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Items: 1 to 50 of 97

1.

Cisplatin-resistant triple-negative breast cancer subtypes: multiple mechanisms of resistance.

Hill DP, Harper A, Malcolm J, McAndrews MS, Mockus SM, Patterson SE, Reynolds T, Baker EJ, Bult CJ, Chesler EJ, Blake JA.

BMC Cancer. 2019 Nov 4;19(1):1039. doi: 10.1186/s12885-019-6278-9.

2.

Gene Ontology Causal Activity Modeling (GO-CAM) moves beyond GO annotations to structured descriptions of biological functions and systems.

Thomas PD, Hill DP, Mi H, Osumi-Sutherland D, Van Auken K, Carbon S, Balhoff JP, Albou LP, Good B, Gaudet P, Lewis SE, Mungall CJ.

Nat Genet. 2019 Oct;51(10):1429-1433. doi: 10.1038/s41588-019-0500-1. No abstract available.

PMID:
31548717
3.

Deep fluid pathways beneath Mammoth Mountain, California, illuminated by migrating earthquake swarms.

Hotovec-Ellis AJ, Shelly DR, Hill DP, Pitt AM, Dawson PB, Chouet BA.

Sci Adv. 2018 Aug 15;4(8):eaat5258. doi: 10.1126/sciadv.aat5258. eCollection 2018 Aug.

4.

Exploring autophagy with Gene Ontology.

Denny P, Feuermann M, Hill DP, Lovering RC, Plun-Favreau H, Roncaglia P.

Autophagy. 2018;14(3):419-436. doi: 10.1080/15548627.2017.1415189. Epub 2018 Feb 17. Review.

5.

Improving Interpretation of Cardiac Phenotypes and Enhancing Discovery With Expanded Knowledge in the Gene Ontology.

Lovering RC, Roncaglia P, Howe DG, Laulederkind SJF, Khodiyar VK, Berardini TZ, Tweedie S, Foulger RE, Osumi-Sutherland D, Campbell NH, Huntley RP, Talmud PJ, Blake JA, Breckenridge R, Riley PR, Lambiase PD, Elliott PM, Clapp L, Tinker A, Hill DP.

Circ Genom Precis Med. 2018 Feb;11(2):e001813. doi: 10.1161/CIRCGEN.117.001813.

6.

Modeling biochemical pathways in the gene ontology.

Hill DP, D'Eustachio P, Berardini TZ, Mungall CJ, Renedo N, Blake JA.

Database (Oxford). 2016 Sep 1;2016. pii: baw126. doi: 10.1093/database/baw126. Print 2016.

7.

The role of visualization and 3-D printing in biological data mining.

Weiss TL, Zieselman A, Hill DP, Diamond SG, Shen L, Saykin AJ, Moore JH; Alzheimer’s Disease Neuroimaging Initiative.

BioData Min. 2015 Aug 5;8:22. doi: 10.1186/s13040-015-0056-2. eCollection 2015.

8.

Application of comparative biology in GO functional annotation: the mouse model.

Drabkin HJ, Christie KR, Dolan ME, Hill DP, Ni L, Sitnikov D, Blake JA.

Mamm Genome. 2015 Oct;26(9-10):574-83. doi: 10.1007/s00335-015-9580-0. Epub 2015 Jul 4.

9.

Methodology for the inference of gene function from phenotype data.

Ascensao JA, Dolan ME, Hill DP, Blake JA.

BMC Bioinformatics. 2014 Dec 12;15:405. doi: 10.1186/s12859-014-0405-z.

10.

Epistasis analysis using artificial intelligence.

Moore JH, Hill DP.

Methods Mol Biol. 2015;1253:327-46. doi: 10.1007/978-1-4939-2155-3_18.

PMID:
25403541
11.

Representing kidney development using the gene ontology.

Alam-Faruque Y, Hill DP, Dimmer EC, Harris MA, Foulger RE, Tweedie S, Attrill H, Howe DG, Thomas SR, Davidson D, Woolf AS, Blake JA, Mungall CJ, O'Donovan C, Apweiler R, Huntley RP.

PLoS One. 2014 Jun 18;9(6):e99864. doi: 10.1371/journal.pone.0099864. eCollection 2014.

12.

A method for increasing expressivity of Gene Ontology annotations using a compositional approach.

Huntley RP, Harris MA, Alam-Faruque Y, Blake JA, Carbon S, Dietze H, Dimmer EC, Foulger RE, Hill DP, Khodiyar VK, Lock A, Lomax J, Lovering RC, Mutowo-Meullenet P, Sawford T, Van Auken K, Wood V, Mungall CJ.

