<h1 id="caltech-center-for-environmental-microbial-interactions-cemi"><a
href="./">Caltech Center for Environmental Microbial Interactions
(CEMI)</a></h1>
<h2 id="section">(““)</h2>
<p><a href="http://www.microbiology.caltech.edu/"
class="uri">http://www.microbiology.caltech.edu/</a></p>
<h3 id="combined-from-caltechauthors">combined from <a
href="https://authors.library.caltech.edu">CaltechAUTHORS</a></h3>
<ul>
<li>Griffin, Catherine; Oz, M. Tufan; et al. (2024) <a
href="https://authors.library.caltech.edu/records/acn1c-cg590">Engineering
plant–microbe communication for plant nutrient use efficiency</a>;
Current Opinion in Biotechnology; Vol. 88; 103150; <a
href="https://doi.org/10.1016/j.copbio.2024.103150">10.1016/j.copbio.2024.103150</a></li>
<li>Hurt, Robert C.; Jin, Zhiyang; et al. (2024) <a
href="https://authors.library.caltech.edu/records/09eq8-exa47">Directed
Evolution of Acoustic Reporter Genes Using High-Throughput Acoustic
Screening</a>; ACS Synthetic Biology; <a
href="https://doi.org/10.1021/acssynbio.4c00283">10.1021/acssynbio.4c00283</a></li>
<li>Tan, Chieh-Hsiang; Wang, Ting-Yu; et al. (2024) <a
href="https://authors.library.caltech.edu/records/zks5d-wkw57">Single-tissue
proteomics in Caenorhabditis elegans reveals proteins resident in
intestinal lysosome-related organelles</a>; Proceedings of the National
Academy of Sciences; Vol. 121; No. 25; <a
href="https://doi.org/10.1073/pnas.2322588121">10.1073/pnas.2322588121</a></li>
<li>Dion-Kirschner, Hannah; Nguyen, Newton H; et al. (2024) <a
href="https://authors.library.caltech.edu/records/g16t4-xhs17">Evaluating
the contribution of methanotrophy kinetics to uncertainty in the soil
methane sink</a>; Environmental Research Letters; Vol. 19; No. 6; 64059;
<a
href="https://doi.org/10.1088/1748-9326/ad4c7a">10.1088/1748-9326/ad4c7a</a></li>
<li>Griffiths, Jessica A.; Yoo, Bryan B.; et al. (2024) <a
href="https://authors.library.caltech.edu/records/mbrmj-h6e60">Peripheral
neuronal activation shapes the microbiome and alters gut physiology</a>;
Cell Reports; Vol. 43; No. 4; 113953; PMCID PMC11132177; <a
href="https://doi.org/10.1016/j.celrep.2024.113953">10.1016/j.celrep.2024.113953</a></li>
<li>Magkiriadou, Sofia; Stepp, Willi L.; et al. (2024) <a
href="https://authors.library.caltech.edu/records/sedrt-1d729">Polyphosphate
affects cytoplasmic and chromosomal dynamics in nitrogen-starved
Pseudomonas aeruginosa</a>; Proceedings of the National Academy of
Sciences; Vol. 121; No. 15; e2313004121; PMCID PMC11009631; <a
href="https://doi.org/10.1073/pnas.2313004121">10.1073/pnas.2313004121</a></li>
<li>Silverman, Shaelyn N.; Wijker, Reto S.; et al. (2024) <a
href="https://authors.library.caltech.edu/records/1e9z3-ykp92">Biosynthetic
and catabolic pathways control amino acid δ²H values in aerobic
heterotrophs</a>; Frontiers in Microbiology; Vol. 15; 1338486; PMCID
PMC11026604; <a
href="https://doi.org/10.3389/fmicb.2024.1338486">10.3389/fmicb.2024.1338486</a></li>
<li>Schwartz, Hillel T.; Tan, Chieh-Hsiang; et al. (2024) <a
href="https://authors.library.caltech.edu/records/n6k3c-dpn19">Molecular
identification of a peroxidase gene controlling body size in the
entomopathogenic nematode Steinernema hermaphroditum</a>; Genetics; Vol.
