Publications

  1. Hieken TJ, Nelson GD, Flotte TJ, Grewal EP, Chen J, McWilliams RR, Kottschade LA, Yang L, Domingo-Musibay E, Dronca RS, Yan Y, Markovic SN, Dimou A, Montane HN, Erskine CL, Piltin MA, Price DL, Khariwala SS, Hui J, Strand CA, Harrington SM, Suman VJ, Dong H, Block MS. Neoadjuvant cobimetinib and atezolizumab with or without vemurafenib for high-risk operable Stage III melanoma: the Phase II NeoACTIVATE trial. Nat Commun. 2024 Feb 16; 15 (1):1430
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  2. Yang L, Wang P, Chen J. 2dGBH: Two-dimensional group Benjamini-Hochberg procedure for false discovery rate control in two-way multiple testing of genomic data. Bioinformatics. 2024 Feb 1; 40 (2)
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  3. Santiago P, Quinn KP, Chen J, Friton JJ, Rypstra CR, Kashyap PC, Raffals LE. Altered Bile Acid and Pouch Microbiota Composition in Patients With Chronic Pouchitis. Inflamm Bowel Dis. 2023 Nov 30. [Epub ahead of print]
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  4. Shi Y, Li H, Wang C, Chen J, Jiang H, Shih YT, Zhang H, Song Y, Feng Y, Liu L. A flexible quasi-likelihood model for microbiome abundance count data. Stat Med. 2023 Nov 10; 42 (25):4632-4643 Epub 2023 Aug 22
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  5. Li G, Yang L, Chen J, Zhang X. Robust Differential Abundance Analysis of Microbiome Sequencing Data. Genes (Basel). 2023 Oct 26; 14(11).
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  6. Yang L, Ng YE, Sun H, Li Y, Chini LCS, LeBrasseur NK, Chen J, Zhang X. Single-cell Mayo Map (scMayoMap): an easy-to-use tool for cell type annotation in single-cell RNA-sequencing data analysis. BMC Biol. 2023 Oct 20; 21(1):223.
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  7. Roy A, Chen J, Zhang X. A general framework for powerful confounder adjustment in omics association studies. Bioinformatics. 2023 Sep 2; 39 (9)
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  8. Balakrishnan B, Luckey D, Wright K, Davis JM, Chen J, Taneja V. Eggerthella lenta augments preclinical autoantibody production and metabolic shift mimicking senescence in arthritis. Sci Adv. 2023 Sep; 9(35):eadg1129.
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  9. Ye H, Zhang X, Wang C, Goode EL, Chen J. Batch-effect correction with sample remeasurement in highly confounded case-control studies. Nat Comput Sci. 2023 Aug; 3 (8):709-719 Epub 2023 Aug 23
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  10. Yang L, Chen J. Benchmarking differential abundance analysis methods for correlated microbiome sequencing data. Brief Bioinform. 2023 Jan 19; 24 (1)
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  11. Asangba AE, Chen J, Goergen KM, Larson MC, Oberg AL, Casarin J, Multinu F, Kaufmann SH, Mariani A, Chia N, Walther-Antonio MRS. Diagnostic and prognostic potential of the microbiome in ovarian cancer treatment response. Sci Rep. 2023 Jan 13; 13 (1):730
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  12. Camilleri M, Carlson P, BouSaba J, McKinzie S, Vijayvargiya P, Magnus Y, Sannaa W, Wang XJ, Chedid V, Zheng T, Maselli D, Atieh J, Taylor A, Nair AA, Kengunte Nagaraj N, Johnson S, Chen J, Burton D, Busciglio I. Comparison of biochemical, microbial and mucosal mRNA expression in bile acid diarrhoea and irritable bowel syndrome with diarrhoea. Gut. 2023 Jan; 72 (1):54-65 Epub 2022 May 17
