Papers

Digital Phenotyping: Methods and Applications

Idiographic prediction of suicidal thoughts: Building personalized machine learning models with real-time monitoring data by SB Wang, RDI Van Genugten, Y Yacoby, W Pan, KH Bentley, SA Bird, RJ Buonopane, A Christie, M Daniel, A Haim, L Follet, RG Fortgang, F Kelly-Brunyak, EM Kleiman, AJ Millner, O Obi-Obasi, JP Onnela, N Ramlal, JR Ricard, JW Smoller, T Tambedou, KL Zuromski, and MK Nock. Nature Mental Health (2024).
Journal

Smartphone screen time characteristics in people with suicidal thoughts: Retrospective observational data analysis study by M Karas, D Huang, Z Clement, A Millner, E Kleiman, K Bentley, K Zuromski, R Fortgang, D DeMarco, A Haim, A Donovan, R Buonopane, S Bird, J Smoller, M Nock, and JP Onnela. JMIR Mhealth Uhealth 12:e57439 (2024).
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Measuring environmental and behavioral drivers of chronic diseases using smartphone-based digital phenotyping: Intensive longitudinal observational mHealth substudy embedded in 2 prospective cohorts of adults by L Yi, J Hart, M Straczkiewicz, M Karas, G Wilt, C Hu, R Librett, F Laden, J Chavarro, JP Onnela , and P James. JMIR Public Health Surveillance 10:e55170 (2024).
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Data missingness in digital phenotyping: implications for clinical inference and decision-baking by J Shen, K Abdelkader, Z Isaac, D Sarno, J Kurz, D Silbersweig, JP Onnela, and D Barron. Submitted (2024).
medRxiv

Vaping habits and respiratory symptoms using a smartphone app platform by MSS Lee, KD Eum, JG Allen, JP Onnela, and DC Christiani. BMC Public Health 24, 2047 (2024).
Journal

Year-long digital phenotyping and natural language processing of daily voice diaries reveal affective and behavioral signatures of real-world life stress by CM Vidal Bustamante, G Coombs, H Rahimi-Eichi, P Mair, JP Onnela, JT Baker, and R Buckner. Submitted (2024).
Preprint

Smartphone-based markers of social connectivity in schizophrenia and bipolar disorder by L Valeri, X Cai, H Rahimi-Eichi, E Liebenthal, S Rauch, D Ongur, R Schutt, L Dixon, JP Onnela^*, and J Baker^*. NPP-Digital Psychiatry and Neuroscience 2, 12 (2024). (^*joint senior authors)
arXiv | Journal

Heterogeneity in suicide risk: Evidence from personalized dynamic models by DDL Coppersmith, EM Kleiman, AJ Millner, SB Wang, C Arizmendi, KH Bentley, D DeMarco, RG Fortgang, KL Zuromski, JS Maimone , A Haim, JP Onnela, SA Bird, JW Smoller, P Mair, and MK Nock. Behaviour Research and Therapy 180:e104574 (2024).
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Irregular cycles, ovulatory disorders, and cardiometabolic conditions in a US-based digital cohort by Z Wang, AMZ Jukic, DD Baird, AJ Wilcox, H Li, CL Curry, T Fischer-Colbrie, JP Onnela, MA Williams, R Hauser, BA Coull, and S Mahalingaiah.  JAMA Network Open 7(5):e249657 (2024).
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Precision assessment of real-world associations between stress and sleep duration using actigraphy data collected continuously for an academic year: individual-level modeling study by C Vidal Bustamante, G Coombs III, H Rahimi-Eichi, P Mair, JP Onnela, J Baker, and R Buckner. JMIR Formative Research, 8:e53441 (2024).
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Assessing mobility in patients with glioblastoma using digital phenotyping – Piloting the digital assessment in neuro-oncology by NLA Nawabi^*, P Emedom-Nnamdi^*, JL Kilgallon, JVE Gerstl, DJ Cote, R Jha, JG Ellen, KM Maniar, C Hong, HY Dawood, JP Onnela^**, and TR Smith^**. Neurosurgery. In print (2024). (^*joint first authors; ^**joint senior authors)

Deep learning framework with uncertainty quantification for survey data: Assessing and predicting diabetes mellitus risk in the American population by M Matabuena, JC Vidal, R Ghosal, and JP Onnela. Submitted (2024).
arXiv

Tracking ALS disease progression using passively collected smartphone sensor data by M Karas^*, J Olsen^*, M Straczkiewicz, S Johnson, K Burke, S Iwasaki, A Lahav, ZA Scheier, A Clark, A Iyer, E Huang, J Berry, and JP Onnela. Annals of Clinical and Translational Neurology. In print (2024). (^*joint first authors)
Journal

Testing unit root non-stationarity in the presence of missing data in univariate time series of mobile health studies by C Fowler, X Cai, JT Baker, JP Onnela, and L Valeri. Journal of the Royal Statistical Society Series C: Applied Statistics, qlae010 (2024).
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Menarche and time to cycle regularity among females born between 1950-2005 in the US by Z Wang^*, G Asokan^*, JP Onnela, DD Baird, AMZ Jukic, AJ Wilcox, CL Curry, T Fischer-Colbrie, MA Williams, R Hauser, BA Coull, and S Mahalingaiah. JAMA Network Open. In print (2024).

