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Synthesis of multi-omic data and community metabolic models reveals insights into the role of hydrogen sulfide in colon cancer.

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.

Methods. 2018 Apr 26. pii: S1046-2023(17)30436-X. doi: 10.1016/j.ymeth.2018.04.024. [Epub ahead of print]


Hong Kong Consensus Statements for the Management of Unresectable Hepatocellular Carcinoma.

Cheung TT, Kwok PC, Chan S, Cheung CC, Lee AS, Lee V, Cheng HC, Chia NH, Chong CCN, Lai TW, Law ALY, Luk MY, Tong CC, Yau TCC.

Liver Cancer. 2018 Mar;7(1):40-54. doi: 10.1159/000485984. Epub 2018 Jan 25.


Identification of Prosthetic Joint Infection Pathogens Using a Shotgun Metagenomics Approach.

Thoendel M, Jeraldo P, Greenwood-Quaintance KE, Yao J, Chia N, Hanssen AD, Abdel MP, Patel R.

Clin Infect Dis. 2018 Apr 10. doi: 10.1093/cid/ciy303. [Epub ahead of print]


Enhanced Pro-Inflammatory Response of Macrophages to Interleukin-33 in an Allergic Environment.

Chia N, Kumar RK, Foster PS, Herbert C.

Int Arch Allergy Immunol. 2018;176(1):74-82. doi: 10.1159/000487573. Epub 2018 Apr 5.


Systematic Bias Introduced by Genomic DNA Template Dilution in 16S rRNA Gene-Targeted Microbiota Profiling in Human Stool Homogenates.

Multinu F, Harrington SC, Chen J, Jeraldo PR, Johnson S, Chia N, Walther-Antonio MR.

mSphere. 2018 Mar 14;3(2). pii: e00560-17. doi: 10.1128/mSphere.00560-17. eCollection 2018 Mar-Apr.


Inferring modes of evolution from colorectal cancer with residual polyp of origin.

Kim M, Druliner BR, Vasmatzis N, Bae T, Chia N, Abyzov A, Boardman LA.

Oncotarget. 2017 Dec 26;9(6):6780-6792. doi: 10.18632/oncotarget.23687. eCollection 2018 Jan 23.


Molecular characterization of colorectal adenomas with and without malignancy reveals distinguishing genome, transcriptome and methylome alterations.

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.

Sci Rep. 2018 Feb 16;8(1):3161. doi: 10.1038/s41598-018-21525-4.


Challenges and recommendations for minimally resourced biobanks in tertiary Australian hospitals.

Chia N, Wen L, Lyons JG, Elliott M, Lee M, Palme CE, Clark JR, Gupta R.

ANZ J Surg. 2018 Jan;88(1-2):115-116. doi: 10.1111/ans.13909. No abstract available.


Hybrid-denovo: a de novo OTU-picking pipeline integrating single-end and paired-end 16S sequence tags.

Chen X, Johnson S, Jeraldo P, Wang J, Chia N, Kocher JA, Chen J.

Gigascience. 2018 Mar 1;7(3):1-7. doi: 10.1093/gigascience/gix129.


Microbiome at the Frontier of Personalized Medicine.

Kashyap PC, Chia N, Nelson H, Segal E, Elinav E.

Mayo Clin Proc. 2017 Dec;92(12):1855-1864. doi: 10.1016/j.mayocp.2017.10.004. Review.


A comprehensive analysis of breast cancer microbiota and host gene expression.

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.

PLoS One. 2017 Nov 30;12(11):e0188873. doi: 10.1371/journal.pone.0188873. eCollection 2017.


Metastatic small cell carcinoma with psammoma bodies: A diagnostic pitfall.

Chia N, Pang B, Nga ME.

Cytopathology. 2018 Feb;29(1):117-120. doi: 10.1111/cyt.12469. Epub 2017 Oct 5. No abstract available.


Draft Genome Sequence of Methanobrevibacter smithii Isolate WWM1085, Obtained from a Human Stool Sample.

Jennings ME, Chia N, Boardman LA, Metcalf WW.

