2022

• Ren H., E. Cromwell, B.S. Kravitz, and X. Chen. 2022. "Technical note: Using Long Short-term Memory Models to Fill Data Gaps in Hydrological Monitoring Networks." Hydrology and Earth System Sciences. PNNL-SA-161724. doi:10.5194/hess-26-1727-2022
• Ward A.S., A.I. Packman, S. Bernal Berenguer, N. Brekenfeld, J. Drummond, E.B. Graham, and D. Hannah, et al. 2022. "Advancing river corridor science beyond disciplinary boundaries with an inductive approach to hypothesis generation." Hydrological Processes. PNNL-SA-162331.

• Dwivedi D., C.I. Steefel, B. Arora, J.F. Banfield, J.R. Bargar, J.R. Bargar, and M.I. Boyanov, et al. 2022. "From Legacy Contamination to Watershed Systems Science: A Review of Scientific Insights and Technologies Developed through DOE-Supported Research in Water and Energy Security." Environmental Research Letters 17, no. 4:043004. PNNL-SA-161347. doi:10.1088/1748-9326/ac59a9

• Hammond G.E. 2022. "The PFLOTRAN Reaction Sandbox." Geoscientific Model Development 15, no. 4:1659-1676. PNNL-SA-165556. doi:10.1016/j.jma.2021.06.004

• Rubinstein R.L., M. Borton, H. Zhou, M. Shaffer, D.W. Hoyt, J.C. Stegen, and C. Henry, et al. 2022. "ORT: A workflow linking genome-scale metabolic models with reactive transport codes." Bioinformatics 38, no. 3:778-784. PNNL-SA-160676. doi:10.1093/bioinformatics/btab753

2021

• Sengupta A., T. Volkmann, R.E. Danczak, J.C. Stegen, K. Dontsova, N. Abramson, and A. Bugaj, et al. 2021. "Contrasting community assembly forces drive microbial structural and functional responses to precipitation in an incipient soil system." Frontiers in Microbiology 12. PNNL-SA-166658. doi:10.3389/fmicb.2021.754698

• He X., S.V. Apte, S. Karra, and O.N. Dogan. 2021. "A LES Study of Secondary Motion and Wall Shear Stresses in a Pipe Bend." Physics of Fluids 33, no. 11:Art. No. 115102. PNNL-SA-165081. doi:10.1063/5.0065338

• Hou Z., H. Ren, C.J. Murray, X. Song, Y. Fang, E.V. Arntzen, and X. Chen, et al. 2021. "A Novel Construct for Scaling Groundwater-River Interactions Based on Machine-Guided Hydromorphic Classification." Environmental Research Letters 16, no. 10:104016. PNNL-SA-151112. doi:10.1088/1748-9326/ac24ce

• Danczak R.E., A.E. Goldman, R.K. Chu, J.G. Toyoda, V.A. Garayburu-Caruso, N. Tolic, and E.B. Graham, et al. 2021. "Ecological theory applied to environmental metabolomes reveals compositional divergence despite conserved molecular properties." Science of the Total Environment 788. PNNL-SA-156110. doi:10.1016/j.scitotenv.2021.147409

• Song X., Y. Fang, J. Bao, H. Ren, Z. Duan, W.A. Perkins, and H. Zhou, et al. 2021. "Scale-dependent spatial variabilities of hydrological exchange flows and transit time in a large regulated river." Journal of Hydrology 598. PNNL-SA-152146. doi:10.1016/j.jhydrol.2021.126283

• Dove N.C., A.M. Veach, W. Muchero, T. Wahl, J.C. Stegen, C.W. Schadt, and M. Cregger. 2021. "Assembly of the Populus microbiome is temporally dynamic and determined by selective and stochastic factors." mSphere 6, no. 3:e01316-20. PNNL-SA-158824. doi:10.1128/mSphere.01316-20

• Chu H., X.R. Luo, Z. Ouyang, W.S. Chan, S. Dengel, S. Biraud, and M.S. Torn, et al. 2021. "Representativeness of Eddy-Covariance flux footprints for areas surrounding AmeriFlux sites." Agricultural and Forest Meteorology 301. PNNL-SA-157254. doi:10.1016/j.agrformet.2021.108350

• Dwivedi D., S.E. Godsey, and T.D. Scheibe. 2021. "Editorial: Linking hydrological and biogeochemical processes in riparian corridors." Frontiers in Water 3. PNNL-SA-161453. doi:10.3389/frwa.2021.693763

• Xiao Y., J.M. Sloan, C. Hepworth, C.P. Osborne, A.J. Flemming, X. Chen, and X. Zhu. 2021. "Estimating uncertainty: A Bayesian approach to modelling photosynthesis in C3 leaves." Plant, Cell & Environment 44, no. 5:1436-1450. PNNL-SA-161702. doi:10.1111/pce.13995

• Missik J.E., H. Liu, Z. Gao, M. Huang, X. Chen, E.V. Arntzen, and D.P. McFarland, et al. 2021. "Groundwater regulates interannual variations in evapotranspiration in a riparian semiarid ecosystem." Journal of Geophysical Research: Atmospheres 126, no. 7:Article No. e2020JD033078. PNNL-SA-153611. doi:10.1029/2020jd033078

