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Nauen DW, Haffner MC, Kim J, Zheng Q, Yin H, DeMarzo AM, Mahairaki V, Colantuoni C, Pickering JG, Johnson TP. Putative Autoantigen Leiomodin-1 Is Expressed in the Human Brain and in the Membrane Fraction of Newly Formed Neurons. Pathogens. 2020 Dec 10;9(12). doi: 10.3390/pathogens9121036. PubMed PMID: 33321732; PubMed Central PMCID: PMC7763904.
Sullivan MN, Brill SA, Mangus LM, Jeong YJ, Solis CV, Knight AC, Colantuoni C, Keceli G, Paolocci N, Queen SE, Mankowski JL. Upregulation of Superoxide Dismutase 2 by Astrocytes in the SIV/Macaque Model of HIV-Associated Neurologic Disease. J Neuropathol Exp Neurol. 2020 Sep 1;79(9):986-997. doi: 10.1093/jnen/nlaa084. PubMed PMID: 32783052; PubMed Central PMCID: PMC7445038.
Sharma G, Colantuoni C, Goff LA, Fertig EJ, Stein-O'Brien G. projectR: an R/Bioconductor package for transfer learning via PCA, NMF, correlation and clustering. Bioinformatics. 2020 Jun 1;36(11):3592-3593. doi: 10.1093/bioinformatics/btaa183. PubMed PMID: 32167521; PubMed Central PMCID: PMC7267840.
Micali N, Kim SK, Diaz-Bustamante M, Stein-O'Brien G, Seo S, Shin JH, Rash BG, Ma S, Wang Y, Olivares NA, Arellano JI, Maynard KR, Fertig EJ, Cross AJ, Bürli RW, Brandon NJ, Weinberger DR, Chenoweth JG, Hoeppner DJ, Sestan N, Rakic P, Colantuoni C, McKay RD. Variation of Human Neural Stem Cells Generating Organizer States In Vitro before Committing to Cortical Excitatory or Inhibitory Neuronal Fates. Cell Rep. 2020 May 5;31(5):107599. doi: 10.1016/j.celrep.2020.107599. PubMed PMID: 32375049; PubMed Central PMCID: PMC7357345.
Burke EE, Chenoweth JG, Shin JH, Collado-Torres L, Kim SK, Micali N, Wang Y, Colantuoni C, Straub RE, Hoeppner DJ, Chen HY, Sellers A, Shibbani K, Hamersky GR, Diaz Bustamante M, Phan BN, Ulrich WS, Valencia C, Jaishankar A, Price AJ, Rajpurohit A, Semick SA, Bürli RW, Barrow JC, Hiler DJ, Page SC, Martinowich K, Hyde TM, Kleinman JE, Berman KF, Apud JA, Cross AJ, Brandon NJ, Weinberger DR, Maher BJ, McKay RDG, Jaffe AE. Dissecting transcriptomic signatures of neuronal differentiation and maturation using iPSCs. Nat Commun. 2020 Jan 23;11(1):462. doi: 10.1038/s41467-019-14266-z. PubMed PMID: 31974374; PubMed Central PMCID: PMC6978526.
Gådin JR, Buil A, Colantuoni C, Jaffe AE, Nielsen J, Shin JH, Hyde TM, Kleinman JE, Plath N, Eriksson P, Brunak S, Didriksen M, Weinberger DR, Folkersen L. Comparison of quantitative trait loci methods: Total expression and allelic imbalance method in brain RNA-seq. PLoS One. 2019;14(6):e0217765. doi: 10.1371/journal.pone.0217765. eCollection 2019. PubMed PMID: 31206532; PubMed Central PMCID: PMC6576752.
Stein-O'Brien GL, Clark BS, Sherman T, Zibetti C, Hu Q, Sealfon R, Liu S, Qian J, Colantuoni C, Blackshaw S, Goff LA, Fertig EJ. Decomposing Cell Identity for Transfer Learning across Cellular Measurements, Platforms, Tissues, and Species. Cell Syst. 2019 May 22;8(5):395-411.e8. doi: 10.1016/j.cels.2019.04.004. PubMed PMID: 31121116; PubMed Central PMCID: PMC6588402.
