bioRxiv Channel: Human Cell Atlas
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This feed contains articles for bioRxiv Channel "Human Cell Atlas"
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https://biorxiv.org
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A cellular census of healthy lung and asthmatic airway wall identifies novel cell states in health and disease
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https://biorxiv.org/cgi/content/short/527408v1?rss=1"
Vieira Braga, F. A.Kar, G.Berg, M.Carpaij, O. A.Polanski, K.Simon, L. M.Brouwer, S.Gomes, T.Hesse, L.Jiang, J.Fasouli, E. S.Efremova, M.Vento-Tormo, R.Affleck, K.Palit, S.Strzelecka, P.Firth, H. V.Mahbubani, K. T.Cvejic, A.Meyer, K. B.Saeb-Parsy, K.Luinge, M.Brandsma, C.-A.Timens, W.Angelidis, I.Strunz, M.Koppelman, G. H.van Oosterhout, A. J.Schiller, H. B.Theis, F. J.van den Berge, M.Nawijn, M. C.Teichmann, S. A.2019-01-23doi:10.1101/527408Cold Spring Harbor Laboratory Press2019-01-23
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Conserved cell types with divergent features between human and mouse cortex
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https://biorxiv.org/cgi/content/short/384826v1?rss=1"
Hodge, R. D.Bakken, T. E.Miller, J. A.Smith, K. A.Barkan, E. R.Graybuck, L. T.Close, J. L.Long, B.Penn, O.Yao, Z.Eggermont, J.Hollt, T.Levi, B. P.Shehata, S. I.Aevermann, B.Beller, A.Bertagnolli, D.Brouner, K.Casper, T.Cobbs, C.Dalley, R.Dee, N.Ding, S.-L.Ellenbogen, R. G.Fong, O.Garren, E.Goldy, J.Gwinn, R. P.Hirschstein, D.Keene, C. D.Keshk, M.Ko, A. L.Lathia, K.Mahfouz, A.Maltzer, Z.McGraw, M.Nguyen, T. N.Nyhus, J.Ojemann, J. G.Oldre, A.Parry, S.Reynolds, S.Rimorin, C.Shapovalova, N. V.Somasundaram, S.2018-08-05doi:10.1101/384826Cold Spring Harbor Laboratory Press2018-08-05
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Reconstructing the human first trimester fetal-maternal interface using single cell transcriptomics
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https://biorxiv.org/cgi/content/short/429589v1?rss=1"
Vento-Tormo, R.Efremova, M.Botting, R. A.Turco, M. Y.Vento-Tormo, M.Meyer, K. B.Park, J.Stephenson, E.Polanski, K.Payne, R. P.Goncalves, A.Zou, A.Henriksson, J.Wood, L.Lisgo, S.Filby, A.Wright, G. J.Stubbington, M. J.Haniffa, M.Moffett, A.Teichmann, S. A.2018-09-29doi:10.1101/429589Cold Spring Harbor Laboratory Press2018-09-29
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Palantir characterizes cell fate continuities in human hematopoiesis
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https://biorxiv.org/cgi/content/short/385328v1?rss=1"
Setty, M.Kiseliovas, V.Levine, J.Gayoso, A.Mazutis, L.Pe'er, D.2018-08-05doi:10.1101/385328Cold Spring Harbor Laboratory Press2018-08-05
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Single-Cell Transcriptomic Analysis of Human Lung Reveals Complex Multicellular Changes During Pulmonary Fibrosis
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https://biorxiv.org/cgi/content/short/296608v1?rss=1"
Reyfman, P. A.Walter, J. M.Joshi, N.Anekalla, K. R.McQuattie-Pimentel, A. C.Chiu, S.Fernandez, R.Akbarpour, M.Chen, C.-I.Ren, Z.Verma, R.Abdala-Valencia, H.Nam, K.Chi, M.Han, S.Gonzalez-Gonzalez, F. J.Soberanes, S.Watanabe, S.Williams, K. J. N.Flozak, A. S.Nicholson, T. T.Morgan, V. K.Hrusch, C. L.Guzy, R. D.Bonham, C. A.Sperling, A. I.Bag, R.Hamanaka, R. B.Mutlu, G. M.Yeldandi, A. V.Marshall, S. A.Shilatifard, A.Amaral, L. A. N.Perlman, H.Sznajder, J. I.Winter, D. R.Hinchcliff, M.Argento, A. C.Gillespie, C. T.Dematt2018-04-06doi:10.1101/296608Cold Spring Harbor Laboratory Press2018-04-06
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Rewiring of the cellular and inter-cellular landscape of the human colon during ulcerative colitis
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https://biorxiv.org/cgi/content/short/455451v1?rss=1"
Smillie, C. S.Biton, M.Ordovas-Montanes, J.Sullivan, K. M.Burgin, G.Graham, D. B.Herbst, R. H.Rogel, N.Slyper, M.Waldman, J.Sud, M.Andrews, E.Haber, A. L.Vickovic, S.Dionne, D.Nguyen, L. T.Villani, A. C.Hofree, M.Creasey, E. A.Huang, H.Rozenblatt-Rosen, O.Garber, J. J.Khalili, H.Desch, A. N.Daly, M. J.Ananthakrishnan, A. N.Shalek, A. K.Xavier, R. J.Regev, A.2018-10-29doi:10.1101/455451Cold Spring Harbor Laboratory Press2018-10-29
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Benchmarking Single-Cell RNA Sequencing Protocols for Cell Atlas Projects
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https://biorxiv.org/cgi/content/short/630087v1?rss=1"
Mereu, E.Lafzi, A.Moutinho, C.Ziegenhain, C.MacCarthy, D. J.Alvarez, A.Batlle, E.Sagar,Grün, D.Lau, J. K.Boutet, S.Sanada, C.Ooi, A.Jones, R. C.Kaihara, K.Brampton, C.Talaga, Y.Sasagawa, Y.Tanaka, K.Hayashi, T.Nikaido, I.Fischer, C.Sauer, S.Trefzer, T.Conrad, C.Adiconis, X.Nguyen, L. T.Regev, A.Levin, J. Z.Janjic, A.Wange, L. E.Bagnoli, J. W.Parekh, S.Enard, W.Gut, M.Sandberg, R.Gut, I.Stegle, O.Heyn, H.2019-05-13doi:10.1101/630087Cold Spring Harbor Laboratory Press2019-05-13
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Systematic comparative analysis of single cell RNA-sequencing methods
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https://biorxiv.org/cgi/content/short/632216v1?rss=1"
Ding, J.Adiconis, X.Simmons, S. K.Kowalczyk, M. S.Hession, C. C.Marjanovic, N. D.Hughes, T. K.Wadsworth, M. H.Burks, T.Nguyen, L. T.Kwon, J. Y. H.Barak, B.Ge, W.Kedaigle, A. J.Carroll, S.Li, S.Hacohen, N.Rozenblatt-Rosen, O.Shalek, A. K.Villani, A.-C.Regev, A.Levin, J. Z.2019-05-09doi:10.1101/632216Cold Spring Harbor Laboratory Press2019-05-09
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Nuclei multiplexing with barcoded antibodies for single-nucleus genomics
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https://biorxiv.org/cgi/content/short/476036v1?rss=1"
Gaublomme, J. T.Li, B.McCabe, C.Knecht, A.Drokhlyansky, E.Van Wittenberghe, N.Waldman, J.Dionne, D.Nguyen, L.De Jager, P.Yeung, B.Zhao, X.Habib, N.Rozenblatt-Rosen, O.Regev, A.2018-11-23doi:10.1101/476036Cold Spring Harbor Laboratory Press2018-11-23
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Molecular architecture of the mouse nervous system
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https://biorxiv.org/cgi/content/short/294918v1?rss=1"
Zeisel, A.Hochgerner, H.Lonnerberg, P.Johnsson, A.Memic, F.van der Zwan, J.Haring, M.Braun, E.Borm, L.La Manno, G.Codeluppi, S.Furlan, A.Skene, N.Harris, K. D.Hjerling Leffler, J.Arenas, E.Ernfors, P.Marklund, U.Linnarsson, S.2018-04-05doi:10.1101/294918Cold Spring Harbor Laboratory Press2018-04-05
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A Human Liver Cell Atlas: Revealing Cell Type Heterogeneity and Adult Liver Progenitors by Single-Cell RNA-sequencing
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https://biorxiv.org/cgi/content/short/649194v1?rss=1"
Aizarani, N.Saviano, A.Sagar,Mailly, L.Durand, S.Pessaux, P.Baumert, T. F.Grün, D.2019-05-24doi:10.1101/649194Cold Spring Harbor Laboratory Press2019-05-24
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Decoding the development of the blood and immune systems during human fetal liver haematopoiesis
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https://biorxiv.org/cgi/content/short/654210v1?rss=1"
Popescu, D.-M.Botting, R. A.Stephenson, E.Green, K.Jardine, L.Calderbank, E. F.Efremova, M.Acres, M.Maunder, D.Vegh, P.Goh, I.Gitton, Y.Park, J.Polanski, K.Vento-Tormo, R.Miao, Z.Rowell, R.McDonald, D.Fletcher, J.Dixon, D.Poyner, E.Reynolds, G.Mather, M.Moldovan, C.Mamanova, L.Greig, F.Young, M. D.Meyer, K.Lisgo, S.Bacardit, J.Fuller, A.Millar, B.Innes, B.Lindsay, S.Stubbington, M. J. T.Kowalczyk, M. D.Li, B. D.Ashenbrg, O.Tabaka, M. D.Dionne, D.Tickle, T. L.Slyper, M.Rozenblatt-Rosen, O.Filby, A.Villani, A2019-05-31doi:10.1101/654210Cold Spring Harbor Laboratory Press2019-05-31
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Generation of human neural retina transcriptome atlas by single cell RNA sequencing
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https://biorxiv.org/cgi/content/short/425223v1?rss=1"
Lukowski, S.Lo, C.Sharov, A.Nguyen, Q.Fang, L.Hung, S.Zhu, L.Zhang, T.Nguyen, T.Senabouth, A.Jabbari, J.Welby, E.Sowden, J.Waugh, H.Mackey, A.Pollock, G.Lamb, T.Wang, P.-Y.Hewitt, A.Gillies, M.Powell, J.Wong, R.2018-09-24doi:10.1101/425223Cold Spring Harbor Laboratory Press2018-09-24
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Single cell transcriptome atlas of immune cells in human small intestine and in celiac disease
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https://biorxiv.org/cgi/content/short/721258v1?rss=1"
Stunnenberg, H.Atlasy, N.Bujko, A.Brazda, P. B.Janssen-Megens, E.Bakkenvold, E. S.Jahnsen, J.Jahsen, F.2019-08-01doi:10.1101/721258Cold Spring Harbor Laboratory Press2019-08-01
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Single nucleus RNA sequencing maps acinar cell states in a human pancreas cell atlas
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https://biorxiv.org/cgi/content/short/733964v1?rss=1"
Tosti, L.Hang, Y.Trefzer, T.Steiger, K.Ten, F. W.Lukassen, S.Ballke, S.Kuehl, A. A.Spieckermann, S.Bottino, R.Weichert, W.Kim, S. K.Eils, R.Conrad, C.2019-08-14doi:10.1101/733964Cold Spring Harbor Laboratory Press2019-08-14
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Gene set inference from single-cell sequencing data using a hybrid of matrix factorization and variational autoencoders
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https://biorxiv.org/cgi/content/short/740415v1?rss=1"
Lukassen, S.Ten, F. W.Eils, R.Conrad, C.2019-08-20doi:10.1101/740415Cold Spring Harbor Laboratory Press2019-08-20
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Lung, spleen and oesophagus tissue remains stable for scRNAseq in cold preservation
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https://biorxiv.org/cgi/content/short/741405v1?rss=1"
Madissoon, E.Wilbrey-Clark, A. L.Miragaia, R. J.Saeb-Parsy, K.Mahbubani, K. T.Georgakopoulos, N.Harding, P.Polanski, K.Nowicki-Osuch, K.Fitzgerald, R. C.Loudon, K. W.Ferdinand, J. R.Clatworthy, M. R.Tsingene, A.van Dongen, S.Dabrowska, M.Patel, M.Stubbington, M. J.Teichmann, S.Stegle, O.Meyer, K. B.2019-08-31doi:10.1101/741405Cold Spring Harbor Laboratory Press2019-08-31
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The enteric nervous system of the human and mouse colon at a single-cell resolution
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https://biorxiv.org/cgi/content/short/746743v1?rss=1"
Drokhlyansky, E.Smillie, C. S.Van Wittenberghe, N.Ericsson, M.Griffin, G. K.Dionne, D.Cuoco, M. S.Goder-Reiser, M. N.Sharova, T.Aguirre, A. J.Boland, G. M.Graham, D.Rozenblatt-Rosen, O.Xavier, R. J.Regev, A.2019-08-28doi:10.1101/746743Cold Spring Harbor Laboratory Press2019-08-28
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Resolving the fibrotic niche of human liver cirrhosis using single-cell transcriptomics
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https://biorxiv.org/cgi/content/short/766113v1?rss=1"
Ramachandran, P.Dobie, R.Wilson-Kanamori, J. R.Dora, E. F.Henderson, B. E.Taylor, R. S.Matchett, K. P.Portman, J. R.Efremova, M.Vento-Tormo, R.Luu, N. T.Weston, C. J.Newsome, P. N.Harrison, E. M.Mole, D. J.Wigmore, S. J.Iredale, J. P.Tacke, F.Pollard, J. W.Ponting, C. P.Marioni, J.Teichmann, S. A.Henderson, N. C.2019-09-12doi:10.1101/766113Cold Spring Harbor Laboratory Press2019-09-12
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A single-cell and single-nucleus RNA-seq toolbox for fresh and frozen human tumors
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https://biorxiv.org/cgi/content/short/761429v1?rss=1"
Slyper, M.Porter, C. B. M.Ashenberg, O.Waldman, J.Drokhlyansky, E.Wakiro, I.Smillie, C.Smith-Rosario, G.Wu, J.Dionne, D.Vigneau, S.Jane-Valbuena, J.Napolitano, S.Su, M.-J.Patel, A. G.Karlstrom, A.Gritsch, S.Nomura, M.Waghray, A.Gohil, S. H.Tsankov, A. M.Jerby-Arnon, L.Cohen, O.Klughammer, J.Rosen, Y.Gould, J.Li, B.Nguyen, L.Wu, C. J.Izar, B.Haq, R.Hodi, F. S.Yoon, C. H.Hata, A. N.Baker, S. J.Suva, M. L.Bueno, R.Stover, E. H.Matulonis, U. A.Clay, M. R.Dyer, M. A.Collins, N. B.Wagle, N.Rotem, A.Johnson, B. E.2019-09-12doi:10.1101/761429Cold Spring Harbor Laboratory Press2019-09-12
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Systematic Comparison of High-throughput Single-Cell and Single-Nucleus Transcriptomes during Cardiomyocyte Differentiation
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https://biorxiv.org/cgi/content/short/585901v1?rss=1"
Selewa, A.Dohn, R.Eckart, H.Lozano, S.Xie, B.Gauchat, E.Elorbany, R.Rhodes, K.Burnett, J.Gilad, Y.Pott, S.Basu, A.2019-03-22doi:10.1101/585901Cold Spring Harbor Laboratory Press2019-03-22
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Segmentation-free inference of cell-types from in situ transcriptomics data
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https://biorxiv.org/cgi/content/short/800748v1?rss=1"
Park, J.Choi, W.Tiesmeyer, S.Long, B.Borm, L. E.Garren, E.Nguyen, T. N.Codeluppi, S.Schlesner, M.Tasic, B.Eils, R.Ishaque, N.2019-10-13doi:10.1101/800748Cold Spring Harbor Laboratory Press2019-10-13
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Deep generative model embedding of single-cell RNA-Seq profiles on hyperspheres and hyperbolic spaces
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https://biorxiv.org/cgi/content/short/853457v1?rss=1"
Ding, J.Regev, A.2019-11-25doi:10.1101/853457Cold Spring Harbor Laboratory Press2019-11-25
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Distinct microbial and immune niches of the human colon
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https://biorxiv.org/cgi/content/short/2019.12.12.871657v1?rss=1"
James, K. R.Gomes, T.Elmentaite, R.Kumar, N.Gulliver, E. L.King, H. W.Stares, M. D.Bareham, B. R.Ferdinand, J. R.Petrova, V.Polanski, K.Forster, S. C.Jarvis, L. B.Suchanek, O.Howlett, S.James, L.Jones, J. L.Meyer, K. B.Clatworthy, M. R.Saeb-Parsy, K.Lawley, T.Teichmann, S. A.2019-12-12doi:10.1101/2019.12.12.871657Cold Spring Harbor Laboratory Press2019-12-12
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Sampling artifacts in single-cell genomics cohort studies
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https://biorxiv.org/cgi/content/short/2020.01.15.897066v1?rss=1"
Massoni-Badosa, R.Iacono, G.Moutinho, C.Kulis, M.Palau, N.Marchese, D.Rodriguez-Ubreva, J.Ballestar, E.Rodriguez-Esteban, G.Marsal, S.Aymerich, M.Colomer, D.Campo, E.Jula, A.Martin-Subero, J. I.Heyn, H.2020-01-15doi:10.1101/2020.01.15.897066Cold Spring Harbor Laboratory Press2020-01-15
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A cell atlas of human thymic development defines T cell repertoire formation
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https://biorxiv.org/cgi/content/short/2020.01.28.911115v1?rss=1"
Park, J.-E.Botting, R. A.Dominguez Conde, C.Popescu, D.-M.Lavaert, M.Kunz, D. J.Stephenson, E.Ragazzini, R.Tuck, E.Wilbrey-Clark, A. L.Ferdinand, J. R.Webb, S.Maunder, D.Vandamme, N.Mahbubani, K. T.Polanski, K.Mamanova, L.Fuller, A.Filby, A.Reynolds, G.Dixon, D.Saeb-Parsy, K.Lisgo, S.Henderson, D.Vento-Tormo, R.Meyer, K. B.Saeys, Y.Bonfanti, P.Behjati, S.Clatworthy, M. R.Taghon, T.Haniffa, M.Teichmann, S. A.2020-01-28doi:10.1101/2020.01.28.911115Cold Spring Harbor Laboratory Press2020-01-28
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SARS-CoV-2 receptor ACE2 and TMPRSS2 are predominantly expressed in a transient secretory cell type in subsegmental bronchial branches
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https://biorxiv.org/cgi/content/short/2020.03.13.991455v1?rss=1"
Lukassen, S.Chua, R. L.Trefzer, T.Kahn, N. C.Schneider, M. A.Muley, T.Winter, H.Meister, M.Veith, C.Boots, A. W.Hennig, B. P.Kreuter, M.Conrad, C.Eils, R.2020-03-14doi:10.1101/2020.03.13.991455Cold Spring Harbor Laboratory Press2020-03-14
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Cells and gene expression programs in the adult human heart
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https://biorxiv.org/cgi/content/short/2020.04.03.024075v1?rss=1"
Litvinukova, M.Talavera-Lopez, C.Maatz, H.Reichart, D.Worth, C. L.Lindberg, E. L.Kanda, M.Polanski, K.Fasouli, E. S.Samari, S.Roberts, K.Tuck, E.Heinig, M.DeLaughter, D.McDonough, B.Wakimoto, H.Gorham, J. M.Nadelmann, E.Mahbubani, K. T.Saeb-Parsy, K.Patone, G.Boyle, J. J.Zhang, H.Zhang, H.Viveiros, A.Oudit, G.Bayraktar, O.Seidman, J. G.Seidman, C.Noseda, M.Hubner, N.Teichmann, S. A.2020-04-05doi:10.1101/2020.04.03.024075Cold Spring Harbor Laboratory Press2020-04-05
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Single-cell atlas of a non-human primate reveals new pathogenic mechanisms of COVID-19
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https://biorxiv.org/cgi/content/short/2020.04.10.022103v1?rss=1"
Han, L.Wei, X.Liu, C.Volpe, G.Wang, Z.Pan, T.Yuan, Y.Lei, Y.Lai, Y.Ward, C.Yu, Y.Wang, M.Shi, Q.Wu, T.Wu, L.Liu, Y.Wang, C.Zhang, Y.Sun, H.Yu, H.Zhuang, Z.Tang, T.Huang, Y.Lu, H.Xu, L.Xu, J.Cheng, M.Liu, Y.Wong, C. W.Tan, T.Ji, W.Maxwell, P. H.Yang, H.Wang, J.Zhu, S.Liu, S.Xu, X.Hou, Y.Esteban, M. A.Liu, L.2020-04-10doi:10.1101/2020.04.10.022103Cold Spring Harbor Laboratory Press2020-04-10
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Single cell profiling of immature human postnatal thymocytes resolves the complexity of intra-thymic lineage differentiation and thymus seeding precursors.
