Publications

  1. Fisher CR, Masters TL, Johnson S, Greenwood-Quaintance KE, Chia N, Abdel MP, Patel R. Comparative transcriptomic analysis of Staphylococcus epidermidis associated with periprosthetic joint infection under in vivo and in vitro conditions. Int J Med Microbiol. 2024 Jun; 315:151620 Epub 2024 Mar 30
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  2. Brunner JD, Chia N. Metabolic model-based ecological modeling for probiotic design. Elife. 2024 Feb 21; 13
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  3. Sandoval L, Mohammed Ismail W, Mazzone A, Dumbrava M, Fernandez J, Munankarmy A, Lasho T, Binder M, Simon V, Kim KH, Chia N, Lee JH, Weroha SJ, Patnaik M, Gaspar-Maia A. Characterization and Optimization of Multiomic Single-Cell Epigenomic Profiling. Genes (Basel). 2023 Jun 10; 14 (6) Epub 2023 June 10
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  4. Lasho T, Finke C, Timm M, Tefferi A, Mangaonkar A, Olteanu H, Reichard K, Ketterling R, Gangat N, Xie Z, Fernandez J, Chia N, Gaspar-Maia A, Binder M, Patnaik MM. Single cell proteogenomic analysis of aberrant monocytosis in TET2 mutant premalignant and malignant hematopoiesis. Leukemia 2023 Jun; 37 (6):1384-1387 Epub 2023 Mar 25
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  5. 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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  6. Byeon SK, Madugundu AK, Garapati K, Ramarajan MG, Saraswat M, Kumar-M P, Hughes T, Shah R, Patnaik MM, Chia N, Ashrafzadeh-Kian S, Yao JD, Pritt BS, Cattaneo R, Salama ME, Zenka RM, Kipp BR, Grebe SKG, Singh RJ, Sadighi Akha AA, Algeciras-Schimnich A, Dasari S, Olson JE, Walsh JR, Venkatakrishnan AJ, Jenkinson G, O'Horo JC, Badley AD, Pandey A. Development of a multiomics model for identification of predictive biomarkers for COVID-19 severity: a retrospective cohort study. Lancet Digit Health. 2022 Sep; 4 (9):e632-e645 Epub 2022 July 11
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  7. Fida M, Cunningham SA, Beisken S, Posch AE, Chia N, Jeraldo PR, Murphy MP, Zinsmaster NM, Patel R, Antibacterial Resistance Leadership Group. Acinetobacter baumannii Genomic Sequence-Based Core Genome Multilocus Sequence Typing Using Ridom SeqSphere+ and Antimicrobial Susceptibility Prediction in ARESdb. J Clin Microbiol. 2022 Aug 17; 60 (8):e0053322 Epub 2022 July 12
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  8. Scott N, Whittle E, Jeraldo P, Chia N. A systemic review of the role of enterotoxic Bacteroides fragilis in colorectal cancer. Neoplasia. 2022 Jul; 29:100797 Epub 2022 Apr 20
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  9. 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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  10. 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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  11. Kim M, Sung J, Chia N. Resource-allocation constraint governs structure and function of microbial communities in metabolic modeling. Metab Eng. 2022 Mar; 70:12-22 Epub 2022 Jan 03
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  12. Yonkus JA, Whittle E, Alva-Ruiz R, Abdelrahman AM, Horsman SE, Suh GA, Cunningham SA, Nelson H, Grotz TE, Smoot RL, Cleary SP, Nagorney DM, Kendrick ML, Patel R, Truty MJ, Chia N. "Answers in hours": A prospective clinical study using nanopore sequencing for bile duct cultures. Surgery. 2022 Mar; 171 (3):693-702 Epub 2021 Dec 29
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  13. Whittle E, Yonkus JA, Jeraldo P, Alva-Ruiz R, Nelson H, Kendrick ML, Grys TE, Patel R, Truty MJ, Chia N. Optimizing Nanopore Sequencing for Rapid Detection of Microbial Species and Antimicrobial Resistance in Patients at Risk of Surgical Site Infections. mSphere. 2022 Feb 23; 7 (1):e0096421 Epub 2022 Feb 16