226; No. 2; iyad209; <a
href="https://doi.org/10.1093/genetics/iyad209">10.1093/genetics/iyad209</a></li>
<li>Osorio-Rodriguez, Daniela; Metcalfe, Kyle S.; et al. (2023) <a
href="https://authors.library.caltech.edu/records/k1ay9-fht81">Microbially
induced precipitation of silica by anaerobic methane-oxidizing consortia
and implications for microbial fossil preservation</a>; Proceedings of
the National Academy of Sciences; Vol. 120; No. 51; e2302156120; PMCID
PMC10743459; <a
href="https://doi.org/10.1073/pnas.2302156120">10.1073/pnas.2302156120</a></li>
<li>Ling, Bill; Ko, Jeong Hoon; et al. (2023) <a
href="https://authors.library.caltech.edu/records/7w289-s1c34">Gas
Vesicle–Blood Interactions Enhance Ultrasound Imaging Contrast</a>; Nano
Letters; Vol. 23; No. 33; 10748-10757; PMCID PMC10722532; <a
href="https://doi.org/10.1021/acs.nanolett.3c02780">10.1021/acs.nanolett.3c02780</a></li>
<li>Jin, Zhiyang; Lakshmanan, Anupama; et al. (2023) <a
href="https://authors.library.caltech.edu/records/qnxrm-ncs15">Ultrasonic
reporters of calcium for deep tissue imaging of cellular signals</a>;
PMCID PMC10659314; <a
href="https://doi.org/10.1101/2023.11.09.566364">10.1101/2023.11.09.566364</a></li>
<li>Hurt, Robert C.; Buss, Marjorie T.; et al. (2023) <a
href="https://resolver.caltech.edu/CaltechAUTHORS:20230317-826078000.2">Genomically
mined acoustic reporter genes for real-time in vivo monitoring of tumors
and tumor-homing bacteria</a>; Nature Biotechnology; Vol. 41; No. 7;
919-931; PMCID PMC10344784; <a
href="https://doi.org/10.1038/s41587-022-01581-y">10.1038/s41587-022-01581-y</a></li>
<li>Dutka, Przemysław; Metskas, Lauren Ann; et al. (2023) <a
href="https://resolver.caltech.edu/CaltechAUTHORS:20230628-257245000.39">Structure
of Anabaena flos-aquae gas vesicles revealed by cryo-ET</a>; Structure;
Vol. 31; No. 5; 518-528; PMCID PMC10185304; <a
href="https://doi.org/10.1016/j.str.2023.03.011">10.1016/j.str.2023.03.011</a></li>
<li>Wang, Grace Z.; Warren, Elizabeth A.; et al. (2023) <a
href="https://resolver.caltech.edu/CaltechAUTHORS:20230316-182348000.27">Staphylococcal
secreted cytotoxins are competition sensing signals for Pseudomonas
aeruginosa</a>; <a
href="https://doi.org/10.1101/2023.01.29.526047">10.1101/2023.01.29.526047</a></li>
<li>Wilkes, Elise B.; Sessions, Alex L.; et al. (2022) <a
href="https://resolver.caltech.edu/CaltechAUTHORS:20220708-948968900">Position-specific
carbon isotope analysis of serine by gas chromatography/Orbitrap mass
spectrometry, and an application to plant metabolism</a>; Rapid
Communications in Mass Spectrometry; Vol. 36; No. 18; Art. No. e9347; <a
href="https://doi.org/10.1002/rcm.9347">10.1002/rcm.9347</a></li>
<li>Zeichner, Sarah S.; Wilkes, Elise B.; et al. (2022) <a
href="https://resolver.caltech.edu/CaltechAUTHORS:20220513-557936000">Methods
and limitations of stable isotope measurements via direct elution of
chromatographic peaks using gas chromotography-Orbitrap mass
spectrometry</a>; International Journal of Mass Spectrometry; Vol. 477;
Art. No. 116848; <a
href="https://doi.org/10.1016/j.ijms.2022.116848">10.1016/j.ijms.2022.116848</a></li>
<li>Dutka, Przemysław; Metskas, Lauren Ann; et al. (2022) <a
href="https://resolver.caltech.edu/CaltechAUTHORS:20220706-965078000">Structure
of Anabaena flos-aquae gas vesicles revealed by cryo-ET</a>; <a
href="https://doi.org/10.1101/2022.06.21.496981">10.1101/2022.06.21.496981</a></li>
<li>Brückner, Adrian; Barnett, Austen A.; et al. (2022) <a
