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See here for only the more technical/statistical/methodological publications

In Submission

Cross validation approaches for penalized Cox regression

Dai B and Breheny P
In submission. [pdf]

Feature-specific inference for penalized regression using local false discovery rates

Miller R and Breheny P
In submission. [pdf] [R package]

The biglasso package: A memory- and computation-efficient solver for lasso model fitting with big data in R

Zeng Y and Breheny P
In submission. [pdf] [R package]

Efficient feature screening for lasso-type problems via hybrid safe-strong rules

Zeng Y, Breheny P and Yang T
In submission. [pdf]


Marginal false discovery rates for penalized regression models

Breheny PJ.
Biostatistics, 20: 299-314. [link] [pdf] [R package] [Reproduce]

Marginal false discovery rate control for likelihood-based penalized regression models

Miller RE and Breheny P
Biometrical Journal, 61: 889-901. [link] [pdf] [R package] [Reproduce]

Genetic Risk Scores for Maternal Lipid Levels and Their Association with Preterm Birth

Smith CJ, Jasper EA, Baer RJ, Breheny PJ, Paynter RA, Bao W, Robinson JG, Dagle JM, Jelliffe-Pawlowski LL and Ryckman KK
Lipids, 54: 641-650. [link]

Development and validation of a clinical model for preconception and early pregnancy risk prediction of gestational diabetes mellitus in nulliparous women

Donovan BM, Breheny PJ, Robinson JG, Baer RJ, Saftlas AF, Bao W, Greiner AL, Carter KD, Oltman SP, Rand L, Jelliffe-Pawlowski LL and Ryckman KK
PLOS ONE, 14: 1-21. [link] [App]

Effective cytoreduction can be achieved in patients with numerous neuroendocrine tumor liver metastases (NETLMs)

Scott AT, Breheny PJ, Keck KJ, Bellizzi AM, Dillon JS, O'Dorisio TM and Howe JR
Surgery, 165: 166 - 175. [link]


p-value histograms: Inference and diagnostics

Breheny P, Stromberg A and Lambert J
High-Throughput, 7: 1–13. [link] [pdf]

A common variant alters SCN5A–miR-24 interaction and associates with heart failure mortality

Zhang X, Yoon J, Morley M, McLendon JM, Mapuskar KA, Gutmann R, Mehdi H, Bloom HL, Dudley SC, Ellinor PT, Shalaby AA, Weiss R, Tang WHW, Moravec CS, Singh M, Taylor AL, Yancy CW, Feldman AM, McNamara DM, Irani K, Spitz DR, Breheny P, Margulies KB, London B and Boudreau RL
The Journal of Clinical Investigation, 128: 1154-1163. [link]

Whole exome sequencing reveals HSPA1L as a genetic risk factor for spontaneous preterm birth

Huusko JM, Karjalainen MK, Graham BE, Zhang G, Farrow EG, Miller NA, Jacobsson B, Eidem HR, Murray JC, Bedell B, Breheny P, Brown NW, Bødker FL, Litterman NK, Jiang P, Russell L, Hinds DA, Hu Y, the 23andMe Research Team, Rokas A, Teramo K, Christensen K, Williams SM, Rämet M, Kingsmore SF, Ryckman KK, Hallman M and Muglia LJ
PLOS Genetics, 14: 1-22. [link]

Association of newborn screening metabolites with risk of wheezing in childhood

Donovan BM, Ryckman KK, Breheny PJ, Gebretsadik T, Turi KN, Larkin EK, Li Y, Dorley MC and Hartert TV
Pediatric Research, 84: 619–624. [link]

Maternal dyslipidemia and risk for preterm birth

Smith CJ, Baer RJ, Oltman SP, Breheny PJ, Bao W, Robinson JG, Dagle JM, Liang L, Feuer SK, Chambers CD, Jelliffe-Pawlowski LL and Ryckman KK
PLOS ONE, 13: 1-10. [link]

Changes in gene expression in small bowel neuroendocrine tumors associated with progression to metastases