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  14. Cho HK, Masters T, Greenwood-Quaintance KE, Johnson S, Jeraldo PR, Chia N, Pu M, Abdel MP, Patel R. Transcriptomic analysis of Streptococcus agalactiae periprosthetic joint infection. Microbiologyopen. 2021 Nov; 10 (6):e1256
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  15. Liu Y, Jeraldo P, Mendes-Soares H, Masters T, Asangba AE, Nelson H, Patel R, Chia N, Walther-Antonio M. Amplification of Femtograms of Bacterial DNA Within 3 h Using a Digital Microfluidics Platform for MinION Sequencing. ACS Omega. 2021 Oct 5; 6 (39):25642-25651 Epub 2021 Sept 23
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  16. 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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  17. Li JJ, Zhu M, Kashyap PC, Chia N, Tran NH, McWilliams RR, Bekaii-Saab TS, Ma WW. The role of microbiome in pancreatic cancer. Cancer Metastasis Rev. 2021 Sep; 40 (3):777-789 Epub 2021 Aug 28
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  18. Le Masters T, Johnson S, Jeraldo PR, Greenwood-Quaintance KE, Cunningham SA, Abdel MP, Chia N, Patel R. Comparative Transcriptomic Analysis of Staphylococcus aureus Associated with Periprosthetic Joint Infection under in Vivo and in Vitro Conditions. J Mol Diagn. 2021 Aug; 23 (8):986-999 Epub 2021 June 05
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  19. Sivaguru M, Saw JJ, Wilson EM, Lieske JC, Krambeck AE, Williams JC, Romero MF, Fouke KW, Curtis MW, Kear-Scott JL, Chia N, Fouke BW. Human kidney stones: a natural record of universal biomineralization. Nat Rev Urol. 2021 Jul; 18 (7):404-432 Epub 2021 May 24
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  20. Li H, Vanarsa K, Zhang T, Soomro S, Cicalese PA, Duran V, Dasari S, Lee KH, Pedroza C, Kisiel JB, Qin H, Bresalier RS, Chia N, Mohan C. Comprehensive aptamer-based screen of 1317 proteins uncovers improved stool protein markers of colorectal cancer. J Gastroenterol. 2021 Jul; 56 (7):659-672 Epub 2021 June 12
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  21. Prototyping CRISP: A Causal Relation and Inference Search Platform applied to Colorectal Cancer Data LifeTech 2021 - 2021 IEEE 3rd Global Conference on Life Sciences and Technologies. 2021.
  22. Saw JJ, Sivaguru M, Wilson EM, Dong Y, Sanford RA, Fields CJ, Cregger MA, Merkel AC, Bruce WJ, Weber JR, Lieske JC, Krambeck AE, Rivera ME, Large T, Lange D, Bhattacharjee AS, Romero MF, Chia N, Fouke BW. In Vivo Entombment of Bacteria and Fungi during Calcium Oxalate, Brushite, and Struvite Urolithiasis. Kidney360. 2021 Feb 25; 2 (2):298-311 Epub 2020 Dec 23
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  23. 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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  24. Seaver SMD, Liu F, Zhang Q, Jeffryes J, Faria JP, Edirisinghe JN, Mundy M, Chia N, Noor E, Beber ME, Best AA, DeJongh M, Kimbrel JA, D'haeseleer P, McCorkle SR, Bolton JR, Pearson E, Canon S, Wood-Charlson EM, Cottingham RW, Arkin AP, Henry CS. The ModelSEED Biochemistry Database for the integration of metabolic annotations and the reconstruction, comparison and analysis of metabolic models for plants, fungi and microbes. Nucleic Acids Res. 2021 Jan 8; 49 (D1):D575-D588
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  25. Crooks TA, Madison JD, Walsh DM, Herbert WG, Jeraldo PR, Chia N, Cliby WA, Kaufmann SH, Walther-Antonio MRS. Porphyromonas somerae Invasion of Endometrial Cancer Cells. Front Microbiol. 2021; 12:674835 Epub 2021 July 23
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  26. Christensen S, Kim J, Chia N, Koyejo O, El-Kebir M. Detecting evolutionary patterns of cancers using consensus trees. Bioinformatics. 2020 Dec 30; 36 (Suppl_2):i684-i691
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  27. Weber LL, Aguse N, Chia N, El-Kebir M. PhyDOSE: Design of follow-up single-cell sequencing experiments of tumors. PLoS Comput Biol. 2020 Oct; 16 (10):e1008240 Epub 2020 Oct 01
