Publications

Recent Publications

Select Publications

Blockchain Technology: Applications in Health Care.Angraal S, Krumholz HM, Schulz WL. Circ Cardiovasc Qual Outcomes. 2017 Sep. PMID: 28912202.
A Dirichlet-tree multinomial regression model for associating dietary nutrients with gut microorganisms.Wang T, Zhao H. Biometrics. 2017 Sep; 2017 Jan 23. PMID: 28112797.
On joint estimation of Gaussian graphical models for spatial and temporal data.Lin Z, Wang T, Yang C, Zhao H. Biometrics. 2017 Sep; 2017 Jan 18. PMID: 28099997.
Multicohort analysis reveals baseline transcriptional predictors of influenza vaccination responses.Sci Immunol. 2017 Aug 25. PMID: 28842433.
Can machine learning complement traditional medical device surveillance? A case study of dual-chamber implantable cardioverter-defibrillators.Ross JS, Bates J, Parzynski CS, Akar JG, Curtis JP, Desai NR, Freeman JV, Gamble GM, Kuntz R, Li SX, Marinac-Dabic D, Masoudi FA, Normand ST, Ranasinghe I, Shaw RE, Krumholz HM. Med Devices (Auckl). 2017; 2017 Aug 16. PMID: 28860874.
Systematic tissue-specific functional annotation of the human genome highlights immune-related DNA elements for late-onset Alzheimer's disease.Lu Q, Powles RL, Abdallah S, Ou D, Wang Q, Hu Y, Lu Y, Liu W, Li B, Mukherjee S, Crane PK, Zhao H. PLoS Genet. 2017 Jul; 2017 Jul 24. PMID: 28742084.
Multiple network-constrained regressions expand insights into influenza vaccination responses.Avey S, Mohanty S, Wilson J, Zapata H, Joshi SR, Siconolfi B, Tsang S, Shaw AC, Kleinstein SH. Bioinformatics. 2017 Jul 15. PMID: 28881994.
Describing the performance of U.S. hospitals by applying big data analytics.Downing NS, Cloninger A, Venkatesh AK, Hsieh A, Drye EE, Coifman RR, Krumholz HM. PLoS One. 2017; 2017 Jun 29. PMID: 28662045.
Joint modeling of genetically correlated diseases and functional annotations increases accuracy of polygenic risk prediction.Hu Y, Lu Q, Liu W, Zhang Y, Li M, Zhao H. PLoS Genet. 2017 Jun; 2017 Jun 9. PMID: 28598966.
Reevaluating the Efficacy and Predictability of Antidepressant Treatments: A Symptom Clustering Approach.Chekroud AM, Gueorguieva R, Krumholz HM, Trivedi MH, Krystal JH, McCarthy G. JAMA Psychiatry. 2017 Apr 1. PMID: 28241180.
Hierarchical Clustering Can Identify B Cell Clones with High Confidence in Ig Repertoire Sequencing Data.Gupta NT, Adams KD, Briggs AW, Timberlake SC, Vigneault F, Kleinstein SH. J Immunol. 2017 Mar 15; 2017 Feb 8. PMID: 28179494.
Statistical Models for the Analysis of Zero-Inflated Pain Intensity Numeric Rating Scale Data.Goulet JL, Buta E, Bathulapalli H, Gueorguieva R, Brandt CA. J Pain. 2017 Mar; 2016 Dec 2. PMID: 27919777.
graph-GPA: A graphical model for prioritizing GWAS results and investigating pleiotropic architecture.Chung D, Kim HJ, Zhao H. PLoS Comput Biol. 2017 Feb; 2017 Feb 17. PMID: 28212402.
Predicting synergistic effects between compounds through their structural similarity and effects on transcriptomes.Liu Y, Zhao H. Bioinformatics. 2016 Dec 15; 2016 Aug 18. PMID: 27540269.
