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Publications

High-throughput discovery of novel developmental phenotypes. Dickinson, Mary E and Flenniken, Ann M and Ji, Xiao and Teboul, Lydia and Wong, Michael D and White, Jacqueline K and Meehan, Terrence F and Weninger, Wolfgang J and Westerberg, Henrik and Adissu, Hibret and Baker, Candice N and Bower, Lynette and Brown, James M and Caddle, L Brianna and Chiani, Francesco and Clary, Dave and Cleak, James and Daly, Mark J and Denegre, James M and Doe, Brendan and Dolan, Mary E and Edie, Sarah M and Fuchs, Helmut and Gailus-durner, Valerie and Galli, Antonella and Gambadoro, Alessia and Gallegos, Juan and Guo, Shiying and Horner, Neil R and Hsu, Chih-wei and Johnson, Sara J and Kalaga, Sowmya and Keith, Lance C and Lanoue, Louise and Lawson, Thomas N and Lek, Monkol and Mark, Manuel and Marschall, Susan and Mason, Jeremy and Mcelwee, Melissa L and Newbigging, Susan and Nutter, Lauryl M J and Peterson, Kevin A and Ramirez-solis, Ramiro and Rowland, Douglas J and Ryder, Edward and Samocha, Kaitlin E and Seavitt, John R and Selloum, Mohammed and Szoke-kovacs, Zsombor and Tamura, Masaru and Wells, Sara and Braun, Robert E and Svenson, Karen L and Angelis, Martin Hrabe De and Herault, Yann and Mohun, Tim.  Nature Publishing Group, 537(7621), 508–514. http://doi.org/10.1038/nature19356

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Applying the ARRIVE Guidelines to an In Vivo Database. Natasha A. Karp , Terry F. Meehan, Hugh Morgan, Jeremy C. Mason, Andrew Blake, Natalja Kurbatova, Damian Smedley, Julius Jacobsen, Richard F. Mott, Vivek Iyer, Peter Matthews, David G. Melvin, Sara Wells, Ann M. Flenniken, Hiroshi Masuya, Shigeharu Wakana, Jacqueline K. White, K. C. Kent Lloyd, Corey L. Reynolds, Richard Paylor, David B. West, Karen L. Svenson, Elissa J. Chesler, Martin Hrabě de Angelis, Glauco P. Tocchini-Valentini, Tania Sorg, Yann Herault, Helen Parkinson, Ann-Marie Mallon, Steve D. M. Brown  PLOS BIOLOGY (2015) Volume:13 Issue:5 Article Number:e1002151

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Targeting of Slc25a21 Is Associated with Orofacial Defects and Otitis Media Due to Disrupted Expression of a Neighbouring Gene. Simon Maguire, Jeanne Estabel, Neil Ingham, Selina Pearson, Edward Ryder, Damian M. Carragher, Nicolas Walker, Sanger MGP Slc25a21 Project Team , James Bussell, Wai-In Chan, Thomas M. Keane, David J. Adams, Cheryl L. Scudamore, Christopher J. Lelliott, Ramiro Ramírez-Solis, Natasha A. Karp, Karen P. Steel, Jacqueline K. White , Anna-Karin Gerdin  PLOS ONE (2015) Volume:9 Issue:3 Article Number:e91807

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PhenStat: A Tool Kit for Standardized Analysis of High Throughput Phenotypic Data. Natalja Kurbatova , Jeremy C. Mason, Hugh Morgan, Terrence F. Meehan, Natasha A. Karp  PLOS ONE (2015) DOI: 10.1371/journal.pone.0131274

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The influence of disease categories on gene candidate predictions from model organism phenotypes. Oellrich A, Koehler S, Washington N; Sanger Mouse Genetic Project, Mungall C,  Lewis S, Haendel M, Robinson PN, Smedley D.  J Biomed Semantics. 2014 Jun 3;5(Suppl 1 Proceedings of the Bio-Ontologies Spec Interest G):S4. doi:  10.1186/2041-1480-5-S1-S4. eCollection 2014. PubMed PMID: 25093073; PubMed Central PMCID: PMC4108905.

