The EUCOMMTools Program

EUCOMMTOOLS – “EUCOMM: Tools for Functional Annotation of the Mouse Genome” – is successor project of EUCOMM and member of the International Knockout Mouse Consortium (IKMC).
EUCOMMTOOLS will complete the IKMC resource of mutations for all protein coding genes.
Furthermore, EUCOMMTOOLS will maximize the utility of the conditional IKMC resource by generating up to 250 different, mostly inducible Cre driver mouse lines.
In addition, EUCOMMTOOLS will develop novel tools to enhance the versatility of the IKMC resource.
EUCOMMTOOLS vectors, mutant ES cells and mutant mice are distributed worldwide:
EUCOMMTOOLS mutant ES cells and vectors can be obtained from the European Mouse Mutant Cell Repository (EuMMCR).
EUCOMMTOOLS mutant mice are archived and distributed by the European Mouse Mutant Archive (EMMA).

EUCOMMTOOLS Project Information

Knockout-first Mutant Alleles

EUCOMMTOOLS will create 3500 C57Bl/6 conditional mutant alleles for single-exon (or otherwise previously conditionally untargeted) protein-coding mouse genes. These alleles will be made predominantly by introducing an ‘artificial intron’, containing a standard EUCOMM promoter-driven targeting cassette, into the coding sequence of the single-exon gene.

Cre Resources

EUCOMMTOOLS will engineer 500 new Cre C57Bl/6 ES cell lines by Cre knock-ins into genes with useful expression patterns. The resource will be made with inducible forms of Cre recombinase such as CreERT2. Up to 250 lines of Cre driver mice on a pure C57Bl/6N background will be generated and the Cre expression patterns documented and annotated in day P14 and P56. These mice will form a matched Cre driver resource for C57Bl/6N mice produced from conditional IKMC resources.

Research, Technology and Complementary Reagents

EUCOMMTOOLS will develop novel technologies to add value, depth and flexibility to existing IKMC ES cell and mouse resources. Key areas include:
• Development of novel recombinase based regulatory switches
• Exploration of zinc-finger nuclease stimulated homologous recombination strategies in fertilized oocytes
• Development and validation of complementary modular vector reagents which enable the construction of new useful knock-in alleles such as fluorescent and other reporters, site specific recombinases, and mutant cDNAs. These novel alleles can be constructed either by re-utilizing existing IKMC modular vector resources or directly modifying existing targeted IKMC ES cell lines by RMCE.

Structure of the EUCOMMTOOLS project

Societal Benefits

• Improvement of health research
• Speedup of drug development, therapy and diagnosis
• Competitive advantage for pharmaceutical industry

Funding & Structure

• Funded by European Union (FP7, THEME Health)
• EU funding: up to 12 million Euros
• Large-scale Integrating Project
• Consortium: 8 participants from five European countries

EUCOMMTOOLS SAB, Participants and Publications

EUCOMMTOOLS Scientific Advisory Board

• Janan Eppig, Bar Harbor, ME, USA
• John Hohmann, Seattle, WA, USA
• Alexandra Joyner, New York, NY, USA
• Monica Justice, Houston, TX, USA
• Björn Löwenadler, Mölndal, Sweden
• Andrew McMahon, Cambridge, MA, USA
• Luis Puelles, Murcia, Spain

EUCOMMTOOLS Coordination

• Wolfgang Wurst
• Allan Bradley


• Cornelia Kaloff
• Derek Matthews
• Karin Simmerl

EUCOMMTOOLS Participants

• Helmholtz Zentrum München, German Research Center for Environmental Health GmbH (formerly GSF), Munich/Neuherberg, Germany
Wolfgang Wurst, Joel Schick, Ralf Kühn, Andreas Hörlein, Cornelia Kaloff, Claudia Seisenberger, Antje Bürger, Karin Simmerl
• The Wellcome Trust Sanger Institute Hinxton, Cambridge, UK
Allan Bradley, William C. Skarnes, Barry Rosen, Anthony West, Wendy Bushell, Haydn Prosser, Vivek Iyer, Ramiro Ramirez-Solis, Derek Matthews, Brendan Doe
• European Molecular Biology Laboratory (EMBL)
– Outstation Monterotondo, Italy
Nadia Rosenthal
– Outstation European Bioinformatics Institute (EBI), Hinxton, Cambridge, UK
Paul Flicek, Damian Smedley
• University of Technology, Dresden, Germany
Francis Stewart, Konstantinos Anastassiadis, Andrea Kranz
• Consiglio Nazionale delle Ricerche, Monterotondo, Italy
Glauco Tocchini-Valentini, Alessia Gambadoro, Francesco Chiani
• Institut Clinique de la Souris, Strasbourg, France
Yann Hérault, Marie-Christine Birling, Guillaume Pavlovic, Mohammed Selloum
• Universidad Miguel Hernández de Elche, Alicante, Spain
Salvador Martínez
• Medical Research Council (MRC)
– Mammalian Genetics Unit, Harwell, UK
Steve Brown
– Human Genetics Unit, Edinburgh, UK
Richard Baldock