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https://biorxiv.org/cgi/content/short/2020.04.07.007237v1?rss=1"
Lavaert, M.Liang, K. L.Vandamme, N.Park, J.-E.Roels, J.Kowalczyk, M. S.Li, B.Ashenberg, O.Tabaka, M.Dionne, D.Tickle, T. L.Slyper, M.Rozenblatt-Rosen, O.Vandekerckhove, B.Leclercq, G.Regev, A.Van Vlierberghe, P.Guilliams, M.Teichmann, S. A.Saeys, Y.Taghon, T.2020-04-08doi:10.1101/2020.04.07.007237Cold Spring Harbor Laboratory Press2020-04-08
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Integrated analyses of single-cell atlases reveal age, gender, and smoking status associations with cell type-specific expression of mediators of SARS-CoV-2 viral entry and highlights inflammatory programs in putative target cells
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https://biorxiv.org/cgi/content/short/2020.04.19.049254v1?rss=1"
Muus, C.Luecken, M. D.Eraslan, G.Waghray, A.Heimberg, G.Sikkema, L.Kobayashi, Y.Vaishnav, E. D.Subramanian, A.Smillie, C.Jagadeesh, K.Duong, E. T.Fiskin, E.Torlai Triglia, E.Ansari, M.Cai, P.Lin, B.Buchanan, J.Chen, S.Shu, J.Haber, A. L.Chung, H.Montoro, D. T.Adams, T.Aliee, H.Allon, S. J.Andrusivova, Z.Angelidis, I.Ashenberg, O.Bassler, K.Becavin, C.Benhar, I.Bergenstrahle, J.Bergenstrahle, L.Bolt, L.Braun, E.Bui, L. T.Chaffin, M.Chichelnitskiy, E.Chiou, J.Conlon, T. M.Cuoco, M. S.Deprez, M.Fischer, D. S.G2020-04-20doi:10.1101/2020.04.19.049254Cold Spring Harbor Laboratory Press2020-04-20
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The Human Cell Atlas
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https://biorxiv.org/cgi/content/short/121202v1?rss=1"
Regev, A.Teichmann, S.Lander, E. S.Amit, I.Benoist, C.Birney, E.Bodenmiller, B.Campbell, P.Carninci, P.Clatworthy, M.Clevers, H.Deplancke, B.Dunham, I.Eberwine, J.Eils, R.Enard, W.Farmer, A.Fugger, L.Gottgens, B.Hacohen, N.Haniffa, M.Hemberg, M.Kim, S. K.Klenerman, P.Kriegstein, A.Lein, E.Linnarsson, S.Lundeberg, J.Majumder, P.Marioni, J.Merad, M.Mhlanga, M.Nawijn, M.Netea, M.Nolan, G.Pe'er, D.Philipakis, A.Ponting, C. P.Quake, S. R.Reik, W.Rozenblatt-Rosen, O.Sanes, J. R.Satija, R.Shumacher, T.Shalek, A. K2017-05-08doi:10.1101/121202Cold Spring Harbor Laboratory Press2017-05-08
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scConsensus: combining supervised and unsupervised clustering for cell type identification in single-cell RNA sequencing data
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https://biorxiv.org/cgi/content/short/2020.04.22.056473v1?rss=1"
Ranjan, B.Schmidt, F.Sun, W.Park, J.Honardoost, M. A.Tan, J.Arul Rayan, N.Prabhakar, S.2020-04-24doi:10.1101/2020.04.22.056473Cold Spring Harbor Laboratory Press2020-04-24
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Spatial and single-cell transcriptional landscape of human cerebellar development
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https://biorxiv.org/cgi/content/short/2020.06.30.174391v1?rss=1"
Aldinger, K. A.Thomson, Z.Haldipur, P.Deng, M.Timms, A. E.Hirano, M.Santpere, G.Roco, C.Rosenberg, A. B.Lorente-Galdos, B.Gulden, F. O.O'Day, D.Overman, L. M.Lisgo, S.Alexandre, P.Sestan, N.Doherty, D.Dobyns, W. B.Seelig, G.Glass, I. A.Millen, K. J.2020-07-01doi:10.1101/2020.06.30.174391Cold Spring Harbor Laboratory Press2020-07-01
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A single-cell atlas of the human healthy airways
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https://biorxiv.org/cgi/content/short/2019.12.21.884759v1?rss=1"
Deprez, M.Zaragosi, L.-E.Truchi, M.Ruiz Garcia, S.Arguel, M.-J.Lebrigand, K.Paquet, A.Pee'r, D.Marquette, C.-H.Leroy, S.BARBRY, P.2019-12-23doi:10.1101/2019.12.21.884759Cold Spring Harbor Laboratory Press2019-12-23
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High throughput, error corrected Nanopore single cell transcriptome sequencing
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https://biorxiv.org/cgi/content/short/831495v1?rss=1"
Lebrigand, K.Magnone, V.BARBRY, P.Waldmann, R.2019-11-05doi:10.1101/831495Cold Spring Harbor Laboratory Press2019-11-05
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Besca, a single-cell transcriptomics analysis toolkit to accelerate translational research
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https://biorxiv.org/cgi/content/short/2020.08.11.245795v1?rss=1"
Maedler, S. C.Julien-Laferriere, A.Wyss, L.Phan, M.Kang, A. S. W.Ulrich, E.Schmucki, R.Zhang, J. D.Ebeling, M.Badi, L.Kam-Thong, T.Schwalie, P. C.Hatje, K.2020-08-12doi:10.1101/2020.08.11.245795Cold Spring Harbor Laboratory Press2020-08-12
<![CDATA[
Deep learning and alignment of spatially-resolved whole transcriptomes of single cells in the mouse brain with Tangram
]]>
https://biorxiv.org/cgi/content/short/2020.08.29.272831v1?rss=1"
Biancalani, T.Scalia, G.Buffoni, L.Avasthi, R.Lu, Z.Sanger, A.Tokcan, N.Vanderburg, C. R.Segerstolpe, A.Zhang, M.Avraham-Davidi, I.Vickovic, S.Nitzan, M.Ma, S.Buenrostro, J. D.Brown, N. B.Fanelli, D.Zhuang, X.Macosko, E.Regev, A.2020-08-30doi:10.1101/2020.08.29.272831Cold Spring Harbor Laboratory Press2020-08-30
<![CDATA[
DUBStepR: correlation-based feature selection for clustering single-cell RNA sequencing data
]]>
https://biorxiv.org/cgi/content/short/2020.10.07.330563v1?rss=1"
Ranjan, B.Sun, W.Park, J.Xie, R.Alipour, F.Singhal, V.Prabhakar, S.2020-10-08doi:10.1101/2020.10.07.330563Cold Spring Harbor Laboratory Press2020-10-08
<![CDATA[
Poised cell circuits in human skin are activated in disease
]]>
https://biorxiv.org/cgi/content/short/2020.11.05.369363v1?rss=1"
Reynolds, G.Vegh, P.Fletcher, J.Poyner, E.Stephenson, E.Goh, I.Botting, R.Huang, N.Olabi, B.Dubois, A.Dixon, D.Green, K.Maunder, D.Engelbert, J.Efremova, M.Polanski, K.Jardine, L.Jones, C.Ness, T.Horsfall, D.McGrath, J.Carey, C.Popescu, D.-M.Webb, S.Wang, X.-n.Sayer, B.Park, J.-E.Negri, V.Belokhvostova, D.Lynch, M.McDonald, D.Filby, A.Hagai, T.Meyer, K.Husain, A.Coxhead, J.Vento-Tormo, R.Behjati, S.Lisgo, S.Villani, A.-C.Bacardit, J.Jones, P.OToole, E.Ogg, G.Rajan, N.Reynolds, N.Teichmann, S.Watt, F.2020-11-05doi:10.1101/2020.11.05.369363Cold Spring Harbor Laboratory Press2020-11-05
<![CDATA[
Single-cell sequencing of developing human gut reveals transcriptional links to childhood Crohns disease
]]>
https://biorxiv.org/cgi/content/short/2020.02.06.937110v1?rss=1"
Elmentaite, R.Ross, A.James, K. R.Ortmann, D.Gomes, T.Roberts, K.Nayak, K.Tuck, L.Bayraktar, O.Heuschkel, R.Vallier, L.Teichmann, S. A.Zilbauer, M.2020-02-07doi:10.1101/2020.02.06.937110Cold Spring Harbor Laboratory Press2020-02-07
<![CDATA[
Robust clustering and interpretation ofscRNA-seq data using reference componentanalysis
]]>
https://biorxiv.org/cgi/content/short/2021.02.16.431527v1?rss=1"
Schmidt, F.Ranjan, B.Xiao Xuan Lin, Q.Krishnan, V.Joanito, I.Honardoost, M. A.Nawaz, Z.Venkatesh, P. N.Tan, J.Rayan, N. A.Ong, S. T.Prabhakar, S.2021-02-17doi:10.1101/2021.02.16.431527Cold Spring Harbor Laboratory Press2021-02-17
<![CDATA[
Systemic Tissue and Cellular Disruption from SARS-CoV-2 Infection revealed in COVID-19 Autopsies and Spatial Omics Tissue Maps
]]>
https://biorxiv.org/cgi/content/short/2021.03.08.434433v1?rss=1"
Park, J.Foox, J.Hether, T.Danko, D.Warren, S.Kim, Y.Reeves, J.Butler, D. J.Mozsary, C.Rosiene, J.Shaiber, A.Afshinnekoo, E.MacKay, M.Bram, Y.Chandar, V.Geiger, H.Craney, A.Velu, P.Melnick, A. M.Hajirasouliha, I.Beheshti, A.Taylor, D.Saravia-Butler, A.Singh, U.Wurtele, E. S.Schisler, J.Fenessey, S.Corvelo, A.Zody, M. C.Germer, S.Salvatore, S.Levy, S.Wu, S.Tatonetti, N.Shapira, S.Salvatore, M.Loda, M.Westblade, L. F.Cushing, M.Rennert, H.Kriegel, A. J.Elemento, O.Imielinski, M.Borczuk, A. C.Meydan, C.Schwar2021-03-09doi:10.1101/2021.03.08.434433Cold Spring Harbor Laboratory Press2021-03-09
<![CDATA[
A single-cell and spatial atlas of autopsy tissues reveals pathology and cellular targets of SARS-CoV-2
]]>
https://biorxiv.org/cgi/content/short/2021.02.25.430130v1?rss=1"
Delorey, T. M.Ziegler, C. G. K.Heimberg, G.Normand, R.Yang, Y.Segerstolpe, A.Abbondanza, D.Fleming, S. J.Subramanian, A.Montoro, D. T.Jagadeesh, K. A.Dey, K.Sen, P.Slyper, M.Pita-Juarez, Y.Phillips, D.Bloom-Ackermann, Z.Barkas, N.Ganna, A.Gomez, J.Normandin, E.Naderi, P.Popov, Y. V.Raju, S. S.Niezen, S.Tsai, L. T.- Y.Siddle, K. J.Sud, M.Tran, V. M.Karuthedath Vellarikkal, S.Amir-Zilberstein, L.Atri, D. S.Beechem, J. M.Brook, O. R.Chen, J.Divakar, P.Dorceus, P.Engreitz, J. M.Essene, A.Fitzgerald, D. M.Fropf, R.Gaz2021-02-25doi:10.1101/2021.02.25.430130Cold Spring Harbor Laboratory Press2021-02-25
<![CDATA[
Single-cell atlas of human oral mucosa reveals a stromal-neutrophil axis regulating tissue immunity in health and inflammatory disease
]]>
https://biorxiv.org/cgi/content/short/2021.04.06.438702v1?rss=1"
Williams, D. W.Greenwell-Wild, T.Brenchley, L.Dutzan, N.Overmiller, A.Sawaya, A. P.Webb, S.Martin, D.Hajishengallis, G.Divaris, K.Morasso, M.Haniffa, M.Moutsopoulos, N. M.2021-04-07doi:10.1101/2021.04.06.438702Cold Spring Harbor Laboratory Press2021-04-07
<![CDATA[
Cells of the human intestinal tract mapped across space and time
]]>
https://biorxiv.org/cgi/content/short/2021.04.07.438755v1?rss=1"
Elmentaite, R.Kumasaka, N.King, H. W.Roberts, K.Dabrowska, M.Pritchard, S.Bolt, L.Vieira, S. F.Mamanova, L.Huang, N.Goh Kai'En, I.Stephenson, E.Engelbert, J.Botting, R. A.Fleming, A.Dann, E.Lisgo, S. N.Katan, M.Leonard, S.Oliver, T. R.Hook, L.Nayak, K.Perrone, F.Campos, L. S.Dominguez Conde, C.Polanski, K.van Dongen, S.Patel, M.Morgan, M.Marioni, J.Bayraktar, O.Meyer, K. B.Zilbauer, M.Uhlig, H.Clatworthy, M. R.Mahbubani, K. T.Saeb-Parsy, K.Haniffa, M. A.James, K. R.Teichmann, S. A.2021-04-07doi:10.1101/2021.04.07.438755Cold Spring Harbor Laboratory Press2021-04-07
<![CDATA[
Profiling of transcribed cis-regulatory elements in single cells
]]>
https://biorxiv.org/cgi/content/short/2021.04.04.438388v1?rss=1"
Moody, J.Kouno, T.Suzuki, A.Shibayama, Y.Terao, C.Chang, J.-C.Lopez-Redondo, F.Yip, C. W.Ando, Y.Yamamoto, K.Carninci, P.Shin, J. W.Hon, C.-C.2021-04-04doi:10.1101/2021.04.04.438388Cold Spring Harbor Laboratory Press2021-04-04
<![CDATA[
A single cell atlas of human cornea that defines its development, limbal stem and progenitor cells and the interactions with the limbal niche
]]>
https://biorxiv.org/cgi/content/short/2020.07.09.195438v1?rss=1"
Joseph CollinRachel QueenDarin ZertiSanja BojicNicky MoyseMarina Moya-MolinaChunbo YangGary ReynoldsRafiqul HussainJonathan M CoxheadSteven LisgoDeborah HendersonAgatha JosephPaul RooneySaurabh GhoshChe ConnonMuzlifah HaniffaFrancisco FigueiredoLyle ArmstrongMajlinda Lako2020-07-10doi:10.1101/2020.07.09.195438Cold Spring Harbor Laboratory Press2020-07-10
<![CDATA[
Integrated Single Cell Atlas of Endothelial Cells of the Human Lung
]]>
https://biorxiv.org/cgi/content/short/2020.10.21.347914v1?rss=1"
Schupp, J. C.Adams, T. S.Cosme, C.Brickman Raredon, M. S.Omote, N.Poli, S.Rose, K.-A.Manning, E.Sauler, M.DeIuliis, G.Ahangari, F.Neumark, N.Yuan, Y.Habermann, A. C.Gutierrez, A. J.Bui, L. T.Meyer, K. B.Nawijn, M. C.Teichmann, S. A.Banovich, N.Kropski, J. A.Niklason, L. E.Pe'er, D.Yan, X.Homer, R.Rosas, I. O.Kaminski, N.2020-10-22doi:10.1101/2020.10.21.347914Cold Spring Harbor Laboratory Press2020-10-22
<![CDATA[
Mapping the temporal and spatial dynamics of the human endometrium in vivo and in vitro
]]>
https://biorxiv.org/cgi/content/short/2021.01.02.425073v1?rss=1"
Garcia-Alonso, L.Handfield, L.-F.Roberts, K.Nikolakopoulou, K.Fernando, R. C.Gardner, L.Woodhams, B.Arutyunyan, A.Polanski, K.Hoo, R.Sancho-Serra, C.Li, T.Kwakwa, K.Tuck, E.Kleshchevnikov, V.Tarkowska, A.Porter, T.Mazzeo, C. I.van Dongen, S.Dabrowska, M.Vaskivskyi, V.Mahbubani, K. T.PARK, J.-E.Jimenez-Linan, M.Campos, L.Kiselev, V.Lindskog, C.Ayuk, P.Prigmore, E.Stratton, M. R.Saeb-Parsy, K.Moffett, A.Moore, L.Bayraktar, O. A.Teichmann, S. A.Turco, M. Y.Vento-Tormo, R.2021-01-04doi:10.1101/2021.01.02.425073Cold Spring Harbor Laboratory Press2021-01-04
<![CDATA[
