MGI-Mouse Genome Informatics Publications
  About   Help   FAQ
Mouse Genome Informatics Publications
The following staff publications derive from work on Mouse Genome Informatics projects and are not meant to be inclusive publication lists for any of the authors. For information about how to cite Mouse Genome Informatics resources in publications, see Citing These Resources.
2024
Baron JA, Johnson CS, Schor MA, Olley D, Nickel L, Felix V, Munro JB, Bello SM, Bearer C, Lichenstein R, Bisordi K, Koka R, Greene C, Schriml LM. 2023. The DO-KB Knowledgebase: a 20-year journey developing the disease open science ecosystem. Nucleic Acids Res. 2024 Jan 5;52(D1):D1305-D1314. PubMed
Gargano MA, Matentzoglu N, Coleman B, Addo-Lartey EB, Anagnostopoulos AV, Anderton J, Avillach P, Bagley AM, Bakštein E, Balhoff JP, Baynam G, Bello SM, […] Smith CL, […] Robinson PN. 2023. The Human Phenotype Ontology in 2024: phenotypes around the world. Nucleic Acids Res. 2024 Jan 5;52(D1):D1333-D1346. PubMed
2023
Begley DA, Krupke DM, Sundberg JP, Jocoy EL, Richardson JE, Neuhauser SB, Bult CJ. 2023. The Mouse Models of Human Cancer database (MMHCdb). Dis Model Mech. 2023;16(4):dmm050001. PubMed
Hill DP, Drabkin HJ, Smith CL, Van Auken KM, D'Eustachio P. 2023. Biochemical Pathways Represented by Gene Ontology Causal Activity Models Identify Distinct Phenotypes Resulting From Mutations in Pathways. Genetics. 2023 Aug 14:iyad152. PubMed
Prakash SJ, Van Auken KM, Hill DP, Sternberg PW. 2023. Semantic representation of neural circuit knowledge in Caenorhabditis elegans. Brain Inform. 2023 Nov 10;10(1):30. PubMed
Perova Z, Martinez M, Mandloi T, Gomez FL, Halmagyi C, Follette A, Mason J, Newhauser S, Begley DA, Krupke DM, Bult C, Parkinson H, Groza T. 2023. PDCM Finder: an open global research platform for patient-derived cancer models. Nucleic Acids Res. 2023 Jan 6;51(D1):D1360-D1366. PubMed
2022
Begley D, Schofield PN, Sundberg JP. The Mouse Online: Open Mouse Biology and Pathology Data Resources for Biomedical Research. 2022 In: Pathology of genetically engineered mice and other mutants. Sundberg JP, Vogel P, and Ward JM, eds., Wiley. 6-21.
Dudová Z, Conte N, Mason J, Stuchlík D, Peša R, Halmagyi C, Perova Z, Mosaku A, Thorne R, Follette A, Pivarč Ľ, Šašinka R, Usman M, Neuhauser S, Begley DA, Krupke DM, Frassà M, Fiori A, Corsi R, Vezzadini L, Isella C, Bertotti A, Bult C, Parkinson H, Medico E, Meehan T, Křenek A. 2022. The EurOPDX Data Portal: an open platform for patient-derived cancer xenograft data sharing and visualization. BMC Genomics. 2022 Feb 22;23(1):156. PubMed
Matentzoglu N, Balhoff JP, Bello SM, Bizon C, Brush M, Callahan TJ, […] Mugall CJ. 2022. A Simple Standard for Sharing Ontological Mappings (SSSOM). 2022. Database (Oxford). 2022 May 25;2022:baac035. PubMed
Richardson JE, Baldarelli RM, Bult CJ. 2022. Multiple genome viewer (MGV): a new tool for visualization and comparison of multiple annotated genomes. Mamm Genome. 2022 Mar;33(1):44-54. PubMed
Ringwald M, Richardson JE, Baldarelli RM, Blake JA, Kadin JA, Smith C, Bult CJ. 2022. Mouse Genome Informatics (MGI): latest news from MGD and GXD. Mamm Genome. 2022 Mar;33(1):4-18. PubMed
Schriml LM, Munro JB, Schor M, Olley D, McCracken C, Felix V, Baron JA, Jackson R, Bello SM, Bearer C, Lichenstein R, Bisordi K, Dialo NC, Giglio M, Greene C. 2022. The Human Disease Ontology 2022 update. Nucleic Acids Res. 2022 Jan 7;50(D1):D1255-D1261. PubMed
Seal RL, Denny P, Bruford EA, Gribkova AK, Landsman D, Marzluff WF, McAndrews M, Panchenko AR, Shaytan AK, Talbert PB. 2022. A standardized nomenclature for mammalian histone genes. Epigenetics Chromatin. 2022 Oct 1;15(1):34. PubMed
Sundberg JP, Begley D, Berry M, Perry MN, Shaw D, Schofield PN. 2022 Mouse Genetic Nomenclature: The Underpinning of Mouse Genetics. In: Pathology of genetically engineered mice and other mutants. Sundberg JP, Vogel P, and Ward JM, eds., Wiley. 22-38.
