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Number Cited by Other Article(s)
51
Huang P, Cai M, Lu X, McKennan C, Wang J. Accurate estimation of rare cell type fractions from tissue omics data via hierarchical deconvolution. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.15.532820. [PMID: 36993280 PMCID: PMC10055056 DOI: 10.1101/2023.03.15.532820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
52
Dai R, Chu T, Zhang M, Wang X, Jourdon A, Wu F, Mariani J, Vaccarino FM, Lee D, Fullard JF, Hoffman GE, Roussos P, Wang Y, Wang X, Pinto D, Wang SH, Zhang C, Chen C, Liu C. Evaluating performance and applications of sample-wise cell deconvolution methods on human brain transcriptomic data. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.13.532468. [PMID: 36993743 PMCID: PMC10054947 DOI: 10.1101/2023.03.13.532468] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
53
Campbell KA, Colacino JA, Puttabyatappa M, Dou JF, Elkin ER, Hammoud SS, Domino SE, Dolinoy DC, Goodrich JM, Loch-Caruso R, Padmanabhan V, Bakulski KM. Placental cell type deconvolution reveals that cell proportions drive preeclampsia gene expression differences. Commun Biol 2023;6:264. [PMID: 36914823 PMCID: PMC10011423 DOI: 10.1038/s42003-023-04623-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 02/22/2023] [Indexed: 03/14/2023]  Open
54
Song X, Ji J, Rothstein JH, Alexeeff SE, Sakoda LC, Sistig A, Achacoso N, Jorgenson E, Whittemore AS, Klein RJ, Habel LA, Wang P, Sieh W. MiXcan: a framework for cell-type-aware transcriptome-wide association studies with an application to breast cancer. Nat Commun 2023;14:377. [PMID: 36690614 PMCID: PMC9871010 DOI: 10.1038/s41467-023-35888-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 01/05/2023] [Indexed: 01/25/2023]  Open
55
Deng W, Li B, Wang J, Jiang W, Yan X, Li N, Vukmirovic M, Kaminski N, Wang J, Zhao H. A novel Bayesian framework for harmonizing information across tissues and studies to increase cell type deconvolution accuracy. Brief Bioinform 2023;24:bbac616. [PMID: 36631398 PMCID: PMC9851324 DOI: 10.1093/bib/bbac616] [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: 10/19/2022] [Revised: 11/28/2022] [Accepted: 12/14/2022] [Indexed: 01/13/2023]  Open
56
Humphrey J, Venkatesh S, Hasan R, Herb JT, de Paiva Lopes K, Küçükali F, Byrska-Bishop M, Evani US, Narzisi G, Fagegaltier D, Sleegers K, Phatnani H, Knowles DA, Fratta P, Raj T. Integrative transcriptomic analysis of the amyotrophic lateral sclerosis spinal cord implicates glial activation and suggests new risk genes. Nat Neurosci 2023;26:150-162. [PMID: 36482247 DOI: 10.1038/s41593-022-01205-3] [Citation(s) in RCA: 67] [Impact Index Per Article: 33.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 10/13/2022] [Indexed: 12/13/2022]
57
Okereke LC, Bello AU, Onwukwe EA. Toward Precision Radiotherapy: A Nonlinear Optimization Framework and an Accelerated Machine Learning Algorithm for the Deconvolution of Tumor-Infiltrating Immune Cells. Cells 2022;11:cells11223604. [PMID: 36429031 PMCID: PMC9688486 DOI: 10.3390/cells11223604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 11/03/2022] [Accepted: 11/09/2022] [Indexed: 11/16/2022]  Open
58
