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For: Chen H, Albergante L, Hsu JY, Lareau CA, Lo Bosco G, Guan J, Zhou S, Gorban AN, Bauer DE, Aryee MJ, Langenau DM, Zinovyev A, Buenrostro JD, Yuan GC, Pinello L. Single-cell trajectories reconstruction, exploration and mapping of omics data with STREAM. Nat Commun 2019;10:1903. [PMID: 31015418 PMCID: PMC6478907 DOI: 10.1038/s41467-019-09670-4] [Citation(s) in RCA: 155] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 03/22/2019] [Indexed: 12/14/2022]  Open
Number Cited by Other Article(s)
1
Zhang H, Zhang W, Zheng X, Li Y. scRDEN: single-cell dynamic gene rank differential expression network and robust trajectory inference. Sci Rep 2025;15:16963. [PMID: 40374885 DOI: 10.1038/s41598-025-01969-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2024] [Accepted: 05/09/2025] [Indexed: 05/18/2025]  Open
2
Labaki WW, Ram S, Namvar A, Bell AJ, Hoff BA, Kazerooni EA, Galban S, Martinez FJ, Hatt CR, Murray S, Mirkes EM, Gorban AN, Zinovyev A, Han MK, Galban CJ. Quantitative CT Scoring for Local COPD Severity. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2025:2025.04.09.25324951. [PMID: 40297437 PMCID: PMC12036413 DOI: 10.1101/2025.04.09.25324951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 04/30/2025]
3
Nesbitt NM, Araldi GL, Pennacchia L, Marchenko N, Assar Z, Muzzarelli KM, Thekke Veedu RR, Medel-Lacruz B, Lee E, Eisenmesser EZ, Kreitler DF, Bahou WF. Small molecule BLVRB redox inhibitor promotes megakaryocytopoiesis and stress thrombopoiesis in vivo. Nat Commun 2025;16:3480. [PMID: 40216753 PMCID: PMC11992022 DOI: 10.1038/s41467-025-58497-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2024] [Accepted: 03/17/2025] [Indexed: 04/14/2025]  Open
4
Perelli L, Zhang L, Mangiameli S, Giannese F, Mahadevan KK, Peng F, Citron F, Khan H, Le C, Gurreri E, Carbone F, Russell AJC, Soeung M, Lam TNA, Lundgren S, Marisetty S, Zhu C, Catania D, Mohamed AMT, Feng N, Augustine JJ, Sgambato A, Tortora G, Draetta GF, Tonon G, Futreal A, Giuliani V, Carugo A, Viale A, Kim MP, Heffernan TP, Wang L, Kalluri R, Cittaro D, Chen F, Genovese G. Evolutionary fingerprints of epithelial-to-mesenchymal transition. Nature 2025;640:1083-1092. [PMID: 40044861 DOI: 10.1038/s41586-025-08671-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 01/17/2025] [Indexed: 04/13/2025]
5
Bell AJ, Ram S, Labaki WW, Murray S, Kazerooni EA, Galban S, Martinez FJ, Hatt CR, Wang JM, Ivanov V, McGettigan P, Khokhlovich E, Maiorino E, Suryadevara R, Boueiz A, Castaldi PJ, Mirkes EM, Zinovyev A, Gorban AN, Galban CJ, Han MK. Temporal Exploration of Chronic Obstructive Pulmonary Disease Phenotypes: Insights from the COPDGene and SPIROMICS Cohorts. Am J Respir Crit Care Med 2025;211:569-576. [PMID: 39269427 PMCID: PMC12005034 DOI: 10.1164/rccm.202401-0127oc] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2024] [Accepted: 09/12/2024] [Indexed: 09/15/2024]  Open
6
Miyazaki K, Horie K, Watanabe H, Hidaka R, Hayashi R, Hayatsu N, Fujiwara K, Kuwata R, Uehata T, Ochi Y, Takenaka M, Kawaguchi RK, Ikuta K, Takeuchi O, Ogawa S, Hozumi K, Holländer GA, Kondoh G, Akiyama T, Miyazaki M. A feedback amplifier circuit with Notch and E2A orchestrates T-cell fate and suppresses the innate lymphoid cell lineages during thymic ontogeny. Genes Dev 2025;39:384-400. [PMID: 39904558 PMCID: PMC11874989 DOI: 10.1101/gad.352111.124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2024] [Accepted: 01/13/2025] [Indexed: 02/06/2025]
7
