Publications
2024
- DNA methylation-based telomere length is associated with HIV infection, physical frailty, cancer, and all-cause mortality.Liang X, Aouizerat BE, So-Armah K, Cohen MH, Marconi VC, Xu K, Justice AC. Aging Cell. 2024 Apr 17; 2024 Apr 17. PMID: 38629454.
- Computationally inferred cell-type specific epigenome-wide DNA methylation analysis unveils distinct methylation patterns among immune cells for HIV infection in three cohorts.Zhang X, Hu Y, Vandenhoudt RE, Yan C, Marconi VC, Cohen MH, Wang Z, Justice AC, Aouizerat BE, Xu K. PLoS Pathog. 2024 Mar; 2024 Mar 11. PMID: 38466776.
- A multi-ancestry genetic study of pain intensity in 598,339 veterans.Toikumo S, Vickers-Smith R, Jinwala Z, Xu H, Saini D, Hartwell EE, Pavicic M, Sullivan KA, Xu K, Jacobson DA, Gelernter J, Rentsch CT, Stahl E, Cheatle M, Zhou H, Waxman SG, Justice AC, Kember RL, Kranzler HR. Nat Med. 2024 Mar 1; 2024 Mar 1. PMID: 38429522.
2023
- Reply to: Genetic differentiation at probe SNPs leads to spurious results in meQTL discovery.Cheng Y, Li B, Zhang X, Aouizerat BE, Zhao H, Xu K. Commun Biol. 2023 Dec 21; 2023 Dec 21. PMID: 38129596.
- Multi-ancestry study of the genetics of problematic alcohol use in over 1 million individuals.Zhou H, Kember RL, Deak JD, Xu H, Toikumo S, Yuan K, Lind PA, Farajzadeh L, Wang L, Hatoum AS, Johnson J, Lee H, Mallard TT, Xu J, Johnston KJA, Johnson EC, Nielsen TT, Galimberti M, Dao C, Levey DF, Overstreet C, Byrne EM, Gillespie NA, Gordon S, Hickie IB, Whitfield JB, Xu K, Zhao H, Huckins LM, Davis LK, Sanchez-Roige S, Madden PAF, Heath AC, Medland SE, Martin NG, Ge T, Smoller JW, Hougaard DM, Børglum AD, Demontis D, Krystal JH, Gaziano JM, Edenberg HJ, Agrawal A, Justice AC, Stein MB, Kranzler HR, Gelernter J. Nat Med. 2023 Dec; 2023 Dec 7. PMID: 38062264.
- Co-occurrence of injection drug use and hepatitis C increases epigenetic age acceleration that contributes to all-cause mortality among people living with HIV.Liang X, Justice AC, Marconi VC, Aouizerat BE, Xu K. Epigenetics. 2023 Dec. PMID: 37191953.
- Multi-ancestry meta-analysis of tobacco use disorder prioritizes novel candidate risk genes and reveals associations with numerous health outcomes.Toikumo S, Jennings MV, Pham BK, Lee H, Mallard TT, Bianchi SB, Meredith JJ, Vilar-Ribó L, Xu H, Hatoum AS, Johnson EC, Pazdernik V, Jinwala Z, Pakala SR, Leger BS, Niarchou M, Ehinmowo M, Jenkins GD, Batzler A, Pendegraft R, Palmer AA, Zhou H, Biernacka JM, Coombes BJ, Gelernter J, Xu K, Hancock DB, Cox NJ, Smoller JW, Davis LK, Justice AC, Kranzler HR, Kember RL, Sanchez-Roige S. medRxiv. 2023 Sep 18; 2023 Sep 18. PMID: 37034728.
- Greater stress and trauma mediate race-related differences in epigenetic age between Black and White young adults in a community sample.Holloway TD, Harvanek ZM, Xu K, Gordon DM, Sinha R. Neurobiol Stress. 2023 Sep; 2023 Jul 21. PMID: 37501940.
- Multi-trait genome-wide association analyses leveraging alcohol use disorder findings identify novel loci for smoking behaviors in the Million Veteran Program.Cheng Y, Dao C, Zhou H, Li B, Kember RL, Toikumo S, Zhao H, Gelernter J, Kranzler HR, Justice AC, Xu K. Transl Psychiatry. 2023 May 5; 2023 May 5. PMID: 37147289.
