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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

2023

Surgical Management of G3 Gastroenteropancreatic Neuroendocrine Neoplasms: A Systematic Review and Meta-analysis

Ziogas IA, Tasoudis PT, Borbon LC, Sherman SK, Breheny PJ, Chandrasekharan C, Dillon JS, Bellizzi AM and Howe JR
Annals of Surgical Oncology, 30: 148–160. Journal

2022

Adaptive hybrid screening for efficient lasso optimization

Wang C and Breheny P
Journal of Statistical Computation and Simulation, 92: 2233–2256. Journal R

Oncogenic RABL6A promotes NF1-associated MPNST progression in vivo

Kohlmeyer JL, Kaemmer CA, Lingo JJ, Voigt E, Leidinger MR, McGivney GR, Scherer A, Koppenhafer SL, Gordon DJ, Breheny P, Meyerholz DK, Tanas MR, Dodd RD and Quelle DE
Neuro-Oncology Advances, 4: 1–11. Journal

Hypertensive disorders of pregnancy among women with a history of leukemia or lymphoma

Anand ST, Ryckman KK, Baer RJ, Charlton ME, Breheny PJ, Terry WW, McLemore MR, Karasek DA, Jelliffe-Pawlowski LL and Chrischilles EA
Pregnancy Hypertension, 29: 101–107. Journal

The risk of preterm birth among women with a history of leukemia or lymphoma

Anand ST, Chrischilles EA, Baer RJ, Charlton ME, Breheny PJ, Terry WW, McLemore MR, Karasek DA, Jelliffe-Pawlowski LL and Ryckman KK
The Journal of Maternal-Fetal & Neonatal Medicine, 35: 6115–6123. Journal

Metabolic differences among newborns born to mothers with a history of leukemia or lymphoma

Anand ST, Ryckman KK, Baer RJ, Charlton ME, Breheny PJ, Terry WW, Kober K, Oltman S, Rogers EE, Jelliffe-Pawlowski LL and Chrischilles EA
The Journal of Maternal-Fetal & Neonatal Medicine, 35: 6751–6758. Journal

2021

Penalized linear mixed models for structured genetic data

Reisetter AC and Breheny P
Genetic Epidemiology, 45: 427–444. Journal

Hybrid safe-strong rules for efficient optimization in lasso-type problems

Zeng Y, Yang T and Breheny P
Computational Statistics and Data Analysis, 153: 107063. Journal PDF Reproduce

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

Zeng Y and Breheny P
R Journal, 12: 6–19. Journal PDF R Reproduce

Prognostic and therapeutic value of the Hippo pathway, RABL6A, and p53-MDM2 axes in sarcomas

Desai C, Thomason J, Kohlmeyer JL, Reisetter AC, Ahirwar P, Jahanseir K, Leidinger M, Ofori-Amanfo G, Fritchie K, Velu SE, Breheny P, Quelle DE and Tanas MR
Oncotarget, 12: 740–755. Journal

Development and comparison of novel bioluminescent mouse models of pancreatic neuroendocrine neoplasm metastasis

Kaemmer CA, Umesalma S, Maharjan CK, Moose DL, Narla G, Mott SL, Zamba GKD, Breheny P, Darbro BW, Bellizzi AM, Henry MD and Quelle DE
Scientific Reports, 11: 10252. Journal

RABL6A promotes pancreatic neuroendocrine tumor angiogenesis and progression in vivo

Maharjan CK, Umesalma S, Kaemmer CA, Muniz VP, Bauchle C, Mott SL, Zamba KD, Breheny P, Leidinger MR, Darbro BW, Stephens SB, Meyerholz DK and Quelle DE
Biomedicines, 9: . Journal

Presacral neuroendocrine tumors associated with the Currarino syndrome

Scott AT, Tessmann JB, Braun T, Brown B, Breheny PJ, Darbro BW, Bellizzi AM, Dillon JS, O'Dorisio TM, Alderson A, Bennett B, Bernat JA, Metz DC and Howe JR
American Journal of Medical Genetics Part A, 185: 1582–1588. Journal

