Papers

Digital Phenotyping

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. In print. (2019).
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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)
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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).
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Design and results of a smartphonebased 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).
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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. In print. (2019).
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Inferring mobility measures from GPS with missing data by I Barnett and JP Onnela. Biostatistics 21:2, e98–e112 (2020).
arXiv | Journal

Activity classification using smartphone gyroscope and accelerometer data by E Huang and JP Onnela. Submitted. (2019).
arXiv

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).
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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 JP.  Journal of the American Medical Informatics Association, 25:12 (2018).
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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).
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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).
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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).
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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 (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 psychiatry25(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

Statistical Network Science

Feature-based classification of networks by I Barnett, N Malek, P Mucha, JP Onnela. Network Science. In print. (2019).

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

Efficient vaccination strategies for epidemic control using network information by Y Yang, A McKhann, S Chen, G Harling, and JP Onnela. Epidemics 115-122 (2019).
PubMed

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).
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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. In print. (2019).
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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. In print. (2019).
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Flexible model selection of mechanistic network models via Super Learner by S Chen, A Mira,  JP Onnela. Submitted. (2019).
aXiv

Connected but segregated: social networks in rural villages by F Montes, RC Jimenez, JP Onnela. Journal of Complex Networks, 6(5), pp.693-705. (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

Efficient vaccination strategies for epidemic control using network information by Y Yang, A McKhann, G Harling* , and JP Onnela* . (* shared senior authors)
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

ABCpy: A high-performance computing perspective to approximate Bayesian computation by R Dutta, M Schoengens, A Ummadisingu, JP Onnela, and A Mira. (2017).
arXiv

Impact of degree truncation on the spread of a contagious process on networks by G Harling and JP Onnela. Network Science. (2017).
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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).
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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).
JournalArXiv

Leveraging contact network information in clustered randomized trials of infectious processes by P Staples, M Prague, V DeGruttola, and JP Onnela. Submitted (2016).
ArXiv

Impact of degree truncation on the spread of a contagious process on networks by G Harling and JP Onnela. Submitted (2016).
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: NPPESPhysician networksPhysician 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).
JournalWorking 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.
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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, 30–33 (2014).
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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).
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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).
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The spontaneous emergence of social influence in online systems by JP Onnela and F Reed-Tsochas. PNAS 107, 18375 (2010).
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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).
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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).
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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).
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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