Publications

Link to Google Scholar

2025

• Neuroimaging endophenotypes reveal underlying mechanisms and genetic factors contributing to progression and development of four brain disorders; J Wen, I Skampardoni, YE Tian, Z Yang, Y Cui, G Erus, G Hwang, E Varol, ...; Nature Biomedical Engineering, 1-18

• Alternative splicing across the C. elegans nervous system; A Weinreb, E Varol, A Barrett, RM McWhirter, SR Taylor, I Courtney, ...; Nature communications 16 (1), 4508

• DREDge: robust motion correction for high-density extracellular recordings across species; C Windolf, H Yu, AC Paulk, D Meszéna, W Muñoz, J Boussard, ...; Nature methods, 1-13

• Decoding neuronal wiring by joint inference of cell identity and synaptic connectivity; HP Gupta, AW Azevedo, K Xing, PA Sims, E Varol, RS Mann; bioRxiv

• Integrating bulk and single cell RNA-seq refines transcriptomic profiles of individual C. elegans neurons; A Barrett, E Varol, A Weinreb, SR Taylor, RM McWhirter, C Cros, B Vidal, ...; BioRxiv, 2025.01. 26.634951

• WormID-Benchmark: Extracting Whole-Brain Neural Dynamics of C. elegans At the Neuron Resolution; J Adhinarta, J Dong, T He, J Huang, D Sprague, J Wan, HJ Lee, Z Yu, ...; bioRxiv, 2025.01. 06.631621

• CellSpliceNet: Interpretable Multimodal Modeling of Alternative Splicing Across Neurons in C. elegans; A Afrasiyabi, J Kovalic, C Liu, E Castro, A Weinreb, E Varol, D Miller, ...; bioRxiv, 2025.06. 22.660966

• Human single neural and columnar dynamics recorded by intraoperative high-density penetrating electrodes; D Meszena, A Paulk, W Munoz, M Jamali, I Caprara, B Coughlin, ...; Neuroscience Applied 4, 105433

2024

• Exploiting correlations across trials and behavioral sessions to improve neural decoding; Y Zhang, H Lyu, C Hurwitz, S Wang, C Findling, F Hubert, A Pouget, ...; bioRxiv

• Genetic and clinical correlates of two neuroanatomical AI dimensions in the Alzheimer’s disease continuum; J Wen, Z Yang, IM Nasrallah, Y Cui, G Erus, D Srinivasan, A Abdulkadir, ...; Translational psychiatry 14 (1), 420

• 2P-NucTag: on-demand phototagging for molecular analysis of functionally identified cortical neurons; J Shi, B Nutkovich, D Kushinsky, BY Rao, SA Herrlinger, E Tsivourakis, ...; bioRxiv

• Alternative splicing across theC. elegansnervous system; A Weinreb, E Varol, A Barrett, RM McWhirter, SR Taylor, I Courtney, ...

• Disorganized Inhibitory Dynamics in Hippocampal area CA1 of 22q11. 2 Deletion Mutant Mice; SA Herrlinger, BY Rao, MEC Paredes, AL Tuttman, H Arain, E Varol, ...; bioRxiv, 2024.04. 28.591464

2023

• Bypassing spike sorting: Density-based decoding using spike localization from dense multielectrode probes; Y Zhang, T He, J Boussard, C Windolf, O Winter, E Trautmann, N Roth, ...; Advances in Neural Information Processing Systems 36, 77604-77631; NeurIPS 2023 (Spotlight)

• Modified Neuropixels probes for recording human neurophysiology in the operating room; B Coughlin, W Muñoz, Y Kfir, MJ Young, D Meszéna, M Jamali, I Caprara, ...; Nature protocols 18 (10), 2927-2953

• Neuroimaging-AI Endophenotypes of Brain Diseases in the General Population: Towards a Dimensional System of Vulnerability; J Wen, I Skampardoni, YE Tian, Z Yang, Y Cui, G Erus, G Hwang, E Varol, ...; Medrxiv: the Preprint Server for Health Sciences