Chatre L, Ducat A, Spradley FT, Palei AC, Chéreau C, Couderc B, Thomas KC, Wilson AR, Amaral LM, Gaillard I, Méhats C, Lagoutte I, Jacques S, Miralles F, Batteux F, Granger JP, Ricchetti M, Vaiman D. Increased NOS coupling by the metabolite tetrahydrobiopterin (BH4) reduces preeclampsia/IUGR consequences. Redox Biol 2022;55:102406. [PMID: 35964341 PMCID: PMC9389306 DOI: 10.1016/j.redox.2022.102406] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 07/04/2022] [Accepted: 07/11/2022] [Indexed: 11/24/2022]  Open
59
Shi C, Zhu J, Shen Y, Luo S, Zhu H, Song R. Off-Policy Confidence Interval Estimation with Confounded Markov Decision Process. J Am Stat Assoc 2022. [DOI: 10.1080/01621459.2022.2110876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
60
Cai M, Yue M, Chen T, Liu J, Forno E, Lu X, Billiar T, Celedón J, McKennan C, Chen W, Wang J. Robust and accurate estimation of cellular fraction from tissue omics data via ensemble deconvolution. Bioinformatics 2022;38:3004-3010. [PMID: 35438146 PMCID: PMC9991889 DOI: 10.1093/bioinformatics/btac279] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 03/22/2022] [Accepted: 04/13/2022] [Indexed: 01/04/2023]  Open
61
Haeusler GM, Garnham AL, Li‐Wai‐Suen CSN, Clark JE, Babl FE, Allaway Z, Slavin MA, Mechinaud F, Smyth GK, Phillips B, Thursky KA, Pellegrini M, Doerflinger M. Blood transcriptomics identifies immune signatures indicative of infectious complications in childhood cancer patients with febrile neutropenia. Clin Transl Immunology 2022;11:e1383. [PMID: 35602885 PMCID: PMC9113042 DOI: 10.1002/cti2.1383] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 03/03/2022] [Accepted: 03/10/2022] [Indexed: 12/13/2022]  Open
62
Haimbaugh A, Meyer D, Akemann C, Gurdziel K, Baker TR. Comparative Toxicotranscriptomics of Single Cell RNA-Seq and Conventional RNA-Seq in TCDD-Exposed Testicular Tissue. FRONTIERS IN TOXICOLOGY 2022;4:821116. [PMID: 35615540 PMCID: PMC9126299 DOI: 10.3389/ftox.2022.821116] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 03/03/2022] [Indexed: 12/18/2022]  Open
63
Studniberg SI, Ioannidis LJ, Utami RAS, Trianty L, Liao Y, Abeysekera W, Li‐Wai‐Suen CSN, Pietrzak HM, Healer J, Puspitasari AM, Apriyanti D, Coutrier F, Poespoprodjo JR, Kenangalem E, Andries B, Prayoga P, Sariyanti N, Smyth GK, Cowman AF, Price RN, Noviyanti R, Shi W, Garnham AL, Hansen DS. Molecular profiling reveals features of clinical immunity and immunosuppression in asymptomatic P. falciparum malaria. Mol Syst Biol 2022;18:e10824. [PMID: 35475529 PMCID: PMC9045086 DOI: 10.15252/msb.202110824] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 03/30/2022] [Accepted: 03/31/2022] [Indexed: 01/12/2023]  Open
64
Girdhar K, Hoffman GE, Bendl J, Rahman S, Dong P, Liao W, Hauberg ME, Sloofman L, Brown L, Devillers O, Kassim BS, Wiseman JR, Park R, Zharovsky E, Jacobov R, Flatow E, Kozlenkov A, Gilgenast T, Johnson JS, Couto L, Peters MA, Phillips-Cremins JE, Hahn CG, Gur RE, Tamminga CA, Lewis DA, Haroutunian V, Dracheva S, Lipska BK, Marenco S, Kundakovic M, Fullard JF, Jiang Y, Roussos P, Akbarian S. Chromatin domain alterations linked to 3D genome organization in a large cohort of schizophrenia and bipolar disorder brains. Nat Neurosci 2022;25:474-483. [PMID: 35332326 PMCID: PMC8989650 DOI: 10.1038/s41593-022-01032-6] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 02/09/2022] [Indexed: 12/19/2022]
65
Comprehensive evaluation of deconvolution methods for human brain gene expression. Nat Commun 2022;13:1358. [PMID: 35292647 PMCID: PMC8924248 DOI: 10.1038/s41467-022-28655-4] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Accepted: 01/28/2022] [Indexed: 11/08/2022]  Open
