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Preuss TM, Cáceres M, Oldham MC, Geschwind DH. Human brain evolution: insights from microarrays. Nat Rev Genet. 2004 Nov;5(11):850-60. doi: 10.1038/nrg1469. Review. PubMed PMID: 15520794.
Oldham MC, Geschwind DH. Evolutionary genetics: the human brain -- adaptation at many levels. Eur J Hum Genet. 2005 May;13(5):520-2. doi: 10.1038/sj.ejhg.5201401. PubMed PMID: 15756295.
Oldham MC, Geschwind DH. Deconstructing language by comparative gene expression: from neurobiology to microarray. Genes Brain Behav. 2006;5 Suppl 1:54-63. doi: 10.1111/j.1601-183X.2006.00195.x. Review. PubMed PMID: 16417618.
Oldham MC, Geschwind DH. Comparative genomics: grasping human transcriptome evolution: what does it all mean?. Heredity (Edinb). 2006 May;96(5):339-40. doi: 10.1038/sj.hdy.6800807. PubMed PMID: 16552432.
Oldham MC, Horvath S, Geschwind DH. Conservation and evolution of gene coexpression networks in human and chimpanzee brains. Proc Natl Acad Sci U S A. 2006 Nov 21;103(47):17973-8. doi: 10.1073/pnas.0605938103. Epub 2006 Nov 13. PubMed PMID: 17101986; PubMed Central PMCID: PMC1693857.
Abrahams BS, Tentler D, Perederiy JV, Oldham MC, Coppola G, Geschwind DH. Genome-wide analyses of human perisylvian cerebral cortical patterning. Proc Natl Acad Sci U S A. 2007 Nov 6;104(45):17849-54. doi: 10.1073/pnas.0706128104. Epub 2007 Oct 31. PubMed PMID: 17978184; PubMed Central PMCID: PMC2077018.
Spiteri E, Konopka G, Coppola G, Bomar J, Oldham M, Ou J, Vernes SC, Fisher SE, Ren B, Geschwind DH. Identification of the transcriptional targets of FOXP2, a gene linked to speech and language, in developing human brain. Am J Hum Genet. 2007 Dec;81(6):1144-57. doi: 10.1086/522237. Epub 2007 Oct 31. PubMed PMID: 17999357; PubMed Central PMCID: PMC2276350.
Miller JA, Oldham MC, Geschwind DH. A systems level analysis of transcriptional changes in Alzheimer's disease and normal aging. J Neurosci. 2008 Feb 6;28(6):1410-20. doi: 10.1523/JNEUROSCI.4098-07.2008. PubMed PMID: 18256261; PubMed Central PMCID: PMC2902235.
Oldham MC, Konopka G, Iwamoto K, Langfelder P, Kato T, Horvath S, Geschwind DH. Functional organization of the transcriptome in human brain. Nat Neurosci. 2008 Nov;11(11):1271-82. doi: 10.1038/nn.2207. Epub 2008 Oct 12. PubMed PMID: 18849986; PubMed Central PMCID: PMC2756411.
Winden KD, Oldham MC, Mirnics K, Ebert PJ, Swan CH, Levitt P, Rubenstein JL, Horvath S, Geschwind DH. The organization of the transcriptional network in specific neuronal classes. Mol Syst Biol. 2009;5:291. doi: 10.1038/msb.2009.46. Epub 2009 Jul 28. PubMed PMID: 19638972; PubMed Central PMCID: PMC2724976.
Mumford JA, Horvath S, Oldham MC, Langfelder P, Geschwind DH, Poldrack RA. Detecting network modules in fMRI time series: a weighted network analysis approach. Neuroimage. 2010 Oct 1;52(4):1465-76. doi: 10.1016/j.neuroimage.2010.05.047. Epub 2010 May 27. PubMed PMID: 20553896; PubMed Central PMCID: PMC3632300.
