Publications

Ma D, Cho S, Meng X, Gulati A, Knight J, Goralsky L, Peng G, Shaw MM, Widomski A, Popa A, Zhao C, Dykas D, Tikhonova I, Bale A, Somlo S, Zhang H, Besse W. Optimizing next-generation sequencing for genetic diagnosis in autosomal dominant polycystic kidney disease. Genet Med. 2026 Feb 3;28(4):102529. doi: 10.1016/j.gim.2026.102529 PubMed: 41653026

Yamada C, Peng G, Johnson JA Jr, Nusbaum A, Sanz N, AlQallaf H, Nichols F, Movila A. Porphyromonas gingivalis-Derived Virulence Lipids Accelerate Osteoclastogenesis Independently of High Mobility Group Box Protein-1 Canonical Signaling. Mol Oral Microbiol. 2025 Dec 7;:e70015. doi: 10.1111/omi.70015 PubMed: 41355213

Xie Y, Peng G, Tikhonova I, Enns G, Zhao H, Cowan T, Scharfe C. Improving newborn screening accuracy through genome sequencing, targeted metabolomics, and machine learning. BMC Med Genomics. 2025 Nov 19;18(1):187. doi: 10.1186/s12920-025-02261-x PubMed: 41257776 | PMCID: PMC12628566

Ackah SA, Karmazyn B, Dewey A, Econs MJ, Peng G, Parks-Schenck C, Skiles JL, Niziolek P, DiMeglio LA, Warden SJ, Imel EA. Can transient neonatal osteosclerosis be differentiated from malignant infantile osteopetrosis? Bone Rep. 2025 Dec;27:101885. doi: 10.1016/j.bonr.2025.101885 PubMed: 41277893 | PMCID: PMC12639257

Xiao C, Miller AH, Paul S, Fedirko V, Peng G, Conneely KN, Felger JC, Shin DM, Saba NF, Bruner DW. Neighborhood Deprivation and Biological and Psychosocial Outcomes for Head and Neck Cancer. JAMA Network Open. 2025;8(10):e2538569. doi: 10.1001/jamanetworkopen.2025.38569 PubMed: 41118167 | PMCID: PMC12541531

Mogavero MP, Peng G, Marchese G, Lanza G, Ferini-Strambi L, Ferri R, Koo BB. Sex differences in cerebrospinal fluid proteomics of patients with restless legs syndrome. Sleep. 2025 Aug 14;48(8). doi: 10.1093/sleep/zsaf112 PubMed: 40289925

Voegtline KM, Raghunathan RS, Sosnowski DW, Peng G, Hoyo C, Murphy SK, Hernandez RG, Johnson SB. PedBE age and age acceleration in umbilical vein endothelial cells: an examination of infant birth outcomes. J Dev Orig Health Dis. 2025;16:e7. doi: 10.1017/S2040174424000333 PubMed: 40071323 | PMCID: PMC12175094

So J, Strobel O, Wann J, Kim K, Paul A, Acri DJ, Dabin LC, Kim J, Peng G, Roh HC. Robust single-nucleus RNA sequencing reveals depot-specific cell population dynamics in adipose tissue remodeling during obesity. eLife. 2025;13. doi: 10.7554/eLife.97981 PubMed: 39804687 | PMCID: PMC11729396

Xiao C, Peng G, Conneely KN, Zhao H, Felger JC, Wommack EC, Higgins KA, Shin DM, Saba NF, Bruner DW, Miller AH. DNA methylation profiles of cancer-related fatigue associated with markers of inflammation and immunometabolism. Molecular Psychiatry. 2025;30(1):76–83. doi: 10.1038/s41380-024-02652-z PubMed: 38977918

Shimonty A, Pin F, Prideaux M, Peng G, Huot J, Kim H, Rosen CJ, Spiegelman BM, Bonewald LF. Deletion of FNDC5/irisin modifies murine osteocyte function in a sex-specific manner. eLife. 2024;12. doi: 10.7554/eLife.92263 PubMed: 38661340 | PMCID: PMC11045224