CCor: A whole genome network-based similarity measure between two genes.Hu Y, Zhao H. Biometrics. 2016 Dec; 2016 Mar 8. PMID: 26953524.
Analysis of Machine Learning Techniques for Heart Failure Readmissions.Mortazavi BJ, Downing NS, Bucholz EM, Dharmarajan K, Manhapra A, Li SX, Negahban SN, Krumholz HM. Circ Cardiovasc Qual Outcomes. 2016 Nov; 2016 Nov 8. PMID: 28263938.
The Promise of Big Data: Opportunities and Challenges.Krumholz HM. Circ Cardiovasc Qual Outcomes. 2016 Nov; 2016 Nov 8. PMID: 28263935.
Estimating healthcare mobility in the Veterans Affairs Healthcare System.Wang KH, Goulet JL, Carroll CM, Skanderson M, Fodeh S, Erdos J, Womack JA, Abel EA, Bathulapalli H, Justice AC, Nunez-Smith M, Brandt CA. BMC Health Serv Res. 2016 Oct 21; 2016 Oct 21. PMID: 27769221.
Evolution of Gene Regulation in Humans.Reilly SK, Noonan JP. Annu Rev Genomics Hum Genet. 2016 Aug 31; 2016 Apr 21. PMID: 27147089.
Origin and evolution of developmental enhancers in the mammalian neocortex.Emera D, Yin J, Reilly SK, Gockley J, Noonan JP. Proc Natl Acad Sci U S A. 2016 May 10; 2016 Apr 25. PMID: 27114548.
The autism-associated chromatin modifier CHD8 regulates other autism risk genes during human neurodevelopment.Cotney J, Muhle RA, Sanders SJ, Liu L, Willsey AJ, Niu W, Liu W, Klei L, Lei J, Yin J, Reilly SK, Tebbenkamp AT, Bichsel C, Pletikos M, Sestan N, Roeder K, State MW, Devlin B, Noonan JP. Nat Commun. 2015 Mar 10; 2015 Mar 10. PMID: 25752243.
Evolutionary genomics. Evolutionary changes in promoter and enhancer activity during human corticogenesis.Reilly SK, Yin J, Ayoub AE, Emera D, Leng J, Cotney J, Sarro R, Rakic P, Noonan JP. Science. 2015 Mar 6. PMID: 25745175.
Automated analysis of high-throughput B-cell sequencing data reveals a high frequency of novel immunoglobulin V gene segment alleles.Gadala-Maria D, Yaari G, Uduman M, Kleinstein SH. Proc Natl Acad Sci U S A. 2015 Feb 24; 2015 Feb 9. PMID: 25675496.
On an Additive Semigraphoid Model for Statistical Networks With Application to Pathway Analysis.Li B, Chun H, Zhao H. J Am Stat Assoc. 2014 Sep. PMID: 26401064.
B cells populating the multiple sclerosis brain mature in the draining cervical lymph nodes.Stern JN, Yaari G, Vander Heiden JA, Church G, Donahue WF, Hintzen RQ, Huttner AJ, Laman JD, Nagra RM, Nylander A, Pitt D, Ramanan S, Siddiqui BA, Vigneault F, Kleinstein SH, Hafler DA, O'Connor KC. Sci Transl Med. 2014 Aug 6. PMID: 25100741.
Big data and new knowledge in medicine: the thinking, training, and tools needed for a learning health system.Krumholz HM. Health Aff (Millwood). 2014 Jul. PMID: 25006142.
Models of somatic hypermutation targeting and substitution based on synonymous mutations from high-throughput immunoglobulin sequencing data.Yaari G, Vander Heiden JA, Uduman M, Gadala-Maria D, Gupta N, Stern JN, O'Connor KC, Hafler DA, Laserson U, Vigneault F, Kleinstein SH. Front Immunol. 2013; 2013 Nov 15. PMID: 24298272.
