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Research Output 1973 2020

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Review article
2020

A rewiring model of intratumoral interaction networks

Sang, M., Rice, S., Jiang, L., Liu, X., Gragnoli, C., Belani, C. P. & Wu, R., 2020, In : Computational and Structural Biotechnology Journal. 18, p. 45-51 7 p.

Research output: Contribution to journal › Review article

Open Access
Tumors
Neoplasms
Cells
Blueprints
Game theory

Systematic integration of GATA transcription factors and epigenomes via IDEAS paints the regulatory landscape of hematopoietic cells

Hardison, R. C., Zhang, Y., Keller, C. A., Xiang, G., Heuston, E. F., An, L., Lichtenberg, J., Giardine, B. M., Bodine, D., Mahony, S., Li, Q., Yue, F., Weiss, M. J., Blobel, G. A., Taylor, J., Hughes, J., Higgs, D. R. & Göttgens, B., Jan 1 2020, In : IUBMB Life. 72, 1, p. 27-38 12 p.

Research output: Contribution to journal › Review article

Open Access
GATA Transcription Factors
Paint
Epigenomics
Genes
Chromatin
2019

A regulatory network for mir156-spl module in arabidopsis thaliana

Zheng, C., Ye, M., Sang, M. & Wu, R., Dec 2 2019, In : International journal of molecular sciences. 20, 24, 6166.

Research output: Contribution to journal › Review article

Open Access
Arabidopsis
modules
sequencing
determinants
genes

A unified mapping framework of multifaceted pharmacodynamic responses to hypertension interventions

Wang, Q., Gan, J., Wei, K., Berceli, S. A., Gragnoli, C. & Wu, R., Mar 1 2019, In : Drug Discovery Today. 24, 3, p. 883-889 7 p.

Research output: Contribution to journal › Review article

Quantitative Trait Loci
Blood Pressure
Hypertension
Pharmaceutical Preparations
Patient Rights
2 Citations (Scopus)

Confronting models with data: The challenges of estimating disease spillover

Cross, P. C., Prosser, D. J., Ramey, A. M., Hanks, E. M. & Pepin, K. M., Sep 30 2019, In : Philosophical Transactions of the Royal Society B: Biological Sciences. 374, 1782, 20180435.

Research output: Contribution to journal › Review article

Pathogens
pathogens
Livestock
Information Systems
prediction
3 Citations (Scopus)

Co-shared genetics and possible risk gene pathway partially explain the comorbidity of schizophrenia, major depressive disorder, type 2 diabetes, and metabolic syndrome

Postolache, T. T., del Bosque-Plata, L., Jabbour, S., Vergare, M., Wu, R. & Gragnoli, C., Apr 1 2019, In : American Journal of Medical Genetics, Part B: Neuropsychiatric Genetics. 180, 3, p. 186-203 18 p.

Research output: Contribution to journal › Review article

Type 2 Diabetes Mellitus
Comorbidity
Schizophrenia
Major Depressive Disorder
Genes
2 Citations (Scopus)

Nutritional status in chronic spinal cord injury: a systematic review and meta-analysis

Farkas, G. J., Pitot, M. A., Berg, A. S. & Gater, D. R., Jan 1 2019, In : Spinal Cord. 57, 1, p. 3-17 15 p.

Research output: Contribution to journal › Review article

United States Department of Agriculture
Nutritional Status
Spinal Cord Injuries
Meta-Analysis
Confidence Intervals
10 Citations (Scopus)

Risk Factors for Elbow and Shoulder Injuries in Adolescent Baseball Players: A Systematic Review

Norton, R., Honstad, C., Joshi, R., Silvis, M., Chinchilli, V. & Dhawan, A., Mar 1 2019, In : American Journal of Sports Medicine. 47, 4, p. 982-990 9 p.

Research output: Contribution to journal › Review article

Baseball
Elbow
Arm Injuries
Fatigue
Arm

Stephen elliott fienberg 1942-2016, founding editor of the annual review of statistics and its application

Carriquiry, A. L., Reid, N. & Slavković, A. B., Mar 7 2019, In : Annual Review of Statistics and Its Application. 6, p. 1-18 18 p.

