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

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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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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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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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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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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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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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Semantics in support of biodiversity knowledge discovery: an introduction to the biological collections ontology and related ontologies von Walls, Ramona L, Deck, John, Guralnick, Robert, Baskauf, Steve, Beaman, Reed, Blum, Stanley, Bowers, Shawn, Buttigieg, Pier Luigi, Davies, Neil, Endresen, Dag, Gandolfo, Maria Alejandra, Hanner, Robert, Janning, Alyssa, Krishtalka, Leonard, Matsunaga, Andréa, Midford, Peter, Morrison, Norman, Ó Tuama, Éamonn, Schildhauer, Mark, Smith, Barry, Stucky, Brian J, Thomer, Andrea, Wieczorek, John, Whitacre, Jamie, Wooley, John

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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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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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A Comparison of Microbial Genome Web Portals von Karp, Peter D, Ivanova, Natalia, Krummenacker, Markus, Kyrpides, Nikos, Latendresse, Mario, Midford, Peter, Ong, Wai Kit, Paley, Suzanne, Seshadri, Rekha

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The EcoCyc Database (2023) von Karp, Peter D, Paley, Suzanne, Caspi, Ron, Kothari, Anamika, Krummenacker, Markus, Midford, Peter E, Moore, Lisa R, Subhraveti, Pallavi, Gama-Castro, Socorro, Tierrafria, Victor H, Lara, Paloma, Muñiz-Rascado, Luis, Bonavides-Martinez, César, Santos-Zavaleta, Alberto, Mackie, Amanda, Sun, Gwanggyu, Ahn-Horst, Travis A, Choi, Heejo, Covert, Markus W, Collado-Vides, Julio, Paulsen, Ian

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