Keck KJ, Breheny P, Braun TA, Darbro B, Li G, Dillon JS, Bellizzi AM, O'Dorisio TM and Howe JR
Surgery, 163: 232 - 239. [link]


Visualization of regression models using visreg

Breheny P and Burchett W
The R Journal, 9: 56–71. [link] [pdf] [R package] [Homepage]

Revisiting the applicability of adult early post-operative nausea and vomiting risk factors for the paediatric patient: A prospective study using cotinine levels in children undergoing adenotonsillectomies

Chau D, Reddy A, Breheny P, Young A, Ashford E, Song M, Zhang C, Taylor T, Younes A and Vazifedan T
Indian Journal of Anaesthesia, 61: 964-971. [link]

68Ga-DOTATOC imaging of neuroendocrine tumors: A systematic review and metaanalysis

Graham MM, Gu X, Ginader T, Breheny P and Sunderland JJ
Journal of Nuclear Medicine, 58: 1452-1458. [link]

Increased grade in neuroendocrine tumor metastases negatively impacts survival

Keck KJ, Choi A, Maxwell JE, Li G, O'Dorisio TM, Breheny P, Bellizzi AM and Howe JR
Annals of Surgical Oncology, 24: 2206–2212. [link]

Genetic predisposition to elevated levels of C-reactive protein is associated with a decreased risk for preeclampsia

Spracklen CN, Smith CJ, Saftlas AF, Triche EW, Bjonnes A, Keating BJ, Saxena R, Breheny PJ, Dewan AT, Robinson JG, Hoh J and Ryckman KK
Hypertension in Pregnancy, 36: 30-35. [link]


The Mnet method for variable selection

Huang J, Breheny P, Lee S, Ma S and Zhang C
Statistica Sinica, 26: 903-923. [link] [pdf] [R package]

Overlapping group logistic regression with applications to genetic pathway selection

Zeng Y and Breheny P
Cancer Informatics, 15: 179–187. [link] [pdf] [R package]

Nonlinear hierarchical modeling of experimental infection data

Singleton MD and Breheny PJ
Preventive Veterinary Medicine, 130: 129 - 136. [link]

DEEPN as an approach for batch processing of yeast 2-hybrid interactions

Pashkova N, Peterson T, Krishnamani V, Breheny P, Stamnes M and Piper R
Cell Reports, 17: 303–315. [link] [pdf] [R package]

Identification of genetic modifiers of age-at-onset for familial Parkinson's disease

Hill-Burns EM, Ross OA, Wissemann WT, Soto-Ortolaza AI, Zareparsi S, Siuda J, Lynch T, Wszolek ZK, Silburn PA, Mellick GD, Ritz B, Scherzer CR, Zabetian CP, Factor SA, Breheny PJ and Payami H
Human Molecular Genetics, 25: 3849. [link]

Genetic risk score for essential hypertension and risk of preeclampsia

Smith CJ, Saftlas AF, Spracklen CN, Triche EW, Bjonnes A, Keating B, Saxena R, Breheny PJ, Dewan AT, Robinson JG, Hoh J and Ryckman KK
American Journal of Hypertension, 29: 17-24. [link] [pdf]


Strong Rules for Nonconvex Penalties and Their Implications for Efficient Algorithms in High-Dimensional Regression

Lee S and Breheny P
Journal of Computational and Graphical Statistics, 24: 1074-1091. [link] [pdf] [R package]

The group exponential lasso for bi-level variable selection

Breheny P.
Biometrics, 71: 731–740. [link] [pdf] [R package]

Group descent algorithms for nonconvex penalized linear and logistic regression models with grouped predictors

Breheny P and Huang J
Statistics and Computing, 25: 173-187. [link] [pdf] [R package]

Penalized multimarker vs. single-marker regression methods for genome-wide association studies of quantitative traits

Yi H, Breheny P, Imam N, Liu Y and Hoeschele I
Genetics, 199: 205-222. [link] [pdf]
Featured article. [link]

Downregulation of dystroglycan glycosyltransferases LARGE2 and ISPD associate with increased mortality in clear cell renal cell carcinoma