2021
Baldarelli RM, Smith CM, Finger JH, Hayamizu TF, McCright IJ, Xu J, Shaw DR, Beal JS, Blodgett O, Campbell J, Corbani LE, Frost PJ, Giannatto SC, Miers DB, Kadin JA, Richardson JE, Ringwald M. 2021. The mouse Gene Expression Database (GXD): 2021 update. Nucleic Acids Res. 2021 Jan 8;49(D1):D924-D931. PubMed
Bello SM, Perry MN, Smith CL. 2021. Know Your Model: A brief history of making mutant mouse genetic models. Lab Anim (NY). 2021 Oct;50:263-266. PubMed
Blake JA, Baldarelli R, Kadin JA, Richardson JE, Smith CL, Bult CJ; Mouse Genome Database Group. 2021. Mouse Genome Database (MGD): Knowledgebase for mouse-human comparative biology. Nucleic Acids Res. 2021 Jan 8;49(D1):D981-D987. PubMed
Blake JA, Dolan ME, Drabkin HJ, Hill DP with The Gene Ontology Consortium. 2021. The Gene Ontology resource: enriching a GOld mine. Nucleic Acids Res. 2021 Jan 8;49(D1):D325-D334. PubMed
Li P, Jiang X, Zhang G, Trabucco JT, Raciti D, Smith C, Ringwald M, Marai GE, Arighi C, Shatkay H. 2021. Utilizing image and caption information for biomedical document classification. Bioinformatics. 2021 Jul 12;37(Suppl_1):i468-i476. PubMed
Perry MN, Smith CL. 2021. Murine allele and transgene symbols: ensuring unique, concise, and informative nomenclature. Mamm Genome (NY). 2021 Aug 14. PubMed
Perry MN, Smith CM, Onda H, Ringwald M, Murray, SA, Smith CL. 2021. Annotated expression and activity data for murine recombinase alleles and transgenes: the CrePortal resource. Mamm Genome (NY). 2021 Sept 4. PubMed
2020
Bello SM, Berry ML, Smith CL. 2020. Know Your Model: How essential is that essential gene? Lab Anim (NY). 2020 Jan;49(1):9-10. PubMed
Bello SM, Perry MN, Smith CL. 2020. Know Your Model: A Knockout Does Not Always Make a Null. Lab Anim (NY). 2020 Mar;49(3):59-60. PubMed
Bello SM, Perry MN, Smith CL. 2020. Know Your Model: When Parental Origin Matters. Lab Anim (NY). 2020 Jun;49(6):161-162. PubMed
Bello SM, Perry MN, Smith CL. 2020. Know Your Model: The role of sex in phenotype penetrance and severity. Lab Anim (NY). 2020 Sep;49(9):239-240. PubMed
Dolan ME, Hill DP, Mukherjee G, McAndrews MS, Chesler EJ, Blake JA. 2020. Investigation of COVID-19 comorbidities reveals genes and pathways coincident with the SARS-CoV-2 viral disease. Scientific Reports 2020 Nov 30;10(1):20848. PubMed
Jiang X, Li P, Kadin J, Blake JA, Ringwald M, Shatkay H. 2020. Integrating image caption information into biomedical document classification in support of biocuration. Database (Oxford). 2020 Jan 1;2020:baaa024. PubMed
Perry MN, Bello SM, Smith CL. 2020. Know Your Model: Why mouse inbred strain contribution matters. Lab Anim (NY). 2020 May;49(5):133-134. PubMed
Perry MN, Bello SM, Smith CL. 2020. Know Your Model: Recombinase-expressing Mice. Lab Anim (NY). 2020 Jul;49(7)187-189. PubMed
Perry MN, Bello SM, Smith CL. 2020. Know Your Model: Microbiota & phenotypes. Lab Anim (NY). 2020 Nov;49(11):301-302. PubMed
Smith CM, Kadin JA, Baldarelli RM, Beal JS, Blodgett O, Giannatto SC, Richardson JE, Ringwald M. 2020. GXD's RNA-Seq and Microarray Experiment Search: using curated metadata to reliably find mouse expression studies of interest. Database 2020 Mar. 4 PubMed
2019
Attrill H, Gaudet P, Huntley RP, Lovering RC, Engel SR, Poux S, Van Auken KM, Georghiou G, Chibucos MC, Berardini TZ, Wood V, Drabkin H, Fey P, Garmiri P, Harris MA, Sawford T, Reiser L, Tauber R, Toro S; Gene Ontology Consortium. 2019. Annotation of gene product function from high-throughput studies using the Gene Ontology. Database. (Oxford) 2019 Jan1;2019:baz007. PubMed
Bult CJ, Blake JA, Smith CL, Kadin JA, Richardson JE , the Mouse Genome Database Group. 2019. Mouse Genome Database (MGD) 2019. Nucleic Acids Res. 2019 Jan. 8;47 (D1): D801–D806. PubMed
Jiang X, Ringwald M, Blake JA, Arighi C, Zhang G, Shatkay H. 2019. An effective biomedical document classification scheme in support of biocuration: addressing class imbalance. Database. (Oxford) 2019 Jan 1;2019:baz045. PubMed
Köhler S, Carmody L, Vasilevsky N, […] Bello SM, […] Smith C, […] Milner JD, Leroux D, Boerkoel CF, Klion A, Carter MC, Groza T, Smedley D, Haendel MA, Mungall C, Robinson PN. 2019. Expansion of the Human Phenotype Ontology (HPO) knowledge base and resources. Nucleic Acids Res. 2019 Jan 8;47(D1):D1018-D1027. PubMed
Kolishovski G, Lamoureux A, Hale P, Richardson JE, Recla JM, Adesanya O, Simons A, Kunde-Ramamoorthy G, Bult CJ. The JAX Synteny Browser for mouse-human comparative genomics. Mamm Genome. 2019 Dec;30(11-12):353-361. PubMed
Smith CM, Hayamizu TF, Finger JH, Bello SM, McCright IJ, Xu J, Baldarelli RM, Beal JS, Campbell JW, Corbani LE, Frost PJ, Lewis, JR, Giannatto SC, Miers DB, Shaw DR, Kadin JA, Richardson JE, Smith CL, Ringwald M. 2019. The mouse Gene Expression Database (GXD): 2019 update. Nucleic Acids Res. 2019 Jan. 8;47 (D1): D774–D779.   PubMed
2018
Bello SM, Shimoyama M, Mitraka E, Laulederkind SJF, Smith CL, Eppig JT, Schriml LM. 2018. Disease Ontology: improving and unifying disease annotations across species. Dis Model Mech.. 2018 Mar 12;11(3). PubMed
Christie KR, Blake JA. 2018. Sensing the cilium, digital capture of ciliary data for comparative genomics investigations. Cilia 2018; 7:3. PubMed
Denny P, Feuermann M, Hill DP, Lovering RC, Plun-Favreau H, Roncaglia P. 2018. Exploring autophagy with Gene Ontology. Autophagy. 2018 Feb. 17:1-18. PubMed
Howe DG, Blake JA, Bradford YM, Bult CJ, Calvi BR, Engel SR, Kadin JA, Kaufman TC, Kishore R, Laulederkind SJF, Lewis SE, Moxon SAT, Richardson JE, Smith C. 2018. Model organism data evolving in support of translational medicine. Lab Anim (NY). 2018 Oct;47(10):277-289. PubMed
Law, M, Shaw DR. 2018. Mouse Genome Informatics (MGI) Is the International Resource for Information on the Laboratory Mouse. In: Eukaryotic Genomic Databases: Methods and Protocols. Kollmar M (ed.) Springer. pp. 141-161.
