2022

Rocks D, Kundakovic M. Hippocampus-based behavioral, structural, and molecular dynamics across the estrous cycle. J Neuroendocrinol. 2022 Nov 14;e13216. doi: 10.1111/jne.13216. Online ahead of print.

Rocks D, Cham H, Kundakovic M. Why the estrous cycle matters for neuroscience. Biol Sex Differ. 2022 Oct 28; 13:62.

Kundakovic M and Rocks D. Sex hormone fluctuation and increased female risk for depression and anxiety disorders: from clinical evidence to molecular mechanisms. Front Neuroendocrinol. 2022 Jul;66:101010.

Kundakovic M (2022). BET-ting on histone proteomics in schizophrenia. Trends in Neurosciences. 2022 Oct;45(10):716-717.

Rocks D, Shukla M, Ouldibbat L, Finnemann SC, Kalluchi A, Rowley MJ, Kundakovic M. Sex-specific multi-level 3D genome dynamics in the mouse brain. Nat Commun. 2022 Jun 15;13(1):3438.

Girdhar K, Hoffman GE, Bendl J, Rahman S, Dong P, Liao W, Hauberg ME, Sloofman L, Brown L, Devillers O, Kassim BS, Wiseman JR, Park R, Zharovsky E, Jacobov R, Flatow E, Kozlenkov A, Gilgenast T, Johnson JS, Couto L, Peters MA, Phillips-Cremins JE, Hahn CG, Gur RE, Tamminga CA, Lewis DA, Haroutunian V; PsychENCODE Consortium, Dracheva S, Lipska BK, Marenco S, Kundakovic M, Fullard JF, Jiang Y, Roussos P, Akbarian S. (2022). Chromatin domain alterations linked to 3D genome organization in a large cohort of schizophrenia and bipolar disorder brains. Nat Neurosci. 25(4):474-483.
2021

Hu B, Won H, Mah W, Park RB, Kassim B, Spiess K, Kozlenkov A, Crowley CA, Pochareddy S; PsychENCODE Consortium, Li Y, Dracheva S, Sestan N, Akbarian S, Geschwind DH. Neuronal and glial 3D chromatin architecture informs the cellular etiology of brain disorders. Nat Commun. 2021 Jun 25;12(1):3968.

Ho AM, Winham SJ, McCauley BM, Kundakovic M, Robertson KD, Sun Z, Ordog T, Webb LM, Frye MA, Veldic M (2021). Plasma Cell-Free DNA Methylomics of Bipolar Disorder With and Without Rapid Cycling. Front Neurosci. 15:774037.

Rocks D, Jaric I, Tesfa L, Greally JM, Suzuki M, Kundakovic M. Cell Type-Specific Chromatin Accessibility Analysis in the Mouse and Human Brain. Epigenetics. 2021 Mar 29:1-18.

 

2019
Jaric I, Rocks D, Greally JM, Suzuki M, Kundakovic M. Chromatin organization in the female mouse brain fluctuates across the oestrous cycle. Nature Commun. 2019 Jun 28;10(1):2851.

Jaric I*, Rocks D*, Cham H, Herchek A, Kundakovic M. Sex and Estrous Cycle Effects on Anxiety- and Depression-related Phenotypes in a Two-hit Developmental Stress Model. Front in Mol Neurosci. 2019 Apr 11;12:74. (*equal contribution).

2018

Li M, Santpere G, Imamura Kawasawa Y, Evgrafov OV, Gulden FO, Pochareddy S, Sunkin SM, Li Z, Shin Y, Zhu Y, Sousa AMM, Werling DM, Kitchen RR, Kang HJ, Pletikos M, Choi J, Muchnik S, Xu X, Wang D, Lorente-Galdos B, Liu S, Giusti-Rodríguez P, Won H, de Leeuw CA, Pardiñas AF; BrainSpan Consortium; PsychENCODE Consortium; PsychENCODE Developmental Subgroup, Hu M, Jin F, Li Y, Owen MJ, O’Donovan MC, Walters JTR, Posthuma D, Levitt P, Weinberger DR, Hyde TM, Kleinman JE, Geschwind DH, Hawrylycz MJ, State MW, Sanders SJ, Sullivan PF, Gerstein MB, Lein ES, Knowles JA, Sestan N. Integrative functional genomic analysis of human brain development and neuropsychiatric risks. Science. 2018 Dec 14;362(6420).