EUCOMMTOOLS Publications


• Gene Targeting and Site-Specific Recombination in Mouse ES Cells.
Anastassiadis K, Schnütgen F, von Melchner H, Stewart AF.
Methods Enzymol. 2013;533:133-55. PMID:24182921 DOI:10.1016/B978-0-12-420067-8.00009-X.
• Direct cloning of isogenic murine DNA in yeast and relevance of isogenicity for targeting in embryonic stem cells.
Andréasson C, Schick AJ, Pfeiffer SM, Sarov M, Stewart F, Wurst W, Schick JA.
PLoS One. 2013 Sep 13;8(9):e74207. PMID:24058528 DOI:10.1371/journal.pone.0074207.
• Combined sequence-based and genetic mapping analysis of complex traits in outbred rats.
Rat Genome Sequencing and Mapping Consortium, Baud A, Hermsen R, Guryev V, Stridh P, Graham D, McBride MW, Foroud T, Calderari S, Diez M, Ockinger J, Beyeen AD, Gillett A, Abdelmagid N, Guerreiro-Cacais AO, Jagodic M, Tuncel J, Norin U, Beattie E, Huynh N, Miller WH, Koller DL, Alam I, Falak S, Osborne-Pellegrin M, Martinez-Membrives E, Canete T, Blazquez G, Vicens-Costa E, Mont-Cardona C, Diaz-Moran S, Tobena A, Hummel O, Zelenika D, Saar K, Patone G, Bauerfeind A, Bihoreau MT, Heinig M, Lee YA, Rintisch C, Schulz H, Wheeler DA, Worley KC, Muzny DM, Gibbs RA, Lathrop M, Lansu N, Toonen P, Ruzius FP, de Bruijn E, Hauser H, Adams DJ, Keane T, Atanur SS, Aitman TJ, Flicek P, Malinauskas T, Jones EY, Ekman D, Lopez-Aumatell R, Dominiczak AF, Johannesson M, Holmdahl R, Olsson T, Gauguier D, Hubner N, Fernandez-Teruel A, Cuppen E, Mott R, Flint J.
Nat Genet. 2013 Jul;45(7):767-75. PMID:23708188 DOI:10.1038/ng.2644.
• FELASA guidelines for the refinement of methods for genotyping genetically-modified rodents: a report of the Federation of European Laboratory Animal Science Associations Working Group.
Bonaparte D, Cinelli P, Douni E, Hérault Y, Maas M, Pakarinen P, Poutanen M, Lafuente MS, Scavizzi F.
Lab Anim. 2013 Jul;47(3):134-45. PMID:23479772
• Human adult periodontal ligament-derived cells integrate and differentiate after implantation into the adult Mammalian brain.
Bueno C, Ramirez C, Rodríguez-Lozano FJ, Tabarés-Seisdedos R, Rodenas M, Moraleda JM, Jones JR, Martinez S.
Cell Transplant. 2013;22(11):2017-28. PMID:23043788 DOI:10.3727/096368912X657305.
• A short G1 phase is an intrinsic determinant of naïve embryonic stem cell pluripotency.
Coronado D, Godet M, Bourillot PY, Tapponnier Y, Bernat A, Petit M, Afanassieff M, Markossian S, Malashicheva A, Iacone R, Anastassiadis K, Savatier P.
Stem Cell Res. 2013 Jan;10(1):118-31. PMID:23178806 DOI:10.1016/j.scr.2012.10.004.
• Report of the Federation of European Laboratory Animal Science Associations Working Group on animal identification.
Dahlborn K, Bugnon P, Nevalainen T, Raspa M, Verbost P, Spangenberg E.
Lab Anim. 2013 Jan;47(1):2-11. PMID:23467487 DOI:10.1177/002367712473290.
• Ensembl 2013.
Flicek P, Ahmed I, Amode MR, Barrell D, Beal K, Brent S, Carvalho-Silva D, Clapham P, Coates G, Fairley S, Fitzgerald S, Gil L, García-Girón C, Gordon L, Hourlier T, Hunt S, Juettemann T, Kähäri AK, Keenan S, Komorowska M, Kulesha E, Longden I, Maurel T, McLaren WM, Muffato M, Nag R, Overduin B, Pignatelli M, Pritchard B, Pritchard E, Riat HS, Ritchie GR, Ruffier M, Schuster M, Sheppard D, Sobral D, Taylor K, Thormann A, Trevanion S, White S, Wilder SP, Aken BL, Birney E, Cunningham F, Dunham I, Harrow J, Herrero J, Hubbard TJ, Johnson N, Kinsella R, Parker A, Spudich G, Yates A, Zadissa A, Searle SM.
Nucleic Acids Res. 2013 Jan;41(Database issue):D48-55. PMID:23203987 DOI:10.1093/nar/gks1236.
• Computational approaches to identify functional genetic variants in cancer genomes.
Gonzalez-Perez A, Mustonen V, Reva B, Ritchie GR, Creixell P, Karchin R, Vazquez M, Fink JL, Kassahn KS, Pearson JV, Bader GD, Boutros PC, Muthuswamy L, Ouellette BF, Reimand J, Linding R, Shibata T, Valencia A, Butler A, Dronov S, Flicek P, Shannon NB, Carter H, Ding L, Sander C, Stuart JM, Stein LD, Lopez-Bigas N; International Cancer Genome Consortium Mutation Pathways and Consequences Subgroup of the Bioinformatics Analyses Working Group.
Nat Methods. 2013 Aug;10(8):723-9. PMID:23900255 DOI:10.1038/nmeth.2562.
• EMAP/EMAPA ontology of mouse developmental anatomy: 2013 update.
Hayamizu TF, Wicks MN, Davidson DR, Burger A, Ringwald M, Baldock RA.
J Biomed Semantics. 2013 Aug 26;4(1):15. PMID:23972281 DOI:10.1186/2041-1480-4-15.