Intrinsic and extrinsic regulation of human fetal bone marrow haematopoiesis and perturbations in Down syndrome
]]>
https://biorxiv.org/cgi/content/short/2021.06.25.449771v1?rss=1"
Jardine, L.Webb, S.Goh, I.Quiroga Londono, M.Reynolds, G.Mather, M.Olabi, B.Stephenson, E.Botting, R. A.Horsfall, D.Engelbert, J.Maunder, D.Mende, N.Murnane, C.Dann, E.McGrath, J.King, H.Kucinski, I.Queen, R.Carey, C. D.Shrubsole, C.Poyner, E.Acres, M.Jones, C.Ness, T.Coultard, R.Elliot, N.O'Byrne, S.Haltalli, M. L.Lawrence, J. E.Lisgo, S.Balogh, P.Meyer, K. B.Prigmore, E.Ambridge, K.Sarkin Jain, M.Efremova, M.Pickard, K.Creasey, T.Bacardit, J.Henderson, D.Coxhead, J.Filby, A.Hussain, R.Dixon, D.McDonald,2021-06-25doi:10.1101/2021.06.25.449771Cold Spring Harbor Laboratory Press2021-06-25
<![CDATA[
Single-nucleus cross-tissue molecular reference maps to decipher disease gene function
]]>
https://biorxiv.org/cgi/content/short/2021.07.19.452954v1?rss=1"
Eraslan, G.Drokhlyansky, E.Anand, S.Subramanian, A.Fiskin, E.Slyper, M.Wang, J.Van Wittenberghe, N.Rouhana, J. M.Waldman, J.Ashenberg, O.Dionne, D.Win, T. S.Cuoco, M. S.Kuksenko, O.Branton, P. A.Marshall, J. L.Greka, A.Getz, G.Segre, A. V.Aguet, F.Rozenblatt-Rosen, O.Ardlie, K. G.Regev, A.2021-07-19doi:10.1101/2021.07.19.452954Cold Spring Harbor Laboratory Press2021-07-19
<![CDATA[
A Web Portal and Workbench for Biological Dissection of Single Cell COVID-19 Host Responses
]]>
https://biorxiv.org/cgi/content/short/2021.06.07.447287v1?rss=1"
Jin, K.Bardes, E. E.Mitelpunkt, A.Wang, Y. J.Bhatnagar, S.Sengupta, S.Krummel, D. P.Rothenberg, M. E.Aronow, B. J.2021-06-07doi:10.1101/2021.06.07.447287Cold Spring Harbor Laboratory Press2021-06-07
<![CDATA[
Anatomical Structures, Cell Types, and Biomarkers Tables Plus 3D Reference Organs in Support of a Human Reference Atlas
]]>
https://biorxiv.org/cgi/content/short/2021.05.31.446440v1?rss=1"
Borner, K.Teichmann, S. A.Quardokus, E. M.Gee, J.Browne, K.Osumi-Sutherland, D.Herr, B. W.Bueckle, A.Paul, H.Haniffa, M. A.Jardine, L.Bernard, A.Ding, S.-L.Miller, J. A.Lin, S.Halushka, M.Boppana, A.Longacre, T. A.Hickey, J.Lin, Y.Valerius, M. T.He, Y.Pryhuber, G.Sun, X.Jorgensen, M.Radtke, A.Wasserfall, C.Ginty, F.Ho, J.Sunshine, J.Beuschel, R. T.Brusko, M.Lee, S.Malhotra, R.Jain, S.Weber, G.2021-06-01doi:10.1101/2021.05.31.446440Cold Spring Harbor Laboratory Press2021-06-01
<![CDATA[
A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche
]]>
https://biorxiv.org/cgi/content/short/2021.11.26.470108v1?rss=1"
Madissoon, E.Oliver, A. J.Kleshchevnikov, V.Wilbrey-Clark, A.Polanski, K.Ribeiro Orsi, A. E.Mamanova, L.Bolt, L.Pett, J. P.Huang, N.Elmentaite, R.Richoz, N.He, P.Dabrowska, M.Tuck, E.Prigmore, E.Knights, A.Oszlanczi, A.Hunter, A.Pritchard, S.Vieira, S. F.Patel, M.Mahbubani, K.Georgakopoulos, N.Clatworthy, M.Stegle, O.Bayraktar, O. A.Saeb-Parsy, K.Kumasaka, N.Teichmann, S. A.Meyer, K. B.2021-11-27doi:10.1101/2021.11.26.470108Cold Spring Harbor Laboratory Press2021-11-27
<![CDATA[
Comprehensive identification of fetal cis-regulatory elements in the human genome by single-cell multi-omics analysis
]]>
https://biorxiv.org/cgi/content/short/2021.11.02.466852v1?rss=1"
Yu, H.Ai, N.Peng, P.Ke, Y. w.Chen, X. p.Li, Y.Zhao, T.Jiang, S.Liu, J.Jiang, L.2021-11-03doi:10.1101/2021.11.02.466852Cold Spring Harbor Laboratory Press2021-11-03
<![CDATA[
Single-Cell Atlas of Common Variable Immunodeficiency reveals germinal center-associated epigenetic dysregulation in B cell responses
]]>
https://biorxiv.org/cgi/content/short/2021.12.20.473453v1?rss=1"
Rodriguez-Ubreva, J.Arutyunyan, A.Bonder, M. J.Del Pino-Molina, L.Clark, S.de la Calle-Fabregat, C.Garcia-Alonso, L.Handfield, L.-F.Ciudad, L.Andres-Leon, E.Krueger, F.Catala-Moll, F.Rodriguez-Cortez, V. C.Polanski, K.Mamanova, L.van Dongen, S.Kiselev, V. Y.Martinez-Saavedra, M. T.Heyn, H.Martin, J.Warnatz, K.Lopez-Granados, E.Rodriguez-Gallego, C.Stegle, O.Kelsey, G. D.Vento-Tormo, R.Ballestar, E.2021-12-21doi:10.1101/2021.12.20.473453Cold Spring Harbor Laboratory Press2021-12-21
<![CDATA[
A human fetal lung cell atlas uncovers proximal-distal gradients of differentiation and key regulators of epithelial fates
]]>
https://biorxiv.org/cgi/content/short/2022.01.11.474933v1?rss=1"
He, P.Lim, K.Sun, D.Pett, J. P.Jeng, Q.Polanski, K.Dong, Z.Bolt, L.Richardson, L.Mamanova, L.Dabrowska, M.Wilbrey-Clark, A. L.Madissoon, E.Tuong, K. Z.Dann, E.Suo, C.Goh, I.He, X.Barker, R. A.Teichmann, S.Marioni, J.Meyer, K. B.Rawlins, E. L.2022-01-11doi:10.1101/2022.01.11.474933Cold Spring Harbor Laboratory Press2022-01-11
<![CDATA[
Mapping the developing human immune system across organs
]]>
https://biorxiv.org/cgi/content/short/2022.01.17.476665v1?rss=1"
Suo, C.Dann, E.Goh, I.Jardine, L.Kleshchevnikov, V.Park, J.-E.Botting, R. A.Stephenson, E.Engelbert, J.Tuong, Z. K.Polanski, K.Yayon, N.Xu, C.Suchanek, O.Elmentaite, R.Dominguez Conde, C.He, P.Pritchard, S.Miah, M.Moldovan, C.Steemers, A. S.Prete, M.Marioni, J. C.Clatworthy, M. R.Haniffa, M.Teichmann, S. A.2022-01-18doi:10.1101/2022.01.17.476665Cold Spring Harbor Laboratory Press2022-01-18
<![CDATA[
Developmental origins of cell heterogeneity in the human lung
]]>
https://biorxiv.org/cgi/content/short/2022.01.11.475631v1?rss=1"
Sountoulidis, A.Marco Salas, S.Braun, E.Avenel, C.Bergenstrahle, J.Vicari, M.Czarnewski Barenco, P. V.Theelke, J.Liontos, A.Abalo, X.Andrusivova, Z.Asp, M.Li, X.Hu, L.Sariyar, S.Martinez Casals, A.Ayoglu, B.Firsova, A. B.Michaelsson, J.Lundberg, E.Wählby, C.Sundström, E.Linnarsson, S.Lundeberg, J.Nilsson, M.Samakovlis, C.2022-01-12doi:10.1101/2022.01.11.475631Cold Spring Harbor Laboratory Press2022-01-12
<![CDATA[
A proximal-to-distal survey of healthy adult human small intestine and colon epithelium by single-cell transcriptomics
]]>
https://biorxiv.org/cgi/content/short/2021.10.05.460818v1?rss=1"
Burclaff, J.Bliton, R. J.Breau, K. A.Ok, M. T.Gomez-Martinez, I.Ranek, J. S.Bhatt, A. P.Purvis, J. E.Woosley, J. T.Magness, S. T.2021-10-06doi:10.1101/2021.10.05.460818Cold Spring Harbor Laboratory Press2021-10-06
<![CDATA[
The Tabula Sapiens: a single cell transcriptomic atlas of multiple organs from individual human donors
]]>
https://biorxiv.org/cgi/content/short/2021.07.19.452956v1?rss=1"
The Tabula Sapiens Consortium,Quake, S. R.2021-07-20doi:10.1101/2021.07.19.452956Cold Spring Harbor Laboratory Press2021-07-20
<![CDATA[
Robust temporal map of human in vitro myelopoiesis using single-cell genomics
]]>
https://biorxiv.org/cgi/content/short/2021.11.17.469005v1?rss=1"
Alsinet, C.Primo, M.Lorenzi, V.Knights, A. J.Sancho-Serra, C.Park, J.-E.Wyspianska, B. S.Tough, D. F.Alvarez, D.Gaffney, D. J.Vento-Tormo, R.2021-11-19doi:10.1101/2021.11.17.469005Cold Spring Harbor Laboratory Press2021-11-19
<![CDATA[
Cross-tissue immune cell analysis reveals tissue-specific adaptations and clonal architecture across the human body
]]>
https://biorxiv.org/cgi/content/short/2021.04.28.441762v1?rss=1"
Dominguez Conde, C.Gomes, T.Jarvis, L. B.Xu, C.Howlett, S.Rainbow, D.Suchanek, O.King, H.Mamanova, L.Polanski, K.Huang, N.Fasouli, E.Mahbubani, K.Prete, M.Campos, L.Mousa, H.Needham, E.Pritchard, S.Li, T.Elmentaite, R.Park, J.Menon, D.Bayraktar, O.James, L.Meyer, K.Clatworthy, M.Saeb-Parsy, K.Jones, J. L.Teichmann, S. A.2021-04-28doi:10.1101/2021.04.28.441762Cold Spring Harbor Laboratory Press2021-04-28
<![CDATA[
Spatial Transcriptomics-correlated Electron Microscopy
]]>
https://biorxiv.org/cgi/content/short/2022.05.18.492475v1?rss=1"
Androvic, P.Schifferer, M.Perez Anderson, K.Cantuti-Castelvetri, L.Ji, H.Liu, L.Besson-Girard, S.Knoferle, J.Simons, M.Gokce, O.2022-05-20doi:10.1101/2022.05.18.492475Cold Spring Harbor Laboratory Press2022-05-20
<![CDATA[
Single-Cell Transcriptome Analyses Reveal the Cell Diversity and Developmental Features of Human Gastric and Metaplastic Mucosa
]]>
https://biorxiv.org/cgi/content/short/2022.05.22.493006v1?rss=1"
Tsubosaka, A.Komura, D.Katoh, H.Kakiuchi, M.Onoyama, T.Yamamoto, A.Abe, H.Seto, Y.Ushiku, T.Ishikawa, S.2022-05-23doi:10.1101/2022.05.22.493006Cold Spring Harbor Laboratory Press2022-05-23
<![CDATA[
Single nucleus pituitary transcriptomic and epigenetic landscape reveals human stem cell heterogeneity with diverse regulatory mechanisms
]]>
https://biorxiv.org/cgi/content/short/2021.06.18.449034v1?rss=1"
Zhang, Z.Zamojski, M.Smith, G. R.Willis, T. L.Yianni, V.Mendelev, N.Pincase, H.Seenarine, N.Amper, M. A. S.Vasoya, M.Nair, V.Turgeon, J. L.Bernard, D. J.Troyanskaya, O. G.Andoniadou, C. L.Sealfon, S. C.Ruf-Zamojski, F. M.2021-06-18doi:10.1101/2021.06.18.449034Cold Spring Harbor Laboratory Press2021-06-18
<![CDATA[
Single nucleus multi-omics regulatory atlas of the murine pituitary
]]>
https://biorxiv.org/cgi/content/short/2020.06.06.138024v1?rss=1"
Ruf-Zamojski, F. M.Zhang, Z.Zamojski, M.Smith, G. R.Mendelev, N.Liu, H.Nudelman, G.Moriwaki, M.Pincas, H.Gomez Castanon, R.Nair, V. D.Seenarine, N.Amper, M. A. S.Zhou, X.Ongaro, L.Toufaily, C.Schang, G.Nery, J. R.Bartlett, A.Aldridge, A.Jain, N.Childs, G. V.Troyanskaya, O. G.Ecker, J. R.Turgeon, J. L.Welt, C. K.Bernard, D. J.Sealfon, S. C.2020-06-07doi:10.1101/2020.06.06.138024Cold Spring Harbor Laboratory Press2020-06-07
<![CDATA[
Singletrome: A method to analyze and enhance the transcriptome with long noncoding RNAs for single cell analysis
]]>
https://biorxiv.org/cgi/content/short/2022.10.31.514182v1?rss=1"
Rahman, R.-U. U.Ahmad, I.Sparks, R.Saad, A. B.Mullen, A.2022-11-02doi:10.1101/2022.10.31.514182Cold Spring Harbor Laboratory Press2022-11-02
<![CDATA[
Single cell antigen receptor analysis reveals lymphocyte developmental origins
]]>
https://biorxiv.org/cgi/content/short/2022.11.18.517068v1?rss=1"
Suo, C.Polanski, K.Dann, E.Lindeboom, R. G. H.Vilarrasa Blasi, R.Vento-Tormo, R.Haniffa, M.Meyer, K. B.Tuong, Z. K.Clatworthy, M. R.Teichmann, S.2022-11-19doi:10.1101/2022.11.18.517068Cold Spring Harbor Laboratory Press2022-11-19
<![CDATA[
Transcriptomic diversity of cell types across the adult human brain
]]>
https://biorxiv.org/cgi/content/short/2022.10.12.511898v1?rss=1"
Siletti, K.Hodge, R. D.Mossi Albiach, A.Hu, L.Lee, K. W.Lönnerberg, P.Bakken, T. E.Ding, S.-L.Clark, M.Casper, T.Dee, N.Gloe, J.Keene, C. D.Nyhus, J.Tung, H.Yanny, A. M.Arenas, E.Lein, E. S.Linnarsson, S.2022-10-14doi:10.1101/2022.10.12.511898Cold Spring Harbor Laboratory Press2022-10-14
<![CDATA[
Comprehensive cell atlas of the first-trimester developing human brain
]]>
https://biorxiv.org/cgi/content/short/2022.10.24.513487v1?rss=1"
Braun, E.Danan-Gotthold, M.Borm, L. E.Vinsland, E.Lee, K. W.Lönnerberg, P.Hu, L.Li, X.He, X.Andrusivova, Z.Lundeberg, J.Arenas, E.Barker, R. A.Sundström, E.Linnarsson, S.2022-10-25doi:10.1101/2022.10.24.513487Cold Spring Harbor Laboratory Press2022-10-25
<![CDATA[
TACCO: Unified annotation transfer and decomposition of cell identities for single-cell and spatial omics
]]>
https://biorxiv.org/cgi/content/short/2022.10.02.508471v1?rss=1"
Mages, S.Moriel, N.Avraham-Davidi, I.Murray, E.Chen, F.Rozenblatt-Rosen, O.Klughammer, J.Regev, A.Nitzan, M.2022-10-05doi:10.1101/2022.10.02.508471Cold Spring Harbor Laboratory Press2022-10-05
<![CDATA[
The emergence of goblet inflammatory or ITGB6hi nasal progenitor cells determines age-associated SARS-CoV-2 pathogenesis
]]>
https://biorxiv.org/cgi/content/short/2023.01.16.524211v1?rss=1"
70y) nasal epithelial cells experimentally infected with SARS-CoV-2. Our data reveal that nasal epithelial cell subtypes show different tropism to SARS-CoV-2, correlating with age, ACE2 and TMPRSS2 expression. Ciliated cells are a viral replication centre across all age groups, but a distinct goblet inflammatory subtype emerges in infected paediatric cultures, identifiable by high expression of interferon stimulated genes and truncated viral genomes. In contrast, infected elderly cultures show a proportional increase in ITGB6hi progenitors, which facilitate viral spread and are associated with dysfunctional epithelial repair pathways.
