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For: Lachmann A, Giorgi FM, Lopez G, Califano A. ARACNe-AP: gene network reverse engineering through adaptive partitioning inference of mutual information. Bioinformatics 2016;32:2233-5. [PMID: 27153652 PMCID: PMC4937200 DOI: 10.1093/bioinformatics/btw216] [Citation(s) in RCA: 226] [Impact Index Per Article: 25.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Accepted: 04/14/2016] [Indexed: 12/22/2022]  Open
Number Cited by Other Article(s)
51
Yashar WM, Estabrook J, Holly HD, Somers J, Nikolova O, Babur Ö, Braun TP, Demir E. Predicting transcription factor activity using prior biological information. iScience 2024;27:109124. [PMID: 38455978 PMCID: PMC10918219 DOI: 10.1016/j.isci.2024.109124] [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: 07/27/2023] [Revised: 10/20/2023] [Accepted: 01/31/2024] [Indexed: 03/09/2024]  Open
52
Yun HY. Leucine rich repeat LGI family member 3: Integrative analyses support its prognostic association with pancreatic adenocarcinoma. Medicine (Baltimore) 2024;103:e37183. [PMID: 38394487 PMCID: PMC11309673 DOI: 10.1097/md.0000000000037183] [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: 09/12/2023] [Accepted: 01/17/2024] [Indexed: 02/25/2024]  Open
53
Winkler I, Tolkachov A, Lammers F, Lacour P, Daugelaite K, Schneider N, Koch ML, Panten J, Grünschläger F, Poth T, Ávila BMD, Schneider A, Haas S, Odom DT, Gonçalves Â. The cycling and aging mouse female reproductive tract at single-cell resolution. Cell 2024;187:981-998.e25. [PMID: 38325365 DOI: 10.1016/j.cell.2024.01.021] [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: 07/25/2022] [Revised: 04/21/2023] [Accepted: 01/12/2024] [Indexed: 02/09/2024]
54
Leuzzi G, Vasciaveo A, Taglialatela A, Chen X, Firestone TM, Hickman AR, Mao W, Thakar T, Vaitsiankova A, Huang JW, Cuella-Martin R, Hayward SB, Kesner JS, Ghasemzadeh A, Nambiar TS, Ho P, Rialdi A, Hebrard M, Li Y, Gao J, Gopinath S, Adeleke OA, Venters BJ, Drake CG, Baer R, Izar B, Guccione E, Keogh MC, Guerois R, Sun L, Lu C, Califano A, Ciccia A. SMARCAL1 is a dual regulator of innate immune signaling and PD-L1 expression that promotes tumor immune evasion. Cell 2024;187:861-881.e32. [PMID: 38301646 PMCID: PMC10980358 DOI: 10.1016/j.cell.2024.01.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 07/23/2023] [Accepted: 01/05/2024] [Indexed: 02/03/2024]
55
Savage TM, Fortson KT, de Los Santos-Alexis K, Oliveras-Alsina A, Rouanne M, Rae SS, Gamarra JR, Shayya H, Kornberg A, Cavero R, Li F, Han A, Haeusler RA, Adam J, Schwabe RF, Arpaia N. Amphiregulin from regulatory T cells promotes liver fibrosis and insulin resistance in non-alcoholic steatohepatitis. Immunity 2024;57:303-318.e6. [PMID: 38309273 PMCID: PMC10922825 DOI: 10.1016/j.immuni.2024.01.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 11/20/2023] [Accepted: 01/10/2024] [Indexed: 02/05/2024]
56
Lu C, Donners MMPC, de Baaij JBJ, Jin H, Otten JJT, Manca M, van Zonneveld AJ, Jukema JW, Kraaijeveld A, Kuiper J, Pasterkamp G, Mees B, Sluimer JC, Cavill R, Karel JMH, Goossens P, Biessen EAL. Identification of a gene network driving the attenuated response to lipopolysaccharide of monocytes from hypertensive coronary artery disease patients. Front Immunol 2024;15:1286382. [PMID: 38410507 PMCID: PMC10894924 DOI: 10.3389/fimmu.2024.1286382] [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: 08/31/2023] [Accepted: 01/24/2024] [Indexed: 02/28/2024]  Open
57
