Finn, D. R., J. Yu, Z. Esra Ilhan, V. M. Fernandes, C. R. Penton, R. Krajmalnik-Brown, F. Garcia-Pichel and T. M. Vogel. 2020. MicroNiche: An R package for assessing microbial niche breadth and overlap from amplicon sequencing data. Microbiology Ecology 96(8): fiaa131. DOI: 10.1093/femsec/fiaa131. (link )

Kalinowski, T., K. McClellan, T. A. Bruton, R. Krajmalnik-Brown, E. Driver and R. U. Halden. 2019. Autonomous screening of groundwater remediation technologies in the subsurface using the In Situ Microcosm Array (ISMA). Journal of Hazardous Materials 367(Apr):668-675. DOI: 0.1016/j.jhazmat.2018.12.054. (link )

Esra Ilhan, Z., J. K. DiBaise, N. G. Isern, D. W. Hoyt, A. K. Marcus, D. Kang, M. D. Crowell, B. E. Rittmann and R. Krajmalnik-Brown. 2017. Distinctive microbiomes and metabolites linked with weight loss after gastric bypass, but not gastric banding. The ISME Journal 11:2047-2058. (link )

Esra Ilhan, Z., A. K. Marcus, D. Kang, B. E. Rittmann and R. Krajmalnik-Brown. 2017. pH-mediated microbial and metabolic interactions in fecal enrichment cultures. mSphere 2(3):e00047-27. DOI: 10.1128/mSphere.00047-17. (link )

Ontiveros Valencia, A. V., C. R. Penton, R. Krajmalnik-Brown and B. E. Rittmann. 2016. Hydrogen-fed biofilm reactors reducing selenite and sulfate: community structure and location of elemental selenium within the biofilm. Biotechnology and Bioengineering 113(8):2736-1744. DOI: 10.1002/bit.25945. (link )

Badalamenti, J. P., C. I. Torres and R. Krajmalnik-Brown. 2014. Coupling dark metabolism to electricity generation using photosynthetic cocultures. Biotechnology and Bioengineering 111(2):223-231. DOI: 10.1002/bit.25011. (link )

Delgado, A. G., D. Fajardo-Williams, S. C. Popat, C. I. Torres and R. Krajmalnik-Brown. 2014. Successful operation of continuous reactors at short retention times results in high-density, fast-rate Dehalococcoides dechlorinating cultures. Applied Microbiology and Biotechnology 98(6):2729-2737. DOI: 10.1007/s00253-013-5263-5. (link )

Delgado, A. G., D. Kang, K. G. Nelson, D. Fajardo-Williams, J. F. Miceli III, H. Y. Done, S. C. Popat and R. Krajmalnik-Brown. 2014. Selective enrichment yields robust ethene-producing dechlorinating cultures from microcosms stalled at cis'dichloroethene. PLOS One 9(6):e100654. DOI: 10.1371/journal.pone.0100654. (link )

Ekre, R., P. C. Johnson, B. E. Rittmann and R. Krajmalnik-Brown. 2014. Method for assessing source zone natural depletion at chlorinated aliphatic spill sites. Groundwater Monitoring & Remediation 34(2):60-70. DOI: 10.1111/gwmr.12049. (link )

Miceli III, J. F., I. Garcia-Pena, P. Parameswaran, C. I. Torres and R. Krajmalnik-Brown. 2014. Combining microbial cultures for efficient production of electricity from butyrate in a microbial electrochemical cell. Bioresource Technology 169:169-174. DOI: 10.1016/j.biortech.2014.06.090. (link )

Ontiveros Valencia, A. V., Y. Tang, R. Krajmalnik-Brown and B. E. Rittmann. 2014. Managing the interactions between sulfate- and perchlorate-reducing bacteria when using hydrogen-fed biofilms to treat a groundwater with a high perchlorate concentration. Water Research 55:215-224. DOI: 10.1016/j.watres.2014.02.020. (link )

