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Prediction of Neighbor-Dependent Microbial Interactions From Limited Population Data.

Lee JY, Haruta S, Kato S, Bernstein HC, Lindemann SR, Lee DY, Fredrickson JK, Song HS.

Front Microbiol. 2020 Jan 21;10:3049. doi: 10.3389/fmicb.2019.03049. eCollection 2019.


Therapeutic challenges in the treatment of systemic inflammatory disease in pregnancy.

Fredrickson JS, Kolfenbach JR, Holmes JL, Cathcart JN, Lynch AM, Palestine AG.

Obstet Med. 2019 Dec;12(4):180-185. doi: 10.1177/1753495X18819929. Epub 2019 Jan 9.


Characterization of TP53 mutations in Pap test DNA of women with and without serous ovarian carcinoma.

Krimmel-Morrison JD, Ghezelayagh TS, Lian S, Zhang Y, Fredrickson J, Nachmanson D, Baker KT, Radke MR, Hun E, Norquist BM, Emond MJ, Swisher EM, Risques RA.

Gynecol Oncol. 2020 Feb;156(2):407-414. doi: 10.1016/j.ygyno.2019.11.124. Epub 2019 Dec 12.


Rapamycin persistently improves cardiac function in aged, male and female mice, even following cessation of treatment.

Quarles E, Basisty N, Chiao YA, Merrihew G, Gu H, Sweetwyne MT, Fredrickson J, Nguyen NH, Razumova M, Kooiker K, Moussavi-Harami F, Regnier M, Quarles C, MacCoss M, Rabinovitch PS.

Aging Cell. 2020 Feb;19(2):e13086. doi: 10.1111/acel.13086. Epub 2019 Dec 10.


Minimal Interspecies Interaction Adjustment (MIIA): Inference of Neighbor-Dependent Interactions in Microbial Communities.

Song HS, Lee JY, Haruta S, Nelson WC, Lee DY, Lindemann SR, Fredrickson JK, Bernstein HC.

Front Microbiol. 2019 Jun 11;10:1264. doi: 10.3389/fmicb.2019.01264. eCollection 2019.


Phase Ib study of the MEK inhibitor cobimetinib (GDC-0973) in combination with the PI3K inhibitor pictilisib (GDC-0941) in patients with advanced solid tumors.

Shapiro GI, LoRusso P, Kwak E, Pandya S, Rudin CM, Kurkjian C, Cleary JM, Pilat MJ, Jones S, de Crespigny A, Fredrickson J, Musib L, Yan Y, Wongchenko M, Hsieh HJ, Gates MR, Chan IT, Bendell J.

Invest New Drugs. 2019 Apr 24. doi: 10.1007/s10637-019-00776-6. [Epub ahead of print]


Correction: 18F-Fluoroestradiol PET/CT Measurement of Estrogen Receptor Suppression during a Phase I Trial of the Novel Estrogen Receptor-Targeted Therapeutic GDC-0810: Using an Imaging Biomarker to Guide Drug Dosage in Subsequent Trials.

Wang Y, Ayres KL, Goldman DA, Dickler MN, Bardia A, Mayer IA, Winer E, Fredrickson J, Arteaga CL, Baselga J, Manning HC, Mahmood U, Ulaner GA.

Clin Cancer Res. 2019 Feb 15;25(4):1435. doi: 10.1158/1078-0432.CCR-18-4266. No abstract available.


Specialty management differences of syphilis and toxoplasmosis surrounding pregnancy: a prospective cross-sectional study.

Fredrickson JS, Holmes J, Cathcart JN, Lynch AM, Kolfenbach JR, Palestine AG.

J Ophthalmic Inflamm Infect. 2018 Jul 3;8(1):10. doi: 10.1186/s12348-018-0152-9.


Phase I study of the anti-α5β1 monoclonal antibody MINT1526A with or without bevacizumab in patients with advanced solid tumors.

Weekes CD, Rosen LS, Capasso A, Wong KM, Ye W, Anderson M, McCall B, Fredrickson J, Wakshull E, Eppler S, Shon-Nguyen Q, Desai R, Huseni M, Hegde PS, Pourmohamad T, Rhee I, Bessudo A.

Cancer Chemother Pharmacol. 2018 Aug;82(2):339-351. doi: 10.1007/s00280-018-3622-8. Epub 2018 Jun 15.


