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Electronic versions of papers are provided as a professional courtesy to ensure timely dissemination of academic work for individual, noncommercial purposes. Copyright resides with the respective copyright holders, as stated within each paper. These files may not be reposted without permission.
Updated February 18th, 2024
Qu Y, Chopra S, Qu S, Cocuzza CV, Labache L, Bauer CCC, Morfini F, Whitfield-Gabrieli S, Slavich GM, Joormann J, Holmes AJ. (Submitted). Shared and unique lifetime stressor characteristics and brain networks predict adolescent anxiety and depression. biorxiv 620373. [preprint]
Orchard ER, Chopra S, Ooi LQR, Chen P, An L, Jamadar SD, Yeo BTT, Rutherford HJV, Holmes AJ. (Submitted). Protective role of parenthood on age-related brain function in mid- to late-life. biorxiv 592382. [preprint]
Chopra S, Cocuzza CV, Lawhead C, Ricard JA, Labache Loic, Patrick LM, Kumar P, Rubenstein A, Moses J, Chen L, Blankenbaker C, Gillis B, Germine LT, Harpaz-Rotem I, Yeo BTT, Baker JT, Holmes AJ. (Submitted). The Transdiagnostic Connectome Project: a richly phenotyped open dataset for advancing the study of brain-behavior relationships in psychiatry. medRxiv 24309054. [preprint]
Dhamala E, Chopra S, Ooi LQR, Rubio JM, Yeo BTT, Malhotra AK, Holmes AJ. (Submitted). Sex differences in the functional network underpinnings of psychotic-like experiences in children. bioRxiv 590660. [preprint]
Ooi LQR, Orban C, Nichols T, Zhang S, Tan TWK, Kong R, Marek S, Dosenbach NUF, Laumann TO, Gordon EM, Zhou JH, Bzdok D, Eickhoff SB, Holmes AJ, BTT Yeo. (Submitted). MRI economics: balancing sample size and scan duration in brain wide association studies. bioRxiv 580448. [preprint]
Segal, A, Tiego J, Parkes L, Holmes AJ, Marquand AF, Fornito A. (In Press). Embracing variability in the search for biological mechanisms of psychiatric illness. Trends in Cognitive Sciences. [preprint]
Qu Y, Chen J, Tam A, Ooi LQR, Dhamala E, Cocuzza C, Lawhead C, Yeo BTT, Holmes AJ. (In Press). Distinct brain network features predict internalizing and externalizing traits in children, adolescents, and adults. Nature Mental Health. [preprint]
Dhamala E, Ricard JA, Uddin LQ, Galea LAM, Jacobs EG, Yip SW, Yeo BTT, Chakravarty MM, Holmes AJ. (In Press). Considering the interconnected nature of social identities in neuroimaging research. Nature Neuroscience.
Zhang X-H, Anderson KM, Dong HM, Chopra S, Dhamala E, Emani PS, Gerstein MB, Margulies D, Holmes AJ. (2024). The cell-type underpinnings of the human functional cortical connectome. Nature Neuroscience. [pdf] [commentary on our paper]
DeYoung CG, Blain SD, Latzman RD, Grazioplene RG, Haltigan JD, Kotov R, Michelini G, et al. (2024). The Hierarchical Taxonomy of Psychopathology (HiTOP) and the search for neurobiological substrates of mental illness: a systematic review and roadmap for future research. Journal of Psychopathology and Clinical Science, 133(8), 697–715. [pdf]
García-Marín LM, Campos AI, Diaz-Torres S, Rabinowitz JA, Ceja Z, Mitchell BL, et al. (2024). Genomic analysis of intracranial and subcortical brain volumes yields polygenic scores accounting for variation across ancestries. Nature Genetics, 56, 2333–2344. [pdf]
Chopra S, Dhamala E, Lawhead C, Ricard JA, Orchard ER, An L, Chen P, Wulan N, Kumar P, Rubenstein A, Moses J, Chen L, Levi P, Aquino K, Fornito A, Harpaz-Rotem I, Germine LT, Baker JT, Yeo BTT, Holmes AJ. (2024). Reliable and generalizable brain-based predictions of cognitive functioning across common psychiatric illness. Science Advances, 10(45), eadn1862. [pdf]
Dong HM, Zhang XH, Labache L, Zhang S, Ooi LQR, Yeo BTT, Margulies DS, Holmes AJ, Zuo X-N. (2024). Ventral attention network connectivity is linked to cortical maturation and cognitive ability in childhood. Nature Neuroscience, 27, 2009-2020. [pdf]
Ricard J, Labache L, Segal A, Dhamala E, Cocussa CV, Jones G, Yip S, Chopra S, Holmes AJ. (2024). A shared spatial topography links the functional connectome correlates of cocaine use disorder and dopamine D2/3 receptor densities. Communications Biology, 7, 1178. [pdf]
