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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)
201
Ru B, Sun J, Kang Q, Tong Y, Zhang J. A framework for identifying dysregulated chromatin regulators as master regulators in human cancer. Bioinformatics 2019;35:1805-1812. [PMID: 30358822 DOI: 10.1093/bioinformatics/bty836] [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: 06/04/2018] [Revised: 08/22/2018] [Accepted: 10/24/2018] [Indexed: 11/12/2022]  Open
202
Mallm JP, Iskar M, Ishaque N, Klett LC, Kugler SJ, Muino JM, Teif VB, Poos AM, Großmann S, Erdel F, Tavernari D, Koser SD, Schumacher S, Brors B, König R, Remondini D, Vingron M, Stilgenbauer S, Lichter P, Zapatka M, Mertens D, Rippe K. Linking aberrant chromatin features in chronic lymphocytic leukemia to transcription factor networks. Mol Syst Biol 2019;15:e8339. [PMID: 31118277 PMCID: PMC6529931 DOI: 10.15252/msb.20188339] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 04/02/2019] [Accepted: 04/17/2019] [Indexed: 12/22/2022]  Open
203
Holding AN, Giorgi FM, Donnelly A, Cullen AE, Nagarajan S, Selth LA, Markowetz F. VULCAN integrates ChIP-seq with patient-derived co-expression networks to identify GRHL2 as a key co-regulator of ERa at enhancers in breast cancer. Genome Biol 2019;20:91. [PMID: 31084623 PMCID: PMC6515683 DOI: 10.1186/s13059-019-1698-z] [Citation(s) in RCA: 18] [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: 02/07/2019] [Accepted: 04/23/2019] [Indexed: 02/06/2023]  Open
204
Arnes L, Liu Z, Wang J, Maurer HC, Sagalovskiy I, Sanchez-Martin M, Bommakanti N, Garofalo DC, Balderes DA, Sussel L, Olive KP, Rabadan R. Comprehensive characterisation of compartment-specific long non-coding RNAs associated with pancreatic ductal adenocarcinoma. Gut 2019;68:499-511. [PMID: 29440233 PMCID: PMC6086768 DOI: 10.1136/gutjnl-2017-314353] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Revised: 12/22/2017] [Accepted: 01/01/2018] [Indexed: 02/06/2023]
205
Ru B, Tong Y, Zhang J. MR4Cancer: a web server prioritizing master regulators for cancer. Bioinformatics 2019;35:636-642. [PMID: 30052770 DOI: 10.1093/bioinformatics/bty658] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Revised: 07/17/2018] [Accepted: 07/20/2018] [Indexed: 01/10/2023]  Open
206
Shi M, Shen W, Chong Y, Wang HQ. Improving GRN re-construction by mining hidden regulatory signals. IET Syst Biol 2019;11:174-181. [PMID: 29125126 PMCID: PMC8687237 DOI: 10.1049/iet-syb.2017.0013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]  Open
207
Heyduk K, Hwang M, Albert V, Silvera K, Lan T, Farr K, Chang TH, Chan MT, Winter K, Leebens-Mack J. Altered Gene Regulatory Networks Are Associated With the Transition From C3 to Crassulacean Acid Metabolism in Erycina (Oncidiinae: Orchidaceae). FRONTIERS IN PLANT SCIENCE 2019;9:2000. [PMID: 30745906 PMCID: PMC6360190 DOI: 10.3389/fpls.2018.02000] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 12/24/2018] [Indexed: 05/21/2023]
208
Manners HN, Roy S, Kalita JK. Intrinsic-overlapping co-expression module detection with application to Alzheimer's Disease. Comput Biol Chem 2018;77:373-389. [PMID: 30466046 DOI: 10.1016/j.compbiolchem.2018.10.014] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Revised: 10/28/2018] [Accepted: 10/29/2018] [Indexed: 11/18/2022]
209
Durón C, Pan Y, Gutmann DH, Hardin J, Radunskaya A. Variability of Betweenness Centrality and Its Effect on Identifying Essential Genes. Bull Math Biol 2018;81:3655-3673. [PMID: 30350013 DOI: 10.1007/s11538-018-0526-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2017] [Accepted: 10/11/2018] [Indexed: 11/27/2022]
