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Items: 37

1.

Meeting the multiscale challenge: representing physiology processes over ApiNATOMY circuits using bond graphs.

de Bono B, Safaei S, Grenon P, Hunter P.

Interface Focus. 2018 Feb 6;8(1):20170026. doi: 10.1098/rsfs.2017.0026. Epub 2017 Dec 15.

2.

Automated PDF highlighting to support faster curation of literature for Parkinson's and Alzheimer's disease.

Wu H, Oellrich A, Girges C, de Bono B, Hubbard TJ, Dobson RJ.

Database (Oxford). 2017 Jan 1;2017(1). doi: 10.1093/database/bax027.

3.

Roadmap for cardiovascular circulation model.

Safaei S, Bradley CP, Suresh V, Mithraratne K, Muller A, Ho H, Ladd D, Hellevik LR, Omholt SW, Chase JG, Müller LO, Watanabe SM, Blanco PJ, de Bono B, Hunter PJ.

J Physiol. 2016 Dec 1;594(23):6909-6928. doi: 10.1113/JP272660. Epub 2016 Sep 29.

4.

The Human Physiome: how standards, software and innovative service infrastructures are providing the building blocks to make it achievable.

Nickerson D, Atalag K, de Bono B, Geiger J, Goble C, Hollmann S, Lonien J, Müller W, Regierer B, Stanford NJ, Golebiewski M, Hunter P.

Interface Focus. 2016 Apr 6;6(2):20150103. doi: 10.1098/rsfs.2015.0103. Review.

5.

Requirements for the formal representation of pathophysiology mechanisms by clinicians.

de Bono B, Helvensteijn M, Kokash N, Martorelli I, Sarwar D, Islam S, Grenon P, Hunter P.

Interface Focus. 2016 Apr 6;6(2):20150099. doi: 10.1098/rsfs.2015.0099.

6.

A physiome interoperability roadmap for personalized drug development.

Thomas S, Wolstencroft K, de Bono B, Hunter PJ.

Interface Focus. 2016 Apr 6;6(2):20150094. doi: 10.1098/rsfs.2015.0094.

7.

Bioinformatics Mining and Modeling Methods for the Identification of Disease Mechanisms in Neurodegenerative Disorders.

Hofmann-Apitius M, Ball G, Gebel S, Bagewadi S, de Bono B, Schneider R, Page M, Kodamullil AT, Younesi E, Ebeling C, Tegnér J, Canard L.

Int J Mol Sci. 2015 Dec 7;16(12):29179-206. doi: 10.3390/ijms161226148. Review.

8.

TARM1 Is a Novel Leukocyte Receptor Complex-Encoded ITAM Receptor That Costimulates Proinflammatory Cytokine Secretion by Macrophages and Neutrophils.

Radjabova V, Mastroeni P, Skjødt K, Zaccone P, de Bono B, Goodall JC, Chilvers ER, Juss JK, Jones DC, Trowsdale J, Barrow AD.

J Immunol. 2015 Oct 1;195(7):3149-59. doi: 10.4049/jimmunol.1401847. Epub 2015 Aug 26.

9.

The Open Physiology workflow: modeling processes over physiology circuitboards of interoperable tissue units.

de Bono B, Safaei S, Grenon P, Nickerson DP, Alexander S, Helvensteijn M, Kok JN, Kokash N, Wu A, Yu T, Hunter P, Baldock RA.

Front Physiol. 2015 Feb 24;6:24. doi: 10.3389/fphys.2015.00024. eCollection 2015.

10.

Transcriptional diversity during lineage commitment of human blood progenitors.

Chen L, Kostadima M, Martens JHA, Canu G, Garcia SP, Turro E, Downes K, Macaulay IC, Bielczyk-Maczynska E, Coe S, Farrow S, Poudel P, Burden F, Jansen SBG, Astle WJ, Attwood A, Bariana T, de Bono B, Breschi A, Chambers JC, Consortium B, Choudry FA, Clarke L, Coupland P, van der Ent M, Erber WN, Jansen JH, Favier R, Fenech ME, Foad N, Freson K, van Geet C, Gomez K, Guigo R, Hampshire D, Kelly AM, Kerstens HHD, Kooner JS, Laffan M, Lentaigne C, Labalette C, Martin T, Meacham S, Mumford A, Nürnberg S, Palumbo E, van der Reijden BA, Richardson D, Sammut SJ, Slodkowicz G, Tamuri AU, Vasquez L, Voss K, Watt S, Westbury S, Flicek P, Loos R, Goldman N, Bertone P, Read RJ, Richardson S, Cvejic A, Soranzo N, Ouwehand WH, Stunnenberg HG, Frontini M, Rendon A.