• Learning Probabilistic Piecewise Rigid Atlases of Model Organisms via Generative Deep Networks; A Nejatbakhsh, N Dey, V Venkatachalam, E Yemini, L Paninski, E Varol; International Conference on Information Processing in Medical Imaging, 332-343; IPMI 2023. (Oral Presentation)

• Multimodal microscopy image alignment using spatial and shape information and a branch-and-bound algorithm; S Chen, BY Rao, S Herrlinger, A Losonczy, L Paninski, E Varol; ICASSP 2023-2023 IEEE International Conference on Acoustics, Speech and …

• Robust online multiband drift estimation in electrophysiology data; C Windolf, AC Paulk, Y Kfir, E Trautmann, D Meszéna, W Muñoz, ...; ICASSP 2023-2023 IEEE International Conference on Acoustics, Speech and …; ICASSP 2023. (Top 3% of papers)

• Assessment of neuroanatomical endophenotypes of autism spectrum disorder and association with characteristics of individuals with schizophrenia and the general population; G Hwang, J Wen, S Sotardi, ES Brodkin, GB Chand, DB Dwyer, G Erus, ...; JAMA psychiatry 80 (5), 498-507

• Psychosis brain subtypes validated in first-episode cohorts and related to illness remission: results from the PHENOM consortium; DB Dwyer, GB Chand, A Pigoni, A Khuntia, J Wen, M Antoniades, ...; Molecular psychiatry 28 (5), 2008-2017

• Subtyping brain diseases from imaging data; J Wen, E Varol, Z Yang, G Hwang, D Dwyer, AF Kazerooni, PA Lalousis, ...; Machine Learning for Brain Disorders, 491-510

2022

• Genetic, clinical underpinnings of brain change along two neuroanatomical dimensions of clinically-defined Alzheimer’s disease; J Wen, Z Yang, IM Nasrallah, Y Cui, G Erus, D Srinivasan, A Abdulkadir, ...

• Genetic, clinical underpinnings of subtle early brain change along Alzheimer’s dimensions; J Wen, Z Yang, IM Nasrallah, Y Cui, G Erus, D Srinivasan, A Abdulkadir, ...; bioRxiv, 2022.09. 16.508329

• Schizophrenia imaging signatures and their associations with cognition, psychopathology, and genetics in the general population; GB Chand, P Singhal, DB Dwyer, J Wen, G Erus, J Doshi, D Srinivasan, ...; American Journal of Psychiatry 179 (9), 650-660

• Three imaging endophenotypes characterize neuroanatomical heterogeneity of autism spectrum disorder; G Hwang, J Wen, S Sotardi, ES Brodkin, GB Chand, DB Dwyer, G Erus, ...; medRxiv, 2022.06. 17.22276543

• P580. Two Schizophrenia Neuroanatomical Signatures From the PHENOM Consortium and Their Association With Psychopathology, Cognition, and Genetics in the Population-Level Samples; G Chand, P Singhal, DB Dwyer, J Wen, G Erus, E Varol, G Hwang, ...; Biological Psychiatry 91 (9), S323-S324

• Characterizing heterogeneity in neuroimaging, cognition, clinical symptoms, and genetics among patients with late-life depression; J Wen, CHY Fu, D Tosun, Y Veturi, Z Yang, A Abdulkadir, E Mamourian, ...; JAMA psychiatry 79 (5), 464-474

• Two schizophrenia imaging signatures and their associations with cognition, psychopathology, and genetics in the general population; GB Chand, P Singhal, DB Dwyer, J Wen, G Erus, J Doshi, D Srinivasan, ...; medRxiv, 2022.01. 07.22268854

• CeNGEN Integrated mRNA data and bulk noncoding RNA lookup table; A Barrett, E Varol, A Weinreb, SR Taylor, R McWhirter, C Cros, ...

