Publications by authors named "Jason H Moore"

100Publications

Corrigendum to: Recommendations to enhance rigor and reproducibility in biomedical research.

Gigascience 2020 Sep;9(9)

Department of Clinical Pharmacy, School of Pharmacy, University of Southern California, 1985 Zonal Avenue, Los Angeles, CA 90089, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/gigascience/giaa103DOI Listing
September 2020

International electronic health record-derived COVID-19 clinical course profiles: the 4CE consortium.

NPJ Digit Med 2020 19;3:109. Epub 2020 Aug 19.

Department of Biomedical Informatics, Harvard Medical School, Boston, MA USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41746-020-00308-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7438496PMC
August 2020

Conservation machine learning.

BioData Min 2020 5;13. Epub 2020 Aug 5.

Institute for Biomedical Informatics, University of Pennsylvania, Philadelphia, 19104-6021 PA USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s13040-020-00220-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7405443PMC
August 2020

Evaluating recommender systems for AI-driven biomedical informatics.

Bioinformatics 2020 Aug 7. Epub 2020 Aug 7.

Institute for Biomedical Informatics, Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania, Philadelphia, PA, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bioinformatics/btaa698DOI Listing
August 2020

treeheatr: an R package for interpretable decision tree visualizations.

Bioinformatics 2020 Jul 23. Epub 2020 Jul 23.

Department of Biostatistics, Epidemiology and Informatics, Institute for Biomedical Informatics, University of Pennsylvania, Philadelphia, PA, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bioinformatics/btaa662DOI Listing
July 2020

WellExplorer: an integrative resource linking hydraulic fracturing chemicals with hormonal pathways and geographic location.

Database (Oxford) 2020 01;2020

Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA, 19104.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/database/baaa053DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7376760PMC
January 2020

Learning from local to global: An efficient distributed algorithm for modeling time-to-event data.

J Am Med Inform Assoc 2020 Jul;27(7):1028-1036

Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania, Philadelphia, Pennsylvania, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/jamia/ocaa044DOI Listing
July 2020

Recommendations to enhance rigor and reproducibility in biomedical research.

Gigascience 2020 Jun;9(6)

Department of Clinical Pharmacy, School of Pharmacy, University of Southern California, 1985 Zonal Avenue, Los Angeles, CA 90089, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/gigascience/giaa056DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7263079PMC
June 2020

Interpretation of machine learning predictions for patient outcomes in electronic health records.

AMIA Annu Symp Proc 2019 4;2019:572-581. Epub 2020 Mar 4.

Biomedical and Translational Informatics Institute/Geisinger, Danville, PA, USA.

View Article

Download full-text PDF

Source
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7153071PMC
June 2020

Case contamination in electronic health records based case-control studies.

Biometrics 2020 Apr 4. Epub 2020 Apr 4.

Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1111/biom.13264DOI Listing
April 2020

Electronic health records and polygenic risk scores for predicting disease risk.

Nat Rev Genet 2020 Aug 31;21(8):493-502. Epub 2020 Mar 31.

Department of Biostatistics, Epidemiology & Informatics, University of Pennsylvania, Philadelphia, PA, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41576-020-0224-1DOI Listing
August 2020

How Computational Experiments Can Improve Our Understanding of the Genetic Architecture of Common Human Diseases.

Artif Life 2020 6;26(1):23-37. Epub 2020 Feb 6.

University of Pennsylvania, Institute for Biomedical Informatics, Perelman School of Medicine.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1162/artl_a_00308DOI Listing
February 2020

OMNIREP: Originating Meaning by Coevolving Encodings and Representations.

Memet Comput 2019 Sep 6;11(3):251-261. Epub 2019 Apr 6.

The authors are with the Institute for Biomedical Informatics (IBI), Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104. M. Sipper is also with the Department of Computer Science, Ben-Gurion University, Beer-Sheva 8410501, Israel.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1007/s12293-019-00285-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6934370PMC
September 2019

Regional imaging genetic enrichment analysis.