Research output: Contribution to journal › Review article

Open Access
Annual
Statistics
Sweeping
Leadership
Categorization
2018
11 Citations (Scopus)

A review of dynamic network models with latent variables

Kim, B., Lee, K. H., Xue, L. & Niu, X., Jan 1 2018, In : Statistics Surveys. 12, p. 105-135 31 p.

Research output: Contribution to journal › Review article

Dynamic Networks
Latent Variables
Network Model
Dynamic Model
Latent Class Model
2 Citations (Scopus)

Bayesian Inference in the Presence of Intractable Normalizing Functions

Park, J. & Haran, M., Jul 3 2018, In : Journal of the American Statistical Association. 113, 523, p. 1372-1390 19 p.

Research output: Contribution to journal › Review article

Bayesian inference
Exponential Model
Graph Model
Bayesian Analysis
Point Process
3 Citations (Scopus)

Mapping genes for drug chronotherapy

Wei, K., Wang, Q., Gan, J., Zhang, S., Ye, M., Gragnoli, C. & Wu, R., Nov 2018, In : Drug Discovery Today. 23, 11, p. 1883-1888 6 p.

Research output: Contribution to journal › Review article

Drug Chronotherapy
Chromosome Mapping
Pharmaceutical Preparations
Genes
Genome-Wide Association Study
4 Citations (Scopus)

The APOGEE-2 Survey of the Orion Star-forming Complex. I. Target Selection and Validation with Early Observations

Cottle, JN., Covey, K. R., Suárez, G., Román-Zúñiga, C., Schlafly, E., Downes, J. J., Ybarra, J. E., Hernandez, J., Stassun, K., Stringfellow, G. S., Getman, K., Feigelson, E., Borissova, J., Kim, J. S., Roman-Lopes, A., Da Rio, N., De Lee, N., Frinchaboy, P. M., Kounkel, M., Majewski, S. R. & 9 others, Mennickent, R. E., Nidever, D. L., Nitschelm, C., Pan, K., Shetrone, M., Zasowski, G., Chambers, K., Magnier, E. & Valenti, J., Jun 2018, In : Astrophysical Journal, Supplement Series. 236, 2, 27.

Research output: Contribution to journal › Review article

stars
field survey
catalogs
wavelength
young
2017
13 Citations (Scopus)

Epigenetic game theory: How to compute the epigenetic control of maternal-to-zygotic transition

Wang, Q., Gosik, K., Xing, S., Jiang, L., Sun, L., Chinchilli, V. & Wu, R., Mar 1 2017, In : Physics of Life Reviews. 20, p. 126-137 12 p.

Research output: Contribution to journal › Review article

game theory
Game Theory
Methylation
embryos
Game theory
44 Citations (Scopus)

Kernel mean embedding of distributions: A review and beyond

Muandet, K., Fukumizu, K., Sriperumbudur, B. & Schölkopf, B., Jan 1 2017, In : Foundations and Trends in Machine Learning. 10, 1-2, p. 1-141 141 p.

Research output: Contribution to journal › Review article

Hilbert spaces
Arsenals
Reinforcement learning
Testing
Support vector machines
2 Citations (Scopus)

Landscaping Crossover Interference Across a Genome

Sun, L., Wang, J., Sang, M., Jiang, L., Zhao, B., Cheng, T., Zhang, Q. & Wu, R., Oct 2017, In : Trends in Plant Science. 22, 10, p. 894-907 14 p.

Research output: Contribution to journal › Review article

landscaping
crossover interference
genome
chromosomes
meiosis
20 Citations (Scopus)

Plant grafting: how genetic exchange promotes vascular reconnection

Wang, J., Jiang, L. & Wu, R., Apr 1 2017, In : New Phytologist. 214, 1, p. 56-65 10 p.

