Johns Hopkins School of Medicine

All peer-reviewed publications:  www.ncbi.nlm.nih.gov/myncbi/1jQ_sYKsbrq/bibliography/public/

Kim SK, Seo S, Stein-O'Brien G, Jaishankar A, Ogawa K, Micali N, Luria V, Karger A, Wang Y, Kim H, Hyde TM, Kleinman JE, Voss T, Fertig EJ, Shin JH, Bürli R, Cross AJ, Brandon NJ, Weinberger DR, Chenoweth JG, Hoeppner DJ, Sestan N, Colantuoni C, McKay RD. Individual variation in the emergence of anterior-to- posterior neural fates from human pluripotent stem cells. Stem Cell Reports. 2024 Aug 5:S2213-6711(24)00213-3. doi: 10.1016/j.stemcr.2024.07.004. Epub ahead of print. PMID: 39151428.

Sonthalia S, Adkins RS, Orvis J, Li G, Mato Blanco X, Casella A, Liu J, Stein-O'Brien G, Caffo B, Hertzano R, Mahurkar A, Gillis J, Werner J, Ma S, Micali N, Sestan N, Rakic P, Santpere G, Ament SA, Colantuoni C. A Curated Compendium of Transcriptomic Data for the Exploration of Neocortical Development. bioRxiv [Preprint]. 2024 Aug 7:2024.02.26.581612. doi: 10.1101/2024.02.26.581612. PMID: 38464021; PMCID: PMC10925183.

Mato-Blanco X, Kim SK, Jourdon A, Ma S, Tebbenkamp ATN, Liu F, Duque A, Vaccarino FM, Sestan N, Colantuoni C, Rakic P, Santpere G, Micali N. Early Developmental Origins of Cortical Disorders Modeled in Human Neural Stem Cells. bioRxiv [Preprint]. 2024 Jun 14:2024.06.14.598925. doi: 10.1101/2024.06.14.598925. PMID: 38915580; PMCID: PMC11195173.

Ament SA, Cortes-Gutierrez M, Herb BR, Mocci E, Colantuoni C, McCarthy MM. A single-cell genomic atlas for maturation of the human cerebellum during early childhood. Sci Transl Med. 2023 Nov 8;15(721):eade1283. doi: 10.1126/scitranslmed.ade1283. Epub 2023 Nov 8. PMID: 37824600.

Herb BR, Glover HJ, Bhaduri A, Colantuoni C, Bale TL, Siletti K, Hodge R, Lein E, Kriegstein AR, Doege CA, Ament SA. Single-cell genomics reveals region- specific developmental trajectories underlying neuronal diversity in the human hypothalamus. Sci Adv. 2023 Nov 10;9(45):eadf6251. doi: 10.1126/sciadv.adf6251. Epub 2023 Nov 8. PMID: 37939194; PMCID: PMC10631741.

Ji L, Wang A, Sonthalia S, Naiman DQ, Younes L, Colantuoni C, Geman D. CellCover Defines Conserved Cell Types and Temporal Progression in scRNA-seq Data across Mammalian Neocortical Development. bioRxiv [Preprint]. 2023 Apr 7:2023.04.06.535943. doi: 10.1101/2023.04.06.535943. PMID: 37383947; PMCID: PMC10299349.

Chen H, Caffo B, Stein-O'Brien G, Liu J, Langmead B, Colantuoni C, Xiao L. Two-stage linked component analysis for joint decomposition of multiple biologically related data sets. Biostatistics. 2022 Oct 14;23(4):1200-1217. doi: 10.1093/biostatistics/kxac005. PMID: 35358296; PMCID: PMC9566367.

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. 2021 Feb 17;12(2):203. doi: 10.1016/j.cels.2021.01.005. Erratum for: Cell Syst. 2019 May 22;8(5):395-411.e8. doi: 10.1016/j.cels.2019.04.004. PMID: 33600760.

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. PMID: 32375049; 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. PMID: 31974374; PMCID: PMC6978526.

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. PMID: 32167521; PMCID: PMC7267840.

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. Erratum in: Cell Syst. 2021 Feb 17;12(2):203. doi: 10.1016/j.cels.2021.01.005. PMID: 31121116; PMCID: PMC6588402.

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; BrainSeq Consortium; 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. PMID: 30050107; PMCID: PMC6438700.

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>3.0.co;2-2. PMID: 10658179.

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. PMID: 11592853.

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. PMID: 12424128.

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(1):e114. doi: 10.1371/journal.pone.0000114. PMID: 17205118; PMCID: PMC1762434.

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. Erratum in: Brain Struct Funct. 2008 Sep;213(1-2):273. PMID: 18470533.

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. PMID: 19913943; PMCID: PMC2891610.

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. PMID: 22031444; PMCID: PMC3510670.