We are also part of the Human Brain Atlas collaboration funded by the Chan Zuckerberg Initiative (CZI).
Read about our commitment to diversity here.


Transcriptional Networks

What are the genes and pathways disrupted in neurodevelopmental disorders such as autism? We are using a combination of computational and wet-bench approaches to elucidate novel signal cascades important for the pathophysiology of autism. We are focused on identifying the neural circuits and cell-type contributions of these genes to brain development. We are also developing new rodent models for testing the behavioral consequences of modifying these genes.

Evolution of Human Cognition

What are the human-specific gene expression signatures and signaling pathways? We are taking a comparative genomics approach to identify genes that have been modified in the human brain. Genes of interest are being further examined using both human neuronal cultures and animal models.

Cognitive Genomics

Which genes are important for human cognition from a functional standpoint? We are examining the correspondence of human brain gene expression with measurements of human brain activity. We are also examining how these correlations are disrupted in cognitive disorders.

Lab Members

Principal Investigator

Assistant Professor

Postdoctoral Fellow

Postdoctoral Fellow

Postdoctoral Fellow

Postdoctoral Fellow

Postdoctoral Fellow

Postdoctoral Fellow

Postdoctoral Fellow

Graduate Student

Graduate Student

Graduate Student

Graduate Student

Graduate Student

Biomedical Engineering
Graduate Student

Lab Technician

Lab Manager


Featured Publication

Molecular features driving cellular complexity of human brain evolution

Human-specific genomic changes contribute to the unique functionalities of the human brain. The cellular heterogeneity of the human brain and the complex regulation of gene expression highlight the need to characterize human-specific molecular features at cellular resolution. Here we analysed single-nucleus RNA-sequencing and single-nucleus assay for transposase-accessible chromatin with sequencing datasets for human, chimpanzee and rhesus macaque brain tissue from posterior cingulate cortex. We show a human-specific increase of oligodendrocyte progenitor cells and a decrease of mature oligodendrocytes across cortical tissues. Human-specific regulatory changes were accelerated in oligodendrocyte progenitor cells, and we highlight key biological pathways that may be associated with the proportional changes. We also identify human-specific regulatory changes in neuronal subtypes, which reveal human-specific upregulation of FOXP2 in only two of the neuronal subtypes. We additionally identify hundreds of new human accelerated genomic regions associated with human-specific chromatin accessibility changes. Our data also reveal that FOS::JUN and FOX motifs are enriched in the human-specifically accessible chromatin regions of excitatory neuronal subtypes. Together, our results reveal several new mechanisms underlying the evolutionary innovation of human brain at cell-type resolution.

All Publications

Khandelwal, N., Kulkarni, A., Ahmed, N., Harper, M., Konopka, G., Gibson, J. FOXP1 regulates the development of excitatory synaptic inputs onto striatal neurons and induces phenotypic reversal with reinstatement. Science Advances 2024 May. https://www.science.org/doi/10.1126/sciadv.adm7039

Ahmed, N., Khandelwal, N., Anderson, A., Kulkarni, A., Gibson, J., Konopka, G. Compensation between FOXP transcription factors maintains proper striatal function Cell Reports 2024 May. https://www.cell.com/cell-reports/fulltext/S2211-1247(24)00585-0

Park, SHE., Kulkarni, A., Konopka, G. FOXP1 orchestrates neurogenesis in human cortical basal radial glial cells. PLoS Biol 2023 Aug. doi: https://doi.org/10.1371/journal.pbio.3001852

Caglayan, E., Ayhan, F., Liu, Y., Vollmer, R., Oh, E., Sherwood, C., Preuss, TM., Soojin, Y., Konopka, G. Molecular features driving cellular complexity of human brain evolution. Nature 2023 July. doi: https://doi.org/10.1038/s41586-023-06338-4

Anderson, A., Kulkarni, A., Konopka, G. A single-cell trajectory atlas of striatal development Sci Rep 2023 June. doi: https://doi.org/10.1038/s41598-023-36255-5

Liu, Y., Fontenot, M., Kulkarni, A., Khandelwal, N., Park, S., Douglas, C., Harper, M., Xu, P., Gupta, N., Gibson, J.R., Takahashi, J.S., Konopka, G. An extra-circadian function for human CLOCK in the neocortex. bioRxiv 2023.03.13.531623; doi: https://doi.org/10.1101/2023.03.13.531623

Caglayan, E., Liu, Y., Konopka, G. Neuronal ambient RNA contamination causes misinterpreted and masked cell types in brain single-nuclei datasets. Neuron E Pub 2022 Oct. PMID: 36240767 PMCID: PMC9789184. doi: https://doi.org/10.1016/j.neuron.2022.09.010

Moore, H., Lega, B.C., Konopka, G. Riding brain "waves" to identify human memory genes. Curr Opin Cell Biol. 2022 Aug. DOI: 10.1016/j.ceb.2022.102118.

Park, SE*, Ortiz, A*, Konopka, G. Corticogenesis across species at single-cell resolution. Dev Neurobiol. 2022 Aug. DOI: 10.1002/dneu.22896 PMID: 35932776.