Research output: Contribution to journal › Review article

vascular tissues
scions
grafting (plants)
phenotypic variation
blood vessels
1 Citation (Scopus)

Predictive Factors of the Effectiveness of Caudal Epidural Steroid Injections in Managing Patients with Chronic Low Back Pain and Radiculopathy

Billy, G. G., Lin, J., Gao, M. & Chow, M. X., Jan 1 2017, In : Clinical Spine Surgery. 30, 6, p. E833-E838

Research output: Contribution to journal › Review article

Epidural Injections
Radiculopathy
Low Back Pain
Steroids
Physical Examination
2016

Editorial

Li, R., Oct 2016, In : Annals of Statistics. 44, 5, p. 1817-1820 4 p.

Research output: Contribution to journal › Review article

12 Citations (Scopus)

Integrating Evolutionary Game Theory into Mechanistic Genotype-Phenotype Mapping

Zhu, X., Jiang, L., Ye, M., Sun, L., Gragnoli, C. & Wu, R., May 1 2016, In : Trends in Genetics. 32, 5, p. 256-268 13 p.

Research output: Contribution to journal › Review article

Game Theory
Genotype
Phenotype
Genetic Selection
Quantitative Trait Loci
11 Citations (Scopus)

Kernel mean shrinkage estimators

Muandet, K., Sriperumbudur, B., Fukumizu, K., Gretton, A. & Schölkopf, B., Apr 1 2016, In : Journal of Machine Learning Research. 17

Research output: Contribution to journal › Review article

Shrinkage Estimator
kernel
Kernel Methods
Hilbert spaces
Estimator
2015
31 Citations (Scopus)

An overview of the prediction of protein DNA-binding sites

Si, J., Zhao, R. & Wu, R., Mar 6 2015, In : International journal of molecular sciences. 16, 3, p. 5194-5215 22 p.

Research output: Contribution to journal › Review article

Binding sites
DNA
deoxyribonucleic acid
Binding Sites
proteins
18 Citations (Scopus)

A selective overview of feature screening for ultrahigh-dimensional data

Liu, J. Y., Zhong, W. & Li, R. Z., Oct 29 2015, In : Science China Mathematics. 58, 10

Research output: Contribution to journal › Review article

Screening
High-dimensional Data
Variable Selection
Biomedical Imaging
Penalized Least Squares
29 Citations (Scopus)

Computational prediction of RNA-binding proteins and binding sites

Si, J., Cui, J., Cheng, J. & Wu, R., Nov 3 2015, In : International journal of molecular sciences. 16, 11, p. 26303-26317 15 p.

Research output: Contribution to journal › Review article

RNA-Binding Proteins
Binding sites
RNA
Protein Binding
Binding Sites
6 Citations (Scopus)

Computational predictions of the site of metabolism of cytochrome P450 2D6 substrates: Comparative analysis, molecular docking, bioactivation and toxicological implications

Ford, K. A., Ryslik, G. A., Sodhi, J., Halladay, J., Diaz, D., Dambach, D. & Masuda, M., Jul 3 2015, In : Drug Metabolism Reviews. 47, 3, p. 291-319 29 p.

Research output: Contribution to journal › Review article

Molecular Docking Simulation
Cytochrome P-450 CYP2D6
Toxicology
Computer Simulation
Small Molecule Libraries
23 Citations (Scopus)

Mapping complex traits as a dynamic system

Sun, L. & Wu, R., Jun 1 2015, In : Physics of Life Reviews. 13, p. 155-185 31 p.

Research output: Contribution to journal › Review article

Endophenotypes
Quantitative Trait Loci
DNA sequences
Biological systems
Machinery
36 Citations (Scopus)

Metabolic reprogramming and dysregulated metabolism: Cause, consequence and/or enabler of environmental carcinogenesis?

Brooks Robey, R., Weisz, J., Kuemmerle, N., Salzberg, A. C., Berg, A., Brown, D. G., Kubik, L., Palorini, R., Al-Mulla, F., Al-Temaimi, R., Colacci, A., Mondello, C., Raju, J., Woodrick, J., Ivana Scovassi, A., Singh, N., Vaccari, M., Roy, R., Forte, S., Memeo, L. & 10 others, Salem, H. K., Amedei, A., Hamid, R. A., Williams, G. P., Lowe, L., Meyer, J., Martin, F. L., Bisson, W. H., Chiaradonna, F. & Ryan, E. P., Jun 1 2015, In : Carcinogenesis. 36, p. S203-S231

Research output: Contribution to journal › Review article

Carcinogenesis
Neoplasms
Toxicology
Gene Expression
1 Citation (Scopus)

Multi-scale biological and physical modelling of the tumour micro-environment

Kunz, R. F., Gaskin, B. J., Li, Q., Davanloo-Tajbakhsh, S. & Dong, C., Feb 2 2015, In : Drug Discovery Today: Disease Models. 16, p. 7-15 9 p.