Cai C, Langfelder P, Fuller TF, Oldham MC, Luo R, van den Berg LH, Ophoff RA, Horvath S. Is human blood a good surrogate for brain tissue in transcriptional studies?. BMC Genomics. 2010 Oct 20;11:589. doi: 10.1186/1471-2164-11-589. PubMed PMID: 20961428; PubMed Central PMCID: PMC3091510.
Langfelder P, Luo R, Oldham MC, Horvath S. Is my network module preserved and reproducible?. PLoS Comput Biol. 2011 Jan 20;7(1):e1001057. doi: 10.1371/journal.pcbi.1001057. PubMed PMID: 21283776; PubMed Central PMCID: PMC3024255.
Iwamoto K, Bundo M, Ueda J, Oldham MC, Ukai W, Hashimoto E, Saito T, Geschwind DH, Kato T. Neurons show distinctive DNA methylation profile and higher interindividual variations compared with non-neurons. Genome Res. 2011 May;21(5):688-96. doi: 10.1101/gr.112755.110. Epub 2011 Apr 5. PubMed PMID: 21467265; PubMed Central PMCID: PMC3083085.
Rosen EY, Wexler EM, Versano R, Coppola G, Gao F, Winden KD, Oldham MC, Martens LH, Zhou P, Farese RV Jr, Geschwind DH. Functional genomic analyses identify pathways dysregulated by progranulin deficiency, implicating Wnt signaling. Neuron. 2011 Sep 22;71(6):1030-42. doi: 10.1016/j.neuron.2011.07.021. Epub 2011 Sep 21. PubMed PMID: 21943601; PubMed Central PMCID: PMC3633414.
Oldham MC, Langfelder P, Horvath S. Network methods for describing sample relationships in genomic datasets: application to Huntington's disease. BMC Syst Biol. 2012 Jun 12;6:63. doi: 10.1186/1752-0509-6-63. PubMed PMID: 22691535; PubMed Central PMCID: PMC3441531.
Konopka G, Friedrich T, Davis-Turak J, Winden K, Oldham MC, Gao F, Chen L, Wang GZ, Luo R, Preuss TM, Geschwind DH. Human-specific transcriptional networks in the brain. Neuron. 2012 Aug 23;75(4):601-17. doi: 10.1016/j.neuron.2012.05.034. PubMed PMID: 22920253; PubMed Central PMCID: PMC3645834.
Han K, Gennarino VA, Lee Y, Pang K, Hashimoto-Torii K, Choufani S, Raju CS, Oldham MC, Weksberg R, Rakic P, Liu Z, Zoghbi HY. Human-specific regulation of MeCP2 levels in fetal brains by microRNA miR-483-5p. Genes Dev. 2013 Mar 1;27(5):485-90. doi: 10.1101/gad.207456.112. Epub 2013 Feb 21. PubMed PMID: 23431031; PubMed Central PMCID: PMC3605462.
Ramos AD, Diaz A, Nellore A, Delgado RN, Park KY, Gonzales-Roybal G, Oldham MC, Song JS, Lim DA. Integration of genome-wide approaches identifies lncRNAs of adult neural stem cells and their progeny in vivo. Cell Stem Cell. 2013 May 2;12(5):616-28. doi: 10.1016/j.stem.2013.03.003. Epub 2013 Apr 11. PubMed PMID: 23583100; PubMed Central PMCID: PMC3662805.
Molofsky AV, Glasgow SM, Chaboub LS, Tsai HH, Murnen AT, Kelley KW, Fancy SP, Yuen TJ, Madireddy L, Baranzini S, Deneen B, Rowitch DH, Oldham MC. Expression profiling of Aldh1l1-precursors in the developing spinal cord reveals glial lineage-specific genes and direct Sox9-Nfe2l1 interactions. Glia. 2013 Sep;61(9):1518-32. doi: 10.1002/glia.22538. Epub 2013 Jul 10. PubMed PMID: 23840004; PubMed Central PMCID: PMC3909648.