Berto, S., Treacher, A.H., Caglayan, E., Luo, D., Haney, J.R., Gandal, M.J., Geschwind, D.H., Montillo, A.A., Konopka, G. Association between resting-state functional brain connectivity and gene expression is altered in autism spectrum disorder. Nat Commun. 2022 Jun. PMID: 35680911; PMCID: PMC9184501. doi: 10.1038/s41467-022-31053-5

Xu P, Berto S, Kulkarni A, Jeong B, Joseph C, Cox KH, Greenberg ME, Kim TK, Konopka G, Takahashi JS. NPAS4 regulates the transcriptional response of the suprachiasmatic nucleus to light and circadian behavior. Neuron. 2021 Aug. PMID: 34416169 DOI: 10.1016/j.neuron.2021.07.026

Solano Fonseca, R., Metang, P., Egge, N., Liu, Y., Zuurbier, K. R., Sivaprakasam, K., Shirazi, S., Chuah, A., Arneaud, S. L., Konopka, G., Qian, D., & Douglas, P. M. Glycolytic preconditioning in astrocytes mitigates trauma-induced neurodegeneration. eLife, 10, e69438. doi: https://doi.org/10.7554/eLife.69438 PMID: 34473622 PMCID: PMC8448530

Ayhan F, Douglas C, Lega BC, Konopka G. Nuclei isolation from surgically resected human hippocampus. STAR Protoc. 2021 Sep 16;2(4):100844. doi: 10.1016/j.xpro.2021.100844. PMID: 34585170; PMCID: PMC8455478.

Ayhan, F., Kulkarni A., Berto S., Sivaprakasam K., Douglas C., Lega B.C., Konopka G. Resolving cellular and molecular diversity along the hippocampal anterior-to-posterior axis in humans. Neuron. May 2021. PMID 34051145 10.1016/j.neuron.2021.05.003

Toriumi K, Berto S, Koike S, Usui N, Dan T, Suzuki K, Miyashita M, Horiuchi Y, Yoshikawa A, Asakura M, Nagahama K, Lin HC, Sugaya Y, Watanabe T, Kano M, Ogasawara Y, Miyata T, Itokawa M, Konopka G, Arai M. Combined glyoxalase 1 dysfunction and vitamin B6 deficiency in a schizophrenia model system causes mitochondrial dysfunction in the prefrontal cortex. Redox Biology. 45: 102057. PMID 34198071. DOI: 10.1016/j.redox.2021.102057 >

Xiao, L., Merullo, D., Cao, M., Co, M., Kulkarni, A., Konopka, G., Roberts, T. Expression of FoxP2 in the Basal Ganglia Regulates Vocal Motor Sequences in the Adult Songbird. In-Press Nature Communications. doi: 10.1101/2020.03.14.991042

Jeong, H., Mendizabal I, Berto S, Chatterjee P, Layman, T., Usui, N., Toriumi, K., Douglas C, Singh, D., Huh, I., Preuss T.M., Konopka, G.,Yi S.V., Evolution of DNA methylation in the human brain. In-Press Nature Communications. doi: 10.1101/2020.07.14.203034

S. Berto, M. R. Fontenot, S. Seger, F. Ayhan, E. Caglayan, A. Kulkarni, C. Douglas, C. A. Tamminga, B. C. Lega, G. Konopka. Gene-expression correlates of the oscillatory signatures supporting human episodic memory encoding. Nat Neurosci (2021). 10.1038/s41593-021-00803-x

Colquitt, B.*, Merullo, D.P.*, Konopka, G., Roberts, T.F., Brainard, M.S., Cellular transcriptomics reveals evolutionary identities of songbird vocal circuits. Science, 12 Feb 2021; Vol. 371, Issue 6530, eabd9704, doi: 10.1126/science.abd9704

Khandelwal, N., Cavalier, S., Rybalchenko, V., Kulkarni, A., Anderson, A.G., Konopka, G., Gibson, J. FOXP1 negatively regulates intrinsic excitability in D2 striatal projection neurons by promoting inwardly rectifying and leak potassium currents. Mol Psychiatry (2021). 10.1038/s41380-020-00995-x

Li Y, Shan Y, Kilaru GK, Berto S, Wang GZ, Cox KH, Yoo SH, Yang S, Konopka G, Takahashi JS. Epigenetic inheritance of circadian period in clonal cells. Elife. 2020 May 27;9:e54186. doi: 10.7554/eLife.54186. PMID: 32459177; PMCID: PMC7289596.

Bjorness T.E.*, Kulkarni A.*, Rybalchenko V.*, Suzuki A., Bridges C, Harrington AJ., Cowan CW., Takahashi JS., Konopka G., Greene RW. An essential role for MEF2C in the cortical response to loss of sleep in mice. Elife. 2020 Aug 27;9:e58331. doi: 10.7554/eLife.58331. PMID: 32851972; PMCID: PMC7490011.

Liu Y, Konopka G. An integrative understanding of comparative cognition: lessons from human brain evolution. Integr Comp Biol. 2020 Jul 18:icaa109. doi: 10.1093/icb/icaa109. Epub ahead of print. PMID: 32681799.

Berto S, Liu Y, Konopka G. Genomics at cellular resolution: insights into cognitive disorders and their evolution. Hum Mol Genet. 2020 Jun 22:ddaa117. doi: 10.1093/hmg/ddaa117. Epub ahead of print. PMID: 32566943.

Co M, Anderson AG, Konopka G. FOXP transcription factors in vertebrate brain development, function, and disorders. Wiley Interdiscip Rev Dev Biol. 2020 Sep;9(5):e375. doi: 10.1002/wdev.375. Epub 2020 Jan 30. PMID: 31999079.

Anderson, A.G., Kulkarni, A., Harper, M., Konopka, G. Single-cell analysis of Foxp1-driven mechanisms essential for striatal development. Cell Reports. 03.03.2020. https://doi.org/10.1016/j.celrep.2020.02.030

Berto S, Mendizabal I, Usui N, Toriumi K, Chatterjee P, Douglas C, Tamminga CA, Preuss TM, Yi SV, Konopka G. Accelerated evolution of oligodendrocytes in the human brain. Proc Natl Acad Sci USA. 2019;116(48):24334-42. doi: 10.1073/pnas.1907982116.