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  28. Gupta VK, Kim M, Bakshi U, Cunningham KY, Davis JM 3rd, Lazaridis KN, Nelson H, Chia N, Sung J. A predictive index for health status using species-level gut microbiome profiling. Nat Commun. 2020 Sep 15; 11 (1):4635 Epub 2020 Sept 15
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  29. Brunner JD, Chia N. Minimizing the number of optimizations for efficient community dynamic flux balance analysis. PLoS Comput Biol. 2020 Sep; 16 (9):e1007786 Epub 2020 Sept 29
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  30. Song SD, Acharya KD, Zhu JE, Deveney CM, Walther-Antonio MRS, Tetel MJ, Chia N. Daily Vaginal Microbiota Fluctuations Associated with Natural Hormonal Cycle, Contraceptives, Diet, and Exercise. mSphere. 2020 Jul 8; 5 (4) Epub 2020 July 08
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  31. 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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  32. Fida M, Cunningham SA, Murphy MP, Bonomo RA, Hujer KM, Hujer AM, Kreiswirth BN, Chia N, Jeraldo PR, Nelson H, Zinsmaster NM, Toraskar N, Chang W, Patel R, Antibacterial Resistance Leadership Group. Core genome MLST and resistome analysis of Klebsiella pneumoniae using a clinically amenable workflow. Diagn Microbiol Infect Dis. 2020 May; 97 (1):114996 Epub 2020 Jan 21
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  33. Kalantari J, Nelson H, Chia N. The Unreasonable Effectiveness of Inverse Reinforcement Learning in Advancing Cancer Research. Proc Conf AAAI Artif Intell. 2020 Apr 3; 34 (1):437-445
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  34. 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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  35. Thoendel M, Jeraldo P, Greenwood-Quaintance KE, Yao J, Chia N, Hanssen AD, Abdel MP, Patel R. Comparison of Three Commercial Tools for Metagenomic Shotgun Sequencing Analysis. J Clin Microbiol. 2020 Feb 24; 58 (3)
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  36. 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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  37. Kalantari J, Nelson H, Chia N. The Unreasonable Effectiveness of Inverse Reinforcement Learning in Advancing Cancer Researchhttps://dotnetprod.mayo.edu/reaims/web/Publications/PublicationCreate#authors Association for the Advancement of Artificial Intelligence. 2020.
  38. Brunner J, Chia N. Confidence in the dynamic spread of epidemics under biased sampling conditions. PeerJ. 2020; 8:e9758 Epub 2020 Aug 14
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  39. 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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  40. Brunner JD, Chia N. Metabolite-mediated modelling of microbial community dynamics captures emergent behaviour more effectively than species-species modelling. J R Soc Interface. 2019 Oct 31; 16 (159):20190423 Epub 2019 Oct 23
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  41. Nelson H, Chia N. Gut Microbiome and Colon Cancer: A Plausible Explanation for Dietary Contributions to Cancer. J Am Coll Surg 2019 Sep; 229 (3):231-235 Epub 2019 May 10
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  42. Park KH, Greenwood-Quaintance KE, Cunningham SA, Rajagopalan G, Chia N, Jeraldo PR, Mandrekar J, Patel R. Lack of correlation of virulence gene profiles of Staphylococcus aureus bacteremia isolates with mortality. Microb Pathog. 2019 Aug; 133:103543 Epub 2019 May 15
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  43. Song S, Acharya K, Zhu J, Walther-Antonio M, Tetel M, Chia N. SUN-198 Vaginal Microbial Diversity Changes across the Menstrual Cycle in Healthy Young Women J Endoc Soc.. 2019.