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  13. Quach HQ, Chen J, Monroe JM, Ratishvili T, Warner ND, Grill DE, Haralambieva IH, Ovsyannikova IG, Poland GA, Kennedy RB. The Influence of Sex, Body Mass Index, and Age on Cellular and Humoral Immune Responses Against Measles After a Third Dose of Measles-Mumps-Rubella Vaccine. J Infect Dis. 2022 Dec 28; 227 (1):141-150
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  14. Chen J, Zhang X. dICC: distance-based intraclass correlation coefficient for metagenomic reproducibility studies. Bioinformatics. 2022 Oct 31; 38 (21):4969-4971
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  15. Aalam SMM, Crasta DN, Roy P, Miller AL 2nd, Gamb SI, Johnson S, Till LM, Chen J, Kashyap P, Kannan N. Genesis of fecal floatation is causally linked to gut microbial colonization in mice. Sci Rep. 2022 Oct 27; 12 (1):18109
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  16. Ling W, Lu J, Zhao N, Lulla A, Plantinga AM, Fu W, Zhang A, Liu H, Song H, Li Z, Chen J, Randolph TW, Koay WLA, White JR, Launer LJ, Fodor AA, Meyer KA, Wu MC. Batch effects removal for microbiome data via conditional quantile regression. Nat Commun. 2022 Sep 15; 13 (1):5418 Epub 2022 Sept 15
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  17. Yang L, Chen J. A comprehensive evaluation of microbial differential abundance analysis methods: current status and potential solutions. Microbiome. 2022 Aug 19; 10 (1):130
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  18. Hussan H, Abu Dayyeh BK, Chen J, Johnson S, Riedl KM, Grainger EM, Brooks J, Hinton A, Simpson C, Kashyap PC. Adjustable Intragastric Balloon Leads to Significant Improvement in Obesity-Related Lipidome and Fecal Microbiome Profiles: A Proof-of-Concept Study. Clin Transl Gastroenterol. 2022 Jul 1; 13 (7):e00508 Epub 2022 June 07
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  19. Hieken TJ, Chen J, Chen B, Johnson S, Hoskin TL, Degnim AC, Walther-Antonio MR, Chia N. The breast tissue microbiome, stroma, immune cells and breast cancer. Neoplasia. 2022 May; 27:100786 Epub 2022 Mar 30
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  20. Edwinson AL, Yang L, Peters S, Hanning N, Jeraldo P, Jagtap P, Simpson JB, Yang TY, Kumar P, Mehta S, Nair A, Breen-Lyles M, Chikkamenahalli L, Graham RP, De Winter B, Patel R, Dasari S, Kashyap P, Griffin T, Chen J, Farrugia G, Redinbo MR, Grover M. Gut microbial ß-glucuronidases regulate host luminal proteases and are depleted in irritable bowel syndrome. Nat Microbiol. 2022 May; 7(5):680-694. Epub 2022 Apr 28.
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  21. Miyabe K, Chandrasekhara V, Wongjarupong N, Chen J, Yang L, Johnson S, Chia N, Walther-Antonio M, Yao JZ, Harrington SC, Nordyke CK, Eaton JE, Gossard AA, Oli S, Ali HA, Lavu S, Giama NH, Hassan FA, Ali HM, Enders FT, Ilyas SI, Gores GJ, Topazian MD, Kashyap PC, Roberts LR. Potential Role of Inflammation-Promoting Biliary Microbiome in Primary Sclerosing Cholangitis and Cholangiocarcinoma. Cancers (Basel). 2022 Apr 24; 14 (9)
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  22. Zhou H, He K, Chen J, Zhang X. LinDA: linear models for differential abundance analysis of microbiome compositional data. Genome Biol. 2022 Apr 14; 23 (1):95
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  23. Deb B, Sharma M, Fletcher JG, Srinivasan SG, Chronopoulou A, Chen J, Bailey KR, Feuerhak KJ, Bharucha AE. Inadequate Rectal Pressure and Insufficient Relaxation and Abdominopelvic Coordination in Defecatory Disorders. Gastroenterology. 2022 Apr; 162 (4):1111-1122.e2 Epub 2021 Dec 22
