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Two Recent Representative Publications

  1. Chen X, Li D*. ERVcaller: Identifying polymorphic endogenous retrovirus and other transposable element insertions using whole-genome sequencing data. Bioinformatics. 2019 Oct 15;35(20):3913-3922. PMID: 30895294. (* corresponding author). (A novel approach to detect and genotype distinct individual ERVs and other TEs on the genome-wide level, named ERVcaller, was developed. This tool allows for genome-wide association studies of TEs with complex diseases.)
  2. Chen X, Kost J, Sulovari A, Wong N, Liang WS, Cao J, Li D*. A virome-wide clonal integration analysis platform for discovering cancer viral etiology. Genome Research. 2019 May;29(5):819-830. PMID: 30872350. (* corresponding author). (A novel approach to detect viral integration events in the human genome on the virome-wide level, named VIcaller, was developed and demonstrated.)

Part I: Peer-reviewed Research Articles

2024

  1. Liu G, Chen X, Luan Y, Li D*. VirusPredictor: XGBoost-based software to predict virus-related sequences in human data. (* corresponding author). Bioinformatics. 2024 Mar 29;40(4):btae192. PMID: 38597887. PMCID: PMC11052659.

2023

  1. Raza A, Diehl SA, Krementsov DN, Case LK, Li D, Kost J, Ball RL, Chesler EJ, Philip VM, Huang R, Chen Y, Ma R, Tyler AL, Mahoney JM, Blankenhorn EP, Teuscher C. A Genetic locus Complements Resistance to Bordetella pertussis-Induced Histamine Sensitization. Communications Biology. 2023 Mar 6;6(1):244. PMID: 36879097. PMCID: PMC9988836.

2021

  1. Chen X, Li D*. Sequencing facility and DNA source associated patterns of virus-mappable reads in whole-genome sequencing data. Genomics. 2021 Jan;113(1 Pt 2):1189-1198. PMID: 33301893. PMCID: PMC7856238. (* corresponding author). (This study describes approach to distinguishing true viral sequences from artifacts and technical variables in human genome sequencing analyses.)
  2. Mathkar PP, Chen X*, Sulovari A, Li D*. Characterization of hepatitis B virus integrations identified in hepatocellular carcinoma genomes. Viruses. 2021 Feb 4;13(2):245. PMID: 33557409. PMCID: PMC7915589. (* corresponding author).

2020

  1. Sulovari A, Li D*. VIpower: Simulation-based tool for estimating power of viral integration detection via high-throughput sequencing. Genomics. 2020 Jan 10;112(1):207-211. PMID: 30710609. (* corresponding author). (This study tells how to design new sequencing experiments to increase the power and accuracy to detect genome-wide viral integrations, and transposable elements.)
  2. Nepotchatykh E, Elremaly W, Caraus I, Godbout C, Leveau C, Chalder L, Beaudin C, Kanamaru E, Kosovskaia R, Lauzon S, Maillet Y, Franco A, Lascau-Coman V, Bouhanik S, Gaitan YP, Li D, Moreau A. Profile of circulating microRNAs in myalgic encephalomyelitis and their relation to symptom severity, and disease pathophysiology. Scientific Reports. 2020 Nov 12;10(1):19620. PMID: 33184353. PMCID: PMC7665057. (This paper received >12,000 downloads in 2020 after published in Nov 2020. One of the top 100 downloaded papers for Scientific Reports in 2020 among >21,000 papers published by this journal in 2020.)

2019

  1. Chen X, Kost J, Sulovari A, Wong N, Liang WS, Cao J, Li D*. A virome-wide clonal integration analysis platform for discovering cancer viral etiology. Genome Research. 2019 May;29(5):819-830. PMID: 30872350. PMCID: PMC6499315. (* corresponding author). (A novel approach to detect viral integration events in the human genome on the virome-wide level, named VIcaller, was developed and demonstrated.)
  2. Chen X, Li D*. ERVcaller: Identifying polymorphic endogenous retrovirus and other transposable element insertions using whole-genome sequencing data. Bioinformatics. 2019 Oct 15;35(20):3913-3922. PMID: 30895294. (* corresponding author). (A novel approach to detect and genotype distinct individual ERVs and other TEs on the genome-wide level, named ERVcaller, was developed. This tool allows for genome-wide association studies of TEs with complex diseases.)
  3. Chen X, Kost J, Li D*. Comprehensive comparative analysis of methods and software for identifying viral integrations. Briefings in Bioinformatics. 2019 Nov 27;20(6):2088-2097. PMID: 30102374. (* corresponding author). (This study is the first to propose the “virome-wide” concept for viral integration detection.)
  4. Nada D, Julien C, Rompré PH, Akoume MY, Gorman KF, Samuels ME, Levy E, Kost J, Li D, Moreau A. Association of Circulating YKL-40 Levels and CHI3L1 Variants with the Risk of Spinal Deformity Progression in Adolescent Idiopathic Scoliosis. Scientific Reports. 2019 Apr 5;9(1):5712. PMID: 30952886. PMCID: PMC6450973.

