Publications

  1. Chen J, King E, Deek R, Wei Z, Yu Y, Grill D, Ballman K. An omnibus test for differential distribution analysis of microbiome sequencing data. Bioinformatics. 2017 Oct 12 [Epub ahead of print]
    View PubMed
  2. 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
    View PubMed
  3. 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
    View PubMed
  4. 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
    View PubMed
  5. 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
    View PubMed
  6. 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.
    View PubMed
  7. 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.
    View PubMed
  8. 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
    View PubMed
  9. 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.
    View PubMed
  10. 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
    View PubMed
  11. 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 immunoglobulinprotein isolate therapy in patients with diarrhea-predominant irritable bowel syndrome. Physiol Rep. 2017 Mar; 5: (5).
    View PubMed
  12. 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 08; 5: (1)17.
    View PubMed
  13. 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.
    View PubMed
  14. 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.
    View PubMed
  15. 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.
    View PubMed
  16. Chen J, Toyomasu Y, Hayashi Y, Linden DR, Szurszewski JH, Nelson H, Farrugia G, Kashyap PC, Chia N, Ordog T. Altered gut microbiota in female mice with persistent low body weights following removal of post-weaning chronic dietary restriction. Genome Med. 2016 Oct 03; 8: (1)103.
    View PubMed
  17. Hieken TJ, Chen J, Hoskin TL, Walther-Antonio M, Johnson S, Ramaker S, Xiao J, Radisky DC, Knutson KL, Kalari KR, Yao JZ, Baddour LM, Chia N, Degnim AC. The Microbiome of Aseptically Collected Human Breast Tissue in Benign and Malignant Disease. Sci Rep. 2016 Aug 03; 6:30751.
    View PubMed
  18. Chen J, Chia N, Kalari KR, Yao JZ, Novotna M, Soldan MM, Luckey DH, Marietta EV, Jeraldo PR, Chen X, Weinshenker BG, Rodriguez M, Kantarci OH, Nelson H, Murray JA, Mangalam AK. Multiple sclerosis patients have a distinct gut microbiota compared to healthy controls. Sci Rep. 2016 Jun 27; 6:28484.
    View PubMed
  19. Wu C, Chen J, Kim J, Pan W. An adaptive association test for microbiome data. Genome Med. 2016 May 19; 8: (1)56.
    View PubMed
  20. Yu Y, Chen J, Li D, Wang L, Wang W, Liu H. Systematic Analysis of Adverse Event Reports for Sex Differences in Adverse Drug Events. Sci Rep. 2016 Apr 22; 6:24955.
    View PubMed
  21. Chen J, Wright K, Davis JM, Jeraldo P, Marietta EV, Murray J, Nelson H, Matteson EL, Taneja V. An expansion of rare lineage intestinal microbes characterizes rheumatoid arthritis. Genome Med. 2016 Apr 21; 8: (1)43.
    View PubMed
  22. Chen J, Just AC, Schwartz J, Hou L, Jafari N, Sun Z, Kocher JP, Baccarelli A, Lin X. CpGFilter: model-based CpG probe filtering with replicates for epigenome-wide association studies. Bioinformatics. 2016 Feb 01; 32: (3)469-71.
    View PubMed
  23. Parthasarathy G, Chen J, Chen X, Chia N, O'Connor HM, Wolf PG, Gaskins HR, Bharucha AE. Relationship Between Microbiota of the Colonic Mucosa vs Feces and Symptoms, Colonic Transit, and Methane Production in Female Patients With Chronic Constipation. Gastroenterology. 2016 Feb; 150: (2)367-79.e1.
    View PubMed
  24. Sinha R, Chen J, Amir A, Vogtmann E, Shi J, Inman KS, Flores R, Sampson J, Knight R, Chia N. Collecting Fecal Samples for Microbiome Analyses in Epidemiology Studies. Cancer Epidemiol Biomarkers Prev. 2016 Feb; 25: (2)407-16.
    View PubMed
  25. Chen J, Chen W, Zhao N, Wu MC, Schaid DJ. Small Sample Kernel Association Tests for Human Genetic and Microbiome Association Studies. Genet Epidemiol. 2016 Jan; 40: (1)5-19.