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. 2018. Improving Interpretation of Cardiac Phenotypes and Enhancing Discovery With Expanded Knowledge in the Gene Ontology. Circ Genom Precis Med. 2018 Feb;11(2):e001813 PubMed
Pujar S, O'Leary NA, Farrell CM, Loveland JE, Mudge JM, Wallin C, Girón CG, Diekhans M, Barnes I, Bennett R, Berry AE, Cox E, Davidson C, Goldfarb T, Gonzalez JM, Hunt T, Jackson J, Joardar V, Kay MP, Kodali VK, Martin FJ, McAndrews M, McGarvey KM, Murphy M, Rajput B, Rangwala SH, Riddick LD, Seal RL, Suner MM, Webb D, Zhu S, Aken BL, Bruford EA, Bult CJ, Frankish A, Murphy T, Pruitt KD. 2018. Consensus coding sequence (CCDS) database: a standardized set of human and mouse protein-coding regions supported by expert curation. Nucleic Acids Res. 2018 Jan. 4;46 (D1): D221–D228. PubMed
Smith CL, Blake JA, Kadin JA, Richardson JE, Bult CJ, the Mouse Genome Database Group. 2018. Mouse Genome Database (MGD)-2018: knowledgebase for the laboratory mouse. Nucleic Acids Res. 2018 Jan. 4;46 (D1): D836–D842. PubMed
2017
Blake JA, Eppig JT, Kadin JA, Richardson JE, Smith CL, Bult CJ, and the Mouse Genome Database Group. 2017. Mouse Genome Database (MGD)-2017: community knowledge resource for the laboratory mouse. Nucleic Acids Res. 2017 Jan. 4;45 (D1): D723-D729. PubMed
Eppig JT. 2017. Mouse Genome Informatics (MGI) Resource: Genetic, Genomic, and Biological Knowledgebase for the Laboratory Mouse. ILAR J. 2017 Jul 1;58(1):17-41 PubMed
Eppig JT, Smith CL, Blake JA, Ringwald M, Kadin JA, Richardson JE, Bult CJ. 2017. Mouse Genome Informatics (MGI): Resources for Mining Mouse Genetic, Genomic, and Biological Data in Support of Primary and Translational Research. Methods Mol Biol. 2017;1488:47-73. PubMed
Finger JH, Smith CM, Hayamizu TF, McCright IJ, Xu J, Law M, Shaw DR, Baldarelli RM, Beal JS, Blodgett O, Campbell JW, Corbani LE, Lewis JR, Forthofer KL, Frost PJ, Giannatto SC, Hutchins LN, Miers DB, Motenko H, Stone KR, Eppig JT, Kadin JA, Richardson JE, Ringwald M. 2017. The mouse Gene Expression Database (GXD): 2017 update. Nucleic Acids Res. 2017 Jan. 4;45 (D1): D730-D736. PubMed
Jiang X, Ringwald M, Blake J, Shatkay H. 2017. Effective biomedical document classification for identifying publications relevant to the mouse Gene Expression Database (GXD). Database. (Oxford) 2017 Mar 24;2017:bax017. PubMed
Knowlton MN, Smith CL. 2017. Naming CRISPR alleles: endonuclease-mediated mutation nomenclature across species. Mamm Genome. 2017 Aug;28,(7–8):367–376. PubMed
Köhler S, Vasilevsky NA, Engelstad M, Foster E, McMurry J, Aymé S, Baynam G, Bello SM, […] Smith CL, […] Smedley D, Mungall CJ, Haendel M, Robinson PN. 2017. The Human Phenotype Ontology in 2017. Nucleic Acids Res. 2017 Jan. 4;45 (D1): D865-D876. PubMed
Krupke DM, Begley DA, Sundberg JP, Richardson JE, Neuhauser SB, Bult CJ. 2017. The Mouse Tumor Biology Database: A Comprehensive Resource for Mouse Models of Human Cancer. Cancer Res. 2017 Nov 1;77(21):e67-e70. PubMed
Meehan TF, Conte N, Goldstein T, Inghirami G, Murakami MA, Brabetz S, Gu Z, Wiser JA, Dunn P, Begley DA, Krupke DM, Bertotti A, Bruna A, Brush MH, Byrne AT, Caldas C, Christie AL, Clark DA, Dowst H, Dry JR, Doroshow JH, Duchamp O, Evrard YA, Ferretti S, Frese KK, Goodwin NC, Greenawalt D, Haendel MA, Hermans E, Houghton PJ, Jonkers J, Kemper K, Khor TO, Lewis MT, Lloyd KCK, Mason J, Medico E, Neuhauser SB, Olson JM, Peeper DS, Rueda OM, Seong JK, Trusolino L, Vinolo E, Wechsler-Reya RJ, Weinstock DM, Welm A, Weroha SJ, Amant F, Pfister SM, Kool M, Parkinson H, Butte AJ, Bult CJ. 2017. PDX-MI: Minimal Information for Patient-Derived Tumor Xenograft Models. Cancer Res. 2017 Nov 1;77(21):e62-e66. PubMed
Natale DA, Arighi CN, Blake JA, Bona J, Chen C, Chen SC, Christie KR, Cowart J, D'Eustachio P, Diehl AD, Drabkin HJ, Duncan WD, Huang H, Ren J, Ross K, Ruttenberg A, Shamovsky V, Smith B, Wang Q, Zhang J, El-Sayed A, Wu CH. 2017. Protein Ontology (PRO): enhancing and scaling up the representation of protein entities. Nucleic Acids Res. 2017 Jan 4;45(D1):D339-D346. PubMed
Roncaglia P, van Dam TJP, Christie KR, Nacheva L, Toedt G, Huynen MA, Huntley RP, Gibson TJ, Lomax J. 2017. The Gene Ontology of eukaryotic cilia and flagella. Cilia 2017. Nov 16;6:10. PubMed
2016
Bello SM, Eppig JT, and the MGI Software Group. 2016. Inferring Gene-to-Phenotype and Gene-to-Disease Relationships at Mouse Genome Informatics: Challenges and Solutions. J Biomed Semantics 2016. 7:14.