Peng G, Deosthale P, Pianeta R, Messersmith HM, Plotkin LI. Sex dimorphic response to osteocyte miR21 deletion in murine calvaria bone as determined by RNAseq analysis. JBMR Plus. 2024;8(6):ziae054. doi: 10.1093/jbmrpl/ziae054 PubMed: 38784723 | PMCID: PMC11114469

Lopez de Rodas M, Wang Y, Peng G, Gu J, Mino-Kenudson M, Riess JW, Velcheti V, Hellmann M, Gainor JF, Zhao H, Schalper KA. Objective Analysis and Clinical Significance of the Spatial Tumor-Infiltrating Lymphocyte Patterns in Non-Small Cell Lung Cancer. Clinical Cancer Research. 2024;30(5):998–1008. doi: 10.1158/1078-0432.CCR-23-2457 PubMed: 38127300 | PMCID: PMC10922461

Nguyen NH, Dodd-Eaton EB, Peng G, Corredor JL, Jiao W, Woodman-Ross J, Arun BK, Wang W. LFSPROShiny: An Interactive R/Shiny App for Prediction and Visualization of Cancer Risks in Families With Deleterious Germline TP53 Mutations. JCO Clinical Cancer Informatics. 2024;8:e2300167. doi: 10.1200/CCI.23.00167 PubMed: 38346271 | PMCID: PMC10871774

Sosnowski DW, Rojo-Wissar DM, Peng G, Parade SH, Sharkey K, Hoyo C, Murphy SK, Hernandez RG, Johnson SB. Maternal Childhood Adversity and Infant Epigenetic Aging: Moderation by Restless Sleep During Pregnancy. Developmental Psychobiology. 2024;66(2). doi: 10.1002/dev.22464 PubMed: 38601952 | PMCID: PMC11003750

Xie Y, Peng G, Zhao H, Scharfe C. Association of Maternal Age and Blood Markers for Metabolic Disease in Newborns. Metabolites. 2023;14(1). doi: 10.3390/metabo14010005 PubMed: 38276295 | PMCID: PMC10821442

Lin Y, Peng G, Bruner DW, Miller AH, Saba NF, Higgins KA, Shin DM, Claussen H, Johnston HR, Houser MC, Wommack EC, Xiao C. Associations of differentially expressed genes with psychoneurological symptoms in patients with head and neck cancer: A longitudinal study. Journal of Psychosomatic Research. 2023;175:111518. doi: 10.1016/j.jpsychores.2023.111518
PubMed: 37832274 | PMCID: PMC11789059

Xiao C, Fedirko V, Claussen H, Johnston HR, Peng G, Paul S, Maner-Smith KM, Higgins KA, Shin DM, Saba NF, Wommack EC, Bruner DW, Miller AH.
Circulating short chain fatty acids and fatigue in patients with head and neck cancer: A longitudinal prospective study.
Brain, Behavior, and Immunity. 2023;113:432–443.
doi: 10.1016/j.bbi.2023.07.025
PubMed: 37543249 | PMCID: PMC10528227

Prideaux M, Smargiassi A, Peng G, Brotto M, Robling AG, Bonewald LF. L-BAIBA Synergizes with Sub-Optimal Mechanical Loading to Promote New Bone Formation. JBMR Plus. 2023;7(6):e10746.
doi: 10.1002/jbm4.10746 PubMed: 37283651 | PMCID: PMC10241089

Peng G, Zhou Q, Chai H, Wen J, Zhao H, Taylor HS, Jiang YH, Li P. Estimation on risk of spontaneous abortions by genomic disorders from a meta-analysis of microarray results on large case series of pregnancy losses. Molecular Genetics & Genomic Medicine. 2023;11(8):e2181. doi: 10.1002/mgg3.2181 PubMed: 37013615 | PMCID: PMC10422064

Habet V, Li N, Qi J, Peng G, Charkoftaki G, Vasiliou V, Sharma L, Pober JS, Dela Cruz C, Yan X, Pierce RW. Integrated Analysis of Tracheobronchial Fluid from Before and After Cardiopulmonary Bypass Reveals Activation of the Integrated Stress Response and Altered Pulmonary Microvascular Permeability. Yale Journal of Biology and Medicine. 2023;96(1):23-42. doi: 10.59249/KFYZ8002 PubMed: 37009190 | PMCID: PMC10052603

