Tirier, S. M., Mallm, J. P., Steiger, S., Poos, A. M., Awwad, M., Giesen, N., Casiraghi, N., Susak, H., Bauer, K., Baumann, A., John, L., Seckinger, A., Hose, D., Müller-Tidow, C., Goldschmidt, H., Stegle, O., Hundemer, M., Weinhold, N., Raab, M. S., & Rippe, K. (2021). Subclone-specific microenvironmental impact and drug response in refractory multiple myeloma revealed by single-cell transcriptomics. Nature communications, 12(1), 6960. https://doi.org/10.1038/s41467-021-26951-z
Gurumurthy, R. K., Kumar, N., & Chumduri, C. (2021). Optimized protocol for isolation of high-quality single cells from the female mouse reproductive tract tissues for single-cell RNA sequencing. STAR protocols, 2(4), 100970. https://doi.org/10.1016/j.xpro.2021.100970
Büttner, M., Ostner, J., Müller, C. L., Theis, F. J., & Schubert, B. (2021). scCODA is a Bayesian model for compositional single-cell data analysis. Nature communications, 12(1), 6876. https://doi.org/10.1038/s41467-021-27150-6
Hickey, J. W., Neumann, E. K., Radtke, A. J., Camarillo, J. M., Beuschel, R. T., Albanese, A., McDonough, E., Hatler, J., Wiblin, A. E., Fisher, J., Croteau, J., Small, E. C., Sood, A., Caprioli, R. M., Angelo, R. M., Nolan, G. P., Chung, K., Hewitt, S. M., Germain, R. N., Spraggins, J. M., … Saka, S. K. (2021). Spatial mapping of protein composition and tissue organization: a primer for multiplexed antibody-based imaging. Nature methods, 10.1038/s41592-021-01316-y. Advance online publication. https://doi.org/10.1038/s41592-021-01316-y
Triana, S., Vonficht, D., Jopp-Saile, L., Raffel, S., Lutz, R., Leonce, D., Antes, M., Hernández-Malmierca, P., Ordoñez-Rueda, D., Ramasz, B., Boch, T., Jann, J. C., Nowak, D., Hofmann, W. K., Müller-Tidow, C., Hübschmann, D., Alexandrov, T., Benes, V., Trumpp, A., Paulsen, M., … Haas, S. (2021). Single-cell proteo-genomic reference maps of the hematopoietic system enable the purification and massive profiling of precisely defined cell states. Nature immunology, 10.1038/s41590-021-01059-0. Advance online publication. https://doi.org/10.1038/s41590-021-01059-0
Xu, Z., Hu, K., Bailey, P., Springfeld, C., Roth, S., Kurilov, R., Brors, B., Gress, T., Buchholz, M., An, J., Wei, K., Peccerella, T., Büchler, M. W., Hackert, T., & Neoptolemos, J. P. (2021). Clinical Impact of Molecular Subtyping of Pancreatic Cancer. Frontiers in cell and developmental biology, 9, 743908. https://doi.org/10.3389/fcell.2021.743908
Rausch, L., Lutz, K., Schifferer, M., Winheim, E., Gruber, R., Oesterhaus, E. F., Rinke, L., Hellmuth, J. C., Scherer, C., Muenchhoff, M., Mandel, C., Bergwelt-Baildon, M., Simons, M., Straub, T., Krug, A. B., Kranich, J., & Brocker, T. (2021). Binding of phosphatidylserine-positive microparticles by PBMCs classifies disease severity in COVID-19 patients. Journal of extracellular vesicles, 10(14), e12173. https://doi.org/10.1002/jev2.12173
Sun, N., Trajkovic-Arsic, M., Li, F., Wu, Y., Münch, C., Kunzke, T., Feuchtinger, A., Steiger, K., Schlitter, A. M., Weichert, W., Esposito, I., Siveke, J. T., & Walch, A. (2021). Native glycan fragments detected by MALDI mass spectrometry imaging are independent prognostic factors in pancreatic ductal adenocarcinoma. EJNMMI research, 11(1), 120. https://doi.org/10.1186/s13550-021-00862-y
Cable, J., Pei, D., Reid, L. M., Wang, X. W., Bhatia, S., Karras, P., Melenhorst, J. J., Grompe, M., Lathia, J. D., Song, E., Kuo, C. J., Zhang, N., White, R. M., Ma, S. K., Ma, L., Chin, Y. R., Shen, M. M., Ng, I., Kaestner, K. H., Zhou, L., … Weissman, I. L. (2021). Cancer stem cells: advances in biology and clinical translation-a Keystone Symposia report. Annals of the New York Academy of Sciences, 10.1111/nyas.14719. Advance online publication. https://doi.org/10.1111/nyas.14719
Glaser, L. V., Steiger, M., Fuchs, A., van Bömmel, A., Einfeldt, E., Chung, H. R., Vingron, M., & Meijsing, S. H. (2021). Assessing genome-wide dynamic changes in enhancer activity during early mESC differentiation by FAIRE-STARR-seq. Nucleic acids research, gkab1100. Advance online publication. https://doi.org/10.1093/nar/gkab1100
Gu, Z., & Hübschmann, D. (2021). spiralize: an R package for Visualizing Data on Spirals. Bioinformatics (Oxford, England), btab778. Advance online publication. https://doi.org/10.1093/bioinformatics/btab778
ElHarouni, D., Berker, Y., Peterziel, H., Gopisetty, A., Turunen, L., Kreth, S., Stainczyk, S. A., Oehme, I., Pietiäinen, V., Jäger, N., Witt, O., Schlesner, M., & Oppermann, S. (2021). iTReX: Interactive exploration of mono- and combination therapy dose response profiling data. Pharmacological research, 105996. Advance online publication. https://doi.org/10.1016/j.phrs.2021.105996
Cardozo Gizzi, AM. A Shift in Paradigms: Spatial Genomics Approaches to Reveal Single-Cell Principles of Genome Organization. Front Genet. 2021;12 :780822. doi: 10.3389/fgene.2021.780822. PubMed PMID:34868269 PubMed Central PMC8640135.
