Journal Publications

    2019

  1. Xu, Min; Stedtfeld, Robert D. ; Wang, Fang ; Hashsham, Syed A. ; Song, Yang ; Chuang, Yahu ; Fan, Jianbo; Li, Hui ; Jiang, Xin ; Tiedje, James M. Composting increased persistence of manure-borne antibiotic resistance genes in soils with different fertilization history. Science of the Total Environment, Volume: 689, Pages: 1172-1180, Published: NOV 1 2019, DOI: 10.1016/j.scitotenv.2019.06.376
  2. Jha, Prabhat N; Gomaa, Abu-Bakr; Yanni, Youssef G; El-Saadany, Abd-Elgawad Y; Stedtfeld, Tiffany M; Stedtfeld, Robert D; Gantner, Stephan; Chai, Benli; Cole, James; Hashsham, Syed A; Dazzo, Frank B. Alterations in the Endophyte-Enriched Root-Associated Microbiome of Rice Receiving Growth-Promoting Treatments of Urea Fertilizer and Rhizobium Biofertilizer. Microbial Ecology. 10.1007/s00248-019-01406-7.
  3. Williams, Maggie R; Hashsham, Syed A. Direct or DNA Extraction-Free Amplification and Quantification of Foodborne Pathogens. Methods in Molecular Biology . Vol. 1918 Pages:21-33. 2019. DOI:10.1007/978-1-4939-9000-9_2
  4. 2018

  5. Dang, HY; Kanitkar, YH; Stedtfeld, RD; Hatzinger, PB; Hashsham, SA; Cupples, AM. Abundance of chlorinated solvent and 1,4-dioxane degrading microorganisms at five chlorinated solvent contaminated sites determined via shotgun sequencing. Environmental Science & Technology. 52 (23):13914-13924. 2018.
  6. Wang, F; Xu, M; Stedtfeld, RD; Sheng, HJ ; Fan, JB; Liu, M; Chai, BL; de Carvalho, TS; Li, H; Hashsham, SA; Tiedje, JM. Long-term effect of different fertilization and cropping systems on the soil antibiotic resistome. Environmental Science & Technology. 52(22): 13037-13046. 2018.
  7. Stedtfeld, RD; Guo, XP; Stedtfeld, TM; Sheng, HJ; Williams, MR; Hauschild, K; Gunturu, S; Tift, L; Wang, F; Howes, A; Chai, BL; Yin, DQ; Cole, JR; Tiedje, JM; Hashsham, SA. Primer set 2.0 for highly parallel qPCR array targeting antibiotic resistance genes and mobile genetic elements. FEMS Microbiology Ecology. 94(9): Article Number: fiy130. 2018.
  8. Waseem, H; Williams, MR; Jameel, S; Hashsham, SA. Antimicrobial resistance in the environment. Water Environment Research. 90(10): 865-884. 2018.
  9. 2017