Zhang H, Zhao Z, Wu Z, Xia Y, Zhao Y. Identifying interactions among air pollutant emissions on diabetes prevalence in Northeast China using a complex network. INTERNATIONAL JOURNAL OF BIOMETEOROLOGY 2024;68:393-400. [PMID: 38110789 DOI: 10.1007/s00484-023-02597-y] [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: 11/30/2023] [Accepted: 12/07/2023] [Indexed: 12/20/2023]
58
Lei W, Zhu H, Cao M, Zhang F, Lai Q, Lu S, Dong W, Sun J, Ru D. From genomics to metabolomics: Deciphering sanguinarine biosynthesis in Dicranostigma leptopodum. Int J Biol Macromol 2024;257:128727. [PMID: 38092109 DOI: 10.1016/j.ijbiomac.2023.128727] [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: 06/15/2023] [Revised: 11/15/2023] [Accepted: 12/08/2023] [Indexed: 12/18/2023]
59
Li J, Meng Z, Cao Z, Lu W, Yang Y, Li Z, Lu S. ADGRE5-centered Tsurv model in T cells recognizes responders to neoadjuvant cancer immunotherapy. Front Immunol 2024;15:1304183. [PMID: 38343549 PMCID: PMC10853338 DOI: 10.3389/fimmu.2024.1304183] [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: 09/29/2023] [Accepted: 01/02/2024] [Indexed: 02/15/2024]  Open
60
Xin J, Wang M, Qu L, Chen Q, Wang W, Wang Z. BIC-LP: A Hybrid Higher-Order Dynamic Bayesian Network Score Function for Gene Regulatory Network Reconstruction. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2024;21:188-199. [PMID: 38127613 DOI: 10.1109/tcbb.2023.3345317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]
61
Tu S, Zuo J. Systematic single cell RNA sequencing analysis reveals unique transcriptional regulatory networks of Atoh1-mediated hair cell conversion in adult mouse cochleae. PLoS One 2023;18:e0284685. [PMID: 38079436 PMCID: PMC10712870 DOI: 10.1371/journal.pone.0284685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 04/05/2023] [Indexed: 12/18/2023]  Open
62
Chen CC, Tran W, Song K, Sugimoto T, Obusan MB, Wang L, Sheu KM, Cheng D, Ta L, Varuzhanyan G, Huang A, Xu R, Zeng Y, Borujerdpur A, Bayley NA, Noguchi M, Mao Z, Morrissey C, Corey E, Nelson PS, Zhao Y, Huang J, Park JW, Witte ON, Graeber TG. Temporal evolution reveals bifurcated lineages in aggressive neuroendocrine small cell prostate cancer trans-differentiation. Cancer Cell 2023;41:2066-2082.e9. [PMID: 37995683 PMCID: PMC10878415 DOI: 10.1016/j.ccell.2023.10.009] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 08/25/2023] [Accepted: 10/30/2023] [Indexed: 11/25/2023]
63
Hicks AR, Reynolds RH, O’Callaghan B, García-Ruiz S, Gil-Martínez AL, Botía J, Plun-Favreau H, Ryten M. The non-specific lethal complex regulates genes and pathways genetically linked to Parkinson's disease. Brain 2023;146:4974-4987. [PMID: 37522749 PMCID: PMC10689904 DOI: 10.1093/brain/awad246] [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: 01/31/2023] [Revised: 05/12/2023] [Accepted: 06/23/2023] [Indexed: 08/01/2023]  Open
64
Tudose C, Bond J, Ryan CJ. Gene essentiality in cancer is better predicted by mRNA abundance than by gene regulatory network-inferred activity. NAR Cancer 2023;5:zcad056. [PMID: 38035131 PMCID: PMC10683780 DOI: 10.1093/narcan/zcad056] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 10/30/2023] [Accepted: 11/09/2023] [Indexed: 12/02/2023]  Open
65
Arriojas A, Patalano S, Macoska J, Zarringhalam K. A Bayesian noisy logic model for inference of transcription factor activity from single cell and bulk transcriptomic data. NAR Genom Bioinform 2023;5:lqad106. [PMID: 38094309 PMCID: PMC10716740 DOI: 10.1093/nargab/lqad106] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 11/12/2023] [Accepted: 11/24/2023] [Indexed: 12/20/2023]  Open
66
