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S. Singer · SciRah

Researcher profile · Semantic Scholar

S. Singer

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S. Singer — researcher profile on SciRah

h-index: 46
Works: 188
Citations: 11K

Most-cited papers

MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets
Yu-Wei Wu, B. Simmons, S. Singer
2016Bioinform.2,619 citations Open access
Semantic Scholar
Critical Assessment of Metagenome Interpretation – a benchmark of computational metagenomics software
A. Sczyrba, P. Hofmann, P. Belmann, D. Koslicki +63 more
2017Nature Methods690 citations Open access
Semantic Scholar
Machine learning for metabolic engineering: A review.
Christopher E. Lawson, Jose Manuel Martí, Tijana Radivojević, Sai Vamshi R. Jonnalagadda +11 more
2020Metabolic Engineering262 citations Open access
Semantic Scholar
Microbial production of advanced biofuels
J. Keasling, Héctor García Martín, T. Lee, A. Mukhopadhyay +2 more
2021Nature Reviews Microbiology240 citations Open access
Semantic Scholar
Comparative genomics and transcriptomics depict ericoid mycorrhizal fungi as versatile saprotrophs and plant mutualists.
E. Martino, E. Morin, G. Grelet, A. Kuo +24 more
2018New Phytologist219 citations Open access
Semantic Scholar
Rhodosporidium toruloides: a new platform organism for conversion of lignocellulose into terpene biofuels and bioproducts
Junko Yaegashi, J. Kirby, Masakazu Ito, Jian Sun +16 more
2017bioRxiv167 citations Open access
Semantic Scholar
Metabolic Engineering of Cupriavidus necator H16 for Sustainable Biofuels from CO2.
Justin Panich, B. Fong, S. Singer
2021Trends in Biotechnology136 citations Open access
Semantic Scholar
Lignin deconstruction by anaerobic fungi
Thomas S. Lankiewicz, Hemant Choudhary, Yu Gao, Bashar Amer +19 more
2023Nature Microbiology120 citations Open access
Semantic Scholar
Adaptive laboratory evolution of Pseudomonas putida KT2440 improves p-coumaric and ferulic acid catabolism and tolerance
E. Mohamed, Allison Z. Werner, Davinia Salvachúa, Christine A Singer +10 more
2020Metabolic Engineering Communications111 citations Open access
Semantic Scholar
Approaches for More Efficient Biological Conversion of Lignocellulosic Feedstocks to Biofuels and Bioproducts
Nawa Raj Baral, Eric Sundstrom, Lalitendu Das, J. Gladden +5 more
2019ACS Sustainable Chemistry and Engineering109 citations Open access
Semantic Scholar
Function-driven single-cell genomics uncovers cellulose-degrading bacteria from the rare biosphere
D. Doud, R. Bowers, F. Schulz, M. de Raad +12 more
2019The ISME Journal74 citations Open access
Semantic Scholar
Ecological Insights into the Dynamics of Plant Biomass-Degrading Microbial Consortia.
D. Jiménez, F. Dini-Andreote, K. DeAngelis, S. Singer +2 more
2017Trends in Microbiology68 citations Open access
Semantic Scholar
Generation of a platform strain for ionic liquid tolerance using adaptive laboratory evolution
E. Mohamed, Shizeng Wang, Rebecca M. Lennen, Markus J. Herrgård +3 more
2017Microbial Cell Factories64 citations Open access
Semantic Scholar
Critical Assessment of Metagenome Interpretation – a benchmark of computational metagenomics software
A. Sczyrba, P. Hofmann, P. Belmann, D. Koslicki +63 more
2017bioRxiv61 citations Open access
Semantic Scholar
Fungi Contribute Critical but Spatially Varying Roles in Nitrogen and Carbon Cycling in Acid Mine Drainage
A. Mosier, C. Miller, K. Frischkorn, R. Ohm +12 more
2016Frontiers in Microbiology57 citations Open access
Semantic Scholar
Generation of Pseudomonas putida KT2440 Strains with Efficient Utilization of Xylose and Galactose via Adaptive Laboratory Evolution
H. Lim, Thomas Eng, Deepanwita Banerjee, Geovanni Alarcon +7 more
2021ACS Sustainable Chemistry and Engineering55 citations Open access
Semantic Scholar
Jungle Express is a versatile repressor system for tight transcriptional control