Perinatal determinants of growth trajectories in children born preterm

Jasper EA, Cho H, Breheny PJ, Bao W, Dagle JM and Ryckman KK
PLOS ONE, 16: 1–20. Journal

2020

Sparsity-regularized skewness estimation for the multivariate skew normal and multivariate skew t distributions

Wang S, Zimmerman DL and Breheny P
Journal of Multivariate Analysis, 179: 104639. Journal

Gene expression signatures identify novel therapeutics for metastatic pancreatic neuroendocrine tumors

Scott AT, Weitz M, Breheny PJ, Ear PH, Darbro B, Brown BJ, Braun TA, Li G, Umesalma S, Kaemmer CA, Maharjan CK, Quelle DE, Bellizzi AM, Chandrasekharan C, Dillon JS, O'Dorisio TM and Howe JR
Clinical Cancer Research, 26: 2011–2021. Journal

Locally invasive, castrate-resistant prostate cancer in a Pten/Trp53 double knockout mouse model of prostate cancer monitored with non-invasive bioluminescent imaging

Yong C, Moose DL, Bannick N, Gutierrez WR, Vanneste M, Svensson R, Breheny P, Brown JA, Dodd RD, Cohen MB and Henry MD
PLOS ONE, 15: 1–15. Journal

Cancer cells resist mechanical destruction in circulation via RhoA/actomyosin-dependent mechano-adaptation

Moose DL, Krog BL, Kim T, Zhao L, Williams-Perez S, Burke G, Rhodes L, Vanneste M, Breheny P, Milhem M, Stipp CS, Rowat AC and Henry MD
Cell Reports, 30: 3864–3874. Journal

Analysis of zebrafish periderm enhancers facilitates identification of a regulatory variant near human KRT8/18

Liu H, Duncan K, Helverson A, Kumari P, Mumm C, Xiao Y, Carlson JC, Darbellay F, Visel A, Leslie E, Breheny P, Erives AJ and Cornell RA
eLife, 9: e51325. Journal

Encoding the odor of cigarette smoke

McClintock TS, Khan N, Alimova Y, Aulisio M, Han DY and Breheny P
Journal of Neuroscience, 40: 7043–7053. Journal

Mixture and Concentration Effects on Odorant Receptor Response Patterns In Vivo

McClintock TS, Wang Q, Sengoku T, Titlow WB and Breheny P
Chemical Senses, 45: 429–438. Journal

Modulation of the combinatorial code of odorant receptor response patterns in odorant mixtures

de March CA, Titlow WB, Sengoku T, Breheny P, Matsunami H and McClintock TS
Molecular and Cellular Neuroscience, 104: 103469. Journal

Key positions of HIV-1 Env and signatures of vaccine efficacy show gradual reduction of population founder effects at the clade and regional levels

Han C, Johnson J, Dong R, Kandula R, Kort A, Wong M, Yang T, Breheny PJ, Brown GD and Haim H
mBio, 11: . Journal

Outdoor light at night and postmenopausal breast cancer risk in the NIH-AARP diet and health study

Xiao Q, James P, Breheny P, Jia P, Park Y, Zhang D, Fisher JA, Ward MH and Jones RR
International Journal of Cancer, 147: 2363–2372. Journal

Early pregnancy prediction of gestational diabetes mellitus risk using prenatal screening biomarkers in nulliparous women

Snyder BM, Baer RJ, Oltman SP, Robinson JG, Breheny PJ, Saftlas AF, Bao W, Greiner AL, Carter KD, Rand L, Jelliffe-Pawlowski LL and Ryckman KK
Diabetes Research and Clinical Practice, 163: 108139. Journal

A randomized control trial evaluating efficacy of antimicrobial impregnated hospital privacy curtains in an intensive care setting

Wilson G, Jackson V, Boyken L, Puig-Asensio M, Marra AR, Perencevich E, Schweizer ML, Diekema D, Breheny P and Petersen C
American Journal of Infection Control, 48: 862–868. Journal