Pearl JR, Colantuoni C, Bergey DE, Funk CC, Shannon P, Basu B, Casella AM, Oshone RT, Hood L, Price ND, Ament SA. Genome-Scale Transcriptional Regulatory Network Models of Psychiatric and Neurodegenerative Disorders. Cell Syst. 2019 Feb 27;8(2):122-135.e7. doi: 10.1016/j.cels.2019.01.002. Epub 2019 Feb 13. PubMed PMID: 30772379.
Jaffe AE, Straub RE, Shin JH, Tao R, Gao Y, Collado-Torres L, Kam-Thong T, Xi HS, Quan J, Chen Q, Colantuoni C, Ulrich WS, Maher BJ, Deep-Soboslay A, Cross AJ, Brandon NJ, Leek JT, Hyde TM, Kleinman JE, Weinberger DR. Developmental and genetic regulation of the human cortex transcriptome illuminate schizophrenia pathogenesis. Nat Neurosci. 2018 Aug;21(8):1117-1125. doi: 10.1038/s41593-018-0197-y. Epub 2018 Jul 26. PubMed PMID: 30050107; PubMed Central PMCID: PMC6438700.
Ursini G, Punzi G, Chen Q, Marenco S, Robinson JF, Porcelli A, Hamilton EG, Mitjans M, Maddalena G, Begemann M, Seidel J, Yanamori H, Jaffe AE, Berman KF, Egan MF, Straub RE, Colantuoni C, Blasi G, Hashimoto R, Rujescu D, Ehrenreich H, Bertolino A, Weinberger DR. Convergence of placenta biology and genetic risk for schizophrenia. Nat Med. 2018 Jun;24(6):792-801. doi: 10.1038/s41591-018-0021-y. Epub 2018 May 28. PubMed PMID: 29808008.
Stein-O'Brien GL, Carey JL, Lee WS, Considine M, Favorov AV, Flam E, Guo T, Li S, Marchionni L, Sherman T, Sivy S, Gaykalova DA, McKay RD, Ochs MF, Colantuoni C, Fertig EJ. PatternMarkers & GWCoGAPS for novel data-driven biomarkers via whole transcriptome NMF. Bioinformatics. 2017 Jun 15;33(12):1892-1894. doi: 10.1093/bioinformatics/btx058. PubMed PMID: 28174896; PubMed Central PMCID: PMC5860188.
Horiuchi Y, Kondo MA, Okada K, Takayanagi Y, Tanaka T, Ho T, Varvaris M, Tajinda K, Hiyama H, Ni K, Colantuoni C, Schretlen D, Cascella NG, Pevsner J, Ishizuka K, Sawa A. Molecular signatures associated with cognitive deficits in schizophrenia: a study of biopsied olfactory neural epithelium. Transl Psychiatry. 2016 Oct 11;6(10):e915. doi: 10.1038/tp.2016.154. PubMed PMID: 27727244; PubMed Central PMCID: PMC5315541.
Jaffe AE, Hyde T, Kleinman J, Weinberger DR, Chenoweth JG, McKay RD, Leek JT, Colantuoni C. Erratum to: Practical impacts of genomic data "cleaning" on biological discovery using surrogate variable analysis. BMC Bioinformatics. 2016 Aug 10;17:302. doi: 10.1186/s12859-016-1152-0. PubMed PMID: 27510709; PubMed Central PMCID: PMC4979135.
Jaffe AE, Hyde T, Kleinman J, Weinbergern DR, Chenoweth JG, McKay RD, Leek JT, Colantuoni C. Practical impacts of genomic data "cleaning" on biological discovery using surrogate variable analysis. BMC Bioinformatics. 2015 Nov 6;16:372. doi: 10.1186/s12859-015-0808-5. PubMed PMID: 26545828; PubMed Central PMCID: PMC4636836.