• Ren H., X. Song, Y. Fang, Z. Hou, and T.D. Scheibe. 2021. "Machine Learning Analysis of Hydrologic Exchange Flows and Transit Time Distributions in a Large Regulated River." Frontiers in Artificial Intelligence 4. PNNL-SA-158855. doi:10.3389/frai.2021.648071

• Conner A., M. Gooseff, X. Chen, E.V. Arntzen, and V.A. Garayburu-Caruso. 2021. "Groundwater Inflows to the Columbia River Along the Hanford Reach and Associated Nitrate Concentrations." Frontiers in Water 3. PNNL-SA-161403. doi:10.3389/frwa.2021.574684

• Zhang Y., D. Zhou, W. Wei, J.M. Frame, H. Sun, A. Sun, and X. Chen. 2021. "Hierarchical Fractional Advection-Dispersion Equation (FADE) to Quantify Anomalous Transport in River Corridor over a Broad Spectrum of Scales: Theory and Applications." Mathematics 9, no. 7:790. PNNL-SA-160334. doi:10.3390/math9070790

• Nayfach S., S. Roux, R. Seshadri, D. Udwary, N. Varghese, F. Schulz, and D. Wu, et al. 2021. "A genomic catalog of Earth‚Äôs microbiomes." Nature Biotechnology 39, no. 4:499‚Äì509. PNNL-SA-150672. doi:10.1038/s41587-020-0718-6

• Damerow J., C. Varadharajan, K.E. Boye, E.L. Brodie, M. Burrus, D. Chadwick, and R. Crystal-Ornelas, et al. 2021. "Sample identifiers and metadata to support data management and reuse in  multidisciplinary ecosystem sciences." Data Science Journal 20, no. 1:Article No. 11. PNNL-SA-158301. doi:10.5334/dsj-2021-011

• Graham E.B., C. Averill, B. Bond-Lamberty, J.E. Knelman, S. Krause, A.L. Peralta, and A. Shade, et al. 2021. "Toward a generalizable framework of disturbance ecology through crowdsourced science." Frontiers in Ecology and Evolution 9. PNNL-SA-151971. doi:10.3389/fevo.2021.588940

• Wu R., X. Chen, G.E. Hammond, G. Bisht, X. Song, M. Huang, and G. Niu, et al. 2021. "Coupling Surface Flow with High-performance Subsurface Reactive Flow and Transport Code PFLOTRAN." Environmental Modelling & Software 137. PNNL-SA-156109. doi:10.1016/j.envsoft.2021.104959

• Zhu B., M. Huang, Y. Cheng, X. Xie, Y. Liu, G. Bisht, and X. Chen. 2021. "Impact of vegetation physiology and phenology on watershed hydrology in a semiarid watershed in the Pacific Northwest in a changing climate." Water Resources Research 57, no. 3:e2020WR028394. PNNL-SA-154491. doi:10.1029/2020WR028394

• Song H., J.C. Stegen, E.B. Graham, and T.D. Scheibe. 2021. "Historical Contingency in Microbial Resilience to Hydrologic Perturbations." Frontiers in Water 3. PNNL-SA-156061. doi:10.3389/frwa.2021.590378

• Fudyma J.D., R.K. Chu, N. Grachet, J.C. Stegen, and M.M. Tfaily. 2021. "Coupled biotic-abiotic processes control biogeochemical cycling of dissolved organic matter in the Columbia River hyporheic zone." Frontiers in Water 2. PNNL-SA-158822. doi:10.3389/frwa.2020.574692

• Liu W., E.B. Graham, Y. Dong, L. Zhong, J. Zhang, C. Qiu, and R. Chen, et al. 2021. "Balanced stochastic versus deterministic assembly processes benefit diverse yet uneven ecosystem functions in representative agroecosystems." Environmental Microbiology 23, no. 1:391-404. PNNL-SA-157815. doi:10.1111/1462-2920.15326

2020

• Garayburu-Caruso V.A., R.E. Danczak, J.C. Stegen, L. Renteria, M.L. McCall, A.E. Goldman, and R.K. Chu, et al. 2020. "Using Community Science to Reveal the Global Chemogeography of River Metabolomes." Metabolites 10, no. 12:518. PNNL-SA-157277. doi:10.3390/metabo10120518
• Danczak R.E., R.K. Chu, S.J. Fansler, A.E. Goldman, E.B. Graham, M.M. Tfaily, and J.G. Toyoda, et al. 2020. "Using metacommunity ecology to understand environmental metabolomes." Nature Communications 11, no. 1:Article No. 6369. PNNL-SA-152827. doi:10.1038/s41467-020-19989-y
• Ahmmed B., M. Mudunuru, S. Karra, S.C. James, H. Viswanathan, and J. Dunbar. 2020. "PFLOTRAN-SIP: A PFLOTRAN Module for Simulating Spectral-induced Polarization of Electrical Impedance Data." Energies 13, no. 24:6552. PNNL-SA-157259. doi:10.3390/en13246552

• Chen X., J.M. Zachara, V.R. Vermeul, G. Hammond, M.D. Freshley, and Y. Fang. 2020. "Understanding Contaminant Migration within a Dynamic River Corridor through Field Experiments and Reactive Transport Modeling." Frontiers in Water 2. PNNL-SA-151389. doi:10.3389/frwa.2020.533796