Bioinformatics 2020 Apr;36(8):2554-2560

Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bioinformatics/btz948DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7178438PMC
April 2020

Correction to: Investigating the parameter space of evolutionary algorithms.

BioData Min 2019;12:22. Epub 2019 Nov 18.

1Institute for Biomedical Informatics, University of Pennsylvania, Philadelphia, PA 19104-6021 USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s13040-019-0210-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6862728PMC
November 2019

Translational Bioinformatics: Biobanks in the Precision Medicine Era.

Pac Symp Biocomput 2020 ;25:743-747

Department of Genetics and Institute for Biomedical Informatics, The Perelman School of Medicine, University of Pennsylvania, A301 Richards Building, 3700 Hamilton Walk, Philadelphia, PA 19104, USA,

View Article

Download full-text PDF

Source
January 2020

Robust-ODAL: Learning from heterogeneous health systems without sharing patient-level data.

Pac Symp Biocomput 2020 ;25:695-706

Department of Biostatistics, Epidemiology & Informatics, University of Pennsylvania, Philadelphia, PA,19104, USA.

View Article

Download full-text PDF

Source
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6905508PMC
January 2020

Mining Regional Imaging Genetic Associations via Voxel-wise Enrichment Analysis.

IEEE EMBS Int Conf Biomed Health Inform 2019 May 12;2019. Epub 2019 Sep 12.

Biostatistics, Epidemiology and Informatics University of Pennsylvania, Philadelphia, PA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1109/BHI.2019.8834450DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6860973PMC
May 2019

A maximum likelihood approach to electronic health record phenotyping using positive and unlabeled patients.

J Am Med Inform Assoc 2020 01;27(1):119-126

Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/jamia/ocz170DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6913222PMC
January 2020

Prevalence and Characterization of Yoga Mentions in the Electronic Health Record.

J Am Board Fam Med 2019 Nov-Dec;32(6):790-800

From the Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA (NMP, SL, JHM); Department of Biostatics, Epidemiology, and Informatics, University of Pennsylvania, Philadelphia, PA (NMP, JHM); Clinical Research Informatics Core, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA (SL); Department of Information Services, Data Analytics Center, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA (ST, NS)

View Article

Download full-text PDF

Source
http://dx.doi.org/10.3122/jabfm.2019.06.190115DOI Listing
September 2020

Model selection for metabolomics: predicting diagnosis of coronary artery disease using automated machine learning.

Bioinformatics 2020 03;36(6):1772-1778

Department of Biostatistics, Epidemiology and Informatics, Institute for Biomedical Informatics, University of Pennsylvania, Philadelphia, PA, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bioinformatics/btz796DOI Listing
March 2020

An augmented estimation procedure for EHR-based association studies accounting for differential misclassification.

J Am Med Inform Assoc 2020 02;27(2):244-253

Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, The University of Pennsylvania, Philadelphia, Pennsylvania, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/jamia/ocz180DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7025368PMC
February 2020

Embracing study heterogeneity for finding genetic interactions in large-scale research consortia.

Genet Epidemiol 2020 01 4;44(1):52-66. Epub 2019 Oct 4.

Department of Biostatistics, Epidemiology, and Informatics, University of Pennsylvania, Philadelphia, Pennsylvania.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1002/gepi.22262DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6980207PMC
January 2020

A regression framework to uncover pleiotropy in large-scale electronic health record data.

J Am Med Inform Assoc 2019 10;26(10):1083-1090

Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/jamia/ocz084DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6748812PMC
October 2019

Global identifiability of latent class models with applications to diagnostic test accuracy studies: A Gröbner basis approach.

Biometrics 2020 03 6;76(1):98-108. Epub 2019 Nov 6.