• Stem cells from wildtype and friedreich’s ataxia mice present similar neuroprotective properties in dorsal root ganglia cells.
Jones J, Estirado A, Redondo C, Martinez S.
PLoS One. 2013 May 9;8(5):e62807. PMID:23671637 DOI:10.1371/journal.pone.0062807.
• Target validation in mice by constitutive and conditional RNAi.
Kleinhammer A, Wurst W, Kühn R.
Methods Mol Biol. 2013;986:307-23. PMID:23436420 DOI:10.1007/978-1-62703-311-4_19.
• The International Mouse Phenotyping Consortium Web Portal, a unified point of access for knockout mice and related phenotyping data.
Koscielny G, Yaikhom G, Iyer V, Meehan TF, Morgan H, Atienza-Herrero J, Blake A, Chen CK, Easty R, Di Fenza A, Fiegel T, Grifiths M, Horne A, Karp NA, Kurbatova N, Mason JC, Matthews P, Oakley DJ, Qazi A, Regnart J, Retha A, Santos LA, Sneddon DJ, Warren J, Westerberg H, Wilson RJ, Melvin DG, Smedley D, Brown SD, Flicek P, Skarnes WC, Mallon AM, Parkinson H.
Nucleic Acids Res. 2013 Nov 4. [Epub ahead of print] PMID:24194600
• Transcriptome and genome sequencing uncovers functional variation in humans.
Lappalainen T, Sammeth M, Friedländer MR, ‘t Hoen PA, Monlong J, Rivas MA, Gonzàlez-Porta M, Kurbatova N, Griebel T, Ferreira PG, Barann M, Wieland T, Greger L, van Iterson M, Almlöf J, Ribeca P, Pulyakhina I, Esser D, Giger T, Tikhonov A, Sultan M, Bertier G, MacArthur DG, Lek M, Lizano E, Buermans HP, Padioleau I, Schwarzmayr T, Karlberg O, Ongen H, Kilpinen H, Beltran S, Gut M, Kahlem K, Amstislavskiy V, Stegle O, Pirinen M, Montgomery SB, Donnelly P, McCarthy MI, Flicek P, Strom TM; Geuvadis Consortium, Lehrach H, Schreiber S, Sudbrak R, Carracedo A, Antonarakis SE, Häsler R, Syvänen AC, van Ommen GJ, Brazma A, Meitinger T, Rosenstiel P, Guigó R, Gut IG, Estivill X, Dermitzakis ET; Geuvadis Consortium.
Nature. 2013 Sep 26;501(7468):506-11. PMID:24037378 DOI:10.1038/nature12531.
• Cardiac fibrosis in mice expressing an inducible myocardial-specific Cre driver.
Lexow J, Poggioli T, Sarathchandra P, Santini MP, Rosenthal N.
Dis Model Mech. 2013 Nov-Dec;6(6):1470-6. PMID:23929940 DOI:10.1242/dmm.010470.
• The piggyBac transposon displays local and distant reintegration preferences and can cause mutations at noncanonical integration sites.
Li MA, Pettitt SJ, Eckert S, Ning Z, Rice S, Cadiñanos J, Yusa K, Conte N, Bradley A.
Mol Cell Biol. 2013 Apr;33(7):1317-30. PMID:23358416 DOI:10.1128/MCB.00670-12.
• Precocious cerebellum development and improved motor functions in mice lacking the astrocyte cilium-, patched 1-associated Gpr37l1 receptor.
Marazziti D, Di Pietro C, Golini E, Mandillo S, La Sala G, Matteoni R, Tocchini-Valentini GP.
Proc Natl Acad Sci USA. 2013 Oct 8;110(41):16486-91. PMID: 24062445 DOI:10.1073/pnas.1314819110.
• Cellular and molecular basis of cerebellar development.
Martinez S, Andreu A, Mecklenburg N, Echevarria D.
Front Neuroanat. 2013 Jun 26;7:18. PMID:23805080 DOI:10.3389/fnana.2013.00018.
• Wnt signal specifies the intrathalamic limit and its organizer properties by regulating Shh induction in the alar plate.
Martinez-Ferre A, Navarro-Garberi M, Bueno C, Martinez S.
J Neurosci. 2013 Feb 27;33(9):3967-80. PMID:23447606 DOI:10.1523/JNEUROSCI.0726-12.2013.
• Efficient generation of rat induced pluripotent stem cells using a non-viral inducible vector.
Merkl C, Saalfrank A, Riesen N, Kühn R, Pertek A, Eser S, Hardt MS, Kind A, Saur D, Wurst W, Iglesias A, Schnieke A.
PLoS One. 2013;8(1):e55170. PMID:23383095 DOI:10.1371/journal.pone.0055170.
• Role of Shh in the development of molecularly characterized tegmental nuclei in mouse rhombomere 1.
Moreno-Bravo JA, Perez-Balaguer A, Martinez-Lopez JE, Aroca P, Puelles L, Martinez S, Puelles E.
Brain Struct Funct. 2013 Mar 14. [Epub ahead of print] PMID:23494735
• Highly Efficient Targeted Mutagenesis in Mice Using TALENs.
Panda SK, Wefers B, Ortiz O, Floss T, Schmid B, Haass C, Wurst W, Kühn R.
Genetics. 2013 Nov;195(3):703-13. PMID: 23979585 DOI:10.1534/genetics.113.156570.
• Highly efficient, in vivo optimized, archaeal endonuclease for controlled RNA splicing in mammalian cells.
Putti S, Calandra P, Rossi N, Scarabino D, Deidda G, Tocchini-Valentini GP.
FASEB J. 2013 Sep;27(9):3466-77. PMID:23682120 DOI:10.1096/fj.13-231993.
• Transposon mediated BAC transgenesis via pronuclear injection of mouse zygotes.
