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For: Hawrylycz M, Ng L, Page D, Morris J, Lau C, Faber S, Faber V, Sunkin S, Menon V, Lein E, Jones A. Multi-scale correlation structure of gene expression in the brain. Neural Netw 2011;24:933-42. [PMID: 21764550 DOI: 10.1016/j.neunet.2011.06.012] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2010] [Revised: 06/16/2011] [Accepted: 06/16/2011] [Indexed: 01/25/2023]
Number Cited by Other Article(s)
1
Chen Z, Xu T, Liu X, Becker B, Li W, Xia L, Zhao W, Zhang R, Huo Z, Hu B, Tang Y, Xiao Z, Feng Z, Chen J, Feng T. Cortical gradient perturbation in attention deficit hyperactivity disorder correlates with neurotransmitter-, cell type-specific and chromosome- transcriptomic signatures. Psychiatry Clin Neurosci 2024;78:309-321. [PMID: 38334172 DOI: 10.1111/pcn.13649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 01/16/2024] [Accepted: 01/18/2024] [Indexed: 02/10/2024]
2
Yuvaraj M, Dey AK, Lyubchich V, Gel YR, Poor HV. Topological clustering of multilayer networks. Proc Natl Acad Sci U S A 2021;118:e2019994118. [PMID: 34006639 PMCID: PMC8166179 DOI: 10.1073/pnas.2019994118] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
3
Topological clustering of multilayer networks. Proc Natl Acad Sci U S A 2021. [DOI: 10.1073/pnas.2019994118 10.1073/pnas.2019994118] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]  Open
4
Distinct Genetic Signatures of Cortical and Subcortical Regions Associated with Human Memory. eNeuro 2019;6:ENEURO.0283-19.2019. [PMID: 31818829 PMCID: PMC6917897 DOI: 10.1523/eneuro.0283-19.2019] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 11/12/2019] [Accepted: 11/19/2019] [Indexed: 11/21/2022]  Open
5
Li J, Wang GZ. Application of Computational Biology to Decode Brain Transcriptomes. GENOMICS PROTEOMICS & BIOINFORMATICS 2019;17:367-380. [PMID: 31655213 PMCID: PMC6943780 DOI: 10.1016/j.gpb.2019.03.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Revised: 02/21/2019] [Accepted: 03/15/2019] [Indexed: 01/03/2023]
6
Cohen I, David E(O, Netanyahu NS. Supervised and Unsupervised End-to-End Deep Learning for Gene Ontology Classification of Neural In Situ Hybridization Images. ENTROPY 2019;21:e21030221. [PMID: 33266936 PMCID: PMC7514702 DOI: 10.3390/e21030221] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 10/22/2018] [Accepted: 12/19/2018] [Indexed: 11/16/2022]
7
Garcia VB, Abbinanti MD, Harris-Warrick RM, Schulz DJ. Effects of Chronic Spinal Cord Injury on Relationships among Ion Channel and Receptor mRNAs in Mouse Lumbar Spinal Cord. Neuroscience 2018;393:42-60. [PMID: 30282002 DOI: 10.1016/j.neuroscience.2018.09.034] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 09/22/2018] [Accepted: 09/24/2018] [Indexed: 01/08/2023]
8
Mladenova D, Barry G, Konen LM, Pineda SS, Guennewig B, Avesson L, Zinn R, Schonrock N, Bitar M, Jonkhout N, Crumlish L, Kaczorowski DC, Gong A, Pinese M, Franco GR, Walkley CR, Vissel B, Mattick JS. Adar3 Is Involved in Learning and Memory in Mice. Front Neurosci 2018;12:243. [PMID: 29719497 PMCID: PMC5914295 DOI: 10.3389/fnins.2018.00243] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 03/27/2018] [Indexed: 11/13/2022]  Open
9
Keil JM, Qalieh A, Kwan KY. Brain Transcriptome Databases: A User's Guide. J Neurosci 2018;38:2399-2412. [PMID: 29437890 PMCID: PMC5858588 DOI: 10.1523/jneurosci.1930-17.2018] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Revised: 01/25/2018] [Accepted: 02/01/2018] [Indexed: 12/20/2022]  Open
10
Huisman SM, van Lew B, Mahfouz A, Pezzotti N, Höllt T, Michielsen L, Vilanova A, Reinders MJ, Lelieveldt BP. BrainScope: interactive visual exploration of the spatial and temporal human brain transcriptome. Nucleic Acids Res 2017;45:e83. [PMID: 28132031 PMCID: PMC5449549 DOI: 10.1093/nar/gkx046] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Revised: 12/22/2016] [Accepted: 01/17/2017] [Indexed: 01/26/2023]  Open
11
