The MetaCyc database of metabolic pathways and enzymes - a 2019 update von Caspi, Ron, Billington, Richard, Keseler, Ingrid M, Kothari, Anamika, Krummenacker, Markus, Midford, Peter E, Ong, Wai Kit, Paley, Suzanne, Subhraveti, Pallavi, Karp, Peter D

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Exploring power and parameter estimation of the BiSSE method for analyzing species diversification von Davis, Matthew P, Midford, Peter E, Maddison, Wayne

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The MetaCyc database of metabolic pathways and enzymes von Caspi, Ron, Billington, Richard, Fulcher, Carol A, Keseler, Ingrid M, Kothari, Anamika, Krummenacker, Markus, Latendresse, Mario, Midford, Peter E, Ong, Quang, Ong, Wai Kit, Paley, Suzanne, Subhraveti, Pallavi, Karp, Peter D

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The BioCyc collection of microbial genomes and metabolic pathways von Karp, Peter D, Billington, Richard, Caspi, Ron, Fulcher, Carol A, Latendresse, Mario, Kothari, Anamika, Keseler, Ingrid M, Krummenacker, Markus, Midford, Peter E, Ong, Quang, Ong, Wai Kit, Paley, Suzanne M, Subhraveti, Pallavi

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Pathway size matters: the influence of pathway granularity on over-representation (enrichment analysis) statistics von Karp, Peter D, Midford, Peter E, Caspi, Ron, Khodursky, Arkady

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Estimating a Binary Character's Effect on Speciation and Extinction von Maddison, Wayne P., Midford, Peter E., Otto, Sarah P.

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Synthesis of phylogeny and taxonomy into a comprehensive tree of life von Hinchliff, Cody E., Smith, Stephen A., Allman, James F., Burleigh, J. Gordon, Chaudhary, Ruchi, Coghill, Lyndon M., Crandall, Keith A., Deng, Jiabin, Drew, Bryan T., Gazis, Romina, Gude, Karl, Hibbett, David S., Katz, Laura A., Laughinghouse, H. Dail, McTavish, Emily Jane, Midford, Peter E., Owen, Christopher L., Ree, Richard H., Rees, Jonathan A., Soltis, Douglas E., Williams, Tiffani, Cranston, Karen A.

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The EcoCyc Database in 2021 von Keseler, Ingrid M, Gama-Castro, Socorro, Mackie, Amanda, Billington, Richard, Bonavides-Martínez, César, Caspi, Ron, Kothari, Anamika, Krummenacker, Markus, Midford, Peter E, Muñiz-Rascado, Luis, Ong, Wai Kit, Paley, Suzanne, Santos-Zavaleta, Alberto, Subhraveti, Pallavi, Tierrafría, Víctor H, Wolfe, Alan J, Collado-Vides, Julio, Paulsen, Ian T, Karp, Peter D

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Within-Species Variation and Measurement Error in Phylogenetic Comparative Methods von Ives, Anthony R., Midford, Peter E., Garland, Theodore, Oakley, Todd

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Patterns in root traits of woody species hosting arbuscular and ectomycorrhizas: implications for the evolution of belowground strategies von Comas, Louise H., Callahan, Hilary S., Midford, Peter E.

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NeXML: Rich, Extensible, and Verifiable Representation of Comparative Data and Metadata von Vos, Rutger A., Balhoff, James P., Caravas, Jason A., Holder, Mark T., Lapp, Hilmar, Maddison, Wayne P., Midford, Peter E., Priyam, Anurag, Sukumaran, Jeet, Xia, Xuhua, Stoltzfus, Arlin

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Phenex: ontological annotation of phenotypic diversity von Balhoff, James P, Dahdul, Wasila M, Kothari, Cartik R, Lapp, Hilmar, Lundberg, John G, Mabee, Paula, Midford, Peter E, Westerfield, Monte, Vision, Todd J

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Evolutionary characters, phenotypes and ontologies: curating data from the systematic biology literature von Dahdul, Wasila M, Balhoff, James P, Engeman, Jeffrey, Grande, Terry, Hilton, Eric J, Kothari, Cartik, Lapp, Hilmar, Lundberg, John G, Midford, Peter E, Vision, Todd J, Westerfield, Monte, Mabee, Paula M

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The Teleost Anatomy Ontology: Anatomical Representation for the Genomics Age von Dahdul, Wasila M., Lundberg, John G., Midford, Peter E., Balhoff, James P., Lapp, Hilmar, Vision, Todd J., Haendel, Melissa A., Westerfield, Monte, Mabee, Paula M.

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Pathway Tools version 23.0 update: software for pathway/genome informatics and systems biology von Karp, Peter D, Midford, Peter E, Billington, Richard, Kothari, Anamika, Krummenacker, Markus, Latendresse, Mario, Ong, Wai Kit, Subhraveti, Pallavi, Caspi, Ron, Fulcher, Carol, Keseler, Ingrid M, Paley, Suzanne M

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Phylotastic! Making tree-of-life knowledge accessible, reusable and convenient von Stoltzfus, Arlin, Lapp, Hilmar, Matasci, Naim, Deus, Helena, Sidlauskas, Brian, Zmasek, Christian M, Vaidya, Gaurav, Pontelli, Enrico, Cranston, Karen, Vos, Rutger, Webb, Campbell O, Harmon, Luke J, Pirrung, Megan, O'Meara, Brian, Pennell, Matthew W, Mirarab, Siavash, Rosenberg, Michael S, Balhoff, James P, Bik, Holly M, Heath, Tracy A, Midford, Peter E, Brown, Joseph W, McTavish, Emily Jane, Sukumaran, Jeet, Westneat, Mark, Alfaro, Michael E, Steele, Aaron, Jordan, Greg

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An Introduction to Phylogenetically Based Statistical Methods, with a New Method for Confidence Intervals on Ancestral Values von GARLAND, THEODORE, MIDFORD, PETER E., IVES, ANTHONY R.

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Taxonomic weighting improves the accuracy of a gap-filling algorithm for metabolic models von Ong, Wai Kit, Midford, Peter E, Karp, Peter D

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Using Pathway Covering to Explore Connections among Metabolites von Midford, Peter E, Latendresse, Mario, O'Maille, Paul E, Karp, Peter D

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Emerging semantics to link phenotype and environment von Thessen, Anne E, Bunker, Daniel E, Buttigieg, Pier Luigi, Cooper, Laurel D, Dahdul, Wasila M, Domisch, Sami, Franz, Nico M, Jaiswal, Pankaj, Lawrence-Dill, Carolyn J, Midford, Peter E, Mungall, Christopher J, Ramírez, Martín J, Specht, Chelsea D, Vogt, Lars, Vos, Rutger Aldo, Walls, Ramona L, White, Jeffrey W, Zhang, Guanyang, Deans, Andrew R, Huala, Eva, Lewis, Suzanna E, Mabee, Paula M

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