Rostovskaya M, Naumann R, Fu J, Obst M, Mueller D, Stewart AF, Anastassiadis K.
Genesis. 2013 Feb;51(2):135-41. PMID:23225373 DOI:10.1002/dvg.22362.
• 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. 2013 Nov 7. [Epub ahead of print] PMID:24197666
• Molecular characterization of mutant mouse strains generated from the EUCOMM/KOMP-CSD ES cell resource.
Ryder E, Gleeson D, Sethi D, Vyas S, Miklejewska E, Dalvi P, Habib B, Cook R, Hardy M, Jhaveri K, Bottomley J, Wardle-Jones H, Bussell JN, Houghton R, Salisbury J, Skarnes WC; Sanger Mouse Genetics Project, Ramirez-Solis R.
Mamm Genome. 2013 Aug;24(7-8):286-94. PMID:23912999 DOI:10.1007/s00335-013-9467-x.
• Genomic analysis of a novel spontaneous albino C57BL/6N mouse strain.
Ryder E, Wong K, Gleeson D, Keane TM, Sethi D, Vyas S, Wardle-Jones H, Bussell JN, Houghton R, Salisbury J, Harvey N, Adams DJ; Sanger Mouse Genetics Project, Ramirez-Solis R.
Genesis. 2013 Jul;51(7):523-8. PMID:23620107 DOI:10.1002/dvg.22398.
• A comparative phenotypic and genomic analysis of C57BL/6J and C57BL/6N mouse strains.
Simon MM, Greenaway S, White JK, Fuchs H, Gailus-Durner V, Wells S, Sorg T, Wong K, Bedu E, Cartwright EJ, Dacquin R, Djebali S, Estabel J, Graw J, Ingham NJ, Jackson IJ, Lengeling A, Mandillo S, Marvel J, Meziane H, Preitner F, Puk O, Roux M, Adams DJ, Atkins S, Ayadi A, Becker L, Blake A, Brooker D, Cater H, Champy MF, Combe R, Danecek P, di Fenza A, Gates H, Gerdin AK, Golini E, Hancock JM, Hans W, Hölter SM, Hough T, Jurdic P, Keane TM, Morgan H, Müller W, Neff F, Nicholson G, Pasche B, Roberson LA, Rozman J, Sanderson M, Santos L, Selloum M, Shannon C, Southwell A, Tocchini-Valentini GP, Vancollie VE, Westerberg H, Wurst W, Zi M, Yalcin B, Ramirez-Solis R, Steel KP, Mallon AM, de Angelis MH, Herault Y, Brown SD.
Genome Biol. 2013 Jul 31;14(7):R82. [Epub ahead of print] PMID:23902802
• Cooperativity and rapid evolution of cobound transcription factors in closely related mammals.
Stefflova K, Thybert D, Wilson MD, Streeter I, Aleksic J, Karagianni P, Brazma A, Adams DJ, Talianidis I, Marioni JC, Flicek P, Odom DT.
Cell. 2013 Aug 1;154(3):530-40. PMID:23911320 DOI:10.1016/j.cell.2013.07.007.
• Reproducibility of high-throughput mRNA and small RNA sequencing across laboratories.
‘t Hoen PA, Friedländer MR, Almlöf J, Sammeth M, Pulyakhina I, Anvar SY, Laros JF, Buermans HP, Karlberg O, Brännvall M; GEUVADIS Consortium, van Ommen GJ, Estivill X, Guigó R, Syvänen AC, Gut IG, Dermitzakis ET, Antonarakis SE, Brazma A, Flicek P, Schreiber S, Rosenstiel P, Meitinger T, Strom TM, Lehrach H, Sudbrak R, Carracedo A, ‘t Hoen PA, Pulyakhina I, Anvar SY, Laros JF, Buermans HP, van Iterson M, Friedländer MR, Monlong J, Lizano E, Bertier G, Ferreira PG, Sammeth M, Almlöf J, Karlberg O, Brännvall M, Ribeca P, Griebel T, Beltran S, Gut M, Kahlem K, Lappalainen T, Giger T, Ongen H, Padioleau I, Kilpinen H, Gonzàlez-Porta M, Kurbatova N, Tikhonov A, Greger L, Barann M, Esser D, Häsler R, Wieland T, Schwarzmayr T, Sultan M, Amstislavskiy V, den Dunnen JT, van Ommen GJ, Gut IG, Guigó R, Estivill X, Syvänen AC, Dermitzakis ET, Lappalainen T.
Nat Biotechnol. 2013 Nov;31(11):1015-22. PMID:24037425 DOI:10.1038/nbt.2702.
• Direct production of mouse disease models by embryo microinjection of TALENs and oligodeoxynucleotides.
Wefers B, Meyer M, Ortiz O, Hrabé de Angelis M, Hansen J, Wurst W, Kühn R.
Proc Natl Acad Sci U S A. 2013 Mar 5;110(10):3782-7. PMID: 23426636 DOI:10.1073/pnas.1218721110.
• Generation of targeted mouse mutants by embryo microinjection of TALEN mRNA.
Wefers B, Panda SK, Ortiz O, Brandl C, Hensler S, Hansen J, Wurst W, Kühn R.
Nat Protoc. 2013 Dec;8(12):2355-79. PMID:24177293 DOI:10.1038/nprot.2013.142.
• Genome-wide generation and systematic phenotyping of knockout mice reveals new roles for many genes.
White JK, Gerdin AK, Karp NA, Ryder E, Buljan M, Bussell JN, Salisbury J, Clare S, Ingham NJ, Podrini C, Houghton R, Estabel J, Bottomley JR, Melvin DG, Sunter D, Adams NC; Sanger Institute Mouse Genetics Project, Tannahill D, Logan DW, Macarthur DG, Flint J, Mahajan VB, Tsang SH, Smyth I, Watt FM, Skarnes WC, Dougan G, Adams DJ, Ramirez-Solis R, Bradley A, Steel KP.
Cell. 2013 Jul 18;154(2):452-64. PMID:23870131 DOI:10.1016/j.cell.2013.06.022.