Bult CJ, Eppig JT, Blake JA, Kadin JA, Richardson JE; and the Mouse Genome Database Group. 2016. The Mouse Genome Database 2016. Nucleic Acids Res. 2016 Jan 4;44 (D1): D840-D847. NAR. PubMed
Hill DP, D'Eustachio P, Berardini T, Mungall CJ, Renedo N, Blake JA. 2016. Modeling biochemical pathways in the gene ontology. Database. 2016. Sep 1. PubMed
Lek M, Karczewski KJ, Minikel EV, Samocha KE, Banks E, Fennell T, O'Donnell-Luria AH, Ware JS, Hill AJ, Cummings BB, Tukiainen T, Birnbaum DP, Kosmicki JA, Duncan LE, Estrada K, Zhao F, Zou J, Pierce-Hoffman E, Berghout J, […], MacArthur DG; Exome Aggregation Consortium. 2016. Analysis of protein-coding genetic variation in 60,706 humans. Nature. 2016. Aug 17;536(7616):285-91. PubMed
Shaw DR. 2016. Searching the Mouse Genome Informatics (MGI) Resources for Information on Mouse Biology from Genotype to Phenotype. Curr Protoc Bioinformatics. 2016 Dec 8;56:1.7.1-1.7.16. PubMed
2015
Begley DA, Sundberg JP, Krupke DM, Neuhauser SB, Bult CJ, Eppig JT, Morse HC 3rd, Ward JM. 2015. Finding mouse models of human lymphomas and leukemia's using the Jackson laboratory mouse tumor biology database. Exp Mol Pathol. 2015. Aug 21;99(3):533-536. PubMed
Bello SM, Smith CL, Eppig JT. 2015. Allele, phenotype and disease data at Mouse Genome Informatics: improving access and analysis. Mamm Genome. 2015 Aug;26(7):285-294. PubMed
Bult CJ, Krupke DM, Begley DA, Richardson JE, Neuhauser SB, Sundberg JP, Eppig JT. Mouse Tumor Biology (MTB): a database of mouse models for human cancer. Nucleic Acids Res. 2015 Jan 28;43(Database issue):D818-24. NAR. PubMed
Deans AR, Lewis SE, Huala E, Anzaldo SS, Ashburner M, Balhoff JP, Blackburn DC, Blake JA, Burleigh JG, Chanet B, Cooper LD, Courtot M, Cs&oumi;sz S, Cui H, Dahdul W, Das S, Dececchi TA, Dettai A, Diogo R, Druzinsky RE, Dumontier M, Franz NM, Friedrich F, Gkoutos GV, Haendel M, Harmon LJ, Hayamizu TF, [ … ], Mabee P. 2015. Finding Our Way through Phenotypes. PLoS Biol. 2015 Jan 6;13(1):e1002033. PubMed
Desvignes T, Batzel P, Berezikov E, Eilbeck K, Eppig JT, McAndrews MS, Singer A, Postlethwait JH. 2015. miRNA Nomenclature: A View Incorporating Genetic Origins, Biosynthetic Pathways, and Sequence Variants. Trends Genet 2015. Nov;31(11):613-626. PubMed
Dolan ME, Baldarelli RM, Bello SM, Ni L, McAndrews MS, Bult CJ, Kadin JA, Richardson JE, Ringwald M, Eppig JT, Blake JA. 2015. Orthology for comparative genomics in the mouse genome database. Mamm Genome. 2015 Aug;26(7):305-313. PubMed
Drabkin HJ, Christie KR, Dolan ME, Hill DP, Ni L, Sitnikov D, Blake JA. 2015. Application of comparative biology in GO functional annotation: the mouse model. Mamm Genome. 2015 Jul;26(9):574-583. PubMed
Eppig JT, Blake JA, Bult CJ, Kadin JA, Richardson JE; The Mouse Genome Database Group. 2015. The Mouse Genome Database (MGD): facilitating mouse as a model for human biology and disease. Nucleic Acids Res. 2015 Jan 28;43(Database issue):D726-36. NAR. PubMed
Eppig JT, Motenko H, Richardson JE, Richards-Smith B, Smith CL. 2015. The International Mouse Strain Resource (IMSR): cataloging worldwide mouse and ES cell line resources. Mamm Genome. 2015 Oct;26(9-10):448-455. PubMed
Eppig JT, Richardson JE, Kadin JA, Ringwald M, Blake JA, Bult CJ. 2015. Mouse Genome Informatics (MGI): reflecting on 25 years. Mamm Genome. 2015 Aug;26(7):272-284. PubMed
Eppig JT, Richardson JE, Kadin JA, Smith CL, Blake JA, Bult CJ and the MGD Team. 2015. Mouse Genome Database: From sequence to phenotypes and disease models. Genesis. 2015 Aug;53(8):458-473. PubMed
Finger JH, Smith CM, Hayamizu TF, McCright IJ, Xu J, Eppig JT, Kadin JA, Richardson JE, Ringwald M. 2015. The mouse gene expression database: New features and how to use them effectively. Genesis. 2015 Aug;53(8):510-522. PubMed
Hayamizu TF, Baldock RA, Ringwald M. 2015. Mouse anatomy ontologies: enhancements and tools for exploring and integrating biomedical data. Mamm Genome. 2015 Oct;26(9-10):422-30. PubMed
Hayamizu TF, Ringwald M. 2015. Textual Anatomics: The Mouse Developmental Anatomy Ontology and the Gene Expression Database for Mouse Development (GXD). In: Kaufman's Atlas of Mouse Development Supplement: With Coronal Sections. Baldock R, Bard J, Davidson DR, Morriss-Kay G (eds). Elsevier, Amsterdam. pp. 283-294.