Department of Biostatistics, Epidemiology, and Informatics, The University of Pennsylvania, Philadelphia, Pennsylvania.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1111/biom.13133DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7036323PMC
March 2020

Using Machine Learning on Home Health Care Assessments to Predict Fall Risk.

Stud Health Technol Inform 2019 Aug;264:684-688

NewCourtland Center for Transitions and Health, School of Nursing, University of Pennsylvania, Philadelphia, PA, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.3233/SHTI190310DOI Listing
August 2019

Comparing drug safety of hepatitis C therapies using post-market data.

BMC Med Inform Decis Mak 2019 08 8;19(Suppl 4):147. Epub 2019 Aug 8.

Departmant of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12911-019-0860-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6686214PMC
August 2019

Integration of genetic and clinical information to improve imputation of data missing from electronic health records.

J Am Med Inform Assoc 2019 10;26(10):1056-1063

Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/jamia/ocz041DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6748821PMC
October 2019

Exploration of a diversity of computational and statistical measures of association for genome-wide genetic studies.

BioData Min 2019 9;12:14. Epub 2019 Jul 9.

1Institute for Biomedical Informatics, University of Pennsylvania, Philadelphia, PA USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s13040-019-0201-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6617598PMC
July 2019

Scalable biclustering - the future of big data exploration?

Gigascience 2019 07;8(7)

Institute for Biomedical Informatics, University of Pennsylvania, 3700 Hamilton Walk, Philadelphia, PA 19104, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/gigascience/giz078DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6598466PMC
July 2019

Anticancer Therapy at the End of Life: Lessons From a Community Cancer Institute.

J Palliat Care 2019 Jun 12:825859719851484. Epub 2019 Jun 12.

3 Section of Palliative Care, Pennsylvania State University College of Medicine, Hershey, PA, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1177/0825859719851484DOI Listing
June 2019

Scaling tree-based automated machine learning to biomedical big data with a feature set selector.

Bioinformatics 2020 01;36(1):250-256

Department of Biostatistics, Epidemiology and Informatics, Institute for Biomedical Informatics, University of Pennsylvania, Philadelphia, PA 19104, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bioinformatics/btz470DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6956793PMC
January 2020

Why mind-body medicine is poised to set a new standard for clinical research.

J Clin Epidemiol 2019 12 18;116:167-170. Epub 2019 May 18.

Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Biostatistics, Epidemiology, and Informatics, University of Pennsylvania, Philadelphia, PA 19104, USA. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.jclinepi.2019.05.001DOI Listing
December 2019

Automated discovery of test statistics using genetic programming.

Genet Program Evolvable Mach 2019 Mar 10;20(1):127-137. Epub 2018 Oct 10.

Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia PA 19104, USA.

View Article

Download full-text PDF

Source
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6519943PMC
March 2019

Workshop during the Pacific Symposium of Biocomputing, Jan 3-7, 2019: Reading between the genes: interpreting non-coding DNA in high-throughput.

Pac Symp Biocomput 2019 ;24:444-448

Center for Biomedical Informatics and Biostatistics, Dept. of Medicine, University of Arizona, 1230 Cherry Ave, Tucson, AZ 85719, USA†all workshop co-chairs contributed equally, and are listed alphabetically,

View Article

Download full-text PDF

Source
January 2020

ODAL: A one-shot distributed algorithm to perform logistic regressions on electronic health records data from multiple clinical sites.

Pac Symp Biocomput 2019 ;24:30-41

Department of Biostatistics, Epidemiology & Informatics, University of Pennsylvania, 423 Guardian Drive, PA, 19104, USA#Co-first author.

View Article

Download full-text PDF

Source
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6417819PMC
August 2019

Testing the assumptions of parametric linear models: the need for biological data mining in disciplines such as human genetics.

BioData Min 2019 11;12. Epub 2019 Feb 11.

3Department of Epidemiology and Biostatistics, Case-Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106 USA.