Graphical Abstract
O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=155 SRC="FIGDIR/small/524211v2_ufig1.gif" ALT="Figure 1">
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]]>Woodall, M.Cujba, A.-M.Worlock, K. B.Case, K.-M.Masonou, T.Yoshida, M.Polanski, K.Huang, N.Lindeboom, R. G.Mamanova, L.Bolt, L.Richardson, L.Ellis, S.Palor, M.Burgoyne, T.Pinto, A.Moulding, D. A.McHugh, T. D.Saleh, A.Kilich, E.Mehta, P.O'Callaghan, C.Zhou, J.Barclay, W.De Coppi, P.Butler, C. R.Vinette, H.Roy, S.Breuer, J.Chambers, R. C.Heywood, W. E.Mills, K.Hynds, R. E.Teichmann, S. A.Meyer, K. B.Nikolic, M. Z.Smith, C. M.2023-01-17doi:10.1101/2023.01.16.524211Cold Spring Harbor Laboratory Press2023-01-17
<![CDATA[
Gene-level alignment of single cell trajectories informs the progression of in vitro T cell differentiation
]]>
https://biorxiv.org/cgi/content/short/2023.03.08.531713v1?rss=1"
Sumanaweera, D.Suo, C.Muraro, D.Dann, E.Polanski, K.Steemers, A.Park, J.-E.Dumitrascu, B.Teichmann, S.2023-03-10doi:10.1101/2023.03.08.531713Cold Spring Harbor Laboratory Press2023-03-10
<![CDATA[
Raman2RNA: Live-cell label-free prediction of single-cell RNA expression profiles by Raman microscopy
]]>
https://biorxiv.org/cgi/content/short/2021.11.30.470655v1?rss=1"
0.96) inferred from Raman images the expression profiles of various cell states and fates, including iPSCs, mesenchymal-epithelial transition (MET) cells, stromal cells, epithelial cells, and fibroblasts. R2R outperformed inference from brightfield images, showing the importance of spectroscopic content afforded by Raman microscopy. Raman2RNA lays a foundation for future investigations into exploring single-cell genome-wide molecular dynamics through imaging data, in vitro and in vivo.
]]>Kobayashi-Kirschvink, K. J.Gaddam, S.James-Sorenson, T.Grody, E.Ounadjela, J. R.Ge, B.Zhang, K.Kang, J. W.Xavier, R.So, P. T. C.Biancalani, T.Shu, J.Regev, A.2021-12-01doi:10.1101/2021.11.30.470655Cold Spring Harbor Laboratory Press2021-12-01
<![CDATA[
Spatially resolved single-cell multiomics map of human trophoblast differentiation in early pregnancy
]]>
https://biorxiv.org/cgi/content/short/2022.11.06.515326v1?rss=1"
Arutyunyan, A.Roberts, K.Sheridan, M. A.Kats, I.Garcia-Alonso, L.Velten, B.Troule-Lozano, K.Hoo, R.Marconato, L.Handfield, L.-F.Tuck, L.Gardner, L.Mazzeo, C. I.Kelava, I.Prigmore, E.Teichmann, S.Bayraktar, O.Moffett, A.Stegle, O.Turco, M. Y.Vento-Tormo, R.2022-11-06doi:10.1101/2022.11.06.515326Cold Spring Harbor Laboratory Press2022-11-06
<![CDATA[
An integrated cell atlas of the human lung in health and disease
]]>
https://biorxiv.org/cgi/content/short/2022.03.10.483747v1?rss=1"
Sikkema, L.Strobl, D. C.Zappia, L.Madissoon, E.Markov, N. S.Zaragosi, L.-E.Ansari, M.Arguel, M.-J.Apperloo, L.Becavin, C.Berg, M.Chichelnitskiy, E.Chung, M.-i.Collin, A.Gay, A. C.Hooshiar Kashani, B.Jain, M.Kapellos, T.Kole, T. M.Mayr, C. H.Papen, von, M.Peter, L.Ramirez-Suastegui, C.Schniering, J.Taylor, C. J.Walzthoeni, T.Xu, C.Bui, L. T.Donno, de, C.Dony, L.Guo, M.Gutierrez, A. J.Heumos, L.Huang, N.Ibarra, I. L.Jackson, N. D.Kadur Lakshminarasimha Murthy, P.Lotfollahi, M.Tabib, T.Talavera-Lopez, C.Travaglini, K.2022-03-11doi:10.1101/2022.03.10.483747Cold Spring Harbor Laboratory Press2022-03-11
<![CDATA[
Spatially resolved multiomics of human cardiac niches
]]>
https://biorxiv.org/cgi/content/short/2023.01.30.526202v1?rss=1"
Kanemaru, K.Cranley, J.Muraro, D.Miranda, A. M. A.Pett, J. P.Litvinukova, M.Kumasaka, N.Ho, S. Y.Polanski, K.Richardson, L.Mach, L.Dabrowska, M.Richoz, N.Barnett, S. N.Perera, S.Wilbrey-Clark, A. L.Talavera-Lopez, C.Mulas, I.Mahbubani, K. T.Bolt, L.Mamanova, L.Tuck, L.Wang, L.Huang, M. M.Prete, M.Pritchard, S.Dark, J.Saeb-Parsy, K.Patel, M.Clatworthy, M. R.Chowdhury, R. A.Noseda, M.Teichmann, S. A.2023-02-01doi:10.1101/2023.01.30.526202Cold Spring Harbor Laboratory Press2023-02-01
<![CDATA[
A Human Breast Cell Atlas Mapping the Homeostatic Cellular Shifts in the Adult Breast
]]>
https://biorxiv.org/cgi/content/short/2023.04.21.537845v1?rss=1"
Khaled, W. T.Reed, A. D.Pensa, S.Steif, A.Stenning, J.Kunz, D.He, P.Twigger, A.-J.Kania, K.Barrow, R.Goulding, I.Gomm, J.Jones, L.Marioni, J.2023-04-21doi:10.1101/2023.04.21.537845Cold Spring Harbor Laboratory Press2023-04-21
<![CDATA[
A spatially resolved single cell genomic atlas of the adult human breast
]]>
https://biorxiv.org/cgi/content/short/2023.04.22.537946v1?rss=1"
Kumar, T.Nee, K.Wei, R.He, S.Nguyen, Q.Bai, S.Blake, K.Pein, M.Gong, Y.Sei, E.Hu, M.Casasent, A.Thennavan, A.Li, J.Tran, T.Chen, K.Nilges, B.Kashikar, N.Braubach, O.Cheikh, B.Nikulina, N.Chen, H.Teshome, M.Menegaz, B.Javaid, H.Nagi, C.Montalvan, J.Lev, T.Tifrea, D.Edwards, R.Lin, E.Parajuli, R.Hanson, S.Winocour, S.Thompson, A.Lim, B.Lawson, D.Kessenbrock, K.Navin, N.2023-04-24doi:10.1101/2023.04.22.537946Cold Spring Harbor Laboratory Press2023-04-24
<![CDATA[
An atlas of healthy and injured cell states and niches in the human kidney
]]>
https://biorxiv.org/cgi/content/short/2021.07.28.454201v1?rss=1"
400,000 nuclei/cells) and spatial imaging technologies to a broad spectrum of healthy reference (n = 42) and disease (n = 42) kidneys. This has provided a high resolution cellular atlas of 100 cell types that include rare and novel cell populations. The multi-omic approach provides detailed transcriptomic profiles, epigenomic regulatory factors, and spatial localizations for major cell types spanning the entire kidney. We further identify and define cellular states altered in kidney injury, encompassing cycling, adaptive or maladaptive repair, transitioning and degenerative states affecting several segments. Molecular signatures of these states permitted their localization within injury neighborhoods using spatial transcriptomics, and large-scale 3D imaging analysis of [~]1.2 million neighborhoods provided linkages to active immune responses. These analyses further defined biological pathways relevant to injury niches, including signatures underlying the transition from reference to predicted maladaptive states that were associated with a decline in kidney function during chronic kidney disease. This human kidney cell atlas, including injury cell states and neighborhoods, will be a valuable resource for future studies.
]]>Lake, B. B.Menon, R.Winfree, S.Hu, Q.Ferreira, R. M.Kalhor, K.Barwinska, D.Otto, E. A.Ferkowicz, M.Diep, D.Plongthongkum, N.Knoten, A.Urata, S.Naik, A. S.Eddy, S.Zhang, B.Wu, Y.Salamon, D.Williams, J. C.Wang, X.Balderrama, K. S.Hoover, P.Murray, E.Vijayan, A.Chen, F.Waikar, S. S.Rosas, S.Wilson, F. P.Palevsky, P. M.Kiryluk, K.Sedor, J. R.Toto, R. D.Parikh, C.Kim, E. H.Macosko, E. Z.Kharchenko, P. V.Gaut, J. P.Hodgin, J. B.Eadon, M. T.Dagher, P. C.El-Achkar, T. M.Zhang, K.Kretzler, M.Jain, S.KPMP Consortium,2021-07-29doi:10.1101/2021.07.28.454201Cold Spring Harbor Laboratory Press2021-07-29
<![CDATA[
Deciphering the spatio-temporal transcriptional and chromatin accessibility of human retinal organoid development at the single cell level
]]>
https://biorxiv.org/cgi/content/short/2023.07.19.549507v1?rss=1"
Dorgau, B.Collin, J.Rozanska, A.Boczonadi, V.MoyaMolina, M.Hussain, R.Coxhead, J.Dhanaseelan, T.Armstrong, L.Queen, R.Lako, M.2023-07-19doi:10.1101/2023.07.19.549507Cold Spring Harbor Laboratory Press2023-07-19
<![CDATA[
Inference of single cell profiles from histology stains with the Single-Cell omics from Histology Analysis Framework (SCHAF)
]]>
https://biorxiv.org/cgi/content/short/2023.03.21.533680v1?rss=1"
Comiter, C.Vaishnav, E. D.Ciapmricotti, M.Li, B.Yang, Y.Rodig, S. J.Turner, M.Pfaff, K. L.Jane-Valbuena, J.Slyper, M.Waldman, J.Vigneau, S.Wu, J.Blosser, T. R.Segerstolpe, A.Abravanel, D.Wagle, N.Zhuang, X.Rudin, C. M.Klughammer, J.Rozenblatt-Rosen, O.Kobayash-Kirschvink, K. J.Shu, J.Regev, A.2023-03-23doi:10.1101/2023.03.21.533680Cold Spring Harbor Laboratory Press2023-03-23
<![CDATA[
Batch-Corrected Distance Mitigates Temporal and Spatial Variability for Clustering and Visualization of Single-Cell Gene Expression Data
]]>
https://biorxiv.org/cgi/content/short/2020.10.08.332080v1?rss=1"
Liang, S.Dou, J.Iqbal, R.Chen, K.2020-10-09doi:10.1101/2020.10.08.332080Cold Spring Harbor Laboratory Press2020-10-09
<![CDATA[
TooManyCellsInteractive: a visualization tool for dynamic exploration of single-cell data
]]>
https://biorxiv.org/cgi/content/short/2023.06.16.544954v1?rss=1"
Klamann, C.Lau, C.Schwartz, G. W.2023-06-18doi:10.1101/2023.06.16.544954Cold Spring Harbor Laboratory Press2023-06-18
<![CDATA[
Conserved coexpression at single cell resolution across primate brains
]]>
https://biorxiv.org/cgi/content/short/2022.09.20.508736v1?rss=1"
Suresh, H.Crow, M.Jorstad, N.Hodge, R.Lein, E.Dobin, A.Bakken, T.Gillis, J.2022-09-22doi:10.1101/2022.09.20.508736Cold Spring Harbor Laboratory Press2022-09-22
<![CDATA[
GRouNdGAN: GRN-guided simulation of single-cell RNA-seq data using causal generative adversarial networks
]]>
https://biorxiv.org/cgi/content/short/2023.07.25.550225v1?rss=1"
Zinati, Y.Takiddeen, A.Emad, A.2023-07-27doi:10.1101/2023.07.25.550225Cold Spring Harbor Laboratory Press2023-07-27
<![CDATA[
Airway epithelial response to RSV is impaired in multiciliated and goblet cells in asthma
]]>
https://biorxiv.org/cgi/content/short/2023.03.16.532356v1?rss=1"
Gay, A. C. A.Banchero, M.Carpaij, O. A.Kole, T.Apperloo, L.van Gosliga, D.Fajar, P. A.Koppelman, G. H.Bont, L.Hendriks, R. W.van den Berge, M.Nawijn, M. C.2023-03-17doi:10.1101/2023.03.16.532356Cold Spring Harbor Laboratory Press2023-03-17
<![CDATA[
Multi-organ functions of yolk sac during human early development
]]>
https://biorxiv.org/cgi/content/short/2022.08.03.502475v1?rss=1"
Botting, R. A.Goh, I.Rose, A.Webb, S.Engelbert, J.Gitton, Y.Stephenson, E.Quiroga Londono, M.Mather, M.Mende, N.Imaz-Rosshandler, I.Horsfall, D.Basurto-Lozada, D.Chipampe, N.-J.Rook, V.Mazin, P.Vijayabaskar, M.Hannah, R.Gambardella, L.Green, K.Ballereau, S.Inoue, M.Tuck, L.Lorenzi, V.Kwakwa, K.Alsinet, C.Olabi, B.Miah, M.Admane, C.Popescu, D.-M.Acres, M.Dixon, D.Coulthard, R.Lisgo, S.Henderson, D. J.Dann, E.Su, C.Kinston, S. J.Park, J.-e.Polanski, K.Van Dongen, S.Meyer, K. B.de Bruijn, M.Palis, J.Behjati, S2022-08-05doi:10.1101/2022.08.03.502475Cold Spring Harbor Laboratory Press2022-08-05
<![CDATA[
Monopogen: single nucleotide variant calling from single cell sequencing
]]>
https://biorxiv.org/cgi/content/short/2022.12.04.519058v1?rss=1"
Dou, J.Tan, Y.Kock, k. H.Wang, J.Cheng, X.Tan, L. M.Han, K. Y.Hon, C.-C.Park, W. Y.Shin, J. W.Chen, H.Prabhakar, S.Navin, N.Chen, R.Chen, K.2022-12-07doi:10.1101/2022.12.04.519058Cold Spring Harbor Laboratory Press2022-12-07
<![CDATA[
A multi-tissue single-cell tumor microenvironment atlas reveals myeloid-derived cell states with significant impact on clinical outcome
]]>
https://biorxiv.org/cgi/content/short/2023.01.04.522727v1?rss=1"
Maklouf, G. R.Guimaraes, G. R.Teixeira, C. E.Pretti, M. A. M.de Oliveira Santos, L.Tessarollo, N. G.Toledo, N. E.Falchetti, M.Dimas, M. M.Serain, A. F.Bastos, N. C.de Macedo, F. C.Rodrigues, F. R.da Silva, J. L.Lummertz-Rocha, E.Chaves, C. B. P.de Melo, A. C.Moraes-Vieira, P. M. M.Mori, M. A.Boroni, M.2023-01-04doi:10.1101/2023.01.04.522727Cold Spring Harbor Laboratory Press2023-01-04
<![CDATA[
SuperCellCyto: enabling efficient analysis of large scale cytometry datasets
]]>
https://biorxiv.org/cgi/content/short/2023.08.14.553168v1?rss=1"
Putri, G. H.Howitt, G.Marsh-Wakefield, F.Ashhurst, T. M.Phipson, B.2023-08-14doi:10.1101/2023.08.14.553168Cold Spring Harbor Laboratory Press2023-08-14
<![CDATA[
A human embryonic limb cell atlas resolved in space and time
]]>
https://biorxiv.org/cgi/content/short/2022.04.27.489800v1?rss=1"
Zhang, B.He, P.Lawrence, J. E.Wang, S.Tuck, E.Williams, B. A.Roberts, K.Kleshchevnikov, V.Mamanova, L.Bolt, L.Polanski, K.Elmentaite, R.Fasouli, E. S.Prete, M.He, X.Yayon, N.Fu, Y.Yang, H.Liang, C.Zhang, H.Fitzpatrick, D.Firth, H.Dean, A.Marioni, J.Barker, R. A.Storer, M. A.Wold, B.Zhang, H.Teichmann, S.2022-04-28doi:10.1101/2022.04.27.489800Cold Spring Harbor Laboratory Press2022-04-28
<![CDATA[
Scalable querying of human cell atlases via a foundational model reveals commonalities across fibrosis-associated macrophages
]]>
https://biorxiv.org/cgi/content/short/2023.07.18.549537v1?rss=1"
Heimberg, G.Kuo, T. C.DePianto, D.Heigl, T.Diamant, N.Salem, O.Scalia, G.Biancalani, T.Rock, J.Turley, S.Bravo, H. C.Kaminker, J.Vander Heiden, J. A.Regev, A.2023-07-19doi:10.1101/2023.07.18.549537Cold Spring Harbor Laboratory Press2023-07-19
<![CDATA[
multiDGD: A versatile deep generative model for multi-omics data
]]>
https://biorxiv.org/cgi/content/short/2023.08.23.554420v1?rss=1"
Schuster, V.Dann, E.Krogh, A.Teichmann, S.2023-08-23doi:10.1101/2023.08.23.554420Cold Spring Harbor Laboratory Press2023-08-23
<![CDATA[
Polybacterial intracellular coinfection of epithelial stem cells in periodontitis
]]>
https://biorxiv.org/cgi/content/short/2023.08.23.554343v1?rss=1"
Easter, Q. T.Matuck, B. F.Stark, G. B.Worth, C. L.Predeus, A. V.Fremin, B.Huynh, K. T.Ranganathan, V.Pereira, D.Weaver, T.Miller, K.Perez, P.Hasuike, A.Chen, Z.Bush, M.Qu, X.Warner, B. M.Lee, J.Wallet, S. M.Sequeira, I.Tyc, K. M.Liu, J.Ko, K. I.Teichmann, S. A.Byrd, K. M.2023-08-24doi:10.1101/2023.08.23.554343Cold Spring Harbor Laboratory Press2023-08-24