- Epigenome-Wide Meta-Analysis Reveals Differential DNA Methylation Associated With Estimated Glomerular Filtration Rate Among African American Men With HIV.Chen J, Hui Q, Wang Z, Wilson FP, So-Armah K, Freiberg MS, Justice AC, Xu K, Zhao W, Ammous F, Smith JA, Kardia SLR, Gwinn M, Marconi VC, Sun YV. Kidney Int Rep. 2023 May; 2023 Mar 2. PMID: 37180517.
- Cell-type specific EWAS identifies genes involved in HIV pathogenesis and oncogenesis among people with HIV infection.Zhang X, Hu Y, Vandenhoudt RE, Yan C, Marconi VC, Cohen MH, Justice AC, Aouizerat BE, Xu K. bioRxiv. 2023 Mar 24; 2023 Mar 24. PMID: 36993343.
- The genetic architecture of pain intensity in a sample of 598,339 U.S. veterans.Toikumo S, Vickers-Smith R, Jinwala Z, Xu H, Saini D, Hartwell E, Venegas MP, Sullivan KA, Xu K, Jacobson DA, Gelernter J, Rentsch CT, Stahl E, Cheatle M, Zhou H, Waxman SG, Justice AC, Kember RL, Kranzler HR. medRxiv. 2023 Mar 13; 2023 Mar 13. PMID: 36993749.
- Epigenetic Age Acceleration Markers Are Associated With Physiologic Frailty and All-Cause Mortality in People With Human Immunodeficiency Virus.Oursler KK, Marconi VC, Wang Z, Xu K, Montano M, So-Armah K, Justice AC, Sun YV. Clin Infect Dis. 2023 Feb 8. PMID: 35970820.
- Multi-ancestry study of the genetics of problematic alcohol use in >1 million individuals.Zhou H, Kember RL, Deak JD, Xu H, Toikumo S, Yuan K, Lind PA, Farajzadeh L, Wang L, Hatoum AS, Johnson J, Lee H, Mallard TT, Xu J, Johnston KJA, Johnson EC, Galimberti M, Dao C, Levey DF, Overstreet C, Byrne EM, Gillespie NA, Gordon S, Hickie IB, Whitfield JB, Xu K, Zhao H, Huckins LM, Davis LK, Sanchez-Roige S, Madden PAF, Heath AC, Medland SE, Martin NG, Ge T, Smoller JW, Hougaard DM, Børglum AD, Demontis D, Krystal JH, Gaziano JM, Edenberg HJ, Agrawal A, Justice AC, Stein MB, Kranzler HR, Gelernter J. medRxiv. 2023 Jan 30; 2023 Jan 30. PMID: 36747741.
- Dissecting the epigenomic differences between smoking and nicotine dependence in a veteran cohort.Nagamatsu ST, Pietrzak RH, Xu K, Krystal JH, Gelernter J, Montalvo-Ortiz JL. Addict Biol. 2023 Jan. PMID: 36577721.
2022
- The Stress and Resilience Town Hall: A systems response to support the health workforce during COVID-19 and beyond.Tebes JK, Awad MN, Connors EH, Fineberg SK, Gordon DM, Jordan A, Kravitz R, Li L, Ponce AN, Prabhu M, Rubman S, Silva MA, Steinfeld M, Tate DC, Xu K, Krystal JH. Gen Hosp Psychiatry. 2022 Jul-Aug; 2022 Apr 22. PMID: 35569322.
- A new monocyte epigenetic clock reveals nonlinear effects of alcohol consumption on biological aging in three independent cohorts (N = 2242).Liang X, Sinha R, Justice AC, Cohen MH, Aouizerat BE, Xu K. Alcohol Clin Exp Res. 2022 May; 2022 Mar 17. PMID: 35257385.
- Incorporating local ancestry improves identification of ancestry-associated methylation signatures and meQTLs in African Americans.Li B, Aouizerat BE, Cheng Y, Anastos K, Justice AC, Zhao H, Xu K. Commun Biol. 2022 Apr 29; 2022 Apr 29. PMID: 35488087.
- A novel graph-based k-partitioning approach improves the detection of gene-gene correlations by single-cell RNA sequencing.Xu H, Hu Y, Zhang X, Aouizerat BE, Yan C, Xu K. BMC Genomics. 2022 Jan 7; 2022 Jan 7. PMID: 34996359.
2021
- Brush swab as a noninvasive surrogate for tissue biopsies in epigenomic profiling of oral cancer.Viet CT, Zhang X, Xu K, Yu G, Asam K, Thomas CM, Callahan NF, Doan C, Walker PC, Nguyen K, Kidd SC, Lee SC, Grandhi A, Allen CT, Young S, Melville JC, Shum JW, Viet DT, Herford AS, Roden DF, Gonzalez ML, Zhong JF, Aouizerat BE. Biomark Res. 2021 Dec 20; 2021 Dec 20. PMID: 34930473.