Ho NCW, Bethlehem RAI, Seidlitz J, Nogovitsyn N, Metzak P, Ballester PL, Hassel S, et al. (2024). Atypical brain aging and its association with working memory performance in major depressive disorder. Biological Psychiatry: Cognitive Neuroscience and Neuroimaging, 9(8), 786-799. [pdf]
Chen P, An L, Wulan N, Zhang C, Zhang S, Ooi LQR, Kong R, Chen J, Wu J, Chopra S, Bzdok D, Eickhoff SB, Holmes AJ, Yeo BTT. (2024). Multilayer meta-matching: translating phenotypic prediction models from multiple datasets to small data. Imaging Neuroscience, 2, 1-21. [pdf]
Wulan N, An L, Zhang C, Kong R, Chen P, Bzdok D, Eickhoff SB, Holmes AJ, Yeo BTT. (2024). Translating phenotypic prediction models from big to small anatomical MRI data using meta-matching. Imaging Neuroscience, 2, 1-21. [pdf]
Dhamala E, Bassett D, Yeo BTT, Holmes A. (2024). Functional brain networks are associated with both sex and gender in children. Science Advances, 10(28), eadn4202. [pdf] [focus article on our paper]
Knol MJ, Poot RA, Evans TE, Satizabal CL, Mishra A, Sargurupremraj M, van der Auwera S, et al. (2024). Genetic variants for head size share genes and pathways with cancer. Cell Reports Medicine, 5(5). [pdf]
Kohler R, Lichenstein SD, Cheng A, Holmes A, Bzdok D, Pearlson G, Yip S. (2024). Identification of a composite latent dimension of reward and impulsivity across clinical, behavioral and neurobiological domains among youth. Biological Psychiatry: Cognitive Neuroscience and Neuroimaging, 9(4), 407-416. [pdf]
Ibrahim K, Iturmendi-Sabater I, Vasishth M, Barron DS, Guardavaccaro M-R, Funaro MC, Holmes A, McCarthy G, Eickhoff SB, Sukhodolsky DG. (2024). Neural circuit disruptions of eye gaze processing in autism spectrum disorder and schizophrenia: an activation likelihood estimation meta-analysis. Schizophrenia Research, 264, 298-313. [pdf]
Boen R, Kaufmann T, van der Meer D, Frei O, Agartz I, Ames D, Andersson M, et al. (2024). Beyond the global brain differences: intra-individual variability differences in 1q21.1 distal and 15q11.2 BP1-BP2 deletion carriers. Biological Psychiatry, 95(2), 147-160. [pdf]
Chopra S, Labache L, Dhamala E, Orchard ER, Holmes AJ. (2023). A practical guide for generating reproducible and programmatic neuroimaging visualizations. Aperture Neuro, 3, 1-12. [pdf] [code repository] [template generator]
Yang E, Milisav F, Kopal J, Holmes AJ, Mitsis GD, Misic B, Finn ES, Bzdok D. (2023). The default network dominates neural responses to evolving movie stories. Nature Communications, 14(1), 4197. [pdf]
Dhamala E, Ooi LQR, Chen J, Ricard JA, Berkeley E, Chopra S, Qu Y, Zhang X-H, Lawhead C, Yeo BTT, Holmes AJ. (2023). Brain-based predictions of psychiatric illness-linked behaviors across the sexes. Biological Psychiatry, 94(6), 479-491. [pdf] [code repository]
Labache L, Ge T, Yeo BTT, Holmes AJ. (2023). Language network lateralization is reflected throughout the macroscale functional organization of cortex. Nature Communications, 14, 3405. [pdf] [code repository]
Tiego J, Martin E, DeYoung CG, Hagan K, Cooper SE, Pasion R, et al. (2023). Precision behavioral phenotyping as a strategy for uncovering the biological correlates of psychopathology. Nature Mental Health, 1, 304–315. [pdf]
Chen J, Ooi LQR, Tan TWK, Zhang S, Li J, Asplund CL, Eickhoff SB, Bzdok D, Holmes AJ, Yeo BTT. (2023). Relationship between prediction accuracy and feature importance reliability: an empirical and theoretical study. NeuroImage, 274, 120115. [pdf]
Chopra S, Zhang X-H, Holmes AJ. (2023). Wavelike properties of functional dynamics across the cortical sheet. Neuron, 11(8), 1171-1173. [pdf] [preview for this paper]
Peng G, Wang Y-S, Lu Q-Y, Rong M-J, Fan X-R, Holmes A, Dong H-M, Li H-F, Zuo X-N. (2023). Brief mock-scan training reduces head motion in real scanning for children: a growth curve study. Developmental Cognitive Neuroscience, 61,101244. [pdf]
Chin R, Chang SWC, Holmes AJ. (2023). Beyond cortex: the evolution of the human brain. Psychological Review, 30(2), 285–307. [pdf]
Yan X, Kong R, Xue A, Yang Q, Orban C, An L, Holmes AJ, Qian X, Chen J, Zuo X-N, Zhou JH, Fortier MV, Tan AP, Gluckman P, Chong YS, Meaney M, Bzdok D, Eickhoff SB, Yeo BTT. (2023). Homotopic local-global parcellation of the human cerebral cortex from resting-state functional connectivity. NeuroImage, 273, 120010. [pdf]