• Ren H., Z. Hou, Z. Duan, X. Song, W.A. Perkins, M.C. Richmond, and E.V. Arntzen, et al. 2020. "Spatial Mapping of Riverbed Grain-size Distribution Using Machine Learning." Frontiers in Water 2. PNNL-SA-151819. doi:10.3389/frwa.2020.551627

• Rizzo C., X. Song, F. De Barros, and X. Chen. 2020. "Temporal flow variations interact with spatial physical heterogeneity to impact solute transport in managed river corridors." Journal of Contaminant Hydrology 235. PNNL-SA-153233. doi:10.1016/j.jconhyd.2020.103713

• Fang Y., X. Song, H. Ren, W.A. Perkins, P. Shuai, M.C. Richmond, and Z. Hou, et al. 2020. "High-performance simulation of dynamic hydrologic exchange and implications for surrogate flow and reactive transport modeling in a large river corridor." Frontiers in Water 2. PNNL-SA-153319. doi:10.3389/frwa.2020.564211

• Song H., J.C. Stegen, E.B. Graham, J. Lee, V.A. Garayburu-Caruso, W.C. Nelson, and X. Chen, et al. 2020. "Representing Organic Matter Thermodynamics in Biogeochemical Reactions via Substrate-Explicit Modeling." Frontiers in Microbiology 11. PNNL-SA-151734. doi:10.3389/fmicb.2020.531756

• Danczak RE, RA Daly, MA Borton, JC Stegen, S Roux, KC Wrighton, and MJ Wilkins. (2020) “Ecological assembly processes are coordinated between bacterial and viral communities in fractured shale ecosystems.” Msystems, 5, e00098-00020; doi: 10.1128/mSystems.00098-20.
• Ji M, W Kong, J Stegen, L Yue, F Wang, X Dong, DA Cowan, and BC Ferrari. (2020) “Distinct assembly mechanisms underlie similar biogeographical patterns of rare and abundant bacteria in Tibetan Plateau grassland soils.” Environmental Microbiology, 22, 2261-2272; doi: 10.1111/1462-2920.14993.
• Liu W, EB Graham, L Zhong, J Zhang, S Li, X Lin, and Y Feng. (2020) “Long-term stochasticity combines with short-term variability in assembly processes to underlie rice paddy sustainability.” Frontiers in Microbiology, 11, 873; doi: 10.3389/fmicb.2020.00873.
• Liu W, EB Graham, L Zhong, J Zhang, W Li, Z Li, X Lin, Y Feng, and J Wang. (2020) “Dynamic microbial assembly processes correspond to soil fertility in sustainable paddy agroecosystems.” Functional Ecology, 34, 1244-1256; doi: 10.1111/1365-2435.13550.
• Graham EB and S Krause. (2020) “Social media sows consensus in disturbance ecology.” Nature, 577, 170; doi: 10.1038/d41586-020-00006-7 download data.

• Kruegler J, J Gomez-Velez, LK Lautz, and TA Endreny. (2020) “Dynamic evapotranspiration alters hyporheic flow and residence times in the intrameander zone.” Water, 12, 424; doi: 10.3390/w12020424 download data.
• Li B, X Liu, MH Kaufman, A Turetcaia, X Chen, and MB Cardenas. (2020) “Flexible and modular simultaneous modeling of flow and reactive transport in rivers and hyporheic zones.” Water Resources Research, 56; doi: 10.1029/2019wr026528download data.
• Nelson WC, EB Graham, AR Crump, SJ Fansler, EV Arntzen, DW Kennedy, and JC Stegen. (2020) “Distinct temporal diversity profiles for nitrogen cycling genes in a hyporheic microbiome.” PLoS ONE, 15, e0228165; doi: 10.1371/journal.pone.0228165 download data.
• Villa JA, GJ Smith, Y Ju, L Renteria, JC Angle, E Arntzen, SF Harding, H Ren, X Chen, AH Sawyer, EB Graham, JC Stegen, KC Wrighton, and G Bohrer. (2020) “Methane and nitrous oxide porewater concentrations and surface fluxes of a egulatedr river.” Science of The Total Environment, 715, 136920; doi: 10.1016/j.scitotenv.2020.136920. download data.
• Wang JJ, P Legendre, J Soininen, CF Yeh, E Graham, JC Stegen, EO Casamayor, JZ Zhou, J Shen, and FY Pan. (2020) “Temperature drives local contributions to beta diversity in mountain streams: Stochastic and deterministic processes.” Global Ecology and Biogeography, 29, 420-432; doi: 10.1111/geb.13035 Front cover download data.
• Wu L, JD Gomez-Velez, S Krause, T Singh, A Wörman, and J Lewandowski. (2020) “Impact of flow alteration and temperature variability on hyporheic exchange.” Water Resources Research, 56; doi: 10.1029/2019wr026225 download data.
• Yao J, H Liu, J Huang, Z Gao, G Wang, D Li, H Yu, and X Chen. (2020) “Accelerated dryland expansion regulates future variability in dryland gross primary production.” Nature Communications, 11, 1665; doi: 10.1038/s41467-020-15515-2download data.
• Zachara JM, X Chen, X Song, P Shuai, C Murray, and CT Resch. (2020) “Kilometer-scale hydrologic exchange flows in a gravel bed river corridor and their implications to solute migration.” Water Resources Research, 56, e2019WR02525; doi: 10.1029/2019wr025258 download data.
• Garayburu-Caruso VA, et al., “Carbon Limitation Leads to Thermodynamic Regulation of Aerobic Metabolism.” Environmental Science & Technology Letters 7, 517-524 (2020). [DOI: 10.1021/acs.estlett.0c00258]