Thomas L. Ruegg, J. H. Pereira, Joseph C. Chen, A. DeGiovanni +8 more
2018Nature Communications53 citations Open access
Semantic Scholar
Microbial Community Structure and Functional Potential Along a Hypersaline Gradient
Jeffrey A. Kimbrel, Nicholas R. Ballor, Yu-Wei Wu, M. David +4 more
2018Frontiers in Microbiology52 citations Open access
Semantic Scholar
The role of organic matter amendment level on soil heating, organic acid accumulation, and development of bacterial communities in solarized soil
C. Simmons, B. Higgins, Simon Staley, Lawrence D. Joh +4 more
201652 citations Open access
Semantic Scholar
Large Circular Plasmids from Groundwater Plasmidomes Span Multiple Incompatibility Groups and Are Enriched in Multimetal Resistance Genes
A. Kothari, Yu-Wei Wu, J. Chandonia, M. Charrier +6 more
2019mBio46 citations Open access
Semantic Scholar
Ionic liquid-tolerant microorganisms and microbial communities for lignocellulose conversion to bioproducts
Chaowei Yu, B. Simmons, S. Singer, M. Thelen +1 more
2016Applied Microbiology and Biotechnology43 citations Open access
Semantic Scholar
Alteration of white-rot basidiomycetes cellulase and xylanase activities in the submerged co-cultivation and optimization of enzyme production by Irpex lacteus and Schizophyllum commune.
E. Metreveli, E. Kachlishvili, S. Singer, V. Elisashvili
2017Bioresource Technology41 citations Open access
Semantic Scholar
Dimethyl Sulfoxide Assisted Ionic Liquid Pretreatment of Switchgrass for Isoprenol Production
Shizeng Wang, Wen-Wen Zhao, T. Lee, S. Singer +4 more
201838 citations
Semantic Scholar
Generation of ionic liquid tolerant Pseudomonas putida KT2440 strains via adaptive laboratory evolution
H. Lim, B. Fong, Geovanni Alarcon, H. D. Magurudeniya +9 more
2020Green Chemistry33 citations Open access
Semantic Scholar
A bacterial pioneer produces cellulase complexes that persist through community succession
Sebastian Kolinko, Yu-Wei Wu, Firehiwot Tachea, Evelyn Denzel +15 more
2017Nature Microbiology33 citations Open access
Semantic Scholar
Xylose induces cellulase production in Thermoascus aurantiacus
Timo Schuerg, Jan-Philip Prahl, Raphael Gabriel, S. Harth +13 more
2017Biotechnology for Biofuels33 citations Open access
Semantic Scholar
Preservation of microbial communities enriched on lignocellulose under thermophilic and high-solid conditions
Chaowei Yu, A. P. Reddy, C. Simmons, B. Simmons +2 more
2015Biotechnology for Biofuels33 citations Open access
Semantic Scholar
Comparative genomic analysis of thermophilic fungi reveals convergent evolutionary adaptations and gene losses
A. Steindorff, M. V. Aguilar-Pontes, Aaron J. Robinson, B. Andreopoulos +26 more
2024Communications Biology29 citations Open access
Semantic Scholar
Trajectories for the evolution of bacterial CO2-concentrating mechanisms
A. Flamholz, Eli J. Dugan, Justin Panich, John James Desmarais +4 more
2022Proceedings of the National Academy of Sciences of the United States of America29 citations Open access
Semantic Scholar
Natural Variation in the Multidrug Efflux Pump SGE1 Underlies Ionic Liquid Tolerance in Yeast
Douglas A. Higgins, Megan K M Young, M. Tremaine, Maria Sardi +13 more
2018Genetics29 citations Open access
Semantic Scholar
Simultaneous carbon catabolite repression governs sugar and aromatic co-utilization in Pseudomonas putida M2
Shilva Shrestha, Deepika Awasthi, Yan Chen, Jennifer W. Gin +4 more
2023bioRxiv28 citations Open access
Semantic Scholar
Experimental and theoretical insights into the effects of pH on catalysis of bond-cleavage by the lignin peroxidase isozyme H8 from Phanerochaete chrysosporium
L. Pham, K. Deng, T. Northen, S. Singer +3 more
2020Biotechnology for Biofuels28 citations Open access
Semantic Scholar
Development and characterization of a thermophilic, lignin degrading microbiota
Shannon J. Ceballos, Chaowei Yu, J. Claypool, S. Singer +4 more
201727 citations Open access
Semantic Scholar
