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Items: 25

1.

Pathway Tools version 23.0 update: software for pathway/genome informatics and systems biology.

Karp PD, Midford PE, Billington R, Kothari A, Krummenacker M, Latendresse M, Ong WK, Subhraveti P, Caspi R, Fulcher C, Keseler IM, Paley SM.

Brief Bioinform. 2019 Dec 8. pii: bbz104. doi: 10.1093/bib/bbz104. [Epub ahead of print]

PMID:
31813964
2.

Taxonomic Weighting Improves the Accuracy of a Gap-Filling Algorithm for Metabolic Models.

Ong WK, Midford PE, Karp PD.

Bioinformatics. 2019 Nov 5. pii: btz813. doi: 10.1093/bioinformatics/btz813. [Epub ahead of print]

PMID:
31688932
3.

The MetaCyc database of metabolic pathways and enzymes-a 2019 update.

Caspi R, Billington R, Keseler IM, Kothari A, Krummenacker M, Midford PE, Ong WK, Paley S, Subhraveti P, Karp PD.

Nucleic Acids Res. 2019 Oct 5. pii: gkz862. doi: 10.1093/nar/gkz862. [Epub ahead of print]

PMID:
31586394
4.

Using Pathway Covering to Explore Connections among Metabolites.

Midford PE, Latendresse M, O'Maille PE, Karp PD.

Metabolites. 2019 May 2;9(5). pii: E88. doi: 10.3390/metabo9050088.

5.

The EcoCyc Database.

Karp PD, Ong WK, Paley S, Billington R, Caspi R, Fulcher C, Kothari A, Krummenacker M, Latendresse M, Midford PE, Subhraveti P, Gama-Castro S, Muñiz-Rascado L, Bonavides-Martinez C, Santos-Zavaleta A, Mackie A, Collado-Vides J, Keseler IM, Paulsen I.

EcoSal Plus. 2018 Nov;8(1). doi: 10.1128/ecosalplus.ESP-0006-2018. Review.

6.

The BioCyc collection of microbial genomes and metabolic pathways.

Karp PD, Billington R, Caspi R, Fulcher CA, Latendresse M, Kothari A, Keseler IM, Krummenacker M, Midford PE, Ong Q, Ong WK, Paley SM, Subhraveti P.

Brief Bioinform. 2019 Jul 19;20(4):1085-1093. doi: 10.1093/bib/bbx085.

7.

The MetaCyc database of metabolic pathways and enzymes.

Caspi R, Billington R, Fulcher CA, Keseler IM, Kothari A, Krummenacker M, Latendresse M, Midford PE, Ong Q, Ong WK, Paley S, Subhraveti P, Karp PD.

Nucleic Acids Res. 2018 Jan 4;46(D1):D633-D639. doi: 10.1093/nar/gkx935.

8.

Emerging semantics to link phenotype and environment.

Thessen AE, Bunker DE, Buttigieg PL, Cooper LD, Dahdul WM, Domisch S, Franz NM, Jaiswal P, Lawrence-Dill CJ, Midford PE, Mungall CJ, Ramírez MJ, Specht CD, Vogt L, Vos RA, Walls RL, White JW, Zhang G, Deans AR, Huala E, Lewis SE, Mabee PM.

PeerJ. 2015 Dec 14;3:e1470. doi: 10.7717/peerj.1470. eCollection 2015.

9.

Synthesis of phylogeny and taxonomy into a comprehensive tree of life.

Hinchliff CE, Smith SA, Allman JF, Burleigh JG, Chaudhary R, Coghill LM, Crandall KA, Deng J, Drew BT, Gazis R, Gude K, Hibbett DS, Katz LA, Laughinghouse HD 4th, McTavish EJ, Midford PE, Owen CL, Ree RH, Rees JA, Soltis DE, Williams T, Cranston KA.

Proc Natl Acad Sci U S A. 2015 Oct 13;112(41):12764-9. doi: 10.1073/pnas.1423041112. Epub 2015 Sep 18.

10.

Finding our way through phenotypes.

Deans AR, Lewis SE, Huala E, Anzaldo SS, Ashburner M, Balhoff JP, Blackburn DC, Blake JA, Burleigh JG, Chanet B, Cooper LD, Courtot M, Csösz S, Cui H, Dahdul W, Das S, Dececchi TA, Dettai A, Diogo R, Druzinsky RE, Dumontier M, Franz NM, Friedrich F, Gkoutos GV, Haendel M, Harmon LJ, Hayamizu TF, He Y, Hines HM, Ibrahim N, Jackson LM, Jaiswal P, James-Zorn C, Köhler S, Lecointre G, Lapp H, Lawrence CJ, Le Novère N, Lundberg JG, Macklin J, Mast AR, Midford PE, Mikó I, Mungall CJ, Oellrich A, Osumi-Sutherland D, Parkinson H, Ramírez MJ, Richter S, Robinson PN, Ruttenberg A, Schulz KS, Segerdell E, Seltmann KC, Sharkey MJ, Smith AD, Smith B, Specht CD, Squires RB, Thacker RW, Thessen A, Fernandez-Triana J, Vihinen M, Vize PD, Vogt L, Wall CE, Walls RL, Westerfeld M, Wharton RA, Wirkner CS, Woolley JB, Yoder MJ, Zorn AM, Mabee P.