Miller M, Ma D, Schappet J, Breheny P, Mott S, Bannick N, Askeland E, Brown J and Henry M
Molecular Cancer, 14: 141. [link]

Implementation and Evaluation of a School-Based Human Papillomavirus Vaccination Program in Rural Kentucky

Vanderpool RC, Breheny PJ, Tiller PA, Huckelby CA, Edwards AD, Upchurch KD, Phillips CA and Weyman CF
American Journal of Preventive Medicine, 49: 317 - 323. [link]

Genetic Predisposition to Dyslipidemia and Risk of Preeclampsia

Spracklen CN, Saftlas AF, Triche EW, Bjonnes A, Keating B, Saxena R, Breheny PJ, Dewan AT, Robinson JG, Hoh J and Ryckman KK
American Journal of Hypertension, 28: 915-923. [link] [pdf]

miR-888: A Novel Cancer-Testis Antigen that Targets the Progesterone Receptor in Endometrial Cancer

Hovey AM, Devor EJ, Breheny PJ, Mott SL, Dai D, Thiel KW and Leslie KK
Translational Oncology, 8: 85 - 96. [link]

Morphine versus Clonidine for Neonatal Abstinence Syndrome

Bada H, Sithisarn T, Gibson J, Garlitz K, Caldwell R, Capilouto G, Li Y, Leggas M and Breheny P
Pediatrics, 135: e383-e391. [link] [pdf]

Do Clinical Parameters Predict First Planned Extubation Outcome in the Pediatric Intensive Care Unit?

Laham JL, Breheny PJ and Rush A
Journal of Intensive Care Medicine, 30: 89-96. [link]


In Vivo identification of eugenol-responsive and muscone-responsive mouse odorant receptors

McClintock TS, Adipietro K, Titlow WB, Breheny P, Walz A, Mombaerts P and Matsunami H
The Journal of Neuroscience, 34: 15669–15678. [link] [pdf]
Featured article. [link]

Semen quality of stallions challenged with the Kentucky 84 strain of equine arteritis virus

Campos JR, Breheny P, Araujo RR, Troedsson MHT, Squires EL, Timoney PJ and Balasuriya UBR
Theriogenology, 82: 1068 - 1079. [link]

Impact of Obesity on the Risk of Venous Thromboembolism in an Inpatient Pediatric Population

Stokes S, Breheny P, Radulescu A and Radulescu VC
Pediatric Hematology-Oncology, 31: 475-480. [link] [pdf]

Procalcitonin to Predict Bacterial Coinfection in Infants With Acute Bronchiolitis: A Preliminary Analysis

Laham JL, Breheny PJ, Gardner BM and Bada H
Pediatric Emergency Care, 30: 11–15. [link]

Impact of Non-HIV Related Comorbidities on Retention in HIV Medical Care: Does Retention Improve Over Time?

Crawford TN, Sanderson WT, Breheny P, Fleming ST and Thornton A
AIDS and Behavior, 18: 617-624. [link] [pdf]

Review of Genomic Clinical Trials and Predictive Medicine, by Richard Simon

Breheny P.
Journal of the American Statistical Association, 109: 868-869. [link] [pdf]

Review of The BUGS Book: A Practical Introduction to Bayesian Analysis, by David Lunn et al.

Schofield M and Breheny P
The American Statistician, 60: 63. [link] [pdf]


Kernel-Based Aggregation of Marker-Level Genetic Association Tests Involving Copy-Number Variation

Li Y and Breheny P
Microarrays, 2: 265–283. [link] [pdf]

Molecular events in the cell types of the olfactory epithelium during adult neurogenesis

Heron P, Stromberg A, Breheny P and McClintock T
Molecular Brain, 6: 49. [link] [pdf]

The effect of bacterial dose and foal age at challenge on Rhodococcus equi infection

Sanz M, Loynachan A, Sun L, Oliveira A, Breheny P and Horohov DW
Veterinary Microbiology, 167: 623–631. [link] [pdf]

Factors Associated With Pharmacy Student Interest in International Study

Owen C, Breheny P, Ingram R, Pfeifle W, Cain J and Ryan M
American Journal of Pharmaceutical Education, 77: 54. [link] [pdf]


Genetic Association Studies of Copy-Number Variation: Should Assignment of Copy Number States Precede Testing?