href="https://resolver.caltech.edu/CaltechAUTHORS:20201214-074948609">Molecular
evolutionary trends and biosynthesis pathways in the Oribatida revealed
by the genome of Archegozetes longisetosus</a>; Acarologia; Vol. 62;
No. 2; 532-573; <a
href="https://doi.org/10.24349/pjye-gkeo">10.24349/pjye-gkeo</a></li>
<li>Douglas, Madison M.; Li, Gen K.; et al. (2022) <a
href="https://resolver.caltech.edu/CaltechAUTHORS:20220520-231800000">Organic
carbon burial by river meandering partially offsets bank erosion carbon
fluxes in a discontinuous permafrost floodplain</a>; Earth Surface
Dynamics; Vol. 10; No. 3; 421-435; <a
href="https://doi.org/10.5194/esurf-10-421-2022">10.5194/esurf-10-421-2022</a></li>
<li>Greenwald, Noah F.; Miller, Geneva; et al. (2022) <a
href="https://resolver.caltech.edu/CaltechAUTHORS:20210303-070232817">Whole-cell
segmentation of tissue images with human-level performance using
large-scale data annotation and deep learning</a>; Nature Biotechnology;
Vol. 40; No. 4; 555-565; PMCID PMC9010346; <a
href="https://doi.org/10.1038/s41587-021-01094-0">10.1038/s41587-021-01094-0</a></li>
<li>Yu, Hang; Chadwick, Grayson L.; et al. (2022) <a
href="https://resolver.caltech.edu/CaltechAUTHORS:20211118-163619344">Comparative
Genomics on Cultivated and Uncultivated Freshwater and Marine
“Candidatus Manganitrophaceae” Species Implies Their Worldwide Reach in
Manganese Chemolithoautotrophy</a>; mBio; Vol. 13; No. 2; Art.
No. 03421-21; PMCID PMC9040806; <a
href="https://doi.org/10.1128/mbio.03421-21">10.1128/mbio.03421-21</a></li>
<li>Needham, Brittany D.; Funabashi, Masanori; et al. (2022) <a
href="https://resolver.caltech.edu/CaltechAUTHORS:20220214-859281700">A
gut-derived metabolite alters brain activity and anxiety behaviour in
mice</a>; Nature; Vol. 602; No. 7899; 647-653; PMCID PMC9170029; <a
href="https://doi.org/10.1038/s41586-022-04396-8">10.1038/s41586-022-04396-8</a></li>
<li>Yu, Hang; Skennerton, Connor T.; et al. (2022) <a
href="https://resolver.caltech.edu/CaltechAUTHORS:20210726-170837328">Sulfate
differentially stimulates but is not respired by diverse anaerobic
methanotrophic archaea</a>; ISME Journal; Vol. 16; No. 1; 168-177; <a
href="https://doi.org/10.1038/s41396-021-01047-0">10.1038/s41396-021-01047-0</a></li>
<li>Magkiriadou, S.; Habel, A.; et al. (2021) <a
href="https://resolver.caltech.edu/CaltechAUTHORS:20220104-461622500">Polyphosphate
affects cytoplasmic and chromosomal dynamics in nitrogen-starved
Pseudomonas aeruginosa</a>; <a
href="https://doi.org/10.1101/2021.12.23.473106">10.1101/2021.12.23.473106</a></li>
<li>Abrams, Michael J.; Tan, Fayth Hui; et al. (2021) <a
href="https://resolver.caltech.edu/CaltechAUTHORS:20201123-131615362">A
conserved strategy for inducing appendage regeneration in moon
jellyfish, Drosophila, and mice</a>; eLife; Vol. 10; e65092; PMCID
PMC8782573; <a
href="https://doi.org/10.7554/eLife.65092">10.7554/eLife.65092</a></li>
<li>Mondragón-Palomino, Octavio; Poceviciute, Roberta; et al. (2021) <a
href="https://resolver.caltech.edu/CaltechAUTHORS:20211015-222210959">3D
imaging for the quantification of spatial patterns in microbiota of the
intestinal mucosa</a>; <a
href="https://doi.org/10.1101/2021.10.07.463215">10.1101/2021.10.07.463215</a></li>
<li>Perry, Elena K.; Siozios, Stefanos; et al. (2021) <a
href="https://resolver.caltech.edu/CaltechAUTHORS:20211008-224629828">Structure
of an ant-myrmecophile-microbe community</a>; <a
href="https://doi.org/10.1101/2021.10.04.462948">10.1101/2021.10.04.462948</a></li>