2019

• Dai H, X Chen, M Ye, X Song, G Hammond, BX Hu, and J Zachara. (2019) “Using Bayesian networks for sensitivity analysis of complex biogeochemical models.” Water Resources Research, 55; doi: 10.1029/2018WR023589 download data.
• Gao Z, H Liu, J Missik, J Yao, M Huang, X Chen, E Arntzen, and D Mcfarland. (2019) “Mechanistic links between underestimated CO₂ fluxes and non-closure of the surface energy balance in a semi-arid sagebrush ecosystem.” Environmental Research Letters, 14, 044016; doi: 10.1088/1748-9326/ab082d download data.
• Graham EB, JC Stegen, M Huang, X Chen, and TD Scheibe. (2019) “Subsurface biogeochemistry is a missing link between ecology and hydrology in dam-impacted river corridors.” Science of The Total Environment, 657, 435-445; doi: 10.1016/j.scitotenv.2018.11.414 download data.
• Hou Z, TD Scheibe, CJ Murray, WA Perkins, EV Arntzen, H Ren, RD Mackley, and MC Richmond. (2019) “Identification and mapping of riverbed sediment facies in the Columbia River through integration of field observations and numerical simulations.” Hydrological Processes, 33, 1245-1259; doi: 10.1002/hyp.13396 download data.
• Knelman JE, SK Schmidt, VA Garayburu-Caruso, K Swatantar, and E Graham. (2019) “Multiple, compounding disturbances in a forest ecosystem: Fire increases susceptibility to extreme precipitation event.” Soil Systems, 3, 40; doi: 10.3390/soilsystems3020040 download data.
• Meile C and TD Scheibe. (2019) “Reactive transport modeling of microbial dynamics.” Elements, 15, 111-116; doi: 10.2138/gselements.15.2.111 download data.
• Missik JEC, HP Liu, ZM Gao, MY Huang, XY Chen, E Arntzen, DP Mcfarland, HY Ren, PS Titzler, JN Thomle, and A Goldman. (2019) “Groundwater-river water exchange enhances growing season evapotranspiration and carbon uptake in a semiarid riparian ecosystem.” Journal of Geophysical Research-Biogeosciences, 124, 99-114; doi: 10.1029/2018jg004666 download data.
• Scott DT, JD Gomez-Velez, CN Jones, and JW Harvey. (2019) “Floodplain inundation spectrum across the United States.” Nature Communications, 10, 5194; doi: 10.1038/s41467-019-13184-4 download data.
• Sengupta A, J Stegen, A Neto, Y Wang, J Neilson, J Chorover, PA Troch, and RM Maier. (2019) “Assessing microbial community patterns during incipient soil formation from basalt.” Journal of Geophysical Research: Biogeosciences, 124; doi: 10.1029/2017JG004315 download data.
• Shuai P, X Chen, X Song, GE Hammond, J Zachara, P Royer, H Ren, WA Perkins, MC Richmond, and M Huang . (2019) “Dam operations and subsurface hydrogeology control dynamics of hydrologic exchange flows in a regulated river reach.” Water Resources Research, 55; doi: 10.1029/2018wr024193 download data.
• Singh T, L Wu, JD Gomez-Velez, J Lewandowski, DM Hannah, and S Krause. (2019) “Dynamic hyporheic zones: exploring the role of peak flow events on bedform-induced hyporheic exchange.” Water Resources Research, 55, 218-235; doi: 10.1029/2018wr022993 download data.
• Song HS, JY Lee, S Haruta, WC Nelson, DY Lee, SR Lindemann, JK Fredrickson, and HC Bernstein. (2019) “Minimal Interspecies Interaction Adjustment (MIIA): Inference of neighbor-dependent interactions in microbial communities.” Frontiers in Microbiology, 10, 1264; doi: 10.3389/fmicb.2019.01264.
• Song X, X Chen, M Ye, Z Dai, G Hammond, and JM Zachara. (2019) “Delineating facies spatial distribution by integrating ensemble data assimilation and indicator geostatistics with level-set transformation.” Water Resources Research, 55; doi: 10.1029/2018wr023262 download data.
• Ward AS, SM Wondzell, NM Schmadel, S Herzog, JP Zarnetske, V Baranov, PJ Blaen, N Brekenfeld, R Chu, R Derelle, J Drummond, JH Fleckenstein, V Garayburu-Caruso, E Graham, D Hannah, CJ Harman, J Hixson, JLA Knapp, S Krause, MJ Kurz, J Lewandowski, AG Li, E Marti, M Miller, AM Milner, K Neil, L Orsini, AI Packman, S Plont, L Renteria, K Roche, T Royer, C Segura, J Stegen, J Toyoda, J Wells, and NI Wisnoski. (2019) “Spatial and temporal variation in river corridor exchange across a 5th-order mountain stream network.” Hydrology and Earth System Sciences, 23, 5199-5225; doi: 10.5194/hess-23-5199-2019 download data.
• Ward AS, JP Zarnetske, V Baranov, PJ Blaen, N Brekenfeld, R Chu, R Derelle, J Drummond, JH Fleckenstein, V Garayburu-Caruso, E Graham, D Hannah, CJ Harman, S Herzog, J Hixson, JLA Knapp, S Krause, MJ Kurz, J Lewandowski, A Li, E Martí, M Miller, AM Milner, K Neil, L Orsini, AI Packman, S Plont, L Renteria, K Roche, T Royer, NM Schmadel, C Segura, J Stegen, J Toyoda, J Wells, NI Wisnoski, and SM Wondzell. (2019) “Co-located contemporaneous mapping of morphological, hydrological, chemical, and biological conditions in a 5th-order mountain stream network, Oregon, USA.” Earth System Science Data, 11, 1567-1581; doi: 10.5194/essd-11-1567-2019 download data.