View Article

Download full-text PDF

Source
https://biodatamining.biomedcentral.com/articles/10.1186/s13
Publisher Site
http://dx.doi.org/10.1186/s13040-019-0194-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6371539PMC
February 2019

Preparing next-generation scientists for biomedical big data: artificial intelligence approaches.

Per Med 2019 05 14;16(3):247-257. Epub 2019 Feb 14.

Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.2217/pme-2018-0145DOI Listing
May 2019

EBIC: an open source software for high-dimensional and big data analyses.

Bioinformatics 2019 09;35(17):3181-3183

Institute for Biomedical Informatics, University of Pennsylvania, Philadelphia, PA, USA.

View Article

Download full-text PDF

Source
https://academic.oup.com/bioinformatics/advance-article/doi/
Publisher Site
http://dx.doi.org/10.1093/bioinformatics/btz027DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6736067PMC
September 2019

Analysis validation has been neglected in the Age of Reproducibility.

PLoS Biol 2018 12 10;16(12):e3000070. Epub 2018 Dec 10.

Department of Biology and Marine Biology, University of North Carolina Wilmington, Wilmington, North Carolina, United States of America.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1371/journal.pbio.3000070DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6301703PMC
December 2018

To know the objective is not (necessarily) to know the objective function.

BioData Min 2018 4;11:21. Epub 2018 Oct 4.

1Institute for Biomedical Informatics, University of Pennsylvania, Philadelphia, 19104-6021 PA USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s13040-018-0182-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6172724PMC
October 2018

Identification of epistatic interactions between the human RNA demethylases FTO and ALKBH5 with gene set enrichment analysis informed by differential methylation.

BMC Proc 2018 17;12(Suppl 9):59. Epub 2018 Sep 17.

Institute for Biomedical Informatics, Richards Medical Research Laboratories, Perelman School of Medicine, University of Pennsylvania, 3700 Hamilton Walk, Philadelphia, PA 19104 USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12919-018-0122-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6157145PMC
September 2018

STatistical Inference Relief (STIR) feature selection.

Bioinformatics 2019 04;35(8):1358-1365

Department of Mathematics, University of Tulsa, Tulsa, OK, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bioinformatics/bty788DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6477983PMC
April 2019

Relief-based feature selection: Introduction and review.

J Biomed Inform 2018 09 18;85:189-203. Epub 2018 Jul 18.

Institute for Biomedical Informatics, University of Pennsylvania, Philadelphia, PA 19104, USA. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.jbi.2018.07.014DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6299836PMC
September 2018

Benchmarking relief-based feature selection methods for bioinformatics data mining.

J Biomed Inform 2018 09 17;85:168-188. Epub 2018 Jul 17.

Institute for Biomedical Informatics, University of Pennsylvania, Philadelphia, PA 19104, USA. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.jbi.2018.07.015DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6299838PMC
September 2018

runibic: a Bioconductor package for parallel row-based biclustering of gene expression data.

Bioinformatics 2018 12;34(24):4302-4304

Institute for Biomedical Informatics, University of Pennsylvania, Philadelphia, PA, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bioinformatics/bty512DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6289127PMC
December 2018

Leveraging epigenomics and contactomics data to investigate SNP pairs in GWAS.

Hum Genet 2018 May 24;137(5):413-425. Epub 2018 May 24.

Department of Biostatistics, Epidemiology, and Informatics, University of Pennsylvania, Philadelphia, PA, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1007/s00439-018-1893-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5996751PMC
May 2018

EBIC: an evolutionary-based parallel biclustering algorithm for pattern discovery.

Bioinformatics 2018 11;34(21):3719-3726

Institute for Biomedical Informatics, University of Pennsylvania, Philadelphia, PA, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bioinformatics/bty401DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6198864PMC
November 2018

A Probabilistic and Multi-Objective Analysis of Lexicase Selection and -Lexicase Selection.

Evol Comput 2019 10;27(3):377-402. Epub 2018 May 10.

