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For: Amit I, Garber M, Chevrier N, Leite AP, Donner Y, Eisenhaure T, Guttman M, Grenier JK, Li W, Zuk O, Schubert LA, Birditt B, Shay T, Goren A, Zhang X, Smith Z, Deering R, McDonald RC, Cabili M, Bernstein BE, Rinn JL, Meissner A, Root DE, Hacohen N, Regev A. Unbiased reconstruction of a mammalian transcriptional network mediating pathogen responses. Science 2009;326:257-63. [PMID: 19729616 PMCID: PMC2879337 DOI: 10.1126/science.1179050] [Citation(s) in RCA: 408] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Number Cited by Other Article(s)
1
Zhang Y, Wang Y, Liu X, Feng X. PbImpute: Precise Zero Discrimination and Balanced Imputation in Single-Cell RNA Sequencing Data. J Chem Inf Model 2025;65:2670-2684. [PMID: 39957720 PMCID: PMC11898086 DOI: 10.1021/acs.jcim.4c02125] [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: 11/15/2024] [Revised: 01/31/2025] [Accepted: 02/03/2025] [Indexed: 02/18/2025]
2
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
3
Moore MM, Wekhande S, Issner R, Collins A, Cruz AJ, Liu YV, Javed N, Casaní-Galdón S, Buenrostro JD, Epstein CB, Mattei E, Doench JG, Bernstein BE, Shoresh N, Najm FJ. Multi-locus CRISPRi targeting with a single truncated guide RNA. Nat Commun 2025;16:1357. [PMID: 39905017 PMCID: PMC11794626 DOI: 10.1038/s41467-025-56144-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: 11/02/2023] [Accepted: 01/10/2025] [Indexed: 02/06/2025]  Open
4
Zhang Y, Wang Y, Liu X, Feng X. CPARI: a novel approach combining cell partitioning with absolute and relative imputation to address dropout in single-cell RNA-seq data. Brief Bioinform 2024;26:bbae668. [PMID: 39715686 DOI: 10.1093/bib/bbae668] [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: 07/26/2024] [Revised: 10/06/2024] [Accepted: 12/06/2024] [Indexed: 12/25/2024]  Open
5
Sheu KM, Pimplaskar A, Hoffmann A. Single-cell stimulus-response gene expression trajectories reveal the stimulus specificities of dynamic responses by single macrophages. Mol Cell 2024;84:4095-4110.e6. [PMID: 39413794 PMCID: PMC11560543 DOI: 10.1016/j.molcel.2024.09.023] [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: 11/03/2023] [Revised: 07/05/2024] [Accepted: 09/19/2024] [Indexed: 10/18/2024]
6
Lensch V, Gabba A, Hincapie R, Bhagchandani SH, Basak A, Alam MM, Noble J, Irvine DJ, Shalek AK, Johnson JA, Finn MG, Kiessling LL. Carbohydrate-Lectin Interactions Reprogram Dendritic Cells to Promote Type 1 Anti-Tumor Immunity. ACS NANO 2024;18:26770-26783. [PMID: 39283240 PMCID: PMC11646345 DOI: 10.1021/acsnano.4c07360] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/02/2024]
7
Kernfeld E, Yang Y, Weinstock J, Battle A, Cahan P. A systematic comparison of computational methods for expression forecasting. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.07.28.551039. [PMID: 37577640 PMCID: PMC10418073 DOI: 10.1101/2023.07.28.551039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
8
Wang Z, Wang H, Zhao J, Xia J, Zheng C. scVSC: Deep Variational Subspace Clustering for Single-Cell Transcriptome Data. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2024;21:1492-1503. [PMID: 38801694 DOI: 10.1109/tcbb.2024.3405731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
9