2018

• Bao J, T Zhou, MY Huang, ZS Hou, W Perkins, S Harding, S Titzler, G Hammond, HY Ren, P Thorne, S Suffield, C Murray, and J Zachara. (2018) “Modulating factors of hydrologic exchanges in a large-scale river reach: Insights from three-dimensional computational fluid dynamics simulations.” Hydrological Processes, 32, 3446-3463; doi: 10.1002/hyp.13266download data.
• Feng Y, R Chen, JC Stegen, Z Guo, J Zhang, Z Li, and X Lin. (2018) “Two key features influencing community assembly processes at regional scale: Initial state and degree of change in environmental conditions.” Molecular Ecology, 27, 5238-5251; doi: 10.1111/mec.14914 download data.
• Gao M, H-Y Li, D Liu, J Tang, X Chen, X Chen, G Blöschl, and RL Leung. (2018) “Identifying the dominant controls on macropore flow velocity in soils: A meta-analysis.” Journal of Hydrology, 567, 590-604; doi: 10.1016/j.jhydrol.2018.10.044download data.
• Graham E, A Crump, D Kennedy, E Arntzen, S Fansler, SO Purvine, C Nicora, W Nelson, M Tfaily, and J Stegen. (2018) “Multi-omics comparison reveals metabolome biochemistry, not microbiome composition or gene expression, corresponds to elevated biogeochemical function in the hyporheic zone.” Science of the Total Environment, 642, 742-753; doi: 10.1016/j.scitotenv.2018.05.256 download data.
• Graham EB, RS Gabor, S Schooler, DM McKnight, DR Nemergut, and JE Knelman. (2018) “Oligotrophic wetland sediments susceptible to shifts in microbiomes and mercury cycling with dissolved organic matter addition.” PeerJ, 6, e4575; doi: 10.7717/peerj.4575 download data.
• Grant SB, JD Gomez-Velez, and M Ghisalberti. (2018) “Modeling the effects of turbulence on hyporheic exchange and local-to-global nutrient processing in streams.” Water Resources Research, 54; doi: 10.1029/2018WR023078 download data.
• Hall EK, ES Bernhard, RL Bier, MA Bradford, CM Boot, JB Cotner, PA del Giorgio, SE Evans, EB Graham, SE Jones, JT Lennon, KJ Locey, D Nemergut, BB Osborne, JD Rocca, JS Schimel, MP Waldrop, and MW Wallenstein. (2018) “Understanding how microbiomes influence the systems they inhabit.” Nature Microbiology, 3, 977-982; doi: 10.1038/s41564-018-0201-z download data.
• Harvey J, J Gomez-Velez, N Schmadel, D Scott, E Boyer, R Alexander, K Eng, H Golden, A Kettner, C Konrad, R Moore, J Pizzuto, G Schwarz, C Soulsby, and J Choi. (2018) “How hydrologic connectivity regulates water quality in river corridors.” JAWRA Journal of the American Water Resources Association, 1-13; doi: 10.1111/1752-1688.12691 download data.
• Korneev SV, X Yang, JM Zachara, TD Scheibe, and I Battiato. (2018) “Downscaling-based segmentation for unresolved images of highly heterogeneous granular porous samples.” Water Resources Research, 54, 2871-2890; doi: 10.1002/2018wr022886 download data.
• Mays DC and TD Scheibe. (2018) “Groundwater contamination, subsurface processes, and remediation methods: Overview of the special issue of water on groundwater contamination and remediation.” Water, 10, 1708; doi: 10.3390/w10121708 download data.
• Meile C and TD Scheibe. (2018) “Reactive transport modeling and biogeochemical cycling.” In Reactive Transport Modeling: Applications in Subsurface Energy and Environmental Problems, Y Xiao, F Whitaker, T Xu, and C Steefel (Eds.), Chapter 10, Wiley Press, 485-510. download data.