Comparing the Expression of Genes Related to Serotonin (5-HT) in C57BL/6J Mice and Humans Based on Data Available at the Allen Mouse Brain Atlas and Allen Human Brain Atlas. Neurol Res Int 2017. [PMID: 28630769 PMCID: PMC5463198 DOI: 10.1155/2017/7138926] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]  Open
12
Mullins RJ, Diehl TC, Chia CW, Kapogiannis D. Insulin Resistance as a Link between Amyloid-Beta and Tau Pathologies in Alzheimer's Disease. Front Aging Neurosci 2017;9:118. [PMID: 28515688 PMCID: PMC5413582 DOI: 10.3389/fnagi.2017.00118] [Citation(s) in RCA: 131] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Accepted: 04/11/2017] [Indexed: 12/19/2022]  Open
13
Diehl T, Mullins R, Kapogiannis D. Insulin resistance in Alzheimer's disease. Transl Res 2017;183:26-40. [PMID: 28034760 PMCID: PMC5393926 DOI: 10.1016/j.trsl.2016.12.005] [Citation(s) in RCA: 90] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Revised: 12/05/2016] [Accepted: 12/06/2016] [Indexed: 12/14/2022]
14
Mahfouz A, Huisman SMH, Lelieveldt BPF, Reinders MJT. Brain transcriptome atlases: a computational perspective. Brain Struct Funct 2017;222:1557-1580. [PMID: 27909802 PMCID: PMC5406417 DOI: 10.1007/s00429-016-1338-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 11/15/2016] [Indexed: 01/31/2023]
15
Mikula S. Progress Towards Mammalian Whole-Brain Cellular Connectomics. Front Neuroanat 2016;10:62. [PMID: 27445704 PMCID: PMC4927572 DOI: 10.3389/fnana.2016.00062] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Accepted: 05/26/2016] [Indexed: 11/13/2022]  Open
16
Pfaffenseller B, da Silva Magalhães PV, De Bastiani MA, Castro MAA, Gallitano AL, Kapczinski F, Klamt F. Differential expression of transcriptional regulatory units in the prefrontal cortex of patients with bipolar disorder: potential role of early growth response gene 3. Transl Psychiatry 2016;6:e805. [PMID: 27163206 PMCID: PMC5070056 DOI: 10.1038/tp.2016.78] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Accepted: 03/23/2016] [Indexed: 01/08/2023]  Open
17
Grange P, Menashe I, Hawrylycz M. Cell-type-specific neuroanatomy of cliques of autism-related genes in the mouse brain. Front Comput Neurosci 2015;9:55. [PMID: 26074809 PMCID: PMC4448060 DOI: 10.3389/fncom.2015.00055] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Accepted: 04/25/2015] [Indexed: 11/28/2022]  Open
18
Mahfouz A, van de Giessen M, van der Maaten L, Huisman S, Reinders M, Hawrylycz MJ, Lelieveldt BP. Visualizing the spatial gene expression organization in the brain through non-linear similarity embeddings. Methods 2015;73:79-89. [DOI: 10.1016/j.ymeth.2014.10.004] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2014] [Revised: 09/18/2014] [Accepted: 10/05/2014] [Indexed: 10/24/2022]  Open
19
Feng D, Lau C, Ng L, Li Y, Kuan L, Sunkin SM, Dang C, Hawrylycz M. Exploration and visualization of connectivity in the adult mouse brain. Methods 2015;73:90-7. [PMID: 25637033 DOI: 10.1016/j.ymeth.2015.01.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Revised: 01/15/2015] [Accepted: 01/16/2015] [Indexed: 02/04/2023]  Open
20
Thompson CL, Ng L, Menon V, Martinez S, Lee CK, Glattfelder K, Sunkin SM, Henry A, Lau C, Dang C, Garcia-Lopez R, Martinez-Ferre A, Pombero A, Rubenstein JLR, Wakeman WB, Hohmann J, Dee N, Sodt AJ, Young R, Smith K, Nguyen TN, Kidney J, Kuan L, Jeromin A, Kaykas A, Miller J, Page D, Orta G, Bernard A, Riley Z, Smith S, Wohnoutka P, Hawrylycz MJ, Puelles L, Jones AR. A high-resolution spatiotemporal atlas of gene expression of the developing mouse brain. Neuron 2014;83:309-323. [PMID: 24952961 DOI: 10.1016/j.neuron.2014.05.033] [Citation(s) in RCA: 213] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/16/2014] [Indexed: 11/30/2022]
21
McCarthy MJ, Liang S, Spadoni AD, Kelsoe JR, Simmons AN. Whole brain expression of bipolar disorder associated genes: structural and genetic analyses. PLoS One 2014;9:e100204. [PMID: 24941232 PMCID: PMC4062532 DOI: 10.1371/journal.pone.0100204] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2014] [Accepted: 05/22/2014] [Indexed: 11/19/2022]  Open
