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Items: 87

1.

Suicide notes: their utility in understanding the motivations behind suicide and preventing future ones.

Niveau G, Frioud E, Aguiar D, Ruch P, Auckenthaler O, Baudraz J, Fracasso T.

Arch Suicide Res. 2018 Jun 8:1-17. doi: 10.1080/13811118.2018.1480985. [Epub ahead of print]

PMID:
29883272
2.

ORBDA: An openEHR benchmark dataset for performance assessment of electronic health record servers.

Teodoro D, Sundvall E, João Junior M, Ruch P, Miranda Freire S.

PLoS One. 2018 Jan 2;13(1):e0190028. doi: 10.1371/journal.pone.0190028. eCollection 2018.

3.

Improving average ranking precision in user searches for biomedical research datasets.

Teodoro D, Mottin L, Gobeill J, Gaudinat A, Vachon T, Ruch P.

Database (Oxford). 2017 Jan 1;2017. doi: 10.1093/database/bax083.

4.

Triage by ranking to support the curation of protein interactions.

Mottin L, Pasche E, Gobeill J, Rech de Laval V, Gleizes A, Michel PA, Bairoch A, Gaudet P, Ruch P.

Database (Oxford). 2017 Jan 1;2017. doi: 10.1093/database/bax040.

5.

SciLite: a platform for displaying text-mined annotations as a means to link research articles with biological data.

Venkatesan A, Kim JH, Talo F, Ide-Smith M, Gobeill J, Carter J, Batista-Navarro R, Ananiadou S, Ruch P, McEntyre J.

Wellcome Open Res. 2017 Jul 10;1:25. doi: 10.12688/wellcomeopenres.10210.2. eCollection 2016.

6.

Development and Evaluation of a Case-Based Retrieval Service.

Pasche E, Chinali M, Gobeill J, Ruch P.

Stud Health Technol Inform. 2017;235:186-190.

PMID:
28423780
7.

Text Mining to Support Gene Ontology Curation and Vice Versa.

Ruch P.

Methods Mol Biol. 2017;1446:69-84.

PMID:
27812936
8.

neXtA5: accelerating annotation of articles via automated approaches in neXtProt.

Mottin L, Gobeill J, Pasche E, Michel PA, Cusin I, Gaudet P, Ruch P.

Database (Oxford). 2016 Jul 3;2016. pii: baw098. doi: 10.1093/database/baw098. Print 2016.

9.

Deep Question Answering for protein annotation.

Gobeill J, Gaudinat A, Pasche E, Vishnyakova D, Gaudet P, Bairoch A, Ruch P.

Database (Oxford). 2015 Sep 16;2015. pii: bav081. doi: 10.1093/database/bav081. Print 2015. Review.

10.

Mixing with herringbone-inspired microstructures: overcoming the diffusion limit in co-laminar microfluidic devices.

Marschewski J, Jung S, Ruch P, Prasad N, Mazzotti S, Michel B, Poulikakos D.

Lab Chip. 2015 Apr 21;15(8):1923-33. doi: 10.1039/c5lc00045a.

PMID:
25737365
11.

Closing the loop: from paper to protein annotation using supervised Gene Ontology classification.

Gobeill J, Pasche E, Vishnyakova D, Ruch P.

Database (Oxford). 2014 Sep 4;2014. pii: bau088. doi: 10.1093/database/bau088. Print 2014.

12.

Electronic processing of informed consents in a global pharmaceutical company environment.

Vishnyakova D, Gobeill J, Oezdemir-Zaech F, Kreim O, Vachon T, Clade T, Haenning X, Mikhailov D, Ruch P.

Stud Health Technol Inform. 2014;205:995-9.

PMID:
25160337
13.

Overview of the gene ontology task at BioCreative IV.

Mao Y, Van Auken K, Li D, Arighi CN, McQuilton P, Hayman GT, Tweedie S, Schaeffer ML, Laulederkind SJ, Wang SJ, Gobeill J, Ruch P, Luu AT, Kim JJ, Chiang JH, Chen YD, Yang CJ, Liu H, Zhu D, Li Y, Yu H, Emadzadeh E, Gonzalez G, Chen JM, Dai HJ, Lu Z.

Database (Oxford). 2014 Aug 25;2014. pii: bau086. doi: 10.1093/database/bau086. Print 2014.

14.

Development and tuning of an original search engine for patent libraries in medicinal chemistry.

Pasche E, Gobeill J, Kreim O, Oezdemir-Zaech F, Vachon T, Lovis C, Ruch P.

BMC Bioinformatics. 2014;15 Suppl 1:S15. doi: 10.1186/1471-2105-15-S1-S15. Epub 2014 Jan 10.

15.

The COMBREX project: design, methodology, and initial results.