    View PubMed
  26. Chen J, Ryu E, Hathcock M, Ballman K, Chia N, Olson JE, Nelson H. Impact of demographics on human gut microbial diversity in a US Midwest population. PeerJ. 2016; 4:e1514.
    View PubMed
  27. Fan W, Chen J, Bao CD. An updated meta-analysis of association of rheumatoid arthritis related interstitial lung disease with anti-cyclic citrullinated peptide antibody or rheumatoid factor International Journal Of Clinical And Experimental Medicine. 2016; 9: (6)10333-43.
  28. Chen L, Liu H, Kocher JP, Li H, Chen J. glmgraph: an R package for variable selection and predictive modeling of structured genomic data. Bioinformatics. 2015 Dec 15; 31: (24)3991-3.
    View PubMed
  29. Nickel JC, Stephens A, Landis JR, Chen J, Mullins C, van Bokhoven A, Lucia MS, Melton-Kreft R, Ehrlich GD, MAPP Research Network. Search for Microorganisms in Men with Urologic Chronic Pelvic Pain Syndrome: A Culture-Independent Analysis in the MAPP Research Network. J Urol. 2015 Jul; 194: (1)127-35.
    View PubMed
  30. Huang J, Chen J, Esparza J, Ding J, Elder JT, Abecasis GR, Lee YA, Mark Lathrop G, Moffatt MF, Cookson WO, Liang L. eQTL mapping identifies insertion- and deletion-specific eQTLs in multiple tissues. Nat Commun. 2015 May 08; 6:6821
    View PubMed
  31. Zhao N, Chen J, Carroll IM, Ringel-Kulka T, Epstein MP, Zhou H, Zhou JJ, Ringel Y, Li H, Wu MC. Testing in Microbiome-Profiling Studies with MiRKAT, the Microbiome Regression-Based Kernel Association Test. Am J Hum Genet. 2015 May 07; 96: (5)797-807.
    View PubMed
  32. Baldwin EA, Walther-Antonio M, MacLean AM, Gohl DM, Beckman KB, Chen J, White B, Creedon DJ, Chia N. Persistent microbial dysbiosis in preterm premature rupture of membranes from onset until delivery. PeerJ. 2015; 3:e1398.
    View PubMed
  33. Albenberg L, Esipova TV, Judge CP, Bittinger K, Chen J, Laughlin A, Grunberg S, Baldassano RN, Lewis JD, Li H, Thom SR, Bushman FD, Vinogradov SA, Wu GD. Correlation between intraluminal oxygen gradient and radial partitioning of intestinal microbiota. Gastroenterology. 2014 Nov; 147(5):1055-63.e8. Epub 2014 Jul 18.
    View PubMed
  34. Tian X, Wang X, Chen J. Network-constrained group lasso for high-dimensional multinomial classification with application to cancer subtype prediction. Cancer Inform. 2014; 13: (Suppl 6)25-33.
    View PubMed
  35. Xia F, Chen J, Fung WK, Li H. A logistic normal multinomial regression model for microbiome compositional data analysis. Biometrics. 2013 Dec; 69(4):1053-63. Epub 2013 Oct 15.
    View PubMed
  36. Huang J, Chen J, Lathrop M, Liang L. A tool for RNA sequencing sample identity check. Bioinformatics. 2013 Jun 1; 29(11):1463-4. Epub 2013 Apr 04.
    View PubMed
  37. Koeth RA, Wang Z, Levison BS, Buffa JA, Org E, Sheehy BT, Britt EB, Fu X, Wu Y, Li L, Smith JD, DiDonato JA, Chen J, Li H, Wu GD, Lewis JD, Warrier M, Brown JM, Krauss RM, Tang WH, Bushman FD, Lusis AJ, Hazen SL. Intestinal microbiota metabolism of L-carnitine, a nutrient in red meat, promotes atherosclerosis. Nat Med. 2013 May; 19(5):576-85. Epub 2013 Apr 07.