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  24. Cao H, Chen J, Zhang X. OPTIMAL FALSE DISCOVERY RATE CONTROL FOR LARGE SCALE MULTIPLE TESTING WITH AUXILIARY INFORMATION. Ann Stat. 2022 Apr; 50 (2):807-857 Epub 2022 Apr 07
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  25. Zhu Y, Prata LGPL, Gerdes EOW, Netto JME, Pirtskhalava T, Giorgadze N, Tripathi U, Inman CL, Johnson KO, Xue A, Palmer AK, Chen T, Schaefer K, Justice JN, Nambiar AM, Musi N, Kritchevsky SB, Chen J, Khosla S, Jurk D, Schafer MJ, Tchkonia T, Kirkland JL. Orally-active, clinically-translatable senolytics restore alpha-Klotho in mice and humans. EBioMedicine. 2022 Mar; 77:103912 Epub 2022 Mar 13
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  26. Banerjee K, Chen J, Zhan X. Adaptive and powerful microbiome multivariate association analysis via feature selection. NAR Genom Bioinform. 2022 Mar; 4 (1):lqab120 Epub 2022 Jan 14
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  27. Jiang Z, He M, Chen J, Zhao N, Zhan X. MiRKAT-MC: A Distance-Based Microbiome Kernel Association Test With Multi-Categorical Outcomes. Front Genet. 2022; 13:841764 Epub 2022 Apr 01
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  28. Chen J, Zhang X. D-MANOVA: fast distance-based multivariate analysis of variance for large-scale microbiome association studies. Bioinformatics. 2021 Dec 22; 38 (1):286-288
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  29. Zhou H, Zhang X, Chen J. Covariate adaptive familywise error rate control for genome-wide association studies. Biometrika. 2021 Dec; 108 (4):915-931 Epub 2020 Nov 27
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  30. Odogwu NM, Onebunne CA, Chen J, Ayeni FA, Walther-Antonio MRS, Olayemi OO, Chia N, Omigbodun AO. Lactobacillus crispatus thrives in pregnancy hormonal milieu in a Nigerian patient cohort. Sci Rep. 2021 Sep 13; 11 (1):18152 Epub 2021 Sept 13
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  31. Leach DA, Chen J, Yang L, Chua HK, Walther-António MRS, Occhino JA. Microbiome diversity predicts surgical success in patients with rectovaginal fistula. Int Urogynecol J. 2021 Sep; 32(9):2491-2501. Epub 2020 Nov 11.
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  32. Acharya KD, Noh HL, Graham ME, Suk S, Friedline RH, Gomez CC, Parakoyi AER, Chen J, Kim JK, Tetel MJ. Distinct Changes in Gut Microbiota Are Associated with Estradiol-Mediated Protection from Diet-Induced Obesity in Female Mice. Metabolites. 2021 Jul 30; 11 (8) Epub 2021 July 30
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  33. Yi S, Zhang X, Yang L, Huang J, Liu Y, Wang C, Schaid DJ, Chen J. 2dFDR: a new approach to confounder adjustment substantially increases detection power in omics association studies. Genome Biol. 2021 Jul 13; 22 (1):208 Epub 2021 July 13
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  34. Wilson N, Zhao N, Zhan X, Koh H, Fu W, Chen J, Li H, Wu MC, Plantinga AM. MiRKAT: kernel machine regression-based global association tests for the microbiome. Bioinformatics. 2021 Jul 12; 37 (11):1595-1597
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  35. Zhan X, Banerjee K, Chen J. Variant-set association test for generalized linear mixed model. Genet Epidemiol. 2021 Jun; 45 (4):402-412 Epub 2021 Feb 19
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  36. Dai Y, Xu A, Li J, Wu L, Yu S, Chen J, Zhao W, Sun XJ, Huang J. CytoTree: an R/Bioconductor package for analysis and visualization of flow and mass cytometry data. BMC Bioinformatics. 2021 Mar 22; 22 (1):138