Chen X, Ma Y, Shi Y, Zhang B, Wu H, Gao J. Fuzzy-Based Identification of Transition Cells to Infer Cell Trajectory for Single-Cell Transcriptomics. J Comput Biol 2025;32:253-273. [PMID: 39670822 DOI: 10.1089/cmb.2023.0432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2024]  Open
8
Cortés-Ríos J, Rodriguez-Fernandez M, Sorger PK, Fröhlich F. Dynamic Modeling of Cell Cycle Arrest Through Integrated Single-Cell and Mathematical Modelling Approaches. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.02.20.639240. [PMID: 40060624 PMCID: PMC11888159 DOI: 10.1101/2025.02.20.639240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 03/18/2025]
9
Ji P, Wang N, Yu Y, Zhu J, Zuo Z, Zhang B, Zhao F. Single-cell delineation of the microbiota-gut-brain axis: Probiotic intervention in Chd8 haploinsufficient mice. CELL GENOMICS 2025;5:100768. [PMID: 39914389 PMCID: PMC11872533 DOI: 10.1016/j.xgen.2025.100768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2024] [Revised: 12/02/2024] [Accepted: 01/14/2025] [Indexed: 02/16/2025]
10
Sun F, Li H, Sun D, Fu S, Gu L, Shao X, Wang Q, Dong X, Duan B, Xing F, Wu J, Xiao M, Zhao F, Han JDJ, Liu Q, Fan X, Li C, Wang C, Shi T. Single-cell omics: experimental workflow, data analyses and applications. SCIENCE CHINA. LIFE SCIENCES 2025;68:5-102. [PMID: 39060615 DOI: 10.1007/s11427-023-2561-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 04/18/2024] [Indexed: 07/28/2024]
11
Paczkowska J, Tang M, Wright KT, Song L, Luu K, Shanmugam V, Welsh EL, Weirather JL, Besson N, Olszewski H, Porter BA, Pfaff KL, Redd RA, Cader FZ, Mandato E, Ouyang J, Calabretta E, Bai G, Lawton LN, Armand P, Rodig SJ, Liu XS, Shipp MA. Cancer-specific innate and adaptive immune rewiring drives resistance to PD-1 blockade in classic Hodgkin lymphoma. Nat Commun 2024;15:10740. [PMID: 39737927 PMCID: PMC11686379 DOI: 10.1038/s41467-024-54512-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Accepted: 11/11/2024] [Indexed: 01/01/2025]  Open
12
Zhang J, Peng Q, Fan J, Liu F, Chen H, Bi X, Yuan S, Jiang W, Pan T, Li K, Tan S, Chen P. Single-cell and spatial transcriptomics reveal SPP1-CD44 signaling drives primary resistance to immune checkpoint inhibitors in RCC. J Transl Med 2024;22:1157. [PMID: 39736762 DOI: 10.1186/s12967-024-06018-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2024] [Accepted: 12/18/2024] [Indexed: 01/01/2025]  Open
13
Zhang J, Zhang N, Mai Q, Zhou C. The frontier of precision medicine: application of single-cell multi-omics in preimplantation genetic diagnosis. Brief Funct Genomics 2024;23:726-732. [PMID: 39486398 DOI: 10.1093/bfgp/elae041] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2024] [Revised: 10/03/2024] [Indexed: 11/04/2024]  Open
14
Do HT, Ono M, Wang Z, Kitagawa W, Dang AT, Yonezawa T, Kuboki T, Oohashi T, Kubota S. Inverse genetics tracing the differentiation pathway of human chondrocytes. Osteoarthritis Cartilage 2024;32:1419-1432. [PMID: 38925474 DOI: 10.1016/j.joca.2024.06.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 06/16/2024] [Accepted: 06/18/2024] [Indexed: 06/28/2024]
15
Farzad N, Enninful A, Bao S, Zhang D, Deng Y, Fan R. Spatially resolved epigenome sequencing via Tn5 transposition and deterministic DNA barcoding in tissue. Nat Protoc 2024;19:3389-3425. [PMID: 38943021 DOI: 10.1038/s41596-024-01013-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 04/11/2024] [Indexed: 06/30/2024]
16