  10. Stedtfeld, Robert Donald, Stedtfeld Tiffany M, Waseem Hassan, Fitschen-Brown Meridith, Guo Xueping, Chai Benli, Williams Maggie Ruth, Shook Trevor, Chae Jong-Chan, Cole James R, Graham Ally, Logan Amanda, Sul Woo-Jun, Tiedje James, Upham Brad L, VanHouten Jacob, Zylstra Gerben, Hashsham, Syed, "Isothermal assay targeting class 1 integrase gene for environmental surveillance of antibiotic resistance markers ". Journal of Environmental Management. Vol. 198. pp. 213-220. Other Information: PMID: 28460328. (August 2017).
  11. Srinivasan, Vidya, Stedtfeld Robert Donald, Tourlousse Dieter, Baushke Samuel, Xin Yu, Miller Sarah, Pham Trinh, Rouillard Jean-Marie, Gulari Erdogan, Tiedje James, Hashsham, Syed, "Diagnostic microarray for 14 water and foodborne pathogens using a flatbed scanner ". Journal of Microbiological Methods. Vol. 139. pp. 15-21. Other Information: PMID: 28438642. (August 2017).
  12. Etchebarne, BE, Li ZG, Stedtfeld RD, Nicholas MC, Williams MR, Johnson TA, (Stedtfeld TM, Kostic T, Khalife WT, Tiedje JM, Hashsham, Syed, Hughes MJ, "Evaluation of nucleic acid isothermal amplification methods for human clinical microbial infection detection ". Frontiers in Microbiology. Vol. 8. pp. 2211. Other Information: Article No. 2211. (DEC 2017)
  13. Kanitkar, Yogendra, Stedtfeld Robert Donald, Hatzinger Paul, Hashsham, Syed, Cupples Alison Meta, "Most probable number with visual based LAMP for the quantification of reductive dehalogenase genes in groundwater samples. ". Journal of Microbiological Methods. Vol. 143. pp. 44-49. (December 2017).
  14. Williams, Maggie Ruth, Stedtfeld Robert Donald, Waseem Hassan, Stedtfeld Tiffany M, Upham Brad L, Khalife Walid T, Etchebarne Brett E, Hughes M., Tiedje James, Hashsham, Syed, "Implications of direct amplification for measuring antimicrobial resistance using point-of-care devices ". Analytical Methods. Vol. 9. No. 8. pp. 1229-1241. Other Information: DOI: 10.1039/C6AY03405E. (February 2017).
  15. Ahmad, Farhan, Stedtfeld Robert Donald, Waseem Hassan, Williams Maggie Ruth, Cupples Alison Meta, Tiedje James, Hashsham, Syed, "Most probable number - loop mediated isothermal amplification (MPNLAMP) for quantifying waterborne pathogens in < 25 min ". Journal of Microbiological Methods. Vol. 132. pp. 27-33. Other Information: PMID: 27856278. (January 2017).
  16. Kanitkar, Yogendra, Stedtfeld Robert Donald, Hatzinger Paul, Hashsham, Syed, Cupples Alison Meta, "Development and application of a rapid, user-friendly, and inexpensive method to detect Dehalococcoides sp reductive dehalogenase genes from groundwater ". Applied Microbiology and Biotechnology. Vol. 101. No. 11. pp. 4827-4835. (June 2017).
  17. Hassan,Waseem, Williams Maggie Ruth, Stedtfeld Tiffany M, Chai Benli, Stedtfeld Robert Donald, Cole James R, Tiedje James, Hashsham, Syed, "Virulence factor activity relationships (VFARs): a bioinformatics perspective". Environmental Science-Processes & Impacts. Vol. 19. No. 3. pp. 247-260. Other Information: PMID: 28261716. (March 2017).
  18. Ahsan, Munir, Waseem Hassan, Williams Maggie Ruth, Stedtfeld Robert Donald, Gulari Erdogan, Tiedje James, Hashsham, Syed. Modeling hybridization kinetics of gene probes in a DNA biochip using FEMLAB. Microarrays. Vol. 6. No. 2. Other Information: PMID: 28555058. (May 2017).
  19. Stedtfeld, Robert Donald, Stedtfeld Tiffany M, Fader Kelly, Williams Maggie Ruth, Bhaduri Prianca, Quensen John, Zacharewski Timothy, Tiedje James, Hashsham, Syed, "TCDD influences reservoir of antibiotic resistance genes in murine gut microbiome ". FEMS Microbiology Ecology. Vol. 93. No. 5. Other Information: PMID: 28475713. (May 2017).
  20. Trebitz, Anett, Hoffman Joel, Darling John, Pilgrim Erik, Kelly John, Brown Emily, Chadderton W. Lindsay, Egan Scott, Grey Erik, Hashsham, Syed, Klymus Katy, Mahon Andrew, Ram Jeffrey, Schultz Martin, Stepien Carol, Schardt James, "Early detection monitoring for aquatic non-indigenous species: Optimizing surveillance, incorporating advanced technologies, and identifying research needs ". Journal of Environmental Management. Vol. 202. pp. 299-310. (November 2017).
  21. Williams, Maggie Ruth, Stedtfeld Robert Donald, Engle Catharine, Salach Paul, Fakher Umama, Stedtfeld Tiffany M, Dreelin Erin A, Stevenson Robert Jan, Latimore Jo Anne, Hashsham, Syed, "Isothermal amplification of environmental DNA (eDNA) for direct field-based monitoring and laboratory confirmation of Dreissena sp ". PLOS ONE. Vol. 12. No. 10. (October 2017).
  22. Stedtfeld, Robert Donald, Sallach J. Brett, Crawford Robert B, Stedtfeld Tiffany M, Williams Maggie Ruth, Waseem Hassan, Johnston Cliff, Li Hui, Boyd Stephen A, Kaminski Norbert E, Teppen Brian J, Tiedje James, Hashsham, Syed, "TCDD administered on activated carbon eliminates bioavailability and subsequent shifts to a key murine gut commensal. Applied Microbiology and Biotechnology. Vol. 101. No. 19. pp. 7409-7415. Other Information: PMID: 28812142. (October 2017).
  23. Hassan,Waseem, Williams Maggie Ruth, Stedtfeld Robert Donald, Hashsham, Syed, "Antimicrobial resistance in the environment ". Water Environment Research. Vol. 89. No. 10. pp. 921-941. (October 2017).
  24. Williams, Maggie Ruth, Stedtfeld Robert Donald, Tiedje James, Hashsham, Syed, "MicroRNAs-based inter-domain communication between the host and members of the gut microbiome ". Frontiers in Microbiology. Vol. 8. Other Information: PMID: 29021788. (September 2017).
  25. Farag,Samhan, Stedtfeld Tiffany M, Waseem Hassan, Williams Maggie Ruth, Stedtfeld Robert Donald, Hashsham, Syed, "On-filter direct amplification of Legionella pneumophila for rapid assessment of its abundance and viability ". Water Research. Vol. 121. pp. 162-170. Other Information: PMID: 28527390. (September 2017).
  26. Stedtfeld, Robert Donald, Chai Benli, Crawford Robert B, Stedtfeld Tiffany M, Williams Maggie Ruth, Shao Xiangwen, Kuwahara Tomomi, Cole James R, Kaminski Norbert E, Tiedje James, Hashsham, Syed. "Modulatory influence of segmented filamentous bacteria on transcriptomic response of gnotobiotic mice exposed to TCDD ". Frontiers in Microbiology. Vol. 8. Other Information: PMID: 28936204. (September 2017).
  27. Williams, Maggie Ruth, Stedtfeld Robert Donald, Stedtfeld Tiffany M, Tiedje James, Hashsham, Syed, "Quantification of microRNAs directly from body fluids using a base-stacking isothermal amplification method in a point-of-care device ". Biomedical Microdevices. Vol. 19. No. 3. Other Information: PMID: 28536858. (September 2017).
  28. 2016