Upper limb movements as digital biomarkers in people with ALS by M Straczkiewicz, M Karas, SA Johnson, KM Burke, Z Scheier, TB Royse, N Calcagno, A Clark, A Iyer, JD Berry, and JP Onnela. eBioMedicine 105036, 101 (2024).
Journal

kNN algorithm for conditional mean and variance estimation with automated uncertainty quantification and variable selection by M Matabuena, JC Vidal, OH Madrid Padilla, and JP Onnela. Submitted (2024).
arXiv

Pain intervention and digital research: An operational report on combining digital research and outpatient chronic disease management by M Fu, J Shen, C Gu, E Oliveira, E Shinchuk, H Isaac, Z Isaac, DL Sarno, JL Kurz, DA Silbersweig, JP Onnela, and DS Barron. Frontiers in Pain Research 5:1327859 (2024).
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Selective acoustic feature enhancement for speech emotion recognition with noisy speech by SG Leem, D Fulford, JP Onnela, D Gard, and C Busso. IEEE/ACM Transactions on Audio, Speech, and Language Processing 32, 917 (2024).
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Validation of an open-source step counting algorithm for smartphone data collected in clinical and non-clinical settings by M Straczkiewicz, NL Keating, E Thompson, UA Matulonis, SM Campos, AA Wright^*, and JP Onnela (^*joint senior authors). JMIR Cancer 2, e47646 (2023).
Journal

Nonparametric additive value functions: Interpretable reinforcement learning with an application to surgical recovery by P Emedom-Nnamdi, TR Smith, JP Onnela, and J Lu. Submitted (2023).
arXiv

Intensive longitudinal assessment of mobility, social activity and loneliness in individuals with severe mental illness during COVID-19 by L Valeri, H Rahimi-Eichi, E Liebenthal, SL Rauch, R Schutt, D Ongur, L Dixon, JP Onnela^*, and J Baker^*. Schizophrenia 9, 62 (2023). (^*joint senior authors)
Journal

Digitally connected diagnostics data in the future of public health by D Mugahid, T Hoffmann, J Olejarz, R Molinaro, C Cooper, R Atun, Y Grad, S Fortune, R Sampath, and JP Onnela.  GEN Biotechnology 2 (3), 181 (2023).
Journal

Menstrual cycle length variation by demographic characteristics from the Apple Women’s Health Study by S Mahalingaiah, H Li, E Gibson, AM Jukic, D Baird, A Wilcox, C Curry, T Fischer-Colbrie, JP Onnela, M Williams, R Hauser, and Brent Coull. npj Digital Medicine 6, 100 (2023).
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Returning individual research results from digital phenotyping in psychiatry by FX Shen, ML Baum, N Martinez-Martin, AS Miner, M Abraham, CA Brownstein, N Cortez, BJ Evans, LT Germine, DC Glahn, C Grady, IA Holm, EA Hurley, S Kimble, G Lázaro-Muñoz, K Leary, M Marks, PJ Monette, JP Onnela, PP O’Rourke, SL Rauch, C Shachar, S Sen, I Vahia, JL Vassy, JT Baker, BE Bierer, and BC Silverman. The American Journal of Bioethics, 0:1 (2023).
Journal

Validation of an open-source smartphone step counting algorithm in clinical and non-clinical settings by M Straczkiewicz, NL Keating, E Thompson, UA Matulonis, SM Campos, AA Wright, and JP Onnela. Submitted (2023).
medRxiv

Wearable device and smartphone data quantify ALS progression and may provide novel outcome measures by S Johnson^*, M Karas^*, K Burke, M Straczkiewicz, Z Scheier, A Clark, S Iwasaki, A Lahav, A Iyer, JP Onnela, and J Berry. npj Digital Medicine 6, 34 (2023). (^*joint first authors)
Journal

Scalable Gaussian Process inference with Stan by T Hoffmann and JP Onnela.
arXiv

A “one-size-fits-most” walking recognition method for smartphones, smartwatches, and wearable accelerometers by M Straczkiewicz, E Huang, and JP Onnela. npj Digital Medicine 6, 29 (2023).
arXiv | Journal

Machine learning and the digital measurement of psychological health by IR Galatzer-Levy and JP Onnela. Annual Review of Clinical Psychology 19, 133 (2023).
Journal