- Psychological and biological resilience modulates the effects of stress on epigenetic aging.Harvanek ZM, Fogelman N, Xu K, Sinha R. Transl Psychiatry. 2021 Nov 27; 2021 Nov 27. PMID: 34839356.
- The impact of removing former drinkers from genome-wide association studies of AUDIT-C.Dao C, Zhou H, Small A, Gordon KS, Li B, Kember RL, Ye Y, Gelernter J, Xu K, Kranzler HR, Zhao H, Justice AC. Addiction. 2021 Nov; 2021 May 6. PMID: 33861876.
- Design of the National Adaptive Trial for PTSD-related Insomnia (NAP Study), VA Cooperative Study Program (CSP) #2016.Krystal JH, Chow B, Vessicchio J, Henrie AM, Neylan TC, Krystal AD, Marx BP, Xu K, Jindal RD, Davis LL, Schnurr PP, Stein MB, Thase ME, Ventura B, Huang GD, Shih MC. Contemp Clin Trials. 2021 Oct; 2021 Aug 18. PMID: 34416369.
- i2d: an R package for simulating data from images and the implications in biomedical research.Liang X, Hu Y, Yan C, Xu K. Bioinformatics. 2021 Aug 25. PMID: 33244599.
- DNA methylation biomarker selected by an ensemble machine learning approach predicts mortality risk in an HIV-positive veteran population.Shu C, Justice AC, Zhang X, Marconi VC, Hancock DB, Johnson EO, Xu K. Epigenetics. 2021 Jun-Jul; 2020 Oct 22. PMID: 33092459.
- DNA methylation signature on phosphatidylethanol, not on self-reported alcohol consumption, predicts hazardous alcohol consumption in two distinct populations.Liang X, Justice AC, So-Armah K, Krystal JH, Sinha R, Xu K. Mol Psychiatry. 2021 Jun; 2020 Feb 7. PMID: 32034291.
- Single-cell meta-analysis of SARS-CoV-2 entry genes across tissues and demographics.Muus C, Luecken MD, Eraslan G, Sikkema L, Waghray A, Heimberg G, Kobayashi Y, Vaishnav ED, Subramanian A, Smillie C, Jagadeesh KA, Duong ET, Fiskin E, Torlai Triglia E, Ansari M, Cai P, Lin B, Buchanan J, Chen S, Shu J, Haber AL, Chung H, Montoro DT, Adams T, Aliee H, Allon SJ, Andrusivova Z, Angelidis I, Ashenberg O, Bassler K, Bécavin C, Benhar I, Bergenstråhle J, Bergenstråhle L, Bolt L, Braun E, Bui LT, Callori S, Chaffin M, Chichelnitskiy E, Chiou J, Conlon TM, Cuoco MS, Cuomo ASE, Deprez M, Duclos G, Fine D, Fischer DS, Ghazanfar S, Gillich A, Giotti B, Gould J, Guo M, Gutierrez AJ, Habermann AC, Harvey T, He P, Hou X, Hu L, Hu Y, Jaiswal A, Ji L, Jiang P, Kapellos TS, Kuo CS, Larsson L, Leney-Greene MA, Lim K, Litviňuková M, Ludwig LS, Lukassen S, Luo W, Maatz H, Madissoon E, Mamanova L, Manakongtreecheep K, Leroy S, Mayr CH, Mbano IM, McAdams AM, Nabhan AN, Nyquist SK, Penland L, Poirion OB, Poli S, Qi C, Queen R, Reichart D, Rosas I, Schupp JC, Shea CV, Shi X, Sinha R, Sit RV, Slowikowski K, Slyper M, Smith NP, Sountoulidis A, Strunz M, Sullivan TB, Sun D, Talavera-López C, Tan P, Tantivit J, Travaglini KJ, Tucker NR, Vernon KA, Wadsworth MH, Waldman J, Wang X, Xu K, Yan W, Zhao W, Ziegler CGK. Nat Med. 2021 Mar; 2021 Mar 2. PMID: 33654293.
2020
- Comparison of methylation capture sequencing and Infinium MethylationEPIC array in peripheral blood mononuclear cells.Shu C, Zhang X, Aouizerat BE, Xu K. Epigenetics Chromatin. 2020 Nov 23; 2020 Nov 23. PMID: 33228774.
