Patrick Breheny

See also: Google Scholar

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

2025

A New Perspective on High Dimensional Confidence Intervals

Harris L and Breheny P

In submission. Preprint

Penalized mixed models to adjust for batch effects and unobserved confounding in high dimensional regression

Lu Y and Breheny P

In submission. Preprint

plmmr: an R package to fit penalized linear mixed models for genome-wide association data with complex correlation structure

Peter TK, Reisetter AC, Lu Y, Rysavy OA and Breheny PJ

Briefings in Bioinformatics, to appear, to appear. Preprint

EHE cell cultures are a platform for mechanistic and therapeutic investigation

Scalora N, DeWane, Gillian, Drebot Y, Khan, Ali A, Sinha S, Ghosh, Krishnendu, Robinson D, Cogswell, Patricia, Bellizzi AM, Snow, Anthony N, Breheny P, Chimenti, Michael S and Tanas MR

Scientific Reports, 15: 35516. Journal

Distinct odorant receptor response patterns to aliphatic odorants in freely behaving mice

de March CA, Breheny P, Titlow WB, Matsunami H and McClintock TS

Chemical Senses, 50: 1–10. Journal

Peptide receptor radionuclide therapy improves survival in patients who progress after resection of gastroenteropancreatic neuroendocrine tumors

Borbon LC, Sherman SK, Breheny PJ, Chandrasekharan C, Menda Y, Bushnell D, Bellizzi AM, Ear PH, O'Dorisio MS, O'Dorisio TM, Dillon JS and Howe JR

Annals of Surgical Oncology, 32: 1136–1148. Journal

Familial oculoauriculovertebral spectrum: a genomic investigation of autosomal dominant inheritance

Petrin AL, Machado-Paula LA, Hinkle A, Hovey L, Awotoye W, Chimenti M, Darbro B, Ribeiro-Bicudo LA, Dabdoub SM, Peter T, Breheny P, Murray JC, Otterloo EV, Venugopalan SR and Moreno-Uribe LM

The Cleft Palate Craniofacial Journal, 0: 10556656241306202. Journal

2024

Cross-validation approaches for penalized Cox regression

Dai B and Breheny P

Statistical Methods in Medical Research, 33: 702–715. Journal

Functional copy-number alterations as diagnostic and prognostic biomarkers in neuroendocrine tumors

Vaughn H, Major H, Kadera E, Keck K, Dunham T, Qian Q, Brown B, Scott A, Bellizzi AM, Braun T, Breheny P, Quelle DE, Howe JR and Darbro B

International Journal of Molecular Sciences, 25: 7532. 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-retest 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