  29. Stedtfeld RD, Williams MR, Fakher U, Johnson TA, Stedtfeld TM, Wang F, Khalife W, Hughes M, Etchebarne BE, Hashsham SA. Antimicrobial resistance dashboard application for mapping environmental occurrence and resistant pathogens. FEMS Microbiology Ecology. 92: fiw020. 2016. PMID: 26850162.
  30. Kostic T, Ellis M, Kronlein M, Stedtfeld TM, Kaneene JB, Stedtfeld RD, Hashsham SA. 30- min screening of antibiotic resistance genes in bacterial isolates with minimal sample-preparation in self-digitizing 64 and 384 assay chips. Applied Microbiology and Biotechnology . 99: 7711-7722. 2016. PMCID: PMC4543423.
  31. Stedtfeld RD, Liu YC, Stedtfeld TM, Kostic T, Kronlein M, Srivannavit O, Khalife WT, Tiedje JM, Gulari E, Hughes M, Etchebarne B, Hashsham SA. Static self-directed sample dispensing into a series of reaction wells on a microfluidic card for parallel genetic detection of microbial pathogens. Biomedical Microdevices . 17: 89. 2015. PMID: 26260693.
  32. Wang, F; Stedtfeld, RD.; Kim, OS; Chai, B; Yang, L; Stedtfeld, TM; Hong, SG; Kim, D; Lim, HS; Hashsham, SA; Tiedje, JM; Sul, WJ. Influence of Soil Characteristics and Proximity to Antarctic Research Stations on Abundance of Antibiotic Resistance Genes in Soils. Environmental Science & Technology. 50(23):12621-12629. 2016.
  33. Stedtfeld, RD; Stedtfeld, TM; Samhan, F; Kanitkar, YH; Hatzinger, PB; Cupples, AM; Hashsham, SA. Direct loop mediated isothermal amplification on filters for quantification of Dehalobacter in groundwater. J. Microbiological Methods. 131: 61-67. DOI: 10.1016/j.mimet.2016.09.025. 2016.
  34. Ahmad, Farhan; Stedtfeld, Robert D; Waseem, Hassan; Williams, Maggie R; Cupples, Alison M; Tiedje, James M; Hashsham, Syed A. Most probable number - loop mediated isothermal amplification (MPN-LAMP) for quantifying waterborne pathogens in <25min. J. Microbiological Methods. 132: p.27-33 DOI:10.1016/j.mimet.2016.11.010. 2016.
  35. Williams, Maggie R; Stedtfeld, Robert D; Guo, Xueping; Hashsham, Syed A. Antimicrobial Resistance in the Environment. Water Environment Research. 88(10):1951-1967. 2016.
  36. Chai, BL; Tsoi, TV; Iwai, S; Liu, C; Fish, JA; Gu, C; Johnson, TA; Zylstra, G; Teppen, BJ; Li, H; Hashsham, SA; Boyd, SA; Cole, JR; Tiedje, JM. Sphingomonas wittichii Strain RW1 Genome-Wide Gene Expression Shifts in Response to Dioxins and Clay. PLoS ONE. 11(6). Article Number: e0157008. DOI: 10.1371/journal.pone.0157008. 2016.
  37. Kanitkar, YH; Stedtfeld, RD; Steffan, RJ; Hashsham, SA; Cupples, AM. Loop-Mediated Isothermal Amplification (LAMP) for Rapid Detection and Quantification of Dehalococcoides Biomarker Genes in Commercial Reductive Dechlorinating Cultures KB-1 and SDC-9. Applied and Environmental Microbiology. 82(6): 1799-1806. DOI: 10.1128/AEM.03660-15. 2016.
  38. Stedtfeld, RD; Williams, MR; Fakher, U; Johnson, TA; Stedtfeld, TM; Wang, F; Khalife, WT; Hughes, M; Etchebarne, BE; Tiedje, JM; Hashsham, SA. Antimicrobial resistance dashboard application for mapping environmental occurrence and resistant pathogens. FEMS Microbiology Ecology. 92(3): Article Number: fiw020. DOI: 10.1093/femsec/fiw020. 2016.
  39. Johnson, T. A.; Stedtfeld, R. D.; Wang Qiong; Cole, J. R.; Hashsham, S. A.; Looft, T.; Zhu YongGuan; Tiedje, J. M. Clusters of antibiotic resistance genes enriched together stay together in swine agriculture. mBio. Vol 7 Issue: 2 Pages: e02214-e02214-15. Published: 2016.
  40. 2015