Wang D, Liu S, Warrell J, Won H, Shi X, Navarro FCP, Clarke D, Gu M, Emani P, Yang YT, Xu M, Gandal MJ, Lou S, Zhang J, Park JJ, Yan C, Rhie SK, Manakongtreecheep K, Zhou H, Nathan A, Peters M, Mattei E, Fitzgerald D, Brunetti T, Moore J, Jiang Y, Girdhar K, Hoffman GE, Kalayci S, Gümüş ZH, Crawford GE; PsychENCODE Consortium, Roussos P, Akbarian S, Jaffe AE, White KP, Weng Z, Sestan N, Geschwind DH, Knowles JA, Gerstein MB. Comprehensive functional genomic resource and integrative model for the human brain. Science. 2018 Dec 14;362(6420).

Gandal MJ, Zhang P, Hadjimichael E, Walker RL, Chen C, Liu S, Won H, van Bakel H, Varghese M, Wang Y, Shieh AW, Haney J, Parhami S, Belmont J, Kim M, Moran Losada P, Khan Z, Mleczko J, Xia Y, Dai R, Wang D, Yang YT, Xu M, Fish K, Hof PR, Warrell J, Fitzgerald D, White K, Jaffe AE; PsychENCODE Consortium, Peters MA, Gerstein M, Liu C, Iakoucheva LM, Pinto D, Geschwind DH. Transcriptome-wide isoform-level dysregulation in ASD, schizophrenia, and bipolar disorder. Science. 2018 Dec 14;362(6420).

PsychENCODE Consortium. Revealing the brain’s molecular architecture. Science. 2018 Dec 14;362(6420):1262-1263.

Girdhar K, Hoffman GE, Jiang Y, Brown L, Kundakovic M, Hauberg ME, Francoeur NJ, Wang Y, Shah H, Kavanagh DH, Zharovsky E, Jacobov R, Wiseman JR, Park R, Johnson JS, Kassim BS, Sloofman L, Mattei E, Weng Z , Sieberts SK, Peters MA, Harris BT, Lipska BK, Sklar P, Roussos P, Akbarian S. Cell-specific histone modification maps in the human frontal lobe link schizophrenia risk to the neuronal epigenome. Nat Neurosci. 2018 Aug;21(8):1126-1136.

2017

Kundakovic M. Sex-specific Epigenetics: Implications for Environmental Studies of Brain and Behavior. Curr Environ Health Rep. 2017 Dec;4(4):385-391.

Kundakovic M, Jaric I. The Epigenetic Link between Prenatal Adverse Environments and Neurodevelopmental Disorders. Genes (Basel). 2017 Mar 18;8(3). pii: E104.

Kundakovic M. Fearing the Mother’s Virus: The Lasting Consequences of Prenatal Immune Activation on the Epigenome and Brain Function. Biol Psychiatry. 2017 Feb 1;81(3):e23-e25.

Kundakovic M, Jiang Y, Kavanagh DH, Dincer A, Brown L, Pothula V, Zharovsky E, Park R, Jacobov R, Magro I, Kassim B, Wiseman J, Dang K, Sieberts SK, Roussos P, Fromer M, Harris B, Lipska BK, Peters MA, Sklar P, Akbarian S. Practical Guidelines for High-Resolution Epigenomic Profiling of Nucleosomal Histones in Postmortem Human Brain Tissue. Biol Psychiatry. 2017 Jan 15;81(2):162-170.