Qiu H, Lee S, Shang Y, Wang WY, Au KF, Kamiya S, Barmada SJ, Finkbeiner S, Lui H, Carlton CE, Tang AA, Oldham MC, Wang H, Shorter J, Filiano AJ, Roberson ED, Tourtellotte WG, Chen B, Tsai LH, Huang EJ. ALS-associated mutation FUS-R521C causes DNA damage and RNA splicing defects. J Clin Invest. 2014 Mar;124(3):981-99. doi: 10.1172/JCI72723. Epub 2014 Feb 10. PubMed PMID: 24509083; PubMed Central PMCID: PMC3938263.
Parchem RJ, Ye J, Judson RL, LaRussa MF, Krishnakumar R, Blelloch A, Oldham MC, Blelloch R. Two miRNA clusters reveal alternative paths in late-stage reprogramming. Cell Stem Cell. 2014 May 1;14(5):617-31. doi: 10.1016/j.stem.2014.01.021. Epub 2014 Mar 13. PubMed PMID: 24630794; PubMed Central PMCID: PMC4305531.
Hwang WW, Salinas RD, Siu JJ, Kelley KW, Delgado RN, Paredes MF, Alvarez-Buylla A, Oldham MC, Lim DA. Distinct and separable roles for EZH2 in neurogenic astroglia. Elife. 2014 May 27;3:e02439. doi: 10.7554/eLife.02439. PubMed PMID: 24867641; PubMed Central PMCID: PMC4032491.
Potts MB, Siu JJ, Price JD, Salinas RD, Cho MJ, Ramos AD, Hahn J, Margeta M, Oldham MC, Lim DA. Analysis of Mll1 deficiency identifies neurogenic transcriptional modules and Brn4 as a factor for direct astrocyte-to-neuron reprogramming. Neurosurgery. 2014 Oct;75(4):472-82; discussion 482. doi: 10.1227/NEU.0000000000000452. PubMed PMID: 24887289; PubMed Central PMCID: PMC4420187.
Lui JH, Nowakowski TJ, Pollen AA, Javaherian A, Kriegstein AR, Oldham MC. Radial glia require PDGFD-PDGFRβ signalling in human but not mouse neocortex. Nature. 2014 Nov 13;515(7526):264-8. doi: 10.1038/nature13973. PubMed PMID: 25391964; PubMed Central PMCID: PMC4231536.
Parchem RJ, Moore N, Fish JL, Parchem JG, Braga TT, Shenoy A, Oldham MC, Rubenstein JL, Schneider RA, Blelloch R. miR-302 Is Required for Timing of Neural Differentiation, Neural Tube Closure, and Embryonic Viability. Cell Rep. 2015 Aug 4;12(5):760-73. doi: 10.1016/j.celrep.2015.06.074. Epub 2015 Jul 23. PubMed PMID: 26212322; PubMed Central PMCID: PMC4741278.
Pollen AA, Nowakowski TJ, Chen J, Retallack H, Sandoval-Espinosa C, Nicholas CR, Shuga J, Liu SJ, Oldham MC, Diaz A, Lim DA, Leyrat AA, West JA, Kriegstein AR. Molecular identity of human outer radial glia during cortical development. Cell. 2015 Sep 24;163(1):55-67. doi: 10.1016/j.cell.2015.09.004. PubMed PMID: 26406371; PubMed Central PMCID: PMC4583716.
Kelley KW, Oldham MC. Transcriptional architecture of the human brain. Nat Neurosci. 2015 Dec;18(12):1699-701. doi: 10.1038/nn.4178. PubMed PMID: 26605877.
Lui H, Zhang J, Makinson SR, Cahill MK, Kelley KW, Huang HY, Shang Y, Oldham MC, Martens LH, Gao F, Coppola G, Sloan SA, Hsieh CL, Kim CC, Bigio EH, Weintraub S, Mesulam MM, Rademakers R, Mackenzie IR, Seeley WW, Karydas A, Miller BL, Borroni B, Ghidoni R, Farese RV Jr, Paz JT, Barres BA, Huang EJ. Progranulin Deficiency Promotes Circuit-Specific Synaptic Pruning by Microglia via Complement Activation. Cell. 2016 May 5;165(4):921-35. doi: 10.1016/j.cell.2016.04.001. Epub 2016 Apr 21. PubMed PMID: 27114033; PubMed Central PMCID: PMC4860138.