  41. Seyrig, G; Stedtfeld, RD; Tourlousse, DM; Ahmad, F; Towery, K; Cupples, AM; Tiedje, JM; Hashsham, SA. Selection of fluorescent DNA dyes for real-time LAMP with portable and simple optics. Journal of Microbiological Methods. 119: 223-227. 2015.
  42. Stedtfeld, RD; Liu, YC; Stedtfeld, TM; Kostic, T; Kronlein, M; Srivannavit, O; Khalife, WT; Tiedje, JM; Gulari, E; Hughes, M; Etchebarne, B; Hashsham, SA. Static self-directed sample dispensing into a series of reaction wells on a microfluidic card for parallel genetic detection of microbial pathogens. Biomedical Microdevices. 17(5): Art No. 89, Oct 2015.
  43. Kostic, T; Ellis, M; Williams, MR; Stedtfeld, TM; Kaneene, JB; Stedtfeld, RD, Hashsham, SA. Thirty-minute screening of antibiotic resistance genes in bacterial isolates with minimal sample preparation in static self-dispensing 64 and 384 assay cards. Applied Microbiology and Biotechnology. 9 (18): 7711-7722, Sep 2015.
  44. Samhan, FA; Kronlein, MR; Fakher, U; Kronlein, C; Stedtfeld, RD; Hashsham, SA. Detection and Occurrence of Indicator Organisms and Pathogens. Water Environment Research. 87 (10): 883-900, 2015.
  45. Chai, Benli; Tsoi, Tamara V; Iwai, Shoko; Liu, Cun; Fish, Jordan; Gu, Cheng; Johnson, Timothy A; Zylstra, Gerben; Teppen, Brian J; Li, Hu; Hashsham, Syed A; Boyd, Stephen A; Cole, James R; Tiedje, James M. GSE74831: Sphingomonas wittichii strain RW1 genome-wide gene expression shifts in response to dioxins and clay. PLoS One. 2016;11(6):e0157008. PMID: 27309357
  46. 2014

  47. Pasco, Elodie V, Shi, H, Xagoraraki, I, Hashsham, SA, Parent, KN, Bruening, ML, Tarabara, VV. Polyelectrolyte multilayers as anti-adhesive membrane coatings for virus concentration and recovery. Journal of Membrane Science. 469: 140-150. 2014.
  48. Stedtfeld,Robert, Tiffany M Stedtfeld, Maggie Kronlein, Gregoire Seyrig, Robert J Steffan, Alison Cupples, Syed A Hashsham. DNA Extraction-free Quantification of Dehalococcoides spp. in Groundwater using a Hand-Held Device. Environmental Science & Technology. 10/2014; DOI: 10.1021/es503472h
  49. Kronlein, MR; Stedtfeld, RD; Farag Samhan; Catherine Kronlein, Hashsham, SA. Detection and Occurrence of Indicator Organisms and Pathogens. Water Environment Research. 86(10): 889-916, 2014.