• An integrated map of genetic variation from 1,092 human genomes. 
1000 Genomes Project Consortium, Abecasis GR, Auton A, Brooks LD, DePristo MA, Durbin RM, Handsaker RE, Kang HM, Marth GT, McVean GA.
Nature. 2012 Nov 1;491(7422):56-65. PMID:23128226 DOI:10.1038/nature11632.
• eMouseAtlas, EMAGE, and the spatial dimension of the transcriptome. 
Armit C, Venkataraman S, Richardson L, Stevenson P, Moss J, Graham L, Ross A, Yang Y, Burton N, Rao J, Hill B, Rannie D, Wicks M, Davidson D, Baldock R.
Mamm Genome. 2012 Oct;23(9-10):514-24. PMID: 22847374 DOI: 10.1007/s00335-012-9407-1
• Mouse large-scale phenotyping initiatives: overview of the European Mouse Disease Clinic (EUMODIC) and of the Wellcome Trust Sanger Institute Mouse Genetics Project.
Ayadi A, Birling MC, Bottomley J, Bussell J, Fuchs H, Fray M, Gailus-Durner V, Greenaway S, Houghton R, Karp N, Leblanc S, Lengger C, Maier H, Mallon AM, Marschall S, Melvin D, Morgan H, Pavlovic G, Ryder E, Skarnes WC, Selloum M, Ramirez-Solis R, Sorg T, Teboul L, Vasseur L, Walling A, Weaver T, Wells S, White JK, Bradley A, Adams DJ, Steel KP, Hrabé de Angelis M, Brown SD, Hérault Y.
Mamm Genome. 2012 Oct;23(9-10):600-10. PMID: 22961258 DOI: 10.1007/s00335-012-9418-y
• Biomedical atlases: systematics, informatics and analysis.
Baldock RA, Burger A.
Adv Exp Med Biol. 2012;736:655-77. PMID: 22161358 DOI: 10.1007/978-1-4419-7210-1_39
• iHealth and economic consequences of fragile X syndrome for caregivers.
Bailey DB Jr, Raspa M, Bishop E, Mitra D, Martin S, Wheeler A, Sacco P.
J Dev Behav Pediatr. 2012 Nov-Dec;33(9):705-12. PMID:23117595 DOI:10.1097/DBP.0b013e318272dcbc.
• Rapid-throughput skeletal phenotyping of 100 knockout mice identifies 9 new genes that determine bone strength.
Bassett JH, Gogakos A, White JK, Evans H, Jacques RM, van der Spek AH; Sanger Mouse Genetics Project, Ramirez-Solis R, Ryder E, Sunter D, Boyde A, Campbell MJ, Croucher PI, Williams GR.
PLoS Genet. 2012 Aug;8(8):e1002858. PMID: 22876197 DOI: 10.1371/journal.pgen.1002858
• Direct cloning, genetic engineering, and heterologous expression of the syringolin biosynthetic gene cluster in E. coli through Red/ET recombineering.
Bian X, Huang F, Stewart FA, Xia L, Zhang Y, Müller R.
Chembiochem. 2012 Sep 3;13(13):1946-52. PMID: 22851214 DOI: 10.1002/cbic.201200310
• Highly-efficient, fluorescent, locus directed Cre and FlpO deleter mice on a pure C57BL/6N genetic background. 
Birling MC, Dierich A, Jacquot S, Hérault Y, Pavlovic G .
Genesis. 2012 Jun;50(6):482-9. PMID: 22121025 DOI: 10.1002/dvg.20826
• 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 KCK, 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 KI, Yoshinaga Y, Wurst W.
Mamm Genome. 2012 Oct;23(9-10):580-6. PMID: 22968824 DOI: 10.1007/s00335-012-9422-2
• 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. PMID: 22940749 DOI: 10.1007/s00335-012-9427-x
• Towards an encyclopaedia of mammalian gene function: the International Mouse Phenotyping Consortium.
Brown SD, Moore MW.
Dis Model Mech. 2012 May;5(3):289-92. PMID: 22566555 DOI: 10.1242/dmm.009878
• Mouse genomics programs and resources: The mouse: pushing the boundaries.
Bucan M, Eppig JT, Brown S.
Mamm Genome. 2012 Oct;23(9-10):479-89. PMID: 22968825 DOI: 10.1007/s00335-012-9429-8
• CreZOO–the European virtual repository of Cre and other targeted conditional driver strains.
Chandras C, Zouberakis M, Salimova E, Smedley D, Rosenthal N, Aidinis V.
Database (Oxford). 2012 Jun 21;2012:bas029. PMID: 22730454 DOI: 10.1093/database/bas029
• The 1000 Genomes Project: data management and community access.
Clarke L, Zheng-Bradley X, Smith R, Kulesha E, Xiao C, Toneva I, Vaughan B, Preuss D, Leinonen R, Shumway M, Sherry S, Flicek P; 1000 Genomes Project Consortium.
Nat Methods. 2012 Apr 27;9(5):459-62. PMID:22543379 DOI:10.1038/nmeth.1974.
• Large-scale identification of microRNA targets in murine Dgcr8-deficient embryonic stem cell lines.
Davis MP, Abreu-Goodger C, van Dongen S, Lu D, Tate PH, Bartonicek N, Kutter C, Liu P, Skarnes WC, Enright AJ, Dunham I.
PLoS One. 2012;7(8):e41762. PMID: 22912678 DOI: 10.1371/journal.pone.0041762
• Centralized mouse repositories.
Donahue LR, Hrabe de Angelis M, Hagn M, Franklin C, Lloyd KC, Magnuson T, McKerlie C, Nakagata N, Obata Y, Read S, Wurst W, Hörlein A, Davisson MT.
Mamm Genome. 2012 Oct;23(9-10):559-71. PMID: 22945696 DOI: 10.1007/s00335-012-9420-4
• An integrated encyclopedia of DNA elements in the human genome.
ENCODE Project Consortium, Dunham I, et al.
Nature. 2012 Sep 6;489(7414):57-74. PMID: 22955616 DOI: 10.1038/nature11247
• Ensembl 2012.