FIR: Efficacy, Safety, and Biomarker Analysis of a Phase II Open-Label Study of Atezolizumab in PD-L1-Selected Patients With NSCLC.

Spigel DR, Chaft JE, Gettinger S, Chao BH, Dirix L, Schmid P, Chow LQM, Hicks RJ, Leon L, Fredrickson J, Kowanetz M, Sandler A, Funke R, Rizvi NA.

J Thorac Oncol. 2018 Nov;13(11):1733-1742. doi: 10.1016/j.jtho.2018.05.004.


The impact of post-traumatic stress disorder symptomatology on quality of life: The sentinel experience of anger, hypervigilance and restricted affect.

Forbes D, Nickerson A, Bryant RA, Creamer M, Silove D, McFarlane AC, Van Hooff M, Phelps A, Felmingham KL, Malhi GS, Steel Z, Fredrickson J, Alkemade N, O'Donnell M.

Aust N Z J Psychiatry. 2019 Apr;53(4):336-349. doi: 10.1177/0004867418772917. Epub 2018 May 4.


Publisher Correction: Influences of organic carbon speciation on hyporheic corridor biogeochemistry and microbial ecology.

Stegen JC, Johnson T, Fredrickson JK, Wilkins MJ, Konopka AE, Nelson WC, Arntzen EV, Chrisler WB, Chu RK, Fansler SJ, Graham EB, Kennedy DW, Resch CT, Tfaily M, Zachara J.

Nat Commun. 2018 Mar 7;9(1):1034. doi: 10.1038/s41467-018-03572-7.


Influences of organic carbon speciation on hyporheic corridor biogeochemistry and microbial ecology.

Stegen JC, Johnson T, Fredrickson JK, Wilkins MJ, Konopka AE, Nelson WC, Arntzen EV, Chrisler WB, Chu RK, Fansler SJ, Graham EB, Kennedy DW, Resch CT, Tfaily M, Zachara J.

Nat Commun. 2018 Feb 8;9(1):585. doi: 10.1038/s41467-018-02922-9. Erratum in: Nat Commun. 2018 Mar 7;9(1):1034.


Harnessing the Periplasm of Bacterial Cells To Develop Biocatalysts for the Biosynthesis of Highly Pure Chemicals.

Yang Y, Wu Y, Hu Y, Wang H, Guo L, Fredrickson JK, Cao B.

Appl Environ Microbiol. 2017 Dec 15;84(1). pii: e01693-17. doi: 10.1128/AEM.01693-17. Print 2018 Jan 1.


Regulation-Structured Dynamic Metabolic Model Provides a Potential Mechanism for Delayed Enzyme Response in Denitrification Process.

Song HS, Thomas DG, Stegen JC, Li M, Liu C, Song X, Chen X, Fredrickson JK, Zachara JM, Scheibe TD.

Front Microbiol. 2017 Sep 29;8:1866. doi: 10.3389/fmicb.2017.01866. eCollection 2017.


Primary and heterotrophic productivity relate to multikingdom diversity in a hypersaline mat.

Bernstein HC, Brislawn CJ, Dana K, Flores-Wentz T, Cory AB, Fansler SJ, Fredrickson JK, Moran JJ.

FEMS Microbiol Ecol. 2017 Oct 1;93(10). doi: 10.1093/femsec/fix121.


Stable Isotope Labeling Reveals Novel Insights Into Ubiquitin-Mediated Protein Aggregation With Age, Calorie Restriction, and Rapamycin Treatment.

Basisty NB, Liu Y, Reynolds J, Karunadharma PP, Dai DF, Fredrickson J, Beyer RP, MacCoss MJ, Rabinovitch PS.

J Gerontol A Biol Sci Med Sci. 2018 Apr 17;73(5):561-570. doi: 10.1093/gerona/glx047.


Geochemical and Microbial Community Attributes in Relation to Hyporheic Zone Geological Facies.

Hou Z, Nelson WC, Stegen JC, Murray CJ, Arntzen E, Crump AR, Kennedy DW, Perkins MC, Scheibe TD, Fredrickson JK, Zachara JM.

Sci Rep. 2017 Sep 20;7(1):12006. doi: 10.1038/s41598-017-12275-w.


Predicting Species-Resolved Macronutrient Acquisition during Succession in a Model Phototrophic Biofilm Using an Integrated 'Omics Approach.

