Early-branching gut fungi possess a large, comprehensive array of biomass-degrading enzymes

Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles

Subramanian, A., Tamayo, P., Mootha, V. K., Mukherjee, S., Ebert, B. L., Gillette, M. A., Paulovich, A., Pomeroy, S. L., Golub, T. R., Lander, E. S., et al. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0506580102 · Cited by 53,625 · see citing works

Full-length transcriptome assembly from RNA-Seq data without a reference genome

Grabherr, M. G., Haas, B. J., Yassour, M., Levin, J. Z., Thompson, D. A., Amit, I., Adiconis, X., Fan, L., Raychowdhury, R., Zeng, Q., et al. (2011) · Nature Biotechnology · doi:10.1038/nbt.1883 · Cited by 20,776 · see citing works

Differential expression analysis for sequence count data

Anders, S., & Huber, W. (2010) · Genome Biology · doi:10.1186/gb-2010-11-10-r106 · Cited by 15,581 · see citing works

Gene Expression Omnibus: NCBI gene expression and hybridization array data repository

Edgar, R. (2002) · Nucleic Acids Research · doi:10.1093/nar/30.1.207 · Cited by 13,288 · see citing works

Cluster analysis and display of genome-wide expression patterns

Eisen, M. B., Spellman, P. T., Brown, P. O., & Botstein, D. (1998) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.95.25.14863 · Cited by 12,617 · see citing works

The carbohydrate-active enzymes database (CAZy) in 2013

Lombard, V., Ramulu, H. G., Drula, É., Coutinho, P. M., & Henrissat, B. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt1178 · Cited by 6,355 · see citing works

Biomass Recalcitrance: Engineering Plants and Enzymes for Biofuels Production

Himmel, M. E., Ding, S.-Y., Johnson, D. K., Adney, W. S., Nimlos, M. R., Brady, J. W., & Foust, T. D. (2007) · Science · doi:10.1126/science.1137016 · Cited by 4,538 · see citing works

High-throughput functional annotation and data mining with the Blast2GO suite

Götz, S., Garcia-Gomez, J. M., Terol, J., Williams, T., Nagaraj, S. H., Nueda, M. J., Robles, M., Talón, M., Dopazo, J., & Conesa, A. (2008) · Nucleic Acids Research · doi:10.1093/nar/gkn176 · Cited by 4,395 · see citing works

Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation

Letunić, I., & Peer Bork, B. (2006) · Bioinformatics · doi:10.1093/bioinformatics/btl529 · Cited by 3,326 · see citing works

A simple gas production method using a pressure transducer to determine the fermentation kinetics of ruminant feeds

Theodorou, M. K., Williams, B. A., Dhanoa, M. S., McAllan, A. B., & France, J. (1994) · Animal Feed Science and Technology · doi:10.1016/0377-8401(94)90171-6 · Cited by 1,809 · see citing works

Analysis Tool Web Services from the EMBL-EBI

McWilliam, H., Li, W., Uludağ, M., Squizzato, S., Park, Y. M., Buso, N., Cowley, A., & López, R. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt376 · Cited by 1,636 · see citing works

MycoCosm portal: gearing up for 1000 fungal genomes

Grigoriev, I. V., Nikitin, R., Haridas, S., Kuo, A., Ohm, R., Otillar, R., Riley, R., Salamov, A., Zhao, X., Korzeniewski, F., et al. (2014) · Nucleic Acids Research · doi:10.1093/nar/gkt1183 · Cited by 1,498 · see citing works

Metagenomic discovery of biomass-degrading genes and genomes from cow rumen

Hess, M., Sczyrba, A., Egan, R., Kim, T.-W., Chokhawala, H., Schroth, G., Luo, S., Clark, D. S., Chen, F., Zhang, T., et al. (2011) · Science · doi:10.1126/science.1200387 · Cited by 1,319 · see citing works

Transcriptome analysis by strand-specific sequencing of complementary DNA

Parkhomchuk, D., Borodina, T. A., Amstislavskiy, V. S., Banaru, M., Hallen, L., Krobitsch, S., Lehrach, H. R., & Солдатов, А. В. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkp596 · Cited by 934 · see citing works

OrthoMCL-DB: querying a comprehensive multi-species collection of ortholog groups

Chen, F. (2005) · Nucleic Acids Research · doi:10.1093/nar/gkj123 · Cited by 885 · see citing works

Inhibition of cellulase, xylanase and β-glucosidase activities by softwood lignin preparations

Berlin, A., Balakshin, M. Y., Gilkes, N. R., Kadla, J. F., Maximenko, V., Kubo, S., & Saddler, J. N. (2006) · Journal of Biotechnology · doi:10.1016/j.jbiotec.2006.02.021 · Cited by 636 · see citing works

Gene regulation by antisense transcription

Pelechano, V., & Steinmetz, L. M. (2013) · Nature Reviews Genetics · doi:10.1038/nrg3594 · Cited by 628 · see citing works

Chemicals from Biomass

Dodds, D. R., & Gross, R. A. (2007) · Science · doi:10.1126/science.1146356 · Cited by 483 · see citing works