Abnormal uterine bleeding patterns determined through menstrual tracking among participants in the Apple Women’s Health Study by Zhang CY, Li H, Zhang S, Suharwardy S, Chaturvedi U, Fischer-Colbrie T, Maratta LA, Onnela JP, Coull BA, Hauser R, Williams MA, Baird DD, Jukic AMC, SMahalingaiah S, and Curry CL.  American Journal of Obstetrics and Gynecology. In print (2022).
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Combining digital pill and smartphone data to quantify medication adherence in an observational psychiatric pilot study by M Straczkiewicz, H Wisniewski, KW Carlson, Z Heidary, J Knights, M Keshavan, JP Onnela^*, and J Torous^*. Psychiatry Research 315, 114707 (2022). (^*joint senior authors)
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Attempts to conceive and the COVID-19 pandemic: data from the Apple Women’s Health Study by V Fruh, G Lyons, AL Scalise, NJ Gallagher, AM Jukic, DD Baird, U Chaturvedi, S Suharwardy, JP Onnela, MA Williams, R Hauser, BA Coull, and S Mahalingaiah. American Journal of Obstetrics and Gynecology 227 (3), 484.e1 (2022).
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Combining accelerometer and gyroscope data in smartphone-based activity recognition using movelets by E Huang, K Yan, and JP Onnela. Sensors 22 (7), 2618 (2022).
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Using smartphones to reduce research burden in a neurodegenerative population and assessing participant adherence: A randomized clinical trial and two observational studies by AL Beukenhorst, KM Burke, Z Scheier, TM Miller, S Paganoni, M Keegan, E Collins, KP Connaghan, A Tay, J Chan, JD Berry, and JP Onnela.  JMIR Mhealth Uhealth 10 (2), e31877 (2022).
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Mentalizing imagery therapy to augment skills training for dementia caregivers: Protocol for a randomized, controlled trial of a mobile application and digital phenotyping by FA Jain, O Okereke, L Gitlin, P Pedrelli, JP Onnela, M Nyer, LA Ramirez Gomez, M Pittman, A Sikder, DJ Ursal, and D Mischoulon. Contemporary Clinical Trials, 106737 (2022).
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Online anomaly detection for smartphone-based multivariate behavioral time series data by G Liu and JP Onnela. Sensors 22 (6), 2110 (2022).
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Fluctuations in behavior and affect in college students measured using deep phenotyping by CMV Bustamante, G Coombs 3^rd, H Rahimi-Eichi, P Mair, JP Onnela, JT Baker, and RL Buckner. Scientific Reports 12, 1932 (2022).
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Design and methods of the Apple Women’s Health Study: a digital longitudinal cohort study by S Mahalingaiah, V Fruh, E Rodriguez, SC Konanki, JP Onnela, A de Figueiredo Veiga, G Lyons, R Ahmed, H Li, N Gallagher, AMZ Jukic, KK. Ferguson, DD Baird, AJ Wilcox, CL Curry, S Suharwardy, T Fischer-Colbrie, G Agrawal, BA Coull, R Hauser, and MA Williams.  American Journal of Obstetrics and Gynecology (2021).
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Beiwe: A data collection platform for high-throughput digital phenotyping by JP Onnela, C Dixon, K Griffin, T Jaenicke, L Minowada, S Esterkin, A Siu, J Zagorsky, and E Jones. Journal of Open Source Software, 6(68), 3417 (2021).
Journal

A systematic review of smartphone-based human activity recognition methods for health research by M Straczkiewicz, P James, and JP Onnela. npj Digital Medicine 4, 148 (2021).
Journal | arXiv

Perceptions of mobile health technology in elective surgery: A qualitative study of North American surgeons by N Panda, R Sinyard, J Margo, N Henrich, CE Cauley, JP Onnela, AB Haynes, and M Brindle. Annals of Surgery. In press, 2021.

Decision models and technology can help psychiatry develop biomarkers by D Barron, J Baker, KS Budde, D Bzdok, SB Eickhoff, K Friston, PT Fox, P Geha, S Heisig, A Holmes, JP Onnela, A Powers, D Silbersweig, and JH Krystal. Frontiers in Psychiatry 12, 1481 (2021).
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Sociodemographic characteristics of missing data in digital phenotyping by Kiang MV, Chen JT, Krieger N, Buckee CO, Alexander MJ, Baker JT, Buckner RL, Coombs G, Rich-Edwards JW, Carlson KW, and JP Onnela. Scientific Reports 11, 15408 (2021).
Journal

Feasibility and performance of smartphone-based daily micro-surveys among patients recovering from cancer surgery by L van den Berg, P Brouwer, N Panda, MM Hoogbergen, I Solsky, JP Onnela, AB Haynes, and CJ Sidey-Gibbons CJ. Quality of Life Research 31, 579 (2022).
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Bidirectional imputation of spatial GPS trajectories with missingness using sparse online Gaussian Process by G Liu and JP Onnela. Journal of the American Medical Informatics Association 28(8), 1777 (2021).
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Expected versus experienced health-related quality of life among patients recovering from cancer surgery: a prospective cohort study by N Panda, I Solsky, B Neal, B Hawrusik, S Lipsitz, CC Lubitz, RD Sinyard, JP Onnela, CE Cauley, AB Haynes. Annals of Surgery Open 2(2), e060, 2021.

Smartphone GPS signatures of patients undergoing spine surgery correlate with mobility and current gold standard outcome measures by A Boaro, J Leung, HT Reeder, F Siddi, E Mezzalira, G Liu, RA Mekary, Y Lu, M Groff, JP Onnela^*, and TR Smith^*. Journal of Neurosurgery: Spine, 2021. (^*joint senior authors)
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Estimating longitudinal depressive symptoms from smartphone data in a transdiagnostic cohort by AM Pellegrini^*, EJ Huang^*, PC Staples, KL Hart, JM Lorme, HE Brown, RH Perlis^**, and JP Onnela^**. Brain and Behavior, e02077, 2021. (^*joint first authors, ^**joint senior authors)
Journal

Open-source longitudinal sleep analysis from accelerometer data (DPSleep): Algorithm development and validation by HR Eichi, G Coombs III, CMV Bustamante, JP Onnela, JT Baker, and RL Buckner. JMIR Mhealth Uhealth 9(10):e29849, 2021.
Journal | medRxiv

Increase in suicidal thinking during COVID-19 by R Fortgang, SB Wang, AJ Millner, A Reid-Russell, A Beukenhorst, EM Kleiman, KH Bentley, KL Zuromski, M Al-Suwaidi, SA Bird, R Buonopane, D Demarco, A Haim, VW Joyce, E Kastman, E Kilbury, H-I Lee, P Mair, CC Nash, JP Onnela, JW Smoller, and MK Nock. Clinical Psychological Science 2167702621993857, 2021.