• Song X, X Chen, J Stegen, G Hammond, H Song, H Dai, EB Graham, and J Zachara. (2018) “Drought conditions maximize the impact of high-frequency flow variations on thermal regimes and biogeochemical function in the hyporheic zone.” Water Resources Research, 54; doi: 10.1029/2018WR022586 download data.
• Stegen J. (2018) “At the nexus of history, ecology, and hydrobiogeochemistry: Improved predictions across scales through integration.” mSystems, 3, e00167-00117; doi: 10.1128/mSystems.00167-17 download data.
• Stegen J, E Bottos, and J Jansson. (2018) “A unified conceptual framework for prediction and control of microbiomes.” Current Opinion in Microbiology, 44, 20-27; doi: 10.1016/j.mib.2018.06.002 download data.
• Stegen J and A Goldman. (2018) “WHONDRS: A community resource for studying dynamic river corridors.” mSystems, 3, e00151-00118; doi: 10.1128/mSystems.00151-18 download data.
• Stegen J, T Johnson, J Fredrickson, MJ Wilkins, A Konopka, WC Nelson, E Arntzen, WB Chrisler, RK Chu, S Fansler, E Graham, D Kennedy, CT Resch, M Tfaily, and JM Zachara. (2018) “Influences of organic carbon speciation on hyporheic corridor biogeochemistry and microbial ecology.” Nature Communications, 9(1) doi: 10.1038/s41467-018-02922-9download data.
• Stern N, J Mejia, SM He, Y Yang, M Ginder-Vogel, and EE Roden. (2018) “Dual role of humic substances as electron donor and shuttle for dissimilatory iron reduction.” Environmental Science & Technology, 52, 5691-5699; doi: 10.1021/acs.est.7b06574 download data.
• Wang C, JD Gomez-Velez, and JL Wilson. (2018) “The importance of capturing topographic features for modeling groundwater flow and transport in mountainous watersheds.” Water Resources Research, 54, 10,313-310,338; doi: 10.1029/2018WR023863 download data.
• Wu L, T Singh, J Gomez-Velez, G Nützmann, A Wörman, S Krause, and J Lewandowski. (2018) “Impact of dynamically changing discharge on hyporheic exchange processes under gaining and losing groundwater conditions.” Water Resources Research, 54, 10,076-010,093; doi: 10.1029/2018wr023185 download data.
• Xu F, Y Liu, and C Liu. (2018) “A generalized-rate model for describing and scaling redox kinetics in sediments containing variable redox-reactive materials.” Environmental Science & Technology, 52, 5268-5276; doi: 10.1021/acs.est.7b06354download data.
• Yan A, C Liu, Y Liu, and F Xu. (2018) “Effect of ion exchange on the rate of aerobic microbial oxidation of ammonium in hyporheic zone sediments.” Environmental Science and Pollution Research, 25, 8880-8887; doi: 10.1007/s11356-018-1217-xdownload data.
• Yang C, YK Zhang, YY Liu, XF Yang, and CX Liu. (2018) “Model-based analysis of the effects of dam-induced river water and groundwater interactions on hydro-biogeochemical transformation of redox sensitive contaminants in a hyporheic zone.” Water Resources Research, 54, 5973-5985; doi: 10.1029/2018wr023286 download data.
• Yang QC, JE Almendinger, XS Zhang, MY Huang, XY Chen, GY Leng, YY Zhou, KG Zhao, GR Asrar, R Srinivasan, and X Li. (2018) “Enhancing SWAT simulation of forest ecosystems for water resource assessment: A case study in the St. Croix River basin.” Ecological Engineering, 120, 422-431; doi: 10.1016/j.ecoleng.2018.06.020 download data.
• Zhou T, J Bao, M Huang, Z Hou, E Arntzen, X Song, S Harding, S Titzler, C Murray, W Perkins, X Chen, J Stegen, G Hammond, J Thorne, and J Zachara. (2018) “Riverbed hydrologic exchange dynamics in a large regulated river reach.” Water Resources Research, 54; doi: 10.1002/2017WR020508 download data.