Lignocellulose: A chewy problem

Sanderson, K. (2011) · Nature · doi:10.1038/474s012a · Cited by 406 · see citing works

Plant Cell Wall Deconstruction by Ascomycete Fungi

Glass, N. L., Schmoll, M., Cate, J. H. D., & Coradetti, S. T. (2013) · Annual Review of Microbiology · doi:10.1146/annurev-micro-092611-150044 · Cited by 376 · see citing works

Preparation of crystalline, amorphous, and dyed cellulase substrates

Wood, T. M. (1988) · Methods in enzymology on CD-ROM/Methods in enzymology · doi:10.1016/0076-6879(88)60103-0 · Cited by 334 · see citing works

Reed Canary Grass (Phalaris arundinacea) as a Biological Model in the Study of Plant Invasions

Lavergne, S., & Molofsky, J. (2004) · Critical Reviews in Plant Sciences · doi:10.1080/07352680490505934 · Cited by 253 · see citing works

The Genome of the Anaerobic Fungus Orpinomyces sp. Strain C1A Reveals the Unique Evolutionary History of a Remarkable Plant Biomass Degrader

Youssef, N. H., Couger, M. B., Struchtemeyer, C. G., Liggenstoffer, A. S., Prade, R. A., Najar, F. Z., Atiyeh, H. K., Wilkins, M. R., & Elshahed, M. S. (2013) · Applied and Environmental Microbiology · doi:10.1128/aem.00821-13 · Cited by 245 · see citing works

Engineering the cell wall by reducing de-methyl-esterified homogalacturonan improves saccharification of plant tissues for bioconversion

Lionetti, V., Francocci, F., Ferrari, S., Volpi, C., Bellincampi, D., Galletti, R., D'Ovidio, R., Lorenzo, G. D., & Cervone, F. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0907549107 · Cited by 211 · see citing works

An optimized microplate assay system for quantitative evaluation of plant cell wall–degrading enzyme activity of fungal culture extracts

King, B. C., Donnelly, M. K., Bergstrom, G. C., et al. (2008) · Biotechnology and Bioengineering · doi:10.1002/bit.22151 · Cited by 163 · see citing works

Role for antisense RNA in regulating circadian clock function in Neurospora crassa

Kramer, C., Loros, J., Dunlap, J., & Crosthwaite, S. K. (2003) · Nature · doi:10.1038/nature01427 · Cited by 159 · see citing works

The Rumen Flagellate Piromonas communis: Its Life-history and Invasion of Plant Material in the Rumen

Orpin, C. G. (1977) · Journal of General Microbiology · doi:10.1099/00221287-99-1-107 · Cited by 155 · see citing works

The pros and cons of peptide-centric proteomics

Duncan, M. W., Aebersold, R. H., & Caprioli, R. M. (2010) · Nature Biotechnology · doi:10.1038/nbt0710-659 · Cited by 142 · see citing works

Strand-specific RNA sequencing reveals extensive regulated long antisense transcripts that are conserved across yeast species

Yassour, M., Pfiffner, J., Levin, J. Z., Adiconis, X., Gnirke, A., Nusbaum, C., Thompson, D. A., Friedman, N., & Regev, A. (2010) · Genome biology · doi:10.1186/gb-2010-11-8-r87 · Cited by 136 · see citing works

Anaerobic gut fungi: Advances in isolation, culture, and cellulolytic enzyme discovery for biofuel production

Haitjema, C. H., Solomon, K., Henske, J. K., Theodorou, M. K., & O'Malley, M. A. (2014) · Biotechnology and Bioengineering · doi:10.1002/bit.25264 · Cited by 135 · see citing works

An endo-β-1,4-xylanase from Rhizopus oryzae: production, partial purification and biochemical characterization

Bakır, U., Yavascaoglu, S., Guvenc, F., et al. (2001) · Enzyme and Microbial Technology · doi:10.1016/s0141-0229(01)00379-9 · Cited by 93 · see citing works

The rapid assignment of ruminal fungi to presumptive genera using ITS1 and ITS2 RNA secondary structures to produce group-specific fingerprints

Tuckwell, D. S., Nicholson, M. J., McSweeney, C. S., et al. (2005) · Microbiology · doi:10.1099/mic.0.27689-0 · Cited by 75 · see citing works

Natural antisense transcripts in fungi

Donaldson, M. E., & Saville, B. J. (2012) · Molecular Microbiology · doi:10.1111/j.1365-2958.2012.08125.x · Cited by 67 · see citing works

Cellulases of Trichoderma reesei

Schülein, M. (1988) · Methods in enzymology on CD-ROM/Methods in enzymology · doi:10.1016/0076-6879(88)60125-x · Cited by 66 · see citing works

Anaerobic fungi in the digestive tract of mammalian herbivores and their potential for exploitation

Theodorou, M. K., Mennim, G., Davies, D. R., Zhu, W., Trinci, A. P. J., & Brookman, J. L. (1996) · Proceedings of The Nutrition Society · doi:10.1079/pns19960088 · Cited by 59 · see citing works

Characterization of a cellulosome dockerin domain from the anaerobic fungus Piromyces equi.