BMC Bioinformatics. 2014 May 21;15:155. doi: 10.1186/1471-2105-15-155.

13.

TermGenie - a web-application for pattern-based ontology class generation.

Dietze H, Berardini TZ, Foulger RE, Hill DP, Lomax J, Osumi-Sutherland D, Roncaglia P, Mungall CJ.

J Biomed Semantics. 2014 Dec 11;5:48. doi: 10.1186/2041-1480-5-48. eCollection 2014.

14.

The Gene Ontology (GO) Cellular Component Ontology: integration with SAO (Subcellular Anatomy Ontology) and other recent developments.

Roncaglia P, Martone ME, Hill DP, Berardini TZ, Foulger RE, Imam FT, Drabkin H, Mungall CJ, Lomax J.

J Biomed Semantics. 2013 Oct 7;4(1):20. doi: 10.1186/2041-1480-4-20.

15.

Gene Ontology annotation of sequence-specific DNA binding transcription factors: setting the stage for a large-scale curation effort.

Tripathi S, Christie KR, Balakrishnan R, Huntley R, Hill DP, Thommesen L, Blake JA, Kuiper M, Lægreid A.

Database (Oxford). 2013 Aug 27;2013:bat062. doi: 10.1093/database/bat062. Print 2013.

16.

Dovetailing biology and chemistry: integrating the Gene Ontology with the ChEBI chemical ontology.

Hill DP, Adams N, Bada M, Batchelor C, Berardini TZ, Dietze H, Drabkin HJ, Ennis M, Foulger RE, Harris MA, Hastings J, Kale NS, de Matos P, Mungall CJ, Owen G, Roncaglia P, Steinbeck C, Turner S, Lomax J.

BMC Genomics. 2013 Jul 29;14:513. doi: 10.1186/1471-2164-14-513.

17.

Gene Ontology annotations and resources.

Gene Ontology Consortium, Blake JA, Dolan M, Drabkin H, Hill DP, Li N, Sitnikov D, Bridges S, Burgess S, Buza T, McCarthy F, Peddinti D, Pillai L, Carbon S, Dietze H, Ireland A, Lewis SE, Mungall CJ, Gaudet P, Chrisholm RL, Fey P, Kibbe WA, Basu S, Siegele DA, McIntosh BK, Renfro DP, Zweifel AE, Hu JC, Brown NH, Tweedie S, Alam-Faruque Y, Apweiler R, Auchinchloss A, Axelsen K, Bely B, Blatter M-, Bonilla C, Bouguerleret L, Boutet E, Breuza L, Bridge A, Chan WM, Chavali G, Coudert E, Dimmer E, Estreicher A, Famiglietti L, Feuermann M, Gos A, Gruaz-Gumowski N, Hieta R, Hinz C, Hulo C, Huntley R, James J, Jungo F, Keller G, Laiho K, Legge D, Lemercier P, Lieberherr D, Magrane M, Martin MJ, Masson P, Mutowo-Muellenet P, O'Donovan C, Pedruzzi I, Pichler K, Poggioli D, Porras Millán P, Poux S, Rivoire C, Roechert B, Sawford T, Schneider M, Stutz A, Sundaram S, Tognolli M, Xenarios I, Foulgar R, Lomax J, Roncaglia P, Khodiyar VK, Lovering RC, Talmud PJ, Chibucos M, Giglio MG, Chang H-, Hunter S, McAnulla C, Mitchell A, Sangrador A, Stephan R, Harris MA, Oliver SG, Rutherford K, Wood V, Bahler J, Lock A, Kersey PJ, McDowall DM, Staines DM, Dwinell M, Shimoyama M, Laulederkind S, Hayman T, Wang S-, Petri V, Lowry T, D'Eustachio P, Matthews L, Balakrishnan R, Binkley G, Cherry JM, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hitz BC, Hong EL, Karra K, Miyasato SR, Nash RS, Park J, Skrzypek MS, Weng S, Wong ED, Berardini TZ, Huala E, Mi H, Thomas PD, Chan J, Kishore R, Sternberg P, Van Auken K, Howe D, Westerfield M.

Nucleic Acids Res. 2013 Jan;41(Database issue):D530-5. doi: 10.1093/nar/gks1050. Epub 2012 Nov 17.

18.

The representation of heart development in the gene ontology.

Khodiyar VK, Hill DP, Howe D, Berardini TZ, Tweedie S, Talmud PJ, Breckenridge R, Bhattarcharya S, Riley P, Scambler P, Lovering RC.