  44. 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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  45. Yan Q, Wi YM, Thoendel MJ, Raval YS, Greenwood-Quaintance KE, Abdel MP, Jeraldo PR, Chia N, Patel R. Evaluation of the CosmosID Bioinformatics Platform for Prosthetic Joint-Associated Sonicate Fluid Shotgun Metagenomic Data Analysis. J Clin Microbiol. 2019 Feb; 57 (2) Epub 2019 Jan 30
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  46. 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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  47. 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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  48. 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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  49. Vijayvargiya P, Jeraldo PR, Thoendel MJ, Greenwood-Quaintance KE, Esquer Garrigos Z, Sohail MR, Chia N, Pritt BS, Patel R. Application of metagenomic shotgun sequencing to detect vector-borne pathogens in clinical blood samples. PLoS One. 2019; 14 (10):e0222915 Epub 2019 Oct 02
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  50. Madigan T, Cunningham SA, Patel R, Greenwood-Quaintance KE, Barth JE, Sampathkumar P, Cole NC, Kohner PC, Colby CE, Asay GF, Fang JL, Baker CA, Heinrich AL, Fjerstad KA, Lujero MJ, Chia N, Jeraldo PR, Nelson H, Huskins WC. Whole-genome sequencing for methicillin-resistant Staphylococcus aureus (MRSA) outbreak investigation in a neonatal intensive care unit. Infect Control Hosp Epidemiol. 2018 Dec; 39 (12):1412-1418 Epub 2018 Oct 04
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  51. Masters TL, Hilker CA, Jeraldo PR, Bhagwate AV, Greenwood-Quaintance KE, Eckloff BW, Chia N, Hanssen AD, Abdel MP, Yao JZ, Jen J, Patel R. Comparative evaluation of cDNA library construction approaches for RNA-Seq analysis from low RNA-content human specimens. J Microbiol Methods. 2018 Nov; 154:55-62 Epub 2018 Oct 14
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  52. 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, 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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  53. 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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  54. Thoendel MJ, Jeraldo PR, Greenwood-Quaintance KE, Yao JZ, Chia N, Hanssen AD, Abdel MP, Patel R. Identification of Prosthetic Joint Infection Pathogens Using a Shotgun Metagenomics Approach. Clin Infect Dis. 2018 Oct 15; 67 (9):1333-1338
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  55. Hale VL, Jeraldo P, Mundy M, Yao J, Keeney G, Scott N, Cheek EH, Davidson J, Greene M, Martinez C, Lehman J, Pettry C, Reed E, Lyke K, White BA, Diener C, Resendis-Antonio O, Gransee J, Dutta T, Petterson XM, Boardman L, Larson D, Nelson H, Chia N. Synthesis of multi-omic data and community metabolic models reveals insights into the role of hydrogen sulfide in colon cancer. Methods. 2018 Oct 1; 149:59-68 Epub 2018 Apr 26
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  56. Sivaguru M, Saw JJ, Williams JC Jr, Williams JC Jr, Lieske JC, Krambeck AE, Romero MF, Chia N, Schwaderer AL, Alcalde RE, Bruce WJ, Wildman DE, Fried GA, Werth CJ, Reeder RJ, Yau PM, Sanford RA, Fouke BW. Geobiology reveals how human kidney stones dissolve in vivo. Sci Rep. 2018 Sep 13; 8 (1):13731 Epub 2018 Sept 13
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  57. Ivy MI, Thoendel MJ, Jeraldo PR, Greenwood-Quaintance KE, Hanssen AD, Abdel MP, Chia N, Yao JZ, Tande AJ, Mandrekar JN, Patel R. Direct Detection and Identification of Prosthetic Joint Infection Pathogens in Synovial Fluid by Metagenomic Shotgun Sequencing. J Clin Microbiol. 2018 Sep; 56 (9) Epub 2018 Aug 27
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  58. Baheti S, Tang X, O'Brien DR, Chia N, Roberts LR, Nelson H, Boughey JC, Wang L, Goetz MP, Kocher JA, Kalari KR. HGT-ID: an efficient and sensitive workflow to detect human-viral insertion sites using next-generation sequencing data. BMC Bioinformatics. 2018 Jul 17; 19 (1):271 Epub 2018 July 17
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  59. 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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  60. 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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  61. Druliner BR, Wang P, Bae T, Baheti S, Slettedahl S, Mahoney D, Vasmatzis N, Xu H, Kim M, Bockol M, O'Brien D, Grill D, Warner N, Munoz-Gomez M, Kossick K, Johnson R, Mouchli M, Felmlee-Devine D, Washechek-Aletto J, Smyrk T, Oberg A, Wang J, Chia N, Abyzov A, Ahlquist D, Boardman LA. Molecular characterization of colorectal adenomas with and without malignancy reveals distinguishing genome, transcriptome and methylome alterations. Sci Rep. 2018 Feb 16; 8 (1):3161
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  62. Kim M, Druliner BR, Vasmatzis N, Bae T, Chia N, Abyzov A, Boardman LA. Inferring modes of evolution from colorectal cancer with residual polyp of origin. Oncotarget. 2018 Jan 23; 9 (6):6780-6792 Epub 2017 Dec 26