Mendizabal I, Berto S, Usui N, Toriumi K, Chatterjee P, Douglas C, Huh I, Jeong H, Layman T, Tamminga CA, Preuss TM, Konopka G, Yi SV. Cell type-specific epigenetic links to schizophrenia risk in the brain. Genome Biology 2019 20:135. https://doi.org/10.1186/s13059-019-1747-7

Hickey, Berto, S., Konopka, G. Chromatin Decondensation by FOXP2 Promotes Human Neuron Maturation and Expression of Neurodevelopmental Disease Genes. Cell Reports, Vol.27, Issue 6, P1699-1711.E9, May 07 2019 https://doi.org/10.1016/j.celrep.2019.04.044

Co, M., Hickey, S.L., Kulkarni, A., Harper, M., Konopka, G. Cortical Foxp2 supports behavioral flexibility and developmental dopamine D1 receptor expression. Cerebral Cortex. Nov 11, 2019. doi: 10.1093/cercor/bhz209.

Kulkarni A., Anderson AG, Merullo DP, Konopka G (2019) Beyond bulk: a review of single cell transcriptomics methodologies and applications. Current Opinion in Biotechnology, Volume 58, August 2019, Pages 129-136. doi: 10.1016/j.copbio.2019.03.001.

Issei S. Shimada, Bandarigoda N. Somatilaka, Sun-Hee Hwang, Ashley G. Anderson, John M. Shelton, Veena Rajaramd, Genevieve Konopka, Saikat Mukhopadhyay (2019) Derepression of sonic hedgehog signaling upon Gpr161 deletion unravels forebrain and ventricular abnormalities. Developmental Biology. Available online 23 March 2019. doi: 10.1016/j.ydbio.2019.03.011.

Richardson RB, Ohlson MB, Eitson JL, Kumar A, McDougal MB, Boys IN, Mar KB, De La Cruz-Rivera PC, Douglas C, Konopka G, Xing C, Schoggins JW. (2018) A CRISPR screen identifies IFI6 as an ER-resident interferon effector that blocks flavivirus replication. Nat Microbiol. 2018 Nov;3(11):1214-1223. doi: 10.1038/s41564-018-0244-1. Epub 2018 Sep 17.

Ayhan, F. and Konopka, G. (2018) Regulatory genes and pathways disrupted in autism spectrum disorders. Prog Neuropsychopharmacol Biol Psychiatry. 2018 Aug 28;89:57-64. doi: 10.1016/j.pnpbp.2018.08.017.

Ayhan, F. and Konopka, G. (2018) Genomics of autism spectrum disorder: approach to therapy. F1000Research 2018, 7(F1000 Faculty Rev):627; DOI: 10.12688/f1000research.13865.1

Fontenot MR, Berto S, Liu Y, Werthmann G, Douglas C, Usui N, Gleason K, Tamminga CA, Takahashi JS, Konopka G. (2017) Novel transcriptional networks regulated by CLOCK in human neurons. Genes Dev. 2017 Nov 1;31(21):2121-2135. doi: 10.1101/gad.305813.117. Epub 2017 Dec 1.

Usui N, Araujo DJ, Kulkarni A, Co M, Ellegood J, Harper M, Toriumi K, Lerch JP, Konopka G. (2017) Foxp1 regulation of neonatal vocalizations via cortical development. Genes Dev. 2017 Oct 15;31(20):2039-2055. doi: 10.1101/gad.305037.117. Epub 2017 Nov 14.

Escamilla CO, Filonova I, Walker AK, Xuan ZX, Holehonnur R, Espinosa F, Liu S, Thyme SB, Lopez-Garcia IA, Mendoza DB, Usui N, Ellegood J, Eisch AJ, Konopka G, Lerch JP, Schier AF, Speed HE, Powell CM. (2017) Kctd13 deletion reduces synaptic transmission via increased RhoA. Nature. 2017 Nov 9;551(7679):227-231. doi: 10.1038/nature24470. Epub 2017 Nov 1.

Araujo DJ, Toriumi K, Escamilla CO, Kulkarni A, Anderson AG, Harper M, Usui N, Ellegood J, Lerch JP, Birnbaum SG, Tucker HO, Powell CM, Konopka G. (2017) Foxp1 in Forebrain Pyramidal Neurons Controls Gene Expression Required for Spatial Learning and Synaptic Plasticity. J Neurosci. 2017 Nov 8;37(45):10917-10931. doi: 10.1523/JNEUROSCI.1005-17.2017. Epub 2017 Oct 4.

Stefano Berto, Guang-Zhong Wang, James Germi, Bradley C. Lega, Genevieve Konopka. (2017) Human Genomic Signatures of Brain Oscillations During Memory Encoding. Cerebral Cortex, April 2017.

Hanners NW, Eitson JL, Usui N, Richardson RB, Wexler EM, Konopka G, Schoggins JW (2016) Western Zika Virus in Human Fetal Neural Progenitors Persists Long Term with Partial Cytopathic and Limited Immunogenic Effects. Volume 15, Issue 11, 14 June 2016 Link

Berto, S., Usui, N., Konopka, G.*, and Fogel, B.L.* (2016) ELAVL2-regulated transcriptional and splicing networks in human neurons link neurodevelopment and autism. In press, Human Molecular Genetics. *Co-corresponding author.

Konopka, G., and Roberts, T.F. (2016) Insights into the neural and genetic basis of speech. Cell164(6):1269-76.

Konopka, G., and Roberts, T.F. (2016) Animal models of speech and vocal communication deficits associated with psychiatric disorders. Biological Psychiatry 79(1):53-61.a.

Usui, N., Co, M., Harper, M., Reiger, M.A., Dougherty, J.D., and Konopka, G. (2016) Sumoylation of FOXP2 regulates motor function and vocal communication through Purkinje cell development. In press, Biological Psychiatry, online Feb 12, doi 10.1016/j.biopsych.2016.02.008.

Wang G.-Z.*, Belgard, T. G.*, Mao, D., Chen, L., Berto, S., Preuss, T. M., Lu, H., Geschwind, D. H.,Konopka, G. (2015) Correspondence between Resting-State Activity and Brain Gene Expression. Neuron. * Equal Contribution.