Science. 2014 Sep 26;345(6204):1251033. doi: 10.1126/science.1251033.

11.

Biophysical constraints on the evolution of tissue structure and function.

Hunter PJ, de Bono B.

J Physiol. 2014 Jun 1;592(11):2389-401. doi: 10.1113/jphysiol.2014.273235.

12.

A vision and strategy for the virtual physiological human: 2012 update.

Hunter P, Chapman T, Coveney PV, de Bono B, Diaz V, Fenner J, Frangi AF, Harris P, Hose R, Kohl P, Lawford P, McCormack K, Mendes M, Omholt S, Quarteroni A, Shublaq N, Skår J, Stroetmann K, Tegner J, Thomas SR, Tollis I, Tsamardinos I, van Beek JH, Viceconti M.

Interface Focus. 2013 Apr 6;3(2):20130004. doi: 10.1098/rsfs.2013.0004.

13.

HuPSON: the human physiology simulation ontology.

Gündel M, Younesi E, Malhotra A, Wang J, Li H, Zhang B, de Bono B, Mevissen HT, Hofmann-Apitius M.

J Biomed Semantics. 2013 Nov 22;4(1):35. doi: 10.1186/2041-1480-4-35.

14.

Functional tissue units and their primary tissue motifs in multi-scale physiology.

de Bono B, Grenon P, Baldock R, Hunter P.

J Biomed Semantics. 2013 Oct 8;4(1):22. doi: 10.1186/2041-1480-4-22.

15.

Eliciting candidate anatomical routes for protein interactions: a scenario from endocrine physiology.

Grenon P, de Bono B.

BMC Bioinformatics. 2013 Apr 16;14:131. doi: 10.1186/1471-2105-14-131.

16.

Integrating knowledge representation and quantitative modelling in physiology.

de Bono B, Hunter P.

Biotechnol J. 2012 Aug;7(8):958-72. doi: 10.1002/biot.201100304.

PMID:
22887885
17.
18.

An infrastructure for ontology-based information systems in biomedicine: RICORDO case study.

Wimalaratne SM, Grenon P, Hoehndorf R, Gkoutos GV, de Bono B.

Bioinformatics. 2012 Feb 1;28(3):448-50. doi: 10.1093/bioinformatics/btr662. Epub 2011 Nov 29.

PMID:
22130590
19.

The RICORDO approach to semantic interoperability for biomedical data and models: strategy, standards and solutions.

de Bono B, Hoehndorf R, Wimalaratne S, Gkoutos G, Grenon P.

BMC Res Notes. 2011 Aug 30;4:313. doi: 10.1186/1756-0500-4-313.

20.

Integrating systems biology models and biomedical ontologies.

Hoehndorf R, Dumontier M, Gennari JH, Wimalaratne S, de Bono B, Cook DL, Gkoutos GV.

BMC Syst Biol. 2011 Aug 11;5:124. doi: 10.1186/1752-0509-5-124.

21.

Transcription profiling in human platelets reveals LRRFIP1 as a novel protein regulating platelet function.

Goodall AH, Burns P, Salles I, Macaulay IC, Jones CI, Ardissino D, de Bono B, Bray SL, Deckmyn H, Dudbridge F, Fitzgerald DJ, Garner SF, Gusnanto A, Koch K, Langford C, O'Connor MN, Rice CM, Stemple D, Stephens J, Trip MD, Zwaginga JJ, Samani NJ, Watkins NA, Maguire PB, Ouwehand WH; Bloodomics Consortium.

Blood. 2010 Nov 25;116(22):4646-56. doi: 10.1182/blood-2010-04-280925. Epub 2010 Sep 10.

22.

A vision and strategy for the virtual physiological human in 2010 and beyond.

Hunter P, Coveney PV, de Bono B, Diaz V, Fenner J, Frangi AF, Harris P, Hose R, Kohl P, Lawford P, McCormack K, Mendes M, Omholt S, Quarteroni A, Skår J, Tegner J, Randall Thomas S, Tollis I, Tsamardinos I, van Beek JH, Viceconti M.

Philos Trans A Math Phys Eng Sci. 2010 Jun 13;368(1920):2595-614. doi: 10.1098/rsta.2010.0048.

23.

A functional genomics approach reveals novel quantitative trait loci associated with platelet signaling pathways.