Tran MT. Identification of TIMP1-induced dysregulation of epithelial-mesenchymal transition as a key pathway in inflammatory bowel disease and small intestinal neuroendocrine tumors shared pathogenesis. Front Genet 2024;15:1376123. [PMID: 39233736 PMCID: PMC11371700 DOI: 10.3389/fgene.2024.1376123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Accepted: 07/29/2024] [Indexed: 09/06/2024]  Open
10
Zandigohar M, Pang J, Rodrigues A, Roberts RE, Dai Y, Koh TJ. Transcription Factor Activity Regulating Macrophage Heterogeneity during Skin Wound Healing. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2024;213:506-518. [PMID: 38940624 PMCID: PMC11300156 DOI: 10.4049/jimmunol.2400172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Accepted: 06/11/2024] [Indexed: 06/29/2024]
11
Luecke S, Guo X, Sheu KM, Singh A, Lowe SC, Han M, Diaz J, Lopes F, Wollman R, Hoffmann A. Dynamical and combinatorial coding by MAPK p38 and NFκB in the inflammatory response of macrophages. Mol Syst Biol 2024;20:898-932. [PMID: 38872050 PMCID: PMC11297158 DOI: 10.1038/s44320-024-00047-4] [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: 10/22/2023] [Revised: 05/27/2024] [Accepted: 05/28/2024] [Indexed: 06/15/2024]  Open
12
Yi X, Jia W, Li W, Jia C, Song C. Diagnostic value of cytokines in severe childhood Mycoplasma pneumoniae pneumonia combined with Adenovirus infection. Ital J Pediatr 2024;50:92. [PMID: 38715105 PMCID: PMC11077701 DOI: 10.1186/s13052-024-01661-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Accepted: 04/25/2024] [Indexed: 05/12/2024]  Open
13
Santos-Rebouças CB, Ferreira CDS, Nogueira JDS, Brustolini OJ, de Almeida LGP, Gerber AL, Guimarães APDC, Piergiorge RM, Struchiner CJ, Porto LC, de Vasconcelos ATR. Immune response stability to the SARS-CoV-2 mRNA vaccine booster is influenced by differential splicing of HLA genes. Sci Rep 2024;14:8982. [PMID: 38637586 PMCID: PMC11026523 DOI: 10.1038/s41598-024-59259-1] [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: 09/12/2023] [Accepted: 04/08/2024] [Indexed: 04/20/2024]  Open
14
Shi Y, Wan J, Zhang X, Liang T, Yin Y. scCRT: a contrastive-based dimensionality reduction model for scRNA-seq trajectory inference. Brief Bioinform 2024;25:bbae204. [PMID: 38701412 PMCID: PMC11066919 DOI: 10.1093/bib/bbae204] [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: 11/29/2023] [Revised: 03/28/2024] [Accepted: 04/15/2024] [Indexed: 05/05/2024]  Open
15
Lensch V, Gabba A, Hincapie R, Bhagchandani SH, Basak A, Alam MM, Irvine DJ, Shalek AK, Johnson JA, Finn MG, Kiessling LL. Glycan-costumed virus-like particles promote type 1 anti-tumor immunity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.18.575711. [PMID: 38293025 PMCID: PMC10827186 DOI: 10.1101/2024.01.18.575711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
16
Cui A, Huang T, Li S, Ma A, Pérez JL, Sander C, Keskin DB, Wu CJ, Fraenkel E, Hacohen N. Dictionary of immune responses to cytokines at single-cell resolution. Nature 2024;625:377-384. [PMID: 38057668 PMCID: PMC10781646 DOI: 10.1038/s41586-023-06816-9] [Citation(s) in RCA: 104] [Impact Index Per Article: 104.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 11/01/2023] [Indexed: 12/08/2023]
17