    2013

  50. Wong,Mark V.M., Syed A Hashsham, Erdogan Gulari, Jean-Marie Rouillard, Tiong Gim AW, Joan B Rose. Detection and characterization of human pathogenic viruses circulating in community wastewater using multi target microarrays and polymerase chain reaction. Journal of Water and Health. 11(4): 659-670. 2013
  51. Zhu, YG; Johnson, TA; Su, JQ; Qiao, M; Guo, GX; Stedtfeld, RD; Hashsham, SA; Tiedje, JM. Diverse and abundant antibiotic resistance genes in Chinese swine farms. Proceedings of the National Academy of Sciences of the United States of America. 110(9): 3435-3440, Feb 2013.
  52. Kronlein, MR; Stedtfeld, RD; Sorensen, J; Bhaduri, P; Stedtfeld, T; Eanes, S; Harichandran, V; Haynes, K; Stevens, M; Hashsham, SA. Detection and Occurrence of Indicator Organisms and Pathogens. Water Environment Research. 85(10): 889-916, 2013.
  53. 2012

  54. Herzog, Amanda B, Alok K Pandey, David Reyes-Gastelum, Charles P Gerba, Joan B Rose, Syed A Hashsham. Evaluation of sample recovery efficiency for Bacteriophage P22 on fomites. Applied and Environmental Microbiology. 78(22): 7915-7922, Nov 2012.
  55. Stedtfeld, Robert D.; Kronlein, Maggie; and; Hashsham, Syed A., Point-of-care platforms, genetic assays and wireless connectivity. Clinical Laboratory International. Page 6-12, November 2012b.
  56. Stedtfeld, Robert D.; Tourlousse, Dieter M.; Seyrig, Gregoire; Stedtfeld, Tiffany M.; Kronlein, Maggie; Price, Scott; Ahmad, Farhan; Gulari, Erdogan; Tiedje, James M.; Hashsham, Syed A. Gene-Z: a device for point of care genetic testing using a smartphone. Lab on a Chip . 12(8): 1454-1462, 2012.
  57. Looft, Torey; Johnson, Timothy A. Allen, Heather K. Bayles, Darrell O.; Alt, David P.; Stedtfeld, Robert D., Woo Jun; Stedtfeld, Tiffany M. Chai, Benli; Cole, James R.; Hashsham, Syed A.; Tiedje, James M.; Stanton, Thad B., In-feed antibiotic effects on the swine intestinal microbiome. Proceedings of the National Academy of Sciences of the United States of America . 109(5): 1691-1696, 2012.
  58. Sinclair, Ryan G.; Rose, Joan B.; Hashsham, Syed A.; Gerba, Charles P.; Haas, Charles N. Criteria for selection of surrogates used to study the fate and control of pathogens in the environment. Applied and Environmental Microbiology. 78(6): 1969-1977, 2012.
  59. Baushke, Samuel W.; Stedtfeld, Robert D.; Tourlousse, Dieter M.; Ahmad, Farhan; Wick, Lukas M.; Gulari, Erdogan; Tiedje, James M.; Hashsham, Syed A. Identification of non-specific hybridization using an empirical equation fitted to non-equilibrium dissociation curves. Journal of Microbiological Methods. 90(1): 29-35. 2012.
  60. Ahmad, Farhan and Hashsham, Syed A. Miniaturized nucleic acid amplification systems for rapid and point-of-care diagnostics: A review. Analytica Chimica Acta. 733: 1-15, 2012.
  61. Tourlousse, Dieter M.; Ahmad, Farhan; Stedtfeld, Robert D.; Seyrig, Gregoire; Tiedje, James M.; Hashsham, Syed A., A polymer microfluidic chip for quantitative detection of multiple water- and foodborne pathogens using real-time fluorogenic loop-mediated isothermal amplification. Biomedical Microdevices. 14(4): 769-778. 2012.
  62. Bhaduri, Prianca, Stedtfeld, RD, Sangeetha Srivanasan, Kostic, Tanja, Amanda B. Herzog, Maggie R. Kronlein, Stedtfeld, T, Liu, YC, Syed A. Hashsham. Detection and occurrence of indicator organisms and pathogens. Water Environment Research. 84(10). 786-813. 2012.
  63. 2011