Genome Announc. 2017 Sep 28;5(39). pii: e01055-17. doi: 10.1128/genomeA.01055-17.


Reproducibility of assessing fecal microbiota in chronic constipation.

Parthasarathy G, Chen J, Chia N, O'Connor HM, Gaskins HR, Bharucha AE.

Neurogastroenterol Motil. 2017 Oct;29(10):1-10. doi: 10.1111/nmo.13172. Epub 2017 Jul 28.


p16 expression in cutaneous squamous cell carcinoma of the head and neck is not associated with integration of high risk HPV DNA or prognosis.

Satgunaseelan L, Chia N, Suh H, Virk S, Ashford B, Lum T, Ranson M, Clark J, Gupta R.

Pathology. 2017 Aug;49(5):494-498. doi: 10.1016/j.pathol.2017.04.002. Epub 2017 Jun 26.


Reversible hemispheric hypoperfusion in two cases of SMART syndrome.

Wai K, Balabanski A, Chia N, Kleinig T.

J Clin Neurosci. 2017 Sep;43:146-148. doi: 10.1016/j.jocn.2017.05.013. Epub 2017 Jun 20.


Global metabolic interaction network of the human gut microbiota for context-specific community-scale analysis.

Sung J, Kim S, Cabatbat JJT, Jang S, Jin YS, Jung GY, Chia N, Kim PJ.

Nat Commun. 2017 Jun 6;8:15393. doi: 10.1038/ncomms15393.


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.

Park KH, Greenwood-Quaintance KE, Uhl JR, Cunningham SA, Chia N, Jeraldo PR, Sampathkumar P, Nelson H, Patel R.

PLoS One. 2017 Jun 2;12(6):e0179003. doi: 10.1371/journal.pone.0179003. eCollection 2017.


Mapping and comparing bacterial microbiota in the sinonasal cavity of healthy, allergic rhinitis, and chronic rhinosinusitis subjects.

Lal D, Keim P, Delisle J, Barker B, Rank MA, Chia N, Schupp JM, Gillece JD, Cope EK.

Int Forum Allergy Rhinol. 2017 Jun;7(6):561-569. doi: 10.1002/alr.21934. Epub 2017 May 8.


Comparison of Whole-Genome Sequencing Methods for Analysis of Three Methicillin-Resistant Staphylococcus aureus Outbreaks.

Cunningham SA, Chia N, Jeraldo PR, Quest DJ, Johnson JA, Boxrud DJ, Taylor AJ, Chen J, Jenkins GD, Drucker TM, Nelson H, Patel R.

J Clin Microbiol. 2017 Jun;55(6):1946-1953. doi: 10.1128/JCM.00029-17. Epub 2017 Apr 12.


A Novel Prosthetic Joint Infection Pathogen, Mycoplasma salivarium, Identified by Metagenomic Shotgun Sequencing.

Thoendel M, Jeraldo P, Greenwood-Quaintance KE, Chia N, Abdel MP, Steckelberg JM, Osmon DR, Patel R.

Clin Infect Dis. 2017 Jul 15;65(2):332-335. doi: 10.1093/cid/cix296.


Mackinac: a bridge between ModelSEED and COBRApy to generate and analyze genome-scale metabolic models.

Mundy M, Mendes-Soares H, Chia N.

Bioinformatics. 2017 Aug 1;33(15):2416-2418. doi: 10.1093/bioinformatics/btx185.


Impact of Contaminating DNA in Whole-Genome Amplification Kits Used for Metagenomic Shotgun Sequencing for Infection Diagnosis.

Thoendel M, Jeraldo P, Greenwood-Quaintance KE, Yao J, Chia N, Hanssen AD, Abdel MP, Patel R.

J Clin Microbiol. 2017 Jun;55(6):1789-1801. doi: 10.1128/JCM.02402-16. Epub 2017 Mar 29.


Assessing the colonic microbiome, hydrogenogenic and hydrogenotrophic genes, transit and breath methane in constipation.

Wolf PG, Parthasarathy G, Chen J, O'Connor HM, Chia N, Bharucha AE, Gaskins HR.