Seo, S, Mace, EM. Diversity of human NK cell developmental pathways defined by single-cell analyses. Curr Opin Immunol. 2021;74 :106-111. doi: 10.1016/j.coi.2021.11.001. PubMed PMID:34861544 .
Wang, YS, Guo, J. Multiplexed Single-Cell in situ RNA Profiling. Front Mol Biosci. 2021;8 :775410. doi: 10.3389/fmolb.2021.775410. PubMed PMID:34859055 PubMed Central PMC8632036.
James, KR, Elmentaite, R, Teichmann, SA, Hold, GL. Redefining intestinal immunity with single-cell transcriptomics. Mucosal Immunol. 2021; :. doi: 10.1038/s41385-021-00470-y. PubMed PMID:34848830 PubMed Central PMC8630196.
Yang, P, Huang, H, Liu, C. Feature selection revisited in the single-cell era. Genome Biol. 2021;22 (1):321. doi: 10.1186/s13059-021-02544-3. PubMed PMID:34847932 PubMed Central PMC8638336.
Search PubMedZhang, Y., An, C., Zhang, Y., Zhang, H., Mohammad, A. F., Li, Q., Liu, W., Shao, F., Sui, J., Ren, C., Sun, K., Cheng, F., Liu, J., & Wang, H. (2021). Microfluidic-templating alginate microgels crosslinked by different metal ions as engineered microenvironment to regulate stem cell behavior for osteogenesis. Materials science & engineering. C, Materials for biological applications, 131, 112497. https://doi.org/10.1016/j.msec.2021.112497
Muskovic, W., & Powell, J. E. (2021). DropletQC: improved identification of empty droplets and damaged cells in single-cell RNA-seq data. Genome biology, 22(1), 329. https://doi.org/10.1186/s13059-021-02547-0
Hutson, N., Zhan, F., Graham, J., Murakami, M., Zhang, H., Ganaparti, S., Hu, Q., Yan, L., Ma, C., Liu, S., Xie, J., & Wei, L. (2021). An adaptive method of defining negative mutation status for multi-sample comparison using next-generation sequencing. BMC medical genomics, 14(Suppl 2), 32. https://doi.org/10.1186/s12920-021-00880-8
Zhang, J., Liu, L., Xu, T., Zhang, W., Zhao, C., Li, S., Li, J., Rao, N., & Le, T. D. (2021). Exploring cell-specific miRNA regulation with single-cell miRNA-mRNA co-sequencing data. BMC bioinformatics, 22(1), 578. https://doi.org/10.1186/s12859-021-04498-6
Dreyer, A. M., & Rieger, J. W. (2021). High-gamma mirror activity patterns in the human brain during reach-to-grasp movement observation, retention, and execution-An MEG study. PloS one, 16(12), e0260304. https://doi.org/10.1371/journal.pone.0260304
Yao, T., Rudak, P. T., Laumont, C. M., Michaud, A. R., Rashu, R., Knier, N. N., Foster, P. J., McWilliam, H., Villadangos, J. A., Nelson, B. H., DiMattia, G. E., Shepherd, T. G., & Haeryfar, S. (2021). MAIT cells accumulate in ovarian cancer-elicited ascites where they retain their capacity to respond to MR1 ligands and cytokine cues. Cancer immunology, immunotherapy : CII, 10.1007/s00262-021-03118-9. Advance online publication. https://doi.org/10.1007/s00262-021-03118-9