<![CDATA[
Human subcutaneous and visceral adipocyte atlases uncover classical and specialized adipocytes and depot-specific patterns
]]>
https://biorxiv.org/cgi/content/short/2023.09.04.555678v1?rss=1"
Lazarescu, O.Ziv Agam, M.Haim, Y.Hekselman, I.Jubran, J.Shneyour, A.Kitsberg, D.Levin, L.Liberty, I. F.Yoel, U.Dukhno, O.Adam, M.Korner, A.Murphy, R.Bluher, M.Habib, N.Rudich, A.Yeger-Lotem, E.2023-09-04doi:10.1101/2023.09.04.555678Cold Spring Harbor Laboratory Press2023-09-04
<![CDATA[
Consensus prediction of cell type labels with popV
]]>
https://biorxiv.org/cgi/content/short/2023.08.18.553912v1?rss=1"
Ergen, C.Xing, G.Xu, C.Jayasuriya, M.McGeever, E.Pisco, A. O.Streets, A. M.Yosef, N.2023-08-21doi:10.1101/2023.08.18.553912Cold Spring Harbor Laboratory Press2023-08-21
<![CDATA[
Cell type-specific gene expression dynamics during human brain maturation
]]>
https://biorxiv.org/cgi/content/short/2023.09.29.560114v1?rss=1"
Steyn, C.Mishi, R.Fillmore, S.Verhoog, M. B.More, J.Rohlwink, U. K.Melvill, R.Butler, J.Enslin, J. M. N.Jacobs, M.Quinones, S.Dulla, C. G.Raimondo, J. V.Figaji, A.Hockman, D.2023-09-29doi:10.1101/2023.09.29.560114Cold Spring Harbor Laboratory Press2023-09-29
<![CDATA[
Single-cell analysis of prenatal and postnatal human cortical development
]]>
https://biorxiv.org/cgi/content/short/2022.10.24.513555v1?rss=1"
Velmeshev, D.Perez, Y.Yan, Z.Valencia, J. E.Castaneda-Castellanos, D. R.Schirmer, L.Mayer, S.Wick, B.Wang, S.Nowakowski, T. J.Paredes, M.Huang, E. J. J.Kriegstein, A.2022-10-25doi:10.1101/2022.10.24.513555Cold Spring Harbor Laboratory Press2022-10-25
<![CDATA[
Spatiotemporal molecular dynamics of the developing human thalamus
]]>
https://biorxiv.org/cgi/content/short/2023.08.21.554174v1?rss=1"
Kim, C.Shin, D.Wang, A.Nowakowski, T.2023-08-22doi:10.1101/2023.08.21.554174Cold Spring Harbor Laboratory Press2023-08-22
<![CDATA[
Inter-individual variation in human cortical cell type abundance and expression
]]>
https://biorxiv.org/cgi/content/short/2022.10.07.511366v1?rss=1"
Johansen, N.Somasundaram, S.Travaglini, K. J.Yanny, A. M.Shumyatcher, M.Casper, T.Cobbs, C.Dee, N.Ellenbogen, R.Ferreira, M.Goldy, J.Guzman, J.Gwinn, R.Hirschstein, D.Jorstad, N. L.Keene, C. D.Ko, A.Levi, B. P.Ojemann, J. G.Pham, T.Shapovalova, N.Silbergeld, D.Sulc, J.Torkelson, A.Tung, H.Smith, K.Lein, E. S.Bakken, T. E.Hodge, R. D.Miller, J. A.2022-10-07doi:10.1101/2022.10.07.511366Cold Spring Harbor Laboratory Press2022-10-07
<![CDATA[
Transcriptomic cytoarchitecture reveals principles of human neocortex organization
]]>
https://biorxiv.org/cgi/content/short/2022.11.06.515349v1?rss=1"
Jorstad, N. L.Close, J.Johansen, N.Yanny, A. M.Barkan, E. R.Travaglini, K. J.Bertagnolli, D.Campos, J.Casper, T.Crichton, K.Dee, N.Ding, S.-L.Gelfand, E.Goldy, J.Hirschstein, D.Kroll, M.Kunst, M.Lathia, K.Long, B.Martin, N.McMillen, D.Pham, T.Rimorin, C.Ruiz, A.Shapovalova, N.Shehata, S.Siletti, K.Somasundaram, S.Sulc, J.Tieu, M.Torkelson, A.Tung, H.Ward, K.Callaway, E. M.Hof, P. R.Keene, C. D.Levi, B. P.Linnarsson, S.Mitra, P. P.Smith, K.Hodge, R. D.Bakken, T. E.Lein, E. S.2022-11-06doi:10.1101/2022.11.06.515349Cold Spring Harbor Laboratory Press2022-11-06
<![CDATA[
Signature morpho-electric properties of diverse GABAergic interneurons in the human neocortex
]]>
https://biorxiv.org/cgi/content/short/2022.11.08.515739v1?rss=1"
Lee, B.Dalley, R.Miller, J. A.Chartrand, T.Close, J.Mann, R.Mukora, A.Ng, L.Alfiler, L.Baker, K.Bertagnolli, D.Brouner, K.Casper, T.Csajbok, E.Dee, N.Donadio, N.Driessens, S. L. W.Egdorf, T.Enstrom, R.Galakhova, A. A.Gary, A.Gelfand, E.Goldy, J.Hadley, K.Heistek, T. S.Hill, D.Johansen, N.Jorstad, N.Kim, L.Kocsis, A. K.Kruse, L.Kunst, M.Leon, G.Long, B.Mallory, M.Maxwell, M.McGraw, M.McMillen, D.Melief, E. J.Molnar, G.Mortrud, M. T.Newman, D.Nyhus, J.Opitz-Araya, X.Pham, T.Pom, A.Potekhina, L.Rajanbabu2022-11-09doi:10.1101/2022.11.08.515739Cold Spring Harbor Laboratory Press2022-11-09
<![CDATA[
Morpho-electric and transcriptomic divergence of the layer 1 interneuron repertoire in human versus mouse neocortex
]]>
https://biorxiv.org/cgi/content/short/2022.10.24.511199v1?rss=1"
Chartrand, T.Dalley, R.Close, J.Goriounova, N. A.Lee, B. R.Mann, R.Miller, J. A.Molnar, G.Mukora, A.Alfiler, L.Baker, K.Bakken, T. E.Berg, J.Bertagnolli, D.Braun, T.Brouner, K.Casper, T.Csajbok, E. A.Dee, N.Egdorf, T.Enstrom, R.Galakhova, A. A.Gary, A.Gelfand, E.Goldy, J.Hadley, K.Heistek, T. S.Hill, D.Jorstad, N.Kim, L.Kocsis, A. K.Kruse, L.Leon, G.Long, B.Mallory, M.McGraw, M.McMillen, D.Melief, E. J.Mihut, N.Ng, L.Nyhus, J.Omstead, V.Peterfi, Z.Pom, A.Potekhina, L.Rajanbabu, R.Rozsa, M.Ruiz, A.Sa2022-10-25doi:10.1101/2022.10.24.511199Cold Spring Harbor Laboratory Press2022-10-25
<![CDATA[
Comparative transcriptomics reveals human-specific cortical features
]]>
https://biorxiv.org/cgi/content/short/2022.09.19.508480v1?rss=1"
Jorstad, N. L.Song, J. H. T.Exposito-Alonso, D.Suresh, H.Castro, N.Krienen, F. M.Yanny, A. M.Close, J.Gelfand, E.Travaglini, K. J.Basu, S.Beaudin, M.Bertagnolli, D.Crow, M.Ding, S.-L.Eggermont, J.Glandon, A.Goldy, J.Kroes, T.Long, B.McMillen, D.Pham, T.Rimorin, C.Siletti, K.Somasundaram, S.Tieu, M.Torkelson, A.Ward, K.Feng, G.Hopkins, W. D.Hollt, T.Keene, C. D.Linnarsson, S.McCarroll, S. A.Lelieveldt, B. P.Sherwood, C. C.Smith, K.Walsh, C. A.Dobin, A.Gillis, J.Lein, E. S.Hodge, R. D.Bakken, T. E.2022-09-19doi:10.1101/2022.09.19.508480Cold Spring Harbor Laboratory Press2022-09-19
<![CDATA[
A comparative atlas of single-cell chromatin accessibility in the human brain
]]>
https://biorxiv.org/cgi/content/short/2022.11.09.515833v1?rss=1"
Li, Y. E.Preissl, S.Miller, M.Johnson, N. D.Wang, Z.Jiao, H.Zhu, C.Wang, Z.Xie, Y.Poirin, O.Kern, C.Pinto-Duarte, A.Tian, W.Siletti, K.Emerson, N.Osteen, J.Lucero, J.Lin, L.Yang, Q.Espinoza, S.Zhu, Q.Zemke, N.Yanny, A. M.Nyhus, J.Dee, N.Casper, T.Shapovalova, N.Hirschstein, D.Hodge, R. D.Linnarsson, S.Bakken, T. E.Levi, B.Keene, C. D.Shang, J.Lein, E. S.Wang, A.Behrens, M. M.Ecker, J. R.Ren, B.2022-11-10doi:10.1101/2022.11.09.515833Cold Spring Harbor Laboratory Press2022-11-10
<![CDATA[
Molecular programs of regional specification and neural stem cell fate progression in developing macaque telencephalon
]]>
https://biorxiv.org/cgi/content/short/2022.10.18.512724v1?rss=1"
Micali, N.Ma, S.Li, M.Kim, S.-K.Mato-Blanco, X.Sindhu, S.Arellano, J. I.Gao, T.Duque, A.Santpere, G.Sestan, N.Rakic, P.2022-10-18doi:10.1101/2022.10.18.512724Cold Spring Harbor Laboratory Press2022-10-18
<![CDATA[
Temporal disparity of action potentials triggered in axon initial segments and distal axons in the neocortex
]]>
https://biorxiv.org/cgi/content/short/2022.08.09.503303v1?rss=1"
Rozsa, M.Toth, M.Olah, G.Baka, J.Lakovics, R.Barzo, P.Tamas, G.2022-08-10doi:10.1101/2022.08.09.503303Cold Spring Harbor Laboratory Press2022-08-10
<![CDATA[
Human voltage-gated Na+ and K+ channel properties underlie sustained fast AP signaling
]]>
https://biorxiv.org/cgi/content/short/2022.11.29.518317v1?rss=1"
Wilbers, R.Metodieva, V. D.Duverdin, S.Heyer, D. B.Galakhova, A. A.Mertens, E. J.Versluis, T. D.Baayen, J. C.Idema, S.Noske, D. P.Verburg, N.Willemse, R. B.de Witt Hamer, P. C.Kole, M. H. P.de Kock, C. P. J.Mansvelder, H. D.Goriounova, N. A.2022-12-02doi:10.1101/2022.11.29.518317Cold Spring Harbor Laboratory Press2022-12-02
<![CDATA[
Whole Human-Brain Mapping of Single Cortical Neurons for Profiling Morphological Diversity and Stereotypy
]]>
https://biorxiv.org/cgi/content/short/2022.10.29.514375v1?rss=1"
Han, X.Guo, S.Ji, N.Li, T.Liu, J.Ye, X.Wang, Y.Yun, Z.Xiong, F.Rong, J.Liu, D.Ma, H.Wang, Y.Huang, Y.Zhang, P.Wu, W.Ding, L.Hawrylycz, M.Lein, E.Ascoli, G. A.Xie, W.Liu, L.Zhang, L.Peng, H.2022-10-30doi:10.1101/2022.10.29.514375Cold Spring Harbor Laboratory Press2022-10-30
<![CDATA[
Structural and functional specializations of human fast spiking neurons support fast cortical signaling
]]>
https://biorxiv.org/cgi/content/short/2022.11.29.518193v1?rss=1"
Wilbers, R.Galakhova, A. A.Heistek, T. S.Metodieva, V. D.Hagemann, J.Heyer, D. B.Mertens, E. J.Deng, S.Idema, S.de Witt Hamer, P. C.Noske, D. P.van Schie, P.Kommers, I.Luan, G.Li, T.Shu, Y.de Kock, C. P. J.Mansvelder, H. D.Goriounova, N. A.2022-11-29doi:10.1101/2022.11.29.518193Cold Spring Harbor Laboratory Press2022-11-29
<![CDATA[
A single-cell multi-omic atlas spanning the adult rhesus macaque brain
]]>
https://biorxiv.org/cgi/content/short/2022.09.30.510346v1?rss=1"
Chiou, K. L.Huang, X.Bohlen, M. O.Tremblay, S.O'Day, D. R.Spurrell, C. H.Gogate, A. A.Zintel, T. M.Cayo Biobank Research Unit,Andrews, M. G.Martinez, M. I.Starita, L. M.Montague, M. J.Platt, M. L.Shendure, J.Snyder-Mackler, N.2022-10-03doi:10.1101/2022.09.30.510346Cold Spring Harbor Laboratory Press2022-10-03
<![CDATA[
Multi-omic profiling of the developing human cerebral cortex at the single cell level
]]>
https://biorxiv.org/cgi/content/short/2022.10.14.512250v1?rss=1"
Zhu, K.Bendl, J.Rahman, S.Vicari, J. M.Coleman, C.Clarence, T.Latouche, O.Tsankova, N. M.Li, A.Brennand, K. J.Lee, D.Yuan, G.Fullard, J. F.Roussos, P.2022-10-17doi:10.1101/2022.10.14.512250Cold Spring Harbor Laboratory Press2022-10-17
<![CDATA[
A marmoset brain cell census reveals persistent influence of developmental origin on neurons
]]>
https://biorxiv.org/cgi/content/short/2022.10.18.512442v1?rss=1"
Krienen, F. M.Levandowski, K. M.Zaniewski, H.del Rosario, R. C.Schroeder, M. E.Goldman, M.Lutservitz, A.Zhang, Q.Li, K. X.Beja-Glasser, V. F.Sharma, J.Shin, T. W.Mauermann, A.Wysoker, A.Nemesh, J.Kashin, S.Vergara, J.Chelini, G.Dimidschstein, J.Berretta, S.Boyden, E.McCarroll, S. A.Feng, G.2022-10-19doi:10.1101/2022.10.18.512442Cold Spring Harbor Laboratory Press2022-10-19
<![CDATA[
Epigenomic complexity of the human brain revealed by single-cell DNA methylomes and 3D genome structures
]]>
https://biorxiv.org/cgi/content/short/2022.11.30.518285v1?rss=1"
Tian, W.Zhou, J.Bartlett, A.Zeng, Q.Liu, H.Castanon, R. G.Kenworthy, M.Altshul, J.Valadon, C.Aldridge, A.Nery, J. R.Chen, H.Xu, J.Johnson, N. D.Lucero, J.Osteen, J. K.Emerson, N.Rink, J.Lee, J.Li, Y.Siletti, K.Liem, M.Claffey, N.OConnor, C.Yanny, A. M.Nyhus, J.Dee, N.Casper, T.Shapovalova, N.Hirschstein, D.Hodge, R.Levi, B. P.Keene, C. D.Linnarsson, S.Lein, E.Ren, B.Behrens, M. M.Ecker, J. R.2022-12-01doi:10.1101/2022.11.30.518285Cold Spring Harbor Laboratory Press2022-12-01
<![CDATA[
A multimodal imaging and analysis pipeline for creating a cellular census of the human cerebral cortex
]]>
https://biorxiv.org/cgi/content/short/2021.10.20.464979v1?rss=1"
Costantini, I.Morgan, L.Yang, J.Balbastre, Y.Varadarajan, D.Pesce, L.Scardigli, M.Mazzamuto, G.Gavryusev, V.Castelli, F. M.Roffilli, M.Silvestri, L.Laffey, J.Raia, S.Varghese, M.Wicinski, B.Chang, S.Chen I-Chun, A.Wang, H.Cordero, D.Vera, M.Nolan, J.Nestor, K.Mora, J.Iglesias, J. E.Pallares, E. G.Evancic, K.Augustinack, J.Fogarty, M.Dalca, A. V.Frosch, M.Magnain, C.Frost, R.van der Kouwe, A.Chen, S.-C.Boas, D. A.Pavone, F. S.Fischl, B.Hof, P. R.2021-10-21doi:10.1101/2021.10.20.464979Cold Spring Harbor Laboratory Press2021-10-21
<![CDATA[
Early-childhood inflammation blunts the transcriptional maturation of cerebellar neurons
]]>
https://biorxiv.org/cgi/content/short/2022.07.26.501598v1?rss=1"
Ament, S. A.Cortes-Gutierrez, M.Herb, B. R.Mocci, E.Colantuoni, C.McCarthy, M. M.2022-07-26doi:10.1101/2022.07.26.501598Cold Spring Harbor Laboratory Press2022-07-26
<![CDATA[
Single-cell genomics reveals region-specific developmental trajectories underlying neuronal diversity in the prenatal human hypothalamus
]]>
https://biorxiv.org/cgi/content/short/2021.07.20.453090v1?rss=1"
Herb, B.Glover, H. J.Bhaduri, A.Casella, A. M.Bale, T. L.Kriegstein, A.Doege, C.Ament, S. A.2021-07-20doi:10.1101/2021.07.20.453090Cold Spring Harbor Laboratory Press2021-07-20
<![CDATA[
Integrated platform for multi-scale molecular imaging andphenotyping of the human brain
]]>
https://biorxiv.org/cgi/content/short/2022.03.13.484171v1?rss=1"
Park, J.Wang, J.Guan, W.Kamentsky, L.Evans, N. B.Gjesteby, L.Pollack, D.Choi, S. W.Snyder, M.Chavez, D.Tian, Y.Su-Arcaro, C.Yun, D. H.Zhao, C.Brattain, L.Frosh, M. P.Chung, K.2022-03-15doi:10.1101/2022.03.13.484171Cold Spring Harbor Laboratory Press2022-03-15
<![CDATA[
An Atlas of Cells in the Human Tonsil
]]>
https://biorxiv.org/cgi/content/short/2022.06.24.497299v1?rss=1"
357,000 cells. We provide a glossary of 121 annotated cell types and states, and disentangle gene regulatory mechanisms that drive cells through specialized lineage trajectories. Exemplarily, we stratify multiple tonsil-resident myeloid slancyte subtypes, establish a distant BCL6 superenhancer as locally active in both follicle-associated T and B cells, and describe SIX5 as a potentially novel transcriptional regulator of plasma cell maturation. Further, our atlas is a reference map to understand alterations observed in disease. Here, we discover immune-phenotype plasticity in tumoral cells and microenvironment shifts of mantle cell lymphomas (MCL). To facilitate such reference-based analysis, we develop HCATonsilData and SLOcatoR, a computational framework that provides programmatic and modular access to our dataset; and allows the straightforward annotation of future single-cell profiles from secondary lymphoid organs.