  64. Ahmad, F., Seyrig G., Tourlousse D. M., Stedtfeld R. D., Hashsham S.A., A CCD-based fluorescence imaging system for real-time loop-mediated isothermal amplification-based rapid and sensitive detection of waterborne pathogens on microchips, Biomedical Microdevices. 13(5):929-37, 2011.
  65. Iwai, S, Johnson TA, Chai B, Hashsham SA, Tiedje JM. Comparison of the specificities and efficacies of primers for aromatic dioxygenase gene analysis of environmental samples. Applied and Environmental Microbiology. 77(11):3551-7, 2011.
  66. Seyrig,Gre?goire, Amanda B. Herzog, Farhan Ahmad, Sangeetha Srivanasan, Maggie R. Kronlein, Prianca Bhaduri, Syed A. Hashsham. Detection and occurrence of indicator organisms and pathogens. Water Environment Research. 83(10). 2011.
  67. 2010

  68. Herzog,Amanda B., Prianca Bhaduri, Robert D. Stedtfeld, Gregoire Seyrig, Farhan Ahmad, Parth K. Dave, and Syed A. Hashsham. Detection and occurrence of indicator organisms and pathogens. Water Environment Research. 82(10):883-907. 2010.
  69. Iwai, Shoko, Benli Chai, Woo Jun Sul, James R Cole, Syed A Hashsham and James M Tiedje. Gene-targeted metagenomics reveals extensive diversity of aromatic dioxygenase genes in the environment. The ISME Journal. 4(2): 279-285. 2010.
  70. 2009

  71. Herzog, Amanda B., McLennan S. Devin, Alok K Pandey, Charles P. Gerba, Charles N. Haas, Joan B. Rose, and Hashsham, Syed. Implications of limits of detection of various methods for Bacillus anthracis in computing risks to human health. Applied and Environmental Microbiology. 75(19):6331-9, 2009.
  72. Callister, Stephen J, J Jacob Parnell, Michael E Pfrender, and Hashsham, Syed. Relating perturbation magnitude to temporal gene expression in biological systems. BMC Research Notes. 2:43. doi: 10.1186/1756-0500-2-43, 2009.
  73. Ahmad,Farhan, Dieter M. Tourlousse, Robert D. Stedtfeld, Gregoire Seyrig, Amanda B. Herzog, Prianca Bhaduri, and Syed Hashsham. Detection and occurrence of indicator organisms and pathogens. Water Environment Research. 81(10): 959-980, 2009.
  74. 2008

  75. Robert, D. Stedtfeld, Samuel M. Baushke, Amanda Herzog, Tiffany Stedtfeld, Erdogan Gulari, James M. Tiedje, and Syed A. Hashsham. Development and experimental validation of a predictive threshold cycle (Ct) equation for quantification of virulence and marker genes using high-throughput nanoliter PCR on OpenArraysTM. Applied and Environmental Microbiology. 74(12):3831-3838, 2008.
  76. Pozhitkov, AE, Rule RA, Stedtfeld RD, Hashsham SA, Noble PA. Concentration dependency of nonequilibrium thermal dissociation curves in complex target samples. Journal of Microbiological Methods. 74(2-3):82-88, 2008.
  77. Tourlousse, M Dieter, Ahmad, Farhan, Stedtfeld, D Robert, Seyrig, Gregoire, Duran, Metin, Alm, W Elizabeth, Hashsham, A Syed. Detection and occurrence of indicator organisms and pathogens. Water Environment Research. 80(10): 898-928, 2008.
  78. Miller,Sarah M., Dieter M. Tourlousse, Robert D. Stedtfeld, Samuel M. Baushke, Amanda B. Herzog, Lukas M. Wick, Jean Marie Rouillard, Erdogan Gulari, James M. Tiedje, and Syed A. Hashsham. An in situ synthesized virulence and marker gene (VMG) biochip for the detection of waterborne pathogens. Applied and Environmental Microbiology. 74: 2200-2209, 2008.
  79. Zhao,Xianda, Reem Musleh, Seth Maher, Milind V. Khire, Thomas C. Voice, Syed A. Hashsham Start-Up Performance of a Bioreactor Landfill Cell Under Cold-Climate Conditions. Waste Management. Mar 2008.
  80. 2007