    View PubMed
  38. Chen J, Bushman FD, Lewis JD, Wu GD, Li H. Structure-constrained sparse canonical correlation analysis with an application to microbiome data analysis. Biostatistics. 2013 Apr; 14(2):244-58. Epub 2012 Oct 15.
    View PubMed
  39. Chen J, Li H. VARIABLE SELECTION FOR SPARSE DIRICHLET-MULTINOMIAL REGRESSION WITH AN APPLICATION TO MICROBIOME DATA ANALYSIS. Ann Appl Stat. 2013 Mar 1; 7(1).
    View PubMed
  40. Hoffmann C, Dollive S, Grunberg S, Chen J, Li H, Wu GD, Lewis JD, Bushman FD. Archaea and fungi of the human gut microbiome: correlations with diet and bacterial residents. PLoS One. 2013; 8(6):e66019. Epub 2013 Jun 17.
    View PubMed
  41. Chen J, Bittinger K, Charlson ES, Hoffmann C, Lewis J, Wu GD, Collman RG, Bushman FD, Li H. Associating microbiome composition with environmental covariates using generalized UniFrac distances. Bioinformatics. 2012 Aug 15; 28(16):2106-13. Epub 2012 Jun 17.
    View PubMed
  42. Charlson ES, Bittinger K, Chen J, Diamond JM, Li H, Collman RG, Bushman FD. Assessing bacterial populations in the lung by replicate analysis of samples from the upper and lower respiratory tracts. PLoS One. 2012; 7(9):e42786. Epub 2012 Sep 06.
    View PubMed
  43. Wu GD, Chen J, Hoffmann C, Bittinger K, Chen YY, Keilbaugh SA, Bewtra M, Knights D, Walters WA, Knight R, Sinha R, Gilroy E, Gupta K, Baldassano R, Nessel L, Li H, Bushman FD, Lewis JD. Linking long-term dietary patterns with gut microbial enterotypes. Science. 2011 Oct 7; 334(6052):105-8. Epub 2011 Sep 01.
    View PubMed
  44. Minot S, Sinha R, Chen J, Li H, Keilbaugh SA, Wu GD, Lewis JD, Bushman FD. The human gut virome: inter-individual variation and dynamic response to diet. Genome Res. 2011 Oct; 21(10):1616-25. Epub 2011 Aug 31.
    View PubMed
  45. Chen J, Xie J, Li H. A penalized likelihood approach for bivariate conditional normal models for dynamic co-expression analysis. Biometrics. 2011 Mar; 67(1):299-308.
    View PubMed
  46. Chen J, Sprouffske K, Huang Q, Maley CC. Solving the puzzle of metastasis: the evolution of cell migration in neoplasms. PLoS One. 2011; 6(4):e17933. Epub 2011 Apr 27.
    View PubMed
  47. Charlson ES, Chen J, Custers-Allen R, Bittinger K, Li H, Sinha R, Hwang J, Bushman FD, Collman RG. Disordered microbial communities in the upper respiratory tract of cigarette smokers. PLoS One. 2010; 5(12):e15216. Epub 2010 Dec 20.
    View PubMed
  48. Wu GD, Lewis JD, Hoffmann C, Chen YY, Knight R, Bittinger K, Hwang J, Chen J, Berkowsky R, Nessel L, Li H, Bushman FD. Sampling and pyrosequencing methods for characterizing bacterial communities in the human gut using 16S sequence tags. BMC Microbiol. 2010; 10:206. Epub 2010 Jul 30.
    View PubMed
  49. Chen J, Yang J. [Synthesis of realistic human faces from CT image and color photos]. Sheng Wu Yi Xue Gong Cheng Xue Za Zhi. 2008 Jun; 25(3):515-9.
    View PubMed
  50. Liu H, Yang J, Chen J, Liu D. Predicting signal peptides based on global alignment similarity. (Chinese). Journal of Shanghai Jiaotong University. 2008; 42:11-15.
  51. Chen J, Liu H, Yang J, Chou KC. Prediction of linear B-cell epitopes using amino acid pair antigenicity scale. Amino Acids. 2007 Sep; 33(3):423-8. Epub 2007 Jan 26.
    View PubMed