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Diversity and geochemical community assembly processes of the living rare biosphere in a sand-and-gravel aquifer ecosystem in the Midwestern United States.

Yamamoto K, Hackley KC, Kelly WR, Panno SV, Sekiguchi Y, Sanford RA, Liu WT, Kamagata Y, Tamaki H.

Sci Rep. 2019 Sep 17;9(1):13484. doi: 10.1038/s41598-019-49996-z.


Effects of triclosan and triclocarban on denitrification and N2O emissions in paddy soil.

Chen S, Chee-Sanford JC, Yang WH, Sanford RA, Chen J, Yan X, Shan J.

Sci Total Environ. 2019 Aug 7;695:133782. doi: 10.1016/j.scitotenv.2019.133782. [Epub ahead of print]


Sequence alignments and validation of PCR primers used to detect phylogenetically diverse nrfA genes associated with dissimilatory nitrate reduction to ammonium (DNRA).

Cannon J, Sanford RA, Connor L, Yang WH, Chee-Sanford J.

Data Brief. 2019 Jun 7;25:104016. doi: 10.1016/j.dib.2019.104016. eCollection 2019 Aug.


Adaptive Evolution of Escherichia coli to Ciprofloxacin in Controlled Stress Environments: Contrasting Patterns of Resistance in Spatially Varying versus Uniformly Mixed Concentration Conditions.

Deng J, Zhou L, Sanford RA, Shechtman LA, Dong Y, Alcalde RE, Sivaguru M, Fried GA, Werth CJ, Fouke BW.

Environ Sci Technol. 2019 Jul 16;53(14):7996-8005. doi: 10.1021/acs.est.9b00881. Epub 2019 Jul 3.


Physiology, Metabolism, and Fossilization of Hot-Spring Filamentous Microbial Mats.

Dong Y, Sanford RA, Inskeep WP, Srivastava V, Bulone V, Fields CJ, Yau PM, Sivaguru M, Ahrén D, Fouke KW, Weber J, Werth CR, Cann IK, Keating KM, Khetani RS, Hernandez AG, Wright C, Band M, Imai BS, Fried GA, Fouke BW.

Astrobiology. 2019 Apr 30. doi: 10.1089/ast.2018.1965. [Epub ahead of print]


Contributions of biotic and abiotic pathways to anaerobic trichloroethene transformation in low permeability source zones.

Berns EC, Sanford RA, Valocchi AJ, Strathmann TJ, Schaefer CE, Werth CJ.

J Contam Hydrol. 2019 Jul;224:103480. doi: 10.1016/j.jconhyd.2019.04.003. Epub 2019 Apr 11.


Optimization of PCR primers to detect phylogenetically diverse nrfA genes associated with nitrite ammonification.

Cannon J, Sanford RA, Connor L, Yang WH, Chee-Sanford J.

J Microbiol Methods. 2019 May;160:49-59. doi: 10.1016/j.mimet.2019.03.020. Epub 2019 Mar 21.


Diffusion-Based Recycling of Flavins Allows Shewanella oneidensis MR-1 To Yield Energy from Metal Reduction Across Physical Separations.

Michelson K, Alcalde RE, Sanford RA, Valocchi AJ, Werth CJ.

Environ Sci Technol. 2019 Apr 2;53(7):3480-3487. doi: 10.1021/acs.est.8b04718. Epub 2019 Mar 19.


Motility of Shewanella oneidensis MR-1 Allows for Nitrate Reduction in the Toxic Region of a Ciprofloxacin Concentration Gradient in a Microfluidic Reactor.

Alcalde RE, Michelson K, Zhou L, Schmitz EV, Deng J, Sanford RA, Fouke BW, Werth CJ.

Environ Sci Technol. 2019 Mar 5;53(5):2778-2787. doi: 10.1021/acs.est.8b04838. Epub 2019 Feb 14.


Geobiology reveals how human kidney stones dissolve in vivo.

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.

Sci Rep. 2018 Sep 13;8(1):13731. doi: 10.1038/s41598-018-31890-9.


Denitrification by Anaeromyxobacter dehalogenans, a Common Soil Bacterium Lacking the Nitrite Reductase Genes nirS and nirK.