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  63. Kashyap PC, Chia N, Nelson H, Segal E, Elinav E. Microbiome at the Frontier of Personalized Medicine. Mayo Clin Proc. 2017 Dec; 92 (12):1855-1864
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  64. Sinha R, Abu-Ali G, Vogtmann E, Fodor AA, Ren B, Amir A, Schwager E, Crabtree J, Ma S, Abnet CC, Knight R, White O, Huttenhower C, Microbiome Quality Control Project Consortium. Assessment of variation in microbial community amplicon sequencing by the Microbiome Quality Control (MBQC) project consortium. Nat Biotechnol. 2017 Nov; 35 (11):1077-1086 Epub 2017 Oct 02
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  65. 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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  66. 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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  67. Jennings ME, Chia N, Boardman LA, Metcalf WW. Draft Genome Sequence of Methanobrevibacter smithii Isolate WWM1085, Obtained from a Human Stool Sample. Genome Announc. 2017 Sep 28; 5 (39) Epub 2017 Sept 28
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  68. Mundy M, Mendes-Soares H, Chia N. Mackinac: a bridge between ModelSEED and COBRApy to generate and analyze genome-scale metabolic models. Bioinformatics. 2017 Aug 1; 33 (15):2416-2418
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  69. Thoendel M, Jeraldo P, Greenwood-Quaintance KE, Chia N, Abdel MP, Steckelberg JM, Osmon DR, Patel R. A Novel Prosthetic Joint Infection Pathogen, Mycoplasma salivarium, Identified by Metagenomic Shotgun Sequencing. Clin Infect Dis. 2017 Jul 15; 65 (2):332-335
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  70. Sung J, Kim S, Cabatbat JJT, Jang S, Jin YS, Jung GY, Chia N, Kim PJ. Global metabolic interaction network of the human gut microbiota for context-specific community-scale analysis. Nat Commun. 2017 Jun 6; 8:15393 Epub 2017 June 06
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  71. Thoendel M, Jeraldo P, Greenwood-Quaintance KE, Yao J, Chia N, Hanssen AD, Abdel MP, Patel R. Impact of Contaminating DNA in Whole-Genome Amplification Kits Used for Metagenomic Shotgun Sequencing for Infection Diagnosis. J Clin Microbiol. 2017 Jun; 55 (6):1789-1801 Epub 2017 Mar 29
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  72. Lal D, Keim P, Delisle J, Barker B, Rank MA, Chia N, Schupp JM, Gillece JD, Cope EK. Mapping and comparing bacterial microbiota in the sinonasal cavity of healthy, allergic rhinitis, and chronic rhinosinusitis subjects. Int Forum Allergy Rhinol. 2017 Jun; 7 (6):561-569 Epub 2017 May 08
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  73. 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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  74. 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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  75. Storlie CB, Therneau TM, Carter RE, Chia N, Bergquist JR, Huddleston JM, Romero-Brufau S. Prediction and Inference with Missing Data in Patient Alert Systems Arxiv.org. 2017.
  76. Mendes-Soares H, Chia N. Community metabolic modeling approaches to understanding the gut microbiome: Bridging biochemistry and ecology. Free Radic Biol Med. 2017 Apr; 105:102-109 Epub 2016 Dec 15
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  77. 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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  78. 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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  79. Sagulenko E, Nouwens A, Webb RI, Green K, Yee B, Morgan G, Leis A, Lee KC, Butler MK, Chia N, Pham UT, Lindgreen S, Catchpole R, Poole AM, Fuerst JA. Nuclear Pore-Like Structures in a Compartmentalized Bacterium. PLoS One. 2017; 12 (2):e0169432 Epub 2017 Feb 01
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  80. Thompson KJ, Ingle JN, Tang X, Chia N, Jeraldo PR, Walther-Antonio MR, Kandimalla KK, Johnson S, Yao JZ, Harrington SC, Suman VJ, Wang L, Weinshilboum RL, Boughey JC, Kocher JP, Nelson H, Goetz MP, Kalari KR. A comprehensive analysis of breast cancer microbiota and host gene expression. PLoS One. 2017; 12 (11):e0188873 Epub 2017 Nov 30
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  81. Park KH, Greenwood-Quaintance KE, Uhl JR, Cunningham SA, Chia N, Jeraldo PR, Sampathkumar P, Nelson H, Patel R. Molecular epidemiology of Staphylococcus aureus bacteremia in a single large Minnesota medical center in 2015 as assessed using MLST, core genome MLST and spa typing. PLoS One. 2017; 12 (6):e0179003 Epub 2017 June 02
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  82. Kao PC, Han QJ, Liu S, Li XJ, Inman KS, Chia N. Letter to the Editor: The Surge of Type 2 Diabetes Mellitus in China - an International Alert: Physical Exercise and Low-Caloric Diet May Reduce the Risks of Type 2 Diabetes Mellitus and Dementia. Ann Clin Lab Sci. 2016 Winter; 46: (1)114-8.
