Publications

Feiglin A, Allen BK, Kohane IS, Kong SW. Comprehensive Analysis of Tissue-wide Gene Expression and Phenotype Data Reveals Tissues Affected in Rare Genetic Disorders. Cell Syst. 2017 Aug 23;5(2):140-148.e2. doi: 10.1016/j.cels.2017.06.016. Epub 2017 Aug 16. PubMed PMID: 28822752.

Yin Xia, Tianxi Cai & T. Tony Cai (preprint): Two-Sample Tests for High-Dimensional Linear Regression with an Application to Detecting Interactions. Statistica Sinica, DOI: 10.5705/ss.202016.0032.

Dai HJ, Su EC, Uddin M, Jonnagaddala J, Wu CS, Syed-Abdul S. Exploring associations of clinical and social parameters with violent behaviors among psychiatric patients. J Biomed Inform. 2017 Aug 16. pii: S1532-0464(17)30188-0. doi: 10.1016/j.jbi.2017.08.009. [Epub ahead of print] PubMed PMID: 28822857.

Clark C, Wellner B, Davis R, Aberdeen J, Hirschman L. Automatic classification of RDoC positive valence severity with a neural network. J Biomed Inform. 2017 Jul 8. pii: S1532-0464(17)30161-2. doi: 10.1016/j.jbi.2017.07.005. [Epub ahead of print] PubMed PMID: 28694118.

Tao C, Filannino M, Uzuner Ö. Prescription extraction using CRFs and word embeddings. J Biomed Inform. 2017 Aug;72:60-66. doi: 10.1016/j.jbi.2017.07.002. Epub 2017 Jul 4. PubMed PMID: 28684255; PubMed Central PMCID: PMC5551970.

Buchan K, Filannino M, Uzuner Ö. Automatic prediction of coronary artery disease from clinical narratives. J Biomed Inform. 2017 Aug;72:23-32. doi: 10.1016/j.jbi.2017.06.019. Epub 2017 Jun 27. PubMed PMID: 28663072; PubMed Central PMCID: PMC5592829.

Stubbs A, Filannino M, Uzuner Ö. De-identification of psychiatric intake records: Overview of 2016 CEGS N-GRID shared tasks Track 1. J Biomed Inform. 2017 Jun 11. pii: S1532-0464(17)30134-X. doi: 10.1016/j.jbi.2017.06.011. [Epub ahead of print] PubMed PMID: 28614702.

Dehghan A, Kovacevic A, Karystianis G, Keane JA, Nenadic G. Learning to identify Protected Health Information by integrating knowledge- and data-driven algorithms: A case study on psychiatric evaluation notes. J Biomed Inform. 2017 Jun 7. pii: S1532-0464(17)30128-4. doi: 10.1016/j.jbi.2017.06.005. [Epub ahead of print] PubMed PMID: 28602908.

Scheurwegs E, Sushil M, Tulkens S, Daelemans W, Luyckx K. Counting trees in Random Forests: Predicting symptom severity in psychiatric intake reports. J Biomed Inform. 2017 Jun 7. pii: S1532-0464(17)30130-2. doi: 10.1016/j.jbi.2017.06.007. [Epub ahead of print] PubMed PMID: 28602906.

Liu Z, Tang B, Wang X, Chen Q. De-identification of clinical notes via recurrent neural network and conditional random field. J Biomed Inform. 2017 Jun  1. pii: S1532-0464(17)30122-3. doi: 10.1016/j.jbi.2017.05.023. [Epub ahead of print] PubMed PMID: 28579533.

Goodwin TR, Maldonado R, Harabagiu SM. Automatic recognition of symptom severity from psychiatric evaluation records. J Biomed Inform. 2017 May 30. pii:  S1532-0464(17)30119-3. doi: 10.1016/j.jbi.2017.05.020. [Epub ahead of print] PubMed PMID: 28576748.

Posada JD, Barda AJ, Shi L, Xue D, Ruiz V, Kuan PH, Ryan ND, Tsui FR. Predictive modeling for classification of positive valence system symptom severity from initial psychiatric evaluation records. J Biomed Inform. 2017 May 29. pii: S1532-0464(17)30118-1. doi: 10.1016/j.jbi.2017.05.019. [Epub ahead of print] PubMed PMID: 28571784.