Smartphone data during the COVID‐19 pandemic can quantify behavioral changes in people with ALS by AL Beukenhorst, E Collins,KM Burke, SM Rahman, M Clapp, SC Konanki, S Paganoni, TM Miller, J Chan, JP Onnela^**, and JD Berry^**. Muscle & Nerve 63(2), 258, 2021. (^** shared senior authors)
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Digital phenotyping to quantify psychosocial well-being trajectories after spinal cord injury by HW Mercier, JW Hamner, J Torous, JP Onnela, and JA Taylor. Am J Phys Med Rehabil. 99(12), 1138, 2020.
Journal

Can mHealth interventions improve quality of life of cancer patients? A systematic review and meta-analysis by I Buneviciene, RA Mekary, TR Smith, JP Onnela, A Bunevicius. Critical Reviews in Oncology/Hematology 103123, 2020.

Smartphone sensing of social interactions in people with and without schizophrenia by D Fulford, J Mote, R Gonzalez, S Abplanalp, Y Zhang, J Luckenbaugh, JP Onnela, C Busso, and D Gard. Journal of Psychiatric Research, 2020.

Consensus statement on ethical & safety practices for conducting digital monitoring studies with people at risk of suicide and related behaviors by MK Nock, E Kleiman, M Abraham, K Bentley, DA Brent, RJ Buonopane, F Castro-Ramirez, CB Cha, W Dempsey, J Draper, CR Glenn, MR Hollander, J Harkavy-Friedman, J Huffman, HUS Lee, A Millner, D Mou, JP Onnela, R Picard, HM Quay, O Rankin, S Sewards, J Torous, J Wheelis, U Whiteside, G Siegel, A Ordóñez, and J Pearson. Psychiatric Research and Clinical Practice (2020).
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Smartphone-based assessment of preoperative decision conflict and postoperative physical activity among patients undergoing cancer surgery: a prospective cohort study by N Panda^*, I Solsky^*, CE Cauley, S Lipsitz, EV Desai, EJ Huang, EM Benjamin, CC Lubitz, JP Onnela^**, and AB Haynes^**. Annals of Surgery, 2020. (^** shared senior authors)

Smartphone Global Positioning System (GPS) data enhances recovery assessment after breast cancer surgery by N Panda^*, I Solsky^*, B Hawrusik, G Liu, H Reeder, S Lipsitz, EV Desai, KW Lowery, K Miller, MA Gadd, CC Lubitz, BL Smith, M Specht, JP Onnela^**, and AB Haynes^**. Annals of Surgical Oncology, 2020. (^** shared senior authors)
Journal

Determining sample size and length of follow-up for smartphone-based digital phenotyping studies by I Barnett, J Torous, HT Reeder, J Baker, and JP Onnela. Journal of the American Medical Informatics Association 27(12), 1844, 2020.
Journal | Calculator

Opportunities and challenges in the collection and analysis of digital phenotyping data by JP Onnela. Neuropsychopharmacology, 46(1), 45, 2021.
Journal | Working paper

Augmented movelet method for activity classification using smartphone gyroscope and accelerometer data by  E Huang and JP Onnela. Sensors 20(13), 3706, 2020.
Journal | Arxiv | Data

Smartphone-based tracking of sleep in depression, anxiety, and psychotic disorders by T Aledavood, J Torous, AM Triana Hoyos, JA Naslund, JP Onnela, M Keshavan. Current Psychiatry Reports Jun 4;21(7):49, 2019.
Journal

Utilizing smartphones to capture novel recovery metrics after cancer surgery by N Panda_*, I Solsky_*, E Huang, C Lipsitz, J Pradarelli, D Delisle, J Cusack, M Gadd, C Lubitz, J Mullen, M Qadan, B Smith, M Specht, A Stephen, K Tanabe, A Gawande, JP Onnela^*, A Haynes^*. JAMA Surgery, 2019. (^*shared senior authors)
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The AURORA Study: a longitudinal, multimodal library of brain biology and function after traumatic stress exposure by S McLean et al. Molecular Psychiatry 25(2), 283, 2019.
Journal

Harnessing digital technology to predict, diagnose, monitor, and develop treatments for brain disorders  by C Stroud, JP Onnela^* and H Manji^*. npj Digital Medicine 2:44, 2019. (^*shared senior authors)
Journal

Assessing the potential of longitudinal smartphone-based cognitive assessment in schizophrenia: A naturalistic pilot study by G Liu, P Henson, M Keshavan, JP Onnela and J Torous. Schizophrenia Research: Cognition, 17:100144, 2019.
Journal

Design and results of a smartphone‐based digital phenotyping study to quantify ALS progression by J Berry, S Paganoni, K Carlson, K Burke, H Weber, P Staples, J Salinas, J Chan, J Green, K Connaghan, J Barback and JP Onnela. Annals of Clinical and Translational Neurology, 6(5):873, 2019.
Journal

Digital phenotyping in patients with spine disease: A novel approach to quantifying mobility and quality of life by J Cote, I Barnett I, JP Onnela, T Smith. World Neurosurgery 126, e241, 2019.
Journal

Inferring mobility measures from GPS with missing data by I Barnett and JP Onnela. Biostatistics 21:2, e98, 2020.
arXiv | Journal

Digital phenotyping for the busy psychiatrist: Clinical implications and relevance by J Torous, A Gershon, R Hays, JP Onnela and J Baker. Psychiatric Annals, 2019.
Journal.