• Multi-scale semi-supervised clustering of brain images: deriving disease subtypes; J Wen, E Varol, A Sotiras, Z Yang, GB Chand, G Erus, H Shou, ...; Medical Image Analysis 75, 102304

2021

• Three-dimensional spike localization and improved motion correction for Neuropixels recordings; J Boussard, E Varol, HD Lee, N Dethe, L Paninski; Advances in Neural Information Processing Systems 34

• Non-parametric vignetting correction for sparse spatial transcriptomics images; BY Rao, AM Peterson, EK Kandror, S Herrlinger, A Losonczy, L Paninski, ...; International Conference on Medical Image Computing and Computer-Assisted …

• Visualizing the organization and differentiation of the male-specific nervous system of C. elegans; T Tekieli, E Yemini, A Nejatbakhsh, C Wang, E Varol, RW Fernandez, ...; Development 148 (18), dev199687

• Molecular topography of an entire nervous system; SR Taylor, G Santpere, A Weinreb, A Barrett, MB Reilly, C Xu, E Varol, ...; Cell

• The Prop1-like homeobox gene unc-42 specifies the identity of synaptically connected neurons; EG Berghoff, L Glenwinkel, A Bhattacharya, HS Sun, E Varol, ...; Elife 10, e64903

• Decentralized Motion Inference and Registration of Neuropixel Data; E Varol, J Boussard, N Dethe, O Winter, A Urai, TIB Laboratory, ...; ICASSP 2021-2021 IEEE International Conference on Acoustics, Speech and …

• Three Distinct Neuroanatomical Subtypes of Autism Spectrum Disorder, Revealed via Machine Learning, and Their Similarities With Schizophrenia Subtypes; G Hwang, ES Brodkin, GB Chand, DB Dwyer, J Wen, G Erus, J Doshi, ...; Biological Psychiatry 89 (9), S374-S375

• Neurocognitive and functional heterogeneity in depressed youth; EB Baller, AN Kaczkurkin, A Sotiras, A Adebimpe, DS Bassett, ME Calkins, ...; Neuropsychopharmacology 46 (4), 783-790

• NeuroPAL Microfluidic Chip Images, GCaMP, and dNMF Neuronal Activity; E Yemini, O Hobert, A Nejatbakhsh, E Varol, L Paninski, ...; (No Title)

• Interaction of the Joining Region in Junctophilin-2 With the L-Type Ca2+ Channel Is Pivotal for Cardiac Dyad Assembly and Intracellular Ca2+ Dynamics; P Gross, J Johnson, CM Romero, DM Eaton, C Poulet, J Sanchez-Alonso, ...; Circulation research 128 (1), 92-114

• NeuroPAL: a multicolor atlas for Whole-Brain neuronal identification in C. elegans; E Yemini, A Lin, A Nejatbakhsh, E Varol, R Sun, GE Mena, ADT Samuel, ...; Cell 184 (1), 272-288. e11

• Neuron matching in C. elegans with robust approximate linear regression without correspondence; A Nejatbakhsh, E Varol; Proceedings of the IEEE/CVF Winter Conference on Applications of Computer …

2020

• Statistical Atlas of C. elegans Neurons; E Varol, A Nejatbakhsh, R Sun, G Mena, E Yemini, O Hobert, L Paninski; International Conference on Medical Image Computing and Computer-Assisted …

• Demixing Calcium Imaging Data in C. elegans via Deformable Non-negative Matrix Factorization; A Nejatbakhsh, E Varol, E Yemini, V Venkatachalam, A Lin, ADT Samuel, ...; International Conference on Medical Image Computing and Computer-Assisted …

• Probabilistic Joint Segmentation and Labeling of C. elegans Neurons; A Nejatbakhsh, E Varol, E Yemini, O Hobert, L Paninski; International conference on medical image computing and computer-assisted …

• MAGIC: Multi-scale heterogeneity analysis and clustering for brain diseases; J Wen, E Varol, G Chand, A Sotiras, C Davatzikos; International Conference on Medical Image Computing and Computer-Assisted …

• Unique homeobox codes delineate all the neuron classes of C. elegans; MB Reilly, C Cros, E Varol, E Yemini, O Hobert; Nature 584 (7822), 595-601