]]>Massoni-Badosa, R.Soler-Vila, P.Aguilar-Fernandez, S.Nieto, J. C.Elosua-Bayes, M.Marchese, D.Kulis, M.Vilas-Zornoza, A.Bühler, M. M.Rashmi, S.Alsinet, C.Caratu, G.Moutinho, C.Ruiz, S.Lorden, P.Lunazzi, G.Colomer, D.Frigola, G.Blevins, W.Palomino, S.Gomez-Cabrero, D.Aguirre, X.Weniger, M. A.Marini, F.Cervera-Paz, F. J.Baptista, P. M.Vilaseca, I.Prosper, F.Küppers, R.Gut, I. G.Campo, E.Martin-Subero, J. I.Heyn, H.2022-06-26doi:10.1101/2022.06.24.497299Cold Spring Harbor Laboratory Press2022-06-26
<![CDATA[
Quantification of the escape from X chromosome inactivation with the million cell-scale human single-cell omics datasets reveals heterogeneity of escape across cell types and tissues
]]>
https://biorxiv.org/cgi/content/short/2023.10.14.561800v1?rss=1"
Tomofuji, Y.Edahiro, R.Shirai, Y.Kock, K. H.Sonehara, K.Wang, Q. S.Namba, S.Moody, J.Ando, Y.Suzuki, A.Yata, T.Ogawa, K.Namkoong, H.Lin, Q. X. X.Buyamin, E. V.Tan, L. M.Sonthalia, R.Han, K. Y.Tanaka, H.Lee, H.Asian Immune Diversity Atlas Network,Japan COVID-19 Task Force,The BioBank Japan Project,Okuno, T.Liu, B.Matsuda, K.Fukunaga, K.Mochizuki, H.Park, W.-Y.Yamamoto, K.Hon, C.-C.Shin, J. W.Prabhakar, S.Kumanogoh, A.Okada, Y.2023-10-18doi:10.1101/2023.10.14.561800Cold Spring Harbor Laboratory Press2023-10-18
<![CDATA[
Integrated spatial protein and RNA analysis on the same section using MICS technology
]]>
https://biorxiv.org/cgi/content/short/2023.10.27.564191v1?rss=1"
Neil, E.Park, D.Hennessey, R. C.DiBiasio, E. C.DiBuono, M.Lafayette, H.Lloyd, E.Lo, H.Femel, J.Makrigiorgos, A.Soliman, S.Mangiardi, D.Praveen, P.Rüberg, S.Staubach, F.Hindman, R.Rothmann, T.Meyer, H.Wantenaar, T.Wang, J.Müller, W.Pinard, R.Bosio, A.2023-10-27doi:10.1101/2023.10.27.564191Cold Spring Harbor Laboratory Press2023-10-27
<![CDATA[
Scaling cross-tissue single-cell annotation models
]]>
https://biorxiv.org/cgi/content/short/2023.10.07.561331v1?rss=1"
Fischer, F.Fischer, D. S.Biederstedt, E.Villani, A.-C.Theis, F. J.2023-10-10doi:10.1101/2023.10.07.561331Cold Spring Harbor Laboratory Press2023-10-10
<![CDATA[
Pan-cancer profiling of tumor-infiltrating natural killer cells through transcriptional reference mapping
]]>
https://biorxiv.org/cgi/content/short/2023.10.26.564050v1?rss=1"
Netskar, H. K.Pfefferle, A.Goodridge, J. P.Sohlberg, E.Dufva, O.Teichmann, S.Clancy, T.horowitz, a.Malmberg, K.-J.2023-10-30doi:10.1101/2023.10.26.564050Cold Spring Harbor Laboratory Press2023-10-30
<![CDATA[
Oncogenic RAS-Pathway Activation Drives Oncofetal Reprogramming and Creates Therapeutic Vulnerabilities in Juvenile Myelomonocytic Leukemia
]]>
https://biorxiv.org/cgi/content/short/2023.10.27.563754v1?rss=1"
Hartmann, M.Schoenung, M.Rajak, J.Maurer, V.Hai, L.Bauer, K.Hakobyan, M.Staeble, S.Langstein, J.Jardine, L.Roelz, R.Bohler, S.Khabirova, E.Maag, A.-H.Vonficht, D.Lebrecht, D.Bernt, K. M.Tan, K.Chen, C.Alikarami, F.Boch, T.Flore, V.Lutsik, P.Milsom, M. D.Raffel, S.Buske, C.Haas, S.Haniffa, M.Mallm, J.-P.Behjati, S.Bonder, M.-J.Froehling, S.Niemeyer, C. M.Hey, J.Flotho, C.Plass, C.Erlacher, M.Schlesner, M.Lipka, D. B.2023-11-01doi:10.1101/2023.10.27.563754Cold Spring Harbor Laboratory Press2023-11-01
<![CDATA[
Integrated multi-omics single cell atlas of the human retina
]]>
https://biorxiv.org/cgi/content/short/2023.11.07.566105v1?rss=1"
Li, J.Wang, J.Ibarra, I. L.Cheng, X.Luecken, M. D.Lu, J.Monavarfeshani, A.Yan, W.Zheng, Y.Zuo, Z.Colborn, S. L. Z.Cortez, B. S.Owen, L. A.Tran, N. M.Shekhar, K.Sanes, J. R.Stout, J. T.Chen, S.Li, Y.DeAngelis, M. M.Theis, F. J.Chen, R.2023-11-08doi:10.1101/2023.11.07.566105Cold Spring Harbor Laboratory Press2023-11-08
<![CDATA[
Early human fetal lung atlas reveals the temporal dynamics of epithelial cell plasticity.
]]>
https://biorxiv.org/cgi/content/short/2023.10.27.564403v1?rss=1"
150,000 single single-cells from 19 healthy human fetal lung tissues from gestational weeks 10-19 and identified at least 58 unique cell types/states contributing to the developing lung. We captured novel dynamic developmental trajectories from various progenitor cells that give rise to club, ciliated, and pulmonary neuroendocrine cells. We also identified four CFTR-expressing progenitor cell types and pinpointed the temporal emergence of these cell types. These developmental dynamics reveal broader epithelial cell plasticity and novel lineage hierarchies that were not previously reported. Combined with spatial transcriptomics, we identified both cell autonomous and non-cell autonomous signalling pathways that may dictate the temporal and spatial emergence of cell lineages. Finally, we showed that human pluripotent stem cell-derived fetal lung models capture cell lineage trajectories specifically through CFTR-expressing progenitor cells, that were also observed in the native fetal tissue. Overall, this study provides a comprehensive single-cell atlas of the developing human lung, outlining the temporal and spatial complexities of cell lineage development.
HighlightsO_LISingle-cell transcriptomics atlas from 19 human fetal lungs reveals cellular heterogeneity and previously unappreciated cellular plasticity in the epithelial compartment.
C_LIO_LIIdentification of novel CFTR-expressing progenitor cells that gives rise to club, ciliated and PNEC.
C_LIO_LINovel RNA velocity facilitated the identification of dynamic lineage trajectories in the epithelial compartment.
C_LIO_LITemporally regulated cell signaling through promiscuous interactions between sender and receiving cells may dictate cell lineage fates.
C_LIO_LIIntegration of human pluripotent stem cell (hPSC)-derived fetal lung cells and organoids with primary lung dataset show hPSC-differentiations captures key developmental trajectories of fetal epithelial cell states.
C_LI
]]>Quach, H. T.Farrell, S.Kanagarajah, K.Wu, M.Xu, X.Kallurkar, P.Turinsky, A.Bear, C.Ratjen, F.Goyal, S.Moraes, T. J.Wong, A.2023-10-28doi:10.1101/2023.10.27.564403Cold Spring Harbor Laboratory Press2023-10-28
<![CDATA[
Spatially resolved single-cell atlas of the lung in fatal Covid19 in an African population reveals a distinct cellular signature and an interferon gamma dominated response
]]>
https://biorxiv.org/cgi/content/short/2023.11.16.566964v1?rss=1"
Nyirenda, J.Hardy, O.Silva Filho, J. L.Herder, V.Attipa, C.Ndovi, C.Siwombo, M.Namalima, T.Suwedi, L.Nyasulu, W.Ngulube, T.Nyirenda, D.Mvaya, L.Phiri, J.Chasweka, D.Eneya, C.Makwinja, C.Phiri, C.Ziwoya, F.Tembo, A.Makwangwala, K.Khoswe, S.Banda, P.Morton, B.Hilton, O.Lawrence, S.Frere dos Reis, M.Cardoso Melo, G.Vinicious Guimaros de Lecerda, M.Trindande Maranhao Costa, F.Marcelo Monteiro, W.Carlos de Lima Fereirra, L.Johnson, C.Mcguinness, D.Jambo, K.Haley, M. J.Kumwenda, B.Palmarini, M.Barnes, K. G.Denno, D. M.Vo2023-11-17doi:10.1101/2023.11.16.566964Cold Spring Harbor Laboratory Press2023-11-17
<![CDATA[
scSemiProfiler: Advancing Large-scale Single-cell Studiesthrough Semi-profiling with Deep Generative Models andActive Learning
]]>
https://biorxiv.org/cgi/content/short/2023.11.20.567929v1?rss=1"
Wang, J.Fonseca, G. J.Ding, J.2023-11-21doi:10.1101/2023.11.20.567929Cold Spring Harbor Laboratory Press2023-11-21
<![CDATA[
A deep lung cell atlas reveals cytokine-mediated lineage switching of a rare cell progenitor of the human airway epithelium
]]>
https://biorxiv.org/cgi/content/short/2023.11.28.569028v1?rss=1"
Waghray, A.Monga, I.Lin, B.Shah, V.Slyper, M.Giotti, B.Xu, J.Waldman, J.Dionne, D.Nguyen, L. T.Lou, W.Cai, P.Park, E.Muus, C.Sun, J.Surve, M. V.Yang, L. C. C.Rozenblatt-Rosen, O.Dolerey, T. M.Saladi, S. V.Tsankov, A. M.Regev, A.Rajagopal, J.2023-11-29doi:10.1101/2023.11.28.569028Cold Spring Harbor Laboratory Press2023-11-29
<![CDATA[
Early human lung immune cell development and its role in epithelial cell fate
]]>
https://biorxiv.org/cgi/content/short/2022.12.13.519713v1?rss=1"
Barnes, J. L.He, P.Yoshida, M.Worlock, K. B.Lindeboom, R. G. H.Suo, C.Pett, J. P.Wilbrey-Clark, A.Dann, E.Mamanova, L.Richardson, L.Oliver, A. J.Pennycuick, A. L.Allen-Hyttinen, J.Herczeg, I. T.Hynds, R. E.Teixeira, V. H.Haniffa, M.Lim, K.Sun, D.Rawlins, E. L.Polanski, K.Lyons, P. A.Marioni, J. C.Tuong, Z. K.Clatworthy, M. R.Reading, J. L.Janes, S. M.Teichmann, S.Meyer, K. B.Nikolic, M. Z.2022-12-15doi:10.1101/2022.12.13.519713Cold Spring Harbor Laboratory Press2022-12-15
<![CDATA[
Automatic cell type harmonization and integration across Human Cell Atlas datasets
]]>
https://biorxiv.org/cgi/content/short/2023.05.01.538994v1?rss=1"
Xu, C.Prete, M.Webb, S.Jardine, L.Stewart, B.Hoo, R.He, P.Teichmann, S.2023-05-01doi:10.1101/2023.05.01.538994Cold Spring Harbor Laboratory Press2023-05-01
<![CDATA[
Human skeletal muscle ageing atlas
]]>
https://biorxiv.org/cgi/content/short/2022.05.24.493094v1?rss=1"
Kedlian, V. R.Wang, Y.Liu, T.Chen, X.Bolt, L.Shen, Z.Fasouli, E. S.Prigmore, E.Kleshchevnikov, V.Li, T.Lawrence, J. E.Huang, N.Guo, Q.Yang, L.Polanski, K.Dabrowska, M.Tudor, C.Li, X.Bayraktar, O. A.Patel, M.Meyer, K. B.Kumasaka, N.Mahbubani, K. T.Xiang, A. P.Saeb-Parsy, K.Teichmann, S. A.Zhang, H.2022-05-25doi:10.1101/2022.05.24.493094Cold Spring Harbor Laboratory Press2022-05-25
<![CDATA[
A single-cell atlas of transcribed cis-regulatory elements in the human genome
]]>
https://biorxiv.org/cgi/content/short/2023.11.13.566791v1?rss=1"
Moody, J.Kouno, T.Kojima, M.Koya, I.Leon, J.Suzuki, A.Hasegawa, A.Akiyama, T.Akiyama, N.Amagai, M.Chang, J.-C.Fukushima-Nomura, A.Handa, M.Hino, K.Hino, M.Hirata, T.Imai, Y.Inoue, K.Kawasaki, H.Kimura, T.Kinoshita, T.Kubo, K.-i.Kunii, Y.Lopez-Redondo, F.Manabe, R.-i.Miyai, T.Morimoto, S.Nagaoka, A.Nakajima, J.Noma, S.Okazaki, Y.Ozaki, K.Saeki, N.Sakai, H.Seyama, K.Shibayama, Y.Sujino, T.Tagami, M.Takahashi, H.Takao, M.Takeshita, M.Takiuchi, T.Terao, C.Yip, C. W.Yoshinaga, S.Okano, H.Yamamoto, K.Kasuka2023-11-14doi:10.1101/2023.11.13.566791Cold Spring Harbor Laboratory Press2023-11-14
<![CDATA[
WebAtlas pipeline for integrated single cell and spatial transcriptomic data
]]>
https://biorxiv.org/cgi/content/short/2023.05.19.541329v1?rss=1"
Li, T.Horsfall, D.Basurto-Lozada, D.Roberts, K.Prete, M.Lawrence, J. E. G.He, P.Tuck, E.Moore, J.Ghazanfar, S.Teichmann, S.Haniffa, M.Bayraktar, O. A.2023-05-22doi:10.1101/2023.05.19.541329Cold Spring Harbor Laboratory Press2023-05-22
<![CDATA[
Single cell-guided prenatal derivation of primary epithelial organoids from the human amniotic and tracheal fluids.