Wang G.-Z., Hickey S. L., Shi L., Huang HC., Nakashe P., Koike N., Tu B.P., Takahashi JS., Konopka G. (2015) Cycling Transcriptional Networks Optimize Energy Utilization on a Genome Scale. Cell Reports.

Araujo, D.J.*, Anderson, A.G.*, Berto, S., Runnels, W., Harper, M., Ammanuel, S., Rieger, M.A., Huang, H-C., Rajkovich, K., Loerwald, K.W., Dekker, J.D., Tucker, H.O., Dougherty, J.D., Gibson, J.R., and Konopka, G. (2015) FoxP1 orchestration of ASD-relevant signaling pathways in the striatum. Genes & Development 29(20): 2081-96. *Equal Contribution.

Frank, E., Benabou, M., Bentzley, B., Bianchi, M., Goldstein, T., Konopka, G, Maywood, E., Pritchett, D., Sheaves, B., Thomas, J. (2014) Influencing circadian and sleep-wake regulation for prevention and intervention in mood and anxiety disorders: what makes a good homeostat? Ann N Y Acad Sci1334:1-25.

Usui, N., Co, M., and Konopka, G. (2014) Decoding the molecular evolution of cognition using comparative genomics. Brain, Behavior, and Evolution 84(2):103-16.

Fontenot, M., and Konopka, G. (2014) Molecular networks and evolution of human cognitive skills. Current Opinion in Genetics & Development 29C:52-59.

Lepp, S., Anderson, A., and Konopka, G. (2013) Connecting signaling pathways underlying communication to ASD vulnerability International Review of Neurobiology: Neurobiology of Autism (ed G. Konopka), Elsevier; 113:97-133.

Miller, D.J., and Konopka, G. (2013) Evolution and Development of Language, in Advances in Evolutionary Developmental Biology (ed J.T. Streelman), John Wiley & Sons, Inc, Hoboken, NJ, USA; 173-201.

Wang, G-Z., and Konopka, G. (2013) Decoding human gene expression signatures in the brain. Transcription 4(3):1-7.

Konopka, G. (2013) FOXP2: linking language and autism, in The Autisms: Molecules to Model Systems (eds. C.M. Powell, C.M. and L.M. Monteggia), Oxford University Press, New York, NY, USA; 367-393.

Bowers, J. M., and Konopka, G. (2012) ASD-relevant animal models of the Foxp family of transcription factors. Autism Open Access S1:010. http://www.omicsgroup.org/journals/2165-7890/2165-7890-S1-010.php?aid=10082

Bowers, JM, and Konopka, G. (2012) The role of the FOXP family of transcription factors in ASD. Dis Markers 33(5):251-60.

Konopka, G., Friedrich, T., Davis-Turak, J., Winden, K., Oldham, M.C., Gao, F., Chen, L., Wang, G-Z., Luo, R., Preuss, T.M., and Geschwind, D.H. (2012) Human-specific transcriptional networks in the brain. Neuron 75(4):601-617.

Wang, G-Z., and Konopka, G. (2012) Differential Functional Constraints on the Evolution of Postsynaptic Density Proteins in Neocortical Laminae. PLOS One 7(6): e39686.

Geschwind, D.H., and Konopka, G. (2012) Neuroscience: genes and human brain evolution. Nature486(7404):481-2.

Konopka, G. (2012) The fetal brain provides a raison d'être for the evolution of new human genes. Brain Behav Evol 79(4):213-4.

Gena's Other Research

Martuscello, R.T., Sivaprakasam, K., Hartstone, W., Kuo, S.H., Konopka, G., Louis, E.D., Faust, P.L. (2022). Gene Expression Analysis of Laser-Captured Purkinje Cells in the Essential Tremor Cerebellum. Cerebellum. 2022 Oct 15. doi: 10.1007/s12311-022-01483-4. Epub ahead of print. PMID: 36242761.

Usui, N., Ono, Y., Aramaki, R., Berto, S., Konopka, G., Matsuzaki, H., & Shimada, S. (2021). Early Life Stress Alters Gene Expression and Cytoarchitecture in the Prefrontal Cortex Leading to Social Impairment and Increased Anxiety. Frontiers in genetics, 12, 754198. https://doi.org/10.3389/fgene.2021.754198

Usui, N., Berto, S., Konishi, A., Kondo, M., Konopka, G., Matsuzaki, H., Shimada, S. Zbtb16 regulates social cognitive behaviors and neocortical development. bioRxiv 2020.08.09.233270; doi: https://doi.org/10.1101/2020.08.09.233270

Perez, J. M., Berto, S., Gleason, K., Ghose, S., Tan, C., Kim, T. K., Konopka, G., & Tamminga, C. A. Hippocampal subfield transcriptome analysis in schizophrenia psychosis. Molecular psychiatry.2020 Mar 9. 10.1038/s41380-020-0696-6. Advance online publication. https://doi.org/10.1038/s41380-020-0696-6

Harrington, A. J., Bridges, C. M., Berto, S., Blankenship, K., Cho, J. Y., Assali, A., Siemsen, B. M., Moore, H. W., Tsvetkov, E., Thielking, A., Konopka, G., Everman, D. B., Scofield, M. D., Skinner, S. A., & Cowan, C. W. MEF2C Hypofunction in Neuronal and Neuroimmune Populations Produces MEF2C Haploinsufficiency Syndrome-like Behaviors in Mice. Biol Psychiatry. 2020 Mar 31;S0006-3223(20)31382-2. doi: 10.1016/j.biopsych.2020.03.011.