Neurogastroenterol Motil. 2017 Oct;29(10):1-9. doi: 10.1111/nmo.13056. Epub 2017 Mar 13.


Comparison of Fecal Collection Methods for Microbiota Studies in Bangladesh.

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.

Appl Environ Microbiol. 2017 May 1;83(10). pii: e00361-17. doi: 10.1128/AEM.00361-17. Print 2017 May 15.


Nuclear Pore-Like Structures in a Compartmentalized Bacterium.

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.

PLoS One. 2017 Feb 1;12(2):e0169432. doi: 10.1371/journal.pone.0169432. eCollection 2017.


Community metabolic modeling approaches to understanding the gut microbiome: Bridging biochemistry and ecology.

Mendes-Soares H, Chia N.

Free Radic Biol Med. 2017 Apr;105:102-109. doi: 10.1016/j.freeradbiomed.2016.12.017. Epub 2016 Dec 15. Review.


Comparison of Collection Methods for Fecal Samples in Microbiome Studies.

Vogtmann E, Chen J, Amir A, Shi J, Abnet CC, Nelson H, Knight R, Chia N, Sinha R.

Am J Epidemiol. 2017 Jan 15;185(2):115-123. doi: 10.1093/aje/kww177. Epub 2016 Dec 16.


Potential contribution of the uterine microbiome in the development of endometrial cancer.

Walther-António MR, Chen J, Multinu F, Hokenstad A, Distad TJ, Cheek EH, Keeney GL, Creedon DJ, Nelson H, Mariani A, Chia N.

Genome Med. 2016 Nov 25;8(1):122.


Beyond Infrastructure: Understanding Why Patients Decline Surgery in the Developing World: An Observational Study in Cameroon.

Lerman BJ, Alsan M, Chia NJ, Brown JA, Wren SM.

Ann Surg. 2017 Dec;266(6):975-980. doi: 10.1097/SLA.0000000000002002.


Comparison of Collection Methods for Fecal Samples for Discovery Metabolomics in Epidemiologic Studies.

Loftfield E, Vogtmann E, Sampson JN, Moore SC, Nelson H, Knight R, Chia N, Sinha R.

Cancer Epidemiol Biomarkers Prev. 2016 Nov;25(11):1483-1490. Epub 2016 Aug 19.


Altered gut microbiota in female mice with persistent low body weights following removal of post-weaning chronic dietary restriction.

Chen J, Toyomasu Y, Hayashi Y, Linden DR, Szurszewski JH, Nelson H, Farrugia G, Kashyap PC, Chia N, Ordog T.

Genome Med. 2016 Oct 3;8(1):103.


Shifts in the Fecal Microbiota Associated with Adenomatous Polyps.

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.

Cancer Epidemiol Biomarkers Prev. 2017 Jan;26(1):85-94. doi: 10.1158/1055-9965.EPI-16-0337. Epub 2016 Sep 26.


Metabolic modeling with Big Data and the gut microbiome.

Sung J, Hale V, Merkel AC, Kim PJ, Chia N.

Appl Transl Genom. 2016 Feb 5;10:10-5. doi: 10.1016/j.atg.2016.02.001. eCollection 2016 Sep. Review.


MMinte: an application for predicting metabolic interactions among the microbial species in a community.

Mendes-Soares H, Mundy M, Soares LM, Chia N.

BMC Bioinformatics. 2016 Sep 2;17(1):343. doi: 10.1186/s12859-016-1230-3.


Programmed cell death-ligand 1 expression in oral squamous cell carcinoma is associated with an inflammatory phenotype.

Satgunaseelan L, Gupta R, Madore J, Chia N, Lum T, Palme CE, Boyer M, Scolyer RA, Clark JR.

Pathology. 2016 Oct;48(6):574-80. doi: 10.1016/j.pathol.2016.07.003. Epub 2016 Aug 30.


Accuracy of a modified axiolateral radiographic hip projection in suspected cases of hip fracture: experience and results from a regional trauma centre.

