Theoretical Systems Biology

Ames RM, Macpherson JI, Pinney JW, Lovell SC, Robertson DL.

PLoS One. 2013 May 3;8(5):e62670. doi: 10.1371/journal.pone.0062670. Print 2013.

Ale A, Kirk P, Stumpf MP.

J Chem Phys. 2013 May 7;138(17):174101. doi: 10.1063/1.4802475.

Harrington HA, Feliu E, Wiuf C, Stumpf MP.

Biophys J. 2013 Apr 16;104(8):1824-31. doi: 10.1016/j.bpj.2013.02.028.

Komorowski M, Miękisz J, Stumpf MP.

Biophys J. 2013 Apr 16;104(8):1783-93. doi: 10.1016/j.bpj.2013.02.027.

Thorne T, Fratta P, Hanna MG, Cortese A, Plagnol V, Fisher EM, Stumpf MP.

Mol Biosyst. 2013 Apr 17. [Epub ahead of print]

Kirk P, Thorne T, Stumpf MP.

Curr Opin Biotechnol. 2013 Apr 8. doi:pii: S0958-1669(13)00069-4. 10.1016/j.copbio.2013.03.012. [Epub ahead of print]

Bryant WA, Sternberg MJ, Pinney JW.

BMC Syst Biol. 2013 Mar 25;7(1):26. [Epub ahead of print]

Filippi S, Barnes CP, Cornebise J, Stumpf MP.

Stat Appl Genet Mol Biol. 2013 Mar 13:1-21. doi: 10.1515/sagmb-2012-0069. [Epub ahead of print]

Liepe J, Filippi S, Komorowski M, Stumpf MP.

PLoS Comput Biol. 2013 Jan;9(1):e1002888. doi: 10.1371/journal.pcbi.1002888. Epub 2013 Jan 31.

MacLean AL, Lo Celso C, Stumpf MP.

J R Soc Interface. 2013 Jan 24;10(81):20120968. doi: 10.1098/rsif.2012.0968. Print 2013 Apr 6.

Barnes CP, Silk D, Stumpf MP.

Interface Focus. 2011 Dec 6;1(6):895-908. doi: 10.1098/rsfs.2011.0056. Epub 2011 Oct 5.

Taylor HB, Liepe J, Barthen C, Bugeon L, Huvet M, Kirk PD, Brown SB, Lamb JR, Stumpf MP, Dallman MJ.

Immunol Cell Biol. 2013 Jan;91(1):60-9. doi: 10.1038/icb.2012.57. Epub 2012 Nov 20.

Thorne T, Stumpf MP.

Bioinformatics. 2012 Dec 15;28(24):3298-305. doi: 10.1093/bioinformatics/bts614. Epub 2012 Oct 16.

Roy A, Cowan G, Mead AJ, Filippi S, Bohn G, Chaidos A, Tunstall O, Chan JK, Choolani M, Bennett P, Kumar S, Atkinson D, Wyatt-Ashmead J, Hu M, Stumpf MP, Goudevenou K, O’Connor D, Chou ST, Weiss MJ, Karadimitris A, Jacobsen SE, Vyas P, Roberts I.

Proc Natl Acad Sci U S A. 2012 Oct 23;109(43):17579-84. doi: 10.1073/pnas.1211405109. Epub 2012 Oct 8.

Harrington HA, Ho KL, Thorne T, Stumpf MP.

Proc Natl Acad Sci U S A. 2012 Sep 25;109(39):15746-51. Epub 2012 Sep 11.

Sheng X, Huvet M, Pinney JW, Stumpf MP.

Adv Exp Med Biol. 2012;751:121-37. doi: 10.1007/978-1-4614-3567-9_6.

Toni T, Ozaki Y, Kirk P, Kuroda S, Stumpf MP.

Mol Biosyst. 2012 Jul 6;8(7):1921-9. doi: 10.1039/c2mb05493k. Epub 2012 May 3.

Thorne T, Stumpf MP.

J R Soc Interface. 2012 Oct 7;9(75):2653-66. doi: 10.1098/rsif.2012.0220. Epub 2012 May 2.