Onley JR, Ahsan S, Sanford RA, Löffler FE.

Appl Environ Microbiol. 2018 Jan 31;84(4). pii: e01985-17. doi: 10.1128/AEM.01985-17. Print 2018 Feb 15.


Year-Round Shotgun Metagenomes Reveal Stable Microbial Communities in Agricultural Soils and Novel Ammonia Oxidizers Responding to Fertilization.

Orellana LH, Chee-Sanford JC, Sanford RA, Löffler FE, Konstantinidis KT.

Appl Environ Microbiol. 2018 Jan 2;84(2). pii: e01646-17. doi: 10.1128/AEM.01646-17. Print 2018 Jan 15.


Nanowires of Geobacter sulfurreducens Require Redox Cofactors to Reduce Metals in Pore Spaces Too Small for Cell Passage.

Michelson K, Sanford RA, Valocchi AJ, Werth CJ.

Environ Sci Technol. 2017 Oct 17;51(20):11660-11668. doi: 10.1021/acs.est.7b02531. Epub 2017 Oct 2.


Genomics and Ecology of Novel N2O-Reducing Microorganisms.

Hallin S, Philippot L, Löffler FE, Sanford RA, Jones CM.

Trends Microbiol. 2018 Jan;26(1):43-55. doi: 10.1016/j.tim.2017.07.003. Epub 2017 Aug 10. Review.


Real rock-microfluidic flow cell: A test bed for real-time in situ analysis of flow, transport, and reaction in a subsurface reactive transport environment.

Singh R, Sivaguru M, Fried GA, Fouke BW, Sanford RA, Carrera M, Werth CJ.

J Contam Hydrol. 2017 Sep;204:28-39. doi: 10.1016/j.jconhyd.2017.08.001. Epub 2017 Aug 4.


Hematite Reduction Buffers Acid Generation and Enhances Nutrient Uptake by a Fermentative Iron Reducing Bacterium, Orenia metallireducens Strain Z6.

Dong Y, Sanford RA, Chang YJ, McInerney MJ, Fouke BW.

Environ Sci Technol. 2017 Jan 3;51(1):232-242. doi: 10.1021/acs.est.6b04126. Epub 2016 Dec 22.


Orenia metallireducens sp. nov. Strain Z6, a Novel Metal-Reducing Member of the Phylum Firmicutes from the Deep Subsurface.

Dong Y, Sanford RA, Boyanov MI, Kemner KM, Flynn TM, O'Loughlin EJ, Chang YJ, Locke RA Jr, Weber JR, Egan SM, Mackie RI, Cann I, Fouke BW.

Appl Environ Microbiol. 2016 Oct 14;82(21):6440-6453. Print 2016 Nov 1.


Tepidibacillus decaturensis sp. nov., a microaerophilic, moderately thermophilic iron-reducing bacterium isolated from 1.7 km depth groundwater.

Dong Y, Sanford RA, Boyanov MI, Kemner KM, Flynn TM, O'Loughlin EJ, Locke RA, Weber JR, Egan SM, Fouke BW.

Int J Syst Evol Microbiol. 2016 Oct;66(10):3964-3971. doi: 10.1099/ijsem.0.001295. Epub 2016 Jul 11.


Nitrous Oxide Reduction Kinetics Distinguish Bacteria Harboring Clade I NosZ from Those Harboring Clade II NosZ.

Yoon S, Nissen S, Park D, Sanford RA, Löffler FE.

Appl Environ Microbiol. 2016 Jun 13;82(13):3793-800. doi: 10.1128/AEM.00409-16. Print 2016 Jul 1.


Detection and Diversity of Fungal Nitric Oxide Reductase Genes (p450nor) in Agricultural Soils.

Higgins SA, Welsh A, Orellana LH, Konstantinidis KT, Chee-Sanford JC, Sanford RA, Schadt CW, Löffler FE.

Appl Environ Microbiol. 2016 May 2;82(10):2919-2928. doi: 10.1128/AEM.00243-16. Print 2016 May 15.