<li>Osorio‐Rodriguez, Daniela; Razo-Mejia, Manuel; et al. (2021) <a
href="https://resolver.caltech.edu/CaltechAUTHORS:20210817-204334443">Sulfur
isotope fractionations constrain the biological cycling of
dimethylsulfoniopropionate in the upper ocean</a>; Limnology and
Oceanography; Vol. 66; No. 10; 3607-3618; <a
href="https://doi.org/10.1002/lno.11901">10.1002/lno.11901</a></li>
<li>Douglas, Madison M.; Lingappa, Usha F.; et al. (2021) <a
href="https://resolver.caltech.edu/CaltechAUTHORS:20210831-221808372">Impact
of River Channel Lateral Migration on Microbial Communities across a
Discontinuous Permafrost Floodplain</a>; Applied and Environmental
Microbiology; Vol. 87; No. 20; Art. No. e01339-21; PMCID PMC8478453; <a
href="https://doi.org/10.1128/aem.01339-21">10.1128/aem.01339-21</a></li>
<li>Dutka, Przemysław; Malounda, Dina; et al. (2021) <a
href="https://resolver.caltech.edu/CaltechAUTHORS:20210125-082358436">Measuring
gas vesicle dimensions by electron microscopy</a>; Protein Science; Vol.
30; No. 5; 1081-1086; PMCID PMC8040859; <a
href="https://doi.org/10.1002/pro.4056">10.1002/pro.4056</a></li>
<li>Hurt, Robert C.; Buss, Marjorie T.; et al. (2021) <a
href="https://resolver.caltech.edu/CaltechAUTHORS:20210429-092722876">Genomically
Mined Acoustic Reporter Genes Enable In Vivo Monitoring of Tumors and
Tumor-Homing Bacteria</a>; <a
href="https://doi.org/10.1101/2021.04.26.441537">10.1101/2021.04.26.441537</a></li>
<li>Yoo, Bryan B.; Griffiths, Jessica A; et al. (2021) <a
href="https://resolver.caltech.edu/CaltechAUTHORS:20210414-072514678">Neuronal
Activation of the Gastrointestinal Tract Shapes the Gut Environment in
Mice</a>; <a
href="https://doi.org/10.1101/2021.04.12.439539">10.1101/2021.04.12.439539</a></li>
<li>Dahlstrom, Kurt M. and Newman, Dianne K. (2021) <a
href="https://resolver.caltech.edu/CaltechAUTHORS:20210419-152102811">Paraburkholderia
edwinii protects Aspergillus sp. from phenazines by acting as a toxin
sponge</a>; <a
href="https://doi.org/10.1101/2021.03.28.437412">10.1101/2021.03.28.437412</a></li>
<li>Nicolas, William J.; Ghosal, Debnath; et al. (2021) <a
href="https://resolver.caltech.edu/CaltechAUTHORS:20200417-145045074">Structure
of the Bacterial Cellulose Ribbon and Its Assembly-Guiding Cytoskeleton
by Electron Cryotomography</a>; Journal of Bacteriology; Vol. 203;
No. 3; Art. No. e00371-20; PMCID PMC7811197; <a
href="https://doi.org/10.1128/JB.00371-20">10.1128/JB.00371-20</a></li>
<li>Morrison, Muir; Razo-Mejia, Manuel; et al. (2021) <a
href="https://resolver.caltech.edu/CaltechAUTHORS:20200615-130249775">Reconciling
kinetic and thermodynamic models of bacterial transcription</a>; PLOS
Computational Biology; Vol. 17; No. 1; Art. No. e1008572; PMCID
PMC7845990; <a
href="https://doi.org/10.1371/journal.pcbi.1008572">10.1371/journal.pcbi.1008572</a></li>
<li>Ling, Bill; Lee, Justin; et al. (2020) <a
href="https://resolver.caltech.edu/CaltechAUTHORS:20200911-133137357">Biomolecular
Ultrasound Imaging of Phagolysosomal Function</a>; ACS Nano; Vol. 14;
No. 9; 12210-12221; PMCID PMC7685203; <a
href="https://doi.org/10.1021/acsnano.0c05912">10.1021/acsnano.0c05912</a></li>
<li>Brückner, Adrian; Kaltenpoth, Martin; et al. (2020) <a
href="https://resolver.caltech.edu/CaltechAUTHORS:20200908-154844861">De
novo biosynthesis of simple aromatic compounds by an arthropod
(Archegozetes longisetosus)</a>; Proceedings of the Royal Society of
London. Series B, Biological Sciences; Vol. 287; No. 1934; Art.