Liu Y, Gu Y, Nguyen JC, Li H, Zhang J, Gao Y, Huang Y. Symptom severity classification with gradient tree boosting. J Biomed Inform. 2017 May 22. pii: S1532-0464(17)30110-7. doi: 10.1016/j.jbi.2017.05.015. [Epub ahead of print] PubMed PMID: 28545836.

Filannino M, Stubbs A, Uzuner Ö. Symptom severity prediction from neuropsychiatric clinical records: Overview of 2016 CEGS N-GRID shared tasks Track 2. J Biomed Inform. 2017 Apr 25. pii: S1532-0464(17)30087-4. doi: 10.1016/j.jbi.2017.04.017. [Epub ahead of print] PubMed PMID: 28455151.

Agniel D, Cai T. Analysis of multiple diverse phenotypes via semiparametric canonical correlation analysis. Biometrics. 2017 Apr 13. doi: 10.1111/biom.12690. [Epub ahead of print] PubMed PMID: 28407213.

McCoy TH Jr, Castro VM, Cagan A, Roberson AM, Perlis RH. Validation of a risk stratification tool for fall-related injury in a state-wide cohort. BMJ Open. 2017 Feb 6;7(2):e012189. doi: 10.1136/bmjopen-2016-012189. PubMed PMID: 28167743; PubMed Central PMCID: PMC5293982.

Yin Xia, Tianxi Cai & T. Tony Cai (2016): Multiple Testing of Submatrices of a Precision Matrix With Applications to Identification of Between Pathway Interactions. Journal of the American Statistical Association, DOI: 10.1080/01621459.2016.1251930

Nazeen S, Palmer NP, Berger B, Kohane IS. Integrative analysis of genetic data sets reveals a shared innate immune component in autism spectrum disorder and its co-morbidities. Genome Biol. 2016 Nov 14;17(1):228. PubMed PMID: 27842596; PubMed Central PMCID: PMC5108086.

Ataman B, Boulting GL, Harmin DA, Yang MG, Baker-Salisbury M, Yap EL, Malik AN, Mei K, Rubin AA, Spiegel I, Durresi E, Sharma N, Hu LS, Pletikos M, Griffith  EC, Partlow JN, Stevens CR, Adli M, Chahrour M, Sestan N, Walsh CA, Berezovskii VK, Livingstone MS, Greenberg ME. Evolution of Osteocrin as an activity-regulated factor in the primate brain. Nature. 2016 Nov 10;539(7628):242-247. doi: 10.1038/nature20111. PubMed PMID: 27830782; PubMed Central PMCID: PMC5499253.

Hyde CL, Nagle MW, Tian C, Chen X, Paciga SA, Wendland JR, Tung JY, Hinds DA, Perlis RH, Winslow AR. Identification of 15 genetic loci associated with risk of major depression in individuals of European descent. Nat Genet. 2016 Sep;48(9):1031-6. doi: 10.1038/ng.3623. Epub 2016 Aug 1. PubMed PMID: 27479909.

Stein MB, Chen CY, Ursano RJ, Cai T, Gelernter J, Heeringa SG, Jain S, Jensen KP, Maihofer AX, Mitchell C, Nievergelt CM, Nock MK, Neale BM, Polimanti R, Ripke S, Sun X, Thomas ML, Wang Q, Ware EB, Borja S, Kessler RC, Smoller JW; Army Study to Assess Risk and Resilience in Servicemembers (STARRS) Collaborators. Genome-wide Association Studies of Posttraumatic Stress Disorder in 2 Cohorts of US Army Soldiers. JAMA Psychiatry. 2016 Jul 1;73(7):695-704. doi: 10.1001/jamapsychiatry.2016.0350. PubMed PMID: 27167565; PubMed Central PMCID: PMC4936936.

Alural B, Genc S, Haggarty SJ. Diagnostic and therapeutic potential of microRNAs in neuropsychiatric disorders: Past, present, and future. Prog Neuropsychopharmacol Biol Psychiatry. 2017 Feb 6;73:87-103. doi: 10.1016/j.pnpbp.2016.03.010. Epub 2016 Apr 9. Review. PubMed PMID: 27072377; PubMed Central PMCID: PMC5292013.