Yu G, Sun B, Zhu Z, Mehareb EM, Teng A, Han J, Zhang H, Liu J, Liu X, Raza G, Zhang B, Zhang Y, Wang K. Genome-wide DNase I-hypersensitive site assay reveals distinct genomic distributions and functional features of open chromatin in autopolyploid sugarcane. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024;117:573-589. [PMID: 37897092 DOI: 10.1111/tpj.16513] [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: 03/06/2023] [Revised: 09/15/2023] [Accepted: 10/09/2023] [Indexed: 10/29/2023]
18
O’Neil JD, Bolimowska OO, Clayton SA, Tang T, Daley KK, Lara-Reyna S, Warner J, Martin CS, Mahida RY, Hardy RS, Arthur JSC, Clark AR. Dexamethasone impairs the expression of antimicrobial mediators in lipopolysaccharide-activated primary macrophages by inhibiting both expression and function of interferon β. Front Immunol 2023;14:1190261. [PMID: 37942320 PMCID: PMC10628473 DOI: 10.3389/fimmu.2023.1190261] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 10/11/2023] [Indexed: 11/10/2023]  Open
19
Ma H, Bosma TJ, Khan AS. Long-Read High-Throughput Sequencing (HTS) Revealed That the Sf-Rhabdovirus X+ Genome Contains a 3.7 kb Internal Duplication. Viruses 2023;15:1998. [PMID: 37896775 PMCID: PMC10612052 DOI: 10.3390/v15101998] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 09/19/2023] [Accepted: 09/20/2023] [Indexed: 10/29/2023]  Open
20
Sabikunnahar B, Caldwell S, Varnum S, Hogan T, Cooper A, Lahue KG, Bivona JJ, Cousens PM, Symeonides M, Ballif BA, Poynter ME, Krementsov DN. Long Noncoding RNA U90926 Is Induced in Activated Macrophages, Is Protective in Endotoxic Shock, and Encodes a Novel Secreted Protein. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2023;210:807-819. [PMID: 36705532 PMCID: PMC9998366 DOI: 10.4049/jimmunol.2200215] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 01/03/2023] [Indexed: 01/28/2023]
21
Slavich GM, Mengelkoch S, Cole SW. Human social genomics: Concepts, mechanisms, and implications for health. LIFESTYLE MEDICINE 2023. [DOI: 10.1002/lim2.75] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/27/2023]  Open
22
Geiger-Schuller K, Eraslan B, Kuksenko O, Dey KK, Jagadeesh KA, Thakore PI, Karayel O, Yung AR, Rajagopalan A, Meireles AM, Yang KD, Amir-Zilberstein L, Delorey T, Phillips D, Raychowdhury R, Moussion C, Price AL, Hacohen N, Doench JG, Uhler C, Rozenblatt-Rosen O, Regev A. Systematically characterizing the roles of E3-ligase family members in inflammatory responses with massively parallel Perturb-seq. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.23.525198. [PMID: 36747789 PMCID: PMC9900845 DOI: 10.1101/2023.01.23.525198] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
23
Joung J, Ma S, Tay T, Geiger-Schuller KR, Kirchgatterer PC, Verdine VK, Guo B, Arias-Garcia MA, Allen WE, Singh A, Kuksenko O, Abudayyeh OO, Gootenberg JS, Fu Z, Macrae RK, Buenrostro JD, Regev A, Zhang F. A transcription factor atlas of directed differentiation. Cell 2023;186:209-229.e26. [PMID: 36608654 PMCID: PMC10344468 DOI: 10.1016/j.cell.2022.11.026] [Citation(s) in RCA: 93] [Impact Index Per Article: 46.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 08/04/2022] [Accepted: 11/23/2022] [Indexed: 01/07/2023]
24
Freimer JW, Shaked O, Naqvi S, Sinnott-Armstrong N, Kathiria A, Garrido CM, Chen AF, Cortez JT, Greenleaf WJ, Pritchard JK, Marson A. Systematic discovery and perturbation of regulatory genes in human T cells reveals the architecture of immune networks. Nat Genet 2022;54:1133-1144. [PMID: 35817986 PMCID: PMC10035359 DOI: 10.1038/s41588-022-01106-y] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 05/26/2022] [Indexed: 12/14/2022]