Impact of Time from Completion of Neoadjuvant Chemotherapy to Surgery on Survival Outcomes in Breast Cancer Patients.

Sanford RA, Lei X, Barcenas CH, Mittendorf EA, Caudle AS, Valero V, Tripathy D, Giordano SH, Chavez-MacGregor M.

Ann Surg Oncol. 2016 May;23(5):1515-21. doi: 10.1245/s10434-015-5020-3. Epub 2015 Dec 17.


Metabolism-Induced CaCO3 Biomineralization During Reactive Transport in a Micromodel: Implications for Porosity Alteration.

Singh R, Yoon H, Sanford RA, Katz L, Fouke BW, Werth CJ.

Environ Sci Technol. 2015 Oct 20;49(20):12094-104. doi: 10.1021/acs.est.5b00152. Epub 2015 Oct 5.


High incidence of germline BRCA mutation in patients with ER low-positive/PR low-positive/HER-2 neu negative tumors.

Sanford RA, Song J, Gutierrez-Barrera AM, Profato J, Woodson A, Litton JK, Bedrosian I, Albarracin CT, Valero V, Arun B.

Cancer. 2015 Oct 1;121(19):3422-7. doi: 10.1002/cncr.29572. Epub 2015 Aug 17.


Nitrite Control over Dissimilatory Nitrate/Nitrite Reduction Pathways in Shewanella loihica Strain PV-4.

Yoon S, Sanford RA, Löffler FE.

Appl Environ Microbiol. 2015 May 15;81(10):3510-7. doi: 10.1128/AEM.00688-15. Epub 2015 Mar 13.


Immobilization of selenite via two parallel pathways during in situ bioremediation.

Tang Y, Werth CJ, Sanford RA, Singh R, Michelson K, Nobu M, Liu WT, Valocchi AJ.

Environ Sci Technol. 2015 Apr 7;49(7):4543-50. doi: 10.1021/es506107r. Epub 2015 Mar 12.


Complete Genome Sequence of Anaeromyxobacter sp. Fw109-5, an Anaerobic, Metal-Reducing Bacterium Isolated from a Contaminated Subsurface Environment.

Hwang C, Copeland A, Lucas S, Lapidus A, Barry K, Glavina Del Rio T, Dalin E, Tice H, Pitluck S, Sims D, Brettin T, Bruce DC, Detter JC, Han CS, Schmutz J, Larimer FW, Land ML, Hauser LJ, Kyrpides N, Lykidis A, Richardson P, Belieav A, Sanford RA, Löeffler FE, Fields MW.

Genome Announc. 2015 Jan 22;3(1). pii: e01449-14. doi: 10.1128/genomeA.01449-14.


Fe-oxide grain coatings support bacterial Fe-reducing metabolisms in 1.7-2.0 km-deep subsurface quartz arenite sandstone reservoirs of the Illinois Basin (USA).

Dong Y, Sanford RA, Locke RA 2nd, Cann IK, Mackie RI, Fouke BW.

Front Microbiol. 2014 Sep 30;5:511. doi: 10.3389/fmicb.2014.00511. eCollection 2014.


Detecting nitrous oxide reductase (NosZ) genes in soil metagenomes: method development and implications for the nitrogen cycle.

Orellana LH, Rodriguez-R LM, Higgins S, Chee-Sanford JC, Sanford RA, Ritalahti KM, Löffler FE, Konstantinidis KT.

MBio. 2014 Jun 3;5(3):e01193-14. doi: 10.1128/mBio.01193-14.


Refined NrfA phylogeny improves PCR-based nrfA gene detection.

Welsh A, Chee-Sanford JC, Connor LM, Löffler FE, Sanford RA.

Appl Environ Microbiol. 2014 Apr;80(7):2110-9. doi: 10.1128/AEM.03443-13. Epub 2014 Jan 24.


Halomonas sulfidaeris-dominated microbial community inhabits a 1.8 km-deep subsurface Cambrian Sandstone reservoir.

