{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T00:15:09Z","timestamp":1772064909872,"version":"3.50.1"},"reference-count":72,"publisher":"Public Library of Science (PLoS)","issue":"11","license":[{"start":{"date-parts":[[2009,11,6]],"date-time":"2009-11-06T00:00:00Z","timestamp":1257465600000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"DOI":"10.1371\/journal.pcbi.1000559","type":"journal-article","created":{"date-parts":[[2009,11,5]],"date-time":"2009-11-05T22:46:36Z","timestamp":1257461196000},"page":"e1000559","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":14,"title":["Looking at Cerebellar Malformations through Text-Mined Interactomes of Mice and Humans"],"prefix":"10.1371","volume":"5","author":[{"given":"Ivan","family":"Iossifov","sequence":"first","affiliation":[]},{"given":"Raul","family":"Rodriguez-Esteban","sequence":"additional","affiliation":[]},{"given":"Ilya","family":"Mayzus","sequence":"additional","affiliation":[]},{"given":"Kathleen J.","family":"Millen","sequence":"additional","affiliation":[]},{"given":"Andrey","family":"Rzhetsky","sequence":"additional","affiliation":[]}],"member":"340","published-online":{"date-parts":[[2009,11,6]]},"reference":[{"key":"ref1","first-page":"xv, 199","article-title":"Working knowledge: how organizations manage what they know","author":"TH Davenport","year":"1998"},{"key":"ref2","doi-asserted-by":"crossref","first-page":"9","DOI":"10.1016\/j.cell.2008.06.029","article-title":"Seeking a new biology through text mining.","volume":"134","author":"A Rzhetsky","year":"2008","journal-title":"Cell"},{"key":"ref3","doi-asserted-by":"crossref","first-page":"S74","DOI":"10.1093\/bioinformatics\/17.suppl_1.S74","article-title":"GENIES: a natural-language processing system for the extraction of molecular pathways from journal articles.","volume":"17","author":"C Friedman","year":"2001","journal-title":"Bioinformatics"},{"key":"ref4","doi-asserted-by":"crossref","first-page":"43","DOI":"10.1016\/j.jbi.2003.10.001","article-title":"GeneWays: a system for extracting, analyzing, visualizing, and integrating molecular pathway data.","volume":"37","author":"A Rzhetsky","year":"2004","journal-title":"J Biomed Inform"},{"key":"ref5","doi-asserted-by":"crossref","first-page":"1120","DOI":"10.1093\/bioinformatics\/16.12.1120","article-title":"A knowledge model for analysis and simulation of regulatory networks.","volume":"16","author":"A Rzhetsky","year":"2000","journal-title":"Bioinformatics"},{"key":"ref6","doi-asserted-by":"crossref","first-page":"e118","DOI":"10.1371\/journal.pcbi.0020118","article-title":"Imitating manual curation of text-mined facts in biomedicine.","volume":"2","author":"R Rodriguez-Esteban","year":"2006","journal-title":"PLoS Comput Biol"},{"key":"ref7","doi-asserted-by":"crossref","first-page":"D411","DOI":"10.1093\/nar\/gkj141","article-title":"Human protein reference database\u20132006 update.","volume":"34","author":"GR Mishra","year":"2006","journal-title":"Nucleic Acids Res"},{"key":"ref8","doi-asserted-by":"crossref","first-page":"D497","DOI":"10.1093\/nar\/gkh070","article-title":"Human protein reference database as a discovery resource for proteomics.","volume":"32","author":"S Peri","year":"2004","journal-title":"Nucleic Acids Res"},{"key":"ref9","doi-asserted-by":"crossref","first-page":"R39","DOI":"10.1186\/gb-2007-8-3-r39","article-title":"Reactome: a knowledge base of biologic pathways and processes.","volume":"8","author":"I Vastrik","year":"2007","journal-title":"Genome Biol"},{"key":"ref10","doi-asserted-by":"crossref","first-page":"D418","DOI":"10.1093\/nar\/gki051","article-title":"The