Onder Y, Laothamatas I, Berto S, Sewart K, Kilaru G, Bordieanu B, Stubblefield JJ, Konopka G, Mishra P, Green CB. The Circadian Protein Nocturnin Regulates Metabolic Adaptation in Brown Adipose Tissue. iScience. 2019;19:83-92. Epub 2019/07/30. doi: 10.1016/j.isci.2019.07.016.

Fogel, B.L., Cho, E., Wahnich, A., Gao, F., Becherel, O.J., Wang, X., Fike, F., Chen, L., Criscuolo, C., De Michele, G., Filla, A., Collins, A., Hahn, A.F., Gatti, R.A., Konopka, G, Perlman, S., Lavin, M.F., Geschwind, D.H., and Coppola, G. (2014) Mutation of senataxin alters disease-specific transcriptional networks in patients with ataxia with oculomotor apraxia type 2. Hum Mol GenetEpub Apr 23.

Zeng, J, Konopka, G, Hunt, BG, Preuss, TM, Geschwind, D, Yi, SV. (2012) Divergent whole-genome methylation maps of human and chimpanzee brains reveal epigenetic basis of human regulatory evolution. Am J Hum Genet. 91(3):455-65.

Fogel, B.L., Wexler, E., Wahnich, A., Friedrich, T., Vijayendran, C., Gao, F., Parikshak, N., Konopka, G., and Geschwind, D.H. (2012) RBFOX1 regulates both splicing and transcriptional networks in human neuronal development. Hum Mol Genet 21(19):4171-86.

Puram, S.V., Yeung, C.M., Jahani-Asl, A., Lin, C., de la Iglesia, N., Konopka, G., Jackson-Grusby, L., and Bonni, A. (2012) STAT3-iNOS signaling mediates EGFRvIII-induced glial proliferation and transformation. Journal of Neuroscience 32(23):7806-18.

DeLaForest, A., Nagaoka, M., Si-Tayeb, K., Noto, F.K., Konopka, G., Battle, M.A., and Duncan, S.A. (2011) HNF4A is essential for specification of hepatic progenitors from human pluripotent stem cells. Development 138(19):4143-53.

Mukamel, Z.*, Konopka, G.*, Wexler, E., Dong, H., Osborn, G., Levitt, P., and Geschwind, D.H. (2011) Regulation of MET by FOXP2, genes implicated in higher cognitive dysfunction and autism risk. Journal of Neuroscience 31(32):11437-42. *Equal Contribution.

Konopka, G., Wexler, E., Rosen, E., Mukamel, Z., Osborn, G. E., Chen, L., Lu, D., Gao, F., Gao, K., Lowe, J.K., and Geschwind D. H. (2012) Modeling the functional genomics of autism using human neurons. Molecular Psychiatry 17(2):202-14.

Konopka, G. (2010) Functional genomics of the brain: uncovering networks in the CNS using a systems approach. WIREs Systems Biology and Medicine, Epub Dec 31.

Konopka, G., and Geschwind, D.H. (2010) Human brain evolution: harnessing the genomics (r)evolution to link genes, cognition, and behavior. Neuron 68(2):231-44.

Konopka, G., Bomar, J.M., Winden, K., Coppola, G., Jonsson, Z.O., Gao, F., Peng, S., Preuss, T.M., Wohlschlegel, J.A., and Geschwind, D.H. (2009) Human-specific transcriptional regulation of CNS development genes by FOXP2. Nature 462 (7270):213-7.

Geschwind, D.H. and Konopka, G. (2009) Neuroscience in the era of functional genomics and systems biology. Nature 461(7266):908-15.

Oldham, M.C., Konopka, G., Iwamoto, K., Langfelder, P., Kato, T., Horvath, S., and Geschwind, D. H. (2008) Functional organization of the transcriptome in human brain. Nature Neuroscience11(11):1271-82.

de la Iglesia, N.*, Konopka, G.*, Nutt, C.L., Bromberg, J.F., Frank, D.A., Mischel, P.S., Louis, D.N., and Bonni, A. (2008) Deregulation of a STAT3-IL8 signaling pathway promotes human glioblastoma cell proliferation and invasiveness. Journal of Neuroscience 28(23):5870-8. *Equal contribution.

de la Iglesia, N.*, Konopka, G.*, Puram, S., Chan, J.A., Bachoo, R.M., You, J.M., Levy, D.E., DePinho, R.A., and Bonni, A. (2008) Identification of a PTEN-regulated STAT3 brain tumor suppressor pathway. Genes and Development 22(4):449-62. * Equal contribution.

Spiteri, E., Konopka, G., Coppola, G., Bomar, J., Oldham, M., Ou, J., Vernes, S.C., Fisher, S.E., Ren, B., and Geschwind, D.H. (2007) Identification of the transcriptional targets of FOXP2, a gene linked to speech and language, in developing human brain. American Journal of Human Genetics81(6): 1144-57.

Konopka, G., Tekiela, J., Iverson, M., Wells, C., Duncan, S.A. (2007) Junctional adhesion molecule-A is critical for the formation of pseudocanaliculi and modulates E-cadherin expression in hepatic cells. Journal of Biological Chemistry 282(38): 28137-48.

Battle MA, Konopka G, Parviz F, Gaggl AL, Yang C, Sladek FM, Duncan SA. (2006) Hepatocyte nuclear factor 4alpha orchestrates expression of cell adhesion proteins during the epithelial transformation of the developing liver. Proc Natl Acad Sci. 2006 May 30;103(22):8419-24.

Chylack LT Jr, Fu L, Mancini R, Martin-Rehrmann MD, Saunders AJ, Konopka G, Tian D, Hedley-Whyte ET, Folkerth RD, Goldstein LE. (2004) Lens epithelium-derived growth factor (LEDGF/p75) expression in fetal and adult human brain. Exp Eye Res. 2004 Dec;79(6):941-8.

Konopka G, Bonni A. (2003) Signaling pathways regulating gliomagenesis. Curr Mol Med. 2003 Feb;3(1):73-84.