210
Wang M, Liu X, Chang G, Chen Y, An G, Yan L, Gao S, Xu Y, Cui Y, Dong J, Chen Y, Fan X, Hu Y, Song K, Zhu X, Gao Y, Yao Z, Bian S, Hou Y, Lu J, Wang R, Fan Y, Lian Y, Tang W, Wang Y, Liu J, Zhao L, Wang L, Liu Z, Yuan R, Shi Y, Hu B, Ren X, Tang F, Zhao XY, Qiao J. Single-Cell RNA Sequencing Analysis Reveals Sequential Cell Fate Transition during Human Spermatogenesis. Cell Stem Cell 2018;23:599-614.e4. [PMID: 30174296 DOI: 10.1016/j.stem.2018.08.007] [Citation(s) in RCA: 311] [Impact Index Per Article: 44.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2018] [Revised: 06/08/2018] [Accepted: 08/09/2018] [Indexed: 11/19/2022]
211
Veras PST, Ramos PIP, de Menezes JPB. In Search of Biomarkers for Pathogenesis and Control of Leishmaniasis by Global Analyses of Leishmania-Infected Macrophages. Front Cell Infect Microbiol 2018;8:326. [PMID: 30283744 PMCID: PMC6157484 DOI: 10.3389/fcimb.2018.00326] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 08/27/2018] [Indexed: 12/12/2022]  Open
212
Smith BA, Balanis NG, Nanjundiah A, Sheu KM, Tsai BL, Zhang Q, Park JW, Thompson M, Huang J, Witte ON, Graeber TG. A Human Adult Stem Cell Signature Marks Aggressive Variants across Epithelial Cancers. Cell Rep 2018;24:3353-3366.e5. [PMID: 30232014 PMCID: PMC6382070 DOI: 10.1016/j.celrep.2018.08.062] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Revised: 07/12/2018] [Accepted: 08/21/2018] [Indexed: 12/23/2022]  Open
213
Lavarenne J, Guyomarc'h S, Sallaud C, Gantet P, Lucas M. The Spring of Systems Biology-Driven Breeding. TRENDS IN PLANT SCIENCE 2018;23:706-720. [PMID: 29764727 DOI: 10.1016/j.tplants.2018.04.005] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 04/12/2018] [Accepted: 04/16/2018] [Indexed: 05/08/2023]
214
Villaverde AF, Becker K, Banga JR. PREMER: A Tool to Infer Biological Networks. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2018;15:1193-1202. [PMID: 28981423 DOI: 10.1109/tcbb.2017.2758786] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
215
Structure Optimization for Large Gene Networks Based on Greedy Strategy. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2018;2018:9674108. [PMID: 30013615 PMCID: PMC6022335 DOI: 10.1155/2018/9674108] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Revised: 04/23/2018] [Accepted: 05/11/2018] [Indexed: 01/04/2023]
216
Tong Y, Sun J, Wong CF, Kang Q, Ru B, Wong CN, Chan AS, Leung SY, Zhang J. MICMIC: identification of DNA methylation of distal regulatory regions with causal effects on tumorigenesis. Genome Biol 2018;19:73. [PMID: 29871649 PMCID: PMC5989391 DOI: 10.1186/s13059-018-1442-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Accepted: 05/03/2018] [Indexed: 12/11/2022]  Open
217
Gao S, Yan L, Wang R, Li J, Yong J, Zhou X, Wei Y, Wu X, Wang X, Fan X, Yan J, Zhi X, Gao Y, Guo H, Jin X, Wang W, Mao Y, Wang F, Wen L, Fu W, Ge H, Qiao J, Tang F. Tracing the temporal-spatial transcriptome landscapes of the human fetal digestive tract using single-cell RNA-sequencing. Nat Cell Biol 2018;20:721-734. [DOI: 10.1038/s41556-018-0105-4] [Citation(s) in RCA: 114] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 04/17/2018] [Indexed: 12/11/2022]
218
Pan Y, Duron C, Bush EC, Ma Y, Sims PA, Gutmann DH, Radunskaya A, Hardin J. Graph complexity analysis identifies an ETV5 tumor-specific network in human and murine low-grade glioma. PLoS One 2018;13:e0190001. [PMID: 29787563 PMCID: PMC5963759 DOI: 10.1371/journal.pone.0190001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2017] [Accepted: 12/06/2017] [Indexed: 01/10/2023]  Open