25
Mishra GP, Jha A, Ahad A, Sen K, Sen A, Podder S, Prusty S, Biswas VK, Gupta B, Raghav SK. Epigenomics of conventional type-I dendritic cells depicted preferential control of TLR9 versus TLR3 response by NCoR1 through differential IRF3 activation. Cell Mol Life Sci 2022;79:429. [PMID: 35849243 PMCID: PMC9293861 DOI: 10.1007/s00018-022-04424-w] [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: 04/15/2022] [Revised: 05/28/2022] [Accepted: 06/13/2022] [Indexed: 11/26/2022]
26
Gan Y, Li N, Guo C, Zou G, Guan J, Zhou S. TiC2D: Trajectory Inference From Single-Cell RNA-Seq Data Using Consensus Clustering. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2022;19:2512-2522. [PMID: 33630737 DOI: 10.1109/tcbb.2021.3061720] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
27
Gao Y, Li J, Cai G, Wang Y, Yang W, Li Y, Zhao X, Li R, Gao Y, Tuo W, Baldwin RL, Li CJ, Fang L, Liu GE. Single-cell transcriptomic and chromatin accessibility analyses of dairy cattle peripheral blood mononuclear cells and their responses to lipopolysaccharide. BMC Genomics 2022;23:338. [PMID: 35501711 PMCID: PMC9063233 DOI: 10.1186/s12864-022-08562-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 04/13/2022] [Indexed: 11/24/2022]  Open
28
Sheu KM, Hoffmann A. Functional Hallmarks of Healthy Macrophage Responses: Their Regulatory Basis and Disease Relevance. Annu Rev Immunol 2022;40:295-321. [PMID: 35471841 PMCID: PMC10074967 DOI: 10.1146/annurev-immunol-101320-031555] [Citation(s) in RCA: 86] [Impact Index Per Article: 28.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
29
Wen W, Chen J, Zhou Y, Li G, Zhang Y. Loss of Ripk3 attenuated neutrophil accumulation in a lipopolysaccharide-induced zebrafish inflammatory model. Cell Death Dis 2022;8:88. [PMID: 35220408 PMCID: PMC8882176 DOI: 10.1038/s41420-022-00891-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 01/27/2022] [Accepted: 02/09/2022] [Indexed: 11/09/2022]
30
Gan Y, Huang X, Zou G, Zhou S, Guan J. Deep structural clustering for single-cell RNA-seq data jointly through autoencoder and graph neural network. Brief Bioinform 2022;23:6529282. [PMID: 35172334 DOI: 10.1093/bib/bbac018] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 12/27/2021] [Accepted: 01/13/2022] [Indexed: 12/20/2022]  Open
31
Troy NM, Strickland D, Serralha M, de Jong E, Jones AC, Read J, Galbraith S, Islam Z, Kaur P, Mincham KT, Holt BJ, Sly PD, Bosco A, Holt PG. Protection against severe infant lower respiratory tract infections by immune training: Mechanistic studies. J Allergy Clin Immunol 2022;150:93-103. [PMID: 35177255 DOI: 10.1016/j.jaci.2022.01.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 12/23/2021] [Accepted: 01/10/2022] [Indexed: 10/19/2022]
32
Kim EY, Che Y, Dean HJ, Lorenzo-Redondo R, Stewart M, Keller CK, Whorf D, Mills D, Dulin NN, Kim T, Votoupal M, Walter M, Fernandez-Sesma A, Kim H, Wolinsky SM. Transcriptome-wide changes in gene expression, splicing, and lncRNAs in response to a live attenuated dengue virus vaccine. Cell Rep 2022;38:110341. [PMID: 35139383 PMCID: PMC8994511 DOI: 10.1016/j.celrep.2022.110341] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 10/20/2021] [Accepted: 01/14/2022] [Indexed: 01/26/2023]  Open
33
