The Neurogenomics page highlights research that connects genomics, computational biology, and neuroscience. These studies use large-scale data, machine learning, and molecular analysis to explore how genes shape the structure, function, and disorders of the human brain. Key papers include “Digital phenotyping from wearables using AI” (Cell, 2025) and “Single-cell genomics and regulatory networks for 388 human brains” (Science, 2024). Other recent work focuses on mapping brain regulatory elements; integrating imaging and genomic modalities; and developing new methods to interpret complex biological networks. Together, these studies reflect our ongoing effort to understand the genomic foundations of brain biology and mental health.

Compression-based Network Interpretability Schemes
J Warrell, H Mohsen, M Gerstein (2020). bioRxiv.

Single-cell transcriptomic and chromatin dynamics of the human brain in PTSD
A Hwang, M Skarica, S Xu, J Coudriet, CY Lee, L Lin, R Terwilliger, AN Sliby, J Wang, T Nguyen, H Li, M Wu, Y Dai, Z Duan, SS Srinivasan, X Zhang, Y Lin, D Cruz, PJM Deans, Traumatic Stress Brain Research Group, BR Huber, D Levey, JR Glausier, DA Lewis, J Gelernter, PE Holtzheimer, MJ Friedman, M Gerstein, N Sestan, KJ Brennand, K Xu, H Zhao, JH Krystal, KA Young, DE Williamson, A Che, J Zhang, MJ Girgenti (2025). Nature 643: 744-754.

Digital phenotyping from wearables using AI characterizes psychiatric disorders and identifies genetic associations
JJ Liu, B Borsari, Y Li, SX Liu, Y Gao, X Xin, S Lou, M Jensen, D Garrido-Martin, TL Verplaetse, G Ash, J Zhang, MJ Girgenti, W Roberts, M Gerstein (2025). Cell 188: 515-529e15.

Deep learning analysis of fMRI data for predicting Alzheimer's Disease: A focus on convolutional neural networks and model interpretability
X Zhou, S Kedia, R Meng, M Gerstein (2024). PLoS One 19: e0312848.

Cross-ancestry atlas of gene, isoform, and splicing regulation in the developing human brain.
C Wen, M Margolis, R Dai, P Zhang, PF Przytycki, DD Vo, A Bhattacharya, N Matoba, M Tang, C Jiao, M Kim, E Tsai, C Hoh, N Aygun, RL Walker, C Chatzinakos, D Clarke, H Pratt, PsychENCODE Consortium, MA Peters, M Gerstein, NP Daskalakis, Z Weng, AE Jaffe, JE Kleinman, TM Hyde, DR Weinberger, NJ Bray, N Sestan, DH Geschwind, K Roeder, A Gusev, B Pasaniuc, JL Stein, MI Love, KS Pollard, C Liu, MJ Gandal, PsychENCODE Consortium (2024). Science 384: eadh0829.

Using a comprehensive atlas and predictive models to reveal the complexity and evolution of brain-active regulatory elements
HE Pratt, G Andrews, N Shedd, N Phalke, T Li, A Pampari, M Jensen, C Wen, P Consortium, MJ Gandal, DH Geschwind, M Gerstein, J Moore, A Kundaje, A Colubri, Z Weng (2024). Sci Adv 10: eadj4452.

The single-cell opioid responses in the context of HIV (SCORCH) consortium
SA Ament, RR Campbell, MK Lobo, JP Receveur, K Agrawal, A Borjabad, SN Byrareddy, L Chang, D Clarke, P Emani, D Gabuzda, KJ Gaulton, M Giglio, FM Giorgi, B Gok, C Guda, E Hadas, BR Herb, W Hu, A Huttner, MR Ishmam, MM Jacobs, J Kelschenbach, DW Kim, C Lee, S Liu, X Liu, BK Madras, AA Mahurkar, DC Mash, EA Mukamel, M Niu, RM O'Connor, CM Pagan, APS Pang, P Pillai, V Repunte-Canonigo, WB Ruzicka, J Stanley, T Tickle, SA Tsai, A Wang, L Wills, AM Wilson, SN Wright, S Xu, J Yang, M Zand, L Zhang, J Zhang, S Akbarian, S Buch, CS Cheng, MJ Corley, HS Fox, M Gerstein, S Gummuluru, M Heiman, YC Ho, M Kellis, PJ Kenny, Y Kluger, TA Milner, DJ Moore, S Morgello, LC Ndhlovu, TM Rana, PP Sanna, JS Satterlee, N Sestan, SA Spector, S Spudich, HU Tilgner, DJ Volsky, OR White, DW Williams, H Zeng (2024). Mol Psychiatry 29: 3950-3961.

Single-cell genomics and regulatory networks for 388 human brains
PS Emani, JJ Liu, D Clarke, M Jensen, J Warrell, C Gupta, R Meng, CY Lee, S Xu, C Dursun, S Lou, Y Chen, Z Chu, T Galeev, A Hwang, Y Li, P Ni, X Zhou, PsychENCODE Consortium, TE Bakken, J Bendl, L Bicks, T Chatterjee, L Cheng, Y Cheng, Y Dai, Z Duan, M Flaherty, JF Fullard, M Gancz, D Garrido-Martin, S Gaynor-Gillett, J Grundman, N Hawken, E Henry, GE Hoffman, A Huang, Y Jiang, T Jin, NL Jorstad, R Kawaguchi, S Khullar, J Liu, J Liu, S Liu, S Ma, M Margolis, S Mazariegos, J Moore, JR Moran, E Nguyen, N Phalke, M Pjanic, H Pratt, D Quintero, AS Rajagopalan, TR Riesenmy, N Shedd, M Shi, M Spector, R Terwilliger, KJ Travaglini, B Wamsley, G Wang, Y Xia, S Xiao, AC Yang, S Zheng, MJ Gandal, D Lee, ES Lein, P Roussos, N Sestan, Z Weng, KP White, H Won, MJ Girgenti, J Zhang, D Wang, D Geschwind, M Gerstein (2024). Science 384: eadi5199.

