COMPLETE PUBLICATION LIST CAN BE FOUND in Google Scholar.

representative Research Publications

Selected Pre-Prints:

  1. Matoba N*, Le BD*, Valone JM*, Wolter JM, Mory J, Liang D, Aygün N, Broadaway KA, Bond ML, Mohlke KL, Zylka MJ, Love MI, Stein JL. (2023). “WNT activity reveals context-specific genetic effects on gene regulation in neural progenitors.”

  2. Glass MR*, Waxman EA*, Yamashita S*, Lafferty M, Beltran A, Farah T, Patel NK, Matoba N, Ahmed S, Srivastava M, Drake E, Davis LT, Yeturi M, Sun K, Love MI, Hashimoto-Torii K+, French DL+, Stein JL+. (2023). “Cross-site reproducibility of human cortical organoids reveals consistent cell type composition and architecture.”

  3. Aygün N, Krupa O, Mory J, Le B, Valone JM, Liang D, Love MI, Stein JL. (2023). “Genetics of cell-type-specific post-transcriptional gene regulation during human neurogenesis.”

Selected Published Papers:

  1. Aygün N, Liang D, Crouse WL, Keele GR, Love MI+, Stein JL+. (2023). “Inferring cell-type-specific causal gene regulatory networks during human neurogenesis.” Genome Biology. 2023 May 30;24(1):130.

  2. Lafferty MJ, Aygün N, Patel NK, Krupa O, Liang D, Wolter JM, Geschwind DH, de la Torre-Ubieta L, Stein JL. (2023). “MicroRNA-eQTLs in the developing human neocortex link miR-4707-3p expression to brain size.” Elife. Jan 11;12:e79488.

  3. Wolter JM, Le BD, Matoba N, Lafferty MJ, Aygün N, Liang D, Courtney K, Song J, Piven J, Zylka MJ, Stein JL. (2022). “Cellular Genome-wide Association Study Identifies Common Genetic Variation Influencing Lithium-Induced Neural Progenitor Proliferation.” Biol Psychiatry. Jan 1;93(1):8-17.

  4. Krupa O, Fragola G, Hadden-Ford E, Mory JT, Liu T, Humphrey Z, Rees BW, Krishnamurthy A, Snider WD, Zylka MJ, Wu G, Xing L+, Stein JL+. (2021). “NuMorph: tools for cortical cellular phenotyping in tissue cleared whole brain images.” Cell Reports. 37(2): 109802.

  5. Aygün N, Elwell AL, Liang D, Lafferty MJ, Cheek KE, Courtney KP, Mory J, Hadden-Ford E, Krupa O, de la Torre-Ubieta L, Geschwind DH, Love MI, Stein JL. (2021). “Brain-trait-associated variants impact cell-type-specific gene regulation during neurogenesis.” Am J Hum Genet 2021 Sep 2;108(9):1647-1668.

  6. Borland D, McCormick CM, Patel NK, Krupa O, Mory JT, Beltran AA, Farah TM, Escobar-Tomlienovich CF, Olson SS, Kim M, Wu G+, Stein JL+. (2021). “Segmentor: a tool for manual refinement of 3D microscopy annotations.” BMC Bioinformatics. 2021 May 22;22(1):260. doi: 10.1186/s12859-021-04202-8.

  7. Liang D, Elwell AL, Aygün N, Krupa O, Wolter JM, Kyere FA, Lafferty MJ, Cheek KE, Courtney KP, Yusupova M, Garrett ME, Ashley-Koch A, Crawford GE, Love MI, de la Torre-Ubieta L, Geschwind DH, Stein JL. (2021). “Cell-type-specific effects of genetic variation on chromatin accessibility during human neuronal differentiation.” Nature Neuroscience. 2021 May 20. doi: 10.1038/s41593-021-00858-w.

  8. Zhu A*, Matoba N*, Wilson EP, Tapia AL, Li Y, Ibrahim JG, Stein JL, Love MI. (2021). “MRLocus: Identifying causal genes mediating a trait through Bayesian estimation of allelic heterogeneity.” PLoS Genetics. 2021 Apr 19;17(4):e1009455. doi: 10.1371/journal.pgen.1009455.