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Using association rule mining to determine promising secondary phenotyping hypotheses. Oellrich A, Jacobsen J, Papatheodorou I; Sanger Mouse Genetics Project, Smedley D.  Bioinformatics. 2014 Jun 15;30(12):i52-59. doi: 10.1093/bioinformatics/btu260. PubMed PMID: 24932005; PubMed Central PMCID: PMC4059059.

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Linking tissues to phenotypes using gene expression profiles. Oellrich A; Sanger Mouse Genetics Project, Smedley D.   Database (Oxford). 2014 Mar 13;201bau017. doi: 10.1093/database/bau017. Print 2014. PubMed PMID: 24634472;  PubMed Central PMCID: PMC3982582.

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Impact of Temporal Variation on Design and Analysis of Mouse Knockout Phenotyping Studies. Karp NA, Speak AO, White JK, Hrabé de Angelis M, Hérault Y, Mott, RF.  PLOS ONE 2014 October 24, 2014 DOI: 10.1371/journal.pone.0111239 PubMed PMID: 25343444

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Disruption of the potassium channel regulatory subunit Kcne2 causes iron-deficient anemia. Salsbury G, Cambridge EL, McIntyre Z, Arends MJ, Karp NA, Isherwood C, Shannon C, Hooks Y; The Sanger Mouse Genetics Project, Ramirez-Solis R, Adams DJ, White JK, Speak AO.  Exp Hematol. 2014 Aug 12. pii: S0301-472X(14)00623-7. doi: 10.1016/j.exphem.2014.07.269. PubMed PMID: 25127743.

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The International Mouse Phenotyping Consortium: past and future perspectives on mouse phenotyping.  Brown SD, Moore MW. Mamm Genome. 2012 Oct;23(9-10):632-40. PubMed PMID: 22940749; PubMed Central PMCID: PMC3774932.

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Rapid conversion of EUCOMM/KOMP-CSD alleles in mouse embryos using a cell-permeable Cre recombinase. Ryder E, Doe B, Gleeson D, Houghton R, Dalvi P, Grau E, Habib B, Miklejewska E, Newman S, Sethi D, Sinclair C, Vyas S, Wardle-Jones H, Sanger Mouse Genetics Project, Bottomley J, Bussell J, Galli A, Salisbury J, Ramirez-Solis R.  Transgenic Res. 2014 Feb;23(1):177-85. PubMed PMID: 24197666; PubMed Central PMCID: PMC3890051.

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The International Mouse Phenotyping Consortium Web Portal, a unified point of access for knockout mice and related phenotyping data.  Gautier Koscielny, Gagarine Yaikhom, Vivek Iyer, Terrence F. Meehan, Hugh Morgan, Julian Atienza-Herrero, Andrew Blake, Chao-Kung Chen, Richard Easty, Armida Di Fenza, Tanja Fiegel, Mark Grifiths, Alan Home, Natasha A. Karp, Natalja Kurbatova, Jeremy C. Mason, Peter Matthews, Darren J. Oakley, Asfand Qazi, Jack Regnart, Ahmad Retha, Luis A. Santos, Duncan J. Sneddon, Jonathan Warren, Henrik Westerberg, Robert J. Wilson, David G. Melvin, Damian Smedley, Steve D. M. Brown, Paul Flicek, William C. Skarnes, Ann-Marie Mallon, Helen Parkinson Nucleic Acids Res. 2014 January; 42(D1): D802-D809. Published online 2013 November 3. doi: 10.1093/nar/gkt977 PMCID: PMC3964955

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The Perfect Host: a mouse host embryo facilitating more efficient germ line transmission of genetically modified embryonic stem cells . Taft RA, Low BE, Byers SL, Murray SA, Kutny P, Wiles MV. 2013.  PLoS ONE 8(7):e67826. PMCID: PMC3699516

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Histopathology reveals correlative and unique phenotypes in a high-throughput mouse phenotyping screen. Adissu HA, Estabel J, Sunter D, Tuck E, Hooks Y, Carragher DM, Clarke K, Karp NA, Project SM, Newbigging S, Jones N, Morikawa L, White JK, McKerlie C.  Dis Model Mech. 2014 May;7(5):515-24. PubMed PMID: 24652767; PubMed Central PMCID: PMC4007403.