No. 20201429; PMCID PMC7542773; <a
href="https://doi.org/10.1098/rspb.2020.1429">10.1098/rspb.2020.1429</a></li>
<li>Saunders, Scott H.; Tse, Edmund C. M.; et al. (2020) <a
href="https://resolver.caltech.edu/CaltechAUTHORS:20191213-144717393">Extracellular
DNA Promotes Efficient Extracellular Electron Transfer by Pyocyanin in
Pseudomonas aeruginosa Biofilms</a>; Cell; Vol. 182; No. 4; 919-932;
PMCID PMC7457544; <a
href="https://doi.org/10.1016/j.cell.2020.07.006">10.1016/j.cell.2020.07.006</a></li>
<li>Khazaei, Tahmineh; Williams, Rory L.; et al. (2020) <a
href="https://resolver.caltech.edu/CaltechAUTHORS:20200813-144241318">Metabolic
multistability and hysteresis in a model aerobe-anaerobe microbiome
community</a>; Science Advances; Vol. 6; No. 33; Art. No. eaba0353;
PMCID PMC7423363; <a
href="https://doi.org/10.1126/sciadv.aba0353">10.1126/sciadv.aba0353</a></li>
<li>Razo-Mejia, Manuel; Marzen, Sarah; et al. (2020) <a
href="https://resolver.caltech.edu/CaltechAUTHORS:20190402-080512452">First-principles
prediction of the information processing capacity of a simple genetic
circuit</a>; Physical Review E; Vol. 102; No. 2; Art. No. 022404; <a
href="https://doi.org/10.1103/PhysRevE.102.022404">10.1103/PhysRevE.102.022404</a></li>
<li>Yu, Hang and Leadbetter, Jared R. (2020) <a
href="https://resolver.caltech.edu/CaltechAUTHORS:20200408-160710037">Bacterial
chemolithoautotrophy via manganese oxidation</a>; Nature; Vol. 583;
No. 7816; 453-458; PMCID PMC7802741; <a
href="https://doi.org/10.1038/s41586-020-2468-5">10.1038/s41586-020-2468-5</a></li>
<li>Hirokawa, Soichi; Chure, Griffin; et al. (2020) <a
href="https://resolver.caltech.edu/CaltechAUTHORS:20191007-074542895">Sequence-Dependent
Dynamics of Synthetic and Endogenous RSSs in V(D)J Recombination</a>;
Nucleic Acids Research; Vol. 48; No. 12; 6726-6739; PMCID PMC7337519; <a
href="https://doi.org/10.1093/nar/gkaa418">10.1093/nar/gkaa418</a></li>
<li>Silva, Rebekah M. B.; Grodick, Michael A.; et al. (2020) <a
href="https://resolver.caltech.edu/CaltechAUTHORS:20200615-113627458">UvrC
Coordinates an O₂-Sensitive [4Fe4S] Cofactor</a>; Journal of the
American Chemical Society; Vol. 142; No. 25; 10964-10977; PMCID
PMC7392197; <a
href="https://doi.org/10.1021/jacs.0c01671">10.1021/jacs.0c01671</a></li>
<li>Donaldson, Gregory P.; Chou, Wen-Chi; et al. (2020) <a
href="https://resolver.caltech.edu/CaltechAUTHORS:20200115-104219274">Spatially
distinct physiology of Bacteroides fragilis within the proximal colon of
gnotobiotic mice</a>; Nature Microbiology; Vol. 5; No. 5; 746-756; <a
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<li>Ward, Lewis M.; Lingappa, Usha F.; et al. (2020) <a
href="https://resolver.caltech.edu/CaltechAUTHORS:20200416-123639965">Microbial
mats in the Turks and Caicos Islands reveal diversity and evolution of
phototrophy in the Chloroflexota order Aggregatilineales</a>;
Environmental Microbiome; Vol. 15; Art. No. 9; PMCID PMC8067394; <a
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<li>Torres, Mark A.; Kemeny, Preston C.; et al. (2020) <a