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  83. 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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  84. Loftfield E, Vogtmann E, Sampson JN, Moore SC, Nelson H, Knight R, Chia N, Sinha R. Comparison of Collection Methods for Fecal Samples for Discovery Metabolomics in Epidemiologic Studies. Cancer Epidemiol Biomarkers Prev. 2016 Nov; 25 (11):1483-1490 Epub 2016 Aug 19
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  85. 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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  86. Mendes-Soares H, Mundy M, Soares LM, Chia N. MMinte: an application for predicting metabolic interactions among the microbial species in a community. BMC Bioinformatics. 2016 Sep 2; 17 (1):343 Epub 2016 Sept 02
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  87. Sung J, Hale V, Merkel AC, Kim PJ, Chia N. Metabolic modeling with Big Data and the gut microbiome. Appl Transl Genom. 2016 Sep; 10:10-5 Epub 2016 Feb 05
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  89. Thoendel M, Jeraldo PR, Greenwood-Quaintance KE, Yao JZ, Chia N, Hanssen AD, Abdel MP, Patel R. Comparison of microbial DNA enrichment tools for metagenomic whole genome sequencing. J Microbiol Methods. 2016 Aug; 127:141-145 Epub 2016 May 26
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  91. Sinha R, Vogtmann E, Chen J, Amir A, Shi J, Sampson J, Flores R, Knight R, Chia N. Fecal Microbiome in Epidemiologic Studies-Response. Cancer Epidemiol Biomarkers Prev 2016 May; 25 (5):870-1 Epub 2016 Mar 09
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  92. Seto CT, Jeraldo P, Orenstein R, Chia N, DiBaise JK. Erratum to: Prolonged use of a proton pump inhibitor reduces microbial diversity: implications for Clostridium difficile susceptibility. Microbiome. 2016 Feb 22; 4:10
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  93. 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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  94. 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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  96. Jeraldo P, Hernandez A, Nielsen HB, Chen X, White BA, Goldenfeld N, Nelson H, Alhquist D, Boardman L, Chia N. Capturing One of the Human Gut Microbiome's Most Wanted: Reconstructing the Genome of a Novel Butyrate-Producing, Clostridial Scavenger from Metagenomic Sequence Data. Front Microbiol. 2016; 7:783 Epub 2016 May 26
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  97. Jeraldo P, Cunningham SA, Quest D, Sikkink RA, O'Brien D, Eckloff BW, Patel R, Chia N. Draft Genome Sequences of Nine Pseudomonas aeruginosa Strains, Including Eight Clinical Isolates. Genome Announc. 2015 Oct 8; 3 (5) Epub 2015 Oct 08
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  98. Jeraldo P, Hernandez A, White BA, O'Brien D, Ahlquist D, Boardman L, Chia N. Draft genome sequences of 24 microbial strains assembled from direct sequencing from 4 stool samples. Genome Announc. 2015 May 28; 3 (3)
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  99. 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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  100. Braundmeier AG, Lenz KM, Inman KS, Chia N, Jeraldo P, Walther-Antonio MR, Berg Miller ME, Yang F, Creedon DJ, Nelson H, White BA. Individualized medicine and the microbiome in reproductive tract. Front Physiol. 2015; 6:97 Epub 2015 Apr 01
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  101. Benedict MN, Mundy MB, Henry CS, Chia N, Price ND. Likelihood-based gene annotations for gap filling and quality assessment in genome-scale metabolic models. PLoS Comput Biol. 2014 Oct; 10 (10):e1003882 Epub 2014 Oct 16
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  102. Theofiles AG, Cunningham SA, Chia N, Jeraldo PR, Quest DJ, Mandrekar JN, Patel R. Pertussis outbreak, southeastern Minnesota, 2012. Mayo Clin Proc. 2014 Oct; 89 (10):1378-88