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  37. Diefenbach CS, Peters BA, Li H, Raphael B, Moskovits T, Hymes K, Schluter J, Chen J, Bennani NN, Witzig TE, Ahn J. Microbial dysbiosis is associated with aggressive histology and adverse clinical outcome in B-cell non-Hodgkin lymphoma. Blood Adv. 2021 Mar 9; 5 (5):1194-1198
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  38. Gu W, Wan F, Chen J, Gan H, Wang B, Wei Y, Zhang G, Zhou J, Ding X, Zhang P, Jin S, Xu Q, Ye D, Zhu Y. Identification of a methylation panel aid in risk stratification in node-positive penile squamous cell carcinoma. Int J Cancer. 2021 Mar 1; 148 (5):1289-1298 Epub 2020 Nov 05
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  39. Zhang H, Chen J, Feng Y, Wang C, Li H, Liu L. Mediation effect selection in high-dimensional and compositional microbiome data. Stat Med. 2021 Feb 20; 40 (4):885-896 Epub 2020 Nov 17
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  40. Pu M, Cho JM, Cunningham SA, Behera GK, Becker S, Amjad T, Greenwood-Quaintance KE, Mendes-Soares H, Jones-Hall Y, Jeraldo PR, Chen J, Dunny G, Patel R, Kashyap PC. Plasmid Acquisition Alters Vancomycin Susceptibility in Clostridioides difficile. Gastroenterology. 2021 Feb; 160 (3):941-945.e8 Epub 2020 Nov 14
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  41. Odogwu NM, Chen J, Onebunne CA, Jeraldo P, Yang L, Johnson S, Ayeni FA, Walther-Antonio MRS, Olayemi OO, Chia N, Omigbodun AO. Predominance of Atopobium vaginae at Midtrimester: a Potential Indicator of Preterm Birth Risk in a Nigerian Cohort. mSphere. 2021 Jan 27; 6 (1)
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  42. Zhang L, Wang Y, Chen J, Chen J. RFtest: A Robust and Flexible Community-Level Test for Microbiome Data Powerfully Detects Phylogenetically Clustered Signals. Front Genet. 2021; 12:749573. Epub 2022 Jan 24.
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  43. Edwinson A, Yang L, Chen J, Grover M. Colonic expression of Ace2, the SARS-CoV-2 entry receptor, is suppressed by commensal human microbiota. Gut Microbes. 2021 Jan-Dec; 13 (1):1984105
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  44. Shen C, Zhu Q, Dong F, Wang W, Fan B, Li K, Chen J, Hu S, He Z, Li X. Identifying Two Novel Clusters in Calcium Oxalate Stones With Urinary Tract Infection Using 16S rDNA Sequencing. Front Cell Infect Microbiol. 2021; 11:723781 Epub 2021 Nov 17
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  45. Balakrishnan B, Luckey D, Bodhke R, Chen J, Marietta E, Jeraldo P, Murray J, Taneja V. Prevotella histicola Protects From Arthritis by Expansion of Allobaculum and Augmenting Butyrate Production in Humanized Mice. Front Immunol. 2021; 12:609644 Epub 2021 May 04
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  46. Balakrishnan B, Selvaraju V, Chen J, Ayine P, Yang L, Babu JR, Geetha T, Taneja V. Ethnic variability associating gut and oral microbiome with obesity in children. Gut Microbes. 2021 Jan-Dec; 13 (1):1-15
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  47. Schaid DJ, Sinnwell JP, Larson NB, Chen J. Penalized variance components for association of multiple genes with traits. Genet Epidemiol. 2020 Oct; 44 (7):665-675 Epub 2020 July 22
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  48. Zhang X, Chen J. Covariate Adaptive False Discovery Rate Control with Applications to Omics-Wide Multiple Testing Journal of the American Statistical Association. 2020.