Raghothama, S., Eberhardt, R. Y., Simpson, P. J., et al. (2001) · Nature Structural Biology · doi:10.1038/nsb0901-775 · Cited by 56 · see citing works

Comparison of automated in‐gel digest methods for femtomole level samples

Finehout, E. J., & Lee, K. H. (2003) · Electrophoresis · doi:10.1002/elps.200305615 · Cited by 49 · see citing works

Molecular analysis of the anaerobic rumen fungus Orpinomyces – insights into an AT-rich genome

Nicholson, M. J., Theodorou, M. K., & Brookman, J. L. (2005) · Microbiology · doi:10.1099/mic.0.27353-0 · Cited by 48 · see citing works

Biomass. Part A. Cellulose and hemicellulose.

Wood, W. A., & Kellogg, S. T. (1988) · PubMed · Cited by 47 · see citing works

Cellulase and Xylanase Production by Penicillium echinulatum in Submerged Media Containing Cellulose Amended with Sorbitol

Ritter, C. E. T., Camassola, M., Zampieri, D., et al. (2013) · Enzyme Research · doi:10.1155/2013/240219 · Cited by 34 · see citing works

Extracting data from the muck: deriving biological insight from complex microbial communities and non-model organisms with next generation sequencing

Solomon, K., Haitjema, C. H., Thompson, D. A., et al. (2014) · Current Opinion in Biotechnology · doi:10.1016/j.copbio.2014.01.007 · Cited by 30 · see citing works

Robust and effective methodologies for cryopreservation and DNA extraction from anaerobic gut fungi

Solomon, K., Henske, J. K., Theodorou, M. K., et al. (2015) · Anaerobe · doi:10.1016/j.anaerobe.2015.11.008 · Cited by 30 · see citing works

Rnnotator: an automated de novo transcriptome assembly pipeline from stranded RNA-Seq reads

Martin, J., Bruno, V. M., Fang, Z., Meng, X., Blow, M., Zhang, T., Sherlock, G., Snyder, M., & Wang, Z. (2010) · BMC Genomics · doi:10.1186/1471-2164-11-663

Cultivation and sequencing of rumen microbiome members from the Hungate1000 Collection

Hungate1000 project collaborators, Seshadri, R., Leahy, S. C., Attwood, G. T., Teh, K. H., Lambie, S. C., Cookson, A. L., Eloe-Fadrosh, E. A., Pavlopoulos, G. A., Hadjithomas, M., et al. (2018) · Nature Biotechnology · doi:10.1038/nbt.4110 · Cited by 624 · see citing works

Addressing global ruminant agricultural challenges through understanding the rumen microbiome: past, present, and future

Huws, S. A., Creevey, C. J., Oyama, L. B., Mizrahi, I., Denman, S. E., Popova, M., Muñoz-Tamayo, R., Forano, E., Waters, S. M., Hess, M., et al. (2018) · Frontiers in Microbiology · doi:10.3389/fmicb.2018.02161 · Cited by 487 · see citing works

Phytogenic Additives Can Modulate Rumen Microbiome to Mediate Fermentation Kinetics and Methanogenesis Through Exploiting Diet–Microbe Interaction

Hassan, F.-U., Arshad, M. A., Ebeid, H. M., Rehman, M. S.-U., Khan, M. S., Shahid, S., & Yang, C. (2020) · Frontiers in Veterinary Science · doi:10.3389/fvets.2020.575801 · Cited by 160 · see citing works

PCR and omics based techniques to study the diversity, ecology and biology of anaerobic fungi: insights, challenges and opportunities

Edwards, J. E., Forster, R. J., Callaghan, T. M., Dollhofer, V., Dagar, S. S., Cheng, Y., Chang, J., Kittelmann, S., Fliegerova, K., Puniya, A. K., et al. (2017) · Frontiers in Microbiology · doi:10.3389/fmicb.2017.01657 · Cited by 130 · see citing works

The kinetics of catabolite repression inEscherichia coli

Janeček, J., & Rickenberg, H. V. (1969) · Folia Microbiologica · doi:10.1007/bf02872693 · Cited by 1 · see citing works

Catabolite Repression, Catabolite Inhibition and the Regulation of β-Galactosidase Synthesis in Escherichia coli

Hamilton, I. D., Fewson, C. A., & Holmes, W. H. (1989) · Elsevier eBooks · doi:10.1016/b978-0-08-036140-6.50052-8

Catabolite modulator factor: a possible mediator of catabolite repression in bacteria.

Ullmann, A., Tillier, F., & Monod, J. (1976) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.73.10.3476 · Cited by 60 · see citing works

Effect of Amino Sugars on Catabolite Repression inEscherichia coli

Dobrogosz, W. J. (1968) · Journal of Bacteriology · doi:10.1128/jb.95.2.578-584.1968 · Cited by 40 · see citing works

Catabolite repression of different inducible enzymes inEscherichia coli and the effect of cAMP

Jirešová, M., Janeček, J., Naprstek, J., et al. (1981) · Folia Microbiologica · doi:10.1007/bf02927249 · Cited by 1 · see citing works