Jones CI, Bray S, Garner SF, Stephens J, de Bono B, Angenent WG, Bentley D, Burns P, Coffey A, Deloukas P, Earthrowl M, Farndale RW, Hoylaerts MF, Koch K, Rankin A, Rice CM, Rogers J, Samani NJ, Steward M, Walker A, Watkins NA, Akkerman JW, Dudbridge F, Goodall AH, Ouwehand WH; Bloodomics Consortium.

Blood. 2009 Aug 13;114(7):1405-16. doi: 10.1182/blood-2009-02-202614. Epub 2009 May 8.

PMID:
19429868
24.

Comparative genomics indicates the mammalian CD33rSiglec locus evolved by an ancient large-scale inverse duplication and suggests all Siglecs share a common ancestral region.

Cao H, de Bono B, Belov K, Wong ES, Trowsdale J, Barrow AD.

Immunogenetics. 2009 May;61(5):401-17. doi: 10.1007/s00251-009-0372-0. Epub 2009 Apr 1.

PMID:
19337729
25.

A HaemAtlas: characterizing gene expression in differentiated human blood cells.

Watkins NA, Gusnanto A, de Bono B, De S, Miranda-Saavedra D, Hardie DL, Angenent WG, Attwood AP, Ellis PD, Erber W, Foad NS, Garner SF, Isacke CM, Jolley J, Koch K, Macaulay IC, Morley SL, Rendon A, Rice KM, Taylor N, Thijssen-Timmer DC, Tijssen MR, van der Schoot CE, Wernisch L, Winzer T, Dudbridge F, Buckley CD, Langford CF, Teichmann S, Göttgens B, Ouwehand WH; Bloodomics Consortium.

Blood. 2009 May 7;113(19):e1-9. doi: 10.1182/blood-2008-06-162958. Epub 2009 Feb 19.

26.

Functional genomics in zebrafish permits rapid characterization of novel platelet membrane proteins.

O'Connor MN, Salles II, Cvejic A, Watkins NA, Walker A, Garner SF, Jones CI, Macaulay IC, Steward M, Zwaginga JJ, Bray SL, Dudbridge F, de Bono B, Goodall AH, Deckmyn H, Stemple DL, Ouwehand WH; Bloodomics Consortium.

Blood. 2009 May 7;113(19):4754-62. doi: 10.1182/blood-2008-06-162693. Epub 2008 Dec 24.

27.

Reactome knowledgebase of human biological pathways and processes.

Matthews L, Gopinath G, Gillespie M, Caudy M, Croft D, de Bono B, Garapati P, Hemish J, Hermjakob H, Jassal B, Kanapin A, Lewis S, Mahajan S, May B, Schmidt E, Vastrik I, Wu G, Birney E, Stein L, D'Eustachio P.

Nucleic Acids Res. 2009 Jan;37(Database issue):D619-22. doi: 10.1093/nar/gkn863. Epub 2008 Nov 3.

28.

SIGLEC16 encodes a DAP12-associated receptor expressed in macrophages that evolved from its inhibitory counterpart SIGLEC11 and has functional and non-functional alleles in humans.

Cao H, Lakner U, de Bono B, Traherne JA, Trowsdale J, Barrow AD.

Eur J Immunol. 2008 Aug;38(8):2303-15. doi: 10.1002/eji.200738078.

29.

Characterization of the opossum immune genome provides insights into the evolution of the mammalian immune system.

Belov K, Sanderson CE, Deakin JE, Wong ES, Assange D, McColl KA, Gout A, de Bono B, Barrow AD, Speed TP, Trowsdale J, Papenfuss AT.

Genome Res. 2007 Jul;17(7):982-91. Epub 2007 May 10.

30.

Reactome: a knowledge base of biologic pathways and processes.

Vastrik I, D'Eustachio P, Schmidt E, Gopinath G, Croft D, de Bono B, Gillespie M, Jassal B, Lewis S, Matthews L, Wu G, Birney E, Stein L.

Genome Biol. 2007;8(3):R39. Erratum in: Genome Biol. 2009 Feb 4;10(2):402. Joshi-Tope, Geeta [removed].

31.

Relationship between SPRY and B30.2 protein domains. Evolution of a component of immune defence?

Rhodes DA, de Bono B, Trowsdale J.

Immunology. 2005 Dec;116(4):411-7. Review.

32.

The transcriptional landscape of the mammalian genome.