Dhamala E, Yeo BTT, Holmes AJ. (2023). One size does not fit all: methodological considerations for predictive modeling in psychiatry. Biological Psychiatry, 93(8), 717-728. [pdf]
Orchard ER, Rutherford HJV, Holmes AJ, Jamadar SD (2023). Matrescence: lifetime impact of motherhood on cognition and the brain. Trends in Cognitive Sciences, 27(3), 302-316. [pdf] [cover art]
Kalantar-Hormozi H, Patel R, Dai A, Ziolkowski J, Dong HM, Holmes A, Raznahan A, Devenyi GA, Chakravarty MM (2023). A cross-sectional and longitudinal study of human brain development: the integration of cortical thickness, surface area, gyrification index, and cortical curvature into a unified analytical framework. Neuroimage, 268, 119885. [pdf]
Ricard JA, Parker TC, Dhamala E, Kwasa J, Allsop A, Holmes AJ. (2023). Confronting racially exclusionary practices in the acquisition and analyses of neuroimaging data. Nature Neuroscience, 26, 4-11. [pdf] [cover art]
Kirk PA, Holmes AJ, Robinson OJ (2022). Anxiety and amygdala connectivity during movie-watching. Biological Psychiatry: Global Open Science, 169(3), 108194. [pdf]
Ooi LQR, Chen J, Shaoshi Z, Kong R, Tam A, Li J, Dhamala E, Zhou JH, Holmes AJ, Yeo BTT. (2022). Comparison of individualized behavioral predictions across anatomical, diffusion and functional connectivity MRI. NeuroImage, 263, 119636. [pdf]
Dhamala E, Ooi LQR, Chen J, Kong R, Anderson KM, Chin R, Yeo BTT, Holmes AJ. (2022). Proportional intracranial volume correction differentially biases behavioral predictions across neuroanatomical features and populations. NeuroImage, 260, 119485. [pdf] [code repository]
Kirk PA, Holmes AJ, Robinson OJ. (2022). Threat vigilance and intrinsic amygdala connectivity. Human Brain Mapping, 43, 3283–3292. [pdf]
Kim GW, Farabaugh AH, Vetterman R, Holmes A, Nyer M, Nasiriavanaki Z, Fava M, Holt DJ. (2022). Diminished frontal pole size and functional connectivity in young adults with high suicidality. Journal of Affective Disorders, 310, 484-492. [pdf]
He T, An L, Feng J, Bzdok D, Holmes AJ, Eickhoff SB, Yeo BTT. (2022). Meta-matching: a simple framework to translate phenotypic predictive models from big to small data. Nature Neuroscience, 25, 795–804. [pdf]
Chen J, Tam A, Kebets V, Orban C, Ooi LQR, Marek S, Dosenbach N, Eickhoff S, Bzdok D, Holmes AJ, Yeo BTT. (2022). Shared and unique brain network features predict cognition, personality and mental health in childhood. Nature Communications, 13, 1-17. [pdf]
Bethlehem RA, Seidlitz J, White SR, Vogel JW, Anderson KM, Adamson C, et al., (2022). Brain charts for the human lifespan. Nature, 604, 525–533. [pdf]
Yip SW, Jordan A, Kohler R, Holmes AJ, Bzdok D. (2022). Transgenerational impacts of the COVID-19 pandemic on minoritized and marginalized communities. JAMA Psychiatry, 79(4), 350–358. [pdf]
Li J, Bzdok D, Chen J, Tam A, Qi Rong Ooi L, Holmes AJ, Ge T, Patil KR, Eickhoff SB, Yeo BTT, Genon S. (2022). Cross-ethnicity/race generalization failure of behavioral prediction from resting-state functional connectivity. Science Advances, 8(11), eabj1812. [pdf]
Sønderby IE, Ching CRK, Thomopoulos SI, van der Meer D, Sun D, Villalo JE, et al. (2022). Effects of copy number variations on brain structure and risk for psychiatric illness: large-scale studies from the ENIGMA Working Groups on CNVs. Human Brain Mapping, 43(1), 300-328. [pdf]
Frangou S, Modabbernia A, Doucet GE, Papachristou E, Williams SCR, Agartz I, et al. (2022). Cortical thickness trajectories across the lifespan: data from 17,075 healthy individuals aged 3-90 years. Human Brain Mapping, 43(1), 431-451. [pdf]
Dima D, Papachristou E, Modabbernia A, Doucet GE, Agartz I, Aghajani M, et al. (2022). Subcortical volume trajectories across the lifespan: data from 17,075 healthy individuals aged 3-90 years. Human Brain Mapping, 43(1), 452-469. [pdf]
Wierenga LW, Doucet G, Dima D, Agartz I, Aghajani M, Akudjedu T, et al. (2022). Greater male than female variability in regional brain structure across the lifespan. Human Brain Mapping, 43(1), 470-499. [pdf]
Chen L-Z, Holmes A, Dong Q, Zuo X-N. (2021). Neuroimaging brain growth charts: A road to mental health. Psychoradiology, 1(4), 272-286. [pdf]