Bioaerosols generated from toilet flushing in rooms of patients with Clostridioides difficile infection

Wilson GM, Jackson VB, Boyken LD, Schweizer ML, Diekema DJ, Petersen CA, Breheny PJ, Nonnenmann MW and Perencevich EN
Infection Control and Hospital Epidemiology, 41: 517–521. Journal

2019

Marginal false discovery rates for penalized regression models

Breheny PJ.
Biostatistics, 20: 299–314. Journal PDF R Reproduce

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

Miller RE and Breheny P
Biometrical Journal, 61: 889–901. Journal PDF R 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. Journal

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. Journal 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. Journal

2018

p-value histograms: Inference and diagnostics

Breheny P, Stromberg A and Lambert J
High-Throughput, 7: 1–13. Journal 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
Journal of Clinical Investigation, 128: 1154–1163. Journal

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, B\"odker FL, Litterman NK, Jiang P, Russell L, Hinds DA, Hu Y, the 23andMe Research Team, Rokas A, Teramo K, Christensen K, Williams SM, R\"amet M, Kingsmore SF, Ryckman KK, Hallman M and Muglia LJ
PLOS Genetics, 14: 1–22. Journal

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. Journal

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. Journal

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. Journal

2017

Visualization of regression models using visreg

Breheny P and Burchett W
R Journal, 9: 56–71. Journal PDF R Website

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. Journal

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. Journal

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. Journal

First-time mothers' breast-feeding maintenance: role of experiences and changes in maternal perceptions

Schafer EJ, Campo S, Colaizy TT, Mulder PJ, Breheny P and Ashida S
Public Health Nutrition, 20: 3099–3108. Journal

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. Journal

2016

The Mnet method for variable selection

Huang J, Breheny P, Lee S, Ma S and Zhang C
Statistica Sinica, 26: 903–923. Journal PDF R

Overlapping group logistic regression with applications to genetic pathway selection

Zeng Y and Breheny P
Cancer Informatics, 15: 179–187. Journal PDF R

Nonlinear hierarchical modeling of experimental infection data

Singleton MD and Breheny PJ
Preventive Veterinary Medicine, 130: 129–136. Journal

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. Journal PDF R

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. Journal

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. Journal PDF

2015

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. Journal PDF R

The group exponential lasso for bi-level variable selection

Breheny P.
Biometrics, 71: 731–740. Journal PDF R

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. Journal PDF R

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. Journal 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. Journal

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. Journal

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. Journal 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. Journal

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: 383–391. Journal 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. Journal

2014

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
Journal of Neuroscience, 34: 15669–15678. Journal 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. Journal

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 and Oncology, 31: 475–480. Journal 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. Journal

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. Journal PDF

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

Breheny P.
Journal of the American Statistical Association, 109: 868–869. Journal PDF

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

Schofield M and Breheny P
American Statistician, 60: 63. Journal PDF

2013

Kernel-based aggregation of marker-level genetic association tests involving copy-number variation

Li Y and Breheny P
Microarrays, 2: 265–283. Journal 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. Journal 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. Journal 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. Journal PDF

2012

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. Journal PDF

A Selective Review of Group Selection in High-Dimensional Models

Huang J, Breheny P and Ma S
Statistical Science, 27: 481–499. Journal PDF

Statistical challenges and opportunities in copy number variant association studies

Breheny P, Li Y and Charnigo R
Journal of Biometrics and Biostatistics, 3: e118. Journal 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. Journal 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. Journal 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. Journal 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 and Environment, 25: 402–418. Journal 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 and Alternative Medicine, 17: 96–103. Journal PDF

2011

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. Journal PDF R

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. Journal 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. Journal PDF

Review of Intuitive Biostatistics, by Harvey Motulsky

Breheny P.
American Statistician, 65: 67–68. Journal PDF

2009

Penalized methods for bi-level variable selection

Breheny P and Huang J
Statistics and Its Interface, 2: 369–380. Journal PDF R

2008

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. Journal 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. Journal
Featured in The Hearing Journal's ""Best of 2008"" issue. Link

2003

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. Journal PDF