66
Brown AL, Wilkins OG, Keuss MJ, Kargbo-Hill SE, Zanovello M, Lee WC, Bampton A, Lee FCY, Masino L, Qi YA, Bryce-Smith S, Gatt A, Hallegger M, Fagegaltier D, Phatnani H, Newcombe J, Gustavsson EK, Seddighi S, Reyes JF, Coon SL, Ramos D, Schiavo G, Fisher EMC, Raj T, Secrier M, Lashley T, Ule J, Buratti E, Humphrey J, Ward ME, Fratta P. TDP-43 loss and ALS-risk SNPs drive mis-splicing and depletion of UNC13A. Nature 2022;603:131-137. [PMID: 35197628 PMCID: PMC8891020 DOI: 10.1038/s41586-022-04436-3] [Citation(s) in RCA: 253] [Impact Index Per Article: 84.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 01/18/2022] [Indexed: 12/12/2022]
67
Hasan R, Humphrey J, Bettencourt C, Newcombe J, Lashley T, Fratta P, Raj T. Transcriptomic analysis of frontotemporal lobar degeneration with TDP-43 pathology reveals cellular alterations across multiple brain regions. Acta Neuropathol 2022;143:383-401. [PMID: 34961893 PMCID: PMC10725322 DOI: 10.1007/s00401-021-02399-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 12/07/2021] [Accepted: 12/10/2021] [Indexed: 12/28/2022]
68
Danaher P, Kim Y, Nelson B, Griswold M, Yang Z, Piazza E, Beechem JM. Advances in mixed cell deconvolution enable quantification of cell types in spatial transcriptomic data. Nat Commun 2022;13:385. [PMID: 35046414 PMCID: PMC8770643 DOI: 10.1038/s41467-022-28020-5] [Citation(s) in RCA: 160] [Impact Index Per Article: 53.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 12/10/2021] [Indexed: 12/11/2022]  Open
69
Hoffman GE, Ma Y, Montgomery KS, Bendl J, Jaiswal MK, Kozlenkov A, Peters MA, Dracheva S, Fullard JF, Chess A, Devlin B, Sieberts SK, Roussos P. Sex Differences in the Human Brain Transcriptome of Cases With Schizophrenia. Biol Psychiatry 2022;91:92-101. [PMID: 34154796 PMCID: PMC8463632 DOI: 10.1016/j.biopsych.2021.03.020] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 03/16/2021] [Accepted: 03/18/2021] [Indexed: 01/03/2023]
70
Nadel BB, Oliva M, Shou BL, Mitchell K, Ma F, Montoya DJ, Mouton A, Kim-Hellmuth S, Stranger BE, Pellegrini M, Mangul S. Systematic evaluation of transcriptomics-based deconvolution methods and references using thousands of clinical samples. Brief Bioinform 2021;22:bbab265. [PMID: 34346485 PMCID: PMC8768458 DOI: 10.1093/bib/bbab265] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 06/07/2021] [Accepted: 06/21/2021] [Indexed: 11/13/2022]  Open
71
Hess JL, Radonjić NV, Patak J, Glatt SJ, Faraone SV. Autophagy, apoptosis, and neurodevelopmental genes might underlie selective brain region vulnerability in attention-deficit/hyperactivity disorder. Mol Psychiatry 2021;26:6643-6654. [PMID: 33339955 PMCID: PMC8760041 DOI: 10.1038/s41380-020-00974-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
72
Qiu Y, Wang J, Lei J, Roeder K. Identification of cell-type-specific marker genes from co-expression patterns in tissue samples. Bioinformatics 2021;37:3228-3234. [PMID: 33904573 PMCID: PMC8504631 DOI: 10.1093/bioinformatics/btab257] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Revised: 03/15/2021] [Accepted: 04/24/2021] [Indexed: 12/16/2022]  Open
73
Cellular, molecular, and therapeutic characterization of pilocarpine-induced temporal lobe epilepsy. Sci Rep 2021;11:19102. [PMID: 34580351 PMCID: PMC8476594 DOI: 10.1038/s41598-021-98534-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 09/09/2021] [Indexed: 12/30/2022]  Open