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Combining sperm plug genotyping and coat color chimerism predicts germline transmission. Lee AY, Evans K, Willis B, Lloyd KC.  Transgenic Res. 2013 Dec;22(6):1265-72. PubMed PMID: 23860911; PubMed Central PMCID: PMC3838463.

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Sestrin-2, a repressor of PDGFRP signalling, promotes cigarette-smoke-induced pulmonary emphysema in mice and is upregulated in individuals with COPD. Heidler J, Fysikopoulos A, Wempe F, Seimetz M, Bangsow T, Tomasovic A, Veit F, Scheibe S, PichI A, Weisel F, Lloyd KC, Jaksch P, Klepetko W, Weissmann N, von Melchner H.  Dis Model Mech. 2013 Nov;6(6):1378-87. PubMed PMID: 24046361; PubMed Central PMCID: PMC3820261.

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The mouse pathology ontology, MPATH; structure and applications. Schofield PN, Sundberg JP, Sundberg BA, McKerlie C, Gkoutos GV. J Biomed Semantics. 2013 Sep 13;4(1):18. PubMed PMID: 24033988; PubMed Central PMCID: PMC3851164.

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Safety, efficacy and efficiency of laser-assisted IVF in subfertile mutant mouse strains. Li MW, Kinchen KL, Vallelunga JM, Young DL, Wright KD, Gorano LN, Wasson K, Lloyd KC. Reproduction. 2013 Mar l;145(3):245-54. PubMed PMID: 23315689; PubMed Central PMCID: PMC3738198.

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The Perfect Host: a mouse host embryo facilitating more efficient germ line transmission of genetically modified embryonic stem cells. Taft RA, Low BE, Byers SL, Murray SA, Kutny P, Wiles MV. 2013.  PLoS ONE 8(7):e67826. PMCID: PMC3699516

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Combining sperm plug genotyping and coat color chimerism predicts germline transmission. Lee AY, Evans K, Willis B, Lloyd KC. Transgenic Res. 2013 Dec;22(6):1265-72. PubMed PMID: 23860911; PubMed Central PMCID: PMC3838463.

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Sestrin-2, a repressor of PDGFRP signalling, promotes cigarette-smoke-induced pulmonary emphysema in mice and is upregulated in individuals with COPD. Heidler J, Fysikopoulos A, Wempe F, Seimetz M, Bangsow T, Tomasovic A, Veit F, Scheibe S, PichI A, Weisel F, Lloyd KC, Jaksch P, Klepetko W, Weissmann N, von Melchner H.  Dis Model Mech. 2013 Nov;6(6):1378-87. PubMed PMID: 24046361; PubMed Central PMCID: PMC3820261.

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The mouse pathology ontology, MPATH; structure and applications. Schofield PN, Sundberg JP, Sundberg BA, McKerlie C, Gkoutos GV. J Biomed Semantics. 2013 Sep 13;4(1):18. PubMed PMID: 24033988; PubMed Central PMCID: PMC3851164.

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Safety, efficacy and efficiency of laser-assisted IVF in subfertile mutant mouse strains. Li MW, Kinchen KL, Vallelunga JM, Young DL, Wright KD, Gorano LN, Wasson K, Lloyd KC. Reproduction. 2013 Mar l;145(3):245-54. PubMed PMID: 23315689; PubMed Central PMCID: PMC3738198.

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The International Mouse Phenotyping Consortium: past and future perspectives on mouse phenotyping. Brown SD, Moore MW. Mamm Genome. 2012 Oct;23(9-10):632-40.  doi: 10.1007/s00335-012-9427-x. Epub 2012 Sep 1. PubMed PMID: 22940749; PubMed Central PMCID: PMC3774932.