Mak J, Peng G, Le A, Gandotra N, Enns GM, Scharfe C, Cowan TM. Validation of a targeted metabolomics panel for improved second-tier newborn screening. Journal of Inherited Metabolic Disease. 2023;46(2):194-205. doi: 10.1002/jimd.12591 PubMed: 36680545 | PMCID: PMC10023470

Qian DC, Ulrich BC, Peng G, Zhao H, Conneely KN, Miller AH, Bruner DW, Eldridge RC, Wommack EC, Higgins KA, Shin DM, Saba NF, Smith AK, Burtness B, Park HS, Stokes WA, Beitler JJ, Xiao C. Outcomes Stratification of Head and Neck Cancer Using Pre- and Post-treatment DNA Methylation From Peripheral Blood. International Journal of Radiation Oncology, Biology, Physics. 2023;115(5):1217-1228. doi: 10.1016/j.ijrobp.2022.11.009 PubMed: 36410685 | PMCID: PMC12272450

Peng G, Pakstis AJ, Gandotra N, Cowan TM, Zhao H, Kidd KK, Scharfe C. Metabolic diversity in human populations and correlation with genetic and ancestral geographic distances. Molecular Genetics and Metabolism. 2022;137(3):292-300. doi: 10.1016/j.ymgme.2022.10.002 PubMed: 36252453 | PMCID: PMC10131177

Peng G, Zhang Y, Zhao H, Scharfe C. dbRUSP: An Interactive Database to Investigate Inborn Metabolic Differences for Improved Genetic Disease Screening. International Journal of Neonatal Screening. 2022;8(3). doi: 10.3390/ijns8030048 PubMed: 36135348 | PMCID: PMC9504335

Peng G, Xi Y, Bellini C, Pham K, Zhuang ZW, Yan Q, Jia M, Wang G, Lu L, Tang MS, Zhao H, Wang H. Nicotine dose-dependent epigenomic-wide DNA methylation changes in the mice with long-term electronic cigarette exposure. American Journal of Cancer Research. 2022;12(8):3679-3692. PubMed: 36119846 | PMCID: PMC9442002

AlOlaby RR, Zafarullah M, Barboza M, Peng G, Varian BJ, Erdman SE, Lebrilla C, Tassone F. Differential Methylation Profile in Fragile X Syndrome-Prone Offspring Mice after in Utero Exposure to Lactobacillus Reuteri. Genes. 2022;13(8). doi: 10.3390/genes13081300 PubMed: 35893036 | PMCID: PMC9331364

Peng G, Chai H, Ji W, Lu Y, Wu S, Zhao H, Li P, Hu Q. Correlating genomic copy number alterations with clinicopathologic findings in 75 cases of hepatocellular carcinoma. BMC Medical Genomics. 2021;14(1):150. doi: 10.1186/s12920-021-00998-9 PubMed: 34103027 | PMCID: PMC8185937

Xiao C, Beitler JJ, Peng G, Levine ME, Conneely KN, Zhao H, Felger JC, Wommack EC, Chico CE, Jeon S, Higgins KA, Shin DM, Saba NF, Burtness BA, Bruner DW, Miller AH. Epigenetic age acceleration, fatigue, and inflammation in patients undergoing radiation therapy for head and neck cancer: A longitudinal study. Cancer. 2021;127(18):3361-3371. doi: 10.1002/cncr.33641 PubMed: 34027995

Xiao C, Miller AH, Peng G, Levine ME, Conneely KN, Zhao H, Eldridge RC, Wommack EC, Jeon S, Higgins KA, Shin DM, Saba NF, Smith AK, Burtness B, Park HS, Irwin ML, Ferrucci LM, Ulrich B, Qian DC, Beitler JJ, Bruner DW. Association of Epigenetic Age Acceleration With Risk Factors, Survival, and Quality of Life in Patients With Head and Neck Cancer. International Journal of Radiation Oncology, Biology, Physics. 2021;111(1):157-167. doi: 10.1016/j.ijrobp.2021.04.002 PubMed: 33882281 | PMCID: PMC8802868