74
Zhang W, Xu H, Qiao R, Zhong B, Zhang X, Gu J, Zhang X, Wei L, Wang X. ARIC: accurate and robust inference of cell type proportions from bulk gene expression or DNA methylation data. Brief Bioinform 2021;23:6361035. [PMID: 34472588 DOI: 10.1093/bib/bbab362] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 08/13/2021] [Accepted: 08/16/2021] [Indexed: 11/12/2022]  Open
75
Thind AS, Monga I, Thakur PK, Kumari P, Dindhoria K, Krzak M, Ranson M, Ashford B. Demystifying emerging bulk RNA-Seq applications: the application and utility of bioinformatic methodology. Brief Bioinform 2021;22:6330938. [PMID: 34329375 DOI: 10.1093/bib/bbab259] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Revised: 06/14/2021] [Accepted: 06/18/2021] [Indexed: 12/13/2022]  Open
76
Sun R, Cui C, Zhou Y, Cui Q. Comprehensive Analysis of RNA Expression Correlations between Biofluids and Human Tissues. Genes (Basel) 2021;12:935. [PMID: 34207420 PMCID: PMC8234006 DOI: 10.3390/genes12060935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 06/12/2021] [Accepted: 06/15/2021] [Indexed: 11/25/2022]  Open
77
Aliee H, Theis FJ. AutoGeneS: Automatic gene selection using multi-objective optimization for RNA-seq deconvolution. Cell Syst 2021;12:706-715.e4. [PMID: 34293324 DOI: 10.1016/j.cels.2021.05.006] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Revised: 07/31/2020] [Accepted: 05/07/2021] [Indexed: 12/25/2022]
78
Kang K, Huang C, Li Y, Umbach DM, Li L. CDSeqR: fast complete deconvolution for gene expression data from bulk tissues. BMC Bioinformatics 2021;22:262. [PMID: 34030626 PMCID: PMC8142515 DOI: 10.1186/s12859-021-04186-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 05/12/2021] [Indexed: 11/10/2022]  Open
79
Amrhein L, Fuchs C. stochprofML: stochastic profiling using maximum likelihood estimation in R. BMC Bioinformatics 2021;22:123. [PMID: 33722188 PMCID: PMC7958472 DOI: 10.1186/s12859-021-03970-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 01/15/2021] [Indexed: 11/10/2022]  Open
80
Hunt GJ, Gagnon-Bartsch JA. The role of scale in the estimation of cell-type proportions. Ann Appl Stat 2021. [DOI: 10.1214/20-aoas1395] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
81
Tai AS, Tseng GC, Hsieh WP. BayICE: A Bayesian hierarchical model for semireference-based deconvolution of bulk transcriptomic data. Ann Appl Stat 2021. [DOI: 10.1214/20-aoas1376] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
82
Nadel BB, Lopez D, Montoya DJ, Ma F, Waddel H, Khan MM, Mangul S, Pellegrini M. The Gene Expression Deconvolution Interactive Tool (GEDIT): accurate cell type quantification from gene expression data. Gigascience 2021;10:giab002. [PMID: 33590863 PMCID: PMC7931818 DOI: 10.1093/gigascience/giab002] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 11/13/2020] [Accepted: 01/07/2021] [Indexed: 12/25/2022]  Open
83
Chen Z, Wu A. Progress and challenge for computational quantification of tissue immune cells. Brief Bioinform 2021;22:6065002. [PMID: 33401306 DOI: 10.1093/bib/bbaa358] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 10/23/2020] [Accepted: 11/07/2020] [Indexed: 12/28/2022]  Open
84