Hawley JE, Obradovic AZ, Dallos MC, Lim EA, Runcie K, Ager CR, McKiernan J, Anderson CB, Decastro GJ, Weintraub J, Virk R, Lowy I, Hu J, Chaimowitz MG, Guo XV, Zhang Y, Haffner MC, Worley J, Stein MN, Califano A, Drake CG. Anti-PD-1 immunotherapy with androgen deprivation therapy induces robust immune infiltration in metastatic castration-sensitive prostate cancer. Cancer Cell 2023;41:1972-1988.e5. [PMID: 37922910 PMCID: PMC11184948 DOI: 10.1016/j.ccell.2023.10.006] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 09/19/2023] [Accepted: 10/10/2023] [Indexed: 11/07/2023]
67
Paas-Oliveros E, Hernández-Lemus E, de Anda-Jáuregui G. Computational single cell oncology: state of the art. Front Genet 2023;14:1256991. [PMID: 38028624 PMCID: PMC10663273 DOI: 10.3389/fgene.2023.1256991] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 10/24/2023] [Indexed: 12/01/2023]  Open
68
Ji P, Liu Y, Yan L, Jia Y, Zhao M, Lv D, Yao Y, Ma W, Yin D, Liu F, Gao S, Wusiman A, Yang K, Zhang L, Liu G. Melatonin improves the vitrification of sheep morulae by modulating transcriptome. Front Vet Sci 2023;10:1212047. [PMID: 37920328 PMCID: PMC10619913 DOI: 10.3389/fvets.2023.1212047] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 07/03/2023] [Indexed: 11/04/2023]  Open
69
Hsieh PH, Lopes-Ramos CM, Zucknick M, Sandve GK, Glass K, Kuijjer ML. Adjustment of spurious correlations in co-expression measurements from RNA-Sequencing data. Bioinformatics 2023;39:btad610. [PMID: 37802917 PMCID: PMC10598588 DOI: 10.1093/bioinformatics/btad610] [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: 11/01/2022] [Revised: 08/05/2023] [Accepted: 10/05/2023] [Indexed: 10/08/2023]  Open
70
Ketteler A, Blumenthal DB. Demographic confounders distort inference of gene regulatory and gene co-expression networks in cancer. Brief Bioinform 2023;24:bbad413. [PMID: 37985453 DOI: 10.1093/bib/bbad413] [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: 06/16/2023] [Revised: 09/19/2023] [Accepted: 10/26/2023] [Indexed: 11/22/2023]  Open
71
Henao JD, Lauber M, Azevedo M, Grekova A, Theis F, List M, Ogris C, Schubert B. Multi-omics regulatory network inference in the presence of missing data. Brief Bioinform 2023;24:bbad309. [PMID: 37670505 PMCID: PMC10516394 DOI: 10.1093/bib/bbad309] [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: 12/08/2022] [Revised: 05/06/2023] [Accepted: 05/29/2023] [Indexed: 09/07/2023]  Open
72
Hoskins JW, Christensen TA, Amundadottir LT. Master regulator activity QTL protocol to implicate regulatory pathways potentially mediating GWAS signals using eQTL data. STAR Protoc 2023;4:102362. [PMID: 37330907 PMCID: PMC10285694 DOI: 10.1016/j.xpro.2023.102362] [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: 01/20/2023] [Revised: 04/26/2023] [Accepted: 05/17/2023] [Indexed: 06/20/2023]  Open
73
Theofilatos K, Stojkovic S, Hasman M, van der Laan SW, Baig F, Barallobre-Barreiro J, Schmidt LE, Yin S, Yin X, Burnap S, Singh B, Popham J, Harkot O, Kampf S, Nackenhorst MC, Strassl A, Loewe C, Demyanets S, Neumayer C, Bilban M, Hengstenberg C, Huber K, Pasterkamp G, Wojta J, Mayr M. Proteomic Atlas of Atherosclerosis: The Contribution of Proteoglycans to Sex Differences, Plaque Phenotypes, and Outcomes. Circ Res 2023;133:542-558. [PMID: 37646165 PMCID: PMC10498884 DOI: 10.1161/circresaha.123.322590] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 08/09/2023] [Accepted: 08/13/2023] [Indexed: 09/01/2023]
74
Li X, Lappalainen T, Bussemaker HJ. Identifying genetic regulatory variants that affect transcription factor activity. CELL GENOMICS 2023;3:100382. [PMID: 37719147 PMCID: PMC10504674 DOI: 10.1016/j.xgen.2023.100382] [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] [Received: 10/20/2022] [Revised: 05/19/2023] [Accepted: 07/21/2023] [Indexed: 09/19/2023]
75