219
Rajbhandari P, Lopez G, Capdevila C, Salvatori B, Yu J, Rodriguez-Barrueco R, Martinez D, Yarmarkovich M, Weichert-Leahey N, Abraham BJ, Alvarez MJ, Iyer A, Harenza JL, Oldridge D, De Preter K, Koster J, Asgharzadeh S, Seeger RC, Wei JS, Khan J, Vandesompele J, Mestdagh P, Versteeg R, Look AT, Young RA, Iavarone A, Lasorella A, Silva JM, Maris JM, Califano A. Cross-Cohort Analysis Identifies a TEAD4-MYCN Positive Feedback Loop as the Core Regulatory Element of High-Risk Neuroblastoma. Cancer Discov 2018;8:582-599. [PMID: 29510988 PMCID: PMC5967627 DOI: 10.1158/2159-8290.cd-16-0861] [Citation(s) in RCA: 109] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Revised: 11/06/2017] [Accepted: 02/23/2018] [Indexed: 01/21/2023]
220
Peng X, Chen Z, Farshidfar F, Xu X, Lorenzi PL, Wang Y, Cheng F, Tan L, Mojumdar K, Du D, Ge Z, Li J, Thomas GV, Birsoy K, Liu L, Zhang H, Zhao Z, Marchand C, Weinstein JN, Bathe OF, Liang H. Molecular Characterization and Clinical Relevance of Metabolic Expression Subtypes in Human Cancers. Cell Rep 2018;23:255-269.e4. [PMID: 29617665 PMCID: PMC5916795 DOI: 10.1016/j.celrep.2018.03.077] [Citation(s) in RCA: 202] [Impact Index Per Article: 28.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Revised: 01/20/2018] [Accepted: 03/19/2018] [Indexed: 12/24/2022]  Open
221
Izzi V, Lakkala J, Devarajan R, Savolainen ER, Koistinen P, Heljasvaara R, Pihlajaniemi T. Vanin 1 (VNN1) levels predict poor outcome in acute myeloid leukemia. Am J Hematol 2018;93:E4-E7. [PMID: 28971505 DOI: 10.1002/ajh.24925] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Accepted: 09/27/2017] [Indexed: 11/10/2022]
222
Chen Y, Widschwendter M, Teschendorff AE. Systems-epigenomics inference of transcription factor activity implicates aryl-hydrocarbon-receptor inactivation as a key event in lung cancer development. Genome Biol 2017;18:236. [PMID: 29262847 PMCID: PMC5738803 DOI: 10.1186/s13059-017-1366-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2017] [Accepted: 11/27/2017] [Indexed: 12/25/2022]  Open
223
He J, Zhou Z, Reed M, Califano A. Accelerated parallel algorithm for gene network reverse engineering. BMC SYSTEMS BIOLOGY 2017;11:83. [PMID: 28950860 PMCID: PMC5615246 DOI: 10.1186/s12918-017-0458-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
224
Single-Cell RNA-Seq Analysis Maps Development of Human Germline Cells and Gonadal Niche Interactions. Cell Stem Cell 2017;20:858-873.e4. [DOI: 10.1016/j.stem.2017.03.007] [Citation(s) in RCA: 237] [Impact Index Per Article: 29.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Revised: 11/30/2016] [Accepted: 03/15/2017] [Indexed: 11/15/2022]
225
Moran B, Rahman A, Palonen K, Lanigan FT, Gallagher WM. Master Transcriptional Regulators in Cancer: Discovery via Reverse Engineering Approaches and Subsequent Validation. Cancer Res 2017;77:2186-2190. [PMID: 28428271 DOI: 10.1158/0008-5472.can-16-1813] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Revised: 09/08/2016] [Accepted: 02/22/2017] [Indexed: 11/16/2022]
226
Koda S, Onda Y, Matsui H, Takahagi K, Uehara-Yamaguchi Y, Shimizu M, Inoue K, Yoshida T, Sakurai T, Honda H, Eguchi S, Nishii R, Mochida K. Diurnal Transcriptome and Gene Network Represented through Sparse Modeling in Brachypodium distachyon. FRONTIERS IN PLANT SCIENCE 2017;8:2055. [PMID: 29234348 PMCID: PMC5712366 DOI: 10.3389/fpls.2017.02055] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Accepted: 11/16/2017] [Indexed: 05/08/2023]
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