Ontiveros Valencia, A., Y. Tang, H. Zhao, D. Friese, R. Overstreet, J. Smith, P. Evans, B. Rittmann and R. Krajmalnik-Brown. 2014. Pyrosequencing analysis yields comprehensive assessment of microbial communities in pilot-scale two-stage membrane biofilm reactors. Environmental Science & Technology 48(13):7511-7518. DOI: 10.1021/es5012466. (link )

Ruiz, V., Z. Esra Ilhan, D. Kang, R. Krajmalnik-Brown and G. Buitron. 2014. The source of inoculum plays a defining role in the development of MEC microbial consortia fed with acetic and propionic acid mixtures. Journal of Biotechnology 182-183:11-18. DOI: 10.1016/j.jbiotec.2014.04.016. (link )

Zhao, H., A. V. Ontiveros Valencia, Y. Tang, B. Kim, S. Van Ginkel, D. Friese, J. Smith, P. Evans and R. Krajmalnik-Brown. 2014. Removal of multiple electron acceptors by pilot-scale, two-stage membrane biofilm reactors. Water Research 54(1):115-122. DOI: 10.1016/j.watres.2014.01.047. (link )

Ziv-El, M., T. Kalinowski, R. Krajmalnik-Brown and R. U. Halden. 2014. Simultaneous determination of chlorinated ethenes and ethene in groundwater using headspace solid-phase microextraction with gas chromatography. Journal of Chromatographic Science 52(2):137-142. DOI: 10.1093/chromsci/bms258. (link )

Badalamenti, J. P., R. Krajmalnik-Brown and C. I. Torres. 2013. Generation of high current densities by pure cultures of anode-respiring Geoalkalibacter spp. under alkaline and saline conditions in microbial electrochemical cells. mBio 4(3):e00144-13. DOI: 10.1128/mBio.00144-13. (link )

Badalamenti, J. P., C. I. Torres and R. Krajmalnik-Brown. 2013. Light-responsive current generation by phototrophically enriched anode biofilms dominated by green sulfur bacteria. Biotechnology and Bioengineering 110(4):1020-1027. DOI: 10.1002/bit.24779. (link )

Gilbert, J. A., R. Krajmalnik-Brown, D. L. Porazinska, S. J. Weiss and R. Knight. 2013. Toward effective probiotics for autism and other neurodevelopmental disorders. Cell 155(7):1446-1448. DOI: 10.1016/j.cell.2013.11.035. (link )

Kang, D., J. Park, Z. Esra Ilhan, G. Wallstrom, J. LaBaer, J. B. Adams and R. Krajmalnik-Brown. 2013. Reduced incidence of Prevotella and other fermenters in intestinal microflora of autistic children. PLOS One 8(7):e68322. DOI: 10.1371/journal.pone.0068322. (link )

Ontiveros Valencia, A. V., Z. Esra Ilhan, D. Kang, B. E. Rittmann and R. Krajmalnik-Brown. 2013. Phylogenetic analysis of nitrate- and sulfate-reducing bacteria in a hydrogen-fed biofilm. FEMS Microbology Ecology 85(1):158-167. DOI: 10.1111/1574-6941.12107. (link )

Ontiveros Valencia, A. V., Y. Tang, R. Krajmalnik-Brown and B. E. Rittmann. 2013. Perchlorate reduction from a highly contaminated groundwater in the presence of sulfate-reducing bacteria in a hydrogen-fed biofilm. Biotechnology and Bioengineering 110(2):3139-3147. DOI: 10.1002/bit.24987. (link )

Tang, Y., R. Krajmalnik-Brown and B. E. Rittmann. 2013. Modeling trichloroethene reduction in a hydrogen-based biofilm. Water Science & Technology 68(5):1158-1163. DOI: 10.2166/wst.2013.362. (link )