Puglielli L, Konopka G, Pack-Chung E, Ingano LA, Berezovska O, Hyman BT, Chang TY, Tanzi RE, Kovacs DM. (2001) Acyl-coenzyme A: cholesterol acyltransferase modulates the generation of the amyloid beta-peptide. Nat Cell Biol. 2001 Oct;3(10):905-12.

Simbulan-Rosenthal CM, Ly DH, Rosenthal DS, Konopka G, Luo R, Wang ZQ, Schultz PG, Smulson ME. (2000) Misregulation of gene expression in primary fibroblasts lacking poly(ADP-ribose) polymerase. Proc Natl Acad Sci U S A. 2000 Oct 10;97(21):11274-9.

Blanchard BJ, Konopka G, Russell M, Ingram VM. (1997) Mechanism and prevention of neurotoxicity caused by beta-amyloid peptides: relation to Alzheimer's disease. Brain Res. 1997 Nov 21;776(1-2):40-50

Keeping up with the Konopka Lab

April 2024: Welcome Dr. Wonjun Hong, new postdoc!

March 2024: Congrats to Rachel for getting F31!!

March 2024: Sid is "off" to med school! Elliot joins the lab!

Jan 2024: Haley got her F30!! Congrats! Welcome Amber!

Oct 2023: Emre defends his PhD and heads off to post-doc lab with Chris Walsh, MD PhD

Oct 2023: Bye rotation students David and Ben!!

Oct 2023: Welcome Gozde! New Computational Biology Postdoc

Sept 2023: Welcome rotation students Anne, David, and Ben!!

August 2023: Spotted, Gena (our fearless leader) and Matt featured on billboards across Dallas!

August 2023: Bye summer research students, Sanjana, Jose, and Imad from high school and Kay Chi from Amgen summer research program! Pics in the gallery!

July 2023: Newaz's going away party :( we'll miss you!

June 2023: Welcome Kay Chi! Undergrad research student working with Miranda!

June 2023: Welcome Sanjana, Jose, and Imad! high school summer research students!

June 2023: Congrats on new striatal development paper Ashley and Ashwinikumar!

May 2023: Bye Emily Oh! Onward to the MSTP program at UT Southwestern!

Jan 2023: Sid transitions from undergrad research volunteer to lab tech! Woot!

Dec 2022: Lab holiday party!!

Oct 2022: Miranda gets on T32 training grant! Congrats

Oct 2022: Bye rotation students Simran and Landry! Had lab lunch!

Sept 2022: Welcome rotation students Simran and Landry!

Aug 2022: Congrats Emre for having paper accepted!

Aug 2022: Congrats Haley, Ana, Emily! Review papers accepted!

July 2022: Congrats Ana! Received Carl Storm fellowship to attend Neural Dev GRC!

July 2022: Bye Husam! Gave great poster for STARS program.

June 2022: Congrats Ana! Accepted to the Cajal Course on single cell!

May 2022: Welcome Husam! STARS student!

May 2022: Welcome Emma!! New post-doc

April 2022: Welcome to the lab David!

March 2022: Welcome to the lab Alia!

Feb 2022: Congrats Karthi on new position!

Feb 2022: First in-person lab meeting in years!!

Jan 2022: Congrats Devin on new position at Parexel!

Dec 2021: Our fearless leader Gena is promoted to Vice Chair of the Neuro Dept!

Dec 2021: Congrats Yuxiang for receiving the AHA fellowship! And Rachael for the NIMH diversity supplement!

Oct 2021: Miranda J joins the Konopka lab as a grad student! Welcome!

Aug 2021: Congrats Ashwinikumar & Stefano on this great paper with the Takahashi lab led by Pin!

Aug 2021: Bye Miranda! Rotation ended. Welcome Emily Oh!

July 2021: End of STARs for Rithvik and Ethan!

June 2021: Fatma starts her new position at Neurocrine!

June 2021: Welcome Miranda, Ethan and Rithvik! Summer lab members.

May 2021: Fatma's paper with the Lega lab collab is out! click here!

May 2021: Graduation celebration! Ashley got hooded by Gena.

April 2021: Welcome Rachael! New lab member!

April 2021: 10 year Konopka lab birthday! New pics are out

March 2021: Stefano's paper is out in press! Gene-expression correlates of the oscillatory signatures supporting human episodic memory encoding

Feb 2021: Congrats Stefano!! New PI!! at MUSC

Jan 2021: New pre-print out! Gene expression and rs-fMRI in ASD click here!

Jan 2021: Check out Nitin's paper! FOXP1 negatively regulates intrinsic excitability in D2 striatal projection neurons by promoting inwardly rectifying and leak potassium currents

Jan 2021: Welcome Andrea! Rotation student

Dec 2020: Congrats Devin Cellular transcriptomics reveals evolutionary identities of songbird vocal circuits

Nov 2020: Congrats Stefano and Nitin for their papers! Nature Neuro and Molecular Psychiatry! Details forthcoming.

September 2020: Congrats Emre! Now a doctoral candidate after passing his qualifying exam!

August 2020: Congrats to Ashwinikumar (@ashwinikumark) for his paper "An essential role for MEF2C in the cortical response to loss of sleep in mice." Excellent work!

August 2020: Welcome to our new grad student/MSTP Haley Moore!

July 2020: Congrats Ana (@anabrains)! Ana is one of the 45 recipients of a Gilliam Fellowship for Advanced Study. Read More.

April/May 2020: Ana (@anabrains) and Newaz (@neuronewaz) got their F31 NRSA grants! Congrats!

March 2020: Ashley (@AGArginine) moves onto her postdoc with Dr. Huda Zoghbi!