Kong X, Kong R, Orban C, Peng W, Zhang S, Anderson KM, Holmes AJ, Murray J, Deco G, van den Heuvel M, Yeo BTT. (2021). Sensory-motor cortices shape functional connectivity dynamics in the human brain. Nature Communications, 12, 6373. [pdf]
Patrick LM, Anderson KM, Holmes AJ. (2021). Local and distributed cortical markers of effort expenditure during sustained goal pursuit. NeuroImage, 244, 118602. [pdf]
Barron DS, Baker JT, Budde KS, Bzdok D, Eickhoff SB, Friston K, et al. (2021). Decision Models and Technology Can Help Psychiatry Develop Biomarkers. Frontiers in Psychiatry, 12, 10.3389/fpsyt.2021.706655. [pdf]
Kong R, Yang Q, Gordon E, Xue A, Yan X, Orban C, Zuo X-N, Spreng N, Ge T, Holmes AJ, Eickhoff S, Yeo BTT. (2021). Individual-specific areal-level parcellations improve functional connectivity prediction of behavior. Cerebral Cortex, 31, 10, 4477–4500. [pdf]
Wang D, Peng X, Pelletier-Baldelli A, Orlov N, Farabaugh A, Nasr S, Eryilmaz H, Fava M, Holmes AJ, Buckner RL, Roffman JL, Liu H. Holt D. (2021). Altered temporal, but intact spatial, features of transient network dynamics in psychosis. Molecular Psychiatry, 26, 2493–2503. [pdf]
Anderson KM, Holmes AJ. (2021). Predicting cognitive ability: brain imaging and genetics. In: AK. Barbey, S. Karama, and R. Haier (Eds.), The Cambridge Handbook of Intelligence and Cognitive Neuroscience. Cambridge University Press, pp. 327-348.
Dong HM, Margulies DS, Zuo X-N, Holmes AJ. (2021). Shifting gradients of macroscale cortical organization mark the transition from childhood to adolescence. Proceedings of the National Academy of Sciences USA, 118(28), e2024448118. [pdf]
Sønderby I, van der Meer D, Moreau C, Kaufmann T, Walters G, Ellegaard M, et al. (2021). 1q21.1 distal copy number variants are associated with cerebral and cognitive alterations in humans. Translational Psychiatry, 11, 182. [pdf]
Nasiriavanaki Z, Barbour T, Farabaugh AH, Fava M, Holmes AJ, Tootell RBH, Holt DJ. (2021). Anxious attachment is associated with heightened responsivity of a parietofrontal cortical network that monitors peri-personal space. Neuroimage: Clinical, 30, 102585. [pdf]
Anderson KM, Ge T, Kong R, Patrick LM, Spreng RN, Sabuncu MR, Yeo BTT, Holmes AJ. (2021). Heritability of individualized cortical network topography. Proceedings of the National Academy of Sciences USA, 118(9), e2016271118. [pdf] [supplementary materials] [code repository]
Kiesow H, Spreng RN, Holmes AJ, Chakravarty MM, Marquand AF, Yeo BTT, Bzdok D. (2021). Deep learning identifies partially overlapping subnetworks in the human social brain. Communications Biology, 4, 65. [pdf]
Chen J, Müller VI, Dukart J, Hoffstaedter F, Baker JT, Holmes AJ, Vatansever D, Nickl-Jockschat T, Liu X, Derntl B, Kogler L, Jardri R, Gruber O, Aleman A, Sommer IE, Eickhoff SB, Patil KR. (2021). Intrinsic connectivity patterns of task-defined brain networks allow individual prediction of cognitive symptom dimension of schizophrenia and are linked to molecular architecture. Biological Psychiatry, 89(3), 308-319. [pdf]
Spreng RN, Dimas E, Mwilambwe-Tshilobo L, Dagher A, Koellinger P, Nave G, Ong A, Kernbach J, Wiecki T, Ge T, Li Y, Holmes AJ, Yeo BTT, Turner GR, Dunbar RIM, Bzdok D (2020). The default network of the human brain is associated with perceived social isolation. Nature Communications, 11, 6393. [pdf]
Dong HM, Castellanos FX, Yang N, Zhang Z, He Y, Zhang L, Xu T, Holmes AJ, et al. (2020). Charting brain growth in tandem with brain templates at school age. Science Bulletin, 65(22), 1924-1934. [pdf]
Anderson KM, Collins MA, Kong R, Fang K, Li J, He T, Chekroud AM, Yeo BTT, Holmes AJ. (2020). Convergent molecular, cellular, and cortical neuroimaging signatures of major depressive disorder. Proceedings of the National Academy of Sciences USA. 117(40), 25138–25149. [pdf] [supplementary materials] [code repository]
Boeke EA, Holmes AJ, Phelps EA. (2020). Toward robust anxiety biomarkers: a machine learning approach in a large-scale sample. Biological Psychiatry: Cognitive Neuroscience and Neuroimaging, 5(8), 799-807. [pdf]