Jethalia M, Jani SP, Ceccarelli M, Mall R. Pancancer network analysis reveals key master regulators for cancer invasiveness. J Transl Med 2023;21:558. [PMID: 37599366 PMCID: PMC10440887 DOI: 10.1186/s12967-023-04435-6] [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: 03/23/2023] [Accepted: 08/12/2023] [Indexed: 08/22/2023]  Open
76
Jiang Z, Wu F, Laise P, Takayuki T, Na F, Kim W, Kobayashi H, Chang W, Takahashi R, Valenti G, Sunagawa M, White RA, Macchini M, Renz BW, Middelhoff M, Hayakawa Y, Dubeykovskaya ZA, Tan X, Chu TH, Nagar K, Tailor Y, Belin BR, Anand A, Asfaha S, Finlayson MO, Iuga AC, Califano A, Wang TC. Tff2 defines transit-amplifying pancreatic acinar progenitors that lack regenerative potential and are protective against Kras-driven carcinogenesis. Cell Stem Cell 2023;30:1091-1109.e7. [PMID: 37541213 PMCID: PMC10414754 DOI: 10.1016/j.stem.2023.07.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 04/06/2023] [Accepted: 07/07/2023] [Indexed: 08/06/2023]
77
Hasman M, Mayr M, Theofilatos K. Uncovering Protein Networks in Cardiovascular Proteomics. Mol Cell Proteomics 2023;22:100607. [PMID: 37356494 PMCID: PMC10460687 DOI: 10.1016/j.mcpro.2023.100607] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 05/01/2023] [Accepted: 06/20/2023] [Indexed: 06/27/2023]  Open
78
Liu Q, Wei F, Wang J, Liu H, Zhang H, Liu M, Liu K, Ye Z. Molecular mechanisms regulating natural menopause in the female ovary: a study based on transcriptomic data. Front Endocrinol (Lausanne) 2023;14:1004245. [PMID: 37564980 PMCID: PMC10411606 DOI: 10.3389/fendo.2023.1004245] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 07/03/2023] [Indexed: 08/12/2023]  Open
79
Ceglia N, Sethna Z, Freeman SS, Uhlitz F, Bojilova V, Rusk N, Burman B, Chow A, Salehi S, Kabeer F, Aparicio S, Greenbaum BD, Shah SP, McPherson A. Identification of transcriptional programs using dense vector representations defined by mutual information with GeneVector. Nat Commun 2023;14:4400. [PMID: 37474509 PMCID: PMC10359421 DOI: 10.1038/s41467-023-39985-2] [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: 07/08/2022] [Accepted: 07/04/2023] [Indexed: 07/22/2023]  Open
80
Li JJ, Vasciaveo A, Karagiannis D, Sun Z, Chen X, Socciarelli F, Frankenstein Z, Zou M, Pannellini T, Chen Y, Gardner K, Robinson BD, de Bono J, Abate-Shen C, Rubin MA, Loda M, Sawyers CL, Califano A, Lu C, Shen MM. NSD2 maintains lineage plasticity and castration-resistance in neuroendocrine prostate cancer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.18.549585. [PMID: 37502956 PMCID: PMC10370123 DOI: 10.1101/2023.07.18.549585] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
81
Laber S, Strobel S, Mercader JM, Dashti H, dos Santos FR, Kubitz P, Jackson M, Ainbinder A, Honecker J, Agrawal S, Garborcauskas G, Stirling DR, Leong A, Figueroa K, Sinnott-Armstrong N, Kost-Alimova M, Deodato G, Harney A, Way GP, Saadat A, Harken S, Reibe-Pal S, Ebert H, Zhang Y, Calabuig-Navarro V, McGonagle E, Stefek A, Dupuis J, Cimini BA, Hauner H, Udler MS, Carpenter AE, Florez JC, Lindgren C, Jacobs SB, Claussnitzer M. Discovering cellular programs of intrinsic and extrinsic drivers of metabolic traits using LipocyteProfiler. CELL GENOMICS 2023;3:100346. [PMID: 37492099 PMCID: PMC10363917 DOI: 10.1016/j.xgen.2023.100346] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 08/22/2022] [Accepted: 05/26/2023] [Indexed: 07/27/2023]
82
Misetic H, Keddar MR, Jeannon JP, Ciccarelli FD. Mechanistic insights into the interactions between cancer drivers and the tumour immune microenvironment. Genome Med 2023;15:40. [PMID: 37277866 PMCID: PMC10240791 DOI: 10.1186/s13073-023-01197-0] [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: 01/14/2023] [Accepted: 05/25/2023] [Indexed: 06/07/2023]  Open