]]>
https://biorxiv.org/cgi/content/short/2023.05.31.539801v1?rss=1"
Gerli, M. F. M.Cala, G.Beesley, M. A.Sina, B.Tullie, L.Panariello, F.Michielin, F.Sun, K. Y.Davidson, J. R.Russo, F. M.Jones, B. C.Lee, D.Savvidis, S.Xenakis, T.Simcock, I. C.Straatman-Iwanowska, A. A.Hirst, R. A.David, A. L.O'Callaghan, C.Olivo, A.Eaton, S.Loukogeorgakis, S. P.Cacchiarelli, D.Deprest, J.Li, V. S.Giobbe, G. G.De Coppi, P.2023-06-01doi:10.1101/2023.05.31.539801Cold Spring Harbor Laboratory Press2023-06-01
<![CDATA[
Spatial transcriptomics of healthy and fibrotic human liver at single-cell resolution
]]>
https://biorxiv.org/cgi/content/short/2024.02.02.578633v1?rss=1"
Watson, B.Paul, B.Amir-Zilberstein, L.Segerstolpe, A.Rahman, R.Shih, A.Deguine, J.Xavier, R.Moffitt, J. R.Mullen, A. C.2024-02-07doi:10.1101/2024.02.02.578633Cold Spring Harbor Laboratory Press2024-02-07
<![CDATA[
Single nucleus and spatial transcriptomic profiling of human healthy hamstring tendon
]]>
https://biorxiv.org/cgi/content/short/2022.12.19.521110v1?rss=1"
Mimpen, J. Y.Ramos-Mucci, L. D.Paul, C.Kurjan, A.Hulley, P.Ikwuanusi, C.Gwilym, S.Baldwin, M. J.Cribbs, A. P.Snelling, S. J. B.2022-12-20doi:10.1101/2022.12.19.521110Cold Spring Harbor Laboratory Press2022-12-20
<![CDATA[
Cellular heterogeneity and dynamics of the human uterus in healthy premenopausal women
]]>
https://biorxiv.org/cgi/content/short/2024.03.07.583985v1?rss=1"
Ulrich, N. D.Vargo, A. H.Ma, Q.Shen, Y.-C.Hannum, D. F.Gurczynski, S. J.Moore, B. B.Schon, S.Lieberman, R.Shikanov, A.Marsh, E. E.Fazleabas, A. T.Li, J. Z.Hammoud, S. S.2024-03-12doi:10.1101/2024.03.07.583985Cold Spring Harbor Laboratory Press2024-03-12
<![CDATA[
Harnessing Agent-Based Modeling in CellAgentChat to Unravel Cell-Cell Interactions from Single-Cell Data
]]>
https://biorxiv.org/cgi/content/short/2023.08.23.554489v1?rss=1"
Raghavan, V.Ding, J.2023-08-24doi:10.1101/2023.08.23.554489Cold Spring Harbor Laboratory Press2023-08-24
<![CDATA[
Spatial landmark detection and tissue registration with deep learning
]]>
https://biorxiv.org/cgi/content/short/2023.08.24.554614v1?rss=1"
Ekvall, M. N.Bergenstrahle, L.Andersson, A.Olegard, J.Czarnewski, P.Kall, L.Lundeberg, J.2023-08-26doi:10.1101/2023.08.24.554614Cold Spring Harbor Laboratory Press2023-08-26
<![CDATA[
A General Framework for Representing and Annotating Multifaceted Cell Heterogeneity in Human Cell Atlas
]]>
https://biorxiv.org/cgi/content/short/2021.09.09.459281v1?rss=1"
Gao, H.Hua, K.Chen, S.Yin, Q.Jiang, R.Zhang, X.2021-09-10doi:10.1101/2021.09.09.459281Cold Spring Harbor Laboratory Press2021-09-10
<![CDATA[
Learning Spatially-Aware Representations of Transcriptomic Data via Transfer Learning
]]>
https://biorxiv.org/cgi/content/short/2022.09.23.509186v1?rss=1"
Hao, M.Wei, L.Zhang, X.2022-09-26doi:10.1101/2022.09.23.509186Cold Spring Harbor Laboratory Press2022-09-26
<![CDATA[
High-parametric protein maps reveal the spatial organization in early-developing human lung
]]>
https://biorxiv.org/cgi/content/short/2024.01.25.577163v1?rss=1"
Sariyar, S.Sountoulidis, A.Hansen, J. N.Salas, S. M.Mardamshina, M.Martinez Sacals, A.Ballllosera Navarro, F.Andrusivova, Z.Li, X.Czarnewski, P.Lundeberg, J.Linnarsson, S.Nilsson, M.Sundstrom, E.Samakovlis, C.Lundberg, E.Ayoglu, B.2024-01-25doi:10.1101/2024.01.25.577163Cold Spring Harbor Laboratory Press2024-01-25
<![CDATA[
An integrated transcriptomic cell atlas of human neural organoids
]]>
https://biorxiv.org/cgi/content/short/2023.10.05.561097v1?rss=1"
He, Z.Dony, L.Fleck, J. S.Szalata, A.Li, K. X.Sliskovic, I.Lin, H.-C.Santel, M.Atamian, A.Quadrato, G.Sun, J.Pasca, S. P.Camp, G.Theis, F.Treutlein, B.2023-10-06doi:10.1101/2023.10.05.561097Cold Spring Harbor Laboratory Press2023-10-06
<![CDATA[
Single nuclei chromatin accessibility and transcriptomic map of breast tissues of women of diverse genetic ancestry
]]>
https://biorxiv.org/cgi/content/short/2023.10.04.560911v1?rss=1"
Bhat-Nakshatri, P.Gao, H.Khatpe, A. S.McGuire, P. C.Erdogan, C.Chen, D.Jiang, G.New, F.German, R.Storniolo, A. M.Liu, Y.Nakshatri, H.2023-10-06doi:10.1101/2023.10.04.560911Cold Spring Harbor Laboratory Press2023-10-06
<![CDATA[
Quantifying Adaptive Evolution of the Human Immune Cell Landscape
]]>
https://biorxiv.org/cgi/content/short/2023.10.06.559946v1?rss=1"
Salvador-Martinez, I.Murga-Moreno, J.Nieto, J. C.Alsinet, C.Enard, D.Heyn, H.2023-10-06doi:10.1101/2023.10.06.559946Cold Spring Harbor Laboratory Press2023-10-06
<![CDATA[
An integrated transcriptomic cell atlas of human endoderm-derived organoids
]]>
https://biorxiv.org/cgi/content/short/2023.11.20.567825v1?rss=1"
Xu, Q.Halle, L.Hediyeh-zadeh, S.Kuijs, M.Kilik, U.Yu, Q.Frum, T.Adam, L.Parikh, S.Gander, M.Kfuri-Rubens, R.Klein, D.He, Z.Fleck, J. S.Oost, K.Kahnwald, M.Barbiero, S.Mitrofanova, O.Maciag, G.Jensen, K. B.Lutolf, M.Liberali, P.Beumer, J.Spence, J. R.Treutlein, B.Theis, F. J.Camp, J. G.2023-11-20doi:10.1101/2023.11.20.567825Cold Spring Harbor Laboratory Press2023-11-20
<![CDATA[
Bering: joint cell segmentation and annotation for spatial transcriptomics with transferred graph embeddings
]]>
https://biorxiv.org/cgi/content/short/2023.09.19.558548v1?rss=1"
Jin, K.Zhang, Z.Zhang, K.Viggiani, F.Callahan, C.Tang, J.Aronow, B. J.Shu, J.2023-09-22doi:10.1101/2023.09.19.558548Cold Spring Harbor Laboratory Press2023-09-22
<![CDATA[
A spatial human thymus cell atlas mapped to a continuous tissue axis
]]>
https://biorxiv.org/cgi/content/short/2023.10.25.562925v1?rss=1"
Yayon, N.Kedlian, V. R.Boehme, L.Suo, C.Wachter, B.Beuschel, R. T.Amsalem, O.Polanski, K.Koplev, S.Tuck, E.Dann, E.Van Hulle, J.Perera, S.Putteman, T.Predeus, A. V.Dabrowska, M.Richardson, L.Tudor, C.Kreins, A. Y.Engelbert, J.Stephenson, E.Kleshchevnikov, V.De Rita, F.Crossland, D.Bosticardo, M.Pala, F.Prigmore, E.Chipampe, N.-J.Prete, M.Fei, L.To, K.Barker, R. A.He, X.Van Nieuwerburgh, F.Bayraktar, O.Patel, M.Davies, G. E.Haniffa, M. A.Uhlmann, V.Notarangelo, L. D.Germain, R. N.Radtke, A. J.Marioni, J. C.Tag2023-10-28doi:10.1101/2023.10.25.562925Cold Spring Harbor Laboratory Press2023-10-28
<![CDATA[
Early infection response of the first trimester human placenta at single-cell scale
]]>
https://biorxiv.org/cgi/content/short/2023.01.02.522155v1?rss=1"
Hoo, R.Ruiz-Morales, E. R.Kelava, I.Sancho-Serra, C.Icoresi Mazzeo, C.Chelaghma, S.Tuck, E.Predeus, A. V.Fernandez-Antoran, D.Waller, R. F.Lee, M.Vento-Tormo, R.2023-01-02doi:10.1101/2023.01.02.522155Cold Spring Harbor Laboratory Press2023-01-02
<![CDATA[
A human prenatal skin cell atlas reveals immune cell regulation of skin morphogenesis
]]>
https://biorxiv.org/cgi/content/short/2023.10.12.556307v1?rss=1"
Gopee, N. H.Huang, N.Olabi, B.Admane, C.Botting, R. A.Foster, A. R.Torabi, F.Winheim, E.Sumanaweera, D. N.Goh, I.Miah, M.Stephenson, E.Tun, W. M.Moghimi, P.Rumney, B.He, P.Lawrence, S.Roberts, K.Sidhpura, K.Englebert, J.Jardine, L.Reynolds, G.Rose, A.Ganier, C.Rowe, V.Pritchard, S.Mulas, I.Fletcher, J.Popescu, D.-M.Poyner, E. F.Dubois, A.Filby, A.Lisgo, S.Barker, R. A.PARK, J.-E.Vento-Tormo, R.Le, P. A.Serdy, S.Kim, J.Deakin, C.Lee, J.Nikolova, M. T.Rajan, N.Ballereau, S.Li, T.Moore, J.Horsfall, D.Bas2023-10-12doi:10.1101/2023.10.12.556307Cold Spring Harbor Laboratory Press2023-10-12
<![CDATA[
An integrated single-cell atlas of the skeleton from development through adulthood
]]>
https://biorxiv.org/cgi/content/short/2022.03.14.484345v1?rss=1"
Herpelinck, T.Ory, L.Nasello, G.Barzegari, M.Bolander, J.Luyten, F. P.Tylzanowski, P.Geris, L.2022-03-15doi:10.1101/2022.03.14.484345Cold Spring Harbor Laboratory Press2022-03-15
<![CDATA[
uniLIVER: a Human Liver Cell Atlas for Data-Driven Cellular State Mapping
]]>
https://biorxiv.org/cgi/content/short/2023.12.09.570903v1?rss=1"
Wu, Y.Fan, Y.Miao, Y.Li, Y.Chen, Z.Du, G.Diao, J.Chen, Y.-A.Ye, M.You, R.Chen, A.Chen, Y.Li, W.Guo, W.Dong, J.Zhang, X.Wang, Y.Gu, J.2023-12-09doi:10.1101/2023.12.09.570903Cold Spring Harbor Laboratory Press2023-12-09
<![CDATA[
Cutaneous T cell lymphoma atlas reveals malignant Th2 cells supported by a B cell-rich microenvironment
]]>
https://biorxiv.org/cgi/content/short/2023.11.06.565474v1?rss=1"
Li, R.Strobl, J.Poyner, E. F. M.Torabi, F.Mazin, P.Chipampe, N.-J.Stephenson, E.Gardner, L.Olabi, B.Coulthard, R.Botting, R. A.Zila, N.Prigmore, E.Gopee, N.Engelbert, J.Goh, I.Chan, H. M.Johnson, H.Ellis, J.Rowe, V.Tun, W.Reynolds, G.Foster, A. R.Gambardella, L.Winheim, E.Admane, C.Rumney, B.Steele, L.Jardine, L.Nenonen, J.Pickard, K.Lumley, J.Hampton, P.Hu, S.Liu, F.Liu, X.Horsfall, D.Basurto-Lozada, D.Grimble, L.Bacon, C. M.Weatherhead, S.Brauner, H.Wang, Y.Bai, F.Reynolds, N. J.Allen, J. E.Jonak, C.2023-11-07doi:10.1101/2023.11.06.565474Cold Spring Harbor Laboratory Press2023-11-07
<![CDATA[
An integrated single-cell reference atlas of the human endometrium
]]>
https://biorxiv.org/cgi/content/short/2023.11.03.564728v1?rss=1"
Mareckova, M.Garcia-Alonso, L.Moullet, M.Lorenzi, V.Petryszak, R.Sancho-Serra, C.Oszlanczi, A.Icoresi Mazzeo, C.Hoffman, S.Krassowski, M.Garbutt, K.Kelava, I.Gaitskell, K.Yancheva, S.Von Woon, E.Male, V.Granne, I.Hellner, K.Mahbubani, K. T.Saeb-Parsy, K.Lotfollahi, M.Prigmore, E.Southcombe, J.Dragovic, R. A.Becker, C. M.Zondervan, K. T.Vento-Tormo, R.2023-11-05doi:10.1101/2023.11.03.564728Cold Spring Harbor Laboratory Press2023-11-05
<![CDATA[
Molecular atlas of the human brain vasculature at the single-cell level
]]>
https://biorxiv.org/cgi/content/short/2021.10.18.464715v1?rss=1"
Wälchli, T.Ghobrial, M.Schwab, M.Takada, S.Zhong, H.Suntharalingham, S.Vetiska, S.Rodrigues Rodrigues, D.Rehrauer, H.Wu, R.Yu, K.Bisschop, J.Farnhammer, F.Regli, L.Schaller, K.Frei, K.Ketela, T.Bernstein, M.Kongkham, P.Carmeliet, P.Valiante, T.Dirks, P. B.Suva, M. L.Zadeh, G.Tabar, V.Schlapbach, R.De Bock, K.Fish, J.Monnier, P.Bader, G.Radovanovic, I.2021-10-19doi:10.1101/2021.10.18.464715Cold Spring Harbor Laboratory Press2021-10-19
<![CDATA[
Cell type-specific effects of age and sex on human cortical neurons
]]>
https://biorxiv.org/cgi/content/short/2023.11.11.566717v1?rss=1"
Chien, J.-F.Liu, H.Wang, B.-A.Luo, C.Bartlett, A.Castanon, R.Johnson, N. D.Nery, J. R.Osteen, J.Li, J.Altshul, J.Kenworthy, M.Valadon, C.Liem, M.Claffey, N.O'Connor, C.Seeker, L. A.Ecker, J. R.Behrens, M. M.Mukamel, E. A.2023-11-15doi:10.1101/2023.11.11.566717Cold Spring Harbor Laboratory Press2023-11-15
<![CDATA[
Single Cell Transcriptomic Landscape of Diabetic Foot Ulcers
]]>
https://biorxiv.org/cgi/content/short/2021.03.11.434413v1?rss=1"
Theocharidis, G.Thomas, B. E.Sarkar, D.Pilcher, W. J.Dwivedi, B.Sandoval-Schaefer, T.Sirbulescu, R. F.Kafanas, A.Mezghani, I.Wang, P.Lobao, A.Vlachos, I.Dash, B.Hsia, H. C.Horsley, V.Bhasin, S. S.Veves, A.Bhasin, M.2021-03-12doi:10.1101/2021.03.11.434413Cold Spring Harbor Laboratory Press2021-03-12
<![CDATA[
Single cell transcriptomics reveals distinct effector profiles of infiltrating T cells in lupus skin and kidney
]]>
https://biorxiv.org/cgi/content/short/2021.10.19.464575v1?rss=1"
Dunlap, G. S.Billi, A. C.Ma, F.Maz, M.Tsoi, L. C.Wasikowski, R.Gudjonsson, J. E.Kahlenberg, J. M.Rao, D. A.2021-10-19doi:10.1101/2021.10.19.464575Cold Spring Harbor Laboratory Press2021-10-19
<![CDATA[
Single cell transcriptomics of human epidermis reveals basal stem cell transition states
]]>
https://biorxiv.org/cgi/content/short/784579v1?rss=1"
Wang, S.Drummond, M. L.Guerrero-Juarez, C. F.Tarapore, E.MacLean, A. L.Stabell, A. R.Wu, S. C.Gutierrez, G.That, B. T.Benavente, C. A.Nie, Q.Atwood, S. X.2019-09-30doi:10.1101/784579Cold Spring Harbor Laboratory Press2019-09-30
<![CDATA[
Myofibroblast transcriptome indicates SFRP2+ fibroblast progenitors in systemic sclerosis skin
]]>
https://biorxiv.org/cgi/content/short/2021.04.30.442148v1?rss=1"
Tabib, T.Huang, M. A.Morse, C.Papazoglou, A.Behera, R.Jia, M.Bulik, M.Monier, D. E.Benos, P. V.Chen, W.Domsic, R.Lafyatis, R.2021-04-30doi:10.1101/2021.04.30.442148Cold Spring Harbor Laboratory Press2021-04-30
<![CDATA[
Defining cellular complexity in human autosomal dominant polycystic kidney disease by multimodal single cell analysis
]]>
https://biorxiv.org/cgi/content/short/2021.10.21.465323v1?rss=1"
Muto, Y.Dixon, E. E.Yoshimura, Y.Wu, H.Omachi, K.King, A. J.Olson, E. N.Gunawan, M. G.Kuo, J. J.Cox, J.Miner, J. H.Seliger, S. L.Woodward, O. M.Welling, P. A.Watnick, T. J.Humphreys, B. D.2021-10-22doi:10.1101/2021.10.21.465323Cold Spring Harbor Laboratory Press2021-10-22
<![CDATA[
The Single Cell Transcriptomic Landscape of Early Human Diabetic Nephropathy
]]>
https://biorxiv.org/cgi/content/short/645424v1?rss=1"
Wilson, P. C.Wu, H.Kirita, Y.Uchimura, K.Rennke, H. G.Welling, P. A.Waikar, S. S.Humphreys, B. D.2019-05-24doi:10.1101/645424Cold Spring Harbor Laboratory Press2019-05-24
<![CDATA[
Harnessing Expressed Single Nucleotide Variation and Single Cell RNA Sequencing to Define Immune Cell Chimerism in the Rejecting Kidney Transplant
]]>
https://biorxiv.org/cgi/content/short/2020.03.10.986075v1?rss=1"
Malone, A. F.Wu, H.Fronick, C.Fulton, R.Gaut, J. P.Humphreys, B. D.2020-03-11doi:10.1101/2020.03.10.986075Cold Spring Harbor Laboratory Press2020-03-11
<![CDATA[
Defining Cardiac Recovery at Single Cell Resolution
]]>
https://biorxiv.org/cgi/content/short/2022.09.11.507463v1?rss=1"
Amrute, J. M.Lai, L.Ma, P.Koenig, A. L.Kamimoto, K.Bredemeyer, A.Shankar, T. S.Kuppe, C.Kadyrov, F. F.Schulte, L. J.Stoutenburg, D.Kopecky, B.Navankasattusas, S.Visker, J.Morris, S. A.Kramann, R.Leuschner, F.Mann, D. L.Drakos, S. G.Lavine, K. J.2022-09-13doi:10.1101/2022.09.11.507463Cold Spring Harbor Laboratory Press2022-09-13
<![CDATA[
Targeting the Immune-Fibrosis Axis in Myocardial Infarction and Heart Failure
]]>
https://biorxiv.org/cgi/content/short/2022.10.17.512579v1?rss=1"
Amrute, J. M.Luo, X.Penna, V.Bredemeyer, A.Yamawaki, T.Heo, G. S.Shi, S.Koenig, A. L.Yang, S.Kadyrov, F. F.Jones, C.Kuppe, C.Kopecky, B.Hayat, S.Ma, P.Feng, G.Terada, Y.Fu, A.Furtado, M.Kreisel, D.Stitziel, N. O.Li, C.-M. K.Kramann, R.Liu, Y.Ason, B.Lavine, K.2022-10-21doi:10.1101/2022.10.17.512579Cold Spring Harbor Laboratory Press2022-10-21
<![CDATA[
Spatial multi-omic map of human myocardial infarction
]]>
https://biorxiv.org/cgi/content/short/2020.12.08.411686v1?rss=1"
Kuppe, C.Ramirez Flores, R. O.Li, Z.Hannani, M. T.Tanevski, J.Halder, M.Cheng, M.Ziegler, S.Zhang, X.Priester, F.Kaesler, N.Xu, Y.Hoogenboezem, R.Bindels, E.Schneider-Kramann, R.Milting, H.Gesteira Costa Filho, I.Saez Rodriguez, J.Kramann, R.2020-12-10doi:10.1101/2020.12.08.411686Cold Spring Harbor Laboratory Press2020-12-10
<![CDATA[
Discriminating Mild from Critical COVID-19 by Innate and Adaptive Immune Single-cell Profiling of Bronchoalveolar Lavages
]]>
https://biorxiv.org/cgi/content/short/2020.07.09.196519v1?rss=1"
Els WautersPierre Van MolAbhishek D. GargSander JansenYannick Van HerckLore VanderbekeAyse BassezBram BoeckxBert Malengier-DevliesAnna TimmermanThomas Van BrusselTina Van BuytenRogier SchepersElisabeth HeylenDieter DauweChristophe DoomsJan GunstGreet HermansPhilippe MeerssemanDries TestelmansJonas YserbytPatrick MatthysSabine TejparCONTAGIOUS collaboratorsJohan NeytsJoost WautersJunbin QianDiether Lambrechts2020-07-10doi:10.1101/2020.07.09.196519Cold Spring Harbor Laboratory Press2020-07-10
<![CDATA[
Expansion of profibrotic monocyte-derived alveolar macrophages in patients with persistent respiratory symptoms and radiographic abnormalities after COVID-19
]]>
https://biorxiv.org/cgi/content/short/2023.07.30.551145v1?rss=1"
Bailey, J. I.Puritz, C. H.Senkow, K. J.Markov, N. S.Diaz, E.Jonasson, E.Yu, Z.Swaminathan, S.Lu, Z.Fenske, S.Grant, R. A.Abdala-Valencia, H.Mylvaganam, R. J.Miller, J.Cumming, R. I.Tighe, R. M.Gowdy, K. M.Kalhan, R.Jain, M.Bharat, A.Kurihara, C.San Jose Estepar, R.San Jose Estepar, R.Washko, G. R.Shilatifard, A.Sznajder, J. I.Ridge, K. M.Budinger, G. S.Braun, R.Misharin, A. V.Sala, M. A.2023-07-31doi:10.1101/2023.07.30.551145Cold Spring Harbor Laboratory Press2023-07-31
<![CDATA[
Single Cell RNA-seq reveals ectopic and aberrant lung resident cell populations in Idiopathic Pulmonary Fibrosis
]]>
https://biorxiv.org/cgi/content/short/759902v1?rss=1"
Adams, T. S.Schupp, J. C.Poli, S.Ayaub, E. A.Neumark, N.Ahangari, F.Chu, S. G.Raby, B.DeIuliis, G.Januszyk, M.Duan, Q.Arnett, H. A.Siddiqui, A.Washko, G. R.Homer, R.Yan, X.Rosas, I. O.Kaminski, N.2019-09-06doi:10.1101/759902Cold Spring Harbor Laboratory Press2019-09-06
<![CDATA[
A Unique Cellular Organization of Human Distal Airways and Its Disarray in Chronic Obstructive Pulmonary Disease
]]>
https://biorxiv.org/cgi/content/short/2022.03.16.484543v1?rss=1"
Rustam, S.Hu, Y.Mahjour, S. B.Rendeiro, A. F.Ravichandran, H.Randell, S. H.Richmond, B.Polosukhin, V.Kropski, J. A.Blackwell, T. S.d'Ovidio, F.Martinez, F. J.Elemento, O.Shaykhiev, R.2022-03-16doi:10.1101/2022.03.16.484543Cold Spring Harbor Laboratory Press2022-03-16
<![CDATA[
Guided construction of single cell reference for human and mouse lung
]]>
https://biorxiv.org/cgi/content/short/2022.05.18.491687v1?rss=1"
Guo, M.Morley, M. P.Wu, Y.Du, Y.Zhao, S.Wagner, A.Kouril, M.Jin, K.Gaddis, N.Kitzmiller, J. A.Stewart, K.Basil, M. C.Lin, S. M.Ying, Y.Babu, A.Wikenheiser-Brokamp, K. A.Mun, K. S.Naren, A. P.Lin, S.Clair, G.Adkins, J. N.Pryhuber, G. S.Misra, R. S.Aronow, B. J.Tickle, T. L.Salomonis, N.Sun, X.Morrisey, E. E.Whitsett, J. A.Xu, Y.2022-05-20doi:10.1101/2022.05.18.491687Cold Spring Harbor Laboratory Press2022-05-20
<![CDATA[
Gene regulatory networks controlling temporal patterning, neurogenesis and cell fate specification in the mammalian retina.