  49. Shogan BD, Chen J, Duchalais E, Collins D, Chang M, Krull K, Krezalek MA, Larson DW, Walther-Antonio MR, Chia N, Nelson H. Alterations of the Rectal Microbiome Are Associated with the Development of Postoperative Ileus in Patients Undergoing Colorectal Surgery. J Gastrointest Surg. 2020 Jul; 24 (7):1663-1672 Epub 2020 Apr 22
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  50. Huang J, Bai L, Cui B, Wu L, Wang L, An Z, Ruan S, Yu Y, Zhang X, Chen J. Leveraging biological and statistical covariates improves the detection power in epigenome-wide association testing. Genome Biol. 2020 Apr 6; 21 (1):88 Epub 2020 Apr 06
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  51. Multinu F, Chen J, Madison JD, Torres M, Casarin J, Visscher D, Shridhar V, Bakkum-Gamez J, Sherman M, Wentzensen N, Mariani A, Walther-Antonio M. Analysis of DNA methylation in endometrial biopsies to predict risk of endometrial cancer. Gynecol Oncol. 2020 Mar; 156 (3):682-688 Epub 2020 Jan 03
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  52. Byrd DA, Sinha R, Hoffman KL, Chen J, Hua X, Shi J, Chia N, Petrosino J, Vogtmann E. Comparison of Methods To Collect Fecal Samples for Microbiome Studies Using Whole-Genome Shotgun Metagenomic Sequencing. mSphere. 2020 Feb 26; 5 (1)
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  53. Kim M, Vogtmann E, Ahlquist DA, Devens ME, Kisiel JB, Taylor WR, White BA, Hale VL, Sung J, Chia N, Sinha R, Chen J. Fecal Metabolomic Signatures in Colorectal Adenoma Patients Are Associated with Gut Microbiota and Early Events of Colorectal Cancer Pathogenesis. mBio. 2020 Feb 18; 11 (1)
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  54. Edogawa S, Edwinson AL, Peters SA, Chikkamenahalli LL, Sundt W, Graves S, Gurunathan SV, Breen-Lyles M, Johnson S, Dyer R, Graham R, Chen J, Kashyap P, Farrugia G, Grover M. Serine proteases as luminal mediators of intestinal barrier dysfunction and symptom severity in IBS. Gut. 2020 Jan; 69 (1):62-73 Epub 2019 Mar 28
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  55. Acharya KD, Gao X, Bless EP, Chen J, Tetel MJ. Estradiol and high fat diet associate with changes in gut microbiota in female ob/ob mice. Sci Rep. 2019 Dec 27; 9 (1):20192
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  56. Walsh DM, Hokenstad AN, Chen J, Sung J, Jenkins GD, Chia N, Nelson H, Mariani A, Walther-Antonio MRS. Postmenopause as a key factor in the composition of the Endometrial Cancer Microbiome (ECbiome). Sci Rep. 2019 Dec 16; 9 (1):19213
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  57. Plantinga AM, Chen J, Jenq RR, Wu MC. pldist: ecological dissimilarities for paired and longitudinal microbiome association analysis. Bioinformatics. 2019 Oct 1; 35 (19):3567-3575
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  58. Ding Y, Dvornikov AV, Ma X, Zhang H, Wang Y, Lowerison M, Packard RR, Wang L, Chen J, Zhang Y, Hsiai T, Lin X, Xu X. Haploinsufficiency of mechanistic target of rapamycin ameliorates bag3 cardiomyopathy in adult zebrafish. Dis Model Mech. 2019 Oct 1; 12 (10) Epub 2019 Oct 01
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  59. Kashyap PC, Johnson S, Geno DM, Lekatz HR, Lavey C, Alexander JA, Chen J, Katzka DA. A decreased abundance of clostridia characterizes the gut microbiota in eosinophilic esophagitis. Physiol Rep. 2019 Oct; 7 (20):e14261
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  60. Zhang H, Chen J, Li Z, Liu L. Testing for Mediation Effect with Application to Human Microbiome Data Statistics in biosciences. 2019.