Institute for Bioinformatics, University of Pennsylvania, Philadelphia, PA, 19104, USA

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1162/evco_a_00224DOI Listing
February 2020

DNAp: A Pipeline for DNA-seq Data Analysis.

Sci Rep 2018 05 1;8(1):6793. Epub 2018 May 1.

Department of Computer Science, Arkansas State University, Jonesboro, Arkansas, 72467, United States of America.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41598-018-25022-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5931599PMC
May 2018

Improving machine learning reproducibility in genetic association studies with proportional instance cross validation (PICV).

BioData Min 2018 19;11. Epub 2018 Apr 19.

2Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s13040-018-0167-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5907739PMC
April 2018

Collective feature selection to identify crucial epistatic variants.

BioData Min 2018 19;11. Epub 2018 Apr 19.

1Biomedical and Translational Bioinformatics Institute, Geisinger Health System, 100 N Academy Avenue, Danville, PA 17822 USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s13040-018-0168-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5907720PMC
April 2018

GPU Accelerated Browser for Neuroimaging Genomics.

Neuroinformatics 2018 10;16(3-4):393-402

Department of Biostatistics, Epidemiology, Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1007/s12021-018-9376-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6092242PMC
October 2018

Eleven quick tips for architecting biomedical informatics workflows with cloud computing.

PLoS Comput Biol 2018 03 29;14(3):e1005994. Epub 2018 Mar 29.

Institute for Biomedical Informatics, Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1371/journal.pcbi.1005994DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5875741PMC
March 2018

Characterizing and Managing Missing Structured Data in Electronic Health Records: Data Analysis.

JMIR Med Inform 2018 Feb 23;6(1):e11. Epub 2018 Feb 23.

Biomedical and Translational Informatics Institute, Geisinger, Danville, PA, United States.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.2196/medinform.8960DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5845101PMC
February 2018

Investigating the parameter space of evolutionary algorithms.

BioData Min 2018 17;11. Epub 2018 Feb 17.

1Institute for Biomedical Informatics, University of Pennsylvania, Philadelphia, 19104-6021 PA USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s13040-018-0164-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5816380PMC
February 2018

Medication class enrichment analysis: a novel algorithm to analyze multiple pharmacologic exposures simultaneously using electronic health record data.

J Am Med Inform Assoc 2018 07;25(7):780-789

Division of Gastroenterology, Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/jamia/ocx162DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6016702PMC
July 2018

Comparing Different Adverse Effects Among Multiple Drugs Using FAERS Data.

Stud Health Technol Inform 2017 ;245:1268

University of Texas Health Science Center at Houston, Houston, TX, USA.

View Article

Download full-text PDF

Source
June 2018

PMLB: a large benchmark suite for machine learning evaluation and comparison.

BioData Min 2017 11;10:36. Epub 2017 Dec 11.

Institute for Biomedical Informatics, University of Pennsylvania, 3700 Hamilton Walk, Philadelphia, 19104 PA USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s13040-017-0154-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5725843PMC
December 2017

Leveraging putative enhancer-promoter interactions to investigate two-way epistasis in Type 2 Diabetes GWAS.

Pac Symp Biocomput 2018 ;23:548-558

Department of Biostatistics, Epidemiology, and Informatics, University of Pennsylvania, 3700 Hamilton Walk, Philadelphia, PA, 19104, USA, ²Division of Human Genetics and Endocrinology, The Children's Hospital of Philadelphia, 3615 Civic Center Boulevard, Philadelphia, PA 19104, USA,

View Article

Download full-text PDF

Source
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5728670PMC
August 2018

Reading Between the Genes: Computational Models to Discover Function from Noncoding DNA.

Pac Symp Biocomput 2018 ;23:507-511

Center for Biomedical Informatics and Biostatistics, The Center for Applied Genetic and Genomic Medicine, BIO5 Institute, UA Cancer Center, and Dept of Medicine; University of Arizona 1657 E Helen St, Tucson, AZ 85719, USA,

View Article

Download full-text PDF

Source
August 2018

A heuristic method for simulating open-data of arbitrary complexity that can be used to compare and evaluate machine learning methods.

