Publications

  1. Sivaguru M, Saw JJ, 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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  2. 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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  3. 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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  4. Hale VL, Jeraldo P, Mundy M, Yao J, Keeney G, Scott N, Cheek EH, Davidson J, Green 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 Apr 26 [Epub ahead of print]
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  5. Thoendel M, Jeraldo P, Greenwood-Quaintance KE, Yao J, Chia N, Hanssen AD, Abdel MP, Patel R. Identification of Prosthetic Joint Infection Pathogens Using a Shotgun Metagenomics Approach. Clin Infect Dis. 2018 Apr 10 [Epub ahead of print]
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  6. Chen X, Johnson S, Jeraldo P, Wang J, Chia N, Kocher JA, Chen J, 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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  7. 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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  8. 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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  9. 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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  10. 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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  11. 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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  12. 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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  13. 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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  14. 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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  15. 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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  16. 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 06; 8:15393.
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  17. 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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  18. 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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  19. 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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  20. 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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  21. 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;
  22. 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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  23. 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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  24. 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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  25. 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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  26. 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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  27. 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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  28. 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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  29. 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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  30. 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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  31. 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.
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  32. 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 02; 17: (1)343.
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  33. 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.
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  34. 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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  35. 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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  36. 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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  37. 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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  38. 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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  39. 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.
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  40. 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.
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  41. 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.
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  42. 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.
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  43. 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 08; 3: (5).
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  44. 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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  45. 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.
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  46. 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.
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  47. 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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  48. 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.
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  49. 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.
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  50. Dong YR, Kumar CG, Chia N, Kim PJ, Miller PA, Price ND, Cann IKO, Flynn TM, Sanford RA, Krapac IG, Locke RA, Hong PY, Tamaki H, Liu WT, Mackie RI, Hernandez AG, Wright CL, Mikel MA, Walker JL, Sivaguru M, Fried G, Yannarell AC, Fouke BW. Halomonas sulfidaeris-dominated microbial community inhabits a 1.8km-deep subsurface Cambrian Sandstone reservoir. Environmental Microbiology. 2014 Jun; 16(6):1695-708.
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  51. 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.
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  52. Jeraldo P, Kalari K, Chen X, Bhavsar J, Mangalam A, White B, Nelson H, Kocher JP, Chia N. IM-TORNADO: a tool for comparison of 16S reads from paired-end libraries. PLoS One. 2014; 9: (12)e114804.
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  53. 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.
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  54. 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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  55. Jeraldo P, Sipos M, Chia N, Brulc JM, Dhillon AS, Konkel ME, Larson CL, Nelson KE, Qu A, Schook LB, Yang F, White BA, Goldenfeld N. Quantification of the relative roles of niche and neutral processes in structuring gastrointestinal microbiomes. Proceedings of the National Academy of Sciences USA.2012;109:9692-9698.
  56. 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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  57. Yeoman CJ, Chia N, Jeraldo P, Sipos M, Goldenfeld N, White BA. The microbiome of the chicken gastrointestinal tract. Animal Health Research Reviews. 2012; 13:89-99.
  58. Jeraldo P, Chia N, Goldenfeld N. On the suitability of short reads of 16S rRNA for phylogeny-based analyses in environmental surveys. Environ Microbiol. 2011 Nov; 13(11):3000-9. Epub 2011 Sep 13.
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  59. 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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  60. Chia N, Goldenfeld N. Statistical mechanics of horizontal gene transfer in evolutionary ecology. Journal Of Statistical Physics. 2011 Apr; 142(6):1287-301.
  61. 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.
  62. Chia N, Goldenfeld N. Dynamics of gene duplication and transposons in microbial genomes following a sudden environmental change. Phys Rev E Stat Nonlin Soft Matter Phys. 2011 Feb; 83(2 Pt 1):021906. Epub 2011 Feb 16.
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  63. 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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  64. 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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  65. 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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  66. 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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  67. 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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  68. 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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  69. 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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  70. 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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