Harrington HA, Komorowski M, Beguerisse-Díaz M, Ratto GM, Stumpf MP.

Phys Biol. 2012 Jun;9(3):036001. doi: 10.1088/1478-3975/9/3/036001. Epub 2012 May 3.

Komorowski M, Zurauskiene J, Stumpf MP.

Bioinformatics. 2012 Mar 1;28(5):731-3. doi: 10.1093/bioinformatics/btr714.

Liepe J, Taylor H, Barnes CP, Huvet M, Bugeon L, Thorne T, Lamb JR, Dallman MJ, Stumpf MP.

Integr Biol (Camb). 2012 Mar;4(3):335-45. doi: 10.1039/c2ib00175f. Epub 2012 Feb 10.

Stumpf MP, Porter MA.

Science. 2012 Feb 10;335(6069):665-6. doi: 10.1126/science.1216142. No abstract available.

Kelly WP, Ingram PJ, Stumpf MP.

Methods Mol Biol. 2012;804:245-62. doi: 10.1007/978-1-61779-361-5_13.

Harmston N, Filsell W, Stumpf MP.

Bioinformatics. 2012 Jan 15;28(2):254-60. doi: 10.1093/bioinformatics/btr640. Epub 2011 Nov 30.

Tang Y, Sheng X, Stumpf MP.

Mol Biosyst. 2011 Dec;7(12):3280-6. doi: 10.1039/c1mb05325f. Epub 2011 Oct 14.

Kirk PD, Witkover A, Courtney A, Lewin AM, Wait R, Stumpf MP, Richardson S, Taylor GP, Bangham CR.

Retrovirology. 2011 Oct 12;8:81. doi: 10.1186/1742-4690-8-81.

Silk D, Kirk PD, Barnes CP, Toni T, Rose A, Moon S, Dallman MJ, Stumpf MP.

Nat Commun. 2011 Oct 4;2:489. doi: 10.1038/ncomms1496.

Barnes CP, Silk D, Sheng X, Stumpf MP.

Proc Natl Acad Sci U S A. 2011 Sep 13;108(37):15190-5. doi: 10.1073/pnas.1017972108. Epub 2011 Aug 29.

Kelly WP, Stumpf MP.

Bull Math Biol. 2012 Feb;74(2):356-74. doi: 10.1007/s11538-011-9680-2. Epub 2011 Aug 26.

Toni T, Jovanovic G, Huvet M, Buck M, Stumpf MP.

BMC Syst Biol. 2011 May 12;5:69. doi: 10.1186/1752-0509-5-69.

Komorowski M, Costa MJ, Rand DA, Stumpf MP.

Proc Natl Acad Sci U S A. 2011 May 24;108(21):8645-50. doi: 10.1073/pnas.1015814108. Epub 2011 May 6.

Erguler K, Stumpf MP.

Mol Biosyst. 2011 May;7(5):1593-602. doi: 10.1039/c0mb00107d. Epub 2011 Mar 4.

Chen CL, Duquenne L, Audit B, Guilbaud G, Rappailles A, Baker A, Huvet M, d’Aubenton-Carafa Y, Hyrien O, Arneodo A, Thermes C.

Mol Biol Evol. 2011 Aug;28(8):2327-37. doi: 10.1093/molbev/msr056. Epub 2011 Mar 2.

Zhou Y, Liepe J, Sheng X, Stumpf MP, Barnes C.

Bioinformatics. 2011 Mar 15;27(6):874-6. doi: 10.1093/bioinformatics/btr015. Epub 2011 Jan 11.

Thorne TW, Ho HL, Huvet M, Haynes K, Stumpf MP.

Fungal Genet Biol. 2011 May;48(5):504-11. doi: 10.1016/j.fgb.2010.12.005. Epub 2010 Dec 28.

Harmston N, Filsell W, Stumpf MP.

Hum Genomics. 2010 Oct;5(1):17-29. Review.

Huvet M, Toni T, Sheng X, Thorne T, Jovanovic G, Engl C, Buck M, Pinney JW, Stumpf MP.