Integrative annotation of variants from 1092 humans: application to cancer genomics.Khurana E, Fu Y, Colonna V, Mu XJ, Kang HM, Lappalainen T, Sboner A, Lochovsky L, Chen J, Harmanci A, Das J, Abyzov A, Balasubramanian S, Beal K, Chakravarty D, Challis D, Chen Y, Clarke D, Clarke L, Cunningham F, Evani US, Flicek P, Fragoza R, Garrison E, Gibbs R, Gümüş ZH, Herrero J, Kitabayashi N, Kong Y, Lage K, Liluashvili V, Lipkin SM, MacArthur DG, Marth G, Muzny D, Pers TH, Ritchie GRS, Rosenfeld JA, Sisu C, Wei X, Wilson M, Xue Y, Yu F, Dermitzakis ET, Yu H, Rubin MA, Tyler-Smith C, Gerstein M. Science. 2013 Oct 4. PMID: 24092746.
Quantitative set analysis for gene expression: a method to quantify gene set differential expression including gene-gene correlations.Yaari G, Bolen CR, Thakar J, Kleinstein SH. Nucleic Acids Res. 2013 Oct; 2013 Aug 5. PMID: 23921631.
Semi-supervised clinical text classification with Laplacian SVMs: an application to cancer case management.Garla V, Taylor C, Brandt C. J Biomed Inform. 2013 Oct; 2013 Jul 8. PMID: 23845911.
The evolution of lineage-specific regulatory activities in the human embryonic limb.Cotney J, Leng J, Yin J, Reilly SK, DeMare LE, Emera D, Ayoub AE, Rakic P, Noonan JP. Cell. 2013 Jul 3. PMID: 23827682.
Complementary ensemble clustering of biomedical data.Fodeh SJ, Brandt C, Luong TB, Haddad A, Schultz M, Murphy T, Krauthammer M. J Biomed Inform. 2013 Jun; 2013 Feb 27. PMID: 23454721.
Architecture of the human regulatory network derived from ENCODE data.Gerstein MB, Kundaje A, Hariharan M, Landt SG, Yan KK, Cheng C, Mu XJ, Khurana E, Rozowsky J, Alexander R, Min R, Alves P, Abyzov A, Addleman N, Bhardwaj N, Boyle AP, Cayting P, Charos A, Chen DZ, Cheng Y, Clarke D, Eastman C, Euskirchen G, Frietze S, Fu Y, Gertz J, Grubert F, Harmanci A, Jain P, Kasowski M, Lacroute P, Leng JJ, Lian J, Monahan H, O'Geen H, Ouyang Z, Partridge EC, Patacsil D, Pauli F, Raha D, Ramirez L, Reddy TE, Reed B, Shi M, Slifer T, Wang J, Wu L, Yang X, Yip KY, Zilberman-Schapira G, Batzoglou S, Sidow A, Farnham PJ, Myers RM, Weissman SM, Snyder M. Nature. 2012 Sep 6. PMID: 22955619.
Quantifying selection in high-throughput Immunoglobulin sequencing data sets.Yaari G, Uduman M, Kleinstein SH. Nucleic Acids Res. 2012 Sep 1; 2012 May 27. PMID: 22641856.
Comparing genomes to computer operating systems in terms of the topology and evolution of their regulatory control networks.Yan KK, Fang G, Bhardwaj N, Alexander RP, Gerstein M. Proc Natl Acad Sci U S A. 2010 May 18; 2010 May 3. PMID: 20439753.
Relating three-dimensional structures to protein networks provides evolutionary insights.Kim PM, Lu LJ, Xia Y, Gerstein MB. Science. 2006 Dec 22. PMID: 17185604.
A Bayesian networks approach for predicting protein-protein interactions from genomic data.Jansen R, Yu H, Greenbaum D, Kluger Y, Krogan NJ, Chung S, Emili A, Snyder M, Greenblatt JF, Gerstein M. Science. 2003 Oct 17. PMID: 14564010.