Poser SW, Chenoweth JG, Colantuoni C, Masjkur J, Chrousos G, Bornstein SR, McKay RD, Androutsellis-Theotokis A. Concise Review: Reprogramming, Behind the Scenes: Noncanonical Neural Stem Cell Signaling Pathways Reveal New, Unseen Regulators of Tissue Plasticity With Therapeutic Implications. Stem Cells Transl Med. 2015 Nov;4(11):1251-7. doi: 10.5966/sctm.2015-0105. Epub 2015 Sep 14. Review. PubMed PMID: 26371344; PubMed Central PMCID: PMC4622411.
Fertig EJ, Stein-O'Brien G, Jaffe A, Colantuoni C. Pattern identification in time-course gene expression data with the CoGAPS matrix factorization. Methods Mol Biol. 2014;1101:87-112. doi: 10.1007/978-1-62703-721-1_6. PubMed PMID: 24233779.
Haberman RP, Colantuoni C, Koh MT, Gallagher M. Behaviorally activated mRNA expression profiles produce signatures of learning and enhanced inhibition in aged rats with preserved memory. PLoS One. 2013;8(12):e83674. doi: 10.1371/journal.pone.0083674. eCollection 2013. PubMed PMID: 24349543; PubMed Central PMCID: PMC3862806.
Horiuchi Y, Kano S, Ishizuka K, Cascella NG, Ishii S, Talbot CC Jr, Jaffe AE, Okano H, Pevsner J, Colantuoni C, Sawa A. Olfactory cells via nasal biopsy reflect the developing brain in gene expression profiles: utility and limitation of the surrogate tissues in research for brain disorders. Neurosci Res. 2013 Dec;77(4):247-50. doi: 10.1016/j.neures.2013.09.010. Epub 2013 Oct 11. PubMed PMID: 24120685; PubMed Central PMCID: PMC4097863.
Mor E, Kano S, Colantuoni C, Sawa A, Navon R, Shomron N. MicroRNA-382 expression is elevated in the olfactory neuroepithelium of schizophrenia patients. Neurobiol Dis. 2013 Jul;55:1-10. doi: 10.1016/j.nbd.2013.03.011. Epub 2013 Mar 29. PubMed PMID: 23542694; PubMed Central PMCID: PMC3959166.
Kano S, Colantuoni C, Han F, Zhou Z, Yuan Q, Wilson A, Takayanagi Y, Lee Y, Rapoport J, Eaton W, Cascella N, Ji H, Goldman D, Sawa A. Genome-wide profiling of multiple histone methylations in olfactory cells: further implications for cellular susceptibility to oxidative stress in schizophrenia. Mol Psychiatry. 2013 Jul;18(7):740-2. doi: 10.1038/mp.2012.120. Epub 2012 Aug 28. PubMed PMID: 22925834; PubMed Central PMCID: PMC3582810.
Kondo MA, Tajinda K, Colantuoni C, Hiyama H, Seshadri S, Huang B, Pou S, Furukori K, Hookway C, Jaaro-Peled H, Kano SI, Matsuoka N, Harada K, Ni K, Pevsner J, Sawa A. Unique pharmacological actions of atypical neuroleptic quetiapine: possible role in cell cycle/fate control. Transl Psychiatry. 2013 Apr 2;3:e243. doi: 10.1038/tp.2013.19. PubMed PMID: 23549417; PubMed Central PMCID: PMC3641406.
Numata S, Ye T, Hyde TM, Guitart-Navarro X, Tao R, Wininger M, Colantuoni C, Weinberger DR, Kleinman JE, Lipska BK. DNA methylation signatures in development and aging of the human prefrontal cortex. Am J Hum Genet. 2012 Feb 10;90(2):260-72. doi: 10.1016/j.ajhg.2011.12.020. Epub 2012 Feb 2. PubMed PMID: 22305529; PubMed Central PMCID: PMC3276664.
Colantuoni C, Lipska BK, Ye T, Hyde TM, Tao R, Leek JT, Colantuoni EA, Elkahloun AG, Herman MM, Weinberger DR, Kleinman JE. Temporal dynamics and genetic control of transcription in the human prefrontal cortex. Nature. 2011 Oct 26;478(7370):519-23. doi: 10.1038/nature10524. PubMed PMID: 22031444; PubMed Central PMCID: PMC3510670.