Breheny P, Chalise P, Batzler A, Wang L and Fridley BL
PLoS ONE, 7: e34262. [link] [pdf]

A Selective Review of Group Selection in High-Dimensional Models

Huang J, Breheny P and Ma S
Statistical Science, 27: 481-499. [link] [pdf]

Statistical Challenges and Opportunities in Copy Number Variant Association Studies

Breheny P, Li Y and Charnigo R
Journal of Biometrics & Biostatistics, 3: e118. [link] [pdf]

New Real-Time PCR Assay Using Allelic Discrimination for Detection and Differentiation of Equine Herpesvirus-1 Strains with A2254 and G2254 Polymorphisms

Smith KL, Li Y, Breheny P, Cook RF, Henney PJ, Sells S, Pronost S, Lu Z, Crossley BM, Timoney PJ and Balasuriya UBR
Journal of Clinical Microbiology, 50: 1981-1988. [link] [pdf]

Genomics of mature and immature olfactory sensory neurons

Nickell MD, Breheny P, Stromberg AJ and McClintock TS
Journal of Comparative Neurology, 520: 2608–2629. [link] [pdf]

Primary radiation therapy for medically inoperable patients with clinical stage I and II endometrial carcinoma

Podzielinski I, Randall ME, Breheny PJ, Escobar PF, Cohn DE, Quick AM, Chino JP, Lopez-Acevedo M, Seitz JL, Zook JE and Seamon LG
Gynecologic Oncology, 124: 36–41. [link] [pdf]

The Long-Term Effects of a Coal Waste Disaster on Social Trust in Appalachian Kentucky

Scott SL, McSpirit S, Breheny P and Howell BM
Organization & Environment, 25: 402-418. [link] [pdf]

Meditation for Quality Improvement of Medical Encounters: Single-Intervention, Vedanta-Based Meditation Effects on Vital Signs and Mood Indices

Srinivasan J and Breheny PJ
Journal of Evidence-Based Complementary & Alternative Medicine, 17: 96-103. [link] [pdf]


Coordinate descent algorithms for nonconvex penalized regression, with applications to biological feature selection

Breheny P and Huang J
Annals of Applied Statistics, 5: 232–253. [link] [pdf] [R package]

Exploration and comparison of methods for combining population- and family-based genetic association using the Genetic Analysis Workshop 17 mini-exome

Fardo D, Druen A, Liu J, Mirea L, Infante-Rivard C and Breheny P
BMC Proceedings, 5: S28. [link] [pdf]

Surface sensing in Vibrio parahaemolyticus triggers a programme of gene expression that promotes colonization and virulence

Gode-Potratz CJ, Kustusch RJ, Breheny PJ, Weiss DS and McCarter LL
Molecular Microbiology, 79: 240–263. [link] [pdf]

Review of Intuitive Biostatistics, by Harvey Motulsky

Breheny P.
The American Statistician, 65: 67-68. [link] [pdf]


Penalized methods for bi-level variable selection

Breheny P and Huang J
Statistics and Its Interface, 2: 369–380. [link] [pdf] [R package]


Impact of travel distance on WISEWOMAN Intervention attendance for a rural population

Oleson JJ, Breheny PJ, Pendergast JF, Ryan S and Litchfield R
Preventive Medicine, 47: 565–569. [link] [pdf]

Multivariate predictors of music perception and appraisal by adult cochlear implant users

Gfeller K, Oleson J, Knutson JF, Breheny P, Driscoll V and Olszewski C
Journal of the American Academy of Audiology, 19: 120. [link]
Featured in The Hearing Journal's "Best of 2008" issue. [link]


Ligand specificity modulated by prolyl imide bond cis/trans isomerization in the Itk SH2 domain: a quantitative NMR study

Breheny PJ, Laederach A, Fulton DB and Andreotti AH
Journal of the American Chemical Society, 125: 15706–15707. [link] [pdf]