2016

Peter CJ, Fischer LK, Kundakovic M, Garg P, Jakovcevski M, Dincer A, Amaral AC, Ginns EI, Galdzicka M, Bryce CP, Ratner C, Waber DP, Mokler D, Medford G, Champagne FA, Rosene DL, McGaughy JA, Sharp AJ, Galler JR, Akbarian S. DNA Methylation Signatures of Early Childhood Malnutrition Associated With Impairments in Attention and Cognition. Biol Psychiatry . 2016 Nov 15;80(10):765-774.

Nestler EJ, Peña CJ, Kundakovic M, Mitchell A, Akbarian S. Epigenetic Basis of Mental Illness. Neuroscientist. 2016 Oct;22(5):447-63.

Kundakovic M (2016). Epigenetics of Psychiatric Disorders. In Tollefsbol (ed) Medical Epigenetics. Elsevier. p 335-350.

Kundakovic M, Peter C, Roussos P, and Akbarian S (2016). Epigenetic approaches towards the molecular and genetic risk architectures of schizophrenia. In Abel (ed) The Neurobiology of Schizophrenia. Elsevier. p 61-82.

Kundakovic M (2016). In utero Bisphenol A exposure and epigenetic programming of neurobehavioral outcomes. In Hollar D (ed), Epigenetics, the Environment, and Children’s Health across Lifespans. Springer. p 67-92.

2015

PsychENCODE Consortium, Akbarian S, Liu C, Knowles JA, Vaccarino FM, Farnham PJ, Crawford GE, Jaffe AE, Pinto D, Dracheva S, Geschwind DH, Mill J, Nairn AC, Abyzov A, Pochareddy S, Prabhakar S, Weissman S, Sullivan PF, State MW, Weng Z, Peters MA, White KP, Gerstein MB, Amiri A, Armoskus C, Ashley-Koch AE, Bae T, Beckel-Mitchener A, Berman BP, Coetzee GA, Coppola G, Francoeur N, Fromer M, Gao R, Grennan K, Herstein J, Kavanagh DH, Ivanov NA, Jiang Y, Kitchen RR, Kozlenkov A, Kundakovic M, Li M, Li Z, Liu S, Mangravite LM, Mattei E, Markenscoff-Papadimitriou E, Navarro FC, North N, Omberg L, Panchision D, Parikshak N, Poschmann J, Price AJ, Purcaro M, Reddy TE, Roussos P, Schreiner S, Scuderi S, Sebra R, Shibata M, Shieh AW, Skarica M, Sun W, Swarup V, Thomas A, Tsuji J, van Bakel H, Wang D, Wang Y, Wang K, Werling DM, Willsey AJ, Witt H, Won H, Wong CC, Wray GA, Wu EY, Xu X, Yao L, Senthil G, Lehner T, Sklar P, Sestan N. The PsychENCODE project. Nat Neurosci. 2015 Dec;18(12):1707-12.

Akbarian S, Kundakovic M. CHRNA7 and CHRFAM7A: psychosis and smoking? Blame the neighbors! Am J Psychiatry. 2015 Nov 1;172(11):1054-6.

Braithwaite EC, Kundakovic M, Ramchandani PG, Murphy SE, Champagne FA. Maternal prenatal depressive symptoms predict infant NR3C1 1F and BDNF IV DNA methylation. Epigenetics. 2015;10(5):408-17.

Morishita H, Kundakovic M, Bicks L, Mitchell A, Akbarian S. Interneuron epigenomes during the critical period of cortical plasticity: Implications for schizophrenia.Neurobiol Learn Mem. 2015 Oct;124:104-10.

Kundakovic M, Gudsnuk K, Herbstman JB, Tang D, Perera FP, Champagne FA. DNA methylation of BDNF as a biomarker of early-life adversity. Proc Natl Acad Sci U S A. 2015 Jun 2;112(22):6807-13.

Kundakovic M, Champagne FA. Early-life experience, epigenetics, and the developing brain. Neuropsychopharmacology. 2015 Jan;40(1):141-53.