Mol Biol Evol. 2011 Mar;28(3):1141-55. doi: 10.1093/molbev/msq301. Epub 2010 Nov 8.

Lèbre S, Becq J, Devaux F, Stumpf MP, Lelandais G.

BMC Syst Biol. 2010 Sep 22;4:130. doi: 10.1186/1752-0509-4-130.

Kelly WP, Stumpf MP.

BMC Bioinformatics. 2010 Sep 20;11:470. doi: 10.1186/1471-2105-11-470.

Toni T, Stumpf MP.

Methods Mol Biol. 2010;673:283-95. doi: 10.1007/978-1-60761-842-3_18. Review.

MacPherson JI, Dickerson JE, Pinney JW, Robertson DL.

PLoS Comput Biol. 2010 Jul 29;6(7):e1000863. doi: 10.1371/journal.pcbi.1000863.

Joly N, Engl C, Jovanovic G, Huvet M, Toni T, Sheng X, Stumpf MP, Buck M.

FEMS Microbiol Rev. 2010 Sep;34(5):797-827. doi: 10.1111/j.1574-6976.2010.00240.x. Epub 2010 Jun 9. Review.

Liepe J, Barnes C, Cule E, Erguler K, Kirk P, Toni T, Stumpf MP.

Bioinformatics. 2010 Jul 15;26(14):1797-9. doi: 10.1093/bioinformatics/btq278.

Dickerson JE, Pinney JW, Robertson DL.

BMC Syst Biol. 2010 Jun 7;4:80. doi: 10.1186/1752-0509-4-80.

Coletta A, Pinney JW, Solís DY, Marsh J, Pettifer SR, Attwood TK.

BMC Syst Biol. 2010 Apr 13;4:43. doi: 10.1186/1752-0509-4-43.

Stumpf MP, Wiuf C.

J R Soc Interface. 2010 Oct 6;7(51):1411-9. doi: 10.1098/rsif.2010.0044. Epub 2010 Apr 8.

Ratmann O, Wiuf C, Pinney JW.

HFSP J. 2009 Oct;3(5):290-306. doi: 10.2976/1.3167215. Epub 2009 Oct 19.

Chen CL, Rappailles A, Duquenne L, Huvet M, Guilbaud G, Farinelli L, Audit B, d’Aubenton-Carafa Y, Arneodo A, Hyrien O, Thermes C.

Genome Res. 2010 Apr;20(4):447-57. doi: 10.1101/gr.098947.109. Epub 2010 Jan 26.

Toni T, Stumpf MP.

Bioinformatics. 2010 Jan 1;26(1):104-10. doi: 10.1093/bioinformatics/btp619. Epub 2009 Oct 29.

Secrier M, Toni T, Stumpf MP.

Mol Biosyst. 2009 Dec;5(12):1925-35. doi: 10.1039/b908951a. Epub 2009 Sep 24.

Humphries JD, Byron A, Bass MD, Craig SE, Pinney JW, Knight D, Humphries MJ.

Sci Signal. 2009 Sep 8;2(87):ra51. doi: 10.1126/scisignal.2000396.

Knight CG, Pinney JW.

Bioessays. 2009 Oct;31(10):1080-90. doi: 10.1002/bies.200900043.

Huvet M, Toni T, Tan H, Jovanovic G, Engl C, Buck M, Stumpf MP.

Biochem Soc Trans. 2009 Aug;37(Pt 4):762-7. doi: 10.1042/BST0370762.

Butler G, Rasmussen MD, Lin MF, Santos MA, Sakthikumar S, Munro CA, Rheinbay E, Grabherr M, Forche A, Reedy JL, Agrafioti I, Arnaud MB, Bates S, Brown AJ, Brunke S, Costanzo MC, Fitzpatrick DA, de Groot PW, Harris D, Hoyer LL, Hube B, Klis FM, Kodira C, Lennard N, Logue ME, Martin R, Neiman AM, Nikolaou E, Quail MA, Quinn J, Santos MC, Schmitzberger FF, Sherlock G, Shah P, Silverstein KA, Skrzypek MS, Soll D, Staggs R, Stansfield I, Stumpf MP, Sudbery PE, Srikantha T, Zeng Q, Berman J, Berriman M, Heitman J, Gow NA, Lorenz MC, Birren BW, Kellis M, Cuomo CA.