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The mammalian gene function resource: the International Knockout Mouse Consortium. Bradley A, Anastassiadis K, Ayadi A, Battey JF, Bell C, Birling MC, Bottomley  J, Brown SD, Bürger A, Bult CJ, Bushell W, Collins FS, Desaintes C, Doe B, Economides A, Eppig JT, Finnell RH, Fletcher C, Fray M, Frendewey D, Friedel RH, Grosveld FG, Hansen J, Hérault Y, Hicks G, Hörlein A, Houghton R, Hrabé de Angelis M, Huylebroeck D, Iyer V, de Jong PJ, Kadin JA, Kaloff C, Kennedy K, Koutsourakis M, Lloyd KC, Marschall S, Mason J, McKerlie C, McLeod MP, von Melchner H, Moore M, Mujica AO, Nagy A, Nefedov M, Nutter LM, Pavlovic G, Peterson JL, Pollock J, Ramirez-Solis R, Rancourt DE, Raspa M, Remacle JE, Ringwald M, Rosen B, Rosenthal N, Rossant J, Ruiz Noppinger P, Ryder E, Schick JZ, Schnütgen F, Schofield P, Seisenberger C, Selloum M, Simpson EM, Skarnes WC,  Smedley D, Stanford WL, Stewart AF, Stone K, Swan K, Tadepally H, Teboul L, Tocchini-Valentini GP, Valenzuela D, West AP, Yamamura K, Yoshinaga Y, Wurst W. Mamm Genome. 2012 Oct;23(9-10):580-6. doi: 10.1007/s00335-012-9422-2. Epub 2012 Sep 12. PubMed PMID: 22968824; PubMed Central PMCID: PMC346380

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A knockout mouse resource for the biomedical research community. Lloyd KC. Ann N Y Acad Sci. 2011 Dec;1245:24-6. doi: 10.1111/j.1749-6632.2011.06311.x. PubMed PMID: 22211970; PubMed Central PMCID: PMC4070945.

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Accessing data from the International Mouse Phenotyping Consortium:state of the art and future plans. Mallon AM, Iyer V, Melvin D, Morgan H, Parkinson H, Brown SD, Flicek P, Skarnes WC. Mamm Genome. 2012 Oct;23(9-10):641-52. doi:10.1007/s00335-012-9428-9. Epub 2012 Sep 19. PubMed PMID: 22991088; PubMed Central PMCID: PMC4106044.

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Beyond knockouts: cre resources for conditional mutagenesis. Murray SA, Eppig JT, Smedley D, Simpson EM, Rosenthal N.  Mamm Genome. 2012 Oct;23(9-10):587-99. doi: 10.1007/s00335-012-9430-2. Epub 2012 Aug 29. Erratum in: Mamm Genome. 2012 Dec;23(11-12):791. PubMed PMID: 22926223; PubMed Central PMCID: PMC3655717.

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A comparative phenotypic and genomic analysis of C57BL/6J and C57BL/6N mouse strains.

Simon, M., Greenaway, S. Blake, A. , White, J., et al.

Genome Biology (2013). in press

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Bloomsbury report on mouse embryo phenotyping: recommendations from the IMPC workshop on embryonic lethal screening.

D. Adams,  R. Baldock, S. Bhattacharya, A.J. Copp, M Dickinson, N.D.E. Greene, M. Henkelman, M. Justice, T. Mohun, S.A. Murray, E. Pauws, M. Raess, J. Rossant, T. Weaver, D. West.

Disease models & mechanisms doi:10.1242/dmm.011833 (2013).

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The mammalian gene function resource: the international knockout mouse consortium.

Bradley A, Anastassiadis K, Ayadi A, Battey JF, Bell C, Birling MC, Bottomley J, Brown SD, Burger A, Bult CJ et al. .

Mamm Genome 23(9-10), 580-586.(2012)

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Towards an encyclopaedia of mammalian gene function: the International Mouse Phenotyping Consortium.

Brown, S.D.M., and Moore, M.W.

Disease models & mechanisms 5, 289-292. (2012).

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High-throughput mouse phenotyping.