Fischer A, Albert TK, Moreno N, Interlandi M, Mormann J, Glaser S, Patil P, de Faria FW, Richter M, Verma A, Balbach ST, Wagener R, Bens S, Dahlum S, Göbel C, Münter D, Inserte C, Graf M, Kremer E, Melcher V, Di Stefano G, Santi R, Chan A, Dogan A, Bush J, Hasselblatt M, Cheng S, Spetalen S, Fosså A, Hartmann W, Herbrüggen H, Robert S, Oyen F, Dugas M, Walter C, Sandmann S, Varghese J, Rossig C, Schüller U, Tzankov A, Pedersen MB, d'Amore FA, Mellgren K, Kontny U, Kancherla V, Veloza L, Missiaglia E, Fataccioli V, Gaulard P, Burkhardt B, Soehnlein O, Klapper W, de Leval L, Siebert R, Kerl K. Lack of SMARCB1 expression characterizes a subset of human and murine peripheral T-cell lymphomas. Nat Commun 2024;15:8571. [PMID: 39362842 PMCID: PMC11452211 DOI: 10.1038/s41467-024-52826-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 09/23/2024] [Indexed: 10/05/2024]  Open
17
Protti G, Spreafico R. A primer on single-cell RNA-seq analysis using dendritic cells as a case study. FEBS Lett 2024. [PMID: 39245787 DOI: 10.1002/1873-3468.15009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Revised: 07/18/2024] [Accepted: 08/12/2024] [Indexed: 09/10/2024]
18
Hendriksen JD, Locallo A, Maarup S, Debnath O, Ishaque N, Hasselbach B, Skjøth-Rasmussen J, Yde CW, Poulsen HS, Lassen U, Weischenfeldt J. Immunotherapy drives mesenchymal tumor cell state shift and TME immune response in glioblastoma patients. Neuro Oncol 2024;26:1453-1466. [PMID: 38695342 PMCID: PMC11300009 DOI: 10.1093/neuonc/noae085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/07/2024]  Open
19
Bonham-Carter B, Schiebinger G. Cellular proliferation biases clonal lineage tracing and trajectory inference. Bioinformatics 2024;40:btae483. [PMID: 39102821 PMCID: PMC11316616 DOI: 10.1093/bioinformatics/btae483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Revised: 03/28/2024] [Accepted: 07/30/2024] [Indexed: 08/07/2024]  Open
20
Liu J, Ma J, Wen J, Zhou X. A Cell Cycle-Aware Network for Data Integration and Label Transferring of Single-Cell RNA-Seq and ATAC-Seq. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024;11:e2401815. [PMID: 38887194 PMCID: PMC11336957 DOI: 10.1002/advs.202401815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 04/22/2024] [Indexed: 06/20/2024]
21
Hirsinger E, Blavet C, Bonnin MA, Bellenger L, Gharsalli T, Duprez D. Limb connective tissue is organized in a continuum of promiscuous fibroblast identities during development. iScience 2024;27:110305. [PMID: 39050702 PMCID: PMC11267076 DOI: 10.1016/j.isci.2024.110305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Revised: 05/21/2024] [Accepted: 06/17/2024] [Indexed: 07/27/2024]  Open
22
Palmer JW, Kumar N, An L, White AC, Mukhtar MS, Harris ML. Molecular heterogeneity of quiescent melanocyte stem cells revealed by single-cell RNA-sequencing. Pigment Cell Melanoma Res 2024;37:480-495. [PMID: 38613320 PMCID: PMC11178447 DOI: 10.1111/pcmr.13169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 03/04/2024] [Accepted: 03/31/2024] [Indexed: 04/14/2024]
23
Hong Y, Li H, Long C, Liang P, Zhou J, Zuo Y. An increment of diversity method for cell state trajectory inference of time-series scRNA-seq data. FUNDAMENTAL RESEARCH 2024;4:770-776. [PMID: 39156571 PMCID: PMC11330101 DOI: 10.1016/j.fmre.2024.01.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 08/29/2023] [Accepted: 01/03/2024] [Indexed: 08/20/2024]  Open
24
Dao L, You Z, Lu L, Xu T, Sarkar AK, Zhu H, Liu M, Calandrelli R, Yoshida G, Lin P, Miao Y, Mierke S, Kalva S, Zhu H, Gu M, Vadivelu S, Zhong S, Huang LF, Guo Z. Modeling blood-brain barrier formation and cerebral cavernous malformations in human PSC-derived organoids. Cell Stem Cell 2024;31:818-833.e11. [PMID: 38754427 PMCID: PMC11162335 DOI: 10.1016/j.stem.2024.04.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 02/24/2024] [Accepted: 04/22/2024] [Indexed: 05/18/2024]
25