Flicek P, Amode MR, Barrell D, Beal K, Brent S, Carvalho-Silva D, Clapham P, Coates G, Fairley S, Fitzgerald S, Gil L, Gordon L, Hendrix M, Hourlier T, Johnson N, Kähäri AK, Keefe D, Keenan S, Kinsella R, Komorowska M, Koscielny G, Kulesha E, Larsson P, Longden I, McLaren W, Muffato M, Overduin B, Pignatelli M, Pritchard B, Riat HS, Ritchie GR, Ruffier M, Schuster M, Sobral D, Tang YA, Taylor K, Trevanion S, Vandrovcova J, White S, Wilson M, Wilder SP, Aken BL, Birney E, Cunningham F, Dunham I, Durbin R, Fernández-Suarez XM, Harrow J, Herrero J, Hubbard TJ, Parker A, Proctor G, Spudich G, Vogel J, Yates A, Zadissa A, Searle SM.
Nucleic Acids Res. 2012 Jan;40(Database issue):D84-90. PMID:22086963 DOI:10.1093/nar/gkr991.
• Full-length RecE enhances linear-linear homologous recombination and facilitates direct cloning for bioprospecting.
Fu J, Bian X, Hu S, Wang H, Huang F, Seibert PM, Plaza A, Xia L, Müller R, Stewart AF, Zhang Y.
Nat Biotechnol. 2012 May;30(5):440-6. PMID: 22544021 DOI: 10.1038/nbt.2183
• Innovations in phenotyping of mouse models in the German Mouse Clinic.
Fuchs H, Gailus-Durner V, Neschen S, Adler T, Afonso LC, Aguilar-Pimentel JA, Becker L, Bohla A, Calzada-Wack J, Cohrs C, Dewert A, Fridrich B, Garrett L, Glasl L, Götz A, Hans W, Hölter SM, Horsch M, Hurt A, Janas E, Janik D, Kahle M, Kistler M, Klein-Rodewald T, Lengger C, Ludwig T, Maier H, Marschall S, Micklich K, Möller G, Naton B, Prehn C, Puk O, Rácz I, Räss M, Rathkolb B, Rozman J, Scheerer M, Schiller E, Schrewe A, Steinkamp R, Stöger C, Sun M, Szymczak W, Treise I, Vargas Panesso IL, Vernaleken AM, Willershäuser M, Wolff-Muscate A, Zeh R, Adamski J, Beckers J, Bekeredjian R, Busch DH, Eickelberg O, Favor J, Graw J, Höfler H, Höschen C, Katus H, Klingenspor M, Klopstock T, Neff F, Ollert M, Schulz H, Stöger T, Wolf E, Wurst W, Yildirim AÖ, Zimmer A, Hrabě de Angelis M.
Mamm Genome. 2012 Oct;23(9-10):611-22. PMID:22926221 DOI:10.1007/s00335-012-9415-1.
• Experimental and husbandry procedures as potential modifiers of the results of phenotyping tests.
Gerdin AK, Igosheva N, Roberson LA, Ismail O, Karp N, Sanderson M, Cambridge E, Shannon C, Sunter D, Ramirez-Solis R, Bussell J, White JK.
Physiol Behav. 2012 Jul 16;106(5):602-11. PMID:22713295 DOI:10.1016/j.physbeh.2012.03.026.
• A practical and efficient cellular substrate for the generation of induced pluripotent stem cells from adults: blood-derived endothelial progenitor cells.
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Stem Cells Transl Med. 2012 Dec;1(12):855-65. PMID:23283547 DOI:10.5966/sctm.2012-0093.
• Extensive compensatory cis-trans regulation in the evolution of mouse gene expression.
Goncalves A, Leigh-Brown S, Thybert D, Stefflova K, Turro E, Flicek P, Brazma A, Odom DT, Marioni JC.
Genome Res. 2012 Aug 23. PMID: 22919075 DOI: 10.1101/gr.142281.112
• Overview of new developments in and the future of cryopreservation in the laboratory mouse.
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. Mamm Genome. 2012 Oct;23(9-10):572-9. PMID:22936001 DOI:10.1007/s00335-012-9423-1.
• Targeted deletion of microRNA-22 promotes stress-induced cardiac dilation and contractile dysfunction.
Gurha P, Abreu-Goodger C, Wang T, Ramirez MO, Drumond AL, van Dongen S, Chen Y, Bartonicek N, Enright AJ, Lee B, Kelm RJ Jr, Reddy AK, Taffet GE, Bradley A, Wehrens XH, Entman ML, Rodriguez A.
Circulation. 2012 Jun 5;125(22):2751-61. PMID: 22570371 DOI: 10.1161/CIRCULATIONAHA.111.044354
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Herault Y, Duchon A, Velot E, Maréchal D, Brault V.
Prog Brain Res. 2012;197:169-97. PMID:22541293 DOI:10.1016/B978-0-444-54299-1.00009-1.
• Isolation of homozygous mutant mouse embryonic stem cells using a dual selection system.
Huang Y, Pettitt SJ, Guo G, Liu G, Li MA, Yang F, Bradley A.
Nucleic Acids Res. 2012 Feb;40(3):e21. PMID:22127858 DOI:10.1093/nar/gkr908.
• Web tools for large-scale 3D biological images and atlases.
Husz ZL, Burton N, Hill B, Milyaev N, Baldock RA.
BMC Bioinformatics. 2012 Jun 7;13:122. PMID: 22676296 DOI: 10.1186/1471-2105-13-122
• Ensembl Genomes: an integrative resource for genome-scale data from non-vertebrate species.
Kersey PJ, Staines DM, Lawson D, Kulesha E, Derwent P, Humphrey JC, Hughes DS, Keenan S, Kerhornou A, Koscielny G, Langridge N, McDowall MD, Megy K, Maheswari U, Nuhn M, Paulini M, Pedro H, Toneva I, Wilson D, Yates A, Birney E.
Nucleic Acids Res. 2012 Jan;40(Database issue):D91-7. PMID:22067447 DOI:10.1093/nar/gkr895.
• Humanized c-Myc mouse.
Lehmann FM, Feicht S, Helm F, Maurberger A, Ladinig C, Zimber-Strobl U, Kühn R, Mautner J, Gerbitz A, Bornkamm GW.
PLoS One. 2012;7(7):e42021. PMID: 22860051 DOI: 10.1371/journal.pone.0042021
• MiR-25 regulates Wwp2 and Fbxw7 and promotes reprogramming of mouse fibroblast cells to iPSCs.
Lu D, Davis MP, Abreu-Goodger C, Wang W, Campos LS, Siede J, Vigorito E, Skarnes WC, Dunham I, Enright AJ, Liu P.