Beyond smartphones and sensors: choosing appropriate statistical methods for the analysis of longitudinal data by I Barnett, J Torous, P Staples, M Keshavan M and JP Onnela.  Journal of the American Medical Informatics Association, 25:12, 2018.
Journal

A crossroad for validating digital tools in schizophrenia and mental health by J Torous, P Staples, I Barnett, JP Onnela and M Keshavan. npj Schizophrenia 4(1), 6, 2018.
Journal

Characterizing the clinical relevance of digital phenotyping data quality with applications to a cohort with schizophrenia by P Staples, J Torous, I Barnett, L Sandoval, M Keshavan and JP Onnela. npj Digital Medicine 1, 15, 2018.
Journal

The HOPE pilot study: Harnessing patient-reported outcomes and biometric data to enhance cancer care by A Wright, N Raman, P Staples, S Schonholz, A Cronin, K Carlson, NL Keating and JP Onnela. JCO Clinical Cancer Informatics 2, 1, 2018.
Journal

Relapse prediction in schizophrenia through digital phenotyping: A pilot study by I Barnett, J Torous, P Staples, L Sandoval, M Keshavan and JP Onnela. Neuropsychopharmacology 43(8), 1660, 2018.
Working Paper  | Journal | Beiwe configuration file | Code

Smartphone applications for monitoring mood disorders: A systematic review by F Or, J Torous and JP Onnela. Submitted, 2017.
Working Paper

High potential but limited evidence: Using voice data from smartphones to monitor and diagnose mood disorders by F Or, J Torous and JP Onnela. Psychiatric Rehabilitation Journal, 2017.
Working Paper | Journal

A comparison of passive and active estimates of sleep in a cohort with schizophrenia by P Staples, J Torous, I Barnett, K Carlson, L Sandoval, M Keshavan and JP Onnela. NPJ Schizophrenia 3 (1), 37, 2017.
Journal | PubMed | Beiwe configuration file

Methodology and reporting of mobile heath and smartphone application studies for schizophrenia by J Torous, J Firth, N Muller, JP Onnela and J Baker. Harvard review of psychiatry, 25(3), 146, 2017.
Journal | PubMed

New dimensions and new tools to realize the potential of RDoC: digital phenotyping via smartphones and connected devices by J Torous, JP Onnela, and M Keshavan. Translational Psychiatry. 7, e1053, 2017.
Journal | PubMed

Harnessing smartphone-based digital phenotyping to enhance behavioral and mental health by JP Onnela and SL Rauch. Neuropsychopharmacology 41, 1691, 2016.
Journal | PubMed

New tools for new research in psychiatry: A scalable and customizable platform to empower data driven smartphone research by J Torous, MV Kiang, J Lorme, and JP Onnela. JMIR Mental Health 3(2):e16, 2016.
Journal | Figure 3 (Multimedia)

Realizing the potential of mobile mental health: new methods for new data in psychiatry by J Torous, P Staples, and JP Onnela. Current Psychiatry Reports 17:61, 2015.
Journal | PubMed

Utilizing a personal smartphone custom app to assess the Patient Health Questionnaire-9 (PHQ-9) depressive symptoms in patients with major depressive disorder by J Torous, P Staples, M Shanahan, C Lin, P Peck, M Keshavan, and JP Onnela. JMIR Mental Health 2(1), e8, 2015.
Journal | PubMed

Network Science: Methods and Applications

Connecting mass-action models and network models for infectious diseases by TM Lee and JP Onnela. Submitted (2024).
arXiv

Temporal configuration model: Statistical inference and spreading processes by TM Le, H Hambridge, and JP Onnela. Submitted (2024).
arXiv

Approximate inference for longitudinal mechanistic HIV contact networks by O Smiley, T Hoffmann^*, and JP Onnela^*. Applied Network Science 9, 12 (2024). (^*joint senior authors)
Journal | arXiv

Insurance-based disparities in stroke center access in California: a network science approach by KS Zachrison, RY Hsia, LH Schwamm, Z Yan, ME Samuels-Kalow, MJ Reeves, CA Camargo, and JP Onnela. Circulation: Cardiovascular Quality and Outcomes, e009868 (2023).
Journal

Framework for converting mechanistic network models to probabilistic models by R Goyal, V DeGruttola, and JP Onnela. Journal of Complex Networks 11 (5) cnad034, (2023).
Journal

Maximum likelihood estimation for reversible mechanistic network models by J Larson and JP Onnela. Physical Review E 108, 024308 (2023).
Journal | arXiv

Digitally connected diagnostics data in the future of public health by D Mugahid, T Hoffmann, J Olejarz, R Molinaro, C Cooper, R Atun, Y Grad, S Fortune, R Sampath, and JP Onnela.  GEN Biotechnology 2 (3), 181 (2023).
Journal

Leveraging contact network information in clustered randomized trials of infectious processes by MH Wan^*, P Staples^*, M Prague, V DeGruttola, and JP Onnela. Observational Studies 9 (2), 157 (2023).
Journal

Cost-based feature selection for network model choice by L Raynal^*, T Hoffmann^*, and JP  Onnela. (^*shared first authors.) Journal of Computational and Graphical Statistics 0, 1 (2023).
Journal | arXiv

Minimizing the expected posterior entropy yields optimal summary statistics by T Hoffmann and JP  Onnela.
arXiv

Ischemic stroke systems of care in California: evolution in the organization during the mechanical thrombectomy era by KS Zachrison, RY Hsia, S Li, MJ Reeves, CA Camargo, Z Yan, JP Onnela, and LH Schwamm. Stroke: Vascular and Interventional Neurology. In print, 2022.