Holmes AJ, MacDonald AW. (2020). Concepts and principles of clinical functional magnetic resonance imaging. In: AGC. Wright and MN. Hallquist (Eds.), Handbook of Research Methods in Clinical Psychology. Cambridge University Press, pp. 153-167. [pdf]
Gruskin, DC, Rosenberg, MD, Holmes, AJ. (2020). Relationships between depressive symptoms and brain responses during emotional movie viewing emerge in adolescence. NeuroImage, 216, 116217. [pdf]
Anderson, KM, Collins, MA, Chin, R, Ge T, Rosenberg MD, Holmes AJ. (2020). Transcriptional and imaging-genetic association of cortical interneurons, brain function, and schizophrenia risk. Nature Communications,11, 2889. [pdf] [supplementary materials] [code repository]
Hofer E, Roshchupkin GV, Adams HHH, Knol MJ, Lin H, Li S, et al. (2020). Genetic correlations and genome-wide associations of cortical structure in general population samples of 22,824 adults. Nature Communications, 11, 4796. [pdf]
Latzman, R.D., DeYoung, C.G., Afzali, M.H. et al. (2020). Using empirically-derived dimensional phenotypes to accelerate clinical neuroscience: the Hierarchical Taxonomy of Psychopathology (HiTOP) framework. Neuropsychopharmacology, 45, 1083–1085. [pdf]
Grasby KL, Jahanshad N, Painter JN, Colodro-Conte L, Bralten J, Hibar DP, et al. (2020). The genetic architecture of the human cerebral cortex. Science, 367(6484), 1340. [pdf] [article summary]
Barbour T, Holmes AJ, DeCross SN, Ward M, Coombs G, Boeke EA, Wolthusen RPF, Beam E, Nyer M, Pedrelli P, Fava M, Harabaugh AH, Holt DJ. (2020). Elevated amygdala activity in youth with familial risk for depression: a potential marker of low resilience. Biological Psychiatry: Cognitive Neuroscience and Neuroimaging, 5(2), 194-202. [pdf]
DeCross SN, Farabugh AH, Holmes AJ, Ward M, Boeke EA, Wolthausen RPF, Coombs G, Nyer M, Fava M, Buckner RL, Holt DJ. (2020). Increased amygdala-visual cortex connectivity in youth with persecutory ideation. Psychological Medicine, 50(2), 273-283. [pdf]
He T, Kong R, Holmes A, Nguyen M, Sabuncu M, Eickhoff SB, Bzdok D, Feng J, Yeo BTT. (2020). Deep neural networks and kernel regression achieve comparable accuracies for functional connectivity prediction of behavior and demographics. NeuroImage, 206, 116276. [pdf]
Satizabal CL, Adams HH, Hibar DP, White CC, Knol MJ, Stein JL, et al. (2019). Genetic architecture of subcortical brain structures in 38,851 individuals. Nature Genetics, 51, 1624–1636. [pdf]
Kebets V, Holmes AJ, Orban C, Tang S, Li J, Sun N, Kong R, Poldrack RA, Yeo BTT. (2019). Somatosensory-motor dysconnectivity spans multiple transdiagnostic dimensions of psychopathology. Biological Psychiatry, 86(10), 779-791. [pdf]
Elliott ML, Belsky DW, Anderson K, Corcoran DL, Ge T, Knodt A, … Hariri AR (2019). A polygenic score for higher educational attainment is associated with larger brains. Cerebral Cortex, 29(8), 3496-3504. [pdf]
Kong R, Li J, Sun N, Sabuncu M, Schaefer A, Scholz M, Zuo XN, Holmes AJ, Eickhoff S, Yeo BTT. (2019). Spatial topography of individual-specific cortical networks predicts human cognition, personality and emotion. Cerebral Cortex, 29(6), 2533–2551. [pdf]
Baker JT, Dillon DG, Patrick LM, Roffman JL, Brady RO, Pizzagalli DA, Öngür D, Holmes AJ. (2019). Functional connectomics of affective and psychotic pathology. Proceedings of the National Academy of Sciences USA, 116, 9050-9059. [pdf] [supplemental materials]
Li J, Kong R, Liegeois R, Orban C, Tan Y, Sun N, Holmes AJ, Sabuncu MR, Ge T, Yeo BTT. (2019). Global signal regression strengthens association between resting-state functional connectivity and behavior. NeuroImage, 196, 126-141. [pdf]
Stanton CH, Holmes AJ, Chang SWC, Joormann J. (2019). From stress to anhedonia: molecular processes through functional circuits. Trends in Neurosciences, 42, 23-42. [pdf]
Kernbach JM, Yeo BTT, Smallwood J, Margulies D, de Schotten MT, Walter H, Sabuncu MR, Holmes AJ, Gramfort A, Varoquaux G, Thirion B, Bzdok D. (2018). Subspecialization within default mode nodes characterized in 10,000 UK Biobank participants. Proceedings of the National Academy of Sciences USA, 115, 12295-12300. [pdf]
Schaefer AL, Kong R, Gordon EM, Laumann TO, Zuo XN, Holmes AJ, Eickhoff SB, Yeo BTT. (2018). Local-Global parcellation of the human cerebral cortex from intrinsic functional connectivity MRI. Cerebral Cortex, 28, 3095-3114. [pdf]