  61. Saffouri GB, Shields-Cutler RR, Chen J, Yang Y, Lekatz HR, Hale VL, Cho JM, Battaglioli EJ, Bhattarai Y, Thompson KJ, Kalari KK, Behera G, Berry JC, Peters SA, Patel R, Schuetz AN, Faith JJ, Camilleri M, Sonnenburg JL, Farrugia G, Swann JR, Grover M, Knights D, Kashyap PC. Small intestinal microbial dysbiosis underlies symptoms associated with functional gastrointestinal disorders. Nat Commun. 2019 May 1; 10 (1):2012 Epub 2019 May 01
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  62. Muniz Pedrogo DA, Chen J, Hillmann B, Jeraldo P, Al-Ghalith G, Taneja V, Davis JM 3rd, Knights D, Nelson H, Faubion WA, Raffals L, Kashyap PC. An Increased Abundance of Clostridiaceae Characterizes Arthritis in Inflammatory Bowel Disease and Rheumatoid Arthritis: A Cross-sectional Study. Inflamm Bowel Dis. 2019 Apr 11; 25 (5):902-913
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  63. Larson NB, Chen J, Schaid DJ. A review of kernel methods for genetic association studies. Genet Epidemiol. 2019 Mar; 43 (2):122-136 Epub 2019 Jan 02
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  64. Song SD, Jeraldo P, Chen J, Chen J, Chia N. Extreme value analysis of gut microbial alterations in colorectal cancer. Phys Rev E. 2019 Mar; 99 (3-1):032413
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  65. Chung W, Chen J, Turman C, Lindstrom S, Zhu Z, Loh PR, Kraft P, Liang L. Efficient cross-trait penalized regression increases prediction accuracy in large cohorts using secondary phenotypes. Nat Commun. 2019 Feb 4; 10 (1):569 Epub 2019 Feb 04
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  66. Greathouse KL, White JR, Padgett RN, Perrotta BG, Jenkins GD, Chia N, Chen J. Gut microbiome meta-analysis reveals dysbiosis is independent of body mass index in predicting risk of obesity-associated CRC. BMJ Open Gastroenterol. 2019; 6 (1):e000247 Epub 2019 Feb 28
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  67. Vogtmann E, Chen J, Kibriya MG, Amir A, Shi J, Chen Y, Islam T, Eunes M, Ahmed A, Naher J, Rahman A, Barmon B, Knight R, Chia N, Ahsan H, Abnet CC, Sinha R. Comparison of Oral Collection Methods for Studies of Microbiota. Cancer Epidemiol Biomarkers Prev. 2019 Jan; 28 (1):137-143 Epub 2018 Sept 27
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  68. Koh H, Li Y, Zhan X, Chen J, Zhao N. A Distance-Based Kernel Association Test Based on the Generalized Linear Mixed Model for Correlated Microbiome Studies. Front Genet. 2019; 10:458 Epub 2019 May 16
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  69. Byrd DA, Chen J, Vogtmann E, Hullings A, Song SJ, Amir A, Kibriya MG, Ahsan H, Chen Y, Nelson H, Knight R, Shi J, Chia N, Sinha R. Reproducibility, stability, and accuracy of microbial profiles by fecal sample collection method in three distinct populations. PLoS One. 2019; 14 (11):e0224757 Epub 2019 Nov 18
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  70. Zhan X, Xue L, Zheng H, Plantinga A, Wu MC, Schaid DJ, Zhao N, Chen J. A small-sample kernel association test for correlated data with application to microbiome association studies. Genet Epidemiol. 2018 Dec; 42 (8):772-782 Epub 2018 Sept 15
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  71. Hale VL, Jeraldo P, Chen J, Mundy M, Chen J, Yao J, Priya S, Keeney G, Lyke K, Ridlon J, White BA, French AJ, Thibodeau SN, Diener C, Resendis-Antonio O, Gransee J, Dutta T, Petterson XM, Sung J, Blekhman R, Boardman L, Larson D, Nelson H, Larson D, Chia N. Distinct microbes, metabolites, and ecologies define the microbiome in deficient and proficient mismatch repair colorectal cancers. Genome Med. 2018 Oct 31; 10 (1):78