Framework for assessing and easing global COVID-19 travel restrictions by TM Le, L Raynal, O Talbot, H Hambridge, C Drovandi, A Mira, K Mengersen, and JP Onnela. Scientific Reports 12, 6985, 2022.
Journal

Effect of a two-dose vs three-dose vaccine strategy in residential colleges using an empirical proximity network by HL Hambridge, R Kahn, and JP Onnela. International Journal of Infectious Diseases 119, 210, 2022.
Journal

Influence of hospital characteristics on hospital transfer destinations for patients with stroke by K Zachrison*, V Amati*, LH Schwamm, Z Yan, V Nielsen, A Christie, MJ Reeves, JP Sauser, A Lomi, and JP Onnela. Circulation: Cardiovascular Quality and Outcomes. In press, 2022.

Examining SARS-CoV-2 interventions in residential colleges using an empirical network by HL Hambridge, R Kahn, and JP Onnela. International Journal of Infectious Diseases 113, 325, 2021.
Journal | medRxiv

Inferring the minimum spanning tree from a sample network by J Larson and JP Onnela. Submitted, 2021.
arXiv

Edge overlap in weighted and directed social networks by H Mattie, JP Onnela. Network Science, 9(2), 179, 2021.
Journal

Scalable approximate Bayesian computation for growing network models via extrapolated and sampled summaries by L Raynal, S Chen, A Mira, JP Onnela. Bayesian Analysis 1(1), 2021.
Journal | arXiv

Assessment of racial disparities in primary care physician subspecialty referrals by BE Landon, JP Onnela, L Meneades, AJ O’Malley, NL Keating. JAMA Network Open 4(1):e2029238, 2020.

The impact of sampling patients on measuring physician patient-sharing networks using Medicare data by AJ O’Malley, JP Onnela, NL Keating, BE Landon. Health Services Research 56(2), 323, 2020.

Evaluating spillover of HIV knowledge from study participants to their network members in a stepped-wedge behavioral intervention in Tanzania by J Rewley, M Smith-Fawzi, SF Kaaya, S Haberlen, H Siril, N Li, K McAdam, D Ainebyona, M Somba, E McAdam, K Oljemark, J Todd, I Andrew, A Simwinga, N Mleli, S Makongwa, G Arthur, Y Liu, JP Onnela. BMJ Open 10:e033759, 2020.
Journal

Bayesian method for inferring the impact of geographical distance on intensity of communication by F Ozga, JP Onnela, V DeGruttola. Scientific Reports 10(1), 1, 2020.
arXiv

Flexible model of network embedding by J Fernandez-Gracia, JP Onnela. Scientific Reports 9, 11710, 2019.
arXiv| PubMed

Feature-based classification of networks by I Barnett, N Malek, M Kuijjer, P Mucha, JP Onnela. Network Science 7(3), 438, 2019.
Journal | arXiv

A network approach to stroke systems of care by K Zachrison, A Dhand, L Schwamm, JP Onnela. Circulation: Cardiovascular Quality and Outcomes 12, e005526, 2019.

Introduction to Social Network Analysis by AJ O’Malley, JP Onnela.  In: Levy A., Goring S., Gatsonis C., Sobolev B., van Ginneken E., Busse R. (eds) Health Services Evaluation. Health Services Research, 2019.
Journal

Influence of peer physicians on intensity of end-of-life care for cancer decedents by N Keating, AJ O’Malley, JP Onnela, S Gray, B Landon. Medical Care 7(6), 468, 2019.
Journal

Flexible model selection of mechanistic network models  by S Chen, A Mira,  JP Onnela. Journal of Complex Networks 8(2), cnz024, 2019.
Journal | aXiv

A bootstrap method for goodness of fit and model selection with a single observed network by S Chen, JP Onnela. Scientific Reports 9, 16674, 2019.
Journal | arXiv

Efficient vaccination strategies for epidemic control using network information by Y Yang, A McKhann, G Harling^*  and JP Onnela^*. Epidemics 27, 115, 2019. (^* shared senior authors)
arXiv| PubMed

Understanding tie strength in social networks using a local “bowtie” framework by H Mattie, K Engo-Monsen, R Ling, JP Onnela. Scientific Reports 8(1), 9349, 2018.
Journal | arXiv

Comparison of physician networks constructed from thresholded ties versus shared clinical episodes by JP Onnela, J O’Malley, N Keating, B Landon. Network Science 3(1), 28, 2018.
Journal

Connected but segregated: social networks in rural villages by F Montes, RC Jimenez, JP Onnela. Journal of Complex Networks, 6(5), 693, 2018.
Journal | arXiv

Bayesian inference of spreading processes on networks by R Dutta, A Mira, and JP Onnela. Proceedings of the Royal Society A, 474:2215, 2018.
Journal | arXiv

Simulations for designing and interpreting intervention trials in infectious diseases by ME Halloran, K Auranen, S Baird, NE Basta, SE Bellan, R Brookmeyer, BS Cooper, V DeGruttola, JP Hughes, J Lessler, ET Lofgren, IM Longini, JP Onnela, B Özler, GR Seage, TA Smith, A Vespignani, E Vynnycky, and M Lipsitch. BMC Med 15 (1),  2017.
PubMed