Biomolecular Interaction Network Database and related tools 2005 update.","volume":"33","author":"C Alfarano","year":"2005","journal-title":"Nucleic Acids Res"},{"key":"ref11","doi-asserted-by":"crossref","first-page":"D449","DOI":"10.1093\/nar\/gkh086","article-title":"The Database of Interacting Proteins: 2004 update.","volume":"32","author":"L Salwinski","year":"2004","journal-title":"Nucleic Acids Res"},{"key":"ref12","doi-asserted-by":"crossref","first-page":"S19","DOI":"10.1186\/1471-2105-7-S5-S19","article-title":"An evaluation of human protein-protein interaction data in the public domain.","volume":"7","author":"S Mathivanan","year":"2006","journal-title":"BMC Bioinformatics"},{"key":"ref13","doi-asserted-by":"crossref","first-page":"39","DOI":"10.1038\/nmeth.1284","article-title":"Literature-curated protein interaction datasets.","volume":"6","author":"ME Cusick","year":"2009","journal-title":"Nat Methods"},{"key":"ref14","doi-asserted-by":"crossref","first-page":"83","DOI":"10.1038\/nmeth.1280","article-title":"An empirical framework for binary interactome mapping.","volume":"6","author":"K Venkatesan","year":"2009","journal-title":"Nat Methods"},{"key":"ref15","doi-asserted-by":"crossref","first-page":"99","DOI":"10.2307\/2412448","article-title":"Distinguishing homologous from analogous proteins.","volume":"19","author":"WM Fitch","year":"1970","journal-title":"Syst Zool"},{"key":"ref16","doi-asserted-by":"crossref","first-page":"2731","DOI":"10.4049\/jimmunol.172.5.2731","article-title":"Of mice and not men: differences between mouse and human immunology.","volume":"172","author":"J Mestas","year":"2004","journal-title":"J Immunol"},{"key":"ref17","doi-asserted-by":"crossref","first-page":"157","DOI":"10.1093\/jhered\/93.3.157","article-title":"The Wilhelmine E. Key 2001 Invitational Lecture. Estimation of divergence times for a few mammalian and several primate species.","volume":"93","author":"M Nei","year":"2002","journal-title":"J Hered"},{"key":"ref18","doi-asserted-by":"crossref","first-page":"D724","DOI":"10.1093\/nar\/gkm961","article-title":"The Mouse Genome Database (MGD): mouse biology and model systems.","volume":"36","author":"CJ Bult","year":"2008","journal-title":"Nucleic Acids Res"},{"key":"ref19","doi-asserted-by":"crossref","first-page":"D476","DOI":"10.1093\/nar\/gkh125","article-title":"The Mouse Genome Database (MGD): integrating biology with the genome.","volume":"32 Database issue","author":"CJ Bult","year":"2004","journal-title":"Nucleic Acids Res"},{"key":"ref20","doi-asserted-by":"crossref","first-page":"367","DOI":"10.1176\/jnp.16.3.367","article-title":"Disorders of the cerebellum: ataxia, dysmetria of thought, and the cerebellar cognitive affective syndrome.","volume":"16","author":"JD Schmahmann","year":"2004","journal-title":"J Neuropsychiatry Clin Neurosci"},{"key":"ref21","doi-asserted-by":"crossref","first-page":"R7","DOI":"10.1186\/gb-2004-6-1-r7","article-title":"The Mammalian Phenotype Ontology as a tool for annotating, analyzing and comparing phenotypic information.","volume":"6","author":"CL Smith","year":"2005","journal-title":"Genome Biol"},{"key":"ref22","doi-asserted-by":"crossref","first-page":"12","DOI":"10.1016\/j.conb.2008.05.010","article-title":"Cerebellar development and disease.","volume":"18","author":"KJ Millen","year":"2008","journal-title":"Curr Opin Neurobiol"},{"key":"ref23","doi-asserted-by":"crossref","first-page":"549","DOI":"10.1146\/annurev.cellbio.23.090506.123237","article-title":"Morphology, molecular codes, and circuitry produce the three-dimensional complexity of the cerebellum.","volume":"23","author":"RV