Research output: Contribution to journal › Review article

Cell Communication
Computing Methodologies
Physics
Hydrodynamics
Biochemistry
2014
139 Citations (Scopus)

An Earth-sized planet in the habitable zone of a cool star

Quintana, E. V., Barclay, T., Raymond, S. N., Rowe, J. F., Bolmont, E., Caldwell, D. A., Howell, S. B., Kane, S. R., Huber, D., Crepp, J. R., Lissauer, J. J., Ciardi, D. R., Coughlin, J. L., Everett, M. E., Henze, C. E., Horch, E., Isaacson, H., Ford, E. B., Adams, F. C., Still, M. & 3 others, Hunter, R. C., Quarles, B. & Selsis, F., Jan 1 2014, In : Science. 344, 6181, p. 277-280 4 p.

Research output: Contribution to journal › Review article

Earth (Planet)
Planets
Water
Orbit
Atmosphere
13 Citations (Scopus)

Architectures of planetary systems and implications for their formation

Ford, E. B., Sep 2 2014, In : Proceedings of the National Academy of Sciences of the United States of America. 111, 35, p. 12616-12621 6 p.

Research output: Contribution to journal › Review article

Planets
Orbit
Planetary Evolution
United States National Aeronautics and Space Administration
Gravitation
28 Citations (Scopus)

Improvements in prevalence trend fitting and incidence estimation in EPP 2013

Brown, T., Bao, L., Eaton, J. W., Hogan, D. R., Mahy, M., Marsh, K., Mathers, B. M. & Puckett, R., Nov 11 2014, In : AIDS. 28, p. S415-S425

Research output: Contribution to journal › Review article

Incidence
Acquired Immunodeficiency Syndrome
United Nations
HIV
Calibration
8 Citations (Scopus)

Incorporating incidence information within the UNAIDS estimation and projection package framework: A study based on simulated incidence assay data

Bao, L., Ye, J. & Hallett, T. B., Nov 11 2014, In : AIDS. 28, p. S515-S522

Research output: Contribution to journal › Review article

Incidence
Sample Size
Uncertainty
Biomarkers
HIV
4 Citations (Scopus)

Systems mapping of genes controlling chemotherapeutic drug efficiency for cancer stem cells

Wu, W., Feng, S., Wang, Y., Wang, N., Hao, H. & Wu, R., Aug 2014, In : Drug Discovery Today. 19, 8, p. 1125-1130 6 p.

Research output: Contribution to journal › Review article

Neoplastic Stem Cells
Chromosome Mapping
Pharmaceutical Preparations
Neoplasms
Genetic Association Studies
2013
14 Citations (Scopus)

A dynamic framework for quantifying the genetic architecture of phenotypic plasticity

Wang, Z., Pang, X., Lv, Y., Xu, F., Zhou, T., Li, X., Feng, S., Li, J., Li, Z. & Wu, R., Jan 1 2013, In : Briefings in bioinformatics. 14, 1, p. 82-95 14 p., bbs009.

Research output: Contribution to journal › Review article

Plasticity
Quantitative Trait Loci
Dynamic models
Genes
Genotype
4 Citations (Scopus)

Conditional inference given partial information in contingency tables using Markov bases

Karwa, V. & Slavkovic, A. B., May 1 2013, In : Wiley Interdisciplinary Reviews: Computational Statistics. 5, 3, p. 207-218 12 p.

Research output: Contribution to journal › Review article

Markov Basis
Conditional Inference
Partial Information
Contingency Table
Algebraic Statistics
8 Citations (Scopus)

Delivering systems pharmacogenomics towards precision medicine through mathematics

Wang, Y., Wang, N., Wang, J., Wang, Z. & Wu, R., Jun 30 2013, In : Advanced Drug Delivery Reviews. 65, 7, p. 905-911 7 p.