Carninci P, Kasukawa T, Katayama S, Gough J, Frith MC, Maeda N, Oyama R, Ravasi T, Lenhard B, Wells C, Kodzius R, Shimokawa K, Bajic VB, Brenner SE, Batalov S, Forrest AR, Zavolan M, Davis MJ, Wilming LG, Aidinis V, Allen JE, Ambesi-Impiombato A, Apweiler R, Aturaliya RN, Bailey TL, Bansal M, Baxter L, Beisel KW, Bersano T, Bono H, Chalk AM, Chiu KP, Choudhary V, Christoffels A, Clutterbuck DR, Crowe ML, Dalla E, Dalrymple BP, de Bono B, Della Gatta G, di Bernardo D, Down T, Engstrom P, Fagiolini M, Faulkner G, Fletcher CF, Fukushima T, Furuno M, Futaki S, Gariboldi M, Georgii-Hemming P, Gingeras TR, Gojobori T, Green RE, Gustincich S, Harbers M, Hayashi Y, Hensch TK, Hirokawa N, Hill D, Huminiecki L, Iacono M, Ikeo K, Iwama A, Ishikawa T, Jakt M, Kanapin A, Katoh M, Kawasawa Y, Kelso J, Kitamura H, Kitano H, Kollias G, Krishnan SP, Kruger A, Kummerfeld SK, Kurochkin IV, Lareau LF, Lazarevic D, Lipovich L, Liu J, Liuni S, McWilliam S, Madan Babu M, Madera M, Marchionni L, Matsuda H, Matsuzawa S, Miki H, Mignone F, Miyake S, Morris K, Mottagui-Tabar S, Mulder N, Nakano N, Nakauchi H, Ng P, Nilsson R, Nishiguchi S, Nishikawa S, Nori F, Ohara O, Okazaki Y, Orlando V, Pang KC, Pavan WJ, Pavesi G, Pesole G, Petrovsky N, Piazza S, Reed J, Reid JF, Ring BZ, Ringwald M, Rost B, Ruan Y, Salzberg SL, Sandelin A, Schneider C, Schönbach C, Sekiguchi K, Semple CA, Seno S, Sessa L, Sheng Y, Shibata Y, Shimada H, Shimada K, Silva D, Sinclair B, Sperling S, Stupka E, Sugiura K, Sultana R, Takenaka Y, Taki K, Tammoja K, Tan SL, Tang S, Taylor MS, Tegner J, Teichmann SA, Ueda HR, van Nimwegen E, Verardo R, Wei CL, Yagi K, Yamanishi H, Zabarovsky E, Zhu S, Zimmer A, Hide W, Bult C, Grimmond SM, Teasdale RD, Liu ET, Brusic V, Quackenbush J, Wahlestedt C, Mattick JS, Hume DA, Kai C, Sasaki D, Tomaru Y, Fukuda S, Kanamori-Katayama M, Suzuki M, Aoki J, Arakawa T, Iida J, Imamura K, Itoh M, Kato T, Kawaji H, Kawagashira N, Kawashima T, Kojima M, Kondo S, Konno H, Nakano K, Ninomiya N, Nishio T, Okada M, Plessy C, Shibata K, Shiraki T, Suzuki S, Tagami M, Waki K, Watahiki A, Okamura-Oho Y, Suzuki H, Kawai J, Hayashizaki Y; FANTOM Consortium; RIKEN Genome Exploration Research Group and Genome Science Group (Genome Network Project Core Group).

Science. 2005 Sep 2;309(5740):1559-63. Erratum in: Science. 2006 Mar 24;311(5768):1713.

33.

IRIS: a database surveying known human immune system genes.

Kelley J, de Bono B, Trowsdale J.

Genomics. 2005 Apr;85(4):503-11.

PMID:
15780753
34.

Reactome: a knowledgebase of biological pathways.

Joshi-Tope G, Gillespie M, Vastrik I, D'Eustachio P, Schmidt E, de Bono B, Jassal B, Gopinath GR, Wu GR, Matthews L, Lewis S, Birney E, Stein L.

Nucleic Acids Res. 2005 Jan 1;33(Database issue):D428-32.

35.

VH gene segments in the mouse and human genomes.

de Bono B, Madera M, Chothia C.

J Mol Biol. 2004 Sep 3;342(1):131-43.

PMID:
15313612
36.

Exploring the immunogenome with bioinformatics.

de Bono B, Trowsdale J.

Semin Immunol. 2003 Aug;15(4):233-8.

PMID:
14690048

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