Simpson S, Kaislasuo J, Peng G, Aldo P, Paidas M, Guller S, Mor G, Pal L. Peri-implantation cytokine profile differs between singleton and twin IVF pregnancies. American Journal of Reproductive Immunology. 2021;85(3):e13348. doi: 10.1111/aji.13348 PubMed: 32946159 | PMCID: PMC8221280

Xiao C, Fedirko V, Beitler J, Bai J, Peng G, Zhou C, Gu J, Zhao H, Lin IH, Chico CE, Jeon S, Knobf TM, Conneely KN, Higgins K, Shin DM, Saba N, Miller A, Bruner D. The role of the gut microbiome in cancer-related fatigue: pilot study on epigenetic mechanisms. Supportive Care in Cancer. 2021;29(6):3173-3182. doi: 10.1007/s00520-020-05820-3 PubMed: 33078326 | PMCID: PMC8055716

Peng G, Tang Y, Cowan TM, Zhao H, Scharfe C. Timing of Newborn Blood Collection Alters Metabolic Disease Screening Performance. Frontiers in Pediatrics. 2020;8:623184. doi: 10.3389/fped.2020.623184 PubMed: 33553077 | PMCID: PMC7854909

Zerjav M, DiAdamo A, Grommisch B, Katherine A, Chai H, Peng G, Li P. Cytogenomic Abnormalities in 19 Cases of Salivary Gland Tumors of Parotid Gland Origin. Case Reports in Genetics. 2020;2020:8897541. doi: 10.1155/2020/8897541 PubMed: 33343950 | PMCID: PMC7725583

Mansuri MS, Peng G, Wilson RS, Lam TT, Zhao H, Williams KR, Nairn AC. Differential Protein Expression in Striatal D1- and D2-Dopamine Receptor-Expressing Medium Spiny Neurons. Proteomes. 2020;8(4). doi: 10.3390/proteomes8040027
PubMed: 33066078 | PMCID: PMC7709116

Johnson RM, Olivares-Strank N, Peng G. A Class II-Restricted CD8γ13 T-Cell Clone Protects During Chlamydia muridarum Genital Tract Infection. Journal of Infectious Diseases. 2020;221(11):1895-1906. doi: 10.1093/infdis/jiz685 PubMed: 31899500 | PMCID: PMC7213565

Zhang YH, Aldo P, You Y, Ding J, Kaislasuo J, Petersen JF, Lokkegaard E, Peng G, Paidas MJ, Simpson S, Pal L, Guller S, Liu H, Liao AH, Mor G. Trophoblast-secreted soluble-PD-L1 modulates macrophage polarization and function. Journal of Leukocyte Biology. 2020;108(3):983-998. doi: 10.1002/JLB.1A0420-012RR PubMed: 32386458 | PMCID: PMC8190653

Ordulu Z, Chai H, Peng G, McDonald AG, De Nictolis M, Garcia-Fernandez E, Hardisson D, Prat J, Li P, Hui P, Oliva E, Buza N. Molecular and clinicopathologic characterization of intravenous leiomyomatosis. Modern Pathology. 2020;33(9):1844-1860. doi: 10.1038/s41379-020-0546-8 PubMed: 32341498 | PMCID: PMC7483566

Peng G, Tang Y, Gandotra N, Enns GM, Cowan TM, Zhao H, Scharfe C. Ethnic variability in newborn metabolic screening markers associated with false-positive outcomes. Journal of Inherited Metabolic Disease. 2020;43(5):934-943. doi: 10.1002/jimd.12236 PubMed: 32216101 | PMCID: PMC7540352

Silasi M, You Y, Simpson S, Kaislasuo J, Pal L, Guller S, Peng G, Ramhorst R, Grasso E, Etemad S, Durosier S, Aldo P, Mor G. Human Chorionic Gonadotropin modulates CXCL10 Expression through Histone Methylation in human decidua. Scientific Reports. 2020;10(1):5785. doi: 10.1038/s41598-020-62593-9 PubMed: 32238853 | PMCID: PMC7113245