Tang, Y., A. V. Ontiveros Valencia, L. Feng, C. Zhou, R. Krajmalnik-Brown and B. E. Rittmann. 2013. A biofilm model to understand the onset of sulfate reduction in denitrifying membrane biofilm reactors. Biotechnology and Bioengineering 110(3):763-772. DOI: 10.1002/bit.24755. (link )

Young, M. N., R. Krajmalnik-Brown, W. Liu, M. L. Doyle and B. E. Rittmann. 2013. The role of anaerobic sludge recycle in improving anaerobic digester performance. Bioresource Technology 128:731-737. DOI: 10.1016/j.biortech.2012.11.079. (link )

Zhao, H., Z. Esra Ilhan, A. V. Ontiveros Valencia, Y. Tang, B. E. Rittmann and R. Krajmalnik-Brown. 2013. Effects of mutiple electron acceptors on microbial interactions in a hydrogen-based biofilm. Environmental Science & Technology 47(13):7396-7403. DOI: 10.1021/es401310j. (link )

Zhao, H., A. V. Ontiveros Valencia, Y. Tang, B. Kim, Z. Esra Ilhan, R. Krajmalnik-Brown and B. Rittmann. 2013. Using a two-stage hydrogen-based membrane biofilm reactor (MBfR) to achieve complete perchlorate reduction in the presence of nitrate and sulfate. Environmental Science & Technology 47(3):1565-1572. DOI: 10.1021/es303823n. (link )

Delgado, A. G., P. Parameswaran, D. Fajardo-Williams, R. U. Halden and R. Krajmalnik-Brown. 2012. Role of bicarbonate as a pH buffer and electron sink in microbial dechlorination of chloroethenes. Microbial Cell Factories 11:128. DOI: 10.1186/1475-2859-11-128. (link )

Hartmann, E. M., J. P. Badalamenti, R. Krajmalnik-Brown and R. U. Halden. 2012. Quantitative PCR for tracking the megaplasmid-borne biodegradation potential of a model sphingomonad. Applied and Environmental Microbiology 78(12):4493-4496. DOI: 10.1128/AEM.00715-12 . (link )

Krajmalnik-Brown, R., Z. Esra Ilhan, D. Kang and J. K. DiBaise. 2012. Effects of gut microbes on nutrient absorption and energy regulation. Nutrition in Clinical Practice 27(2):201-214. DOI: 10.1177/0884533611436116 . (link )

Miceli III, J. F., P. Parameswaran, D. Kang, R. Krajmalnik-Brown and C. I. Torres. 2012. Enrichment and analysis of anode-respiring bacteria from diverse aneraobic inocula. Environmental Science & Technology 46(18):10349-10355. DOI: 10.1021/es301902h. (link )

Ontiveros Valencia, A. V., M. Ziv-El, H. Zhao, L. Feng, B. E. Rittmann and R. Krajmalnik-Brown. 2012. Interactions between nitrate-reducing and sulfate-reducing bacteria coexisting in a hydrogen-fed biofilm. Environmental Science and Technology 46(20):11289-11298. DOI: 10.1021/es302370t. (link )

Parameswaran, P., C. I. Torres, D. Kang, B. E. Rittmann and R. Krajmalnik-Brown. 2012. The role of homoacetogenic bacteria as efficient hydrogen scavengers in microbial electrochemical cells (MXCs). Water Science & Technology 65(1):1-6. DOI: 10.2166/wst.2011.519. (link )

Tang, Y., H. Zhao, A. K. Marcus, R. Krajmalnik-Brown and B. E. Rittmann. 2012. A steady-state biofilm model for simultaneous reduction of nitrate and perchlorate, Part 1: Model development and numerical solution. Environmental Science & Technology 46(3):1598-1607. DOI: 10.1021/es203129s. (link )