Payne R, Yang M, Zheng Y, Jensen MK, Cai T. Robust risk prediction with biomarkers under two-phase stratified cohort design. Biometrics. 2016 Dec;72(4):1037-1045. doi: 10.1111/biom.12515. Epub 2016 Apr 1. PubMed PMID: 27037494; PubMed Central PMCID: PMC5045782.

Agniel D, Liao KP, Cai T. Estimation and testing for multiple regulation of multivariate mixed outcomes. Biometrics. 2016 Dec;72(4):1194-1205. doi: 10.1111/biom.12495. Epub 2016 Feb 22. PubMed PMID: 26910481; PubMed Central PMCID: PMC5459434.

Haggarty SJ, Silva MC, Cross A, Brandon NJ, Perlis RH. Advancing drug discovery for neuropsychiatric disorders using patient-specific stem cell models. Mol Cell Neurosci. 2016 Jun;73:104-15. doi: 10.1016/j.mcn.2016.01.011. Epub 2016  Jan 28. Review. PubMed PMID: 26826498; PubMed Central PMCID: PMC5292010.

Castro VM, Kong SW, Clements CC, Brady R, Kaimal AJ, Doyle AE, Robinson EB, Churchill SE, Kohane IS, Perlis RH. Absence of evidence for increase in risk for autism or attention-deficit hyperactivity disorder following antidepressant exposure during pregnancy: a replication study. Transl Psychiatry. 2016 Jan 5;6:e708. doi: 10.1038/tp.2015.190. PubMed PMID: 26731445; PubMed Central PMCID:  PMC5068870.

Loebrich S, Rathje M, Hager E, Ataman B, Harmin DA, Greenberg ME, Nedivi E. Genomic mapping and cellular expression of human CPG2 transcripts in the SYNE1 gene. Mol Cell Neurosci. 2016 Mar;71:46-55. doi: 10.1016/j.mcn.2015.12.007. Epub  2015 Dec 15. PubMed PMID: 26704904.

Prilutsky D, Kho AT, Palmer NP, Bhakar AL, Smedemark-Margulies N, Kong SW, Margulies DM, Bear MF, Kohane IS. Gene expression analysis in Fmr1KO mice identifies an immunological signature in brain tissue and mGluR5-related signaling in primary neuronal cultures. Mol Autism. 2015 Dec 21;6:66. doi: 10.1186/s13229-015-0061-9. eCollection 2015. PubMed PMID: 26697163; PubMed Central PMCID: PMC4687343.

Payne R, Neykov M, Jensen MK, Cai T. Kernel machine testing for risk prediction with stratified case cohort studies. Biometrics. 2016 Jun;72(2):372-81. doi: 10.1111/biom.12452. Epub 2015 Dec 21. PubMed PMID: 26692376; PubMed Central PMCID: PMC4899160.

Lodato MA, Woodworth MB, Lee S, Evrony GD, Mehta BK, Karger A, Lee S, Chittenden TW, D'Gama AM, Cai X, Luquette LJ, Lee E, Park PJ, Walsh CA. Somatic mutation in single human neurons tracks developmental and transcriptional history. Science. 2015 Oct 2;350(6256):94-98. doi: 10.1126/science.aab1785. PubMed PMID: 26430121; PubMed Central PMCID: PMC4664477.

McCoy TH, Castro VM, Cagan A, Roberson AM, Kohane IS, Perlis RH. Sentiment Measured in Hospital Discharge Notes Is Associated with Readmission and Mortality Risk: An Electronic Health Record Study. PLoS One. 2015 Aug 24;10(8):e0136341. doi: 10.1371/journal.pone.0136341. eCollection 2015. PubMed PMID: 26302085; PubMed Central PMCID: PMC4547711.

Minnier J, Yuan M, Liu JS, Cai T. Risk Classification with an Adaptive Naive Bayes Kernel Machine Model. J Am Stat Assoc. 2015 Apr 22;110(509):393-404. PubMed PMID: 26236061; PubMed Central PMCID: PMC4519995.

Shen Y, Cai T, Chen Y, Yang Y, Chen J. Retrospective likelihood-based methods for analyzing case-cohort genetic association studies. Biometrics. 2015 Dec;71(4):960-8. doi: 10.1111/biom.12342. Epub 2015 Jul 14. PubMed PMID: 26177343; PubMed Central PMCID: PMC4751872.