Gaudet A, Zheng X, Kambham N, Bhalla V. Esm-1 mediates transcriptional polarization associated with diabetic kidney disease. Am J Physiol Renal Physiol 2024;326:F1016-F1031. [PMID: 38601985 PMCID: PMC11386982 DOI: 10.1152/ajprenal.00419.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 03/20/2024] [Accepted: 04/04/2024] [Indexed: 04/12/2024]  Open
26
Radley A, Boeing S, Smith A. Branching topology of the human embryo transcriptome revealed by Entropy Sort Feature Weighting. Development 2024;151:dev202832. [PMID: 38691188 PMCID: PMC11213519 DOI: 10.1242/dev.202832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Accepted: 04/24/2024] [Indexed: 05/03/2024]
27
Kuraz Abebe B, Wang J, Guo J, Wang H, Li A, Zan L. A review of the role of epigenetic studies for intramuscular fat deposition in beef cattle. Gene 2024;908:148295. [PMID: 38387707 DOI: 10.1016/j.gene.2024.148295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 01/23/2024] [Accepted: 02/15/2024] [Indexed: 02/24/2024]
28
Su Y, Yu Z, Yang Y, Wong K, Li X. Distribution-Agnostic Deep Learning Enables Accurate Single-Cell Data Recovery and Transcriptional Regulation Interpretation. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024;11:e2307280. [PMID: 38380499 PMCID: PMC11040354 DOI: 10.1002/advs.202307280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 01/16/2024] [Indexed: 02/22/2024]
29
Zeng Y, Luo M, Shangguan N, Shi P, Feng J, Xu J, Chen K, Lu Y, Yu W, Yang Y. Deciphering cell types by integrating scATAC-seq data with genome sequences. NATURE COMPUTATIONAL SCIENCE 2024;4:285-298. [PMID: 38600256 DOI: 10.1038/s43588-024-00622-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 03/18/2024] [Indexed: 04/12/2024]
30
Croizer H, Mhaidly R, Kieffer Y, Gentric G, Djerroudi L, Leclere R, Pelon F, Robley C, Bohec M, Meng A, Meseure D, Romano E, Baulande S, Peltier A, Vincent-Salomon A, Mechta-Grigoriou F. Deciphering the spatial landscape and plasticity of immunosuppressive fibroblasts in breast cancer. Nat Commun 2024;15:2806. [PMID: 38561380 PMCID: PMC10984943 DOI: 10.1038/s41467-024-47068-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 03/19/2024] [Indexed: 04/04/2024]  Open
31
Maroni G, Krishnan I, Alfieri R, Maymi VA, Pandell N, Csizmadia E, Zhang J, Weetall M, Branstrom A, Braccini G, Cabrera San Millán E, Storti B, Bizzarri R, Kocher O, Bassères DS, Welner RS, Magli MC, Merelli I, Clohessy JG, Ali A, Tenen DG, Levantini E. Tumor Microenvironment Landscapes Supporting EGFR-mutant NSCLC Are Modulated at the Single-cell Interaction Level by Unesbulin Treatment. CANCER RESEARCH COMMUNICATIONS 2024;4:919-937. [PMID: 38546390 PMCID: PMC10964845 DOI: 10.1158/2767-9764.crc-23-0161] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 01/26/2024] [Accepted: 03/12/2024] [Indexed: 11/03/2024]
32
Xia L, Lee C, Li JJ. Statistical method scDEED for detecting dubious 2D single-cell embeddings and optimizing t-SNE and UMAP hyperparameters. Nat Commun 2024;15:1753. [PMID: 38409103 PMCID: PMC10897166 DOI: 10.1038/s41467-024-45891-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 02/06/2024] [Indexed: 02/28/2024]  Open
33
Tietze E, Barbosa AR, Araujo B, Euclydes V, Spiegelberg B, Cho HJ, Lee YK, Wang Y, McCord A, Lorenzetti A, Feltrin A, van de Leemput J, Di Carlo P, Ursini G, Benjamin KJ, Brentani H, Kleinman JE, Hyde TM, Weinberger DR, McKay R, Shin JH, Sawada T, Paquola ACM, Erwin JA. Human archetypal pluripotent stem cells differentiate into trophoblast stem cells via endogenous BMP5/7 induction without transitioning through naive state. Sci Rep 2024;14:3291. [PMID: 38332235 PMCID: PMC10853519 DOI: 10.1038/s41598-024-53381-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 01/31/2024] [Indexed: 02/10/2024]  Open