Anton BP, Chang YC, Brown P, Choi HP, Faller LL, Guleria J, Hu Z, Klitgord N, Levy-Moonshine A, Maksad A, Mazumdar V, McGettrick M, Osmani L, Pokrzywa R, Rachlin J, Swaminathan R, Allen B, Housman G, Monahan C, Rochussen K, Tao K, Bhagwat AS, Brenner SE, Columbus L, de Crécy-Lagard V, Ferguson D, Fomenkov A, Gadda G, Morgan RD, Osterman AL, Rodionov DA, Rodionova IA, Rudd KE, Söll D, Spain J, Xu SY, Bateman A, Blumenthal RM, Bollinger JM, Chang WS, Ferrer M, Friedberg I, Galperin MY, Gobeill J, Haft D, Hunt J, Karp P, Klimke W, Krebs C, Macelis D, Madupu R, Martin MJ, Miller JH, O'Donovan C, Palsson B, Ruch P, Setterdahl A, Sutton G, Tate J, Yakunin A, Tchigvintsev D, Plata G, Hu J, Greiner R, Horn D, Sjölander K, Salzberg SL, Vitkup D, Letovsky S, Segrè D, DeLisi C, Roberts RJ, Steffen M, Kasif S.

PLoS Biol. 2013;11(8):e1001638. doi: 10.1371/journal.pbio.1001638. Epub 2013 Aug 27. No abstract available.

16.

Use of controlled vocabularies to improve biomedical information retrieval tasks.

Pasche E, Gobeill J, Vishnyakova D, Ruch P, Lovis C.

Stud Health Technol Inform. 2013;192:1068.

PMID:
23920842
17.

Managing the data deluge: data-driven GO category assignment improves while complexity of functional annotation increases.

Gobeill J, Pasche E, Vishnyakova D, Ruch P.

Database (Oxford). 2013 Jul 9;2013:bat041. doi: 10.1093/database/bat041. Print 2013.

18.

Improving data and knowledge management to better integrate health care and research.

Cases M, Furlong LI, Albanell J, Altman RB, Bellazzi R, Boyer S, Brand A, Brookes AJ, Brunak S, Clark TW, Gea J, Ghazal P, Graf N, Guigó R, Klein TE, López-Bigas N, Maojo V, Mons B, Musen M, Oliveira JL, Rowe A, Ruch P, Shabo A, Shortliffe EH, Valencia A, van der Lei J, Mayer MA, Sanz F.

J Intern Med. 2013 Oct;274(4):321-8. doi: 10.1111/joim.12105. Epub 2013 Jul 15. No abstract available.

19.

Assisted knowledge discovery for the maintenance of clinical guidelines.

Pasche E, Ruch P, Teodoro D, Huttner A, Harbarth S, Gobeill J, Wipfli R, Lovis C.

PLoS One. 2013 Apr 30;8(4):e62874. doi: 10.1371/journal.pone.0062874. Print 2013. Erratum in: PLoS One. 2013;8(5). doi:10.1371/annotation/b38c6896-f340-45cb-a9ca-ceff49330c3f.

20.

Utilization of ontology look-up services in information retrieval for biomedical literature.

Vishnyakova D, Pasche E, Lovis C, Ruch P.

Stud Health Technol Inform. 2013;186:155-9.

PMID:
23542988
21.

Application of text-mining for updating protein post-translational modification annotation in UniProtKB.

Veuthey AL, Bridge A, Gobeill J, Ruch P, McEntyre JR, Bougueleret L, Xenarios I.

BMC Bioinformatics. 2013 Mar 22;14:104. doi: 10.1186/1471-2105-14-104.

22.

Using binary classification to prioritize and curate articles for the Comparative Toxicogenomics Database.

Vishnyakova D, Pasche E, Ruch P.

Database (Oxford). 2012 Dec 5;2012:bas050. doi: 10.1093/database/bas050. Print 2012.

24.

Classification and prioritization of biomedical literature for the comparative toxicogenomics database.

Vishnyakova D, Pasche E, Gobeill J, Gaudinat A, Lovis C, Ruch P.

Stud Health Technol Inform. 2012;180:210-4.

PMID:
22874182
25.

An advanced search engine for patent analytics in medicinal chemistry.

Pasche E, Gobeill J, Teodoro D, Gaudinat A, Vishnykova D, Lovis C, Ruch P.

Stud Health Technol Inform. 2012;180:204-9.

PMID:
22874181
26.

Building a transnational biosurveillance network using semantic web technologies: requirements, design, and preliminary evaluation.

Teodoro D, Pasche E, Gobeill J, Emonet S, Ruch P, Lovis C.

J Med Internet Res. 2012 May 29;14(3):e73. doi: 10.2196/jmir.2043.

