Publications

  1. 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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  2. 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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  3. 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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  4. Xiang Zhan, Kalins Banerjee, Jun Chen. Variant-set association test for generalized linear mixed model Genetic Epidemiology. 2021.
  5. 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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  6. 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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  7. Balakrishnan B, Selvaraju V, Chen J, Ayine P, Yang L, Ramesh Babu J, 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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  8. Leach DA, Chen J, Yang L, Chua HK, Walther-Antonio MRS, Occhino JA. Microbiome diversity predicts surgical success in patients with rectovaginal fistula. Int Urogynecol J. 2020 Nov 11 [Epub ahead of print]
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  9. 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. 2020 Nov 3 Epub 2020 Nov 03
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  10. Huijuan Zhou, Xianyang Zhang, Jun Chen. Covariate Adaptive Family-wise Error Rate Control for Genome-Wide Association Studies arXiv preprint arXiv:2011.01107. 2020.
  11. 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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  12. Xianyang Zhang, Jun Chen . Covariate Adaptive False Discovery Rate Control with Applications to Omics-Wide Multiple Testing Journal of the American Statistical Association. 2020.
  13. 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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  14. 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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  15. 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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  16. 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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  17. 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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  18. 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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  19. 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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  20. 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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  21. 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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  22. 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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  23. Plantinga AM, Chen J, Jun Chen, 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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  24. Zhang H, Chen J, Li Z, Liu L. Testing for Mediation Effect with Application to Human Microbiome Data Statistics in biosciences. 2019.
  25. 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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  26. 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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  27. 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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  28. 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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  29. 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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  30. 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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  31. 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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  32. 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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  33. 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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  34. 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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  35. 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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  36. 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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  37. 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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  38. 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; fj201800560R Epub 2018 June 13
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  39. 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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  40. 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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  41. 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 1; 7 (3):1-7
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  42. 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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  43. 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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  44. 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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  45. 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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  46. 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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  47. 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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  48. 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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  49. 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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  50. 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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  51. 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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  52. 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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  53. 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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  54. 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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  55. 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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  56. 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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  57. 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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  58. 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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  59. Xiao J, Chen J. Phylogeny-Based Kernels with Application to Microbiome Association Studies New Advances in Statistics and Data Science. 2017; 217-237.
  60. Chen J, Chen L. GMPR: A novel normalization method for microbiome sequencing data BioRxiv. 2017.
  61. 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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  62. 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 3; 8 (1):103 Epub 2016 Oct 03
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  63. 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 3; 6:30751 Epub 2016 Aug 03
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  64. Chen J, Chia N, Kalari KR, Yao JZ, Novotna M, Paz 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 Epub 2016 June 27
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  65. Wu C, Chen J, Kim J, Pan W. An adaptive association test for microbiome data. Genome Med. 2016 May 19; 8 (1):56
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  66. 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
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  67. 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
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  68. 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 1; 32 (3):469-71 Epub 2015 Oct 07
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  69. 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 Epub 2015 Oct 13
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  70. 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 Epub 2015 Nov 24
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  71. 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 Epub 2015 Dec 07
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  72. 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 Epub 2016 Jan 07
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  73. 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.
  74. 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 Epub 2015 Aug 26
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  75. 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 Epub 2015 Jan 14
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  76. 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 8; 6:6821 Epub 2015 May 08
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  77. Zhao N, Chen J, Carroll IM, Chen J, 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 7; 96 (5):797-807
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  78. 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 Epub 2015 Nov 26
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  79. 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.
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  80. 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 Epub 2015 Jan 12
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  81. 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.
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  82. 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.
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  83. 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.
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  84. 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.
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  85. 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).
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  86. 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.
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  87. Chen J, Li H . Kernel Methods for Regression Analysis of Microbiome Compositional Data Topics in Applied Statistics, Springer Proceedings in Mathematics & Statistics. 2013; 55:191-201.
  88. 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.
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  89. 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.
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  90. Chen J. Statistical methods for human microbiome data analysis Dissertation, University of Pennsylvania. 2012.
  91. 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.
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  92. 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.
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  93. Gary Wu, Meenakshi, Christian, Ying-Yu, Sue, Kyle, Rob, Jennifer, Jun, Erin, Kernika, Lisa, Robert, Hongzhe Li, Frederic, James. Controlled Feeding Experiments Demonstrate the Impact of Diet on the Composition of the Human Gut Microbiome Gastroenterology. 2011; 140(5):S-47.
  94. 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.
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  95. 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.
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  96. 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.
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  97. 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.
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  98. 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.
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  99. 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.
  100. 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.
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