Nature. 2009 Jun 4;459(7247):657-62. doi: 10.1038/nature08064.

Pinney JW, Stumpf MP.

Genome Biol. 2009;10(4):307. doi: 10.1186/gb-2009-10-4-307. Epub 2009 Apr 17.

Huxley-Jones J, Pinney JW, Archer J, Robertson DL, Boot-Handford RP.

Int J Exp Pathol. 2009 Apr;90(2):95-100. doi: 10.1111/j.1365-2613.2008.00637.x. Review.

Macpherson JI, Pinney JW, Robertson DL.

BMC Bioinformatics. 2009 Mar 26;10:95. doi: 10.1186/1471-2105-10-95.

Kirk PD, Stumpf MP.

Bioinformatics. 2009 May 15;25(10):1300-6. doi: 10.1093/bioinformatics/btp139. Epub 2009 Mar 16.

Gaskell EA, Smith JE, Pinney JW, Westhead DR, McConkey GA.

PLoS One. 2009;4(3):e4801. doi: 10.1371/journal.pone.0004801. Epub 2009 Mar 11.

Pinney JW, Dickerson JE, Fu W, Sanders-Beer BE, Ptak RG, Robertson DL.

AIDS. 2009 Mar 13;23(5):549-54. doi: 10.1097/QAD.0b013e328325a495. No abstract available.

Toni T, Welch D, Strelkowa N, Ipsen A, Stumpf MP.

J R Soc Interface. 2009 Feb 6;6(31):187-202.

Ptak RG, Fu W, Sanders-Beer BE, Dickerson JE, Pinney JW, Robertson DL, Rozanov MN, Katz KS, Maglott DR, Pruitt KD, Dieffenbach CW.

AIDS Res Hum Retroviruses. 2008 Dec;24(12):1497-502. doi: 10.1089/aid.2008.0113. Review.

Ingram PJ, Stumpf MP, Stark J.

PLoS Comput Biol. 2008 Oct;4(10):e1000192. doi: 10.1371/journal.pcbi.1000192. Epub 2008 Oct 10.

Erguler K, Stumpf MP.

Math Biosci. 2008 Nov;216(1):90-9. doi: 10.1016/j.mbs.2008.08.012.

Archer J, Pinney JW, Fan J, Simon-Loriere E, Arts EJ, Negroni M, Robertson DL.

PLoS Comput Biol. 2008 Sep 12;4(9):e1000178. doi: 10.1371/journal.pcbi.1000178.

Eales JM, Pinney JW, Stevens RD, Robertson DL.

BMC Bioinformatics. 2008 Sep 1;9:359. doi: 10.1186/1471-2105-9-359.

Adamo A, Pinney JW, Kunova A, Westhead DR, Meyer P.

PLoS One. 2008 Aug 6;3(8):e2889. doi: 10.1371/journal.pone.0002889.

Stumpf MP, Thorne T, de Silva E, Stewart R, An HJ, Lappe M, Wiuf C.

Proc Natl Acad Sci U S A. 2008 May 13;105(19):6959-64. doi: 10.1073/pnas.0708078105. Epub 2008 May 12.

Kirk PD, Toni T, Stumpf MP.

Biophys J. 2008 Jul;95(2):540-9. doi: 10.1529/biophysj.107.126086. Epub 2008 May 2.

Audit B, Nicolay S, Huvet M, Touchon M, d’Aubenton-Carafa Y, Thermes C, Arneodo A.

Phys Rev Lett. 2007 Dec 14;99(24):248102. Epub 2007 Dec 12.

Bland ND, Pinney JW, Thomas JE, Turner AJ, Isaac RE.

BMC Evol Biol. 2008 Jan 23;8:16. doi: 10.1186/1471-2148-8-16.