  81. Tourlousse, DM, Stedtfeld, RD, Baushke, SW, Wick, LM, and SA Hashsham. Virulence factor activity relationships (VFAR): Challenges and development approaches. Water Environment Research. 79(3):246-59, 2007.
  82. Stedtfeld, RD, Tourlousse, DM, Baushke, SW, Chai, B, Cole, JR, and SA Hashsham. Multiplex approach for screening genetic markers of microbial indicators. Water Environment Research. 79(3):260-9, 2007.
  83. Robert D. Stedtfeld, Dieter M. Tourlousse, Gregoire Seyrig, Elizabeth W. Alm, and Syed A. Hashsham. Detection and occurrence of indicator organisms and pathogens. Water Environment Research. 1085-1108, 2007.
  84. Pozhitkov AE, Stedtfeld RD, Hashsham SA, Noble PA. Revision of the nonequilibrium thermal dissociation and stringent washing approaches for identification of mixed nucleic acid targets by microarrays. Nucleic Acids Research. 35(9):e70. 2007.
  85. Stedtfeld, R.D., Jean-Marie Rouillard, Erdogan Gulari, James M. Tiedje, and Syed A. Hashsham. 2006. Influence of dangling end and surface proximal tail of targets on probe- target duplex formation in 16S rRNA gene-based diagnostic arrays. Applied and Environmental Microbiology. 73(2): 380-389, 2007.
  86. Maqbool, S.B., A. Ahmad, M.B. Sicklen, and S.A. Hashsham. Real time PCR assay for polyphosphate kinase genes in activated sludge. 2007. Research Journal of Environmental Sciences. 1 (5): 229-236, 2007.
  87. Hashsham, Syed A., Erdogan Gulari, and James M. Tiedje. Microfluidic systems being adapted for microbial and molecular biological analysis. Microbe. 29(11):531-536, 2007.
  88. 2006

  89. Parnell J.J., Park, J. , Denef, V. , Tsoi, T., Hashsham, S., Quensen, J., and J.M. Tiedje. Coping with PCB toxicity: Physiological and genome-wide responses of Burkholderia xenovorans LB400 to PCB (polychlorinated biphenyl)-mediated stress. Applied and Environmental Microbiology. doi:10.1128/AEM.01129-06. 2006.
  90. Dhawan, Alok, Julian S. Taurozzi, Alok K. Pandey, Wenqian Shan, Sarah M. Miller, Syed A. Hashsham, and Volodymyr V. Tarabara. Stable colloidal dispersions of C60 fullerenes in water: Evidence for genotoxicity. Environmental Science & Technology. (40) 7394-7401, 2006.
  91. Stedtfeld, R.D., Duran M., Alm, E.W., and Hashsham, S.A. Detection and occurrence of indicator organisms and pathogens. Water Environment Research. 78(10) 1054-1077: 2006.
  92. Wick, Lukas M Jean-Marie Rouillard, Thomas S. Whittam, Erdogan Gulari, James M. Tiedje, and Syed A. Hashsham. On-chip non-equilibrium dissociation curves and dissociation rate constants as methods to assess specificity of oligonucleotide probes. Nucleic Acids Research. 34(3):e26; doi:10.1093/nar/gnj024. 2006.
  93. Maqbool S.B., Ahmad A., Dhawan A., Callister S.J., Tsoi T., Sticklen M.B., and Hashsham S.A. Response of selected genes of Burkholderia xenovorans strain LB400 to onion extract using a DNA:RNA hybrid capture detection system. Research Journal of Microbiology. 1(5): 378-391. 2006.
  94. 2005

  95. Duran M., Alm, E.W., Stedtfeld, R.D., Haznedaroglu, B., and Hashsham, S.A., Detection and occurrence of indicator organisms and pathogens. Water Environment Research. 77: 659-717: 2005.
  96. 2004