• Extracting neural signals from semi-immobilized animals with deformable non-negative matrix factorization; A Nejatbakhsh, E Varol, E Yemini, V Venkatachalam, A Lin, ADT Samuel, ...; bioRxiv, 2020.07. 07.192120

• Sinkhorn em: an expectation-maximization algorithm based on entropic optimal transport; G Mena, A Nejatbakhsh, E Varol, J Niles-Weed; arXiv preprint arXiv:2006.16548

• NeuroPAL Data; E Yemini, A Lin, A Nejatbakhsh, E Varol, R Sun, G Mena, A Samuel, ...; (No Title)

• Neurostructural Heterogeneity in Youth With Internalizing Symptoms; A Kaczkurkin, A Sotiras, E Baller, R Barzilay, ME Calkins, G Chand, Z Cui, ...; Biological Psychiatry 87 (9), S28

• Two Neuroanatomical Subtypes of Schizophrenia Defined by Multi-Site Machine Learning; D Wolf, G Chand, D Dwyer, G Erus, A Sotiras, E Varol, D Srinivasan, ...; Biological Psychiatry 87 (9), S28-S29

• Neuroanatomical Dimensional Phenotypes of Schizophrenia: Expression in Youth With Psychosis-Spectrum Symptoms and Correlation With Cognition; G Chand, DH Wolf, G Erus, D Srinivasan, DB Dwyer, R Pomponio, ...; Biological Psychiatry 87 (9), S119

• Two distinct neuroanatomical subtypes of schizophrenia revealed using machine learning; GB Chand, DB Dwyer, G Erus, A Sotiras, E Varol, D Srinivasan, J Doshi, ...; Brain 143 (3), 1027-1038

• Neurostructural heterogeneity in youths with internalizing symptoms; AN Kaczkurkin, A Sotiras, EB Baller, R Barzilay, ME Calkins, GB Chand, ...; Biological psychiatry 87 (5), 473-482

• A multidimensional neural maturation index reveals reproducible developmental patterns in children and adolescents; M Truelove-Hill, G Erus, V Bashyam, E Varol, C Sako, RC Gur, RE Gur, ...; Journal of Neuroscience 40 (6), 1265-1275

• Sinkhorn permutation variational marginal inference; G Mena, E Varol, A Nejatbakhsh, E Yemini, L Paninski; Symposium on advances in approximate Bayesian inference, 1-9

• NeuroPAL: a neuronal polychromatic atlas of landmarks for whole-brain imaging in C. elegans; E Yemini, A Lin, A Nejatbakhsh, E Varol, R Sun, GE Mena, ADT Samuel, ...; BioRxiv, 676312

2019

• Temporal Wasserstein non-negative matrix factorization for non-rigid motion segmentation and spatiotemporal deconvolution; E Varol, A Nejatbakhsh, C McGrory; arXiv preprint arXiv:1912.03463

• Neurocognitive and functional heterogeneity in depressed youth; EB Baller, AN Kaczkurkin, A Sotiras, A Adebimpe, DS Bassett, ME Calkins, ...; bioRxiv, 778878

• T195. Neuroanatomical heterogeneity of schizophrenia quantified via semi-supervised machine learning reveals two distinct subtypes: Results from the PHENOM consortium; GB Chand, DB Dwyer, G Erus, A Sotiras, E Varol, D Srinivasan, RC Gur, ...; Biological Psychiatry 85 (10), S205-S206

• Expression profiling of the mature C. elegans Nervous system by single-Cell RNA-sequencing. bioRxiv: 737577; SR Taylor, G Santpere, M Reilly, L Glenwinkel, A Poff, R McWhirter, C Xu, ...; Publisher: Cold Spring Harbor Laboratory Section: New Results

2018

• Semi-Supervised Machine Learning Reveals 3 Patterns of Cognitive Function in Depressed Youth; E Baller, A Kaczkurkin, A Sotiras, E Varol, T Moore, C Xia, M Calkins, ...; NEUROPSYCHOPHARMACOLOGY 43, S443-S444