Mitra I, Tsang K, Ladd-Acosta C, Croen LA, Aldinger KA, Hendren RL, Traglia M, Lavillaureix A, Zaitlen N, Oldham MC, Levitt P, Nelson S, Amaral DG, Hertz-Picciotto I, Fallin MD, Weiss LA. Pleiotropic Mechanisms Indicated for Sex Differences in Autism. PLoS Genet. 2016 Nov;12(11):e1006425. doi: 10.1371/journal.pgen.1006425. eCollection 2016 Nov. PubMed PMID: 27846226; PubMed Central PMCID: PMC5147776.
Seidel K, Marangoni P, Tang C, Houshmand B, Du W, Maas RL, Murray S, Oldham MC, Klein OD. Resolving stem and progenitor cells in the adult mouse incisor through gene co-expression analysis. Elife. 2017 May 5;6. doi: 10.7554/eLife.24712. PubMed PMID: 28475038; PubMed Central PMCID: PMC5419740.
Hu JK, Du W, Shelton SJ, Oldham MC, DiPersio CM, Klein OD. An FAK-YAP-mTOR Signaling Axis Regulates Stem Cell-Based Tissue Renewal in Mice. Cell Stem Cell. 2017 Jul 6;21(1):91-106.e6. doi: 10.1016/j.stem.2017.03.023. Epub 2017 Apr 27. PubMed PMID: 28457749; PubMed Central PMCID: PMC5501749.
Sorrells SF, Paredes MF, Cebrian-Silla A, Sandoval K, Qi D, Kelley KW, James D, Mayer S, Chang J, Auguste KI, Chang EF, Gutierrez AJ, Kriegstein AR, Mathern GW, Oldham MC, Huang EJ, Garcia-Verdugo JM, Yang Z, Alvarez-Buylla A. Human hippocampal neurogenesis drops sharply in children to undetectable levels in adults. Nature. 2018 Mar 15;555(7696):377-381. doi: 10.1038/nature25975. Epub 2018 Mar 7. PubMed PMID: 29513649; PubMed Central PMCID: PMC6179355.
Griveau A, Seano G, Shelton SJ, Kupp R, Jahangiri A, Obernier K, Krishnan S, Lindberg OR, Yuen TJ, Tien AC, Sabo JK, Wang N, Chen I, Kloepper J, Larrouquere L, Ghosh M, Tirosh I, Huillard E, Alvarez-Buylla A, Oldham MC, Persson AI, Weiss WA, Batchelor TT, Stemmer-Rachamimov A, Suvà ML, Phillips JJ, Aghi MK, Mehta S, Jain RK, Rowitch DH. A Glial Signature and Wnt7 Signaling Regulate Glioma-Vascular Interactions and Tumor Microenvironment. Cancer Cell. 2018 May 14;33(5):874-889.e7. doi: 10.1016/j.ccell.2018.03.020. Epub 2018 Apr 19. PubMed PMID: 29681511; PubMed Central PMCID: PMC6211172.
Raju CS, Spatazza J, Stanco A, Larimer P, Sorrells SF, Kelley KW, Nicholas CR, Paredes MF, Lui JH, Hasenstaub AR, Kriegstein AR, Alvarez-Buylla A, Rubenstein JL, Oldham MC. Secretagogin is Expressed by Developing Neocortical GABAergic Neurons in Humans but not Mice and Increases Neurite Arbor Size and Complexity. Cereb Cortex. 2018 Jun 1;28(6):1946-1958. doi: 10.1093/cercor/bhx101. PubMed PMID: 28449024; PubMed Central PMCID: PMC6019052.
Oldham MC, Kreitzer AC. Sequencing Diversity One Cell at a Time. Cell. 2018 Aug 9;174(4):777-779. doi: 10.1016/j.cell.2018.07.024. PubMed PMID: 30096308.