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  72. Battaglioli EJ, Hale VL, Chen J, Jeraldo P, Ruiz-Mojica C, Schmidt BA, Rekdal VM, Till LM, Huq L, Smits SA, Moor WJ, Jones-Hall Y, Smyrk T, Khanna S, Pardi DS, Grover M, Patel R, Chia N, Nelson H, Sonnenburg JL, Farrugia G, Kashyap PC. Clostridioides difficile uses amino acids associated with gut microbial dysbiosis in a subset of patients with diarrhea. Sci Transl Med. 2018 Oct 24; 10 (464)
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  73. Muniz Pedrogo DA, Jensen MD, Van Dyke CT, Murray JA, Woods JA, Chen J, Kashyap PC, Nehra V. Gut Microbial Carbohydrate Metabolism Hinders Weight Loss in Overweight Adults Undergoing Lifestyle Intervention With a Volumetric Diet. Mayo Clin Proc. 2018 Aug; 93 (8):1104-1110
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  74. Edogawa S, Peters SA, Jenkins GD, Gurunathan SV, Sundt WJ, Johnson S, Lennon RJ, Dyer RB, Camilleri M, Kashyap PC, Farrugia G, Chen J, Singh RJ, Grover M. Sex differences in NSAID-induced perturbation of human intestinal barrier function and microbiota. FASEB J. 2018 Jun 13; 32 (12):fj201800560R Epub 2018 June 13
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  75. Zhang J, Wei Z, Chen J. A distance-based approach for testing the mediation effect of the human microbiome. Bioinformatics. 2018 Jun 1; 34 (11):1875-1883
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  76. Chen X, Johnson S, Jeraldo P, Wang J, Chia N, Kocher JA, Chen J. Hybrid-denovo: a de novo OTU-picking pipeline integrating single-end and paired-end 16S sequence tags. Gigascience. 2018 Mar 01; 7(3):1-7.
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  77. Multinu F, Harrington SC, Chen J, Jeraldo PR, Johnson S, Chia N, Walther-Antonio MR. Systematic Bias Introduced by Genomic DNA Template Dilution in 16S rRNA Gene-Targeted Microbiota Profiling in Human Stool Homogenates. mSphere. 2018 Mar-Apr; 3 (2) Epub 2018 Mar 14
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  78. Chen J, King E, Deek R, Wei Z, Yu Y, Grill D, Ballman K, Stegle O. An omnibus test for differential distribution analysis of microbiome sequencing data. Bioinformatics. 2018 Feb 15; 34(4):643-651.
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  79. Xiao J, Chen L, Yu Y, Zhang X, Chen J. A Phylogeny-Regularized Sparse Regression Model for Predictive Modeling of Microbial Community Data. Front Microbiol. 2018; 9:3112. Epub 2018 Dec 19.
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  80. Chen L, Reeve J, Zhang L, Huang S, Wang X, Chen J. GMPR: A robust normalization method for zero-inflated count data with application to microbiome sequencing data. PeerJ. 2018; 6:e4600 Epub 2018 Apr 02
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  81. Xiao J, Chen L, Johnson S, Yu Y, Zhang X, Chen J. Predictive Modeling of Microbiome Data Using a Phylogeny-Regularized Generalized Linear Mixed Model. Front Microbiol. 2018; 9:1391 Epub 2018 June 27
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  82. Herzog EM, Eggink AJ, Willemsen SP, Slieker RC, Wijnands KPJ, Felix JF, Chen J, Stubbs A, van der Spek PJ, van Meurs JB, Steegers-Theunissen RPM. Early- and late-onset preeclampsia and the tissue-specific epigenome of the placenta and newborn. Placenta. 2017 Oct; 58:122-132 Epub 2017 Aug 30
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  83. Parthasarathy G, Chen J, Chia N, O'Connor HM, Gaskins HR, Bharucha AE. Reproducibility of assessing fecal microbiota in chronic constipation. Neurogastroenterol Motil. 2017 Oct; 29 (10):1-10 Epub 2017 July 28
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  84. Wolf PG, Parthasarathy G, Chen J, O'Connor HM, Chia N, Bharucha AE, Gaskins HR. Assessing the colonic microbiome, hydrogenogenic and hydrogenotrophic genes, transit and breath methane in constipation. Neurogastroenterol Motil. 2017 Oct; 29 (10):1-9 Epub 2017 Mar 13