Sillitoe","year":"2007","journal-title":"Annu Rev Cell Dev Biol"},{"key":"ref24","doi-asserted-by":"crossref","first-page":"36","DOI":"10.1016\/j.ymgme.2003.08.010","article-title":"Human malformations of the midbrain and hindbrain: review and proposed classification scheme.","volume":"80","author":"MA Parisi","year":"2003","journal-title":"Mol Genet Metab"},{"key":"ref25","doi-asserted-by":"crossref","first-page":"62","DOI":"10.1055\/s-2004-815728","article-title":"A case of Kallmann syndrome associated with Dandy-Walker malformation.","volume":"112","author":"H Ueno","year":"2004","journal-title":"Exp Clin Endocrinol Diabetes"},{"key":"ref26","doi-asserted-by":"crossref","first-page":"492","DOI":"10.1177\/0883073807299862","article-title":"Isolated posterior cerebellar vermal defect: a morphological study of midsagittal cerebellar vermis in 4 fetuses\u2013early stage of Dandy-Walker continuum or new vermal dysgenesis?","volume":"22","author":"R Russo","year":"2007","journal-title":"J Child Neurol"},{"key":"ref27","doi-asserted-by":"crossref","first-page":"170","DOI":"10.1177\/08830738050200021301","article-title":"Extreme microcephaly with agyria-pachygyria, partial agenesis of the corpus callosum, and pontocerebellar dysplasia.","volume":"20","author":"L Sztriha","year":"2005","journal-title":"J Child Neurol"},{"key":"ref28","first-page":"253","article-title":"A fatal case of cerebellar hypoplasia associated with anterior horn cell disease.","volume":"14","author":"G Deda","year":"2003","journal-title":"Genet Couns"},{"key":"ref29","doi-asserted-by":"crossref","first-page":"155","DOI":"10.1097\/00000433-200006000-00013","article-title":"Unappreciated agenesis of cerebellum in an adult: case report of a 38-year-old man.","volume":"21","author":"JE Leestma","year":"2000","journal-title":"Am J Forensic Med Pathol"},{"key":"ref30","doi-asserted-by":"crossref","first-page":"302","DOI":"10.1006\/exnr.1993.1064","article-title":"Cerebellectomy eliminates the motor syndrome of the genetically dystonic rat.","volume":"120","author":"MS LeDoux","year":"1993","journal-title":"Exp Neurol"},{"key":"ref31","doi-asserted-by":"crossref","first-page":"438","DOI":"10.1097\/WCO.0b013e3281fbd3dd","article-title":"Spinocerebellar ataxias: an update.","volume":"20","author":"BW Soong","year":"2007","journal-title":"Curr Opin Neurol"},{"key":"ref32","doi-asserted-by":"crossref","first-page":"1243","DOI":"10.1038\/nbt1005-1243","article-title":"Emergent behavior of growing knowledge about molecular interactions.","volume":"23","author":"M Cokol","year":"2005","journal-title":"Nat Biotechnol"},{"key":"ref33","doi-asserted-by":"crossref","first-page":"1173","DOI":"10.1038\/nature04209","article-title":"Towards a proteome-scale map of the human protein-protein interaction network.","volume":"437","author":"JF Rual","year":"2005","journal-title":"Nature"},{"key":"ref34","doi-asserted-by":"crossref","first-page":"957","DOI":"10.1016\/j.cell.2005.08.029","article-title":"A human protein-protein interaction network: a resource for annotating the proteome.","volume":"122","author":"U Stelzl","year":"2005","journal-title":"Cell"},{"key":"ref35","doi-asserted-by":"crossref","first-page":"15148","DOI":"10.1073\/pnas.0404315101","article-title":"Molecular triangulation: Bridging linkage and molecular-network information for identifying candidate genes in Alzheimer's disease.","volume":"101","author":"M Krauthammer","year":"2004","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref36","doi-asserted-by":"crossref","first-page":"483","DOI":"10.1038\/nn0504-483","article-title":"Gene expression nervous system