Kelley KW, Nakao-Inoue H, Molofsky AV, Oldham MC. Variation among intact tissue samples reveals the core transcriptional features of human CNS cell classes. Nat Neurosci. 2018 Sep;21(9):1171-1184. doi: 10.1038/s41593-018-0216-z. Epub 2018 Aug 28. PubMed PMID: 30154505; PubMed Central PMCID: PMC6192711.
Paredes MF, Sorrells SF, Cebrian-Silla A, Sandoval K, Qi D, Kelley KW, James D, Mayer S, Chang J, Auguste KI, Chang EF, Gutierrez Martin AJ, Kriegstein AR, Mathern GW, Oldham MC, Huang EJ, Garcia-Verdugo JM, Yang Z, Alvarez-Buylla A. Does Adult Neurogenesis Persist in the Human Hippocampus?. Cell Stem Cell. 2018 Dec 6;23(6):780-781. doi: 10.1016/j.stem.2018.11.006. PubMed PMID: 30526879; PubMed Central PMCID: PMC6800191.
Munji RN, Soung AL, Weiner GA, Sohet F, Semple BD, Trivedi A, Gimlin K, Kotoda M, Korai M, Aydin S, Batugal A, Cabangcala AC, Schupp PG, Oldham MC, Hashimoto T, Noble-Haeusslein LJ, Daneman R. Profiling the mouse brain endothelial transcriptome in health and disease models reveals a core blood-brain barrier dysfunction module. Nat Neurosci. 2019 Nov;22(11):1892-1902. doi: 10.1038/s41593-019-0497-x. Epub 2019 Oct 14. PubMed PMID: 31611708; PubMed Central PMCID: PMC6858546.
Torres R, Lang UE, Hejna M, Shelton SJ, Joseph NM, Shain AH, Yeh I, Wei ML, Oldham MC, Bastian BC, Judson-Torres RL. MicroRNA Ratios Distinguish Melanomas from Nevi. J Invest Dermatol. 2020 Jan;140(1):164-173.e7. doi: 10.1016/j.jid.2019.06.126. Epub 2019 Sep 30. PubMed PMID: 31580842; PubMed Central PMCID: PMC6926155.
Huie JR, Ferguson AR, Kyritsis N, Pan JZ, Irvine KA, Nielson JL, Schupp PG, Oldham MC, Gensel JC, Lin A, Segal MR, Ratan RR, Bresnahan JC, Beattie MS. Machine intelligence identifies soluble TNFa as a therapeutic target for spinal cord injury. Sci Rep. 2021 Feb 9;11(1):3442. doi: 10.1038/s41598-021-82951-5. PubMed PMID: 33564058; PubMed Central PMCID: PMC7873211.
Kyritsis N, Torres-Espín A, Schupp PG, Huie JR, Chou A, Duong-Fernandez X, Thomas LH, Tsolinas RE, Hemmerle DD, Pascual LU, Singh V, Pan JZ, Talbott JF, Whetstone WD, Burke JF, DiGiorgio AM, Weinstein PR, Manley GT, Dhall SS, Ferguson AR, Oldham MC, Bresnahan JC, Beattie MS. Diagnostic blood RNA profiles for human acute spinal cord injury. J Exp Med. 2021 Mar 1;218(3). doi: 10.1084/jem.20201795. PubMed PMID: 33512429; PubMed Central PMCID: PMC7852457.
Sorrells SF, Paredes MF, Zhang Z, Kang G, Pastor-Alonso O, Biagiotti S, Page CE, Sandoval K, Knox A, Connolly A, Huang EJ, Garcia-Verdugo JM, Oldham MC, Yang Z, Alvarez-Buylla A. Positive Controls in Adults and Children Support That Very Few, If Any, New Neurons Are Born in the Adult Human Hippocampus. J Neurosci. 2021 Mar 24;41(12):2554-2565. doi: 10.1523/JNEUROSCI.0676-20.2020. Review. PubMed PMID: 33762407; PubMed Central PMCID: PMC8018729.
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