January 2020: Congrats Ashley (@AGArginine)!! Paper accepted in Cell Reports! "Single-cell analysis of Foxp1-driven mechanisms essential for striatal development"

Nov 2019: Stefano's paper is out in PNAS! "Accelerated evolution of oligodendrocytes in the human brain."

August 2019: Marissa goes off to OHSU and Stephanie is off to MSU for their Post Docs! Good luck!

August 2019: Congrats to Marissa on your Cerebral Cortex paper "Cortical Foxp2 supports behavioral flexibility and developmental dopamine D1 receptor expression."

August 2019: Congrats Dr. Ashley Anderson on defending your PhD!

July 2019: Stefano's new paper is out in Genome Biology. "Cell type-specific epigenetic links to schizophrenia risk in the brain." More

June 2019: Congrats Dr. Marissa Co on defending your PhD thesis! pics to follow

June 2019: Welcome Haley, Jack and Abel! Bye Amena, good luck in med school!

April 2019: Ashley wins Best Poster at the Neuroscience Retreat!! Second year in a row!

April 2019: Ashwinikumar's review paper accepted in Current Opinion in Biotechnology "Beyond bulk: a review of single cell transcriptomics methodologies and applications." Congrats!!

April 2019: Stephanie's paper accepted in Cell Reports "Chromatin decondensation by FOXP2 promotes human neuron maturation and expression of neurodevelopmental disease genes". Congrats Steph!

April 2019: Yuxiang presents at Texas Society for Circadian Biology & Medicine meeting, and Ana has poster at NIMH conference!

March 2019: Ashley collaborates on paper, out now: "Derepression of sonic hedgehog signaling upon Gpr161 deletion unravels forebrain and ventricular abnormalities"

January 2019: Welcome new graduate student Emre Caglayan!

December 2018: Konopka lab outing! Pics in the gallery.

October 2018: Welcome rotation student Lauretta!

October 2018: Ana and Newaz pass quals & are PhD candidates. Congrats!

September 2018: Welcome rotation students Yoheilly and Emre!

August 2018: Trevor heads off to UT; Bye Trevor!

July 2018: Stephanie's Public PhD Defense! Congrats Dr. Lepp Hickey!

July 2018: Shelly presents at STARS poster session. Bye Shelly!

June 2018: Welcome to our summer high school students Trevor and Shelly!

April 2018: Stephanie wins Best Talk and Ashley wins Best Student Poster at the UTSW Neuroscience retreat! Konopka lab sweep!

March 2018: Congrats on all the new papers!

February 2018: Welcome to our new graduate student Ana!

January 2018: Welcome to our new green fellow Amena!

November 2017: ODonnell Brain Institute at UT Southwestern joins global effort to map human cells. Read More

October 2017: Welcome to our new graduate student Newaz!

Spetember 2017: Congrats Ashley on winning a travel award to present her research at the Basal Ganglia Gordon Conference in March 2018!

July 2017: DJ is officially a PhD neuroscientist! Good luck at UC Berkeley in the Saijo Lab!

June 2017: North Texas Researchers Identify More Than 100 Genes Linked To Human Memory. More at KERA Radio.

June 2017: STAR Student Trevor joins the lab for the summer! Welcome!

May 2017: Scientists ID 100 memory genes, open new avenues of brain study. More at UTSW Newsroom. Watch Video at YouTube

April 2017: Gena is promoted to Associate Professor with tenure! Congrats fearless leader!

April 2017: Stefano's paper "Human Genomic Signatures of Brain Oscillations During Memory Encoding" is published in Cerebral Cortex!

March 2017: Miles passed his dissertation defense entitled "The Evolution and Function of the Genomic Landscape of the Human Brain"! Congrats and good luck!

March 2017: Welcome to our new post-docs Fatma and Yuxiang!

March 2017: Our rotation student Emily joins the lab! Welcome Emily!

January 2017: Connor joins the lab! Welcome Connor!

November 2016: Marissa wins a Keystone Symposia Travel Award! Congrats!

September 2016: Konopka Lab wins the golden brain in the 2016 Summer Lab Olympics! Congrats to Team Dragon-Thunder!

August 2016: Aarin finishes her rotation in the Konopka Lab- good luck with your future studies!

August 2016: The new lab website goes live! Thanks for checking it out!

June 2016: STAR Student Yosiah joins the lab for the summer! Welcome!

May 2016: Nori teams up with members of the Schoggins lab to publish a study on Zika virus in Human Neural Progenitors in Cell Reports!

April 2016: Stefano's paper, "ELAVL2-regulated transcriptional and splicing networks in human neurons link neurodevelopment and autism", is accepted at Human Molecular Genetics. Congrats Stefano!

Former Lab Members

Dan Miller

Visiting Scientist

(May-Jul 2011)

Regan Allen

Summer Intern

(Jun-Aug 2012)

Lupita Rios

STARS Fellow

(Jun-Jul 2012)

Christine Ochoa

Rotation student

(Oct-Dec 2012)

Maria Funes

Research assistant

(Sep 2011-Sep 2012)

Mike Bowers, Ph.D.

Postdoctoral Fellow

(Jan 2012-Mar 2013)

Julia Mandel

Student Intern

(Jun 2012-Mar 2013)

Steven Wen Qi, M.S.


(Jan-Jul 2013)

Emma Konopka

Summer Intern

(Jul-Aug 2013)

Dean Itani

SURF Fellow

(Jun-Aug 2012, Jun-Aug 2013)

Rodney Chen

Summer Intern

(Jun-Aug 2013)

Wesley Runnels

STARS Student

(Jun 2013-Aug 2014)

Taylor Stefanik

SURF Fellow

(Jun 2014-Aug 2014)

Jayant Madugula

STARS Student

(Jun 2014-Jul 2015)

Chandler Werthmann

SURF Fellow

(Jun-Aug 2015)

Enrique De Alba

STARS Student

(Jun-Aug 2015)

Hanqing (Kathy) Shang

Undergraduate Intern

(Oct 2015-Jan 2016)

Guang-Zhong Wang, Ph.D.