Hakes L, Pinney JW, Robertson DL, Lovell SC.

Nat Biotechnol. 2008 Jan;26(1):69-72. doi: 10.1038/nbt0108-69. No abstract available.

Pinney JW, Amoutzias GD, Rattray M, Robertson DL.

Proc Natl Acad Sci U S A. 2007 Dec 18;104(51):20449-53. Epub 2007 Dec 12.

Thorne T, Stumpf MP.

BMC Bioinformatics. 2007 Nov 30;8:467.

Pinney JW, Papp B, Hyland C, Wambua L, Westhead DR, McConkey GA.

Trends Parasitol. 2007 Nov;23(11):548-54. Epub 2007 Oct 22. Review.

Hakes L, Pinney JW, Lovell SC, Oliver SG, Robertson DL.

Genome Biol. 2007;8(10):R209.

Holden BJ, Pinney JW, Lovell SC, Amoutzias GD, Robertson DL.

BMC Bioinformatics. 2007 Aug 6;8:289.

Huvet M, Nicolay S, Touchon M, Audit B, d’Aubenton-Carafa Y, Arneodo A, Thermes C.

Genome Res. 2007 Sep;17(9):1278-85. Epub 2007 Aug 3.

Stumpf MP, Kelly WP, Thorne T, Wiuf C.

Trends Ecol Evol. 2007 Jul;22(7):366-73. Epub 2007 May 1. Review.

Agrafioti I, Stumpf MP.

Nucleic Acids Res. 2007 Jan;35(Database issue):D71-5.

Stumpf MP, Robertson BD, Duncan K, Young DB.

Prog Drug Res. 2007;64:1, 3-20. Review.

de Silva E, Thorne T, Ingram P, Agrafioti I, Swire J, Wiuf C, Stumpf MP.

BMC Biol. 2006 Nov 3;4:39.

Thomas MG, Stumpf MP, Härke H.

Proc Biol Sci. 2006 Oct 22;273(1601):2651-7.

de Silva E, Stumpf MP.

J R Soc Interface. 2005 Dec 22;2(5):419-30. Review.

Hyland C, Pinney JW, McConkey GA, Westhead DR.

Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W725-8.

Manfield IW, Jen CH, Pinney JW, Michalopoulos I, Bradford JR, Gilmartin PM, Westhead DR.

Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W504-9.

Jovanovic G, Lloyd LJ, Stumpf MP, Mayhew AJ, Buck M.

J Biol Chem. 2006 Jul 28;281(30):21147-61. Epub 2006 May 17.

Stumpf MP, Wilkinson-Herbots HM.

Trends Ecol Evol. 2004 Apr;19(4):166-8.

Wiuf C, Brameier M, Hagberg O, Stumpf MP.

Proc Natl Acad Sci U S A. 2006 May 16;103(20):7566-70. Epub 2006 May 8.

Ingram PJ, Stumpf MP, Stark J.

BMC Genomics. 2006 May 5;7:108.

Jen CH, Manfield IW, Michalopoulos I, Pinney JW, Willats WG, Gilmartin PM, Westhead DR.

Plant J. 2006 Apr;46(2):336-48.

Stumpf MP, Wiuf C.

Phys Rev E Stat Nonlin Soft Matter Phys. 2005 Sep;72(3 Pt 2):036118. Epub 2005 Sep 19.

Jansen VA, Stumpf MP.

Science. 2005 Sep 23;309(5743):2005-7. No abstract available.

Taib M, Pinney JW, Westhead DR, McDowall KJ, Adams DJ.

Arch Microbiol. 2005 Oct;184(1):78-81. Epub 2005 Nov 3.

De Iorio M, de Silva E, Stumpf MP.

Philos Trans R Soc Lond B Biol Sci. 2005 Aug 29;360(1460):1597-603.

Stumpf MP, Goldstein DB, Wood NW.

Philos Trans R Soc Lond B Biol Sci. 2005 Aug 29;360(1460):1539-41. No abstract available.

Both M, Csukai M, Stumpf MP, Spanu PD.