Bornholdt J, Broholm C, Chen Y, Rago A, Sloth S, Hendel J, Melsæther C, Müller CV, Juul Nielsen M, Strickertsson J, Engelholm L, Vitting-Seerup K, Jensen KB, Baker A, Sandelin A. Personalized B cell response to the Lactobacillus rhamnosus GG probiotic in healthy human subjects: a randomized trial. Gut Microbes 2020;12:1-14. [PMID: 33274667 PMCID: PMC7722709 DOI: 10.1080/19490976.2020.1854639] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]  Open
85
Benchmarking of cell type deconvolution pipelines for transcriptomics data. Nat Commun 2020;11:5650. [PMID: 33159064 PMCID: PMC7648640 DOI: 10.1038/s41467-020-19015-1] [Citation(s) in RCA: 243] [Impact Index Per Article: 48.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 09/16/2020] [Indexed: 01/05/2023]  Open
86
Hauberg ME, Creus-Muncunill J, Bendl J, Kozlenkov A, Zeng B, Corwin C, Chowdhury S, Kranz H, Hurd YL, Wegner M, Børglum AD, Dracheva S, Ehrlich ME, Fullard JF, Roussos P. Common schizophrenia risk variants are enriched in open chromatin regions of human glutamatergic neurons. Nat Commun 2020;11:5581. [PMID: 33149216 PMCID: PMC7643171 DOI: 10.1038/s41467-020-19319-2] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 10/08/2020] [Indexed: 01/04/2023]  Open
87
Li Z, Guo Z, Cheng Y, Jin P, Wu H. Robust partial reference-free cell composition estimation from tissue expression. Bioinformatics 2020;36:3431-3438. [PMID: 32167531 DOI: 10.1093/bioinformatics/btaa184] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 03/05/2020] [Accepted: 03/10/2020] [Indexed: 12/13/2022]  Open
88
Li H, Sharma A, Ming W, Sun X, Liu H. A deconvolution method and its application in analyzing the cellular fractions in acute myeloid leukemia samples. BMC Genomics 2020;21:652. [PMID: 32967610 PMCID: PMC7510109 DOI: 10.1186/s12864-020-06888-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 07/07/2020] [Indexed: 12/20/2022]  Open
89
Bortolomeazzi M, Keddar MR, Ciccarelli FD, Benedetti L. Identification of non-cancer cells from cancer transcriptomic data. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2020;1863:194445. [PMID: 31654804 PMCID: PMC7346884 DOI: 10.1016/j.bbagrm.2019.194445] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 09/20/2019] [Accepted: 10/07/2019] [Indexed: 02/07/2023]
90
Li H, Sharma A, Luo K, Qin ZS, Sun X, Liu H. DeconPeaker, a Deconvolution Model to Identify Cell Types Based on Chromatin Accessibility in ATAC-Seq Data of Mixture Samples. Front Genet 2020;11:392. [PMID: 32547592 PMCID: PMC7269180 DOI: 10.3389/fgene.2020.00392] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 03/30/2020] [Indexed: 12/26/2022]  Open
91
EPIC: A Tool to Estimate the Proportions of Different Cell Types from Bulk Gene Expression Data. Methods Mol Biol 2020;2120:233-248. [PMID: 32124324 DOI: 10.1007/978-1-0716-0327-7_17] [Citation(s) in RCA: 323] [Impact Index Per Article: 64.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
92
Fang S, Xu T, Xiong M, Zhou X, Wang Y, Haydu LE, Ross MI, Gershenwald JE, Prieto VG, Cormier JN, Wargo J, Sui D, Wei Q, Amos CI, Lee JE. Role of Immune Response, Inflammation, and Tumor Immune Response-Related Cytokines/Chemokines in Melanoma Progression. J Invest Dermatol 2019;139:2352-2358.e3. [PMID: 31176707 PMCID: PMC6814532 DOI: 10.1016/j.jid.2019.03.1158] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 03/07/2019] [Accepted: 03/24/2019] [Indexed: 01/12/2023]
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