2018

  1. Sulovari A, Liu Z, Zhu Z*, Li D*. Genome-wide meta-analysis of copy number variations with alcohol dependence. Pharmacogenomics Journal. 2018 May 22;18(3):398-405. PMID: 28696413. (* corresponding author). (First genome-wide meta-analysis of CNVs in any substance abuse)
  2. Zhao FQ, Misra Y, Li DB, Wadsworth MP, Krag D, Weaver D, Tessitore J, Li DW, Zhang G, Tian Q, Buss K. Differential expression of Oct3/4 in human breast cancer and normal tissues. International Journal of Oncology. 2018 Jun;52(6):2069-2078. PMID: 29620155.

2017

  1. Sulovari A, Chen YH, Hudziak JJ, Li D*. Atlas of human diseases influenced by genetic variants with extreme allele frequency differences. Human Genetics. 2017 Jan;136(1):39-54. PMID: 27699474. (* corresponding author). (This study paves a new avenue to identify disease genes.)

2015

  1. Li D*, Zhao H, Kranzler HR, Li M, Jensen KP, Zayats T, Farrer LA, Gelernter J. Genome-wide Association Study of Copy Number Variations (CNVs) With Opioid Dependence. Neuropsychopharmacology. 2015 Mar;40(4):1016-26. PMID: 25345593. PMCID: PMC4330517. (* corresponding author) (First genome-wide CNV study in any drug dependence)
  2. Sulovari A, Kranzler HR, Farrer LA, Gelernter J, Li D*. Eye Color: A Potential Indicator of Alcohol Dependence Risk in European Americans. American Journal of Medical Genetics Part B: Neuropsychiatric Genetics. 2015 Jul;168(5):347-53. PMID: 25921801. (* corresponding author). (Featured in Huffington Post, ABC news, CBS News, WPTZ-TV, and other media reports in July 2015)

2014

  1. Sulovari A, Li D*. GACT: a Genome build and Allele definition Conversion Tool for SNP imputation and meta-analysis in genetic association studies. BMC Genomics. 2014 Jul 19;15(1):610. PMID: 25038819. PMCID: PMC4223508. (* corresponding author)
  2. Li D*, Sulovari A, Cheng C, Zhao H, Kranzler HR, Gelernter J. Association of Gamma-Aminobutyric Acid A Receptor α 2 Gene (GABRA2) with Alcohol Use Disorder. Neuropsychopharmacology. 2014 Mar;39(4):907-18. PMID: 24136292. PMCID: PMC3924525. (* corresponding author) (Citations >115; NIH Relative Citation Ratio = 3.90; NIH Percentile = 90.3). (First meta-analysis of drug dependence with GABA receptor genes)
  3. Cao J, Liu X, Han S, Zhang CK, Liu Z, Li D*. Association of the HTR2A gene with alcohol and heroin abuse. Human Genetics. 2014 Mar;133(3):357-65. PMID: 24178752. PMCID: PMC4085799. (* corresponding author)
  4. Yang H, Li D, Cheng C. Relating gene expression evolution with CpG content changes. BMC Genomics. 2014 Aug 20;15(1):693. PMID: 25142157. PMCID: PMC4148958.

2013

  1. Cao J, Hudziak J, Li D*. Multi-cultural Association of the Serotonin Transporter Gene (SLC6A4) with Substance Use Disorder. Neuropsychopharmacology. 2013 Aug;38(9):1737-47. PMID: 23518607. PMCID: PMC3717550. (* corresponding author)
  2. Cao J, LaRocque E, Li D*. Associations of the 5-hydroxytryptamine (Serotonin) Receptor 1B Gene (HTR1B) with Alcohol, Cocaine, and Heroin Abuse. American Journal of Medical Genetics Part B: Neuropsychiatric Genetics. 2013 Mar;162(2):169-76. PMID: 23335468. PMCID: PMC4089973. (* corresponding author)
  3. Wang L, Jiao Y, Huang Y, Liu X, Gibson G, Bennett B, Hamre KM, Li D, Zhao H, Gelernter J, Kranzler HR, Farrer LA, Lu L, Wang Y, Gu W. Critical evaluation of transcription factor Atf2 as a candidate modulator of alcohol preference in mouse and human populations. Genetics and Molecular Research. 2013 Nov 26;12(4):5992-6005. PMID: 24338393. PMCID: PMC4108070.