- Genome-wide association study of smoking trajectory and meta-analysis of smoking status in 842,000 individuals.Xu K, Li B, McGinnis KA, Vickers-Smith R, Dao C, Sun N, Kember RL, Zhou H, Becker WC, Gelernter J, Kranzler HR, Zhao H, Justice AC. Nat Commun. 2020 Oct 20; 2020 Oct 20. PMID: 33082346.
- Searching for Genomic Biomarkers for Major Depressive Disorder in Peripheral Immune Cells.Xu K, Aouizerat BE. Biol Psychiatry. 2020 Oct 15. PMID: 32972513.
- Association of OPRM1 Functional Coding Variant With Opioid Use Disorder: A Genome-Wide Association Study.Zhou H, Rentsch CT, Cheng Z, Kember RL, Nunez YZ, Sherva RM, Tate JP, Dao C, Xu K, Polimanti R, Farrer LA, Justice AC, Kranzler HR, Gelernter J. JAMA Psychiatry. 2020 Oct 1. PMID: 32492095.
- DNA methylation mediates the effect of cocaine use on HIV severity.Shu C, Justice AC, Zhang X, Wang Z, Hancock DB, Johnson EO, Xu K. Clin Epigenetics. 2020 Sep 14; 2020 Sep 14. PMID: 32928285.
- Single-cell Transcriptome Mapping Identifies Common and Cell-type Specific Genes Affected by Acute Delta9-tetrahydrocannabinol in Humans.Hu Y, Ranganathan M, Shu C, Liang X, Ganesh S, Osafo-Addo A, Yan C, Zhang X, Aouizerat BE, Krystal JH, D'Souza DC, Xu K. Sci Rep. 2020 Feb 26; 2020 Feb 26. PMID: 32103029.
- Epigenetic Associations With Estimated Glomerular Filtration Rate Among Men With Human Immunodeficiency Virus Infection.Chen J, Huang Y, Hui Q, Mathur R, Gwinn M, So-Armah K, Freiberg MS, Justice AC, Xu K, Marconi VC, Sun YV. Clin Infect Dis. 2020 Feb 3. PMID: 30893429.
2019
- Retrospective Association Analysis of Longitudinal Binary Traits Identifies Important Loci and Pathways in Cocaine Use.Wu W, Wang Z, Xu K, Zhang X, Amei A, Gelernter J, Zhao H, Justice AC, Wang Z. Genetics. 2019 Dec; 2019 Oct 7. PMID: 31591132.
- Patterns and Correlates of Prescription Opioid Receipt Among US Veterans: A National, 18-Year Observational Cohort Study.Rentsch CT, Edelman EJ, Justice AC, Marshall BDL, Xu K, Smith AH, Crystal S, Gaither JR, Gordon AJ, Smith RV, Kember RL, Polimanti R, Gelernter J, Fiellin DA, Tate JP, Kranzler HR, Becker WC. AIDS Behav. 2019 Dec. PMID: 31317364.
- Epigenome-Wide DNA Methylation Association Analysis Identified Novel Loci in Peripheral Cells for Alcohol Consumption Among European American Male Veterans.Xu K, Montalvo-Ortiz JL, Zhang X, Southwick SM, Krystal JH, Pietrzak RH, Gelernter J. Alcohol Clin Exp Res. 2019 Oct; 2019 Aug 30. PMID: 31386212.
- Using DNA methylation to validate an electronic medical record phenotype for smoking.McGinnis KA, Justice AC, Tate JP, Kranzler HR, Tindle HA, Becker WC, Concato J, Gelernter J, Li B, Zhang X, Zhao H, Crothers K, Xu K. Addict Biol. 2019 Sep; 2018 Oct 4. PMID: 30284751.
- DNA Methylation Markers of Type 2 Diabetes Mellitus Among Male Veterans With or Without Human Immunodeficiency Virus Infection.Mathur R, Hui Q, Huang Y, Gwinn M, So-Armah K, Freiberg MS, Justice AC, Xu K, Marconi VC, Sun YV. J Infect Dis. 2019 May 24. PMID: 30649532.
- Genome-wide association study of alcohol consumption and use disorder in 274,424 individuals from multiple populations.Kranzler HR, Zhou H, Kember RL, Vickers Smith R, Justice AC, Damrauer S, Tsao PS, Klarin D, Baras A, Reid J, Overton J, Rader DJ, Cheng Z, Tate JP, Becker WC, Concato J, Xu K, Polimanti R, Zhao H, Gelernter J. Nat Commun. 2019 Apr 2; 2019 Apr 2. PMID: 30940813.