Seo B, Lin L, Li J. Block-Wise Variable Selection for Clustering Via Latent States of Mixture Models. J Comput Graph Stat 2021. [DOI: 10.1080/10618600.2021.1982724] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
34
Sloan RP, Cole SW. Parasympathetic neural activity and the reciprocal regulation of innate antiviral and inflammatory genes in the human immune system. Brain Behav Immun 2021;98:251-256. [PMID: 34400237 PMCID: PMC8511100 DOI: 10.1016/j.bbi.2021.08.217] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 07/18/2021] [Accepted: 08/09/2021] [Indexed: 12/26/2022]  Open
35
Shin MR, Lee JH, Lee JA, Kim MJ, Park HJ, Park BW, Seo SB, Roh SS. Immunomodulatory and anti-inflammatory effects of Phellinus linteus mycelium. BMC Complement Med Ther 2021;21:269. [PMID: 34702240 PMCID: PMC8547106 DOI: 10.1186/s12906-021-03441-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 10/08/2021] [Indexed: 12/17/2022]  Open
36
Hodges NA, Sussman EM, Stegemann JP. Aseptic and septic prosthetic joint loosening: Impact of biomaterial wear on immune cell function, inflammation, and infection. Biomaterials 2021;278:121127. [PMID: 34564034 DOI: 10.1016/j.biomaterials.2021.121127] [Citation(s) in RCA: 84] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Revised: 09/01/2021] [Accepted: 09/07/2021] [Indexed: 12/17/2022]
37
Stimulus-specific responses in innate immunity: Multilayered regulatory circuits. Immunity 2021;54:1915-1932. [PMID: 34525335 DOI: 10.1016/j.immuni.2021.08.018] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 03/07/2021] [Accepted: 08/16/2021] [Indexed: 12/24/2022]
38
Goldwater DS, Leng M, Karlamangla A, Seeman T, Elashoff D, Wanagat JM, Reuben DB, Lindman BR, Cole S. Baseline pro-inflammatory gene expression in whole blood is related to adverse long-term outcomes after transcatheter aortic valve replacement: a case control study. BMC Cardiovasc Disord 2021;21:368. [PMID: 34340660 PMCID: PMC8327421 DOI: 10.1186/s12872-021-02186-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 07/28/2021] [Indexed: 12/12/2022]  Open
39
Peng Q, Ehlers CL. Long tracks of homozygosity predict the severity of alcohol use disorders in an American Indian population. Mol Psychiatry 2021;26:2200-2211. [PMID: 33398086 PMCID: PMC8254832 DOI: 10.1038/s41380-020-00989-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 11/30/2020] [Accepted: 12/07/2020] [Indexed: 11/20/2022]
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Cheemalavagu N, Gottschalk RA. Time will tell: The temporal code of immune threats. Immunity 2021;54:845-847. [PMID: 33979580 DOI: 10.1016/j.immuni.2021.04.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
41
Allelign Ashagre H, Zaltzman D, Idan-Molakandov A, Romano H, Tzfadia O, Harpaz-Saad S. FASCICLIN-LIKE 18 Is a New Player Regulating Root Elongation in Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2021;12:645286. [PMID: 33897736 PMCID: PMC8058476 DOI: 10.3389/fpls.2021.645286] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 02/19/2021] [Indexed: 05/26/2023]
42
Johnson JS, De Veaux N, Rives AW, Lahaye X, Lucas SY, Perot BP, Luka M, Garcia-Paredes V, Amon LM, Watters A, Abdessalem G, Aderem A, Manel N, Littman DR, Bonneau R, Ménager MM. A Comprehensive Map of the Monocyte-Derived Dendritic Cell Transcriptional Network Engaged upon Innate Sensing of HIV. Cell Rep 2021;30:914-931.e9. [PMID: 31968263 PMCID: PMC7039998 DOI: 10.1016/j.celrep.2019.12.054] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 06/25/2019] [Accepted: 12/13/2019] [Indexed: 01/12/2023]  Open
