Geuder, Johanna, Nguyen, Phong, Richter, Daniel, Vieth, Beate, Vick, Binje, Jeremias, Irmela, Ziegenhain, Christoph, Hellmann, Ines, Enard, Wolfgang

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Tissue-specific RNA Polymerase II promoter-proximal pause release and burst kinetics in a Drosophila embryonic patterning network von Hunt, George, Vaid, Roshan, Pirogov, Sergei, Pfab, Alexander, Ziegenhain, Christoph, Sandberg, Rickard, Reimegård, Johan, Mannervik, Mattias

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Single-cell new RNA sequencing reveals principles of transcription at the resolution of individual bursts von Ramsköld, Daniel, Hendriks, Gert-Jan, Larsson, Anton J. M., Mayr, Juliane V., Ziegenhain, Christoph, Hagemann-Jensen, Michael, Hartmanis, Leonard, Sandberg, Rickard

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Low spatial structure and selection against secreted virulence factors attenuates pathogenicity in Pseudomonas aeruginosa von Granato, Elisa T., Ziegenhain, Christoph, Marvig, Rasmus L., Kümmerli, Rolf

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Transcriptional bursts explain autosomal random monoallelic expression and affect allelic imbalance von Larsson, Anton J. M., Ziegenhain, Christoph, Hagemann-Jensen, Michael, Reinius, Bjorn, Jacob, Tina, Dalessandri, Tim, Hendriks, Gert-Jan, Kasper, Maria, Sandberg, Rickard

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Ly6D+Siglec-H+ precursors contribute to conventional dendritic cells via a Zbtb46+Ly6D+ intermediary stage von Lutz, Konstantin, Musumeci, Andrea, Sie, Christopher, Dursun, Ezgi, Winheim, Elena, Bagnoli, Johannes, Ziegenhain, Christoph, Rausch, Lisa, Bergen, Volker, Luecken, Malte D., Oostendorp, Robert A. J., Schraml, Barbara U., Theis, Fabian J., Enard, Wolfgang, Korn, Thomas, Krug, Anne B.

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Alternative platelet differentiation pathways initiated by nonhierarchically related hematopoietic stem cells von Carrelha, Joana, Mazzi, Stefania, Winroth, Axel, Hagemann-Jensen, Michael, Ziegenhain, Christoph, Högstrand, Kari, Seki, Masafumi, Brennan, Margs S., Lehander, Madeleine, Wu, Bishan, Meng, Yiran, Markljung, Ellen, Norfo, Ruggiero, Ishida, Hisashi, Belander Strålin, Karin, Grasso, Francesca, Simoglou Karali, Christina, Aliouat, Affaf, Hillen, Amy, Chari, Edwin, Siletti, Kimberly, Thongjuea, Supat, Mead, Adam J., Linnarsson, Sten, Nerlov, Claus, Sandberg, Rickard, Yoshizato, Tetsuichi, Woll, Petter S., Jacobsen, Sten Eirik W.

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Erythroid Differentiation Enhances RNA Mis-Splicing in SF3B1-Mutant Myelodysplastic Syndromes with Ring Sideroblasts von Moura, PL, Mortera-Blanco, T, Hofman, IJ, Todisco, G, Kretzschmar, WW, Bjoerklund, AC, Creignou, M, Hagemann-Jensen, M, Ziegenhain, C, Granados, DC, 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

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