Postdoctoral Fellow

(Aug 2011-Mar 2016)

Professor @PICB Wang lab

Kazuya Toriumi, Ph.D.


(Mar 2015-Mar 2017)

Asst. Professor Tokyo Metropolitan Institute of Medical Science

Noriyoshi Usui, Ph.D.


(Oct 2012-Mar 2017)

Asst. Professor @Osaka University

Miles Fontenot, Ph.D., M.D.

MD/PhD Neuroscience Graduate Student

(Jul 2013-Mar 2017)

Resident at U Wash

Yosiah Fetahi

STARS Student

(Jun 2016-Apr 2017)

Student at Harvard

Daniel Araujo, Ph.D.

PhD Neuroscience Graduate Student

(Jan 2012-Jul 2017)

Scientific Editor Hendrick Lab at La Jolla Institute for Immunology

Trevor Thai Nguyen

STARS Student

(Jun-Aug 2017; Jun-Aug 2018)

Student at UT Austin

Aarin Jones

Rotation Student

(July-Aug 2016)

Grad student in Kraus lab

Jennifer Gibson

Rotation Student

(Oct-Nov 2017)

Grad student in Tsai lab

Kathan Trivedi

UTD Green Fellow


Islam Oguz Tuncay

Rotation Student

(Jan-Feb 2018)

Grad student in Chahrour lab

Shelly Goel

STARS Student

(Jun-Aug 2018)

Yoheilly Velazquez Gonzalez

Rotation Student

(Aug-Oct 2018)

Grad student in Tsai lab

Lauretta El Hayek

Rotation Student

(Oct - Nov 2018)

Grad student in Chahrour lab

Amena Qavi

UTD Green Fellow

(Jan 2018-June 2019)

now medical student

Jack Casey

STARS Student

(Jun-Aug 2019)

Abel Fetahi

STARS Student

(Jun-Aug 2019)

Haley Moore

MSTP Rotation student

(Jun-July 2019)

Marissa Co, Ph.D.

PhD Neuroscience Graduate Student

(2013 - Aug 2019)

Post Doc in the Wright and O'Roak labs @OHSU

Stephanie Lepp Hickey, Ph.D.

PhD Neuroscience Graduate Student

(2012 - Aug 2019)

Post Doc at Michigan State University with Dr. Arjun Krishnan, Ph.D.

Ashley A. Anderson Ph.D.

PhD Neuroscience Graduate Student

(2014 - Apr 2020)

Post Doc in Dr. Huda Zoghbi's lab

Carlos Orozco

Rotation Student

Fall (Aug-Oct) 2019

Grad student in Roberts lab

Humay (Gulhumay) Gardashova

Rotation Student

Fall 2019 (Oct-Dec)

Grad student in Diamond lab

Lupita Rios

Rotation Student

Fall 2019 (Oct-Dec)

Grad student in Shabel lab

Nisha Gupta

UTD Green Fellow

2018 -2020

now medical student

Andrea Boitnott

Rotation Student

Spring 2021

Grad student in Gray lab

Rachael Vollmer

Rotation Student

Spring 2021

Miranda Jankovic

MSTP Rotation Student

Summer 2021

Ethan Lotan

STARS Student

Summer 2021

Rithvik Ganesh

STARS Student

Summer 2021

Husam Elnager

STARS Student

Summer 2022

Stefano Berto, Ph.D.

Post-doctoral scholar

Feb 2016 - Feb 2021

Ass. Profesor at MUSC

Fatma Ayhan, Ph.D.

Post-doctoral scholar

March 2017 - June 2021

Scientist at Neurocrine Biosciences

Devin Merullo, Ph.D.

Post-doctoral scholar

June 2018 - Jan 2022

Senior Scientist Bioinformatics at Parexel

Karthigayini Sivaprakasam, Ph.D.

Post-doctoral scholar

Jan 2019 - Feb 2022

Senior Bioinformatician at Memorial Sloan Kettering Cancer Center

Emily Park, Ph.D.

PhD Neuroscience Graduate Student

March 2017 - May 2022

Post-doc at Bristol-Myers Squibb

Landry Johnson

rotation student

Sept 2022 - Oct 2022

Simran Rastogi

rotation student

Sept 2022 - Oct 2022

Siddhartha Lavu

Undergraduate researcher

Sept 2022 - Dec 2022

Emily Oh

Research Assistant

Aug 2021 - May 2023

MSTP at UT Southwestern

Joanna Zepeda

rotation student

Feb-April 2023

Imad Ahmed

STARS student

June-July 2023

Jose Hernandez

STARS student

June-July 2023

Newaz Ahmed

Graduate student

Oct 2017 - August 2023

Postdoc at Ian Maze Lab

Sanjana Kota

Summer student

May - July 2023

Kay Chi Pua


June-Aug 2023

David Atkinson


April 2022 - Sept 2023

Emre Caglayan

PhD student

Sept 2018 - Oct 2023

Ben Harrington

Rotation Student

Sept 2023 - Oct 2023

David Guarin

Rotation Student

Sept 2023 - Oct 2023

Anne Freelin

Rotation Student

Nov 2023 - Dec 2023

Wei-Chen Chen

Rotation Student

Nov 2023 - Dec 2023

Elliot Outland

Rotation Student

Nov 2023 - Dec 2023

Alison Mueller

Rotation Student

Jan 2024 - Feb 2024

Siddhartha Lavu

Lab Technician

Jan 2023 - March 2024

Get in touch

Konopka lab
Department of Neuroscience
UT Southwestern Medical Center
5323 Harry Hines Blvd., ND4.300
Dallas, TX 75390-9111
Ph: 214-648-5135 (Office), 214-648-5136 (Lab)
Twitter: @KonopkaLab