See also: Google scholar
See here for only the more technical/statistical/methodological publications
2024
Cross-validation approaches for penalized Cox regression
Dai B and Breheny P
Statistical Methods in Medical Research, 33: 702–715. Journal
2023
Feature-specific inference for penalized regression using local false discovery rates
Miller R and Breheny P
Statistics in Medicine, 42: 1412–1429. Journal PDF R
CDK4/6-MEK Inhibition in MPNSTs Causes Plasma Cell Infiltration, Sensitization to PD-L1 Blockade, and Tumor Regression
Kohlmeyer JL, Lingo JJ, Kaemmer CA, Scherer A, Warrier A, Voigt E, Raygoza Garay JA, McGivney GR, Brockman QR, Tang A, Calizo A, Pollard K, Zhang X, Hirbe AC, Pratilas CA, Leidinger M, Breheny P, Chimenti MS, Sieren JC, Monga V, Tanas MR, Meyerholz DK, Darbro BW, Dodd RD and Quelle DE
Clinical Cancer Research, 29: 3484–3497. Journal
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
Global expression analysis of endometrial cancer cells in response to progesterone identifies new therapeutic targets
Thiel KW, Newtson AM, Devor EJ, Zhang Y, Malmrose PK, Bi J, Losh HA, Davies S, Smith LE, Padilla J, Leiva SM, Grueter CE, Breheny P, Hagan CR, Pufall MA, Gertz J, Guo Y and Leslie KK
The Journal of Steroid Biochemistry and Molecular Biology, 234: 106399. 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: 633. 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
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
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
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
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
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
Quantitative Test\textendashRetest Measurement of 68Ga-PSMA-HBED-CC in Tumor and Normal Tissue
Pollard JH, Raman C, Zakharia Y, Tracy CR, Nepple KG, Ginader T, Breheny P and Sunderland JJ
Journal of Nuclear Medicine, 61: 1145–1152. 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
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
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
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
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: 3849–3862. 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
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