Lee WC, Luo FY, Tiong KK, Chia NW, Tham LM, Tan TJ.

Emerg Radiol. 2017 Feb;24(1):7-11. doi: 10.1007/s10140-016-1434-x. Epub 2016 Aug 24.


What Public Policies Should Be Developed to Cope with the Myopia Epidemic?

Verkicharla PK, Chia NE, Saw SM.

Optom Vis Sci. 2016 Sep;93(9):1055-7. doi: 10.1097/OPX.0000000000000982. Review.


The Microbiome of Aseptically Collected Human Breast Tissue in Benign and Malignant Disease.

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.

Sci Rep. 2016 Aug 3;6:30751. doi: 10.1038/srep30751.


Multiple sclerosis patients have a distinct gut microbiota compared to healthy controls.

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.

Sci Rep. 2016 Jun 27;6:28484. doi: 10.1038/srep28484.


Capturing One of the Human Gut Microbiome's Most Wanted: Reconstructing the Genome of a Novel Butyrate-Producing, Clostridial Scavenger from Metagenomic Sequence Data.

Jeraldo P, Hernandez A, Nielsen HB, Chen X, White BA, Goldenfeld N, Nelson H, Alhquist D, Boardman L, Chia N.

Front Microbiol. 2016 May 26;7:783. doi: 10.3389/fmicb.2016.00783. eCollection 2016.


Comparison of microbial DNA enrichment tools for metagenomic whole genome sequencing.

Thoendel M, Jeraldo PR, Greenwood-Quaintance KE, Yao JZ, Chia N, Hanssen AD, Abdel MP, Patel R.

J Microbiol Methods. 2016 Aug;127:141-145. doi: 10.1016/j.mimet.2016.05.022. Epub 2016 May 26.


Determining the Number of Ischemic Strokes Potentially Eligible for Endovascular Thrombectomy: A Population-Based Study.

Chia NH, Leyden JM, Newbury J, Jannes J, Kleinig TJ.

Stroke. 2016 May;47(5):1377-80. doi: 10.1161/STROKEAHA.116.013165. Epub 2016 Mar 17.


Fecal Microbiome in Epidemiologic Studies-Response.

Sinha R, Vogtmann E, Chen J, Amir A, Shi J, Sampson J, Flores R, Knight R, Chia N.

Cancer Epidemiol Biomarkers Prev. 2016 May;25(5):870-1. doi: 10.1158/1055-9965.EPI-16-0161. Epub 2016 Mar 9. No abstract available.


Erratum to: Prolonged use of a proton pump inhibitor reduces microbial diversity: implications for Clostridium difficile susceptibility.

Seto CT, Jeraldo P, Orenstein R, Chia N, DiBaise JK.

Microbiome. 2016 Feb 22;4:10. doi: 10.1186/s40168-016-0158-1. No abstract available.


Molecular classification of gastric cancer.

Chia NY, Tan P.

Ann Oncol. 2016 May;27(5):763-9. doi: 10.1093/annonc/mdw040. Epub 2016 Feb 9. Review.


Impact of demographics on human gut microbial diversity in a US Midwest population.

Chen J, Ryu E, Hathcock M, Ballman K, Chia N, Olson JE, Nelson H.

PeerJ. 2016 Jan 7;4:e1514. doi: 10.7717/peerj.1514. eCollection 2016.


A multi-channel biomimetic neuroprosthesis to support treadmill gait training in stroke patients.

Chia N, Ambrosini E, Baccinelli W, Nardone A, Monticone M, Ferrigno G, Pedrocchi A, Ferrante S.

Conf Proc IEEE Eng Med Biol Soc. 2015;2015:7159-62. doi: 10.1109/EMBC.2015.7320043.


Persistent microbial dysbiosis in preterm premature rupture of membranes from onset until delivery.

Baldwin EA, Walther-Antonio M, MacLean AM, Gohl DM, Beckman KB, Chen J, White B, Creedon DJ, Chia N.

PeerJ. 2015 Nov 26;3:e1398. doi: 10.7717/peerj.1398. eCollection 2015.

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