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  85. Xiao J, Cao H, Chen J. False discovery rate control incorporating phylogenetic tree increases detection power in microbiome-wide multiple testing. Bioinformatics. 2017 Sep 15; 33 (18):2873-2881
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  86. Cunningham SA, Chia N, Jeraldo PR, Quest DJ, Johnson JA, Boxrud DJ, Taylor AJ, Chen J, Jenkins GD, Drucker TM, Nelson H, Patel R. Comparison of Whole-Genome Sequencing Methods for Analysis of Three Methicillin-Resistant Staphylococcus aureus Outbreaks. J Clin Microbiol. 2017 Jun; 55 (6):1946-1953 Epub 2017 Apr 12
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  87. Chen J, Behnam E, Huang J, Moffatt MF, Schaid DJ, Liang L, Lin X. Fast and robust adjustment of cell mixtures in epigenome-wide association studies with SmartSVA. BMC Genomics. 2017 May 26; 18 (1):413
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  88. Vogtmann E, Chen J, Kibriya MG, Chen Y, Islam T, Eunes M, Ahmed A, Naher J, Rahman A, Amir A, Shi J, Abnet CC, Nelson H, Knight R, Chia N, Ahsan H, Sinha R. Comparison of Fecal Collection Methods for Microbiota Studies in Bangladesh. Appl Environ Microbiol. 2017 May 15; 83 (10) Epub 2017 May 01
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  89. Zhan X, Tong X, Zhao N, Maity A, Wu MC, Chen J. A small-sample multivariate kernel machine test for microbiome association studies. Genet Epidemiol. 2017 Apr; 41 (3):210-220 Epub 2016 Dec 26
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  90. Wijnands KP, Chen J, Liang L, Verbiest MM, Lin X, Helbing WA, Gittenberger-de Groot AC, van der Spek PJ, Uitterlinden AG, Steegers-Theunissen RP. Genome-wide methylation analysis identifies novel CpG loci for perimembranous ventricular septal defects in human. Epigenomics. 2017 Mar; 9 (3):241-251 Epub 2017 Jan 31
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  91. Valentin N, Camilleri M, Carlson P, Harrington SC, Eckert D, O'Neill J, Burton D, Chen J, Shaw AL, Acosta A. Potential mechanisms of effects of serum-derived bovine immunoglobulin/protein isolate therapy in patients with diarrhea-predominant irritable bowel syndrome. Physiol Rep. 2017 Mar; 5 (5)
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  92. Plantinga A, Zhan X, Zhao N, Chen J, Jenq RR, Wu MC. MiRKAT-S: a community-level test of association between the microbiota and survival times. Microbiome. 2017 Feb 8; 5 (1):17 Epub 2017 Feb 08
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  93. Vogtmann E, Chen J, Amir A, Shi J, Abnet CC, Nelson H, Knight R, Chia N, Sinha R. Comparison of Collection Methods for Fecal Samples in Microbiome Studies. Am J Epidemiol. 2017 Jan 15; 185: (2)115-123.
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  94. Hale VL, Chen J, Johnson S, Harrington SC, Yab TC, Smyrk TC, Nelson H, Boardman LA, Druliner BR, Levin TR, Rex DK, Ahnen DJ, Lance P, Ahlquist DA, Chia N. Shifts in the Fecal Microbiota Associated with Adenomatous Polyps. Cancer Epidemiol Biomarkers Prev. 2017 Jan; 26 (1):85-94 Epub 2016 Sept 26
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  95. Xiao J, Chen J. Phylogeny-Based Kernels with Application to Microbiome Association Studies New Advances in Statistics and Data Science. 2017; 217-237.
  96. Chen J, Chen L. GMPR: A novel normalization method for microbiome sequencing data BioRxiv. 2017.
  97. Walther-Antonio MR, Chen J, Multinu F, Hokenstad A, Distad TJ, Cheek EH, Keeney GL, Creedon DJ, Nelson H, Mariani A, Chia N. Potential contribution of the uterine microbiome in the development of endometrial cancer. Genome Med. 2016 Nov 25; 8 (1):122
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