Lindemann SR, Mobberley JM, Cole JK, Markillie LM, Taylor RC, Huang E, Chrisler WB, Wiley HS, Lipton MS, Nelson WC, Fredrickson JK, Romine MF.

Front Microbiol. 2017 Jun 13;8:1020. doi: 10.3389/fmicb.2017.01020. eCollection 2017.


Targeted quantification of functional enzyme dynamics in environmental samples for microbially mediated biogeochemical processes.

Li M, Gao Y, Qian WJ, Shi L, Liu Y, Nelson WC, Nicora CD, Resch CT, Thompson C, Yan S, Fredrickson JK, Zachara JM, Liu C.

Environ Microbiol Rep. 2017 Oct;9(5):512-521. doi: 10.1111/1758-2229.12558. Epub 2017 Jul 13.


Effect of Water Chemistry and Hydrodynamics on Nitrogen Transformation Activity and Microbial Community Functional Potential in Hyporheic Zone Sediment Columns.

Liu Y, Liu C, Nelson WC, Shi L, Xu F, Liu Y, Yan A, Zhong L, Thompson C, Fredrickson JK, Zachara JM.

Environ Sci Technol. 2017 May 2;51(9):4877-4886. doi: 10.1021/acs.est.6b05018. Epub 2017 Apr 18.


Indirect Interspecies Regulation: Transcriptional and Physiological Responses of a Cyanobacterium to Heterotrophic Partnership.

Bernstein HC, McClure RS, Thiel V, Sadler NC, Kim YM, Chrisler WB, Hill EA, Bryant DA, Romine MF, Jansson JK, Fredrickson JK, Beliaev AS.

mSystems. 2017 Mar 7;2(2). pii: e00181-16. doi: 10.1128/mSystems.00181-16. eCollection 2017 Mar-Apr.


Deterministic influences exceed dispersal effects on hydrologically-connected microbiomes.

Graham EB, Crump AR, Resch CT, Fansler S, Arntzen E, Kennedy DW, Fredrickson JK, Stegen JC.

Environ Microbiol. 2017 Apr;19(4):1552-1567. doi: 10.1111/1462-2920.13720. Epub 2017 Mar 28.


Coupling Spatiotemporal Community Assembly Processes to Changes in Microbial Metabolism.

Graham EB, Crump AR, Resch CT, Fansler S, Arntzen E, Kennedy DW, Fredrickson JK, Stegen JC.

Front Microbiol. 2016 Dec 16;7:1949. doi: 10.3389/fmicb.2016.01949. eCollection 2016.


Syntrophic anaerobic photosynthesis via direct interspecies electron transfer.

Ha PT, Lindemann SR, Shi L, Dohnalkova AC, Fredrickson JK, Madigan MT, Beyenal H.

Nat Commun. 2017 Jan 9;8:13924. doi: 10.1038/ncomms13924.


Improved detection of mineral oil toxicity using an extended mouse embryo assay.

Ainsworth AJ, Fredrickson JR, Morbeck DE.

J Assist Reprod Genet. 2017 Mar;34(3):391-397. doi: 10.1007/s10815-016-0856-4. Epub 2017 Jan 7.


18F-Fluoroestradiol PET/CT Measurement of Estrogen Receptor Suppression during a Phase I Trial of the Novel Estrogen Receptor-Targeted Therapeutic GDC-0810: Using an Imaging Biomarker to Guide Drug Dosage in Subsequent Trials.

Wang Y, Ayres KL, Goldman DA, Dickler MN, Bardia A, Mayer IA, Winer E, Fredrickson J, Arteaga CL, Baselga J, Manning HC, Mahmood U, Ulaner GA.

Clin Cancer Res. 2017 Jun 15;23(12):3053-3060. doi: 10.1158/1078-0432.CCR-16-2197. Epub 2016 Dec 23. Erratum in: Clin Cancer Res. 2019 Feb 15;25(4):1435.


Trade-offs between microbiome diversity and productivity in a stratified microbial mat.

Bernstein HC, Brislawn C, Renslow RS, Dana K, Morton B, Lindemann SR, Song HS, Atci E, Beyenal H, Fredrickson JK, Jansson JK, Moran JJ.

ISME J. 2017 Feb;11(2):405-414. doi: 10.1038/ismej.2016.133. Epub 2016 Nov 1.