• Generative discriminative models for multivariate inference and statistical mapping in medical imaging; E Varol, A Sotiras, K Zeng, C Davatzikos; International Conference on Medical Image Computing and Computer-Assisted …

• MIDAS: Regionally linear multivariate discriminative statistical mapping; E Varol, A Sotiras, C Davatzikos; NeuroImage 174, 111-126

• Regionally discriminative multivariate statistical mapping; E Varol, A Sotiras, C Davatzikos; 2018 IEEE 15th International Symposium on Biomedical Imaging (ISBI 2018 …

• Advancing Statistical Inference For Population Studies In Neuroimaging Using Machine Learning; E Varol; University of Pennsylvania

2017

• Heterogeneity of neuroanatomical patterns in prodromal Alzheimer’s disease: links to cognition, progression and biomarkers; A Dong, JB Toledo, N Honnorat, J Doshi, E Varol, A Sotiras, D Wolk, ...; Brain 140 (3), 735-747

• HYDRA: Revealing heterogeneity of imaging and genetic patterns through a multiple max-margin discriminative analysis framework; E Varol, A Sotiras, C Davatzikos, ADN Initiative; Neuroimage 145, 346-364

2016 & Older

• Structured outlier detection in neuroimaging studies with minimal convex polytopes; E Varol, A Sotiras, C Davatzikos; International Conference on Medical Image Computing and Computer-Assisted …

• Automated Characterization and Quantification of Cardiomyocyte Proliferation and Apoptosis in Post Myocardial Infarction Tissue Images; P Gross, N Honnorat, E Varol, M Wallner, D Trappanese, T Sharp, ...; Circulation Research 119 (suppl_1), A28-A28

• Crowdsourced estimation of cognitive decline and resilience in Alzheimer's disease; GI Allen, N Amoroso, C Anghel, V Balagurusamy, CJ Bare, D Beaton, ...; Alzheimer's & Dementia 12 (6), 645-653

• Nuquantus: Machine learning software for the characterization and quantification of cell nuclei in complex immunofluorescent tissue images; P Gross, N Honnorat, E Varol, M Wallner, DM Trappanese, TE Sharp, ...; Scientific reports 6 (1), 23431

• Heterogeneity of neuroanatomical patterns in prodromal Alzheimer’s disease: links to cognition, progression and biomarkers. ; A Dong, JB Toledo, N Honnorat, J Doshi, E Varol, A Sotiras, D Wolk, ...

• Machine learning as a means toward precision diagnostics and prognostics; A Sotiras, B Gaonkar, H Eavani, N Honnorat, E Varol, A Dong, ...; Machine learning and medical imaging, 299-334

• Disentangling disease heterogeneity with max-margin multiple hyperplane classifier; E Varol, A Sotiras, C Davatzikos; International Conference on Medical Image Computing and Computer-Assisted …

• Supervised block sparse dictionary learning for simultaneous clustering and classification in computational anatomy; E Varol, C Davatzikos; International Conference on Medical Image Computing and Computer-Assisted …

• Classifying medical images using morphological appearance manifolds; E Varol, B Gaonkar, C Davatzikos; 2013 IEEE 10th International Symposium on Biomedical Imaging, 744-747

• Feature ranking based nested support vector machine ensemble for medical image classification; E Varol, B Gaonkar, G Erus, R Schultz, C Davatzikos; 2012 9th IEEE international symposium on biomedical imaging (ISBI), 146-149

• Neuroanatomical Pattern Classification in Unmedicated First-Episode Psychosis: Influence of Different Imaging Feature Selection; MH Serpa, MV Zanetti, E Varol, TM Chaim, B Gaonkar, J Doshi, MT BILT, ...; ELSEVIER SCIENCE INC

• High-Dimensional Pattern Classification of Brain Morphometric and DTI Data of Adult ADHD; TM Chaim, MA Silva, E Varol, J Doshi, MV Zanetti, B Gaonkar, M Serpa, ...; ELSEVIER SCIENCE INC