He T, Kong R, Holmes AJ, Sabuncu MR, Eickhoff SB, Bzdok D, Feng J, Yeo BTT. (2018). Is deep learning better than kernel regression for functional connectivity prediction of fluid intelligence? 8th International Workshop on Pattern Recognition in Neuroimaging (PRNI), Runner-Up, PRNI Best Paper Award. [pdf]
Anderson KM, Krienen FM, Choi EY, Reinen JM, Yeo BTT, Holmes AJ. (2018). Gene expression links functional networks across cortex and striatum. Nature Communications, 9, 1428. [pdf] [supplemental materials] [code repository]
Reinen JM, Chen OY, Hutchison RM, Yeo BTT, Anderson KM, Sabuncu MR, Öngür D, Roffman JL, Smoller JW, Baker JT, Holmes AJ. (2018). The human cerebral cortex possesses a reconfigurable dynamic architecture that is disrupted in psychotic illness. Nature Communications, 9, 1157. [pdf] [supplemental materials]
Rosenberg MD, Casey BJ, Holmes AJ. (2018). Prediction complements explanation in understanding the developing brain. Nature Communications, 9, 589. [pdf]
Holmes AJ, Patrick LM. (2018). The myth of optimality in clinical neuroscience. Trends in Cognitive Sciences, 22(3), 241-257. [pdf]
Ge T, Holmes AJ, Buckner RL, Smoller JW, Sabuncu MR. (2018). Reply to Risk and Zhu: Mixed effects modeling as a more principled approach to heritability analysis with repeat measurements. Proceedings of the National Academy of Sciences USA, 115(2), E123. [pdf]
Ge T, Holmes AJ, Buckner RL, Smoller JW, Sabuncu MR. (2017). Heritability analysis with repeat measurements and its application to resting-state functional connectivity. Proceedings of the National Academy of Sciences USA, 114(21), 5521-5526. [pdf]
Dal Monte O, Piva M, Anderson KA, Marios T, Holmes AJ, Chang SWC. (2017). Oxytocin under opioid antagonism leads to supralinear enhancement of social attention. Proceedings of the National Academy of Sciences USA, 114(20), 5247-5252. [pdf]
Hibar DP, Adams HH, Jahanshad N, Chauhan G, Stein JL, Hofer E, et al. (2017). Novel genetic loci associated with hippocampal volume. Nature Communications, 8, 13264. [pdf]
Germine L, Robinson EB, Smoller JW, Calkins ME, Moore TM, Hakonarson H, et al. (2016). Association between polygenic risk for schizophrenia, neurocognition, and social cognition across development. Translational Psychiatry, 6, e924. [pdf]
Adams HH, Hibar DP, Chouraki V, Stein J, Nyquist P, Renteria E, et al. (2016). Novel genetic loci underlying human intracranial volume identified through genome-wide association. Nature Neuroscience, 19, 1569–1582. [pdf]
Lee PH, Baker J, Holmes AJ, Jahanshad N, Ge T, Jung J-Y, et al. (2016). Partitioning heritability analysis reveals a shared genetic basis of brain anatomy and schizophrenia. Molecular Psychiatry, 21, 1680-1689. [pdf]
Ge T, Reuter M, Winkler AM, Holmes AJ, Lee PH, Tirrell L, Roffman JL, Buckner RB, Smoller JW, Sabuncu MR. (2016). Multidimensional heritability analysis of neuroanatomical shape. Nature Communications, 7, 13291. [pdf]
Sabuncu M, Ge T, Holmes AJ, Smoller JW, Buckner RL, Fischl B. (2016). Morphometricity as a measure of the neuroanatomical signature of a trait. Proceedings of the National Academy of Sciences, 113(39), E5749-E5756. [pdf]
Mormino B, Sperling RA, Holmes AJ, Buckner RL, De Jager PL, Smoller JW, Sabuncu MR, for the ADNI Initiative. (2016). Polygenic risk of Alzheimer’s disease dementia is associated with early and late life processes within clinically normal individuals. Neurology, 87(5), 481-488. [pdf]
Holmes AJ, Hollinshead MO, Roffman JL, Smoller JW, Buckner RL. (2016). Individual differences in cognitive control circuit anatomy link sensation seeking, impulsivity, and substance use. Journal of Neuroscience, 36(14), 4038-4049. [pdf]
Chekroud AM, Ward EJ, Rosenberg MD, Holmes AJ. (2016). Patterns in the human brain mosaic discriminate males from females. Proceedings of the National Academy of Sciences, 113(14), E1968. [pdf] [letter in response to this paper]
Franke B, Stein J, Ripke S, Anttilla V, Hibar DP, Kimm JE, et al. (2016). Genetic influences on schizophrenia and subcortical brain volumes: large-scale proof of concept. Nature Neuroscience, 19(3), 420-431. [pdf]