In Situ Molecular Imaging of the Biofilm and Its Matrix.

Ding Y, Zhou Y, Yao J, Szymanski C, Fredrickson J, Shi L, Cao B, Zhu Z, Yu XY.

Anal Chem. 2016 Nov 15;88(22):11244-11252. Epub 2016 Oct 21.


Extracellular electron transfer mechanisms between microorganisms and minerals.

Shi L, Dong H, Reguera G, Beyenal H, Lu A, Liu J, Yu HQ, Fredrickson JK.

Nat Rev Microbiol. 2016 Oct;14(10):651-62. doi: 10.1038/nrmicro.2016.93. Epub 2016 Aug 30. Review.


Coupling among Microbial Communities, Biogeochemistry, and Mineralogy across Biogeochemical Facies.

Stegen JC, Konopka A, McKinley JP, Murray C, Lin X, Miller MD, Kennedy DW, Miller EA, Resch CT, Fredrickson JK.

Sci Rep. 2016 Jul 29;6:30553. doi: 10.1038/srep30553.


Unlocking the Constraints of Cyanobacterial Productivity: Acclimations Enabling Ultrafast Growth.

Bernstein HC, McClure RS, Hill EA, Markillie LM, Chrisler WB, Romine MF, McDermott JE, Posewitz MC, Bryant DA, Konopka AE, Fredrickson JK, Beliaev AS.

mBio. 2016 Jul 26;7(4). pii: e00949-16. doi: 10.1128/mBio.00949-16.


Treatment with a human recombinant monoclonal IgG antibody against oxidized LDL in atherosclerosis-prone pigs reduces cathepsin S in coronary lesions.

Poulsen CB, Al-Mashhadi AL, von Wachenfeldt K, Bentzon JF, Nielsen LB, Al-Mashhadi RH, Thygesen J, Tolbod L, Larsen JR, Frøkiær J, Tawakol A, Vucic E, Fredrickson J, Baruch A, Frendéus B, Robertson AK, Moestrup SK, Drouet L, Falk E.

Int J Cardiol. 2016 Jul 15;215:506-15. doi: 10.1016/j.ijcard.2016.03.222. Epub 2016 Apr 2.


Mitochondrial-targeted catalase is good for the old mouse proteome, but not for the young: 'reverse' antagonistic pleiotropy?

Basisty N, Dai DF, Gagnidze A, Gitari L, Fredrickson J, Maina Y, Beyer RP, Emond MJ, Hsieh EJ, MacCoss MJ, Martin GM, Rabinovitch PS.

Aging Cell. 2016 Aug;15(4):634-45. doi: 10.1111/acel.12472. Epub 2016 Apr 8.


Groundwater-surface water mixing shifts ecological assembly processes and stimulates organic carbon turnover.

Stegen JC, Fredrickson JK, Wilkins MJ, Konopka AE, Nelson WC, Arntzen EV, Chrisler WB, Chu RK, Danczak RE, Fansler SJ, Kennedy DW, Resch CT, Tfaily M.

Nat Commun. 2016 Apr 7;7:11237. doi: 10.1038/ncomms11237.


Functional roles of CymA and NapC in reduction of nitrate and nitrite by Shewanella putrefaciens W3-18-1.

Wei H, Dai J, Xia M, Romine MF, Shi L, Beliav A, Tiedje JM, Nealson KH, Fredrickson JK, Zhou J, Qiu D.

Microbiology. 2016 Jun;162(6):930-941. doi: 10.1099/mic.0.000285. Epub 2016 Mar 23.


Engineering microbial consortia for controllable outputs.

Lindemann SR, Bernstein HC, Song HS, Fredrickson JK, Fields MW, Shou W, Johnson DR, Beliaev AS.

ISME J. 2016 Sep;10(9):2077-84. doi: 10.1038/ismej.2016.26. Epub 2016 Mar 11.


Clinical translation of ferumoxytol-based vessel size imaging (VSI): Feasibility in a phase I oncology clinical trial population.

Fredrickson J, Serkova NJ, Wyatt SK, Carano RA, Pirzkall A, Rhee I, Rosen LS, Bessudo A, Weekes C, de Crespigny A.

Magn Reson Med. 2017 Feb;77(2):814-825. doi: 10.1002/mrm.26167. Epub 2016 Feb 26.