Research output: Contribution to journal › Review article

Precision Medicine
Mathematics
Pharmacogenetics
Biomarkers
Pharmaceutical Preparations
7 Citations (Scopus)

Selection of multinomial logit models via association rules analysis

Changpetch, P. & Lin, D. K. J., Jan 1 2013, In : Wiley Interdisciplinary Reviews: Computational Statistics. 5, 1, p. 68-77 10 p.

Research output: Contribution to journal › Review article

Multinomial Logit Model
Association Rules
Model Selection
Interaction
Interaction Effects
1 Citation (Scopus)

Statistical resolution of missing longitudinal data in clinical pharmacogenomics

Wang, Z., Li, H., Wang, J., Li, J. & Wu, R., Jun 30 2013, In : Advanced Drug Delivery Reviews. 65, 7, p. 980-986 7 p.

Research output: Contribution to journal › Review article

Pharmacogenetics
Pharmaceutical Preparations
Precision Medicine
Statistical Models
Haplotypes
5 Citations (Scopus)

Stochastic modeling of systems mapping in pharmacogenomics

Wang, Z., Luo, J., Fu, G., Wang, Z. & Wu, R., Jun 30 2013, In : Advanced Drug Delivery Reviews. 65, 7, p. 912-917 6 p.

Research output: Contribution to journal › Review article

Pharmacogenetics
Precision Medicine
Pharmaceutical Preparations
Drug Design
Pharmacology
5 Citations (Scopus)

Systems mapping of metabolic genes through control theory

Liu, G., Kong, L., Wang, Z., Wang, C. & Wu, R., Jun 30 2013, In : Advanced Drug Delivery Reviews. 65, 7, p. 918-928 11 p.

Research output: Contribution to journal › Review article

Chromosome Mapping
Quantitative Trait Loci
Phenotype
Metabolic Networks and Pathways
Genotype

Theoretical Biology and Medical Modelling: Ensuring continued growth and future leadership

Nishiura, H., Rietman, E. A. & Wu, R., Jul 16 2013, In : Theoretical Biology and Medical Modelling. 10, 1, 43.

Research output: Contribution to journal › Review article

Leadership
Biology
Growth
Modeling
Mathematical Biology
29 Citations (Scopus)

Variation in the transcriptional response of threatened coral larvae to elevated temperatures

Polato, N. R., Altman, N. S. & Baums, I. B., Mar 1 2013, In : Molecular ecology. 22, 5, p. 1366-1382 17 p.

Research output: Contribution to journal › Review article

Anthozoa
Larva
corals
coral
larva
2012
2 Citations (Scopus)

A pattern-mixture model for haplotype analysis of longitudinal traits with non-ignorable dropout

Li, H. & Wu, R., Jan 1 2012, In : Statistica Sinica. 22, 1, p. 337-357 21 p.

Research output: Contribution to journal › Review article

Pattern-mixture Model
Haplotype
Drop out
Dobutamine
Model
748 Citations (Scopus)

ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia

Landt, S. G., Marinov, G. K., Kundaje, A., Kheradpour, P., Pauli, F., Batzoglou, S., Bernstein, B. E., Bickel, P., Brown, J. B., Cayting, P., Chen, Y., DeSalvo, G., Epstein, C., Fisher-Aylor, K. I., Euskirchen, G., Gerstein, M., Gertz, J., Hartemink, A. J., Hoffman, M. M., Iyer, V. R. & 27 others, Jung, Y. L., Karmakar, S., Kellis, M., Kharchenko, P. V., Li, Q., Liu, T., Liu, X. S., Ma, L., Milosavljevic, A., Myers, R. M., Park, P. J., Pazin, M. J., Perry, M. D., Raha, D., Reddy, T. E., Rozowsky, J., Shoresh, N., Sidow, A., Slattery, M., Stamatoyannopoulos, J. A., Tolstorukov, M. Y., White, K. P., Xi, S., Farnham, P. J., Lieb, J. D., Wold, B. J. & Snyder, M., Sep 1 2012, In : Genome research. 22, 9, p. 1813-1831 19 p.