2018
- Machine learning selected smoking-associated DNA methylation signatures that predict HIV prognosis and mortality.Zhang X, Hu Y, Aouizerat BE, Peng G, Marconi VC, Corley MJ, Hulgan T, Bryant KJ, Zhao H, Krystal JH, Justice AC, Xu K. Clin Epigenetics. 2018 Dec 13; 2018 Dec 13. PMID: 30545403.
- AUDIT-C and ICD codes as phenotypes for harmful alcohol use: association with ADH1B polymorphisms in two US populations.Justice AC, Smith RV, Tate JP, McGinnis K, Xu K, Becker WC, Lee KY, Lynch K, Sun N, Concato J, Fiellin DA, Zhao H, Gelernter J, Kranzler HR. Addiction. 2018 Dec; 2018 Aug 1. PMID: 29972609.
- Similar psychotic and cognitive profile between ketamine dependence with persistent psychosis and schizophrenia.Cheng WJ, Chen CH, Chen CK, Huang MC, Pietrzak RH, Krystal JH, Xu K. Schizophr Res. 2018 Sep; 2018 Mar 3. PMID: 29510925.
- Epigenome-wide association analysis revealed that SOCS3 methylation influences the effect of cumulative stress on obesity.Xu K, Zhang X, Wang Z, Hu Y, Sinha R. Biol Psychol. 2018 Jan; 2016 Nov 5. PMID: 27826092.
2017
- DNA methylation signatures of illicit drug injection and hepatitis C are associated with HIV frailty.Zhang X, Hu Y, Justice AC, Li B, Wang Z, Zhao H, Krystal JH, Xu K. Nat Commun. 2017 Dec 21; 2017 Dec 21. PMID: 29269866.
- Validating Harmful Alcohol Use as a Phenotype for Genetic Discovery Using Phosphatidylethanol and a Polymorphism in ADH1B.Justice AC, McGinnis KA, Tate JP, Xu K, Becker WC, Zhao H, Gelernter J, Kranzler HR. Alcohol Clin Exp Res. 2017 May; 2017 Apr 10. PMID: 28295416.
- Identification of HIV infection-related DNA methylation sites and advanced epigenetic aging in HIV-positive, treatment-naive U.S. veterans.Nelson KN, Hui Q, Rimland D, Xu K, Freiberg MS, Justice AC, Marconi VC, Sun YV. AIDS. 2017 Feb 20. PMID: 27922854.
- Alcohol Triggers Reemergence of Ketamine-Like Experience in a Ketamine Ex-User.Chang F, Xu K, Huang MC, Krystal JH. J Clin Psychopharmacol. 2017 Feb. PMID: 28027112.
2016
- Epigenome-wide differential DNA methylation between HIV-infected and uninfected individuals.Zhang X, Justice AC, Hu Y, Wang Z, Zhao H, Wang G, Johnson EO, Emu B, Sutton RE, Krystal JH, Xu K. Epigenetics. 2016 Oct 2; 2016 Sep 27. PMID: 27672717.
2015
- Preliminary analysis of positive and negative syndrome scale in ketamine-associated psychosis in comparison with schizophrenia.Xu K, Krystal JH, Ning Y, Chen DC, He H, Wang D, Ke X, Zhang X, Ding Y, Liu Y, Gueorguieva R, Wang Z, Limoncelli D, Pietrzak RH, Petrakis IL, Zhang X, Fan N. J Psychiatr Res. 2015 Feb; 2014 Dec 24. PMID: 25560772.
2012
- Genetic modulation of plasma NPY stress response is suppressed in substance abuse: association with clinical outcomes.Xu K, Hong KA, Zhou Z, Hauger RL, Goldman D, Sinha R. Psychoneuroendocrinology. 2012 Apr; 2011 Sep 13. PMID: 21917383.
2008
- Genetic variation in human NPY expression affects stress response and emotion.Zhou Z, Zhu G, Hariri AR, Enoch MA, Scott D, Sinha R, Virkkunen M, Mash DC, Lipsky RH, Hu XZ, Hodgkinson CA, Xu K, Buzas B, Yuan Q, Shen PH, Ferrell RE, Manuck SB, Brown SM, Hauger RL, Stohler CS, Zubieta JK, Goldman D. Nature. 2008 Apr 24; 2008 Apr 2. PMID: 18385673.