Oscar-Berman M, Urban TA, Holmes AJ. (2016). Effects of Alcoholism on Neurological Function and Disease in Adulthood. The Oxford Handbook of Substance Use Disorders, Volume 2. Medicine-US. [pdf]
Wang D, Buckner RL, Fox MD, Holt DJ, Holmes AJ, Mueller S, Langs G, Pan R, Qian T, Baker J, Stufflebeam SM, Wang K, Wang X, Hong B, Liu H. (2015). Parcellating cortical functional networks in individuals. Nature Neuroscience, 18(12), 1853–1860. [pdf] [supplemental materials]
Holmes AJ, Yeo BTT. (2015). From phenotypic chaos to neurobiological order. Nature Neuroscience, 18(11), 1532-1534. [pdf] [news & views for this paper]
Holmes AJ, Hollinshead M, O’Keefe TM, Petrov VI, Fariello GR, Wald LL, Fischl B, Rosen BR, Mair RW, Roffman JL, Smoller JW, Buckner RL. (2015). Brain Genomics Superstruct Project initial data release with structural, functional, and behavioral measures. Scientific Data, 2, 150031. [pdf][supplemental materials]
Hibar D, Stein JL, Renteria ME, Arias-Vasquez A, Desrivières S, Jahanshad N, et al. (2015). Common genetic variants influence human subcortical brain structures. Nature, 520, 224-229. [pdf]
Ge T, Nichols TE, Lee PH, Holmes AJ, Roffman JL, Buckner RL, Sabuncu M, Smoller JW. (2015). Massively expedited genome-wide heritability analysis (MEGHA). Proceedings of the National Academy of Sciences, 112(8), 2479–2484. [pdf]
Treadway MT, Waskom ML, Dillon DG, Holmes AJ, Park MTM, Chakravarty MM, Dutra SJ, Polli FE, Iosifescu DV, Fava M, Gabrieli JDE, Pizzagalli DA. (2015). Illness progression, recent stress, and morphometry of hippocampal subfields and medial prefrontal cortex in major depression. Biological Psychiatry, 77, 285-294. [pdf]
Admon R, Nickerson LD, Dillon DG, Holmes AJ, Bogdan R, Kumar P, et al. (2015). Dissociable cortico-striatal connectivity abnormalities in major depression in response to monetary gains and penalties. Psychological Medicine, 45, 121-131. [pdf]
Zuo XN, Anderson J, Bellec P, Birn RM, Biswal BB, Blautzik J, et al. (2014). An open science resource for establishing reliability and reproducibility in functional connectomics. Scientific Data, 1, 140049. [pdf]
Smoller JW, Gallagher PJ, Duncan LE, McGrath L, Haddad S, Holmes AJ, et al. (2014). The human ortholog of acid-sensing ion channel gene ASIC1a is associated with panic disorder and amygdala structure and function. Biological Psychiatry, 76, 902-910. [pdf]
Thomson PM, Stein JL, Medland SE, Hibar DP, Vasquez AA, Renteria M, et al. (2014) The ENIGMA Consortium: large-scale collaborative analyses of neuroimaging and genetic data. Brain Imaging and Behavior, 8(2), 153-182. [pdf]
Pearson-Fuhrhop KM, Dunn EC, Mortero S, Devan WJ, Falcone GJ, Holmes AJ, et al. (2014). Dopamine genetic risk score predicts depressive symptoms in healthy adults and adults with depression. PLoS ONE, 9(5), e93772. [pdf]
Baker JT, Holmes AJ, Masters G, Yeo BT, Krienen F, Buckner RL, Öngür D. (2014). Disruption of cortical association networks in schizophrenia and psychotic bipolar disorder. JAMA Psychiatry, 71(2), 109-118. [pdf]
Holmes AJ, Lee PH, Hollinshead M, Bakst L, Roffman JL, Smoller JW, Buckner RL. (2012). Individual differences in amygdala-medial prefrontal anatomy link negative affect, impaired social functioning, and polygenic depression risk. Journal of Neuroscience, 32(50), 18087-18100. [pdf]
Bis JC, DeCarli C, Smith AV, van der Lijn F, Crivello F, Fornage M, et al. (2012). Common variants at 12q14 and 12q24 are associated with hippocampal volume. Nature Genetics, 44(5), 545-551. [pdf]
Stein JL, Medland SE, Vasquez AA, Hibar DP, Senstad RE, Winkler AM, et al. (2012). Identification of common variants associated with human hippocampal and intracranial volumes. Nature Genetics, 44(5), 552-561. [pdf]
Santesso DL, Bogdan R, Birk JL, Goetz EL, Holmes AJ, Pizzagalli DA. (2012). Neural responses to negative feedback are related to negative emotionality in healthy adults. Social Cognitive and Affective Neuroscience, 7(7), 794-803. [pdf]
Pizzagalli DA, Dillon DG, Bogdan R, Holmes A. (2011). Reward and punishment processing in the human brain: Clues from affective neuroscience and implications for depression research. In: O. Vartanian and D. Mandel (Eds.), Neuroscience of Decision Making. New York: Psychology Press, pp. 199-220.