Research output: Contribution to journal › Review article

Chromatin Immunoprecipitation
Practice Guidelines
Histone Code
Guidelines
High-Throughput Nucleotide Sequencing
9 Citations (Scopus)

Key observations from the NHLBI Asthma Clinical Research Network

Szefler, S. J., Chinchilli, V. M., Israel, E., Denlinger, L. C., Lemanske, R. F., Calhoun, W. & Peters, S. P., May 2012, In : Thorax. 67, 5, p. 450-455 6 p.

Research output: Contribution to journal › Review article

National Heart, Lung, and Blood Institute (U.S.)
Asthma
Research
Clinical Trials
Leukotriene Antagonists
106 Citations (Scopus)

Piecing together the past: Statistical insights into paleoclimatic reconstructions

Tingley, M. P., Craigmile, P. F., Haran, M., Li, B., Mannshardt, E. & Rajaratnam, B., Mar 5 2012, In : Quaternary Science Reviews. 35, p. 1-22 22 p.

Research output: Contribution to journal › Review article

reconstruction
climate
statistics
modeling
paleoclimate
533 Citations (Scopus)

Planet occurrence within 0.25AU of solar-type stars from Kepler

Howard, A. W., Marcy, G. W., Bryson, S. T., Jenkins, J. M., Rowe, J. F., Batalha, N. M., Borucki, W. J., Koch, D. G., Dunham, E. W., Gautier, T. N., Van Cleve, J., Cochran, W. D., Latham, D. W., Lissauer, J. J., Torres, G., Brown, T. M., Gilliland, R. L., Buchhave, L. A., Caldwell, D. A., Christensen-Dalsgaard, J. & 47 others, Ciardi, D., Fressin, F., Haas, M. R., Howell, S. B., Kjeldsen, H., Seager, S., Rogers, L., Sasselov, D. D., Steffen, J. H., Basri, G. S., Charbonneau, D., Christiansen, J., Clarke, B., Dupree, A., Fabrycky, D. C., Fischer, D. A., Ford, E. B., Fortney, J. J., Tarter, J., Girouard, F. R., Holman, M. J., Johnson, J. A., Klaus, T. C., MacHalek, P., Moorhead, A. V., Morehead, R. C., Ragozzine, D., Tenenbaum, P., Twicken, J. D., Quinn, S. N., Isaacson, H., Shporer, A., Lucas, P. W., Walkowicz, L. M., Welsh, W. F., Boss, A., Devore, E., Gould, A., Smith, J. C., Morris, R. L., Prsa, A., Morton, T. D., Still, M., Thompson, S. E., Mullally, F., Endl, M. & MacQueen, P. J., Aug 1 2012, In : Astrophysical Journal, Supplement Series. 201, 2, 15.

Research output: Contribution to journal › Review article

planets
planet
occurrences
stars
orbitals
5 Citations (Scopus)

Private forest landowners: Estimating population parameters

Metcalf, A. L., Finley, J. C., Luloff, A. E., Shumway, D. & Stedman, R. C., Oct 1 2012, In : Journal of Forestry. 110, 7, p. 362-370 9 p.

Research output: Contribution to journal › Review article

private forestry
landowners
landowner
USDA Forest Service
wildlife habitats
2011
18 Citations (Scopus)

A conceptual framework for pharmacodynamic genome-wide association studies in pharmacogenomics

Wu, R., Tong, C., Wang, Z., Mauger, D., Tantisira, K., Szefler, S. J., Chinchilli, V. M. & Israel, E., Oct 1 2011, In : Drug Discovery Today. 16, 19-20, p. 884-890 7 p.

Research output: Contribution to journal › Review article

Genome-Wide Association Study
Pharmacogenetics
Pharmaceutical Preparations
Genetic Testing
Genetic Association Studies
10 Citations (Scopus)

A note on small composite designs for sequential experimentation

Nguyen, N. K. & Lin, D. K. J., Mar 1 2011, In : Journal of Statistical Theory and Practice. 5, 1, p. 109-117 9 p.

Research output: Contribution to journal › Review article

Experimentation
Composite
Design
First-order
Second-order Model