Haberman RP, Colantuoni C, Stocker AM, Schmidt AC, Pedersen JT, Gallagher M. Prominent hippocampal CA3 gene expression profile in neurocognitive aging. Neurobiol Aging. 2011 Sep;32(9):1678-92. doi: 10.1016/j.neurobiolaging.2009.10.005. Epub 2009 Nov 13. PubMed PMID: 19913943; PubMed Central PMCID: PMC2891610.
Hyde TM, Lipska BK, Ali T, Mathew SV, Law AJ, Metitiri OE, Straub RE, Ye T, Colantuoni C, Herman MM, Bigelow LB, Weinberger DR, Kleinman JE. Expression of GABA signaling molecules KCC2, NKCC1, and GAD1 in cortical development and schizophrenia. J Neurosci. 2011 Jul 27;31(30):11088-95. doi: 10.1523/JNEUROSCI.1234-11.2011. PubMed PMID: 21795557; PubMed Central PMCID: PMC3758549.
Barth AS, Kumordzie A, Colantuoni C, Margulies KB, Cappola TP, Tomaselli GF. Reciprocal regulation of metabolic and signaling pathways. BMC Genomics. 2010 Mar 24;11:197. doi: 10.1186/1471-2164-11-197. PubMed PMID: 20334672; PubMed Central PMCID: PMC2861677.
Tajinda K, Ishizuka K, Colantuoni C, Morita M, Winicki J, Le C, Lin S, Schretlen D, Sawa A, Cascella NG. Neuronal biomarkers from patients with mental illnesses: a novel method through nasal biopsy combined with laser-captured microdissection. Mol Psychiatry. 2010 Mar;15(3):231-2. doi: 10.1038/mp.2009.73. PubMed PMID: 20168323.
Ishizuka K, Tajinda K, Colantuoni C, Morita M, Winicki J, Le C, Lin S, Schretlen D, Sawa A, Cascella NG. Negative symptoms of schizophrenia correlate with impairment on the University of Pennsylvania smell identification test. Neurosci Res. 2010 Jan;66(1):106-10. doi: 10.1016/j.neures.2009.10.001. Epub 2009 Oct 9. PubMed PMID: 19819272; PubMed Central PMCID: PMC4064297.
Barth AS, Aiba T, Halperin V, DiSilvestre D, Chakir K, Colantuoni C, Tunin RS, Dimaano VL, Yu W, Abraham TP, Kass DA, Tomaselli GF. Cardiac resynchronization therapy corrects dyssynchrony-induced regional gene expression changes on a genomic level. Circ Cardiovasc Genet. 2009 Aug;2(4):371-8. doi: 10.1161/CIRCGENETICS.108.832345. Epub 2009 May 15. PubMed PMID: 20031609; PubMed Central PMCID: PMC2801868.
Colantuoni C, Hyde TM, Mitkus S, Joseph A, Sartorius L, Aguirre C, Creswell J, Johnson E, Deep-Soboslay A, Herman MM, Lipska BK, Weinberger DR, Kleinman JE. Age-related changes in the expression of schizophrenia susceptibility genes in the human prefrontal cortex. Brain Struct Funct. 2008 Sep;213(1-2):255-71. doi: 10.1007/s00429-008-0181-5. Epub 2008 May 10. PubMed PMID: 18470533.
Haberman RP, Lee HJ, Colantuoni C, Koh MT, Gallagher M. Rapid encoding of new information alters the profile of plasticity-related mRNA transcripts in the hippocampal CA3 region. Proc Natl Acad Sci U S A. 2008 Jul 29;105(30):10601-6. doi: 10.1073/pnas.0804292105. Epub 2008 Jul 23. PubMed PMID: 18650386; PubMed Central PMCID: PMC2492487.
Williams EP, Lee JH, Bishai WR, Colantuoni C, Karakousis PC. Mycobacterium tuberculosis SigF regulates genes encoding cell wall-associated proteins and directly regulates the transcriptional regulatory gene phoY1. J Bacteriol. 2007 Jun;189(11):4234-42. doi: 10.1128/JB.00201-07. Epub 2007 Mar 23. PubMed PMID: 17384187; PubMed Central PMCID: PMC1913405.
