Alex Nord, Ph.D.

Alex Nord

Associate Professor

  • Neurobiology, Physiology and Behavior; Psychiatry and Behavioral Sciences

Genomic control of transcription in the brain

Research Interest

My research explores gene regulatory circuits and chromatin dynamics in the brain, studying how these features contribute to brain development, evolution, and function. I apply a combination of genomics, mouse and cell-based models, and human genetics.  My work is rooted in basic and translational science, with an ultimate goal of understanding the biological components of human diseases and disorders of the brain and improving clinical care of afflicted individuals.  To that end, I perform both experimental work and computational analysis to reveal function of primary DNA sequence, epigenomic modifications, and chromatin structure.

I am always looking for motivated undergraduates, graduate students, and postdocs who are interested in contributing to projects addressing:

  • Chromatin and gene regulation in brain development, evolution, and function 
  • Genetic models of neurodevelopmental and psychiatric disorders 
  • Development and implementation of genomic applications in the clinic

Selected Publications

  • Wu H, Nord AS, Akiyama JA, Shoukry M, Afzal V, Rubin EM, Pennacchio LA, Visel A. Tissue-specific RNA expression marks distant-acting developmental enhancers. PLoS Genet. 2014 Sep 4;10(9):e1004610. PMID: 25188404.

  • Attanasio C*, Nord AS*, Zhu Y, Blow MJ, Biddie SC, Mendenhall EM, Dixon J, Wright C, Hosseini R, Akiyama JA, Holt A, Plajzer-Frick I, Shoukry M, Afzal V, Ren B, Bernstein BE, Rubin EM, Visel A, Pennacchio LA.  Tissue-specific SMARCA4 binding at active and repressed regulatory elements during embryogenesis.   Genome Res. 2014 Jun;24(6):920-9. PMID: 24752179

  • Pattabiraman K, Golonzhka O, Lindtner S, Nord AS, Taher L, Hoch R, Silberberg SN, Zhang D, Chen B, Zeng H, Pennacchio LA, Puelles L, Visel A, Rubenstein JL.  Transcriptional regulation of enhancers active in protodomains of the developing cerebral cortex.  Neuron. 2014 Jun 4;82(5):989-1003.  PMID: 24814534

  • Dickel, DE, Zhu Y, Nord AS, Wylie J, Akiyama JA, Plajzer-Frick I, Bruneau BG, Cisel A, Pennacchio LA. Function-based Identification of Mammalian Enhancers. Nat Methods2014 May;11(5):566-71. PMID: 24658141

  • Nord AS, Lee M, King MC, Walsh T. Accurate and exact CNV identification from targeted high-throughput sequence data. BMC Genomics. 2011 Apr 12;12:184. PMCID: PMC3088570

  • Nord AS, Blow MJ, Attanasio C, Akiyama JA, Holt A, Hosseini R, Phouanenavong S, Plajzer-Frick I, Shoukry M, Afzal V, Rubenstein JLR, Rubin EM, Pennacchio LA, Visel A. Rapid and Pervasive Changes in Genome-Wide Enhancer Usage During Mammalian Development. Cell. 2013. Dec 19;155(7): 1521-31 PMID: 24360275

  • Attanasio C, Nord AS, Zhu Y, Blow MJ, Li Z, Liberton DK, Morrison H, Plajzer-Frick I, Holt A, Hosseini R, Phouanenavong S, Akiyama JA, Shoukry M, Afzal V, Rubin EM, FitzPatrick DR, Ren B, Hallgrímsson B, Pennacchio LA, Visel A. Fine tuning of craniofacial morphology by distant-acting enhancers. Science. 2013. Oct 25;342(6157):1241006. PMID: 24159046

  • Visel A, Taher L, Girgis H, May D, Golonzhka O, Hoch RV, McKinsey GL, Pattabiraman K, Silberberg SN, Blow MJ, Hansen DV, Nord AS, Akiyama JA, Holt A, Hosseini R, Phouanenavong S, Plajzer-Frick I, Shoukry M, Afzal V, Kaplan T, Kriegstein AR, Rubin EM, Ovcharenko I, Pennacchio LA, Rubenstein JL. A high-resolution enhancer atlas of the developing telencephalon. Cell. 2013 Feb 14;152(4):895-908. PMCID: PMC3660042

  • Nord AS, Roeb W, Dickel DE, Walsh T, Kusenda M, O'Connor KL, Malhotra D, McCarthy SE, Stray SM, Taylor SM, Sebat J; STAART Psychopharmacology Network, King B, King MC, McClellan JM. Reduced transcript expression of genes affected by inherited and de novo CNVs in autism. Eur J Hum Genet. 2011 Jun;19(6):727-31. PMCID: PMC3110052

  • Walsh T, McClellan JM, McCarthy SE, Addington AM, Pierce SB, Cooper GM, Nord AS, Kusenda M, Malhotra D, Bhandari A, Stray SM, Rippey CF, Roccanova P, Makarov V, Lakshmi B, Findling RL, Sikich L, Stromberg T, Merriman B, Gogtay N, Butler P, Eckstrand K, Noory L, Gochman P, Long R, Chen Z, Davis S, Baker C, Eichler EE, Meltzer PS, Nelson SF, Singleton AB, Lee MK, Rapoport JL, King MC, Sebat J. Rare structural variants disrupt multiple genes in neurodevelopmental pathways in schizophrenia. Science. 2008 Apr 25;320(5875):539-43. PMID: 18369103

  • Nord AS, Vranizan K, Tingley W, Zambon AC, Hanspers K, Fong LG, Hu Y, Bacchetti P, Ferrin TE, Babbitt PC, Doniger SW, Skarnes WC, Young SG, Conklin BR. Modeling insertional mutagenesis using gene length and expression in murine embryonic stem cells. PLoS One. 2007 Jul 18;2(7):e617. PMCID: PMC1910612

  • Nord AS, Chang PJ, Conklin BR, Cox AV, Harper CA, Hicks GG, Huang CC, Johns SJ, Kawamoto M, Liu S, Meng EC, Morris JH, Rossant J, Ruiz P, Skarnes WC, Soriano P, Stanford WL, Stryke D, von Melchner H, Wurst W, Yamamura K, Young SG, Babbitt PC, Ferrin TE. The International Gene Trap Consortium Website: a portal to all publicly available gene trap cell lines in mouse. Nucleic Acids Res. 2006 Jan 1;34(Database issue):D642-8. PMCID: PMC1347459

Affiliations

Center for Neuroscience
Neurobiology, Physiology, and Behavior (College of Biological Sciences)
Psychiatry (School of Medicine)
UC Davis Genome Center
UC Davis MIND Institute