Dev Biol. 2011 Jun 1;354(1):9-17. doi: 10.1016/j.ydbio.2011.03.011. Epub 2011 Mar 17.

19.

Wound healing trajectories to determine pressure ulcer treatment efficacy.

Payne WG, Bhalla R, Hill DP, Pierpont YN, Robson MC.

Eplasty. 2011 Jan 10;11:e1.

20.

Integrating text mining into the MGI biocuration workflow.

Dowell KG, McAndrews-Hill MS, Hill DP, Drabkin HJ, Blake JA.

Database (Oxford). 2009;2009:bap019. Epub 2009 Nov 21.

21.

Cross-product extensions of the Gene Ontology.

Mungall CJ, Bada M, Berardini TZ, Deegan J, Ireland A, Harris MA, Hill DP, Lomax J.

J Biomed Inform. 2011 Feb;44(1):80-6. doi: 10.1016/j.jbi.2010.02.002. Epub 2010 Feb 10.

22.

Ontology engineering.

Alterovitz G, Xiang M, Hill DP, Lomax J, Liu J, Cherkassky M, Dreyfuss J, Mungall C, Harris MA, Dolan ME, Blake JA, Ramoni MF.

Nat Biotechnol. 2010 Feb;28(2):128-30. doi: 10.1038/nbt0210-128. No abstract available.

23.

Representing ontogeny through ontology: a developmental biologist's guide to the gene ontology.

Hill DP, Berardini TZ, Howe DG, Van Auken KM.

Mol Reprod Dev. 2010 Apr;77(4):314-29. doi: 10.1002/mrd.21130. Review.

24.

Big data: The future of biocuration.

Howe D, Costanzo M, Fey P, Gojobori T, Hannick L, Hide W, Hill DP, Kania R, Schaeffer M, St Pierre S, Twigger S, White O, Rhee SY.

Nature. 2008 Sep 4;455(7209):47-50. doi: 10.1038/455047a. No abstract available.

25.

An en masse phenotype and function prediction system for Mus musculus.

Taşan M, Tian W, Hill DP, Gibbons FD, Blake JA, Roth FP.

Genome Biol. 2008;9 Suppl 1:S8. doi: 10.1186/gb-2008-9-s1-s8. Epub 2008 Jun 27.

26.

A critical assessment of Mus musculus gene function prediction using integrated genomic evidence.

Peña-Castillo L, Tasan M, Myers CL, Lee H, Joshi T, Zhang C, Guan Y, Leone M, Pagnani A, Kim WK, Krumpelman C, Tian W, Obozinski G, Qi Y, Mostafavi S, Lin GN, Berriz GF, Gibbons FD, Lanckriet G, Qiu J, Grant C, Barutcuoglu Z, Hill DP, Warde-Farley D, Grouios C, Ray D, Blake JA, Deng M, Jordan MI, Noble WS, Morris Q, Klein-Seetharaman J, Bar-Joseph Z, Chen T, Sun F, Troyanskaya OG, Marcotte EM, Xu D, Hughes TR, Roth FP.

Genome Biol. 2008;9 Suppl 1:S2. doi: 10.1186/gb-2008-9-s1-s2. Epub 2008 Jun 27.

27.

Gene Ontology annotations: what they mean and where they come from.

Hill DP, Smith B, McAndrews-Hill MS, Blake JA.

BMC Bioinformatics. 2008 Apr 29;9 Suppl 5:S2. doi: 10.1186/1471-2105-9-S5-S2.

28.

AgBase: a functional genomics resource for agriculture.

McCarthy FM, Wang N, Magee GB, Nanduri B, Lawrence ML, Camon EB, Barrell DG, Hill DP, Dolan ME, Williams WP, Luthe DS, Bridges SM, Burgess SC.

BMC Genomics. 2006 Sep 8;7:229.

29.

Monitoring super-volcanoes: geophysical and geochemical signals at Yellowstone and other large caldera systems.

Lowenstern JB, Smith RB, Hill DP.

Philos Trans A Math Phys Eng Sci. 2006 Aug 15;364(1845):2055-72.

PMID:
16844648
30.

Wound-healing trajectories as outcome measures of venous stasis ulcer treatment.

Steed DL, Hill DP, Woodske ME, Payne WG, Robson MC.

Int Wound J. 2006 Mar;3(1):40-7.

PMID:
16650209
31.

Ontological visualization of protein-protein interactions.

Drabkin HJ, Hollenbeck C, Hill DP, Blake JA.

BMC Bioinformatics. 2005 Feb 11;6:29.

32.

Initial healing rates of venous ulcers: are they useful as predictors of healing?