Lehrmann E, Colantuoni C, Deep-Soboslay A, Becker KG, Lowe R, Huestis MA, Hyde TM, Kleinman JE, Freed WJ. Transcriptional changes common to human cocaine, cannabis and phencyclidine abuse. PLoS One. 2006 Dec 27;1:e114. doi: 10.1371/journal.pone.0000114. PubMed PMID: 17205118; PubMed Central PMCID: PMC1762434.
Gallagher M, Colantuoni C, Eichenbaum H, Haberman RP, Rapp PR, Tanila H, Wilson IA. Individual differences in neurocognitive aging of the medial temporal lobe. Age (Dordr). 2006 Sep;28(3):221-33. doi: 10.1007/s11357-006-9017-5. Epub 2006 Nov 25. PubMed PMID: 22253491; PubMed Central PMCID: PMC3259151.
Bencherif B, Guarda AS, Colantuoni C, Ravert HT, Dannals RF, Frost JJ. Regional mu-opioid receptor binding in insular cortex is decreased in bulimia nervosa and correlates inversely with fasting behavior. J Nucl Med. 2005 Aug;46(8):1349-51. PubMed PMID: 16085593.
Abounader R, Reznik T, Colantuoni C, Martinez-Murillo F, Rosen EM, Laterra J. Regulation of c-Met-dependent gene expression by PTEN. Oncogene. 2004 Dec 9;23(57):9173-82. doi: 10.1038/sj.onc.1208146. PubMed PMID: 15516982.
Colantuoni C, Henry G, Zeger S, Pevsner J. SNOMAD (Standardization and NOrmalization of MicroArray Data): web-accessible gene expression data analysis. Bioinformatics. 2002 Nov;18(11):1540-1. doi: 10.1093/bioinformatics/18.11.1540. PubMed PMID: 12424128.
Colantuoni C, Henry G, Zeger S, Pevsner J. Local mean normalization of microarray element signal intensities across an array surface: quality control and correction of spatially systematic artifacts. Biotechniques. 2002 Jun;32(6):1316-20. doi: 10.2144/02326mt02. PubMed PMID: 12074162.
Colantuoni C, Rada P, McCarthy J, Patten C, Avena NM, Chadeayne A, Hoebel BG. Evidence that intermittent, excessive sugar intake causes endogenous opioid dependence. Obes Res. 2002 Jun;10(6):478-88. doi: 10.1038/oby.2002.66. PubMed PMID: 12055324.
Colantuoni C, Schwenker J, McCarthy J, Rada P, Ladenheim B, Cadet JL, Schwartz GJ, Moran TH, Hoebel BG. Excessive sugar intake alters binding to dopamine and mu-opioid receptors in the brain. Neuroreport. 2001 Nov 16;12(16):3549-52. doi: 10.1097/00001756-200111160-00035. PubMed PMID: 11733709.
Colantuoni C, Jeon OH, Hyder K, Chenchik A, Khimani AH, Narayanan V, Hoffman EP, Kaufmann WE, Naidu S, Pevsner J. Gene expression profiling in postmortem Rett Syndrome brain: differential gene expression and patient classification. Neurobiol Dis. 2001 Oct;8(5):847-65. doi: 10.1006/nbdi.2001.0428. PubMed PMID: 11592853.
Colantuoni C, Purcell AE, Bouton CM, Pevsner J. High throughput analysis of gene expression in the human brain. J Neurosci Res. 2000 Jan 1;59(1):1-10. doi: 10.1002/(sici)1097-4547(20000101)59:1<1::aid-jnr1>;2-2. Review. PubMed PMID: 10658179.
Ward RJ, Colantuoni C, Dahchour A, Quertemont E, De Witte P. Acetaldehyde-induced changes in monoamine and amino acid extracellular microdialysate content of the nucleus accumbens. Neuropharmacology. 1997 Feb;36(2):225-32. doi: 10.1016/s0028-3908(97)00007-5. PubMed PMID: 9144660.
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