]]>
https://biorxiv.org/cgi/content/short/2021.07.31.454200v1?rss=1"
Lyu, P.Hoang, T.Santiago, C. P.Thomas, E.Timms, A.Appel, H.Gimmen, M.Le, N.Jiang, L.Kim, D. W.Chen, S.Espinoza, D.Tegler, A.Weir, K.Clark, B.Cherry, T. M.Qian, J.Blackshaw, S.2021-08-02doi:10.1101/2021.07.31.454200Cold Spring Harbor Laboratory Press2021-08-02
<![CDATA[
CELL ATLAS OF THE HUMAN FOVEA AND PERIPHERAL RETINA
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https://biorxiv.org/cgi/content/short/2020.02.11.943779v1?rss=1"
Yan, W.Peng, Y.-R.van Zyl, T.Regev, A.Shekhar, K.Juric, D.Sanes, J.2020-02-12doi:10.1101/2020.02.11.943779Cold Spring Harbor Laboratory Press2020-02-12
<![CDATA[
Maturation of human intestinal epithelium from pluripotency in vitro
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https://biorxiv.org/cgi/content/short/2021.09.24.460132v1?rss=1"
Kilik, U.Yu, Q.Holtackers, R.Seimiya, M.Xavier da Silveira dos Santos, A.Treutlein, B.Spence, J. R.Camp, G.2021-09-24doi:10.1101/2021.09.24.460132Cold Spring Harbor Laboratory Press2021-09-24
<![CDATA[
Integrative Transcriptomics Reveals Layer 1 Astrocytes Altered in Schizophrenia
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https://biorxiv.org/cgi/content/short/2024.06.27.601103v1?rss=1"
Leon, J.Yoshinaga, S.Hino, M.Nagaoka, A.Ando, Y.Moody, J.Kojima, M.Kitazawa, A.Hayashi, K.Nakajima, K.Condello, C.Carninci, P.Kunii, Y.Hon, C.-C.Shin, J. W.Kubo, K.-i.2024-06-28doi:10.1101/2024.06.27.601103Cold Spring Harbor Laboratory Press2024-06-28
<![CDATA[
An organoid and multi-organ developmental cell atlas reveals multilineage fate specification in the human intestine
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https://biorxiv.org/cgi/content/short/2020.07.24.219147v1?rss=1"
Yu, Q.Kilik, U.Holloway, E. M.Tsai, Y.-H.Wu, A.Wu, J. H.Czerwinski, M.Childs, C.He, Z.Glass, I. A.Higgins, P. D. R.Treutlein, B.Spence, J. R.Camp, J. G.2020-07-25doi:10.1101/2020.07.24.219147Cold Spring Harbor Laboratory Press2020-07-25
<![CDATA[
Multi-modal refinement of the human heart atlas during the first gestational trimester
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https://biorxiv.org/cgi/content/short/2024.11.21.624698v1?rss=1"
De Bono, C.Xu, Y.Kausar, S.Herbane, M.Humbert, C.Rafatov, S.Missirian, C.Moreno, M.Shi, W.Gitton, Y. I.Lombardini, A.Vanzetta, I.Mazaud-Guittot, S.Chedotal, A.Baudot, A.Zaffran, S.Etchevers, H. C.2024-11-21doi:10.1101/2024.11.21.624698Cold Spring Harbor Laboratory Press2024-11-21
<![CDATA[
Single-cell transcriptomics reveals the impact of sex and age in the healthy human liver
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https://biorxiv.org/cgi/content/short/2025.01.27.635138v1?rss=1"
Rahman, R.Epstein, E. T.Murphy, S.Amir-Zilberstein, L.McCabe, C.Delorey, T.Koene, H.Fernandes, L.Tanabe, K. K.Qadan, M.Ferrone, C.Berger, D. L.Shih, A.Deguine, J.Mullen, A.2025-01-30doi:10.1101/2025.01.27.635138Cold Spring Harbor Laboratory Press2025-01-30
<![CDATA[
Systematic evaluation of single-cell multimodal data integration for comprehensive human reference atlas.
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https://biorxiv.org/cgi/content/short/2025.03.06.637075v1?rss=1"
Acera-Mateos, M.Adiconis, X.Li, J.-K.Marchese, D.Caratu, G.Hon, C.-C.Tiwari, P.Kojima, M.Vieth, B.Murphy, M. A.Simmons, S. K.Lefevre, T.Claes, I.O'Connor, C. L.Menon, R.Otto, E. A.Ando, Y.Vandereyken, K.Kretzler, M.Bitzer, M.Fraenkel, E.Voet, T.Enard, W.Carnici, P.Heyn, H.Levin, J. Z.Mereu, E.2025-03-06doi:10.1101/2025.03.06.637075Cold Spring Harbor Laboratory Press2025-03-06
<![CDATA[
Human HYPOMAP: A comprehensive spatio-cellular map of the human hypothalamus
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https://biorxiv.org/cgi/content/short/2023.09.15.557967v1?rss=1"
Tadross, J. A.Steuernagal, L.Dowsett, G.Kentistou, K. A.Lundh, S.Porniece, M.Klemm, P.Rainbow, K.Hvid, H.Kania, K.Polex-Wolf, J.Knudsen, L. B.Pyke, C.Perry, J.Lam, B. Y.Bruening, J. C.Yeo, G. S. H.2023-09-15doi:10.1101/2023.09.15.557967Cold Spring Harbor Laboratory Press2023-09-15
<![CDATA[
A Single-Cell Atlas Of Human Pediatric Liver Reveals Age-Related Hepatic Gene Signatures
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https://biorxiv.org/cgi/content/short/2025.04.16.649149v1?rss=1"
View larger version (43K):
org.highwire.dtl.DTLVardef@8d4131org.highwire.dtl.DTLVardef@1b336d2org.highwire.dtl.DTLVardef@d43ddeorg.highwire.dtl.DTLVardef@29fadf_HPS_FORMAT_FIGEXP M_FIG C_FIG
]]>Edgar, R. D.Nakib, D.Camat, D.Chung, S.Lumanto, P.Atif, J.Perciani, C. T.Ma, X. Z.Thoeni, C.Selvakumaran, N.Manuel, J.Sayed, B.Huysentruyt, K.Ricciuto, A.McGilvray, I.Avitzur, Y.Bader, G. D.MacParland, S. A.2025-04-20doi:10.1101/2025.04.16.649149Cold Spring Harbor Laboratory Press2025-04-20
<![CDATA[
Multimodal learning of transcriptomes and text enables interactive single-cell RNA-seq data exploration with natural-language chats
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https://biorxiv.org/cgi/content/short/2024.10.15.618501v1?rss=1"
Schaefer, M.Peneder, P.Malzl, D.Peycheva, M.Burton, J.Hakobyan, A.Sharma, V.Krausgruber, T.Menche, J.Tomazou, E. M.Bock, C.2024-10-18doi:10.1101/2024.10.15.618501Cold Spring Harbor Laboratory Press2024-10-18
<![CDATA[
A single cell and spatial genomics atlas of human skin fibroblasts in health and disease
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https://biorxiv.org/cgi/content/short/2024.12.23.629194v1?rss=1"
Steele, L.Admane, C.Chakala, K. P.Foster, A.Gopee, N. H.Koplev, S.Mazin, P.Olabi, B.Roberts, K.Tudor, C.Winheim, E.Annusver, K.Correa-Gallegos, D.Forsthuber, A.Francis, L.Frech, S.Ganier, C.Layton, T.Liu, Y.Yuan, H.Gudjonsson, J.Lichtenberger, B. M.Mahil, S.Nanchahal, J.O'Toole, E. A.Plikus, M.Rinkevich, Y.Rognoni, E.Smith, C.Teichmann, S. A.Kasper, M.Lotfollahi, M.Haniffa, M.2024-12-23doi:10.1101/2024.12.23.629194Cold Spring Harbor Laboratory Press2024-12-23
<![CDATA[
Polybacterial Intracellular Macromolecules Shape Single-Cell Epikine Profiles in Upper Airway Mucosa
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https://biorxiv.org/cgi/content/short/2024.10.08.617279v1?rss=1"
Easter, Q. T.Alvarado-Martinez, Z.Kunz, M.Matuck, B.Rupp, B.Weaver, T.Ren, Z.Tata, A. T.Caballero-Perez, J.Oscarson, N.Hasuike, A.Ghodke, A.Kimple, A.Tata, P. R.Randell, S. H.Koo, H.Ko, K. I.Byrd, K. M.2024-10-09doi:10.1101/2024.10.08.617279Cold Spring Harbor Laboratory Press2024-10-09
<![CDATA[
Spatial Deconvolution of Cell Types and Cell States at Scale Utilizing TACIT
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https://biorxiv.org/cgi/content/short/2024.05.31.596861v1?rss=1"
Huynh, K.Tyc, K. M.Matuck, B. F.Easter, Q. T.Pratapa, A.Kumar, N. V.Perez, P.Kulchar, R.Pranzatelli, T.Souza, D.Weaver, T. M.Qu, X.Alberto Valente Soares Junior, L.Dolhnokoff, M.Kleiner, D. E.Hewitt, S. M.Fernando Ferraz da Silva, L.Rocha, V.Warner, B. M.Byrd, K. M.Liu, J.2024-06-03doi:10.1101/2024.05.31.596861Cold Spring Harbor Laboratory Press2024-06-03
<![CDATA[
STARComm Scalably Detects Emergent Modules of Spatial Cell-Cell Communication in Inflammation and Cancer.
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https://biorxiv.org/cgi/content/short/2025.08.07.669133v1?rss=1"
14million cells across 8 cancers, STARComm revealed 24 conserved and tumor-specific MCIMs, including a fibro-immune module with targetable axes linked to immune exclusion and immunotherapy resistance. In chronic graft-versus-host disease, STARComm identified three salivary gland MCIMs predictive of patient death and two druggable axes (CXCL12-CXCR4, CCL5-SDC4), both with FDA-approved therapeutics. STARComm demonstrated that peripheral tissue profiling can forecast fatality nearly 3 years in advance using minor salivary glands. By enabling scalable biomarker discovery, drug targeting, and spatially resolved precision profiling, STARComm bridges the gap between spatial biology and clinical translation, advancing the field of spatial medicine.
SUMMARYDespite major advances in spatial biology, no framework has yet linked spatially resolved intercellular communication networks, independent of cell types, to clinical outcomes in human disease. Here, we present STARComm, a scalable method that identifies Multicellular Interaction MCIMs (MCIMs). Applying STARComm to minor salivary gland biopsies from patients with chronic graft-versus-host disease (GVHD), we identify MCIMs that not only distinguish healthy from diseased tissue but also stratify patient survival. High-risk MCIMs are enriched for actionable immune and stromal pathways, including those targetable with existing therapies. These findings establish the first outcome-linked spatial communication framework in any human disease and highlight the translational potential of oral tissues as minimally invasive platforms for real-time immune diagnostics, prognostic modeling, and therapeutic screening.
]]>Huynh, K.Matuck, B. F.de Souza, D.Zhang, X.Fatobene, G.Soares Junior, L. A. V.Ferraz da Silva, L. F.Rocha, V.Byrd, K.Liu, J.2025-08-11doi:10.1101/2025.08.07.669133Cold Spring Harbor Laboratory Press2025-08-11
<![CDATA[
Identifying the Minimal Number of Protein Markers for Cell Type Annotation Using MiniMarS
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https://biorxiv.org/cgi/content/short/2025.07.14.664825v1?rss=1"
0.9). Additionally, we showed that by appropriately combining clusters, MiniMarS improves the F1 score of a rare population identification (<1% of total cells) by 28.7%. Together, these findings highlight the broad applicability of MiniMarS in identifying appropriate markers for distinguishing cell populations.
]]>Parikh, D.Xue, A.Liao, H.-C.Wishart, C.Ashhurst, T. M.Putri, G.Luciani, F.Naik, S.Salim, A.Marsh-Wakefield, F.Louie, R.2025-07-18doi:10.1101/2025.07.14.664825Cold Spring Harbor Laboratory Press2025-07-18
<![CDATA[
Spatiotemporal map of the developing human reproductive tract at single-cell resolution
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https://biorxiv.org/cgi/content/short/2024.10.30.621114v1?rss=1"
Lorenzi, V.Mazzeo, C. I.Yayon, N.Ruiz-Morales, E. R.Sancho-Serra, C.Wong, F. C. K.Mareckova, M.Tuck, L.Roberts, K.Li, T.Jacques, M.-A.He, X.Barker, R.Crespo, B.Cakir, B.Murray, S.Prete, M.Gu, Y.Kelava, I.Garcia-Alonso, L.Marioni, J. C.Tormo, R. V.2024-10-31doi:10.1101/2024.10.30.621114Cold Spring Harbor Laboratory Press2024-10-31
<![CDATA[
CD38⁺ Endothelial Remodeling Defines Spatially Diverse Vasculopathy Programs in Rapidly Advancing Oral Inflammation
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https://biorxiv.org/cgi/content/short/2025.07.29.667333v1?rss=1"
Easter, Q. T.Huynh, K.Stolf, C.Xie, J.Matuck, B.Hasuike, A.Alvarado-Martinez, Z.Chen, Z.Aguiar Ribeiro, A.Pareek, N.Azcarate-Peril, A. M.Wu, D.Casarin, R.Ko, K. I.Liu, J.Byrd, K. M.2025-08-01doi:10.1101/2025.07.29.667333Cold Spring Harbor Laboratory Press2025-08-01
<![CDATA[
A molecular cell atlas of endocrine signalling in human neural organoids
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https://biorxiv.org/cgi/content/short/2025.08.14.669814v1?rss=1"
Caporale, N.Matassa, G.Rigoli, M. T.Castaldi, D.Valenti, A.Lessi, M.Stucchi, S.Muda, B.Nagni, R.Mainardi, L.Melon, A.Tintori, A.Bulgheresi, D.Kubacki, M.Trattaro, S.Evangelista, S.Leonards, P.Human Cell Atlas, B. N. O.Villa, C. E.Cheroni, C.Testa, G.2025-08-15doi:10.1101/2025.08.14.669814Cold Spring Harbor Laboratory Press2025-08-15
<![CDATA[
The normal human lymph node cell classification and landscape defined by high-dimensional spatial proteomic.
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https://biorxiv.org/cgi/content/short/2025.10.19.683341v1?rss=1"
Bolognesi, M. M.Dall'Olio, L.Mandelli, G. E.Lorenzi, L.Bosisio, F. M.Haberman, A. M.Bhagat, G.Borghesi, S.Faretta, M.Castellani, G.CATTORETTI, G.2025-10-20doi:10.1101/2025.10.19.683341Cold Spring Harbor Laboratory Press2025-10-20