Impact of degree truncation on the spread of a contagious process on networks by G Harling and JP Onnela. Network Science 1, 2017.
Journal

ABCpy: A user-friendly, extensible, and parallel library for approximate Bayesian computation by R Dutta, M Schoengens, JP Onnela, and A Mira. Proceedings of the Platform for Advanced Scientific Computing Conference. Article No. 8, 2017.
Journal

Leveraging contact network structure in the design of cluster randomized trials by G Harling, R Wang, JP Onnela, and V DeGruttola. Clinical Trials. 1740774516673355, 2016.
Journal|ArXiv

Social and spatial clustering of people at humanity’s largest gathering by I Barnett, T Khanna, and JP Onnela. PLoS ONE 11(6): e0156794, 2016.
Journal | ArXiv

The social geography of American medicine by D Kim, AJ O’Malley, and JP Onnela. Submitted (2016).
Working paper | Interactive figures: 1, 3, 4a, 4b, 4c, 4d | Code
Data: NPPES, Physician networks, Physician billing, Physician prescribing

Spread of pathogens in the patient transfer network of US hospitals by J Fernandez-Gracia^*, JP Onnela^*, M Barnett, VM Eguiluz, and NA Christakis. Scientific Reports, 7(1), 2930, 2017.
Journal |ArXiv

Incorporating contact network structure in cluster randomized trials by P Staples, E Ogburn, and JP Onnela. Scientific Reports 5, 17581, 2015.
Journal | ArXiv | Code

Polio vaccine hesitancy in the networks and neighborhoods of Malegaon, India by JP Onnela, BE Landon, AL Kahn, D Ahmed, H Verma, AJ O’Malley, S Bahl, RW Sutter, and NA Christakis. Social Science and Medicine 153, 999, 2016.
Journal | Working paper | High-resolution network figure

Multiple contexts and adolescent body mass index: schools, neighborhoods, and social networks by CR Evans, JP Onnela, DR Williams, and SV Subramanian. Social Science and Medicine 162, 21, 2016.
Journal

Investigating population dynamics of the Kumbh through the lens of cell phone data by JP Onnela and T Khanna.  In T Khanna, R Mehrotra, F Vera, and D Eck (Eds.), Kumbh Mela: Mapping the ephemeral mega city. Hatje Cantz, 2015.
ArXiv

Change point detection in correlation networks by Ian Barnett and JP Onnela. Scientific Reports 6, 18893, 2016.
Journal | ArXiv | Data | Code

Mapping Ebola: Why cell phone data could be the key to tracking the next pandemic by S Balsari, J Leaning, JP Onnela, and T Khanna. Emergency Physicians International 15, 30, 2014.
Journal

Flow of control in networks by JP Onnela. Science 343 (6177), 1373, 2014.
Journal  |  PubMed

Topics in social network analysis and network science by AJ O’Malley and JP Onnela. Submitted to Handbook of Health Services Research, 2014.
ArXiv

Adding network structure onto the map of collective behavior by S Fortunato, J Saramäki, and JP Onnela. Behavioral and Brain Sciences 37 (1), 82, 2014.
Journal  |  PubMed

A simple generative model of collective online behaviour by JP Gleeson, D Cellai, JP Onnela, MA Porter, and F Reed-Tsochas. PNAS 111, 10411, 2014.
Journal  |  PubMed  |  ArXiv

Using sociometers to quantify social interaction patterns by JP Onnela, B Waber, A Pentland, S Schnorf, and D Lazer. Scientific Reports 4, 5604, 2014.
Journal  |  PubMed  |  ArXiv 

Using administrative data to identify naturally occurring networks of physicians by B Landon, JP Onnela, NL Keating, M Barnett, S Paul, AJ O’Malley, T Keegan, and NA Christakis. Medical Care 51 (8), 715, 2013.
PubMed  |  ArXiv

Establishing a culture of reproducibility and openness in medical research with an emphasis on the training years by CD Barr and JP Onnela. Chance 25 (3), 8, 2012.
Journal

Variation in patient-sharing networks of physicians across the United States by B Landon, NL Keating, M Barnett, JP Onnela, S Paul, AJ O’Malley, and NA Christakis. JAMA 308 (3), 265, 2012.
Journal  |  PubMed

Spreading paths in partially observed social networks by JP Onnela and NA Christakis. Physical Review E 85, 036106, 2012.
Journal  |  PubMed  |  ArXiv

Taxonomies of networks from community structure by JP Onnela^*, DJ Fenn^*, S Reid, MA Porter, PJ Mucha, MD Fricker, and NS Jones. Physical Review E 86, 036104, 2012.
Journal  | PubMed  | ArXiv | Code

Physician patient-sharing networks and the cost and intensity of care in US hospitals by M Barnett, NA Christakis, AJ O’Malley, JP Onnela, NL Keating, and B Landon. Medical Care 50 (2), 152, 2012.
PubMed

Geographic constraints on social network groups by JP Onnela^*, S Arbesman^*, MC Gonzalez, AL Barabasi, and NA Christakis. PLoS one 6, e16939, 2011.
Journal  |  PubMed  |  ArXiv 

Network automata: Coupling structure and function in real-world networks by DMD Smith, JP Onnela, CF Lee, M Fricker, and NF Johnson. Advances in Complex Systems 14, 317, 2011.
ArXiv 