atlas (GENSAT).","volume":"7","author":"N Heintz","year":"2004","journal-title":"Nat Neurosci"},{"key":"ref37","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1111\/j.2517-6161.1995.tb02031.x","article-title":"Controlling the False Discovery Rate - a Practical and Powerful Approach to Multiple Testing.","volume":"57","author":"Y Benjamini","year":"1995","journal-title":"Journal of the Royal Statistical Society Series B-Methodological"},{"key":"ref38","doi-asserted-by":"crossref","first-page":"1165","DOI":"10.1214\/aos\/1013699998","article-title":"The control of the false discovery rate in multiple testing under dependency.","volume":"29","author":"Y Benjamini","year":"2001","journal-title":"Annals of Statistics"},{"key":"ref39","doi-asserted-by":"crossref","first-page":"770","DOI":"10.1038\/nn1706","article-title":"Ascl1 and Gsh1\/2 control inhibitory and excitatory cell fate in spinal sensory interneurons.","volume":"9","author":"R Mizuguchi","year":"2006","journal-title":"Nat Neurosci"},{"key":"ref40","doi-asserted-by":"crossref","first-page":"1301","DOI":"10.1242\/dev.02807","article-title":"The Zic family member, odd-paired, regulates the Drosophila BMP, decapentaplegic, during adult head development.","volume":"134","author":"H Lee","year":"2007","journal-title":"Development"},{"key":"ref41","doi-asserted-by":"crossref","first-page":"763","DOI":"10.1038\/nrg1178","article-title":"From developmental disorder to heritable cancer: it's all in the BMP\/TGF-beta family.","volume":"4","author":"KA Waite","year":"2003","journal-title":"Nat Rev Genet"},{"key":"ref42","doi-asserted-by":"crossref","first-page":"422","DOI":"10.1016\/j.ydbio.2009.02.008","article-title":"Origins and control of the differentiation of inhibitory interneurons and glia in the cerebellum.","volume":"328","author":"P Grimaldi","year":"2009","journal-title":"Dev Biol"},{"key":"ref43","doi-asserted-by":"crossref","first-page":"389","DOI":"10.1016\/S0896-6273(00)80172-5","article-title":"Embryonic precursor cells from the rhombic lip are specified to a cerebellar granule neuron identity.","volume":"17","author":"J Alder","year":"1996","journal-title":"Neuron"},{"key":"ref44","doi-asserted-by":"crossref","first-page":"2793","DOI":"10.1242\/dev.02441","article-title":"The roof plate regulates cerebellar cell-type specification and proliferation.","volume":"133","author":"VV Chizhikov","year":"2006","journal-title":"Development"},{"key":"ref45","doi-asserted-by":"crossref","first-page":"91","DOI":"10.1016\/S0925-4773(00)00378-6","article-title":"Human SPRY2 inhibits FGF2 signalling by a secreted factor.","volume":"96","author":"J Glienke","year":"2000","journal-title":"Mech Dev"},{"key":"ref46","first-page":"529","article-title":"FGF signaling inhibitor, SPRY4, is evolutionarily conserved target of WNT signaling pathway in progenitor cells.","volume":"17","author":"Y Katoh","year":"2006","journal-title":"Int J Mol Med"},{"key":"ref47","doi-asserted-by":"crossref","first-page":"5556","DOI":"10.1158\/0008-5472.CAN-04-1669","article-title":"SPRY2 is an inhibitor of the ras\/extracellular signal-regulated kinase pathway in melanocytes and melanoma cells with wild-type BRAF but not with the V599E mutant.","volume":"64","author":"D Tsavachidou","year":"2004","journal-title":"Cancer Res"},{"key":"ref48","doi-asserted-by":"crossref","first-page":"94","DOI":"10.1002\/9780470751251.ch8","article-title":"The fibroblast growth factor family and mood disorders.","volume":"289","author":"H Akil","year":"2008","journal-title":"Novartis Found Symp"},{"key":"ref49","doi-asserted-by":"crossref","first-page":"344","DOI":"10.1111\/j.1601-183X.2007.00357.x","article-title":"Abnormal