Low-abundance populations distinguish microbiome performance in plant cell wall deconstruction
L. Tom, Martina Aulitto, Yu-Wei Wu, K. Deng +12 more
2022Microbiome25 citations Open access
Semantic Scholar
Doing it alone: Unisexual reproduction in filamentous ascomycete fungi
A. Wilson, Raphael Gabriel, S. Singer, Timo Schuerg +4 more
202125 citations Open access
Semantic Scholar
Assessment of biogas production and microbial ecology in a high solid anaerobic digestion of major California food processing residues
Y. Achmon, J. Claypool, Sara A Pace, B. Simmons +2 more
2019Bioresource Technology Reports25 citations Open access
Semantic Scholar
Thermoascus aurantiacus is an Intriguing Host for the Industrial Production of Cellulases
Timo Schuerg, Raphael Gabriel, Nora Baecker, S. Baker +1 more
201724 citations
Semantic Scholar
The response of Pseudomonas putida to complex aromatic-rich fractions from biomass.
Mee-Rye Park, Yan Chen, M. Thompson, V. Benites +8 more
2020ChemSusChem23 citations Open access
Semantic Scholar
Guanidine Riboswitch-Regulated Efflux Transporters Protect Bacteria against Ionic Liquid Toxicity
Douglas A. Higgins, J. Gladden, Jeffery A. Kimbrel, B. Simmons +2 more
2019Journal of Bacteriology21 citations Open access
Semantic Scholar
Nitrogen amendment of green waste impacts microbial community, enzyme secretion and potential for lignocellulose decomposition
Chaowei Yu, D. Harrold, J. Claypool, B. Simmons +3 more
201721 citations Open access
Semantic Scholar
Revisiting Theoretical Tools and Approaches for the Valorization of Recalcitrant Lignocellulosic Biomass to Value-Added Chemicals
L. Pham, Hemant Choudhary, Rahul Gauttam, S. Singer +4 more
2022Frontiers in Energy Research19 citations Open access
Semantic Scholar
Comparative Community Proteomics Demonstrates the Unexpected Importance of Actinobacterial Glycoside Hydrolase Family 12 Protein for Crystalline Cellulose Hydrolysis
Jennifer Hiras, Yu-Wei Wu, K. Deng, C. Nicora +9 more
2016mBio19 citations Open access
Semantic Scholar
Recovering Individual Genomes from Metagenomes Using MaxBin 2.0
Yu-Wei Wu, S. Singer
2021Current Protocols18 citations
Semantic Scholar
The F-box protein gene exo-1 is a target for reverse engineering enzyme hypersecretion in filamentous fungi
Raphael Gabriel, Nils Thieme, Qian Liu, Fangya Li +13 more
2021Proceedings of the National Academy of Sciences of the United States of America18 citations Open access
Semantic Scholar
Comparison of soil biosolarization with mesophilic and thermophilic solid digestates on soil microbial quantity and diversity
J. Fernández-Bayo, Y. Achmon, D. Harrold, J. Claypool +6 more
201718 citations Open access
Semantic Scholar
Transcriptomic analysis of the highly efficient oil-degrading bacterium Acinetobacter venetianus RAG-1 reveals genes important in dodecane uptake and utilization
A. Kothari, M. Charrier, Yu-Wei Wu, S. Malfatti +4 more
2016FEMS Microbiology Letters18 citations Open access
Semantic Scholar
Construction of a novel dual-inducible duet-expression system for gene (over)expression in Pseudomonas putida.
Rahul Gauttam, A. Mukhopadhyay, S. Singer
2020Plasmid17 citations Open access
Semantic Scholar
CAZymes from the thermophilic fungus Thermoascus aurantiacus are induced by C5 and C6 sugars
Raphael Gabriel, Rebecca Mueller, Lena Floerl, Cynthia Hopson +4 more
2021Biotechnology for Biofuels16 citations Open access
Semantic Scholar
A single-cell genomics pipeline for environmental microbial eukaryotes
D. Ciobanu, A. Clum, S. Ahrendt, William B. Andreopoulos +18 more
2021iScience16 citations Open access
Semantic Scholar
Whole-Genome Sequence of Brevibacillus borstelensis SDM, Isolated from a Sorghum-Adapted Microbial Community
Martina Aulitto, L. Tom, J. Ceja-Navarro, B. Simmons +1 more
2020Microbiology Resource Announcements16 citations Open access
Semantic Scholar

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