2014

Kundakovic M. Postnatal risk environments, epigenetics, and psychosis: putting the pieces together.Soc Psychiatry Psychiatr Epidemiol. 2014 Oct;49(10):1535-6.

Kundakovic M (2014). DNA Methyltransferase Inhibitors and Psychiatric Disorders, In Peedicayil J, Avramopoulos D, and Grayson D (eds), Epigenetics in Psychiatry. Elsevier, p 497-514.

 

2013

Kundakovic M, Lim S, Gudsnuk K, Champagne FA. Sex-specific and strain-dependent effects of early life adversity on behavioral and epigenetic outcomes. Front Psychiatry. 2013 Aug 1;4:78.

Kundakovic M, Gudsnuk K, Franks B, Madrid J, Miller RL, Perera FP, Champagne FA. Sex-specific epigenetic disruption and behavioral changes following low-dose in utero bisphenol A exposure. Proc Natl Acad Sci U S A. 2013 Jun 11;110(24):9956-61.

Kundakovic M. Prenatal programming of psychopathology: the role of epigenetic mechanisms. J Med Biochem. 2013; 32 (4): 313–324.

2011-2012

Kirkbride JB, Susser E, Kundakovic M, Kresovich JK, Davey Smith G, Relton CL. Prenatal nutrition, epigenetics and schizophrenia risk: can we test causal effects? Epigenomics. 2012 Jun;4(3):303-15.

Kundakovic M, Champagne FA. Epigenetic perspective on the developmental effects of bisphenol A. Brain Behav Immun. 2011 Aug;25(6):1084-93.

2009-2010

Grayson DR, Kundakovic M, Sharma RP. Is there a future for histone deacetylase inhibitors in the pharmacotherapy of psychiatric disorders? Mol Pharmacol. 2010 Feb;77(2):126-35.

Grayson DR, Chen Y, Dong E, Kundakovic M, Guidotti A. From trans-methylation to cytosine methylation: evolution of the methylation hypothesis of schizophrenia. Epigenetics. 2009 Apr 1;4(3):144-9.

Guidotti A, Dong E, Kundakovic M, Satta R, Grayson DR, Costa E. Characterization of the action of antipsychotic subtypes on valproate-induced chromatin remodeling. Trends Pharmacol Sci. 2009 Feb;30(2):55-60.

Costa E, Chen Y, Dong E, Grayson DR, Kundakovic M, Maloku E, Ruzicka W, Satta R, Veldic M, Zhubi A, Guidotti A. GABAergic promoter hypermethylation as a model to study the neurochemistry of schizophrenia vulnerability. Expert Rev Neurother. 2009 Jan;9(1):87-98.

Kundakovic M, Chen Y, Guidotti A, Grayson DR. The reelin and GAD67 promoters are activated by epigenetic drugs that facilitate the disruption of local repressor complexes. Mol Pharmacol. 2009 Feb;75(2):342-54.

2005-2008

Chen Y, Kundakovic M, Agis-Balboa RC, Pinna G, Grayson DR. Induction of the reelin promoter by retinoic acid is mediated by Sp1. J Neurochem. 2007 Oct;103(2):650-65.

Kundakovic M, Chen Y, Costa E, Grayson DR. DNA methyltransferase inhibitors coordinately induce expression of the human reelin and glutamic acid decarboxylase 67 genes. Mol Pharmacol. 2007 Mar;71(3):644-53.

Grayson DR, Chen Y, Costa E, Dong E, Guidotti A, Kundakovic M, Sharma RP. The human reelin gene: transcription factors (+), repressors (-) and the methylation switch (+/-) in schizophrenia. Pharmacol Ther. 2006 Jul;111(1):272-86.

Mitchell CP, Chen Y, Kundakovic M, Costa E, Grayson DR. Histone deacetylase inhibitors decrease reelin promoter methylation in vitro. J Neurochem. 2005 Apr;93(2):483-92.