Peng G, Tang Y, Cowan TM, Enns GM, Zhao H, Scharfe C. Reducing False-Positive Results in Newborn Screening Using Machine Learning. International Journal of Neonatal Screening. 2020;6(1). doi: 10.3390/ijns6010016 PubMed: 32190768 | PMCID: PMC7080200

Shin SJ, Dodd-Eaton EB, Peng G, Bojadzieva J, Chen J, Amos CI, Frone MN, Khincha PP, Mai PL, Savage SA, Ballinger ML, Thomas DM, Yuan Y, Strong LC, Wang W. Penetrance of Different Cancer Types in Families with Li-Fraumeni Syndrome: A Validation Study Using Multicenter Cohorts. Cancer Research. 2020;80(2):354-360. doi: 10.1158/0008-5472.CAN-19-0728 PubMed: 31719101 | PMCID: PMC6980689

Kaislasuo J, Simpson S, Petersen JF, Peng G, Aldo P, Lokkegaard E, Paidas M, Pal L, Guller S, Mor G. IL-10 to TNFα ratios throughout early first trimester can discriminate healthy pregnancies from pregnancy losses. American Journal of Reproductive Immunology. 2020;83(1):e13195. doi: 10.1111/aji.13195 PubMed: 31585488 | PMCID: PMC8295882

Peng G, Wilson R, Tang Y, Lam TT, Nairn AC, Williams K, Zhao H. ProteomicsBrowser: MS/proteomics data visualization and investigation. Bioinformatics. 2019;35(13):2313-2314. doi: 10.1093/bioinformatics/bty958 PubMed: 30462190 | PMCID: PMC6596887

Xie Y, Ostriker AC, Jin Y, Hu H, Sizer AJ, Peng G, Morris AH, Ryu C, Herzog EL, Kyriakides T, Zhao H, Dardik A, Yu J, Hwa J, Martin KA. LMO7 Is a Negative Feedback Regulator of Transforming Growth Factor β Signaling and Fibrosis. Circulation. 2019;139(5):679-693. doi: 10.1161/CIRCULATIONAHA.118.034615 PubMed: 30586711 | PMCID: PMC6371979

Peng G, de Fontnouvelle CA, Enns GM, Cowan TM, Zhao H, Scharfe C. Elevated methylmalonic acidemia (MMA) screening markers in Hispanic and preterm newborns. Molecular Genetics and Metabolism. 2019;126(1):39-42. doi: 10.1016/j.ymgme.2018.11.006 PubMed: 30448007 | PMCID: PMC6361520

Peng G, Shen P, Gandotra N, Le A, Fung E, Jelliffe-Pawlowski L, Davis RW, Enns GM, Zhao H, Cowan TM, Scharfe C. Combining newborn metabolic and DNA analysis for second-tier testing of methylmalonic acidemia. Genetics in Medicine. 2019;21(4):896-903. doi: 10.1038/s41436-018-0272-5 PubMed: 30209273 | PMCID: PMC6416784

Zhang X, Hu Y, Aouizerat BE, Peng G, Marconi VC, Corley MJ, Hulgan T, Bryant KJ, Zhao H, Krystal JH, Justice AC, Xu K. Machine learning selected smoking-associated DNA methylation signatures that predict HIV prognosis and mortality. Clinical Epigenetics. 2018;10(1):155. doi: 10.1186/s13148-018-0591-z PubMed: 30545403 | PMCID: PMC6293604

Madsen T, Braun D, Peng G, Parmigiani G, Trippa L. Efficient computation of the joint probability of multiple inherited risk alleles from pedigree data. Genetic Epidemiology. 2018;42(6):528-538. doi: 10.1002/gepi.22130 PubMed: 29943416 | PMCID: PMC6129424