2012

  1. Li D, Zhao H, Kranzler HR, Oslin D, Anton RF, Farrer LA, Gelernter J. Association of COL25A1 with comorbid antisocial personality disorder and substance dependence. Biological Psychiatry. 2012 Apr 15;71(8):733-40. PMID: 22297151. PMCID: PMC3548659. (First genome-wide association study of this disorder; another study showed COL25A1 was a driver gene for behavioral alteration in mice.)
  2. Li D*, Zhao H, Gelernter J. Further clarification of the contribution of the ADH1C gene to vulnerability of alcoholism and selected liver diseases. Human Genetics. 2012 Aug;131(8):1361-74. PMID: 22476623. PMCID: PMC3557796. (* corresponding author)
  3. Li D*, Zhao H, Gelernter J. Strong protective effect of the aldehyde dehydrogenase gene (ALDH2) 504lys (*2) allele against alcoholism and alcohol-induced medical diseases in Asians. Human Genetics. 2012 May;131(5):725-37. PMID: 22102315. PMCID: PMC3548401. (* corresponding author) (Citations >185) (NIH Relative Citation Ratio = 2.70; NIH Percentile = 83.1)
  4. Zhang H, Li D, Su Y, Jiang S, Xu Y, Jiang K, Cui D. Identification of the N-acylsphingosine amidohydrolase 1 gene (ASAH1) for susceptibility to schizophrenia in a Han Chinese population. World Journal Biological Psychiatry. 2012 Feb;13(2):106-13. PMID: 21375364.

2011

  1. Li D*, Zhao H, Gelernter J. Strong association of the alcohol dehydrogenase 1B gene (ADH1B) with alcohol dependence and alcohol-induced medical diseases. Biological Psychiatry. 2011 Sep 15;70(6):504-12. PMID: 21497796. PMCID: PMC3142297. (* corresponding author) (Citations >185; NIH Relative Citation Ratio = 3.71; NIH Percentile = 89.5)
  2. Cui D, Zhang H, Yang BZ, Listman JB, Li D, Price LH, Carpenter LL, Tyrka AR, Anton RF, Kranzler HR, Gelernter J. Variation in NGFB is associated with primary affective disorders in women. American Journal of Medical Genetics Part B: Neuropsychiatric Genetics. 2011 Jun;156B(4):401-12. PMID: 21294249. PMCID: PMC3108453.

2010

  1. Bertisch H, Li D, Hoptman MJ, Delisi LE. Heritability estimates for cognitive factors and brain white matter integrity as markers of schizophrenia. American Journal of Medical Genetics Part B: Neuropsychiatric Genetics. 2010 Jun 5;153B(4):885-94. PMID: 20052692. PMCID: PMC3446203.
  2. Proudnikov D, Kroslak T, Sipe JC, Randesi M, Li D, Hamon S, Ho A, Ott J, Kreek MJ. Association of polymorphisms of the cannabinoid receptor (CNR1) and fatty acid amide hydrolase (FAAH) genes with heroin addiction: impact of long repeats of CNR1. Pharmacogenomics Journal. 2010 Jun;10(3):232-42. PMID: 20010914. PMCID: PMC3810151.
  3. Hilner JE, Perdue LH, Sides EG, Pierce JJ, Wägner AM, Aldrich A, Loth A, Albret L, Wagenknecht LE, Nierras C, Akolkar B; Type 1 Diabetes Genetics Consortium. Designing and implementing sample and data collection for an international genetics study: the Type 1 Diabetes Genetics Consortium (T1DGC). Clinical Trials. 2010;7(1 Suppl):S5-S32. PMID: 20603248. PMCID: PMC2917852.