Holmes AJ, Pizzagalli D. (2010). Effects of task-relevant incentives on the electrophysiological correlates of error processing in major depressive disorder. Cognitive Affective and Behavioral Neuroscience, 10(1), 119-128. [pdf]
Holmes AJ, Bogdan R, Pizzagalli D. (2010). Serotonin transporter genotype and action monitoring dysfunction: A possible substrate underlying increased vulnerability to depression. Neuropsychopharmacology, 35, 1186-1197. [pdf]
Janes AC, Pizzagalli DA, Richard S, Frederick BB, Holmes AJ, Sousa A, Fava M, Evins AE, Kaufman M. (2010). Neural substrates of attentional bias for smoking-related cues: An fMRI study. Neuropsychopharmacology, 35(12), 2339-2345. [pdf]
Janes AC, Pizzagalli DA, Richardt S, Frederick BB, Chuzi S, Pachas G, Culhane MA, Holmes AJ, Fava M, Evins AE, Kaufman M. (2010). Brain reactivity to smoking cues prior to smoking cessation predicts ability to maintain tobacco abstinence. Biological Psychiatry, 67, 722-729. [pdf]
Petersen, T, Pava J, Buchin J, Matthews J, Nierenberg A, Holmes AJ, Bogdan R, Graves L, Harley R, Fava M. (2010). The role of cognitive-behavioral therapy and fluoxetine in prevention of recurrence of major depressive disorder. Cognitive Therapy and Research, 34(1), 13-23. [pdf]
Dillon DG, Bogdan R, Fagerness J, Holmes AJ, Perlis RH, Pizzagalli DA. (2010). Variation in TREK1 gene linked to depression-resistant phenotype is associated with potentiated neural responses to rewards in humans. Human Brain Mapping, 31, 210-221. [pdf]
Dillon DG, Holmes AJ, Birk JL, Brooks N, Lyons-Ruth K, Pizzagalli DA. (2009). Childhood adversity is associated with left basal ganglia dysfunction during reward anticipation in adulthood. Biological Psychiatry, 66, 206-213. [pdf]
Pizzagalli DA, Holmes AJ, Dillon DG, Goetz EL, Birk JL, Bogdan R, Dougherty DD, Iosifescu DV, Rauch SL, Fava M. (2009). Reduced caudate and nucleus accumbens response to rewards in unmedicated subjects with major depressive disorder. American Journal of Psychiatry, 166, 702-710. [pdf]
Holmes AJ, Pizzagalli DA. (2008). Response conflict and frontocingulate dysfunction in unmedicated participants with major depression. Neuropsychologia, 46, 2904-2913. [pdf]
Chiu P, Holmes AJ, Pizzagalli DA. (2008) Neural dynamics of affective response inhibition: Dissociable recruitment of rostral anterior cingulate and inferior frontal cortex. NeuroImage, 42, 988-997. [pdf]
Holmes AJ, Pizzagalli DA. (2008). Spatiotemporal dynamics of action monitoring dysfunctions in major depressive disorder. Archives of General Psychiatry, 65(2), 179-188. [pdf]
Meites TM, Deveney CM, Steele KT, Holmes AJ, Pizzagalli DA. (2008). Implicit depression and hopelessness in remitted depressed individuals. Behaviour Research and Therapy, 46, 1078-1084. [pdf]
Dillon DG, Holmes AJ, Jahn AL, Bogdan R, Wald L, Pizzagalli DA. (2008). Dissociation of neural regions associated with anticipatory versus consummatory phases of incentive processing. Psychophysiology, 45, 36-49. [pdf]
Santesso DL, Dillon DG, Birk JL, Holmes AJ, Goetz E, Bogdan R, Pizzagalli DA. (2008). Individual differences in reinforcement learning: Behavioral, electrophysiological, and neuroimaging correlates. NeuroImage, 42, 807-816. [pdf]
Santesso DL, Steele KT, Bogdan R, Holmes AJ, Deveney CM, Meites TM, Pizzagalli DA (2008) Enhanced negative feedback responses in remitted depression. NeuroReport, 19, 1045-1048. [pdf]
Holmes AJ, Pizzagalli DA. (2007) Task feedback effects on conflict monitoring and executive control: Relationship to subclinical measures of mood. Emotion, 7(1), 68-76. [pdf]
Peterson T, Feldman G, Harley R, Fresco D, Graves L, Holmes A, Bogdan R, Papakostas G, Bohn L, Lury A, Fava M, Segal Z. (2007) Extreme response style in recurrent and chronically depressed patients: Change with antidepressant administration and stability during continuation treatment. Journal of Consulting and Clinical Psychology, 75(1), 145-153. [pdf]
Holmes AJ, MacDonald AW, Carter C S, Barch D M, Stenger AV, Cohen JD. (2005). Prefrontal functioning during context processing in schizophrenia and major depression: An event-related fMRI study. Schizophrenia Research, 76, 199-206. [pdf]
MacDonald AW, Carter CS, Kerns JG, Ursu S, Barch DB, Holmes AJ, Stenger AV, Cohen JD. (2005). Specificity of prefrontal dysfunction and context processing deficits to schizophrenia in never medicated first-episode patients with first episode psychosis. American Journal of Psychiatry, 62, 475-484. [pdf]