Hill DP, Poore S, Wilson J, Robson MC, Cherry GW.

Am J Surg. 2004 Jul;188(1A Suppl):22-5.

PMID:
15223498
33.

The mouse Gene Expression Database (GXD): updates and enhancements.

Hill DP, Begley DA, Finger JH, Hayamizu TF, McCright IJ, Smith CM, Beal JS, Corbani LE, Blake JA, Eppig JT, Kadin JA, Richardson JE, Ringwald M.

Nucleic Acids Res. 2004 Jan 1;32(Database issue):D568-71.

34.

The Gene Ontology (GO) database and informatics resource.

Harris MA, Clark J, Ireland A, Lomax J, Ashburner M, Foulger R, Eilbeck K, Lewis S, Marshall B, Mungall C, Richter J, Rubin GM, Blake JA, Bult C, Dolan M, Drabkin H, Eppig JT, Hill DP, Ni L, Ringwald M, Balakrishnan R, Cherry JM, Christie KR, Costanzo MC, Dwight SS, Engel S, Fisk DG, Hirschman JE, Hong EL, Nash RS, Sethuraman A, Theesfeld CL, Botstein D, Dolinski K, Feierbach B, Berardini T, Mundodi S, Rhee SY, Apweiler R, Barrell D, Camon E, Dimmer E, Lee V, Chisholm R, Gaudet P, Kibbe W, Kishore R, Schwarz EM, Sternberg P, Gwinn M, Hannick L, Wortman J, Berriman M, Wood V, de la Cruz N, Tonellato P, Jaiswal P, Seigfried T, White R; Gene Ontology Consortium.

Nucleic Acids Res. 2004 Jan 1;32(Database issue):D258-61.

35.

Development and evaluation of an automated annotation pipeline and cDNA annotation system.

Kasukawa T, Furuno M, Nikaido I, Bono H, Hume DA, Bult C, Hill DP, Baldarelli R, Gough J, Kanapin A, Matsuda H, Schriml LM, Hayashizaki Y, Okazaki Y, Quackenbush J.

Genome Res. 2003 Jun;13(6B):1542-51.

36.

Connecting sequence and biology in the laboratory mouse.

Baldarelli RM, Hill DP, Blake JA, Adachi J, Furuno M, Bradt D, Corbani LE, Cousins S, Frazer KS, Qi D, Yang L, Ramachandran S, Reed D, Zhu Y, Kasukawa T, Ringwald M, King BL, Maltais LJ, McKenzie LM, Schriml LM, Maglott D, Church DM, Pruitt K, Eppig JT, Richardson JE, Kadin JA, Bult CJ.

Genome Res. 2003 Jun;13(6B):1505-19.

37.

Human disease genes and their cloned mouse orthologs: exploration of the FANTOM2 cDNA sequence data set.

Schriml LM, Hill DP, Blake JA, Bono H, Wynshaw-Boris A, Pavan WJ, Ring BZ, Beisel K, Setou M, Okazaki Y; RIKEN GER Group; GSL Members.

Genome Res. 2003 Jun;13(6B):1496-500.

38.

G protein-coupled receptor genes in the FANTOM2 database.

Kawasawa Y, McKenzie LM, Hill DP, Bono H, Yanagisawa M; RIKEN GER Group; GSL Members.

Genome Res. 2003 Jun;13(6B):1466-77.

39.

The 2002 Denali fault earthquake, Alaska: a large magnitude, slip-partitioned event.

Eberhart-Phillips D, Haeussler PJ, Freymueller JT, Frankel AD, Rubin CM, Craw P, Ratchkovski NA, Anderson G, Carver GA, Crone AJ, Dawson TE, Fletcher H, Hansen R, Harp EL, Harris RA, Hill DP, Hreinsdóttir S, Jibson RW, Jones LM, Kayen R, Keefer DK, Larsen CF, Moran SC, Personius SF, Plafker G, Sherrod B, Sieh K, Sitar N, Wallace WK.

Science. 2003 May 16;300(5622):1113-8.

40.

The effect of TGF-beta2 in various vehicles on incisional wound healing.

Wright TE, Hill DP, Ko F, Soler PM, Smith PD, Franz M, Nichols EH, Robson MC.

Int J Surg Investig. 2000;2(2):133-43.

PMID:
12678511
41.

Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs.