2017

• Bisht G, M Huang, T Zhou, X Chen, H Dai, G Hammond, W Riley, J Downs, Y Liu, and J Zachara. (2017) “Coupling a three-dimensional subsurface flow and transport model with a land surface model to simulatestream-aquifer-land interactions (CP v1.0).” Geoscientific Model Development, 10, 4539-4562, doi: 10.5194/gmd-10-4539-2017 download data.
• Dai H, M Ye, AP Walker, and X Chen. (2017) “A new process sensitivity index to identify important system processes under process model and parametric uncertainty.” Water Resources Research, 53(4): 3476-3490, doi: 10.1002/2016WR019715download data.
• Dai H, X Chen, M Ye, X Song, and J Zachara. (2017) “A geostatistics informed hierarchical sensitivity analysis method for complex groundwater flow and transport modeling.” Water Resources Research, 53(5): 4327-4343, doi: 10.1002/2016WR019756 download data.
• Gao Z, ES Russell, JEC Missik, M Huang, X Chen, CE Strickland, R Clayton, E Arntzen, Y Ma, and H Liu.* (2017) “A novel approach to evaluate soil heat flux calculation: An analytical review of nine methods.” Journal of Geophysical Research - Atmospheres, 122, doi: 10.1002/2017JD027160 download data.
• Goldman AE, EB Graham, AR Crump, DW Kennedy, EB Romero, CG Anderson, KL Dana, CT Resch, JK Fredrickson, and JC Stegen. (2017), “Biogeochemical cycling at the aquatic-terrestrial interface is linked to parafluvial hyporheic zone inundation history.” Biogeosciences, 14, 4229-4241, doi: 10.5194/bg-14-4229-2017 download data.
• Graham, EB, AR Crump, CT Resch, S Fansler, E Arntzen, DW Kennedy, JK Fredrickson, and JC Stegen. (2017), “Deterministic influences exceed dispersal effects on hydrologically-connected microbiomes.” Environ Microbiol, 19: 1552-1567. doi: 10.1111/1462-2920.13720 download data.
• Graham E and J Stegen. (2017) “Dispersal-based microbial community assembly decreases biogeochemical function.” Processes, 5, 65, doi: 10.3390/pr5040065 download data.
• Graham EB, M Tfaily, AR Crump, A Goldman, L Bramer, E Arntzen, E Romero, CT Resch, D Kennedy, and J Stegen. (2017) “Carbon inputs from riparian vegetation limit oxidation of physically bound organic carbon via biochemical and thermodynamic processes.” JGR Biogeosciences, 122, 3188-3205; doi: 10.1101/105486 download data.
• Hou Z, WC Nelson, J Stegen, E Arntzen, C Murray, AR Crump, TD Scheibe, J Fredrickson, and J Zachara. (2017) “Geochemical and microbial community attributes in relation to hyporheic zone geological facies.” Scientific Reports, 7, 12006, doi:10.1038/s41598-017-12275-w download data.
• Jiao Y, H Lei, D Yang, M Huang, D Liu, and X Yuan. (2017) “Impact of vegetation dynamics on hydrological processes in a semi-arid basin using a land surface-hydrology coupled model.” Journal of Hydrology, 551:116-131, doi:10.1029/2006WR005588.
• Johnson T, GE Hammond, and X Chen. (2017) “PFLOTRAN-E4D: A parallel open source PFLOTRAN module for simulating time-lapse electrical resistivity data.” Computers and Geosciences, 99, 72-80; doi:10.1016/j.cageo.2016.09.006 download data.
• Johnson T and J Thomle. (2017) “3-D decoupled inversion of complex conductivity data in the real number domain.” Geophysical Journal International, 212, 284-296, doi: 10.1093/gji/ggx416 download data.
• Li L, K Maher, A Navarre-Sitchler, J Druhan, C Meile, C Lawrence, J Moore, J Perdrial, P Sullivan, A Thompson, L Jin, EW Bolton, SL Brantley, WE Dietrich, KU Mayer, CI Steefel, A Valocchi, J Zachara. B, Kocar, J McIntosh, BM Tutolo, M Kumar, E Sonnenthal, C Bao, and J Beisman. (2017) “Expanding the role of reactive transport models in critical zone processes.” Earth-Science Reviews, 165, 280-301; doi: 10.1016/j.earscirev.2016.09.001 download data.
• Li M, Y Gao, WJ Qian, L Shi, Y Liu, WC Nelson, CD Nicora, CT Resch, C Thompson, S Yan, JK Fredrickson, JM Zachara, and C Liu. (2017) “Targeted quantification of functional enzyme dynamics in environmental samples for microbially mediated biogeochemical processes.” Environmental Microbiology Reports, 9, 512-521; doi: 10.1111/1758-2229.12558 download data.
• Li M, WJ Qian, Y Gao, L Shi, and C Liu. (2017) “Functional enzyme-based approach for linking microbial community functions with biogeochemical process kinetics.” Environmental Science & Technology," 51, 11848-11857; doi: 10.1021/acs.est.7b03158 download data.
• Ling B, J Bao, M Oostrom, I Battiato, and AM Tartakovsky. (2017) “Modeling variability in porescale multiphase flow experiments.” Advances in Water Resources, 105: 29-38, doi: 10.1016/j.advwatres.2017.04.005 download data.
• Liu C, M Yao, J Stegen, J Rui, J Li, and X Li. (2017) “Long-term nitrogen addition affects the phylogenetic turnover of soil microbial community responding to moisture pulse.” Scientific Reports, 7, 17492;doi: 10.1038/s41598-017-17736-w 1download data.
• Liu Y, F Xu ,and C Liu. (2017) “Coupled hydro-biogeochemical processes controlling Cr reductive immobilization in Columbia River hyporheic zone.” Environmental Science & Technology, 51(3), 1508-1517, doi: 10.1021/acs.est.6b05099 download data.