22
Scott-Van Zeeland AA, Bloss CS, Tewhey R, Bansal V, Torkamani A, Libiger O, Duvvuri V, Wineinger N, Galvez L, Darst BF, Smith EN, Carson A, Pham P, Phillips T, Villarasa N, Tisch R, Zhang G, Levy S, Murray S, Chen W, Srinivasan S, Berenson G, Brandt H, Crawford S, Crow S, Fichter MM, Halmi KA, Johnson C, Kaplan AS, La Via M, Mitchell JE, Strober M, Rotondo A, Treasure J, Woodside DB, Bulik CM, Keel P, Klump KL, Lilenfeld L, Plotnicov K, Topol EJ, Shih PB, Magistretti P, Bergen AW, Berrettini W, Kaye W, Schork NJ. Evidence for the role of EPHX2 gene variants in anorexia nervosa. Mol Psychiatry 2014;19:724-32. [PMID: 23999524 PMCID: PMC3852189 DOI: 10.1038/mp.2013.91] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/11/2013] [Revised: 06/19/2013] [Accepted: 06/24/2013] [Indexed: 01/08/2023]
23
Cell-type-based model explaining coexpression patterns of genes in the brain. Proc Natl Acad Sci U S A 2014;111:5397-402. [PMID: 24706869 DOI: 10.1073/pnas.1312098111] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]  Open
24
Ye R, Carneiro AMD, Han Q, Airey D, Sanders-Bush E, Zhang B, Lu L, Williams R, Blakely RD. Quantitative trait loci mapping and gene network analysis implicate protocadherin-15 as a determinant of brain serotonin transporter expression. GENES BRAIN AND BEHAVIOR 2014;13:261-75. [PMID: 24405699 DOI: 10.1111/gbb.12119] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2013] [Revised: 12/23/2013] [Accepted: 01/02/2014] [Indexed: 12/15/2022]
25
Pollock JD, Wu DY, Satterlee JS. Molecular neuroanatomy: a generation of progress. Trends Neurosci 2014;37:106-23. [PMID: 24388609 PMCID: PMC3946666 DOI: 10.1016/j.tins.2013.11.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2013] [Revised: 11/08/2013] [Accepted: 11/14/2013] [Indexed: 11/22/2022]
26
Liscovitch N, Shalit U, Chechik G. FuncISH: learning a functional representation of neural ISH images. Bioinformatics 2013;29:i36-43. [PMID: 23813005 PMCID: PMC3694670 DOI: 10.1093/bioinformatics/btt207] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
27
Ye R, Carneiro AMD, Airey D, Sanders-Bush E, Williams RW, Lu L, Wang J, Zhang B, Blakely RD. Evaluation of heritable determinants of blood and brain serotonin homeostasis using recombinant inbred mice. GENES BRAIN AND BEHAVIOR 2013;13:247-60. [PMID: 24102824 DOI: 10.1111/gbb.12092] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Revised: 10/01/2013] [Accepted: 10/01/2013] [Indexed: 12/31/2022]
28
Menashe I, Grange P, Larsen EC, Banerjee-Basu S, Mitra PP. Co-expression profiling of autism genes in the mouse brain. PLoS Comput Biol 2013;9:e1003128. [PMID: 23935468 PMCID: PMC3723491 DOI: 10.1371/journal.pcbi.1003128] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2013] [Accepted: 05/21/2013] [Indexed: 11/17/2022]  Open
29
Grange P, Hawrylycz M, Mitra PP. Computational neuroanatomy and co-expression of genes in the adult mouse brain, analysis tools for the Allen Brain Atlas. QUANTITATIVE BIOLOGY 2013. [DOI: 10.1007/s40484-013-0011-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
30
Kirsch L, Liscovitch N, Chechik G. Localizing genes to cerebellar layers by classifying ISH images. PLoS Comput Biol 2012;8:e1002790. [PMID: 23284274 PMCID: PMC3527225 DOI: 10.1371/journal.pcbi.1002790] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2011] [Accepted: 08/31/2012] [Indexed: 11/18/2022]  Open
31
Neural networks including microRNAs. Neural Netw 2012;25:200-4. [DOI: 10.1016/j.neunet.2011.08.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2011] [Revised: 08/14/2011] [Accepted: 08/16/2011] [Indexed: 01/14/2023]
32
Ishii S, Diesmann M, Doya K. Multi-scale, multi-modal neural modeling and simulation. Neural Netw 2011;24:917. [PMID: 21840687 DOI: 10.1016/j.neunet.2011.07.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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