Tang, Y., H. Zhao, A. K. Marcus, R. Krajmalnik-Brown and B. E. Rittmann. 2012. A steady-state biofilm model for simultaneous reduction of nitrate and perchlorate, Part 2: Parameter optimization and results and discussion. Environmental Science & Technology 46(3):1608-1615. DOI: 10.1021/es203130r. (link )

Ziv-El, M., A. G. Delgado, Y. Yao, D. Kang, K. G. Nelson, R. U. Halden and R. Krajmalnik-Brown. 2012. Erratum to: Development and characterization of DehaloR^2, a novel anaerobic microbial consortium performing rapid dechlorination of TCE to ethene. Applied Microbiology and Biotechnology 95(1):273-274. DOI: 10.1007/s00253-012-4161-6. (link )

Ziv-El, M., S. C. Popat, K. Cai, R. U. Halden, R. Krajmalnik-Brown and B. E. Rittmann. 2012. Managing methanogens and homoacetogens to promote reductive dechlorination of trichloroethene with direct delivery of H2 in a membrane biofilm reactor. Biotechnology and Bioengineering 109(9):2200-2210. DOI: 10.1002/bit.24487. (link )

Ziv-El, M., S. C. Popat, P. Parameswaran, D. Kang, A. Polasko, R. U. Halden, B. E. Rittmann and R. Krajmalnik-Brown. 2012. Using electron balances and molecular techniques to assess trichoroethene-induced shifts to a dechlorinating microbial community. Biotechnology and Bioengineering 109(9):2230-2239. DOI: 10.1002/bit.24504. (link )

Garcia-Pena, E. I., P. Parameswaran, D. Kang, M. Canul-Chan and R. Krajmalnik-Brown. 2011. Anaerobic digestion and co-digestion processes of vegetable and fruit residues: Process and microbial ecology. Bioresource Technology 102(20):9447-9455. DOI: 10.1016/j.biortech.2011.07.068. (link )

Parameswaran, P., C. I. Torres, H. Lee, B. E. Rittmann and R. Krajmalnik-Brown. 2011. Hydrogen consumption in microbial electrochemical systems (MXCs): The role of homo-acetogenic bacteria. Bioresources Technology 102(1):263-271. DOI: 10.1016/j.biortech.2010.03.133. (link )

Sheng, J., H. W. Kim, J. P. Badalamenti, C. Zhou, S. Sridharakrishnan, R. Krajmalnik-Brown, B. E. Rittmann and R. Vannela. 2011. Effects of temperature shifts on growth rate and lipid characteristics of Synechocystis sp. PCC6803 in a bench-top photobioreactor. Bioresource Technology 102(24):11218-11225. DOI: 10.1016/j.biortech.2011.09.083. (link )

Torres, C. I., S. Ramakrishna, C. Chiu, K. G. Nelson, P. K. Westerhoff and R. Krajmalmik-Brown. 2011. Fate of sucralose during wastewater treatment. Environmental Engineering Science 28(5):325-331. (link )

Zhao, H., S. Van Ginkel, Y. Tang, D. Kang, B. E. Rittmann and R. Krajmalnik-Brown. 2011. Interactions between perchlorate and nitrate reductions in the biofilm of a hydrogen-based membrane biofilm reactor. Environmental Science & Technology 45(23):10155-10162. DOI: 10.1021/es202569b. (link )

Ziv-El, M., A. G. Delgado, Y. Yao, D. Kang, K. G. Nelson, R. U. Halden and R. Krajmalnik-Brown. 2011. Development and characterization of DehaloR^2, a novel anaerobic microbial consortium performing rapid dechlorination of TCE to ethene. Applied Microbiology and Biotechnology 92(5):1063-1071. DOI: 10.1007/s00253-011-3388-y. (link )

Parameswaran, P., H. Zhang, C. I. Torres, B. E. Rittmann and R. Krajmalnik-Brown. 2010. Microbial community structure in a biofilm anode fed with a fermentable substrate: The significance of hydrogen scavengers. Biotechnology and Bioengineering 105(1):69-78. DOI: 10.1002/bit.22508. (link )