• Liu Y, C Liu, WC Nelson, L Shi. F, Xu, YD Liu, A Yan, LR Zhong, C Thompson, J Fredrickson, and J Zachara. (2017) “Effect of water chemistry and hydrodynamics on nitrogen transformation and microbial community functional potential in hyporheic zone sediment columns.” Environmental Science & Technology, 51(9): 4877-4886, doi: 10.1021/acs.est.6b05018download data.
• Miller BL, EV Arntzen, A Goldman, and MC Richmond. (2017) “Methane ebullition in temperate hydropower reservoirs and implications for U.S. policy on greenhouse gas emissions.” Environmental Management, 56, 1-15; doi: 10.1007/s00267-017-0909-1 download data.
• Percak-Dennett E, S He, B Converse, H Konishi, H Xu, A Corcoran, D Noguera, C Chan, A Bhattacharyya, T Borch, E Boyd, and EE Roden. (2017) “Microbial acceleration of aerobic pyrite oxidation at circumneutral pH.” Geobiology, 15, 690-703; DOI: 10.1111/gbi.12241 download data.
• Qafoku O, CI Pearce, A Neumann, L Kovarik, M Zhu, ES Ilton, ME Bowden, CT Resch, BW Arey, E Arenholz, AR Felmy, and KM Rosso. (2017) “Tc(VII) and Cr(VI) interaction with naturally reduced ferruginous smectite from a redox transition zone.” Environmental Science & Technology, 51, 9042-9052; doi: 10.1021/acs.est.7b02191 download data.
• Renslow R, B Ahmed, JR Nunez, B Cao, PD Majors, JK Fredrickson, and H Beyenal. (2017) “Modeling substrate utilization, metabolite production, and uranium immobilization in Shewanella oneidensis biofilms.” Frontiers in Environmental Science, 50: 30, doi: 10.3389/fenvs.2017.00030 download data.
• Song H-S, N Goldberg, A Mahajan, and D Ramkrishna. (2017) “Sequential computation of elementary modes and minimal cut sets in genome-scale metabolic networks using alternate integer linear programming.” Bioinformatics, 33, 2345-2353; DOI: 10.1093/bioinformatics/btx171 download data.
• Song H-S, D Thomas, J Stegen, M Li, C Liu, X Song, X Chen, J Fredrickson, J Zachara, and TD Scheibe. (2017) “Regulation-structured dynamic metabolic model provides a potential mechanism for delayed enzyme response in denitrification process.” Frontiers in Microbiology, 8, 1866; DOI: 10.3389/fmicb.2017.01866 download data.
• Stern N, MA Ginder-Vogel, JC Stegen, E Arntzen, D Kennedy, BR Larget, and E Roden. (2017) “Colonization habitat controls biomass, composition, and metabolic activity of attached microbial communities in the Columbia River hyporheic corridor.” Applied Environmental Microbiology, 83, e00260-00217; DOI: 10.1128/AEM.00260-17 download data.
• Tartakovsky AM, M Panzeri, GD Tartakovsky, and A Guadagnini. (2017) “Uncertainty quantification in scale-dependent models of flow in porous media.” Water Resources Research, 53: 9392-9401, doi: 10.1002/2017WR020905 download data.
• Wu T, AM Griffin, CA Gorski, ES Shelobolina, H Xu, RK Kukkadapu, and EE Roden. (2017) “Interactions between Fe(III)-oxides and Fe(III)-phyllosilicates during microbial reduction 2: Natural subsurface sediments.” Geomicrobiology Journal; DOI: 10.1080/01490451.2016.1174758 download data.
• Xia Y, D Mocko, M Huang, M Rodell, KE Mitchell, X Cai, and MB Ek. (2017) “Comparison and assessment of three advanced land surface models in simulating terrestrial water storage components over the United States.” Journal of Hydrometeorology; DOI: 10.1175/JHM-D-16-0112.1 download data.
• Xu F, Y Liu, J Zachara, M Bowden, D Kennedy, AE Plymale, and C Liu. (2017) “Redox transformation and reductive immobilization of Cr(VI) in Columbia River hyporheic zone sediments.” Journal of Hydrology, 555, 278-287; doi: 10.1016/j.jhydrol.2017.10.016 download data.
• Xu Z and AM Tartakovsky. (2017) “Method of model reduction and multifidelity models for solute transport in random layered porous media.” Physical Review E, 96, 033314; doi: 10.1103/PhysRevE.96.033314 download data.
• Yan Q, J Stegen, Y Yu, Y Deng, XB Li, S Wu, L Dai, X Zhang, J Li, C Wang, J Ni, XB Li, H Hu, W Feng, D Ning, Z He, JD Von Nostrand, L Wu, and J Zhou. (2017) “Nearly a decade-long repeatable seasonal diversity patterns of bacterioplankton communities in the eutrophic Lake Donghu (Wuhan, China).” Molecular Ecology, 26(14): 3839-3850, doi: 10.1111/mec.14151 download data.
• Yan Z, C Liu, Y Liu, and VL Bailey. (2017) “Multiscale investigation on biofilm distribution and its impact on macroscopic biogeochemical reaction rates.” Water Resources Research, 53(11): 8698-8714, doi: 10.1002/2017WR020570 download data.
• Yang X, T Varga, C Liu, and TD Scheibe. (2017) “What can we learn from in-soil imaging of a live plant: X-ray computed tomography and 3D numerical simulation of root-soil system.” Rhizosphere, 3(2): 259-262, doi: 10.1016/j.rhisph.2017.04.017download data.
• Zhou T, M Huang, J Bao, Z Hou, E Arntzen, RD Mackley, A Crump, A Goldman, X Song, Y Xu, and J Zachara. (2017) “A new approach to quantify shallow water hydrologic exchanges in a large regulated river reach.” Water 9, 703; DOI: 10.3390/w9090703 download data.