social behaviors in mice lacking Fgf17.","volume":"7","author":"K Scearce-Levie","year":"2008","journal-title":"Genes Brain Behav"},{"key":"ref50","doi-asserted-by":"crossref","first-page":"266","DOI":"10.1002\/ajmg.10775","article-title":"FGFs, their receptors, and human limb malformations: clinical and molecular correlations.","volume":"112","author":"AO Wilkie","year":"2002","journal-title":"Am J Med Genet"},{"key":"ref51","doi-asserted-by":"crossref","first-page":"889","DOI":"10.1242\/dev.011569","article-title":"Specific regions within the embryonic midbrain and cerebellum require different levels of FGF signaling during development.","volume":"135","author":"MA Basson","year":"2008","journal-title":"Development"},{"key":"ref52","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.bcp.2006.06.024","article-title":"PAX genes: roles in development, pathophysiology, and cancer.","volume":"73","author":"D Lang","year":"2007","journal-title":"Biochem Pharmacol"},{"key":"ref53","doi-asserted-by":"crossref","first-page":"52","DOI":"10.1038\/nrc1778","article-title":"A PANorama of PAX genes in cancer and development.","volume":"6","author":"EJ Robson","year":"2006","journal-title":"Nat Rev Cancer"},{"key":"ref54","doi-asserted-by":"crossref","first-page":"417","DOI":"10.1083\/jcb.125.2.417","article-title":"Differential induction of Pax genes by NGF and BDNF in cerebellar primary cultures.","volume":"125","author":"C Kioussi","year":"1994","journal-title":"J Cell Biol"},{"key":"ref55","doi-asserted-by":"crossref","first-page":"237","DOI":"10.1007\/s00439-008-0467-y","article-title":"Linkage to chromosome 2q36.1 in autosomal dominant Dandy-Walker malformation with occipital cephalocele and evidence for genetic heterogeneity.","volume":"123","author":"A Jalali","year":"2008","journal-title":"Hum Genet"},{"key":"ref56","doi-asserted-by":"crossref","DOI":"10.1007\/978-0-387-68990-6","article-title":"HOX gene expression","author":"S Papageorgiou","year":"2007"},{"key":"ref57","doi-asserted-by":"crossref","first-page":"e1000215","DOI":"10.1371\/journal.pcbi.1000215","article-title":"Biomedical discovery acceleration, with applications to craniofacial development.","volume":"5","author":"SM Leach","year":"2009","journal-title":"PLoS Comput Biol"},{"key":"ref58","doi-asserted-by":"crossref","first-page":"78","DOI":"10.1186\/1471-2105-9-78","article-title":"OpenDMAP: an open source, ontology-driven concept analysis engine, with applications to capturing knowledge regarding protein transport, protein interactions and cell-type-specific gene expression.","volume":"9","author":"L Hunter","year":"2008","journal-title":"BMC Bioinformatics"},{"key":"ref59","article-title":"A mouse protein interactome through combined literature mining with multiple sources of interaction evidence.","author":"X Li","year":"2009","journal-title":"Amino Acids"},{"key":"ref60","doi-asserted-by":"crossref","first-page":"233","DOI":"10.1186\/1471-2105-10-233","article-title":"A realistic assessment of methods for extracting gene\/protein interactions from free text.","volume":"10","author":"R Kabiljo","year":"2009","journal-title":"BMC Bioinformatics"},{"key":"ref61","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1007\/978-1-60761-175-2_1","article-title":"Mining Protein-Protein Interactions from Published Literature Using Linguamatics I2E.","volume":"563","author":"J Bandy","year":"2009","journal-title":"Methods Mol Biol"},{"key":"ref62","doi-asserted-by":"crossref","first-page":"W160","DOI":"10.1093\/nar\/gkp484","article-title":"PLAN2L: a web tool for