Dong Y, Kumar CG, Chia N, Kim PJ, Miller PA, Price ND, Cann IK, Flynn TM, Sanford RA, Krapac IG, Locke RA 2nd, Hong PY, Tamaki H, Liu WT, Mackie RI, Hernandez AG, Wright CL, Mikel MA, Walker JL, Sivaguru M, Fried G, Yannarell AC, Fouke BW.

Environ Microbiol. 2014 Jun;16(6):1695-708. doi: 10.1111/1462-2920.12325. Epub 2013 Dec 12.


Functional microbial diversity explains groundwater chemistry in a pristine aquifer.

Flynn TM, Sanford RA, Ryu H, Bethke CM, Levine AD, Ashbolt NJ, Santo Domingo JW.

BMC Microbiol. 2013 Jun 24;13:146. doi: 10.1186/1471-2180-13-146.


Shewanella spp. Use acetate as an electron donor for denitrification but not ferric iron or fumarate reduction.

Yoon S, Sanford RA, Löffler FE.

Appl Environ Microbiol. 2013 Apr;79(8):2818-22. doi: 10.1128/AEM.03872-12. Epub 2013 Feb 8.


Management and outcome of focal low-grade brainstem tumors in pediatric patients: the St. Jude experience.

Klimo P Jr, Pai Panandiker AS, Thompson CJ, Boop FA, Qaddoumi I, Gajjar A, Armstrong GT, Ellison DW, Kun LE, Ogg RJ, Sanford RA.

J Neurosurg Pediatr. 2013 Mar;11(3):274-81. doi: 10.3171/2012.11.PEDS12317. Epub 2013 Jan 4.


Disease control after reduced volume conformal and intensity modulated radiation therapy for childhood craniopharyngioma.

Merchant TE, Kun LE, Hua CH, Wu S, Xiong X, Sanford RA, Boop FA.

Int J Radiat Oncol Biol Phys. 2013 Mar 15;85(4):e187-92. doi: 10.1016/j.ijrobp.2012.10.030. Epub 2012 Dec 11.


Unexpected nondenitrifier nitrous oxide reductase gene diversity and abundance in soils.

Sanford RA, Wagner DD, Wu Q, Chee-Sanford JC, Thomas SH, Cruz-García C, Rodríguez G, Massol-Deyá A, Krishnani KK, Ritalahti KM, Nissen S, Konstantinidis KT, Löffler FE.

Proc Natl Acad Sci U S A. 2012 Nov 27;109(48):19709-14. doi: 10.1073/pnas.1211238109. Epub 2012 Nov 12.


Headaches in children with craniopharyngioma.

Khan RB, Merchant TE, Boop FA, Sanford RA, Ledet D, Onar-Thomas A, Kun LE.

J Child Neurol. 2013 Dec;28(12):1622-5. doi: 10.1177/0883073812464817. Epub 2012 Nov 8.


Patterns of care for non-small-cell lung cancer at an academic institution affiliated with a national cancer institute-designated cancer center.

Nguyen KS, Sanford RA, Huberman MS, Goldstein MA, McDonald DM, Farquhar M, Gangadharan SP, Kent MS, Michaud G, Majid A, Berman SM, Aronovitz JA, Nedea EA, Boiselle PM, Cohen DW, Kobayashi S, Costa DB.

J Oncol Pract. 2012 Jan;8(1):57-62. doi: 10.1200/JOP.2011.000274. Epub 2011 Nov 22.


Distinct disease-risk groups in pediatric supratentorial and posterior fossa ependymomas.

Godfraind C, Kaczmarska JM, Kocak M, Dalton J, Wright KD, Sanford RA, Boop FA, Gajjar A, Merchant TE, Ellison DW.

Acta Neuropathol. 2012 Aug;124(2):247-57. doi: 10.1007/s00401-012-0981-9. Epub 2012 Apr 21.


Resection of infantile brain tumors after neoadjuvant chemotherapy: the St. Jude experience.

Van Poppel M, Klimo P Jr, Dewire M, Sanford RA, Boop F, Broniscer A, Wright K, Gajjar AJ.

J Neurosurg Pediatr. 2011 Sep;8(3):251-6. doi: 10.3171/2011.6.PEDS11158.


Primary neurosurgery for pediatric low-grade gliomas: a prospective multi-institutional study from the Children's Oncology Group.