Understanding the demographics of Twitter users by A Mislove, S Lehmann, YY Ahn, JP Onnela, and JN Rosenquist. Proceedings of the Fifth International AAAI Conference on Weblogs and Social Media (ICWSM’11), Barcelona, Spain, 2011.
Journal

The spontaneous emergence of social influence in online systems by JP Onnela and F Reed-Tsochas. PNAS 107, 18375, 2010.
Journal  |  PubMed  |  ArXiv

Community structure in time-dependent, multiscale, and multiplex networks by PJ Mucha, T Richardson, K Macon, MA Porter, and JP Onnela. Science 328, 876, 2010.
Journal  |  PubMed  |  ArXiv

Competition for popularity in catalog networks by M Beguerisse-Díaz, MA Porter, and JP Onnela. Chaos 20, 043101, 2010.
Journal  |  PubMed  |  ArXiv 

Tick size and stock returns by JP Onnela, J Töyli, and K Kaski. Physica A 388, 441, 2009.
Journal

A comparative study of stochastic algorithmic models for social networks by R Toivonen, L Kovanen, M Kivelä, JP Onnela, J Saramäki, and K Kaski. Social Networks 31, 240, 2009.
Journal  |  ArXiv 

Communities in networks by MA Porter, JP Onnela, and PJ Mucha. Notices of the American Mathematical Society 56, 1082, 2009.
Journal  |  ArXiv 

Master-equation analysis of accelerating networks by DMD Smith, JP Onnela, and NS Jones. Physical Review E 79, 056101, 2009.
Journal  |  PubMed  |  ArXiv 

Sampling bias due to structural heterogeneity and limited internal diffusion by JP Onnela, NF Johnson, S Gourley, G Reinert, and M Spagat. Europhysics Letters 85, 28001, 2009.
Journal   |  ArXiv 

Model of community emergence in weighted social networks by JM Kumpula, JP Onnela, J Saramäki, J Kertész, and K Kaski. Computer Physics Communications 180, 517, 2009.
Journal   |  ArXiv 

Bias in epidemiological studies of conflict mortality by NF Johnson, M Spagat, S Gourley, JP Onnela, and G Reinert. Journal of Peace Research 45 (5), 653, 2008.
Journal  |

Link-space formalism for network analysis by DMD Smith, CF Lee, JP Onnela, and NF Johnson. Physical Review E 77, 036112, 2008.
Journal  |  PubMed  |  ArXiv 

Emergence of communities in weighted networks by JM Kumpula, JP Onnela, J Saramäki, K Kaski, and J Kertész. Physical Review Letters 99, 228701, 2007.
Journal  |  PubMed  |  ArXiv 

Structure and tie strengths in mobile communication networks by JP Onnela, J Saramäki, J Hyvönen, G Szabó, D Lazer, K Kaski, J Kertész, and AL Barabási. PNAS 104, 7332, 2007.
Journal  |  PubMed  |  ArXiv 

Analysis of a large-scale weighted network of one-to-one human communication by JP Onnela, J Saramäki, J Hyvönen, G Szabó, M Argollo de Menezes, K Kaski, AL Barabási, and J Kertész. New Journal of Physics 9, 179, 2007.
Journal  | ArXiv 

Accelerating networks by DMD Smith, JP Onnela, and NF Johnson. New Journal of Physics 9, 181, 2007.
Journal  |  ArXiv 

Spectral and network methods in the analysis of correlation matrices of stock returns by T Heimo, J Saramäki, JP Onnela, and K Kaski. Physica A 383, 147, 2007.
Journal  |  ArXiv 

Generalizations of the clustering coefficient to weighted complex networks by J Saramäki, M Kivelä, JP Onnela, K Kaski, and J Kertész. Physical Review E 75, 027105, 2007.
Journal  |  PubMed  |  ArXiv 

Spectrum, intensity and coherence in weighted networks of a financial market by G Tibély, JP Onnela, J Saramäki, K Kaski, and J Kertész. Physica A 370, 145, 2006.
Journal  |  ArXiv 

Model for social networks by R Toivonen, JP Onnela, J Saramäki, J Hyvönen, and K Kaski. Physica A371, 851, 2006.
Journal  |  ArXiv 

Intensity and coherence of motifs in weighted complex networks JP Onnela, J Saramäki, J Kertész, and K Kaski. Physical Review E 71, 065103, 2005.
Journal  |  PubMed  |  ArXiv 

Clustering and information in correlation based financial networks by JP Onnela, K Kaski, and J Kertész. European Physical Journal B 38, 353, 2004.
Journal  |  ArXiv 

Asset trees and asset graphs in financial markets by JP Onnela, A Chakraborti, K Kaski, J Kertész, and A Kanto. Physica Scripta 106, 48, 2003.
Journal  |  ArXiv 

Dynamics of market correlations: Taxonomy and portfolio analysis by JP Onnela, A Chakraborti, K Kaski, J Kertész, and A Kanto. Physical Review E 68, 056110, 2003.
Journal  |  PubMed  |  ArXiv 

Dynamic asset trees and Black Monday by JP Onnela, A Chakraborti, K Kaski, and J Kertész. Physica A 324/1, 247, 2003.
Journal   |  ArXiv | Data

Dynamic asset trees and portfolio analysis by JP Onnela, A Chakraborti, K Kaski, and J Kertész. European Physical Journal B 30, 285, 2002.
Journal  |  ArXiv | Data