Goffredo M, Santoro N, Tricò D, Giannini C, D'Adamo E, Zhao H, Peng G, Yu X, Lam TT, Pierpont B, Caprio S, Herzog RI. A Branched-Chain Amino Acid-Related Metabolic Signature Characterizes Obese Adolescents with Non-Alcoholic Fatty Liver Disease. Nutrients. 2017;9(7). doi: 10.3390/nu9070642 PubMed: 28640216 | PMCID: PMC5537762

Rauniyar N, Peng G, Lam TT, Zhao H, Mor G, Williams KR. Data-Independent Acquisition and Parallel Reaction Monitoring Mass Spectrometry Identification of Serum Biomarkers for Ovarian Cancer. Biomarker Insights. 2017;12:1177271917710948. doi: 10.1177/1177271917710948 PubMed: 28615921 | PMCID: PMC5462478

Peng G, Bojadzieva J, Ballinger ML, Li J, Blackford AL, Mai PL, Savage SA, Thomas DM, Strong LC, Wang W. Estimating TP53 Mutation Carrier Probability in Families with Li-Fraumeni Syndrome Using LFSPRO. Cancer Epidemiology, Biomarkers & Prevention. 2017;26(6):837-844. doi: 10.1158/1055-9965.EPI-16-0695 PubMed: 28137790 | PMCID: PMC5457344

Lefterova MI, Shen P, Odegaard JI, Fung E, Chiang T, Peng G, Davis RW, Wang W, Kharrazi M, Schrijver I, Scharfe C. Next-Generation Molecular Testing of Newborn Dried Blood Spots for Cystic Fibrosis. Journal of Molecular Diagnostics. 2016;18(2):267-82. doi: 10.1016/j.jmoldx.2015.11.005 PubMed: 26847993 | PMCID: PMC4816703

Peng G, Fan Y, Wang W. FamSeq: a variant calling program for family-based sequencing data using graphics processing units. PLoS Computational Biology. 2014;10(10):e1003880. doi: 10.1371/journal.pcbi.1003880 PubMed: 25357123 | PMCID: PMC4214554

Yuan X, Song H, Peng G, Hua X, Tang X. Prevalence of Corneal Astigmatism in Patients before Cataract Surgery in Northern China. Journal of Ophthalmology. 2014;2014:536412. doi: 10.1155/2014/536412 PubMed: 24991429 | PMCID: PMC4060487

Peng G, Fan Y, Palculict TB, Shen P, Ruteshouser EC, Chi AK, Davis RW, Huff V, Scharfe C, Wang W. Rare variant detection using family-based sequencing analysis. Proceedings of the National Academy of Sciences. 2013;110(10):3985-90. doi: 10.1073/pnas.1222158110 PubMed: 23426633 | PMCID: PMC3593912

Wu X, Dong H, Luo L, Zhu Y, Peng G, Reveille JD, Xiong M. A novel statistic for genome-wide interaction analysis. PLoS Genetics. 2010;6(9):e1001131. doi: 10.1371/journal.pgen.1001131 PubMed: 20885795 | PMCID: PMC2944798

Luo L, Peng G, Zhu Y, Dong H, Amos CI, Xiong M. Genome-wide gene and pathway analysis. European Journal of Human Genetics. 2010;18(9):1045-53. doi: 10.1038/ejhg.2010.62 PubMed: 20442747 | PMCID: PMC2924916

Peng G, Luo L, Siu H, Zhu Y, Hu P, Hong S, Zhao J, Zhou X, Reveille JD, Jin L, Amos CI, Xiong M. Gene and pathway-based second-wave analysis of genome-wide association studies. European Journal of Human Genetics. 2010;18(1):111-7. doi: 10.1038/ejhg.2009.115 PubMed: 19584899 | PMCID: PMC2987176

Seitsonen SP, Onkamo P, Peng G, Xiong M, Tommila PV, Ranta PH, Holopainen JM, Moilanen JA, Palosaari T, Kaarniranta K, Meri S, Immonen IR, Järvelä IE. Multifactor effects and evidence of potential interaction between complement factor H Y402H and LOC387715 A69S in age-related macular degeneration. PLoS One. 2008;3(12):e3833. doi: 10.1371/journal.pone.0003833 PubMed: 19048105 | PMCID: PMC2585793