PLoS One. 2012;7(8):e40938. PMID:22912667 DOI:10.1371/journal.pone.0040938.
• 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. PMID: 22991088 DOI: 10.1007/s00335-012-9428-9
• The transcriptional and epigenomic foundations of ground state pluripotency.
Marks H, Kalkan T, Menafra R, Denissov S, Jones K, Hofemeister H, Nichols J, Kranz A, Stewart AF, Smith A, Stunnenberg HG.
Cell. 2012 Apr 27;149(3):590-604. PMID: 22541430 DOI: 10.1016/j.cell.2012.03.026
• Molecular regionalization of the diencephalon.
Martinez-Ferre A, Martinez S.
Front Neurosci. 2012 May 25;6:73. PMID:22654731 DOI:10.3389/fnins.2012.00073.
• Orphan receptor IL-17RD tunes IL-17A signalling and is required for neutrophilia. 
Mellett M, Atzei P, Horgan A, Hams E, Floss T, Wurst W, Fallon PG, Moynagh PN.
Nat Commun. 2012 Oct 9;3:1119 PMID: 23047677 DOI: 10.1038/ncomms2127
• Modeling disease mutations by gene targeting in one-cell mouse embryos.
Meyer M, Ortiz O, Hrabé de Angelis M, Wurst W, Kühn R.
Proc Natl Acad Sci U S A. 2012 Jun 12;109(24):9354-9. PMID: 22660928 DOI: 10.1073/pnas.1121203109
• 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. PMID: 22926223 DOI: 10.1007/s00335-012-9430-2
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• Large-scale mouse knockouts and phenotypes.
Ramírez-Solis R, Ryder E, Houghton R, White JK, Bottomley J.
Wiley Interdiscip Rev Syst Biol Med. 2012 Nov;4(6):547-63. PMID: 22899600 DOI: 10.1002/wsbm.1183
• Transposon-mediated BAC transgenesis in human ES cells.
Rostovskaya M, Fu J, Obst M, Baer I, Weidlich S, Wang H, Smith AJ, Anastassiadis K, Stewart AF.
Nucleic Acids Res. 2012 Oct;40(19):e150. PMID: 22753106 DOI: 10.1093/nar/gks643
• Network compression as a quality measure for protein interaction networks.
Royer L, Reimann M, Stewart AF, Schroeder M.
PLoS One. 2012;7(6):e35729. PMID:22719828 DOI:10.1371/journal.pone.0035729.
• A genome-scale resource for in vivo tag-based protein function exploration in C. elegans.
Sarov M, Murray JI, Schanze K, Pozniakovski A, Niu W, Angermann K, Hasse S, Rupprecht M, Vinis E, Tinney M, Preston E, Zinke A, Enst S, Teichgraber T, Janette J, Reis K, Janosch S, Schloissnig S, Ejsmont RK, Slightam C, Xu X, Kim SK, Reinke V, Stewart AF, Snyder M, Waterston RH, Hyman AA.
Cell. 2012 Aug 17;150(4):855-66. PMID: 22901814 DOI: 10.1016/j.cell.2012.08.001
• Waves of retrotransposon expansion remodel genome organization and CTCF binding in multiple mammalian lineages.
Schmidt D, Schwalie PC, Wilson MD, Ballester B, Gonçalves A, Kutter C, Brown GD, Marshall A, Flicek P, Odom DT.
Cell. 2012 Jan 20;148(1-2):335-48. Erratum in: Cell. 2012 Feb 17;148(4):832. PMID:22244452 DOI:10.1016/j.cell.2011.11.058.
• Building and sharing resources. Interview by Krystie Nybo.
Skarnes WC.
Biotechniques. 2012 May;52(5):299. PMID: 22578120 DOI: 10.2144/000113846
• Large-scale phenotyping of an accurate genetic mouse model of JNCL identifies novel early pathology outside the central nervous system.
Staropoli JF, Haliw L, Biswas S, Garrett L, Hölter SM, Becker L, Skosyrski S, Da Silva-Buttkus P, Calzada-Wack J, Neff F, Rathkolb B, Rozman J, Schrewe A, Adler T, Puk O, Sun M, Favor J, Racz I, Bekeredjian R, Busch DH, Graw J, Klingenspor M, Klopstock T, Wolf E, Wurst W, Zimmer A, Lopez E, Harati H, Hill E, Krause DS, Guide J, Dragileva E, Gale E, Wheeler VC, Boustany RM, Brown DE, Breton S, Ruether K, Gailus-Durner V, Fuchs H, de Angelis MH, Cotman SL.
PLoS One. 2012;7(6):e38310. PMID: 22701626 DOI: 10.1371/journal.pone.0038310
• Avatar pre-tRNAs help elucidate the properties of tRNA-splicing endonucleases that produce tRNA from permuted genes.
Tocchini-Valentini GD, Tocchini-Valentini GP.
Proc Natl Acad Sci U S A. 2012 Dec 26;109(52):21325-9. PMID:23236183 DOI:10.1073/pnas.1219336110.
• Locally expressed IGF1 propeptide improves mouse heart function in induced dilated cardiomyopathy by blocking myocardial fibrosis and SRF-dependent CTGF induction.
Touvron M, Escoubet B, Mericskay M, Angelini A, Lamotte L, Santini MP, Rosenthal N, Daegelen D, Tuil D, Decaux JF.
Dis Model Mech. 2012 Jul;5(4):481-91. PMID:22563064 DOI:10.1242/dmm.009456.
• Srgap3-/- mice present a neurodevelopmental disorder with schizophrenia-related intermediate phenotypes.
Waltereit R, Leimer U, von Bohlen Und Halbach O, Panke J, Hölter SM, Garrett L, Wittig K, Schneider M, Schmitt C, Calzada-Wack J, Neff F, Becker L, Prehn C, Kutscherjawy S, Endris V, Bacon C, Fuchs H, Gailus-Durner V, Berger S, Schönig K, Adamski J, Klopstock T, Esposito I, Wurst W, de Angelis MH, Rappold G, Wieland T, Bartsch D.
FASEB J. 2012 Jul 20. PMID: 22820399 DOI: 10.1096/fj.11-202317i
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Zheng-Bradley X, Flicek P.
Hum Mutat. 2012 Jun;33(6):1016-9. PMID:22253119 DOI:10.1002/humu.22024.