Li Y, Klena N, Gabriel G, Liu X, Lemke K, Chen Y, Kim A, Chatterjee B, Damerla R, Devine W, Chang C-f, Yagi H, San Augustin JT, Thahir M, Anderton S, Lawhead C, Vescovi A, Pratt H, Morgan J, Smith C, Eppig J, Reinholdt L, Leatherby L, Tobita K, Francis R, Ganapathiraju M, Pazour GJ, Lo CW. 2015. Global genetic analysis in mice unveils central role for cilia in congenital heart disease. Nature 2015 521(7553):520-4. PubMed
Lyne R, Sullivan J, Butano D, Contrino S, Heimbach J, Hu F, Kalderimis A, Lyne M, Smith R, Štěpán R, Balakrishnan R, Binkley G, Harris T, Karra K, Moxon S, Motenko H, Neuhauser S, Ruzicka L, Cherry M, Richardson J, Stein L, Westerfield M, Worthey E, Micklem G. 2015. Cross-organism analysis using InterMine. Genesis. 2015 Aug;53(8):547-560. PubMed
Motenko H, Neuhauser SB, O'Keefe M, Richardson JE. 2015. MouseMine: a new data warehouse for MGI. Mamm Genome. 2015 Aug;26(7):325-30. PubMed
Richardson JE, Bult CJ. 2015. Visual annotation display (VLAD): a tool for finding functional themes in lists of genes. Mamm Genome. 2015 Oct;26(9):567-573. PubMed
Schofield PN, Hoehndorf R, Smith CL, Eppig JT, Gkoutos GV. 2015. The Informatics of Developmental Phenotypes. In: Kaufman's Atlas of Mouse Development Supplement: With Coronal Sections. Baldock R, Bard J, Davidson DR, Morriss-Kay G (eds). Elsevier, Amsterdam. pp. 307-318.
Smith C, Eppig JT. 2015. Expanding the mammalian phenotype ontology to support automated exchange of high throughput mouse phenotyping data generated by large-scale mouse knockout screens. J Biomed Semantics. 2015 Mar 25; 6:11. PubMed
Smith CM, Finger JH, Hayamizu TF, McCright IJ, Xu J, Eppig JT, Kadin JA, Richardson JE, Ringwald M. 2015. GXD: a community resource of mouse Gene Expression Data. Mamm Genome. 2015 Aug;26(7):314-324. PubMed
Zhu Y, Richardson JE, Hale P, Baldarelli RM, Reed DJ, Recla JM, Sinclair R, Reddy TBK, Bult CJ. 2015. A unified gene catalog for the laboratory mouse reference genome. Mamm Genome. 2015 Aug;26(7):295-304. PubMed
2014
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. 2014. Representing kidney development using the gene ontology. PLoS One. Jun 18;9(6):e99864. PubMed
Anagnostopoulos A and Eppig JT. 2014. Databases, Internet Resources, and Genetic Nomencalture. In: Pinkert C (ed). Transgenic Animal Technology 3e, Third Edition, Elsevier, pp 657-689. DOI: 10.1016/B978-0-12-410490-7.00024-4.
Ascensao JA, Dolan ME, Hill DP, Blake JA. 2014. Methodology for the inference of gene function from phenotype data. BMC Bioinformatics. 2014 Dec 12;15(1):405. PubMed
Begley DA, Krupke DM, Neuhauser SB, Richardson JE, Schofield PN, Bult CJ, Eppig JT, Sundberg JP. 2014. Identifying mouse models for skin cancer using the Mouse Tumor Biology Database. Exp Dermatol. 2014 Oct; 23(10):761-3. PubMed
Blake JA, Bult CJ, Eppig JT, Kadin JA, Richardson JE; The Mouse Genome Database Group. 2014. The Mouse Genome Database: integration of and access to knowledge about the laboratory mouse. Nucleic Acids Res. 2014 Jan 1;42(D1):D810-D817. NAR. PubMed
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. 2014. A method for increasing expressivity of Gene Ontology annotations using a compositional approach. BMC Bioinformatics. 2014 May 21;15(1):155. PubMed
Köhler S, Doelken SC, Mungall CJ, Bauer S, Firth HV, Bailleul-Forestier I, Black GC, Brown DL, Brudno M, Campbell J, Fitzpatrick DR, Eppig JT, Jackson AP, Freson K, Girdea M, Helbig I, Hurst JA, Jähn J, Jackson LG, Kelly AM, Ledbetter DH, Mansour S, Martin CL, Moss C, Mumford A, Ouwehand WH, Park SM, Riggs ER, Scott RH, Sisodiya S, Vooren SV, Wapner RJ, Wilkie AO, Wright CF, Vulto-van Silfhout AT, Leeuw ND, de Vries BB, Washingthon NL, Smith CL, Westerfield M, Schofield P, Ruef BJ, Gkoutos GV, Haendel M, Smedley D, Lewis SE, Robinson PN. 2014. The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data. Nucleic Acids Res. 2014 42 (D1): D966-D974. NAR. PubMed
Natale DA, Arighi CN, Blake JA, Bult CJ, Christie KR, Cowart J, D'Eustachio P, Diehl AD, Drabkin HJ, Helfer O, Huang H, Masci AM, Ren J, Roberts NV, Ross K, Ruttenberg A, Shamovsky V, Smith B, Yerramalla MS, Zhang J, Aljanahi A, Celen I, Gan C, Lv M, Schuster-Lezell E, Wu CH. 2014. Protein Ontology: a controlled structured network of protein entities. Nucleic Acids Res. 2014 Jan 1;42(1):D415-21. NAR. PubMed