83
Ding J, Lee SJ, Vlahos L, Yuki K, Rada CC, van Unen V, Vuppalapaty M, Chen H, Sura A, McCormick AK, Tomaske M, Alwahabi S, Nguyen H, Nowatzke W, Kim L, Kelly L, Vollrath D, Califano A, Yeh WC, Li Y, Kuo CJ. Therapeutic blood-brain barrier modulation and stroke treatment by a bioengineered FZD4-selective WNT surrogate in mice. Nat Commun 2023;14:2947. [PMID: 37268690 PMCID: PMC10238527 DOI: 10.1038/s41467-023-37689-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 03/27/2023] [Indexed: 06/04/2023]  Open
84
Pan TC, Chockalingam SP, Aluru M, Aluru S. MCPNet: a parallel maximum capacity-based genome-scale gene network construction framework. Bioinformatics 2023;39:btad373. [PMID: 37289522 PMCID: PMC10287961 DOI: 10.1093/bioinformatics/btad373] [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: 04/29/2022] [Revised: 04/06/2023] [Accepted: 06/06/2023] [Indexed: 06/10/2023]  Open
85
Obradovic A, Ager C, Turunen M, Nirschl T, Khosravi-Maharlooei M, Iuga A, Jackson CM, Yegnasubramanian S, Tomassoni L, Fernandez EC, McCann P, Rogava M, DeMarzo AM, Kochel CM, Allaf M, Bivalacqua T, Lim M, Realubit R, Karan C, Drake CG, Califano A. Systematic elucidation and pharmacological targeting of tumor-infiltrating regulatory T cell master regulators. Cancer Cell 2023;41:933-949.e11. [PMID: 37116491 PMCID: PMC10193511 DOI: 10.1016/j.ccell.2023.04.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 09/13/2022] [Accepted: 04/06/2023] [Indexed: 04/30/2023]
86
Arriojas A, Patalano S, Macoska J, Zarringhalam K. A Bayesian Noisy Logic Model for Inference of Transcription Factor Activity from Single Cell and Bulk Transcriptomic Data. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.03.539308. [PMID: 37205561 PMCID: PMC10187261 DOI: 10.1101/2023.05.03.539308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
87
Wang Q, Guo M, Chen J, Duan R. A gene regulatory network inference model based on pseudo-siamese network. BMC Bioinformatics 2023;24:163. [PMID: 37085776 PMCID: PMC10122305 DOI: 10.1186/s12859-023-05253-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Accepted: 03/24/2023] [Indexed: 04/23/2023]  Open
88
Blatti C, de la Fuente J, Gao H, Marín-Goñi I, Chen Z, Zhao SD, Tan W, Weinshilboum R, Kalari KR, Wang L, Hernaez M. Bayesian Machine Learning Enables Identification of Transcriptional Network Disruptions Associated with Drug-Resistant Prostate Cancer. Cancer Res 2023;83:1361-1380. [PMID: 36779846 PMCID: PMC10102853 DOI: 10.1158/0008-5472.can-22-1910] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 07/29/2022] [Accepted: 02/08/2023] [Indexed: 02/14/2023]
89
Neyret-Kahn H, Fontugne J, Meng XY, Groeneveld CS, Cabel L, Ye T, Guyon E, Krucker C, Dufour F, Chapeaublanc E, Rapinat A, Jeffery D, Tanguy L, Dixon V, Neuzillet Y, Lebret T, Gentien D, Davidson I, Allory Y, Bernard-Pierrot I, Radvanyi F. Epigenomic mapping identifies an enhancer repertoire that regulates cell identity in bladder cancer through distinct transcription factor networks. Oncogene 2023;42:1524-1542. [PMID: 36944729 PMCID: PMC10162941 DOI: 10.1038/s41388-023-02662-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 03/01/2023] [Accepted: 03/06/2023] [Indexed: 03/23/2023]
90
Griffin AT, Vlahos LJ, Chiuzan C, Califano A. NaRnEA: An Information Theoretic Framework for Gene Set Analysis. ENTROPY (BASEL, SWITZERLAND) 2023;25:e25030542. [PMID: 36981431 PMCID: PMC10048242 DOI: 10.3390/e25030542] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 03/03/2023] [Accepted: 03/13/2023] [Indexed: 05/26/2023]
91