• High-efficiency counterselection recombineering for site-directed mutagenesis in bacterial artificial chromosomes.
Bird AW, Erler A, Fu J, Hériché JK, Maresca M, Zhang Y, Hyman AA, Stewart AF.
Nat Methods. 2011 Dec 4;9(1):103-9. PMID: 22138824 DOI: 10.1038/nmeth.1803
• A high-resolution anatomical atlas of the transcriptome in the mouse embryo.
Diez-Roux G, Banfi S, Sultan M, Geffers L, Anand S, Rozado D, Magen A, Canidio E, Pagani M, Peluso I, Lin-Marq N, Koch M, Bilio M, Cantiello I, Verde R, De Masi C, Bianchi SA, Cicchini J, Perroud E, Mehmeti S, Dagand E, Schrinner S, Nürnberger A, Schmidt K, Metz K, Zwingmann C, Brieske N, Springer C, Hernandez AM, Herzog S, Grabbe F, Sieverding C, Fischer B, Schrader K, Brockmeyer M, Dettmer S, Helbig C, Alunni V, Battaini MA, Mura C, Henrichsen CN, Garcia-Lopez R, Echevarria D, Puelles E, Garcia-Calero E, Kruse S, Uhr M, Kauck C, Feng G, Milyaev N, Ong CK, Kumar L, Lam M, Semple CA, Gyenesei A, Mundlos S, Radelof U, Lehrach H, Sarmientos P, Reymond A, Davidson DR, Dollé P, Antonarakis SE, Yaspo ML, Martinez S, Baldock RA, Eichele G, Ballabio A.
PLoS Biol. 2011 Jan 18;9(1):e1000582. PMID: 21267068 DOI: 10.1371/journal.pbio.1000582
• Towards BioDBcore: a community-defined information specification for biological databases.
Gaudet P, Bairoch A, Field D, Sansone SA, Taylor C, Attwood TK, Bateman A, Blake JA, Bult CJ, Cherry JM, Chisholm RL, Cochrane G, Cook CE, Eppig JT, Galperin MY, Gentleman R, Goble CA, Gojobori T, Hancock JM, Howe DG, Imanishi T, Kelso J, Landsman D, Lewis SE, Karsch Mizrachi I, Orchard S, Ouellette BF, Ranganathan S, Richardson L, Rocca-Serra P, Schofield PN, Smedley D, Southan C, Tan TW, Tatusova T, Whetzel PL, White O, Yamasaki C; BioDBCore Working Group.
Database (Oxford). 2011 Jan 4;2011:baq027. PMID: 21205783 DOI: 10.1093/database/baq027
• CD19-independent instruction of murine marginal zone B-cell development by constitutive Notch2 signaling.
Hampel F, Ehrenberg S, Hojer C, Draeseke A, Marschall-Schröter G, Kühn R, Mack B, Gires O, Vahl CJ, Schmidt-Supprian M, Strobl LJ, Zimber-Strobl U.
Blood. 2011 Dec 8;118(24):6321-31. PMID: 21795747 DOI: 10.1182/blood-2010-12-325944
• Automatically identifying and annotating mouse embryo gene expression patterns.
Han L, van Hemert JI, Baldock RA.
Bioinformatics. 2011 Apr 15;27(8):1101-7. PMID: 21357576 DOI: 10.1093/bioinformatics/btr105
• Digital atlasing and standardization in the mouse brain.
Hawrylycz M, Baldock RA, Burger A, Hashikawa T, Johnson GA, Martone M, Ng L, Lau C, Larson SD, Nissanov J, Puelles L, Ruffins S, Verbeek F, Zaslavsky I, Boline J.
PLoS Comput Biol. 2011 Feb 3;7(2):e1001065. Erratum in: PLoS Comput Biol. 2011 Feb;7(2). PMID: 21304938 DOI:10.1371/journal.pcbi.1001065
• Requirement of the RNA-editing enzyme ADAR2 for normal physiology in mice.
Horsch M, Seeburg PH, Adler T, Aguilar-Pimentel JA, Becker L, Calzada-Wack J, Garrett L, Götz A, Hans W, Higuchi M, Hölter SM, Naton B, Prehn C, Puk O, Rácz I, Rathkolb B, Rozman J, Schrewe A, Adamski J, Busch DH, Esposito I, Graw J, Ivandic B, Klingenspor M, Klopstock T, Mempel M, Ollert M, Schulz H, Wolf E, Wurst W, Zimmer A, Gailus-Durner V, Fuchs H, de Angelis MH, Beckers J.
J Biol Chem. 2011 May 27;286(21):18614-22. PMID: 21467037 DOI: 10.1074/jbc.M110.200881
• A scalable pipeline for highly effective genetic modification of a malaria parasite.
Pfander C, Anar B, Schwach F, Otto TD, Brochet M, Volkmann K, Quail MA, Pain A, Rosen B, Skarnes W, Rayner JC, Billker O.
Nat Methods. 2011 Oct 23;8(12):1078-82. PMID: 22020067 DOI: 10.1038/nmeth.1742
• A resource of vectors and ES cells for targeted deletion of microRNAs in mice.
Prosser HM, Koike-Yusa H, Cooper JD, Law FC, Bradley A.
Nat Biotechnol. 2011 Aug 7;29(9):840-5. PMID: 21822254 DOI: 10.1038/nbt.1929
• A conditional knockout resource for the genome-wide study of mouse gene function.
Skarnes WC, Rosen B, West AP, Koutsourakis M, Bushell W, Iyer V, Mujica AO, Thomas M, Harrow J, Cox T, Jackson D, Severin J, Biggs P, Fu J, Nefedov M, de Jong PJ, Stewart AF, Bradley A.
Nature. 2011 Jun 15;474(7351):337-42. PMID: 21677750 DOI: 10.1038/nature10163
• Cre recombinase resources for conditional mouse mutagenesis.
Smedley D, Salimova E, Rosenthal N.
Methods. 2011 Apr;53(4):411-6. PMID: 21195764 DOI: 10.1016/j.ymeth.2010.12.027
• The BioMart interface to the eMouseAtlas gene expression database EMAGE.
Stevenson P, Richardson L, Venkataraman S, Yang Y, Baldock R.
Database (Oxford). 2011 Sep 18;2011:bar029. PMID: 21930504 DOI: 10.1093/database/bar029
• Sprouty genes prevent excessive FGF signalling in multiple cell types throughout development of the cerebellum.
Yu T, Yaguchi Y, Echevarria D, Martinez S, Basson MA.
Development. 2011 Jul;138(14):2957-68. PMID: 21693512 DOI: 10.1242/dev.063784