Smith CM, Finger JH, Hayamizu TF, McCright IJ, Xu J, Berghout J, Campbell J, Corbani LE, Forthofer KL, Frost PJ, Miers D, Shaw DR, Stone KR, Eppig JT, Kadin JA, Richardson JE, Ringwald M. The mouse Gene Expression Database (GXD): 2014 update. Nucleic Acids Res. 2014 Jan 1;42(D1):D818-D824. NAR. PubMed
Smith CM, Finger JH, Kadin JA, Richardson JE, Ringwald M. The gene expression database for mouse development (GXD): Putting developmental expression information at your fingertips. 2014. Dev Dyn. Oct;243(10):1176-1186. PubMed
Wick HC, Drabkin H, Ngu H, Sackman M, Fournier C, Haggett J, Blake JA, Bianchi DW, Slonim DK. 2014. DFLAT: functional annotation for human development. BMC Bioinformatics. 2014 Feb 7;15:45. PubMed
2013
Arighi CN, Carterette B, Cohen KB, Krallinger M, Wilbur WJ, Fey P, Dodson R, Cooper L, Van Slyke CE, Dahdul W, Mabee P, Li D, Harris B, Gillespie M, Jimenez S, Roberts P, Matthews L, Becker K, Drabkin H, Bello S, Licata L, Chatr-Aryamontri A, Schaeffer ML, Park J, Haendel M, Van Auken K, Li Y, Chan J, Muller HM, Cui H, Balhoff JP, Chi-Yang Wu J, Lu Z, Wei CH, Tudor CO, Raja K, Subramani S, Natarajan J, Cejuela JM, Dubey P, Wu C. 2013. An overview of the BioCreative 2012 Workshop Track III: interactive text mining task. Database. (Oxford) 2013 Jan 17;2013:bas056. PubMed
Blake JA. 2013. Ten quick tips for using the Gene Ontology. PLoS Comput Biol. 2013 Nov;9(11):e1003343.
Bult CJ, Eppig JT, Blake JA, Kadin JA, Richardson JE; the Mouse Genome Database Group. 2013.The Mouse Genome Database: Genotypes, Phenotypes, and Models of Human Disease. Nucleic Acids Res. 2013 Jan 1;41(D1):D885-D891. NAR. PubMed
Doelken SC, K&oumi;hler S, Mungall CJ, Gkoutos GV, Ruef BJ, Smith C, Smedley D, Bauer S, Klopocki E, Schofield PN, Westerfield M, Robinson PN, Lewis SE. 2013. Phenotypic overlap in the contribution of individual genes to CNV pathogenicity revealed by cross-species computational analysis of single-gene mutations in humans, mice and zebrafish. Dis Model Mech. 2013 Mar;6(2):358-72. PubMed
Hayamizu TF, Wicks MN, Davidson DR, Burger A, Ringwald M, Baldock RA. 2013. EMAP/EMAPA ontology of mouse developmental anatomy: 2013 update. J Biomed Semantics. 2013 Aug 26;4(1):15. PubMed
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. 2013. Dovetailing biology and chemistry: integrating the Gene Ontology with the ChEBI chemical ontology. BMC Genomics 2013 Jul 29; 14:513. PubMed
Meehan TF, Vasilevsky NA, Mungall CJ, Dougall DS, Haendel MA, Blake JA, Diehl AD. 2013. Ontology based molecular signatures for immune cell types via gene expression analysis. BMC Bioinformatics. 2013 Aug 30;14(1):263. PubMed
Oetting WS, Robinson PN, Greenblatt MS, Cotton RG, Beck T, Carey JC, Doelken SC, Girdea M, Groza T, Hamilton CM, Hamosh A, Kerner B, MacArthur JA, Maglott DR, Mons B, Rehm HL, Schofield PN, Searle BA, Smedley D, Smith CL, Bernstein IT, Zankl A, Zhao EY. Getting ready for the Human Phenome Project: the 2012 forum of the Human Variome Project. Hum Mutat 2013; 34(4):661-6. PubMed
Park CA, Bello SM, Smith CL, Hu ZL, Munzenmaier DH, Nigam R, Smith JR, Shimoyama M, Eppig JT, Reecy JM. 2013. The Vertebrate Trait Ontology: a controlled vocabulary for the annotation of trait data across species. J Biomed Semantics. 2013 Aug 9;4(1):13. PubMed
Sullivan J, Karra K, Moxon SA, Vallejos A, Motenko H, Wong JD, Aleksic J, Balakrishnan R, Binkley G, Harris T, Hitz B, Jayaraman P, Lyne R, Neuhauser S, Pich C, Smith RN, Trinh Q, Cherry JM, Richardson J, Stein L, Twigger S, Westerfield M, Worthey E, Micklem G. InterMOD: integrated data and tools for the unification of model organism research. Sci Rep 2013 May 8; 3:1802. PubMed
Tripathi S, Christie KR, Balakrishnan R, Huntley R, Hill DP, Thommesen L, Blake JA, Kuiper M, Lægreid A. Gene Ontology annotation of sequence-specific DNA binding transcription factors: setting the stage for a large-scale curation effort. Database (Oxford). 2013 Aug 27;2013(0):bat062. PubMed
2012
Bada M, Eckert M, Evans D, Garcia K, Shipley K, Sitnikov D, Baumgartner WA Jr, Cohen KB, Verspoor K, Blake JA, Hunter LE. 2012. Concept annotation in the CRAFT corpus. BMC Bioinformatics. 2012 Jul 9;13:161. PubMed
Baldarelli RM. 2012. Drug discovery: In defence of the animal model. Nature. 2012 May 16;485(7398):309. PubMed
Begley DA, Krupke DM, Neuhauser SB, Richardson JE, Bult CJ, Eppig JT, Sundberg JP. 2012. The Mouse Tumor Biology Database (MTB): A Central Electronic Resource for Locating and Integrating Mouse Tumor Pathology Data. Vet Pathol. 2012 49(1):218-23. PubMed