34
Liu J, Ma J, Wen J, Zhou X. A Cell Cycle-aware Network for Data Integration and Label Transferring of Single-cell RNA-seq and ATAC-seq. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.31.578213. [PMID: 38352302 PMCID: PMC10862874 DOI: 10.1101/2024.01.31.578213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
35
Murakami M, Hara K, Ikeda K, Horino M, Okazaki R, Niitsu Y, Takeuchi A, Aoki J, Shiba K, Tsujimoto K, Komiya C, Nakamura Y, Kurata M, Akashi T, Fujii Y, Yamada T. Single-Nucleus Analysis Reveals Tumor Heterogeneity of Aldosterone-Producing Adenoma. Hypertension 2024;81:361-371. [PMID: 38095094 DOI: 10.1161/hypertensionaha.123.21446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 12/03/2023] [Indexed: 01/19/2024]
36
Guise AJ, Misal SA, Carson R, Chu JH, Boekweg H, Van Der Watt D, Welsh NC, Truong T, Liang Y, Xu S, Benedetto G, Gagnon J, Payne SH, Plowey ED, Kelly RT. TDP-43-stratified single-cell proteomics of postmortem human spinal motor neurons reveals protein dynamics in amyotrophic lateral sclerosis. Cell Rep 2024;43:113636. [PMID: 38183652 PMCID: PMC10926001 DOI: 10.1016/j.celrep.2023.113636] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 11/02/2023] [Accepted: 12/14/2023] [Indexed: 01/08/2024]  Open
37
Sprooten J, Vanmeerbeek I, Datsi A, Govaerts J, Naulaerts S, Laureano RS, Borràs DM, Calvet A, Malviya V, Kuballa M, Felsberg J, Sabel MC, Rapp M, Knobbe-Thomsen C, Liu P, Zhao L, Kepp O, Boon L, Tejpar S, Borst J, Kroemer G, Schlenner S, De Vleeschouwer S, Sorg RV, Garg AD. Lymph node and tumor-associated PD-L1+ macrophages antagonize dendritic cell vaccines by suppressing CD8+ T cells. Cell Rep Med 2024;5:101377. [PMID: 38232703 PMCID: PMC10829875 DOI: 10.1016/j.xcrm.2023.101377] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 08/23/2023] [Accepted: 12/18/2023] [Indexed: 01/19/2024]
38
Yan M, Liu M, Davis AG, Stoner SA, Zhang DE. Single-cell RNA sequencing of a new transgenic t(8;21) preleukemia mouse model reveals regulatory networks promoting leukemic transformation. Leukemia 2024;38:31-44. [PMID: 37838757 PMCID: PMC10776403 DOI: 10.1038/s41375-023-02063-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 09/22/2023] [Accepted: 10/05/2023] [Indexed: 10/16/2023]
39
Craig AJ, Silveira MAD, Ma L, Revsine M, Wang L, Heinrich S, Rae Z, Ruchinskas A, Dadkhah K, Do W, Behrens S, Mehrabadi FR, Dominguez DA, Forgues M, Budhu A, Chaisaingmongkol J, Hernandez JM, Davis JL, Tran B, Marquardt JU, Ruchirawat M, Kelly M, Greten TF, Wang XW. Genome-wide profiling of transcription factor activity in primary liver cancer using single-cell ATAC sequencing. Cell Rep 2023;42:113446. [PMID: 37980571 PMCID: PMC10750269 DOI: 10.1016/j.celrep.2023.113446] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Revised: 09/24/2023] [Accepted: 10/31/2023] [Indexed: 11/21/2023]  Open
40
Li R, Guan J, Wang Z, Zhou S. A new and effective two-step clustering approach for single cell RNA sequencing data. BMC Genomics 2023;23:864. [PMID: 37946133 PMCID: PMC10636845 DOI: 10.1186/s12864-023-09577-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 08/10/2023] [Indexed: 11/12/2023]  Open
41
Rao J, Djeffal Y, Chal J, Marchianò F, Wang CH, Al Tanoury Z, Gapon S, Mayeuf-Louchart A, Glass I, Sefton EM, Habermann B, Kardon G, Watt FM, Tseng YH, Pourquié O. Reconstructing human brown fat developmental trajectory in vitro. Dev Cell 2023;58:2359-2375.e8. [PMID: 37647896 PMCID: PMC10873093 DOI: 10.1016/j.devcel.2023.08.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 08/23/2022] [Accepted: 08/01/2023] [Indexed: 09/01/2023]