2009

  1. Barrett JC, Clayton DG, Concannon P, Akolkar B, Cooper JD, Erlich HA, Julier C, Morahan G, Nerup J, Nierras C, Plagnol V, Pociot F, Schuilenburg H, Smyth DJ, Stevens H, Todd JA, Walker NM, Rich SS; Type 1 Diabetes Genetics Consortium. Genome-wide association study and meta-analysis find that over 40 loci affect risk of type 1 diabetes. Nature Genetics. 2009 Jun;41(6):703-7. PMID: 19430480. PMCID: PMC2889014.
  2. Li D*, Feng G, He L*. Case-control study of association between the functional candidate gene ERBB3 and schizophrenia in Caucasian population. World Journal of Biological Psychiatry. 2009;10(4 Pt 2):595-8. PMID: 19995212. (* co-corresponding author)
  3. Li D*, He G, Xu Y, Duan Y, Gu N, Li X, Shi Y, Qin W, Feng G, He L. Schizophrenia is not associated with the ERBB3 gene in a Han Chinese population sample: Results from case-control and family-based studies. Genetics and Molecular Biology. 2009 Oct;32(4):729-30. PMID: 21637446. PMCID: PMC3036886. (* co-corresponding author)
  4. He C, Hamon S, Li D, Barral S, Ott J. MHC fine mapping of human type 1 diabetes using the T1DGC data. Diabetes, Obesity and Metabolism. Vol 11, Suppl 1, 2009 Jan, 53-9. PMID: 19143815. PMCID: PMC2753855.

2008

  1. Li D*, He L*. Meta-study on association between the monoamine oxidase A gene (MAOA) and schizophrenia. American Journal of Medical Genetics Part B: Neuropsychiatric Genetics. 2008 Mar 5;147B(2):174-8. PMID: 17894408. (* co-corresponding author)
  2. Levran O, O'Hara K, Peles E, Li D, Barral S, Ray B, Borg L, Ott J, Adelson M, Kreek MJ. ABCB1 (MDR1) genetic variants are associated with methadone doses required for effective treatment of heroin dependence. Human Molecular Genetics. 2008 Jul 15;17(14):2219-27. PMID: 18424454. PMCID: PMC2599947. (Citations >195; NIH Relative Citation Ratio = 3.45; NIH Percentile = 88.2)

2007

  1. Li D, He L. Meta-analysis supports association between serotonin transporter (5-HTT) and suicidal behavior. Molecular Psychiatry (impact factor: 13.44). 2007 Jan;12(1):47-54. PMID: 16969368. (Citations >250)
  2. Li D*, He L*. Association study between the NMDA receptor 2B subunit gene (GRIN2B) and schizophrenia: a HuGE review and meta-analysis. Genetics in Medicine. 2007 Jan;9(1):4-8. PMID: 17224684. (*co-corresponding author) (Citations >105)
  3. Li D*, He L. G72/G30 genes and schizophrenia: a systematic meta-analysis of association studies. Genetics. 2007 Feb;175(2):917-22. PMID: 17179078. PMCID: PMC1800627. (* corresponding author)
  4. Li D*, He L*. Association study between the dystrobrevin binding protein 1 gene (DTNBP1) and schizophrenia: a meta-analysis. Schizophrenia Research. 2007 Nov;96(1-3):112-8. PMID: 17604607. (*co-corresponding author)

2006

  1. Li D, Sham PC, Owen MJ, He L. Meta-analysis shows significant association between dopamine system genes and attention deficit hyperactivity disorder (ADHD). Human Molecular Genetics. 2006 Jul 15;15(14):2276-84. PMID: 16774975. (Citations >795; NIH Relative Citation Ratio = 10.13; NIH Percentile = 98.3)
  2. Li D, Collier DA, He L. Meta-analysis shows strong positive association of the neuregulin 1 (NRG1) gene with schizophrenia. Human Molecular Genetics. 2006 Jun 15;15(12):1995-2002. PMID: 16687441. (Citations >385; NIH Relative Citation Ratio = 6.12; NIH Percentile = 95.5)
  3. Li D, He L. Further clarification of the contribution of the tryptophan hydroxylase (TPH) gene to suicidal behavior using systematic allelic and genotypic meta-analyses. Human Genetics. 2006 Apr;119(3):233-40. PMID: 16450114. (Citations >140)
  4. Li D, He L. Meta-analysis shows association between the tryptophan hydroxylase (TPH) gene and schizophrenia. Human Genetics. 2006 Aug;120(1):22-30. PMID: 16741719.
  5. Li D, He L. Association study of the G-protein signaling 4 (RGS4) and proline dehydrogenase (PRODH) genes with schizophrenia: a meta-analysis. European Journal of Human Genetics. 2006 Oct;14(10):1130-5. PMID: 16791139.
  6. Li D, Duan Y, He L. Association study of serotonin 2A receptor (5-HT2A) gene with schizophrenia and suicidal behavior using systematic meta-analysis. Biochemical and Biophysical Research Communications. 2006 Feb 17;340(3):1006-15. PMID: 16405867. (Citations >140)
  7. Zhang X, Li D, Duan S, Duan Y, Chen Q, Li X, Liu Z, Feng G, He L. Analysis of the association between Apolipoprotein D and schizophrenia. Neuropsychobiology. 2006Nov;54(1):40-4. PMID: 16966838.
  8. Liu X, Li H, Qin W, He G, Li D, Shen Y, Shen J, Gu N, Feng G, He L. Association of TPH1 with suicidal behaviour and psychiatric disorders in the Chinese population. Journal of Medical Genetics. 2006 Feb;43(2):e4. PMID: 16467214. PMCID: PMC2564644.