Bello SM, Richardson JE, Davis AP, Wiegers TC, Mattingly CJ, Dolan ME, Smith CL, Blake JA, Eppig JT. 2012. Disease model curation improvements at Mouse Genome Informatics. Database. (Oxford) 2012; Mar 20; 2012:bar063. PubMed
Bradley A, Anastassiadis K, Ayadi A, Battey JF, Bell C, Birling MC, Bottomley J, Brown SD, B&uumi;rger 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, H&oumi;rlein A, Houghton R, Hrabé de Angelis M, Huylebroeck D, Iyer V, de Jong PJ, Kadin JA, Kaloff C, Kennedy K, Koutsourakis M, Kent 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, Schn&uumi;tgen F, Schofield P, Seisenberger C, Selloum M, Simpson EM, Skarnes WC, Smedley D, Stanford WL, Francis Stewart A, Stone K, Swan K, Tadepally H, Teboul L, Tocchini-Valentini GP, Valenzuela D, West AP, Yamamura KI, Yoshinaga Y, Wurst W. 2012. The mammalian gene function resource: the international knockout mouse consortium. Mamm Genome. 2012 Oct;23(9-10):580-6. PubMed
Bucan M, Eppig JT, Brown S. 2012. Mouse genomics programs and resources : The mouse: pushing the boundaries. Mamm Genome. 2012 Oct;23(9-10):479-89. PubMed
Bult CJ. 2012. Bioinformatics resources for behavior studies in the laboratory mouse. Int Rev Neurobiol. 2012;104:71-90. PubMed
Chen CK, Mungall CJ, Gkoutos GV, Doelken SC, Köhler S, Ruef BJ, Smith C, Westerfield M, Robinson PN, Lewis SE, Schofield PN, Smedley D. 2012. MouseFinder: Candidate disease genes from mouse phenotype data. Hum Mutat. 2012 May;33(5):858-66. PubMed
Dahdul WM, Balhoff JP, Blackburn DC, Diehl AD, Haendel MA, Hall BK, Lapp H, Lundberg JG, Mungall CJ, Ringwald M, Segerdell E, Van Slyke CE, Vickaryous MK, Westerfield M, Mabee PM. 2012. A unified anatomy ontology of the vertebrate skeletal system. PLoS One. 2012;7(12):e51070. PubMed
Drabkin HJ, Blake JA; for the Mouse Genome Informatics Database. Manual Gene Ontology annotation workflow at the Mouse Genome Informatics Database. Database (Oxford). 2012 Oct 29; 2012:bas045. PubMed
Eppig JT, Blake JA, Bult CJ, Kadin JA, Richardson JE; the Mouse Genome Database Group. 2012. The Mouse Genome Database (MGD): comprehensive resource for genetics and genomics of the laboratory mouse. Nucleic Acids Res 2012; 40(1):D881-86. NAR PubMed
Gaudet P, Arighi C, Bastian F, Bateman A, Blake JA, Cherry MJ, D'Eustachio P, Finn R, Giglio M, Hirschman L, Kania R, Klimke W, Martin MJ, Karsch-Mizrachi I, Munoz-Torres M, Natale D, O'Donovan C, Ouellette F, Pruitt KD, Robinson-Rechavi M, Sansone SA, Schofield P, Sutton G, Van Auken K, Vasudevan S, Wu C, Young J, Mazumder R. Recent advances in biocuration: Meeting Report from the fifth International Biocuration Conference. Database (Oxford). 2012 Oct 29; 2012:bas036. PubMed
Hayamizu TF, de Coronado S, Fragoso G, Sioutos N, Kadin JA, Ringwald M. 2012. The mouse-human anatomy ontology mapping project. Database. 2012 Mar 20. PubMed
Heffner CS, Herbert Pratt C, Babiuk RP, Sharma Y, Rockwood SF, Donahue LR, Eppig JT, Murray SA. Supporting conditional mouse mutagenesis with a comprehensive cre characterization resource. Nat Commun 2012 Nov 20; 3:1218. PubMed
Murray SA, Eppig JT, Smedley D, Simpson EM, Rosenthal N. 2012. Beyond knockouts: cre resources for conditional mutagenesis. Mamm Genome. 2012 Oct;23(9-10):587-99. PubMed
Ringwald M, Wu C, Su AI. 2012. BioGPS and GXD: mouse gene expression data-the benefits and challenges of data integration. Mamm Genome. 2012 Oct;23(9-10):550-8. PubMed
Smith CL, Eppig JT. 2012. The Mammalian Phenotype Ontology as a unifying standard for experimental and high-throughput phenotyping data. Mamm Genome. 2012 Oct;23(9-10):653-68. PubMed
Taşan M, Drabkin HJ, Beaver JE, Chua HN, Dunham J, Tian W, Blake JA, Roth FP. 2012. A Resource of Quantitative Functional Annotation for Homo sapiens Genes. G3 (Bethesda). 2012 Feb;2(2):223-33. PubMed
Thomas PD, Wood V, Mungall CJ, Lewis SE, Blake JA; Gene Ontology Consortium. 2012. On the Use of Gene Ontology Annotations to Assess Functional Similarity among Orthologs and Paralogs: A Short Report. PLoS Comput Biol. 2012;8(2):e1002386. PubMed
2011
Blake JA, Bult CJ, Kadin JA, Richardson JE, Eppig JT and the Mouse Genome Database Group. 2011. The Mouse Genome Database (MGD): premier model organism resource for mammalian genomics and genetics. Nucleic Acids Res 39(suppl 1): D842-D848. NAR PubMed
Fairfield H, Gilbert GJ, Barter M, Corrigan RR, Curtain M, Ding Y, D'Ascenzo M, Gerhardt DJ, He C, Huang W, Richmond T, Rowe L, Probst FJ, Bergstrom DE, Murray SA, Bult C, Richardson J, et al. 2011. Mutation discovery in mice by whole exome sequencing. Genome Biol. 12(9):R86. PubMed