Gates H, Mallon AM, Brown SD.

Methods 53(4), 394-404. (2011).

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PhenomeNET: a whole-phenome approach to disease gene discovery.

Hoehndorf, R., Schofield, P.N., and Gkoutos, G.V.

Nucleic acids research 39, e119. (2011).

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A conditional knockout resource for the genome-wide study of mouse gene function.

Skarnes, W.C., Rosen, B., West, A.P., Koutsourakis, M., Bushell, W., Iyer, V., Mujica, A.O., Thomas, M., Harrow, J., Cox, T., et al.

Nature 474, 337-342. (2011).

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EuroPhenome: a repository for high-throughput mouse phenotyping data.

Morgan, H., Beck, T., Blake, A., Gates, H., Adams, N., Debouzy, G., Leblanc, S., Lengger, C., Maier, H., Melvin, D., et al.

Nucleic acids research 38, D577-585. (2010).

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The functional annotation of mammalian genomes: the challenge of phenotyping.

Brown, S.D., Wurst, W., Kuhn, R., and Hancock, J.M.

Annual review of genetics 43, 305-333. (2009).

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EuroPhenome and EMPReSS: online mouse phenotyping resource.

Mallon, A.M., Blake, A., and Hancock, J.M.

Nucleic acids research 36, D715-718.(2008).

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Commentary: A Mouse for All Reasons.

Francis S. Collins, Janet Rossant, Wolfgang Wurst, The International Mouse Knockout Consortium.

Cell 128(1), 9-13. (2007).

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Understanding mammalian genetic systems: the challenge of phenotyping in the mouse.

Brown, S.D., Hancock, J.M., and Gates, H. 

PLoS genetics 2, e118. (2006).

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EMPReSS: standardized phenotype screens for functional annotation of the mouse genome

Brown, S.D., Chambon, P., and de Angelis, M.H.

Nature genetics 37, 1155. (2005).

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Introducing the German Mouse Clinic: open access platform for standardized phenotyping.

Gailus-Durner, V., Fuchs, H., Becker, L., Bolle, I., Brielmeier, M., Calzada-Wack, J., Elvert, R., Ehrhardt, N., Dalke, C., Franz, T.J., et al.

Nature methods 2, 403-404. (2005).

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The knockout mouse project.

C.P. Austin, J.F. Battey, A. Bradley, M. Bucan, M. Capecchi, F.S. Collins, W.F. Dove, G. Duyk, S. Dymecki, J.T. Eppig, F.B. Grieder, N. Heintz, G. Hicks, T.R. Insel, A. Joyner, B. HKoller, K.C. Lloyd, T. Magnuson, M.WMoore, A.  Nagy, J.D. Pollock, A.D. Roses, A.T. Sands, B. Seed, W.C. Skarnes, J. Snoddy, P. Soriano, D.J. Stewart, F.  Stewart, B.  Stillman, H. Varmus, L. Varticovski, I.M. Verma, T.F. Vogt, H. von Melchner, J. Witkowski, R.P. Woychik, W. Wurst, G.D. Yancopoulos, S.G. Young, B. Zambrowicz.

Nature Genetics 36(9), 921-924. (2004).

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The European dimension for the mouse genome mutagenesis program.

J. Auwerx, P. Avner, R. Baldock, A. Ballabio, R. Balling, M. Barbacid, A. Berns, A. Bradley, S.D.M. Brown, P. Carmeliet, P. Chambon, R. Cox, D. Davidson, K. Davies, D. Duboule, J. Forejt, F. Granucci, N. Hastie, M. Hrabé de Angelis, I. Jackson, D. Kioussis, G. Kollias, M. Lathrop, U. Lendahl, M. Malumbres, H. von Melchner, W. Müller, J. Partanen, P. Ricciardi-Castagnoli, P. Rigby, B. Rosen, N. Rosenthal, B. Skarnes, A.F. Stewart, J. Thornton, G. Tocchini-Valentini, E. Wagner, W. Wahl, W. Wurst.

Nature Genetics 36(9), 925-927.(2004). 

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