href="https://resolver.caltech.edu/CaltechAUTHORS:20200317-150608382">Long-term
storage and age‐biased export of fluvial organic carbon: field evidence
from West Iceland</a>; Geochemistry, Geophysics, Geosystems; Vol. 21;
No. 4; Art. No. e2019GC008632; <a
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<li>Davis, Hunter C.; Kang, Sunghwi; et al. (2020) <a
href="https://resolver.caltech.edu/CaltechAUTHORS:20200203-092720672">Nanoscale
Heat Transfer from Magnetic Nanoparticles and Ferritin in an Alternating
Magnetic Field</a>; Biophysical Journal; Vol. 118; No. 6; 1502-1510;
PMCID PMC7091488; <a
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<li>Challis, Collin; Hori, Acacia; et al. (2020) <a
href="https://resolver.caltech.edu/CaltechAUTHORS:20191209-154036633">Gut-seeded
α-synuclein fibrils promote gut dysfunction and brain pathology
specifically in aged mice</a>; Nature Neuroscience; Vol. 23; No. 3;
327-336; PMCID PMC7065967; <a
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<li>Khazaei, Tahmineh; Williams, Rory L.; et al. (2020) <a
href="https://resolver.caltech.edu/CaltechAUTHORS:20200303-084602692">Metabolic
multi-stability and hysteresis in a model aerobe-anaerobe microbiome
community</a>; <a
href="https://doi.org/10.1101/2020.02.28.968941">10.1101/2020.02.28.968941</a></li>
<li>Moen, Erick; Borba, Enrico; et al. (2019) <a
href="https://resolver.caltech.edu/CaltechAUTHORS:20191014-100546775">Accurate
cell tracking and lineage construction in live-cell imaging experiments
with deep learning</a>; <a
href="https://doi.org/10.1101/803205">10.1101/803205</a></li>
<li>Porter, Michael K.; Steinberg, Asher Preska; et al. (2019) <a
href="https://resolver.caltech.edu/CaltechAUTHORS:20190823-085722494">Interplay
of motility and polymer-driven depletion forces in the initial stages of
bacterial aggregation</a>; Soft Matter; Vol. 15; No. 35; 7071-7079; <a
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<li>Hanewich-Hollatz, Mikhail H.; Chen, Zhewei; et al. (2019) <a
href="https://resolver.caltech.edu/CaltechAUTHORS:20190123-124341981">Conditional
Guide RNAs: Programmable Conditional Regulation of CRISPR/Cas Function
in Bacterial and Mammalian Cells via Dynamic RNA Nanotechnology</a>; ACS
Central Science; Vol. 5; No. 7; 1241-1249; PMCID PMC6661866; <a
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<li>Preska Steinberg, Asher; Wang, Zhen-Gang; et al. (2019) <a
href="https://resolver.caltech.edu/CaltechAUTHORS:20190619-091518942">Food
Polyelectrolytes Compress the Colonic Mucus Hydrogel by a Donnan
Mechanism</a>; Biomacromolecules; Vol. 20; No. 7; 2675-2683; <a
href="https://doi.org/10.1021/acs.biomac.9b00442">10.1021/acs.biomac.9b00442</a></li>
<li>Chalkley, Matthew J.; Oyala, Paul H.; et al. (2019) <a
href="https://resolver.caltech.edu/CaltechAUTHORS:20190221-125557747">Cp*
Noninnocence Leads to a Remarkably Weak C–H Bond via Metallocene
Protonation</a>; Journal of the American Chemical Society; Vol. 141;
No. 11; 4721-4729; <a
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