integrated text mining and literature-based bioentity relation extraction.","volume":"37","author":"M Krallinger","year":"2009","journal-title":"Nucleic Acids Res"},{"key":"ref63","doi-asserted-by":"crossref","first-page":"263","DOI":"10.1021\/ci800332w","article-title":"Extraction of CYP chemical interactions from biomedical literature using natural language processing methods.","volume":"49","author":"D Jiao","year":"2009","journal-title":"J Chem Inf Model"},{"key":"ref64","doi-asserted-by":"crossref","first-page":"1536","DOI":"10.1093\/bioinformatics\/btp245","article-title":"Bayesian inference of protein-protein interactions from biological literature.","volume":"25","author":"R Chowdhary","year":"2009","journal-title":"Bioinformatics"},{"key":"ref65","doi-asserted-by":"crossref","first-page":"S6","DOI":"10.1186\/1471-2105-10-S2-S6","article-title":"Pharmspresso: a text mining tool for extraction of pharmacogenomic concepts and relationships from full text.","volume":"10","author":"Y Garten","year":"2009","journal-title":"BMC Bioinformatics"},{"key":"ref66","doi-asserted-by":"crossref","first-page":"S4","DOI":"10.1186\/gb-2008-9-s2-s4","article-title":"Overview of the protein-protein interaction annotation extraction task of BioCreative II.","volume":"9","author":"M Krallinger","year":"2008","journal-title":"Genome Biol"},{"key":"ref67","doi-asserted-by":"crossref","first-page":"S12","DOI":"10.1186\/gb-2008-9-s2-s12","article-title":"Mining physical protein-protein interactions from the literature.","volume":"9","author":"M Huang","year":"2008","journal-title":"Genome Biol"},{"key":"ref68","doi-asserted-by":"crossref","first-page":"222","DOI":"10.1016\/S1532-0464(03)00012-1","article-title":"Two biomedical sublanguages: a description based on the theories of Zellig Harris.","volume":"35","author":"C Friedman","year":"2002","journal-title":"J Biomed Inform"},{"key":"ref69","doi-asserted-by":"crossref","first-page":"S249","DOI":"10.1093\/bioinformatics\/18.suppl_1.S249","article-title":"Of truth and pathways: chasing bits of information through myriads of articles.","volume":"18","author":"M Krauthammer","year":"2002","journal-title":"Bioinformatics"},{"key":"ref70","doi-asserted-by":"crossref","first-page":"e61","DOI":"10.1371\/journal.pone.0000061","article-title":"Self-correcting maps of molecular pathways.","volume":"1","author":"A Rzhetsky","year":"2006","journal-title":"PLoS ONE"},{"key":"ref71","doi-asserted-by":"crossref","first-page":"4940","DOI":"10.1073\/pnas.0600591103","article-title":"Microparadigms: chains of collective reasoning in publications about molecular interactions.","volume":"103","author":"A Rzhetsky","year":"2006","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref72","doi-asserted-by":"crossref","first-page":"512","DOI":"10.1016\/j.jbi.2004.08.004","article-title":"Term identification in the biomedical literature.","volume":"37","author":"M Krauthammer","year":"2004","journal-title":"J Biomed Inform"}],"container-title":["PLoS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pcbi.1000559","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,2,13]],"date-time":"2025-02-13T03:06:01Z","timestamp":1739415961000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1000559"}},"subtitle":[],"editor":[{"given":"Eran","family":"Segal","sequence":"first","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2009,11,6]]},"references-count":72,"journal-issue":{"issue":"11","published-online":{"date-parts":[[2009,11,6]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1000559","relation":{},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2009,11,6]]}}}