Torres, C. I., A. K. Marcus, H. Lee, P. Parameswaran, R. Krajmalnik-Brown and B. E. Rittmann. 2010. A kinetic perspective on extracellular electron transfer by anode-respiring bacteria. FEMS Microbiology Reviews 34(1):3-17. DOI: 10.1111/j.1574-6976.2009.00191.x. (link )

Zhang, H., M. Ziv-El, B. E. Rittmann and R. Krajmalnik-Brown. 2010. Effect of dechlorination and sulfate reduction on the microbial community structure in denitrifying membrane-biofilm reactors. Environmental Science & Technology 44(13):5159-5164. DOI: 10.1021/es100695n. (link )

Lee, H., R. Krajmalnik-Brown, H. Zhang and B. E. Rittmann. 2009. An electron-flow model can predict complex redox reactions in mixed-culture fermentative BioH₂: Microbial ecology evidence. Biotechnology and Bioengineering 104(4):687-697. DOI: 10.1002/bit.22442. (link )

Parameswaran, P., C. I. Torres, H. Lee, R. Krajmalnik-Brown and B. E. Rittmann. 2009. Syntrophic interactions among anode respiring bacteria (ARB) and Non-ARB in a biofilm anode: electron balances. Biotechnology and Bioengineering 103(3):513-523. DOI: 10.1002/bit.22267. (link )

Torres, C. I., R. Krajmalnik-Brown, P. Parameswaran, A. K. Marcus, G. Wanger, Y. A. Gorby and B. E. Rittmann. 2009. Selecting anode-respiring bacteria based on anode potential: Phylogenetic, eletrochemical, and microscopic characterization. Environmental Science & Technology 43(24):9519-9524. DOI: 10.1021/es902165y. (link )

Zhang, H., J. E. Banaszak, P. Parameswaran, J. Alder, R. Krajmalnik-Brown and B. E. Rittmann. 2009. Focused-pulsed sludge pre-treatment increases the bacterial diversity and relative abundance of acetoclastic methanogens in a full-scale anaerobic digester. Water Research 43(18):4517-4526. DOI: 10.1016/j.watres.2009.07.034. (link )

Zhang, H., J. K. DiBaise, A. Zuccolo, D. Kudma, M. Braidotti, Y. Yu, P. Parameswaran, M. D. Crowell, B. E. Rittmann and R. Krajmalnik-Brown. 2009. Human gut microbiota in obesity and after gastric bypass. Proceedings of the National Academy of Sciences of the United States of America 106(7):2365-2370. DOI: 10.1073/pnas.0812600106. (link )

Chung, J., R. Krajmalnik-Brown and B. E. Rittmann. 2008. Bioreduction of trichloroethene using a hydrogen-based membrane biofilm reactor. Environmental Science & Technology 42(2):477-483. DOI: 10.1021/es702422d. (link )

DiBaise, J. K., H. Zhang, M. D. Crowell, R. Krajmalnik-Brown, G. A. Decker and B. E. Rittmann. 2008. Gut microbiota and its possible relationship with obesity. Mayo Clinic Proceedings 83(4):460-469. DOI: 10.4065/83.4.460. (link )

Rittmann, B. E., R. Krajmalnik-Brown and R. U. Halden. 2008. Opinion: Pre-genomic, genomic and post-genomic study of microbial communities involved in bioenergy. Nature Reviews Microbiology 6:604-612. DOI: 10.1038/nrmicro1939. (link )

Krajmalnik-Brown, R., Y. Sung, K. M. Ritalahti, F. M. Saunders and F. E. Loffler. 2007. Environmental distribution of the trichloroethene reductive dehalogenase gene (tceA) suggests lateral gene transfer among Dehalococcoides. FEMS Microbiology Ecology (59):1. DOI: 10.1111/j.1574-6941.2006.00243.x. (link )