Pac Symp Biocomput 2018 ;23:259-267

Institute for Biomedical Informatics, University of Pennsylvania, D202 Richards Building, 3700 Hamilton Walk, Philadelphia, PA 19104, USA,

View Article

Download full-text PDF

Source
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5728661PMC
August 2018

Data-driven advice for applying machine learning to bioinformatics problems.

Pac Symp Biocomput 2018 ;23:192-203

Institute for Biomedical Informatics, University of Pennsylvania Philadelphia, PA 19104, USA,

View Article

Download full-text PDF

Source
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5890912PMC
August 2018

Mapping Patient Trajectories using Longitudinal Extraction and Deep Learning in the MIMIC-III Critical Care Database.

Pac Symp Biocomput 2018 ;23:123-132

Computational Genetics Lab, Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, 3700 Hamilton Walk, Philadelphia PA, 19104, United States of America,

View Article

Download full-text PDF

Source
August 2018

A Pilot Characterization of the Human Chronobiome.

Sci Rep 2017 12 7;7(1):17141. Epub 2017 Dec 7.

Department of Systems Pharmacology and Translational Therapeutics, at the University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41598-017-17362-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5719427PMC
December 2017

Artificial intelligence: more human with human.

BioData Min 2017 1;10:34. Epub 2017 Dec 1.

Institute for Biomedical Informatics, University of Pennsylvania, Philadelphia, 19104-6021 PA USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s13040-017-0157-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5709984PMC
December 2017

On meta- and mega-analyses for gene-environment interactions.

Genet Epidemiol 2017 12 7;41(8):876-886. Epub 2017 Nov 7.

Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1002/gepi.22085DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5775907PMC
December 2017

Analysis of Gene-Gene Interactions.

Curr Protoc Hum Genet 2017 10 18;95:1.14.1-1.14.10. Epub 2017 Oct 18.

Department of Biostatistics and Epidemiology, Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1002/cphg.45DOI Listing
October 2017

Phenotype validation in electronic health records based genetic association studies.

Genet Epidemiol 2017 12 11;41(8):790-800. Epub 2017 Oct 11.

Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1002/gepi.22080DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5891135PMC
December 2017

Up For A Challenge (U4C): Stimulating innovation in breast cancer genetic epidemiology.

PLoS Genet 2017 09 28;13(9):e1006945. Epub 2017 Sep 28.

Epidemiology and Genomics Research Program, Division of Cancer Control and Population Sciences, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1371/journal.pgen.1006945DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5619686PMC
September 2017

Evolutionarily derived networks to inform disease pathways.

Genet Epidemiol 2017 12 25;41(8):866-875. Epub 2017 Sep 25.

Department of Genetics, The Geisel School of Medicine at Dartmouth College, Hanover, New Hampshire, United States of America.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1002/gepi.22078DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5696086PMC
December 2017

Evolutionary computation: the next major transition of artificial intelligence?

BioData Min 2017 29;10:26. Epub 2017 Jul 29.

Institute for Biomedical Informatics, University of Pennsylvania, Philadelphia, 19104-6021 PA USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s13040-017-0147-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5534026PMC
July 2017

Tissue-specific network-based genome wide study of amygdala imaging phenotypes to identify functional interaction modules.

Bioinformatics 2017 Oct;33(20):3250-3257

Department of BioHealth Informatics, Indiana University School of Informatics & Computing, Indianapolis, IN 46202, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bioinformatics/btx344DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6410887PMC
October 2017

Gene Set Enrichment Analyses: lessons learned from the heart failure phenotype.

BioData Min 2017 26;10:18. Epub 2017 May 26.