Editorial: Systems Biology and Ecology of Microbial Mat Communities.

Klotz MG, Bryant DA, Fredrickson JK, Inskeep WP, Kühl M.

Front Microbiol. 2016 Feb 9;7:115. doi: 10.3389/fmicb.2016.00115. eCollection 2016. No abstract available.


Phase I Study of Apitolisib (GDC-0980), Dual Phosphatidylinositol-3-Kinase and Mammalian Target of Rapamycin Kinase Inhibitor, in Patients with Advanced Solid Tumors.

Dolly SO, Wagner AJ, Bendell JC, Kindler HL, Krug LM, Seiwert TY, Zauderer MG, Lolkema MP, Apt D, Yeh RF, Fredrickson JO, Spoerke JM, Koeppen H, Ware JA, Lauchle JO, Burris HA 3rd, de Bono JS.

Clin Cancer Res. 2016 Jun 15;22(12):2874-84. doi: 10.1158/1078-0432.CCR-15-2225. Epub 2016 Jan 19.


Integrating Ecological and Engineering Concepts of Resilience in Microbial Communities.

Song HS, Renslow RS, Fredrickson JK, Lindemann SR.

Front Microbiol. 2015 Dec 1;6:1298. doi: 10.3389/fmicb.2015.01298. eCollection 2015.


Direct involvement of ombB, omaB, and omcB genes in extracellular reduction of Fe(III) by Geobacter sulfurreducens PCA.

Liu Y, Fredrickson JK, Zachara JM, Shi L.

Front Microbiol. 2015 Oct 1;6:1075. doi: 10.3389/fmicb.2015.01075. eCollection 2015.


Advancing understanding of microbial bioenergy conversion processes by activity-based protein profiling.

Liu Y, Fredrickson JK, Sadler NC, Nandhikonda P, Smith RD, Wright AT.

Biotechnol Biofuels. 2015 Sep 25;8:156. doi: 10.1186/s13068-015-0343-7. eCollection 2015. Review.


Regulation of electron transfer processes affects phototrophic mat structure and activity.

Ha PT, Renslow RS, Atci E, Reardon PN, Lindemann SR, Fredrickson JK, Call DR, Beyenal H.

Front Microbiol. 2015 Sep 3;6:909. doi: 10.3389/fmicb.2015.00909. eCollection 2015.


Nitrate bioreduction in redox-variable low permeability sediments.

Yan S, Liu Y, Liu C, Shi L, Shang J, Shan H, Zachara J, Fredrickson J, Kennedy D, Resch CT, Thompson C, Fansler S.

Sci Total Environ. 2016 Jan 1;539:185-195. doi: 10.1016/j.scitotenv.2015.08.122. Epub 2015 Sep 9.


The impact of the protein stabilizer octanoic acid on embryonic development and fetal growth in a murine model.

Fredrickson J, Krisher R, Morbeck DE.

J Assist Reprod Genet. 2015 Oct;32(10):1517-24. doi: 10.1007/s10815-015-0560-9. Epub 2015 Sep 5.


Redox Linked Flavin Sites in Extracellular Decaheme Proteins Involved in Microbe-Mineral Electron Transfer.

Edwards MJ, White GF, Norman M, Tome-Fernandez A, Ainsworth E, Shi L, Fredrickson JK, Zachara JM, Butt JN, Richardson DJ, Clarke TA.

Sci Rep. 2015 Jul 1;5:11677. doi: 10.1038/srep11677.


ECOLOGY. Ecological communities by design.

Fredrickson JK.

Science. 2015 Jun 26;348(6242):1425-7. doi: 10.1126/science.aab0946. No abstract available.


Weight perception in overweight adolescents: Associations with body change intentions, diet and physical activity.

Fredrickson J, Kremer P, Swinburn B, de Silva A, McCabe M.

J Health Psychol. 2015 Jun;20(6):774-84. doi: 10.1177/1359105315580223.


The Aurora A-HP1γ pathway regulates gene expression and mitosis in cells from the sperm lineage.

Leonard PH, Grzenda A, Mathison A, Morbeck DE, Fredrickson JR, de Assuncao TM, Christensen T, Salisbury J, Calvo E, Iovanna J, Coddington CC, Urrutia R, Lomberk G.

BMC Dev Biol. 2015 May 29;15:23. doi: 10.1186/s12861-015-0073-x.

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