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  103. Kang SS, Jeraldo PR, Kurti A, Miller ME, Cook MD, Whitlock K, Goldenfeld N, Woods JA, White BA, Chia N, Fryer JD. Diet and exercise orthogonally alter the gut microbiome and reveal independent associations with anxiety and cognition. Mol Neurodegener. 2014 Sep 13; 9:36 Epub 2014 Sept 13
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  105. Seto CT, Jeraldo P, Orenstein R, Chia N, DiBaise JK. Prolonged use of a proton pump inhibitor reduces microbial diversity: implications for Clostridium difficile susceptibility. Microbiome. 2014; 2:42 Epub 2014 Nov 25
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  106. Walther-Antonio MR, Jeraldo P, Berg Miller ME, Yeoman CJ, Nelson KE, Wilson BA, White BA, Chia N, Creedon DJ. Pregnancy's stronghold on the vaginal microbiome. PLoS One. 2014; 9 (6):e98514 Epub 2014 June 04
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  108. Yang F, Chia N, White BA, Schook LB. Compression-based distance (CBD): a simple, rapid, and accurate method for microbiota composition comparison. BMC Bioinformatics. 2013; 14:136. Epub 2013 Apr 23.
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  111. Berg Miller ME, Yeoman CJ, Chia N, Tringe SG, Angly FE, Edwards RA, Flint HJ, Lamed R, Bayer EA, White BA. Phage-bacteria relationships and CRISPR elements revealed by a metagenomic survey of the rumen microbiome. Environ Microbiol. 2012 Jan; 14(1):207-27. Epub 2011 Oct 17.
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  113. Chia N , Guttenberg N . Commentary: Dynamics of gene duplication and transposons in microbial genomes following a sudden environmental change. Mobile Genetic Elements. September/October 2011.
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  114. Chia N, Goldenfeld N. Statistical mechanics of horizontal gene transfer in evolutionary ecology. Journal Of Statistical Physics. 2011 Apr; 142(6):1287-301.
  115. Yeoman CJ, Chia N, Yildirim S, Berg Miller ME, Kent A, Stumpf R, Leigh SR, Nelson KE, White BA, Wilson BA. Towards an evolutionary model of animal-associated microbiomes. Entropy. 2011 Mar; 13(3):570-94.
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  117. Li Y, Chia N, Lauria M, Bundschuh R. A performance enhanced PSI-BLAST based on hybrid alignment. Bioinformatics. 2011 Jan 1; 27(1):31-7. Epub 2010 Nov 24.
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  118. Sipos M, Jeraldo P, Chia N, Qu A, Dhillon AS, Konkel ME, Nelson KE, White BA, Goldenfeld N. Robust computational analysis of rRNA hypervariable tag datasets. PLoS One. 2010; 5(12):e15220. Epub 2010 Dec 31.
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  119. Chia N, Cann I, Olsen GJ. Evolution of DNA replication protein complexes in eukaryotes and Archaea. PLoS One. 2010; 5(6):e10866. Epub 2010 Jun 02.
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  120. Chia N, Golding I, Goldenfeld N. Lambda-prophage induction modeled as a cooperative failure mode of lytic repression. Phys Rev E Stat Nonlin Soft Matter Phys. 2009 Sep; 80(3 Pt 1):030901. Epub 2009 Sep 01.
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  121. Chia N, Woese CR, Goldenfeld N. A collective mechanism for phase variation in biofilms. Proc Natl Acad Sci U S A. 2008 Sep 23; 105(38):14597-602. Epub 2008 Sep 17.
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  122. Chia N, Bundschuh R. A practical approach to significance assessment in alignment with gaps. J Comput Biol. 2006 Mar; 13(2):429-41.
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  123. Chia N, Bundschuh R. Numerical method for accessing the universal scaling function for a multiparticle discrete time asymmetric exclusion process. Phys Rev E Stat Nonlin Soft Matter Phys. 2005 Nov; 72(5 Pt 1):051102. Epub 2005 Nov 07.
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  124. Chia N, Bundschuh R. Finite width model sequence comparison. Phys Rev E Stat Nonlin Soft Matter Phys. 2004 Aug; 70(2 Pt 1):021906. Epub 2004 Aug 17.
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