Flores-Díaz A, Escoto-Sandoval C, Cervantes-Hernández F, Ordaz-Ortiz JJ, Hayano-Kanashiro C, Reyes-Valdés H, Garcés-Claver A, Ochoa-Alejo N, Martínez O. Gene Functional Networks from Time Expression Profiles: A Constructive Approach Demonstrated in Chili Pepper (Capsicum annuum L.). PLANTS (BASEL, SWITZERLAND) 2023;12:1148. [PMID: 36904008 PMCID: PMC10005043 DOI: 10.3390/plants12051148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 02/20/2023] [Accepted: 02/27/2023] [Indexed: 06/18/2023]
92
Lachmann A, Rizzo KA, Bartal A, Jeon M, Clarke DJB, Ma’ayan A. PrismEXP: gene annotation prediction from stratified gene-gene co-expression matrices. PeerJ 2023;11:e14927. [PMID: 36874981 PMCID: PMC9979837 DOI: 10.7717/peerj.14927] [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: 10/06/2022] [Accepted: 01/30/2023] [Indexed: 03/03/2023]  Open
93
Rosenberger G, Li W, Turunen M, He J, Subramaniam PS, Pampou S, Griffin AT, Karan C, Kerwin P, Murray D, Honig B, Liu Y, Califano A. Network-based elucidation of colon cancer drug resistance by phosphoproteomic time-series analysis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.15.528736. [PMID: 36824919 PMCID: PMC9949144 DOI: 10.1101/2023.02.15.528736] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
94
The role of non-additive gene action on gene expression variation in plant domestication. EvoDevo 2023;14:3. [PMID: 36765382 PMCID: PMC9912502 DOI: 10.1186/s13227-022-00206-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 12/05/2022] [Indexed: 02/12/2023]  Open
95
Yan J, Wang X. Machine learning bridges omics sciences and plant breeding. TRENDS IN PLANT SCIENCE 2023;28:199-210. [PMID: 36153276 DOI: 10.1016/j.tplants.2022.08.018] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 08/15/2022] [Accepted: 08/23/2022] [Indexed: 06/16/2023]
96
Sebastian S, Roy S, Kalita J. A generic parallel framework for inferring large-scale gene regulatory networks from expression profiles: application to Alzheimer's disease network. Brief Bioinform 2023;24:6868522. [PMID: 36534961 DOI: 10.1093/bib/bbac482] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 09/14/2022] [Accepted: 10/11/2022] [Indexed: 12/23/2022]  Open
97
Zhang Y, Zhang Y, Song C, Zhao X, Ai B, Wang Y, Zhou L, Zhu J, Feng C, Xu L, Wang Q, Sun H, Fang Q, Xu X, Li E, Li C. CRdb: a comprehensive resource for deciphering chromatin regulators in human. Nucleic Acids Res 2023;51:D88-D100. [PMID: 36318256 PMCID: PMC9825595 DOI: 10.1093/nar/gkac960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 10/04/2022] [Accepted: 10/12/2022] [Indexed: 11/05/2022]  Open
98
Wang YQ, Wu DH, Wei D, Shen JY, Huang ZW, Liang XY, Cho WC, Ma J, Lv J, Chen YP. TEAD4 is a master regulator of high-risk nasopharyngeal carcinoma. SCIENCE ADVANCES 2023;9:eadd0960. [PMID: 36608137 PMCID: PMC9821866 DOI: 10.1126/sciadv.add0960] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Accepted: 12/06/2022] [Indexed: 06/17/2023]
99
Multi-omics inference of differential breast cancer-related transcriptional regulatory network gene hubs between young Black and White patients. Cancer Genet 2023;270-271:1-11. [PMID: 36410105 DOI: 10.1016/j.cancergen.2022.11.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 10/25/2022] [Accepted: 11/04/2022] [Indexed: 11/09/2022]
100
Galindez G, Sadegh S, Baumbach J, Kacprowski T, List M. Network-based approaches for modeling disease regulation and progression. Comput Struct Biotechnol J 2022;21:780-795. [PMID: 36698974 PMCID: PMC9841310 DOI: 10.1016/j.csbj.2022.12.022] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 12/14/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022]  Open
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