The association between evening social media use and delayed sleep may be causal: Suggestive evidence from 120 million Reddit timestamps
WU Meyerson, SK Fineberg, FC Andrade, P Corlett, MB Gerstein, RH Hoyle (2023). Sleep Med 107: 212-218.

Estimation of Bedtimes of Reddit Users: Integrated Analysis of Time Stamps and Surveys
WU Meyerson, SK Fineberg, YK Song, A Faber, G Ash, FC Andrade, P Corlett, MB Gerstein, RH Hoyle (2023). JMIR Form Res 7: e38112.

Illuminating links between cis-regulators and trans-acting variants in the human prefrontal cortex.
S Liu, H Won, D Clarke, N Matoba, S Khullar, Y Mu, D Wang, M Gerstein (2022). Genome Med 14: 133.

Cyclic and Multilevel Causation in Evolutionary Processes
J Warrell, M Gerstein (2020). Biology & Philosophy, 35(5), pp.1-36.

A Single-Cell Transcriptomic Atlas of Human Neocortical Development during Mid-gestation.
D Polioudakis, L de la Torre-Ubieta, J Langerman, AG Elkins, X Shi, JL Stein, CK Vuong, S Nichterwitz, M Gevorgian, CK Opland, D Lu, W Connell, EK Ruzzo, JK Lowe, T Hadzic, FI Hinz, S Sabri, WE Lowry, MB Gerstein, K Plath, DH Geschwind (2019). Neuron 103: 785-801e8.

Revealing the brain's molecular architecture.
PsychENCODE Consortium (2018). Science 362: 1262-1263.

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

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

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

Transcriptome and epigenome landscape of human cortical development modeled in organoids.
A Amiri, G Coppola, S Scuderi, F Wu, T Roychowdhury, F Liu, S Pochareddy, Y Shin, A Safi, L Song, Y Zhu, AMM Sousa, PsychENCODE Consortium, M Gerstein, GE Crawford, N Sestan, A Abyzov, FM Vaccarino (2018). Science 362.

A multiregional proteomic survey of the postnatal human brain.
BC Carlyle, RR Kitchen, JE Kanyo, EZ Voss, M Pletikos, AMM Sousa, TT Lam, MB Gerstein, N Sestan, AC Nairn (2017). Nat Neurosci 20: 1787-1795.

Molecular and cellular reorganization of neural circuits in the human lineage.
AMM Sousa, Y Zhu, MA Raghanti, RR Kitchen, M Onorati, ATN Tebbenkamp, B Stutz, KA Meyer, M Li, YI Kawasawa, F Liu, RG Perez, M Mele, T Carvalho, M Skarica, FO Gulden, M Pletikos, A Shibata, AR Stephenson, MK Edler, JJ Ely, JD Elsworth, TL Horvath, PR Hof, TM Hyde, JE Kleinman, DR Weinberger, M Reimers, RP Lifton, SM Mane, JP Noonan, MW State, ES Lein, JA Knowles, T Marques-Bonet, CC Sherwood, MB Gerstein, N Sestan (2017). Science 358: 1027-1032.

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

FOXG1-Dependent Dysregulation of GABA/Glutamate Neuron Differentiation in Autism Spectrum Disorders.
J Mariani, G Coppola, P Zhang, A Abyzov, L Provini, L Tomasini, M Amenduni, A Szekely, D Palejev, M Wilson, M Gerstein, EL Grigorenko, K Chawarska, KA Pelphrey, JR Howe, FM Vaccarino (2015). Cell 162: 375-390.

Decoding neuroproteomics: integrating the genome, translatome and functional anatomy.
RR Kitchen, JS Rozowsky, MB Gerstein, AC Nairn (2014). Nat Neurosci 17: 1491-9.

Transcriptional landscape of the prenatal human brain.
JA Miller, SL Ding, SM Sunkin, KA Smith, L Ng, A Szafer, A Ebbert, ZL Riley, JJ Royall, K Aiona, JM Arnold, C Bennet, D Bertagnolli, K Brouner, S Butler, S Caldejon, A Carey, C Cuhaciyan, RA Dalley, N Dee, TA Dolbeare, BA Facer, D Feng, TP Fliss, G Gee, J Goldy, L Gourley, BW Gregor, G Gu, RE Howard, JM Jochim, CL Kuan, C Lau, CK Lee, F Lee, TA Lemon, P Lesnar, B McMurray, N Mastan, N Mosqueda, T Naluai-Cecchini, NK Ngo, J Nyhus, A Oldre, E Olson, J Parente, PD Parker, SE Parry, A Stevens, M Pletikos, M Reding, K Roll, D Sandman, M Sarreal, S Shapouri, NV Shapovalova, EH Shen, N Sjoquist, CR Slaughterbeck, M Smith, AJ Sodt, D Williams, L Zollei, B Fischl, MB Gerstein, DH Geschwind, IA Glass, MJ Hawrylycz, RF Hevner, H Huang, AR Jones, JA Knowles, P Levitt, JW Phillips, N Sestan, P Wohnoutka, C Dang, A Bernard, JG Hohmann, ES Lein (2014). Nature 508: 199-206.

Annual Research Review: The promise of stem cell research for neuropsychiatric disorders.
FM Vaccarino, AE Urban, HE Stevens, A Szekely, A Abyzov, EL Grigorenko, M Gerstein, S Weissman (2011). J Child Psychol Psychiatry 52: 504-16.

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