Wisoff JH, Sanford RA, Heier LA, Sposto R, Burger PC, Yates AJ, Holmes EJ, Kun LE.

Neurosurgery. 2011 Jun;68(6):1548-54; discussion 1554-5. doi: 10.1227/NEU.0b013e318214a66e.


Subtypes of medulloblastoma have distinct developmental origins.

Gibson P, Tong Y, Robinson G, Thompson MC, Currle DS, Eden C, Kranenburg TA, Hogg T, Poppleton H, Martin J, Finkelstein D, Pounds S, Weiss A, Patay Z, Scoggins M, Ogg R, Pei Y, Yang ZJ, Brun S, Lee Y, Zindy F, Lindsey JC, Taketo MM, Boop FA, Sanford RA, Gajjar A, Clifford SC, Roussel MF, McKinnon PJ, Gutmann DH, Ellison DW, Wechsler-Reya R, Gilbertson RJ.

Nature. 2010 Dec 23;468(7327):1095-9. doi: 10.1038/nature09587. Epub 2010 Dec 8.


Cross-species genomics matches driver mutations and cell compartments to model ependymoma.

Johnson RA, Wright KD, Poppleton H, Mohankumar KM, Finkelstein D, Pounds SB, Rand V, Leary SE, White E, Eden C, Hogg T, Northcott P, Mack S, Neale G, Wang YD, Coyle B, Atkinson J, DeWire M, Kranenburg TA, Gillespie Y, Allen JC, Merchant T, Boop FA, Sanford RA, Gajjar A, Ellison DW, Taylor MD, Grundy RG, Gilbertson RJ.

Nature. 2010 Jul 29;466(7306):632-6. doi: 10.1038/nature09173. Epub 2010 Jul 18.


Uranium 238U/235U isotope ratios as indicators of reduction: results from an in situ biostimulation experiment at Rifle, Colorado, U.S.A.

Bopp CJ 4th, Lundstrom CC, Johnson TM, Sanford RA, Long PE, Williams KH.

Environ Sci Technol. 2010 Aug 1;44(15):5927-33. doi: 10.1021/es100643v.


Irradiation of pediatric high-grade spinal cord tumors.

Tendulkar RD, Pai Panandiker AS, Wu S, Kun LE, Broniscer A, Sanford RA, Merchant TE.

Int J Radiat Oncol Biol Phys. 2010 Dec 1;78(5):1451-6. doi: 10.1016/j.ijrobp.2009.09.071. Epub 2010 Mar 24.


Prevention of growing skull fractures: report of 2 cases.

Sanford RA.

J Neurosurg Pediatr. 2010 Feb;5(2):213-8. doi: 10.3171/2009.9.PEDS09180.


Malignant transformation of irradiated craniopharyngioma in children: report of 2 cases.

Aquilina K, Merchant TE, Rodriguez-Galindo C, Ellison DW, Sanford RA, Boop FA.

J Neurosurg Pediatr. 2010 Feb;5(2):155-61. doi: 10.3171/2009.9.PEDS09257.


Unique ecophysiology among U(VI)-reducing bacteria as revealed by evaluation of oxygen metabolism in Anaeromyxobacter dehalogenans strain 2CP-C.

Thomas SH, Sanford RA, Amos BK, Leigh MB, Cardenas E, Löffler FE.

Appl Environ Microbiol. 2010 Jan;76(1):176-83. doi: 10.1128/AEM.01854-09. Epub 2009 Nov 6.


Chiari I malformation after cranial radiation therapy in childhood: a dynamic process associated with changes in clival growth.

Aquilina K, Merchant TE, Boop FA, Sanford RA.

Childs Nerv Syst. 2009 Nov;25(11):1429-36. doi: 10.1007/s00381-009-0982-8.


Phase II trial of conformal radiation therapy for pediatric low-grade glioma.

Merchant TE, Kun LE, Wu S, Xiong X, Sanford RA, Boop FA.

J Clin Oncol. 2009 Aug 1;27(22):3598-604. doi: 10.1200/JCO.2008.20.9494. Epub 2009 Jul 6.

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