  97. Hashsham, S.A., Wick, L.M., Rouillard, J-M., Gulari, E., and J.M. Tiedje, 2004. Potential of DNA microarrays for developing parallel detection tools (PDTs) for microorganisms relevant to biodefense and related research needs. Biosensors and Bioelectronics. 20(4): 668-683, 2004.
  98. Hashsham, S.A., Alm, E.W., Stedtfeld, R.D., Traver, R.G., and M. Duran. Detection and occurrence of indicator organisms and pathogens. Water Environment Research. 75(6): 2004.
  99. Jenkins, T.M., T.M. Scott, J.R. Cole, S.A. Hashsham, and J.B. Rose, Assessment of virulence-factor activity relationships (VFARs) for waterborne diseases. Water Science and Technology. 50(1):309-314, 2004.
  100. Denef, VJ, Park J, Tsoi TV, Rouillard JM, Zhang H, Wibbenmeyer JA, Verstraete W, Gulari E, Hashsham SA, Tiedje JM., Biphenyl and benzoate metabolism in a genomic context: Outlining genome-wide metabolic networks in Burkholderia xenovorans LB400. Applied and Environmental Microbiology. 70 (8):4961-70. 2004.
  101. 2003

  102. Dollhopf SL, Pariseau ML, Hashsham SA, Tiedje J.M., Competitive and cooperative interactions affecting a fermentative spirochete in anaerobic chemostats. Microbial Ecology. 46 (1):1-11, 2003.
  103. Callister, SJ., Ayala-del-Rio H.L., and S.A. Hashsham. Quantification of a single population in a mixed community using a laser integrated microarray scanner. Environmental Engineering and Science. 2(4):247-253, 2003.
  104. Hashsham, S.A. and D.L. Freedman, Adsorption of vitamin B12 to alumina, kaolinite, sand and sandy soil. Water Research. 37: 3189-3193, 2003.
  105. Musarrat J., and S.A. Hashsham. Customized cDNA microarray for expression profiling of environmentally important genes of Pseudomonas stutzeri strain KC. Teratogenesis Carcinogenesis and Mutagenesis. 283-294. Suppl. 2003.
  106. Denef, V.J., J. Park, J.L.M. Rodrigues1, T.V. Tsoi, S.A. Hashsham and J.M. Tiedje. Validation of a more sensitive method for using spotted oligonucleotide DNA microarrays for functional genomics studies on bacterial communities. Environmental Microbiology. 5 (10), 933-943, 2003.
  107. 2002

  108. Sun, B., B.M. Griffin, R.K. Kehrer, S.A. Hashsham, and J.M. Tiedje. Microbial reductive dechlorination of 1,1,1-trichloroethane to chloroethane. Science. 298: 1023, 2002.
  109. 2001

  110. Dollhopf, S.L., S.A. Hashsham S. A., F.B. Dazzo, R.F. Hickey, C.S. Criddle, and J.M. Tiedje. The impact of fermentative organisms on carbon flow in methanogenic systems under constant low-substrate conditions. Applied Microbiology and Biotechnology. 56: 531-538, 2001.
  111. Dollhopf, S.L., S.A. Hashsham, and J.M. Tiedje. Interpreting 16S rDNA T-RFLP Data: Application of self-organizing maps and principal component analysis to describe community dynamics and convergence. Microbial Ecology. 42 (4): 495-505, 2001.
  112. 2000

  113. Fernandez, A., S. Hashsham, S. Dollhopf, L. Raskin, O. Glagoleva, F. Dazzo, R. Hickey, C. Criddle, and J. Tiedje. Flexible community structure correlates with stable community function in methanogenic bioreactor communities perturbed by glucose. Applied and Environmental Microbiology. 66 (9):4058-4067, 2000.
  114. Hashsham S. , A. Fernandez, S. Dollhopf, F. Dazzo, R. Hickey, J. Tiedje, and C. Criddle. Parallel processing of substrate correlates with greater functional stability in methanogenic bioreactor communities perturbed by glucose. Applied and Environmental Microbiology. 66 (9):4050-4057, 2000.
  115. 1999

  116. Hashsham, S.A. and D.L. Freedman. Enhanced biotransformation of carbon tetrachloride by Acetobacterium woodii upon addition of hydroxocobalamin and fructose. Applied and Environmental Microbiology. 65(10): 4537-4542, 1999.
  117. 1995

  118. Hashsham, S.A., R. Scholze, and D.L. Freedman. Cobalamin-enhanced anaerobic biotransformation of carbon tetrachloride. Environmental Science & Technology. 29(11):2856-2863, 1995.
  119. 1992

  120. Qasim, R., A. Hashsham, and N. I. Ansari. Optimizing TOC removal by coagulation and softening, Journal of Environmental Engineering Division, American Society of Civil Engineers. Vol. 118, No. 3, p. 432 437. 1992.
  121. Qasim, S.R., S.A. Hashsham, and G.M. Middleton. Study aimed at odor reduction in water from reservoir. Water/Engineering and Management. April 1992, p. 58-62, 1992.