43
Sun X, Zhang J, Nie Q. Inferring latent temporal progression and regulatory networks from cross-sectional transcriptomic data of cancer samples. PLoS Comput Biol 2021;17:e1008379. [PMID: 33667222 PMCID: PMC7968745 DOI: 10.1371/journal.pcbi.1008379] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Revised: 03/17/2021] [Accepted: 02/15/2021] [Indexed: 12/19/2022]  Open
44
Jet T, Gines G, Rondelez Y, Taly V. Advances in multiplexed techniques for the detection and quantification of microRNAs. Chem Soc Rev 2021;50:4141-4161. [PMID: 33538706 DOI: 10.1039/d0cs00609b] [Citation(s) in RCA: 203] [Impact Index Per Article: 50.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
45
Chen T, Delano MJ, Chen K, Sperry JL, Namas RA, Lamparello AJ, Deng M, Conroy J, Moldawer LL, Efron PA, Loughran P, Seymour C, Angus DC, Vodovotz Y, Chen W, Billiar TR. A road map from single-cell transcriptome to patient classification for the immune response to trauma. JCI Insight 2021;6:145108. [PMID: 33320841 PMCID: PMC7934885 DOI: 10.1172/jci.insight.145108] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 12/09/2020] [Indexed: 01/07/2023]  Open
46
Gelaye B, Foster S, Bhasin M, Tawakol A, Fricchione G. SARS-CoV-2 morbidity and mortality in racial/ethnic minority populations: A window into the stress related inflammatory basis of health disparities? Brain Behav Immun Health 2020;9:100158. [PMID: 33052326 PMCID: PMC7543984 DOI: 10.1016/j.bbih.2020.100158] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 09/30/2020] [Accepted: 10/05/2020] [Indexed: 12/12/2022]  Open
47
Ghasemi T, Khalaj-Kondori M, Hosseinpour Feizi MA, Asadi P. lncRNA-miRNA-mRNA interaction network for colorectal cancer; An in silico analysis. Comput Biol Chem 2020;89:107370. [PMID: 32932199 DOI: 10.1016/j.compbiolchem.2020.107370] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 05/26/2020] [Accepted: 09/01/2020] [Indexed: 12/13/2022]
48
Herrera-Uribe J, Liu H, Byrne KA, Bond ZF, Loving CL, Tuggle CK. Changes in H3K27ac at Gene Regulatory Regions in Porcine Alveolar Macrophages Following LPS or PolyIC Exposure. Front Genet 2020;11:817. [PMID: 32973863 PMCID: PMC7468443 DOI: 10.3389/fgene.2020.00817] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Accepted: 07/08/2020] [Indexed: 12/17/2022]  Open
49
Katzenelenbogen Y, Sheban F, Yalin A, Yofe I, Svetlichnyy D, Jaitin DA, Bornstein C, Moshe A, Keren-Shaul H, Cohen M, Wang SY, Li B, David E, Salame TM, Weiner A, Amit I. Coupled scRNA-Seq and Intracellular Protein Activity Reveal an Immunosuppressive Role of TREM2 in Cancer. Cell 2020;182:872-885.e19. [PMID: 32783915 DOI: 10.1016/j.cell.2020.06.032] [Citation(s) in RCA: 318] [Impact Index Per Article: 63.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 05/06/2020] [Accepted: 06/19/2020] [Indexed: 01/08/2023]
50
Han J, Wang P, Wang Q, Lin Q, Chen Z, Yu G, Miao C, Dao Y, Wu R, Schnable JC, Tang H, Wang K. Genome-Wide Characterization of DNase I-Hypersensitive Sites and Cold Response Regulatory Landscapes in Grasses. THE PLANT CELL 2020;32:2457-2473. [PMID: 32471863 PMCID: PMC7401015 DOI: 10.1105/tpc.19.00716] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 05/11/2020] [Accepted: 05/23/2020] [Indexed: 05/05/2023]
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