Finger JH, Smith CM, Hayamizu TF, McCright IJ, Eppig JT, Kadin JA, Richardson JE, Ringwald M. 2011. The mouse Gene Expression Database (GXD): 2011 update. Nucleic Acids Res 39(suppl 1): D835-D841. NAR PubMed
Gaudet P, Bairoch A, Field D, Sansone S-A, 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, Mizrachi IK, Orchard S, Ouellette BFF, Ranganathan S, Richardson L, Rocca-Serra P, Schofield PN, Smedley D, Southan C, Tan TW, Tatusova T, Whetzel PL, White O, Yamasaki C on behalf of the BioDBCore working group. 2011. Towards BioDBcore: a community-defined information specification for biological databases. Nucleic Acids Res 39 (suppl 1): D7-D10. NAR PubMed
Köhler S, Bauer S, Mungall CJ, Carletti G, Smith CL, Schofield P, Gkoutos GV, Robinson PN. 2011. Improving ontologies by automatic reasoning and evaluation of logical definitions. BMC Bioinformatics. 2011 Oct 27;12:418. PubMed
Meehan TF, Carr CJ, Jay JJ, Bult CJ, Chesler EJ, Blake JA. Autism candidate genes via mouse phenomics. 2011. J Biomed Inform. 44 Suppl 1: S5-S11. PubMed
Ringwald M, Eppig JT. Mouse mutants and phenotypes: accessing information for the study of mammalian gene function. Methods 2011 Apr;53(4):405-10. PubMed
Ringwald M, Iyer V, Mason JC, Stone KR, Tadepally HD, Kadin JA, Bult CJ, Eppig JT, Oakley DJ, Briois S, Stupka E, Maselli V, Smedley D, Liu S, Hansen J, Baldock R, Hicks GG, Skarnes WC. 2011. The IKMC web portal: a central point of entry to data and resources from the International Knockout Mouse Consortium. Nucleic Acids Res 39(suppl 1): D849-D855. NAR PubMed
2010
Bult CJ, Kadin JA, Richardson JE, Blake JA, Eppig JT; Mouse Genome Database Group. The Mouse Genome Database: enhancements and updates. Nucl. Acids Res. 2010 Jan;38(Database issue):D586-92. NAR   PubMed
Gene Ontology Consortium. The Gene Ontology in 2010: extensions and refinements. Nucleic Acids Res. 2010 Jan;38(Database issue):D331-5. NAR  PubMed
Hill DP, Berardini TZ, Howe DG, Van Auken KM. Representing ontogeny through ontology: a developmental biologist's guide to the gene ontology. Mol Reprod Dev 2010; 77(4):314-29. PubMed
Hirschman J, Berardini TZ, Drabkin HJ, Howe D. 2010. A MOD(ern) perspective on literature curation. Mol Genet Genomics. 283(5):415-425. PubMed
Holmes RS, Wright MW, Laulederkind SJ, Cox LA, Hosokawa M, Imai T, Ishibashi S, Lehner R, Miyazaki M, Perkins EJ, Potter PM, Redinbo MR, Robert J, Satoh T, Yamashita T, Yan B, Yokoi T, Zechner R, Maltais LJ. Recommended nomenclature for five mammalian carboxylesterase gene families: human, mouse, and rat genes and proteins. Mamm Genome. 2010 Oct;21(9-10):427-41. Epub 2010 Oct 8. PubMed.
International Arabidopsis Information Consoritum (JT Eppig). 2010. An international bioinformatics infrastructure to underpin the Arabidopsis community. Plant Cell. 22(8):2530-2536. PubMed
Mungall CJ, Gkoutos GV, Smith CL, Haendel MA, Lewis SE, Ashburner M. Integrating phenotype ontologies across multiple species. Genome Biol. 2010 Jan 8;11(1):R2. PubMed
Reference Genome Group of the Gene Ontology Consortium. 2009. The Gene Ontology's Reference Genome Project: a unified framework for functional annotation across species. PLoS Comput Biol 5:e1000431. PubMed
Schofield PN, Eppig J, Huala E, de Angelis MH, Harvey M, Davidson D, Weaver T, Brown S, Smedley D, Rosenthal N, Schughart K, Aidinis V, Tocchini-Valentini G, Hancock JM. 2010. Research funding. Sustaining the data and bioresource commons. Science 330(6004): 592-593. PubMed
Smedley D, Schofield P, Chen C-K, Aidinis V, Ainali C, Bard J, Balling R, Birney E, Blake A, Bongcam-Rudloff, Brookes AJ, Cesareni G, Chandras C, Eppig J, Flicek P, Gkoutos G, Greenaway S, Gruenberger M, Heriche J-K, Lyall A, Mallon A-M, Muddyman D, Reisinger F, Ringwald M, Rosenthal N, Schughart K, Swertz M, Swertz M, Thorisson GA, Zouberakis M, Hancock JM. 2010. Finding and sharing; new approaches to registries of resources and services for the biomedical sciences. Database (Oxford). 2010:baq014. PubMed
Contributing Projects:
Mouse Genome Database (MGD), Gene Expression Database (GXD), Mouse Models of Human Cancer database (MMHCdb) (formerly Mouse Tumor Biology (MTB)), Gene Ontology (GO)
Citing These Resources
Funding Information
Warranty Disclaimer, Privacy Notice, Licensing, & Copyright
Send questions and comments to User Support. 		last database update
04/16/2024
MGI 6.23 		The Jackson Laboratory