Okazaki Y, Furuno M, Kasukawa T, Adachi J, Bono H, Kondo S, Nikaido I, Osato N, Saito R, Suzuki H, Yamanaka I, Kiyosawa H, Yagi K, Tomaru Y, Hasegawa Y, Nogami A, Schönbach C, Gojobori T, Baldarelli R, Hill DP, Bult C, Hume DA, Quackenbush J, Schriml LM, Kanapin A, Matsuda H, Batalov S, Beisel KW, Blake JA, Bradt D, Brusic V, Chothia C, Corbani LE, Cousins S, Dalla E, Dragani TA, Fletcher CF, Forrest A, Frazer KS, Gaasterland T, Gariboldi M, Gissi C, Godzik A, Gough J, Grimmond S, Gustincich S, Hirokawa N, Jackson IJ, Jarvis ED, Kanai A, Kawaji H, Kawasawa Y, Kedzierski RM, King BL, Konagaya A, Kurochkin IV, Lee Y, Lenhard B, Lyons PA, Maglott DR, Maltais L, Marchionni L, McKenzie L, Miki H, Nagashima T, Numata K, Okido T, Pavan WJ, Pertea G, Pesole G, Petrovsky N, Pillai R, Pontius JU, Qi D, Ramachandran S, Ravasi T, Reed JC, Reed DJ, Reid J, Ring BZ, Ringwald M, Sandelin A, Schneider C, Semple CA, Setou M, Shimada K, Sultana R, Takenaka Y, Taylor MS, Teasdale RD, Tomita M, Verardo R, Wagner L, Wahlestedt C, Wang Y, Watanabe Y, Wells C, Wilming LG, Wynshaw-Boris A, Yanagisawa M, Yang I, Yang L, Yuan Z, Zavolan M, Zhu Y, Zimmer A, Carninci P, Hayatsu N, Hirozane-Kishikawa T, Konno H, Nakamura M, Sakazume N, Sato K, Shiraki T, Waki K, Kawai J, Aizawa K, Arakawa T, Fukuda S, Hara A, Hashizume W, Imotani K, Ishii Y, Itoh M, Kagawa I, Miyazaki A, Sakai K, Sasaki D, Shibata K, Shinagawa A, Yasunishi A, Yoshino M, Waterston R, Lander ES, Rogers J, Birney E, Hayashizaki Y; FANTOM Consortium; RIKEN Genome Exploration Research Group Phase I & II Team.

Nature. 2002 Dec 5;420(6915):563-73.

PMID:
12466851
42.

Extension and integration of the gene ontology (GO): combining GO vocabularies with external vocabularies.

Hill DP, Blake JA, Richardson JE, Ringwald M.

Genome Res. 2002 Dec;12(12):1982-91.

43.

Program description: Strategies for biological annotation of mammalian systems: implementing gene ontologies in mouse genome informatics.

Hill DP, Davis AP, Richardson JE, Corradi JP, Ringwald M, Eppig JT, Blake JA.

Genomics. 2001 May 15;74(1):121-8. No abstract available.

PMID:
11374909
44.

Long-term outcome study of growth factor-treated pressure ulcers.

Payne WG, Ochs DE, Meltzer DD, Hill DP, Mannari RJ, Robson LE, Robson MC.

Am J Surg. 2001 Jan;181(1):81-6.

PMID:
11248182
45.

XXXIV international congress of physiological sciences: It's for anatomists, Too!

Hill DP.

Anat Rec. 2000 Dec 15;261(6):222-3. No abstract available.

46.

In vitro fibroblast populated collagen lattices are not good models of in vivo clinical wound healing.

Kuhn MA, Smith PD, Hill DP, Ko F, Meltzer DD, Vande Berg JS, Robson MC.

Wound Repair Regen. 2000 Jul-Aug;8(4):270-6.

PMID:
11013018
47.

Wound healing trajectories as predictors of effectiveness of therapeutic agents.

Robson MC, Hill DP, Woodske ME, Steed DL.

Arch Surg. 2000 Jul;135(7):773-7.

PMID:
10896369
48.

Gene ontology: tool for the unification of biology. The Gene Ontology Consortium.

Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G.

Nat Genet. 2000 May;25(1):25-9. No abstract available.

49.

Sequential cytokine therapy for pressure ulcers: clinical and mechanistic response.

Robson MC, Hill DP, Smith PD, Wang X, Meyer-Siegler K, Ko F, VandeBerg JS, Payne WG, Ochs D, Robson LE.

Ann Surg. 2000 Apr;231(4):600-11.

50.

The Mouse Gene Expression Database (GXD).

Ringwald M, Eppig JT, Begley DA, Corradi JP, McCright IJ, Hayamizu TF, Hill DP, Kadin JA, Richardson JE.

Nucleic Acids Res. 2001 Jan 1;29(1):98-101.

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