42
Tian W, Zhou J, Bartlett A, Zeng Q, Liu H, Castanon RG, Kenworthy M, Altshul J, Valadon C, Aldridge A, Nery JR, Chen H, Xu J, Johnson ND, Lucero J, Osteen JK, Emerson N, Rink J, Lee J, Li Y, Siletti K, Liem M, Claffey N, O’Connor C, Yanny AM, Nyhus J, Dee N, Casper T, Shapovalova N, Hirschstein D, Ding SL, Hodge R, Levi BP, Keene CD, Linnarsson S, Lein E, Ren B, Behrens MM, Ecker JR. Single-cell DNA methylation and 3D genome architecture in the human brain. Science 2023;382:eadf5357. [PMID: 37824674 PMCID: PMC10572106 DOI: 10.1126/science.adf5357] [Citation(s) in RCA: 61] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 09/05/2023] [Indexed: 10/14/2023]
43
Yi D, Nam JW, Jeong H. Toward the functional interpretation of somatic structural variations: bulk- and single-cell approaches. Brief Bioinform 2023;24:bbad297. [PMID: 37587831 PMCID: PMC10516374 DOI: 10.1093/bib/bbad297] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 07/05/2023] [Accepted: 07/23/2023] [Indexed: 08/18/2023]  Open
44
Xia L, Lee C, Li JJ. scDEED: a statistical method for detecting dubious 2D single-cell embeddings and optimizing t-SNE and UMAP hyperparameters. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.21.537839. [PMID: 37163087 PMCID: PMC10168265 DOI: 10.1101/2023.04.21.537839] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
45
Wang L, Trasanidis N, Wu T, Dong G, Hu M, Bauer DE, Pinello L. Dictys: dynamic gene regulatory network dissects developmental continuum with single-cell multiomics. Nat Methods 2023;20:1368-1378. [PMID: 37537351 DOI: 10.1038/s41592-023-01971-3] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 07/05/2023] [Indexed: 08/05/2023]
46
Mao S, Liu J, Zhao W, Zhou X. LVPT: Lazy Velocity Pseudotime Inference Method. Biomolecules 2023;13:1242. [PMID: 37627306 PMCID: PMC10452358 DOI: 10.3390/biom13081242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 08/09/2023] [Accepted: 08/10/2023] [Indexed: 08/27/2023]  Open
47
Erbe R, Stein-O’Brien G, Fertig EJ. Transcriptomic forecasting with neural ordinary differential equations. PATTERNS (NEW YORK, N.Y.) 2023;4:100793. [PMID: 37602211 PMCID: PMC10435954 DOI: 10.1016/j.patter.2023.100793] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 04/03/2023] [Accepted: 06/13/2023] [Indexed: 08/22/2023]
48
Fouché A, Zinovyev A. Omics data integration in computational biology viewed through the prism of machine learning paradigms. FRONTIERS IN BIOINFORMATICS 2023;3:1191961. [PMID: 37600970 PMCID: PMC10436311 DOI: 10.3389/fbinf.2023.1191961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 07/26/2023] [Indexed: 08/22/2023]  Open
49
Orrapin S, Thongkumkoon P, Udomruk S, Moonmuang S, Sutthitthasakul S, Yongpitakwattana P, Pruksakorn D, Chaiyawat P. Deciphering the Biology of Circulating Tumor Cells through Single-Cell RNA Sequencing: Implications for Precision Medicine in Cancer. Int J Mol Sci 2023;24:12337. [PMID: 37569711 PMCID: PMC10418766 DOI: 10.3390/ijms241512337] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 07/25/2023] [Accepted: 07/27/2023] [Indexed: 08/13/2023]  Open
50
Li C, Chen X, Chen S, Jiang R, Zhang X. simCAS: an embedding-based method for simulating single-cell chromatin accessibility sequencing data. Bioinformatics 2023;39:btad453. [PMID: 37494428 PMCID: PMC10394124 DOI: 10.1093/bioinformatics/btad453] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 06/25/2023] [Accepted: 07/25/2023] [Indexed: 07/28/2023]  Open
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