PLoS Biol. 2015 Jan 6;13(1):e1002033. doi: 10.1371/journal.pbio.1002033. eCollection 2015 Jan.

11.

Patterns in root traits of woody species hosting arbuscular and ectomycorrhizas: implications for the evolution of belowground strategies.

Comas LH, Callahan HS, Midford PE.

Ecol Evol. 2014 Aug;4(15):2979-90. doi: 10.1002/ece3.1147. Epub 2014 Jul 3.

12.

The vertebrate taxonomy ontology: a framework for reasoning across model organism and species phenotypes.

Midford PE, Dececchi TA, Balhoff JP, Dahdul WM, Ibrahim N, Lapp H, Lundberg JG, Mabee PM, Sereno PC, Westerfield M, Vision TJ, Blackburn DC.

J Biomed Semantics. 2013 Nov 22;4(1):34. doi: 10.1186/2041-1480-4-34.

13.

Phylotastic! Making tree-of-life knowledge accessible, reusable and convenient.

Stoltzfus A, Lapp H, Matasci N, Deus H, Sidlauskas B, Zmasek CM, Vaidya G, Pontelli E, Cranston K, Vos R, Webb CO, Harmon LJ, Pirrung M, O'Meara B, Pennell MW, Mirarab S, Rosenberg MS, Balhoff JP, Bik HM, Heath TA, Midford PE, Brown JW, McTavish EJ, Sukumaran J, Westneat M, Alfaro ME, Steele A, Jordan G.

BMC Bioinformatics. 2013 May 13;14:158. doi: 10.1186/1471-2105-14-158.

14.

Exploring power and parameter estimation of the BiSSE method for analyzing species diversification.

Davis MP, Midford PE, Maddison W.

BMC Evol Biol. 2013 Feb 11;13:38. doi: 10.1186/1471-2148-13-38.

15.

500,000 fish phenotypes: The new informatics landscape for evolutionary and developmental biology of the vertebrate skeleton.

Mabee BP, Balhoff JP, Dahdul WM, Lapp H, Midford PE, Vision TJ, Westerfield M.

J Appl Ichthyol. 2012 Jun 1;28(3):300-305. Epub 2012 May 21.

16.

NeXML: rich, extensible, and verifiable representation of comparative data and metadata.

Vos RA, Balhoff JP, Caravas JA, Holder MT, Lapp H, Maddison WP, Midford PE, Priyam A, Sukumaran J, Xia X, Stoltzfus A.

Syst Biol. 2012 Jul;61(4):675-89. doi: 10.1093/sysbio/sys025. Epub 2012 Feb 22.

17.

The teleost anatomy ontology: anatomical representation for the genomics age.

Dahdul WM, Lundberg JG, Midford PE, Balhoff JP, Lapp H, Vision TJ, Haendel MA, Westerfield M, Mabee PM.

Syst Biol. 2010 Jul;59(4):369-83. doi: 10.1093/sysbio/syq013. Epub 2010 Mar 29.

18.

Evolutionary characters, phenotypes and ontologies: curating data from the systematic biology literature.

Dahdul WM, Balhoff JP, Engeman J, Grande T, Hilton EJ, Kothari C, Lapp H, Lundberg JG, Midford PE, Vision TJ, Westerfield M, Mabee PM.

PLoS One. 2010 May 20;5(5):e10708. doi: 10.1371/journal.pone.0010708.

19.

Phenex: ontological annotation of phenotypic diversity.

Balhoff JP, Dahdul WM, Kothari CR, Lapp H, Lundberg JG, Mabee P, Midford PE, Westerfield M, Vision TJ.

PLoS One. 2010 May 5;5(5):e10500. doi: 10.1371/journal.pone.0010500.

20.

Robots aren't the only physical models.

Midford PE.

Behav Brain Sci. 2001 Dec;24(6):1069-1070. doi: 10.1017/S0140525X01420127.

PMID:
18241381
21.

Estimating a binary character's effect on speciation and extinction.

Maddison WP, Midford PE, Otto SP.

Syst Biol. 2007 Oct;56(5):701-10.

PMID:
17849325
22.

Linking of digital images to phylogenetic data matrices using a morphological ontology.

Ramírez MJ, Coddington JA, Maddison WP, Midford PE, Prendini L, Miller J, Griswold CE, Hormiga G, Sierwald P, Scharff N, Benjamin SP, Wheeler WC.

Syst Biol. 2007 Apr;56(2):283-94.

PMID:
17464883
23.

Within-species variation and measurement error in phylogenetic comparative methods.

Ives AR, Midford PE, Garland T Jr.

Syst Biol. 2007 Apr;56(2):252-70.

PMID:
17464881
24.

Ontologies for behavior.

Midford PE.

Bioinformatics. 2004 Dec 12;20(18):3700-1. Epub 2004 Jul 29.

PMID:
15284105
25.

Social learning of a novel foraging patch in families of free-living Florida scrub-jays.

Midford PE, Hailman JP, Woolfenden GE.

Anim Behav. 2000 Jun;59(6):1199-1207.

PMID:
10877899

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