2005

  1. Pan Y, Li D, Duan Y, Zhang Z, Xu M, Feng G, He L. Predicting protein subcellular location using digital signal processing. Acta Biochimica et Biophysica Sinica. 2005 Feb;37(2):88-96. PMID: 15685365.
  2. Liu X, Qin W, He G, Yang Y, Chen Q, Zhou J, Li D, Gu N, Xu Y, Feng G, Sang H, Hao X, Zhang K, Wang S, He L. A family-based association study of the MOG gene with schizophrenia in the Chinese population. Schizophrenia Research. 2005 Mar 1;73(2-3):275-80. PMID: 15653272.
  3. Liu J, Shi Y, Tang W, Guo T, Li D, Yang Y, Yang Y, Zhao X, Wang H, Li X, Feng G, Gu N, Zhu S, Liu H, Guo Y, Shi J, Sang H, Yan L, He L. Positive association of the human GABA-A-receptor beta 2 subunit gene haplotype with schizophrenia in the Chinese Han population. Biochemical and Biophysical Research Communications. 2005 Sep 2;334(3):817-23. PMID: 16023997.

2004

  1. Li D, Pan Y, Duan Y, Hung Z, Xu M, He L. Understanding SARS with Wolfram approach. Acta Biochimica et Biophysica Sinica. 2004 Jan;36(1):1-10. PMID: 14732867. PMCID: PMC7109819.
  2. Liu X, He G, Wang X, Chen Q, Qian X, Lin W, Li D, Gu N, Feng G, He L. Association of DAAO with schizophrenia in the Chinese population. Neuroscience Letters. 2004 Oct 21;369(3):228-33. PMID: 15464270.
  3. Yang Y, Xiao Z, Chen W, Sang H, Guan Y, Peng Y, Zhang D, Gu Z, Qian M, He G, Qin W, Li D, Gu N, He L. Tumor suppressor gene TP53 is genetically associated with schizophrenia in the Chinese population. Neuroscience Letters. 2004 Oct 14;369(2):126-31. PMID: 15450681.

 

Part II: Invited Peer-reviewed Review Articles

2024

  1. Obraitis D, Li D*. Blood virome research in myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS): challenges and opportunities. (* corresponding author). Current Opinion in Virology. 2024. Invited.

2018

  1. Cao* J, Li D*. Searching for human oncoviruses: histories, challenges, and opportunities. Journal of Cellular Biochemistry. 2018 Jun;119(6):4897-4906. PMID: 29377246. (* corresponding author). (This study is the first to propose the “clonal integration analysis” concept.)

 

Part III: Invited Commentary

2024

  1. Li D*. Mosaic chromosomal alterations/somatic copy number variations: a new frontier in genetic association studies of complex diseases. (* corresponding author). Biological Psychiatry. 2024. Invited. In Press.

Part IV: Non-Peer Reviewed Journal Publications

 

Letters to editor

  1. Sulovari A, Kranzler HR, Farrer LA, Gelernter J, Li D*. Further analyses support the association between light eye color and alcohol dependence. American Journal of Medical Genetics Part B: Neuropsychiatric Genetics. 2015 Dec;168(8):757-60. PMID: 26290254. (* corresponding author).
  2. Han S, Ma L, Li D, Yang BZ. Is the tail-strength measure more powerful in tests of genetic association? American Journal of Human Genetics. 2009 Feb;84(2):295-8. PMID: 19215734. PMCID: PMC2668021.

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