Plant Cell. 2005 Jul;17(7):2107-22. Epub 2005 Jun 10.

Kauppi L, Stumpf MP, Jeffreys AJ.

Genomics. 2005 Jul;86(1):13-24.

Agrafioti I, Swire J, Abbott J, Huntley D, Butcher S, Stumpf MP.

BMC Evol Biol. 2005 Mar 18;5:23.

Stumpf MP, Wiuf C, May RM.

Proc Natl Acad Sci U S A. 2005 Mar 22;102(12):4221-4. Epub 2005 Mar 14.

Pinney JW, Shirley MW, McConkey GA, Westhead DR.

Nucleic Acids Res. 2005 Mar 3;33(4):1399-409. Print 2005.

de Silva E, Kelley LA, Stumpf MP.

Hum Genomics. 2004 Nov;1(6):410-20.

de Silva E, Stumpf MP.

FEMS Microbiol Lett. 2004 Dec 1;241(1):1-12. Review.

Alsmark CM, Frank AC, Karlberg EO, Legault BA, Ardell DH, Canbäck B, Eriksson AS, Näslund AK, Handley SA, Huvet M, La Scola B, Holmberg M, Andersson SG.

Proc Natl Acad Sci U S A. 2004 Jun 29;101(26):9716-21. Epub 2004 Jun 21.

Stumpf MP.

Eur J Hum Genet. 2004 Jun;12(6):469-77.

McConkey GA, Pinney JW, Westhead DR, Plueckhahn K, Fitzpatrick TB, Macheroux P, Kappes B.

Trends Parasitol. 2004 Feb;20(2):60-5. Review.

Pinney JW, Westhead DR, McConkey GA.

Biochem Soc Trans. 2003 Dec;31(Pt 6):1513-5. Review.

Stumpf MP, McVean GA.

Nat Rev Genet. 2003 Dec;4(12):959-68. Review.

Wiuf C, Laidlaw Z, Stumpf MP.

Math Biosci. 2003 Oct;185(2):205-16.

Capelli C, Redhead N, Abernethy JK, Gratrix F, Wilson JF, Moen T, Hervig T, Richards M, Stumpf MP, Underhill PA, Bradshaw P, Shaha A, Thomas MG, Bradman N, Goldstein DB.

Curr Biol. 2003 May 27;13(11):979-84.

Mead S, Stumpf MP, Whitfield J, Beck JA, Poulter M, Campbell T, Uphill JB, Goldstein D, Alpers M, Fisher EM, Collinge J.

Science. 2003 Apr 25;300(5619):640-3. Epub 2003 Apr 10.

Stumpf MP, Goldstein DB.

Curr Biol. 2003 Jan 8;13(1):1-8.

Stumpf MP, Laidlaw Z, Jansen VA.

Proc Natl Acad Sci U S A. 2002 Nov 12;99(23):15234-7. Epub 2002 Oct 30.

Stumpf MP, Pybus OG.

FEMS Microbiol Lett. 2002 Sep 10;214(2):143-52. Review.

Stumpf MP.

Trends Genet. 2002 May;18(5):226-8.

Pletcher SD, Stumpf MP.

Curr Biol. 2002 Apr 30;12(9):R328-30.

Krebs JR, May RM, Stumpf MP.

Nature. 2002 Jan 10;415(6868):115. No abstract available.

Stumpf MP, Zitzmann N.

Proc Biol Sci. 2001 Oct 7;268(1480):1993-9.

Stumpf MP, Goldstein DB.

Science. 2001 Mar 2;291(5509):1738-42. Review.

May RM, Stumpf MP.

Science. 2000 Dec 15;290(5499):2084-6.

Capelli C, Wilson JF, Richards M, Stumpf MP, Gratrix F, Oppenheimer S, Underhill P, Pascali VL, Ko TM, Goldstein DB.

Am J Hum Genet. 2001 Feb;68(2):432-43. Epub 2001 Jan 22.

Stumpf MP, Krakauer DC.

Proc Natl Acad Sci U S A. 2000 Sep 12;97(19):10573-7.