  9. Tilot AK, Khramtsova EA, Liang D, Grasby KL, Jahanshad N, Painter J, Colodro-Conde L, Bralten J, Hibar DP, Lind PA, Liu S, Brotman SM, Thompson PM, Medland SE, Macciardi F, Stranger BE, Davis LK, Fisher SE+, Stein JL+. (2020). “The Evolutionary History of Common Genetic Variants Influencing Human Cortical Surface Area.” Cerebral Cortex. Dec 9:bhaa327. doi: 10.1093/cercor/bhaa327.

  10. Matoba N, Love MI, Stein JL. (2020). “Evaluating brain structure traits as endophenotypes using polygenicity and discoverability.” Human Brain Mapp. 2020 Oct 24. doi: 10.1002/hbm.25257.

  11. Matoba N, Liang D, Sun H, Aygün N, McAfee JC, Davis JE, Raffield LM, Qian H, Piven J, Li Y, Kosuri S, Won H+, Stein JL+. (2020). “Common genetic risk variants identified in the SPARK cohort support DDHD2 as a candidate risk gene for autism.” Translational Psychiatry. 10(1):265.

  12. Grasby KL*, Jahanshad N*, [330 addition co-authors], Stein JL+, Thompson PM+, Medland SE+. (2020). “The genetic architecture of the human cerebral cortex.” Science. 367, 1340.

  13. Le BD, Stein JL. “Mapping causal pathways from genetics to neuropsychiatric disorders using imaging genetics.” (2019). Psychiatry and Clinical Neuroscience. Jul;73(7):357-369.

  14. de la Torre Ubieta L*, Stein JL*, Won H, Opland CK, Liang D, Lu D, Geschwind DH. (2018). “The dynamic landscape of open chromatin during human cortical neurogenesis.” Cell. 172(1-2):289-304.

  15. Hibar DP*, Adams HH*, Jahanshad N*, Chauhan G*, Stein JL*, Hofer E*, Renteria ME*, Bis JC*, [300 additional authors]. (2017). “Novel genetic loci associated with hippocampal volume.” Nat Commun. Jan 18;8:13624.

  16. de la Torre-Ubieta L*, Won H*, Stein JL*, Geschwind DH. (2016). "Advancing the understanding of autism mechanisms through genetics." Nature Medicine. 22:345-61. Review.

  17. Franke B*, Stein JL*, Ripke S*, Anttila V, Hibar DP, van Hulzen KJE, Arias-Vasquez A, Smoller JW, Nichols TE, Neale MC, McIntosh AM, Lee PH, McMahon FJ, Meyer-Lindenberg A, Mattheisen M, Andreassen OA, Gruber O, Sachdev PS, Roiz-Santiañez R, Saykin AJ, Ehrlich S, Mather KA, Turner JA, Schwarz E, Thalamuthu A, Yao Y, Ho YYW, G Martin NG, Wright MJ, Schizophrenia Working Group of the Psychiatric Genomics Consortium, ENIGMA Consortium, O’Donovan MC*, Thompson PM*, Neale BM*, Medland SE*, Sullivan PF*. (2016). "Genetic influences on schizophrenia and subcortical brain volumes: large-scale proof of concept." Nature Neuroscience. 19(3):420-31.

  18. Hibar DP*, Stein JL*, Renteria ME*, Arias-Vasquez A*, Desrivières S*, [276 additional co-authors], Martin NG, Wright MJ, Schumann G, Franke B, Thompson PM, Medland SE. (2015). “Common genetic variants influence human subcortical brain structures.” Nature. 520(7546):224-9.

  19. Stein JL*, de la Torre-Ubieta L*, Tian Y, Parikshak NN, Hernandez IA, Marchetto MC, Baker DK, Lu D, Lowe JK, Wexler EM, Muotri AR, Gage FH, Kosik KS, Geschwind DH. (2014). “A quantitative framework to evaluate modeling of cortical development by neural stem cells.” Neuron. Jul 2;83(1):69-86. Cover article.

  20. Stein JL*, Medland SE*, Vasquez AA*, Hibar DP*, Senstad RE, [193 additional co-authors], Martin NG*, Franke B*, Wright MJ*, Thompson PM* for the Enhancing Neuro Imaging Genetics through Meta-Analysis (ENIGMA) Consortium. (2012). “Identification of common variants associated with human hippocampal and intracranial volumes.” Nature Genetics. 44(5):552-561.

* indicates equal first-author contribution
+ indicates equal last-author contribution