Department of Cardiology, Division Heart & Lungs, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s13040-017-0137-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5446754PMC
May 2017

Multi-class computational evolution: development, benchmark evaluation and application to RNA-Seq biomarker discovery.

BioData Min 2017 24;10:13. Epub 2017 Apr 24.

Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, FDA, Jefferson, AR USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s13040-017-0134-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5404302PMC
April 2017

Genetic Effects on the Correlation Structure of CVD Risk Factors: Exome-Wide Data From a Ghanaian Population.

Glob Heart 2017 06 10;12(2):133-140. Epub 2017 Apr 10.

Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, OH, USA; Department of Genetics, Geisel School of Medicine, Dartmouth College, Hanover, NH, USA. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.gheart.2017.01.013DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5642993PMC
June 2017

Variant Set Enrichment: an R package to identify disease-associated functional genomic regions.

BioData Min 2017 22;10. Epub 2017 Feb 22.

Princess Margaret Cancer Centre, University Health Network, Toronto, ON Canada.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s13040-017-0129-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5320724PMC
February 2017

Complex systems analysis of bladder cancer susceptibility reveals a role for decarboxylase activity in two genome-wide association studies.

BioData Min 2016 12;9:40. Epub 2016 Dec 12.

Department of Biostatistics and Epidemiology, Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104-6116 USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s13040-016-0119-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5154053PMC
December 2016

NO-BOUNDARY THINKING IN BIOINFORMATICS.

Pac Symp Biocomput 2017 ;22:646-648

Institute for Biomedical Informatics, University of Pennsylvania Philadelphia, PA 19104, USA,

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1142/9789813207813_0060DOI Listing
March 2017

THE TRAINING OF NEXT GENERATION DATA SCIENTISTS IN BIOMEDICINE.

Pac Symp Biocomput 2017 ;22:640-645

2Epidemiology Program, University of Hawaii Cancer Center,Honolulu, HI, 96813, USA†Work partially supported by grant NIH Big Data 2 Knowledge Award K01ES025434 (to LXG), K01ES026839 (to SG), K01ES025433 (to QCN), K01ES026837 (to JHC), K01ES025445 (to SN), U24 ES026465 (to JDV), by the National Institute of Environmental Health Sciences through funds provided by the trans-NIH Big Data to Knowledge (BD2K) initiative,*work is also partially supported by P20 COBRE GM103457 awarded by NIH/NIGMS, NICHD R01 HD084633, NLM R01 LM012373, and Hawaii Community Foundation Medical Research Grant 14ADVC-64566.,

View Article

Download full-text PDF

Source
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5425257PMC
http://dx.doi.org/10.1142/9789813207813_0059DOI Listing
March 2017

MISSING DATA IMPUTATION IN THE ELECTRONIC HEALTH RECORD USING DEEPLY LEARNED AUTOENCODERS.

Pac Symp Biocomput 2017 ;22:207-218

Genomics and Computational Biology Graduate Group, Computational Genetics Lab, Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, 3700 Hamilton Walk, Philadelphia PA, 19104, USA,

View Article

Download full-text PDF

Source
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5144587PMC
http://dx.doi.org/10.1142/9789813207813_0021DOI Listing
June 2017

Considerations for higher efficiency and productivity in research activities.

BioData Min 2016 9;9:35. Epub 2016 Nov 9.

Department of Biostatistics and Epidemiology, Institute for Biomedical Informatics, Perelman School or Medicine, University of Pennsylvania, Philadelphia, PA 19104-6116 USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s13040-016-0115-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5103420PMC
November 2016

Identifying significant gene-environment interactions using a combination of screening testing and hierarchical false discovery rate control.

Genet Epidemiol 2016 11 31;40(7):544-557. Epub 2016 Aug 31.

Departments of Biomedical Data Science and Genetics, Institute for Quantitative Biomedical Sciences, Geisel School of Medicine, Dartmouth College, Hanover, NH 03755, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1002/gepi.21997DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5108431PMC
November 2016