27.

A user-friendly tool for medical-related patent retrieval.

Pasche E, Gobeill J, Teodoro D, Gaudinat A, Vishnyakova D, Lovis C, Ruch P.

Stud Health Technol Inform. 2012;174:121-5.

PMID:
22491124
28.

Pathogens and gene product normalization in the biomedical literature.

Vishnyakova D, Pasche E, Teodoro D, Lovis C, Ruch P.

Stud Health Technol Inform. 2012;174:89-93.

PMID:
22491118
29.

The gene normalization task in BioCreative III.

Lu Z, Kao HY, Wei CH, Huang M, Liu J, Kuo CJ, Hsu CN, Tsai RT, Dai HJ, Okazaki N, Cho HC, Gerner M, Solt I, Agarwal S, Liu F, Vishnyakova D, Ruch P, Romacker M, Rinaldi F, Bhattacharya S, Srinivasan P, Liu H, Torii M, Matos S, Campos D, Verspoor K, Livingston KM, Wilbur WJ.

BMC Bioinformatics. 2011 Oct 3;12 Suppl 8:S2. doi: 10.1186/1471-2105-12-S8-S2.

31.

Using multimodal mining to drive clinical guidelines development.

Pasche E, Gobeill J, Teodoro D, Vishnyakova D, Gaudinat A, Ruch P, Lovis C.

Stud Health Technol Inform. 2011;169:477-81.

PMID:
21893795
32.

Interoperability driven integration of biomedical data sources.

Teodoro D, Choquet R, Schober D, Mels G, Pasche E, Ruch P, Lovis C.

Stud Health Technol Inform. 2011;169:185-9.

PMID:
21893739
33.

Findings from the yearbook 2010 section on decision support systems.

Ruch P; Section Editor for the IMIA Yearbook Section on Decision Support Systems.

Yearb Med Inform. 2010:55-7. Review.

PMID:
20938571
34.

Comparing a Rule Based vs. Statistical System for Automatic Categorization of MEDLINE Documents According to Biomedical Specialty.

Humphrey SM, Névéol A, Gobeil J, Ruch P, Darmoni SJ, Browne A.

J Am Soc Inf Sci Technol. 2009 Dec 1;60(12):2530-2539.

36.

Automatic medical knowledge acquisition using question-answering.

Pasche E, Teodoro D, Gobeill J, Ruch P, Lovis C.

Stud Health Technol Inform. 2009;150:569-73.

PMID:
19745375
37.

Biomedical data management: a proposal framework.

Teodoro D, Choquet R, Pasche E, Gobeill J, Daniel C, Ruch P, Lovis C.

Stud Health Technol Inform. 2009;150:175-9.

PMID:
19745292
38.

DebugIT: building a European distributed clinical data mining network to foster the fight against microbial diseases.

Lovis C, Douglas T, Pasche E, Ruch P, Colaert D, Stroetmann K.

Stud Health Technol Inform. 2009;148:50-9.

PMID:
19745235
39.

QA-driven guidelines generation for bacteriotherapy.

Pasche E, Teodoro D, Gobeill J, Ruch P, Lovis C.

AMIA Annu Symp Proc. 2009 Nov 14;2009:509-13.

40.

Automatic medical encoding with SNOMED categories.

Ruch P, Gobeill J, Lovis C, Geissbühler A.

BMC Med Inform Decis Mak. 2008 Oct 27;8 Suppl 1:S6. doi: 10.1186/1472-6947-8-S1-S6.

41.

From episodes of care to diagnosis codes: automatic text categorization for medico-economic encoding.

Ruch P, Gobeilla J, Tbahritia I, Geissbühlera A.

AMIA Annu Symp Proc. 2008 Nov 6:636-40.

42.

Introducing meta-services for biomedical information extraction.

Leitner F, Krallinger M, Rodriguez-Penagos C, Hakenberg J, Plake C, Kuo CJ, Hsu CN, Tsai RT, Hung HC, Lau WW, Johnson CA, Saetre R, Yoshida K, Chen YH, Kim S, Shin SY, Zhang BT, Baumgartner WA Jr, Hunter L, Haddow B, Matthews M, Wang X, Ruch P, Ehrler F, Ozgür A, Erkan G, Radev DR, Krauthammer M, Luong T, Hoffmann R, Sander C, Valencia A.

Genome Biol. 2008;9 Suppl 2:S6. doi: 10.1186/gb-2008-9-s2-s6. Epub 2008 Sep 1.

43.

Overview of BioCreative II gene normalization.

Morgan AA, Lu Z, Wang X, Cohen AM, Fluck J, Ruch P, Divoli A, Fundel K, Leaman R, Hakenberg J, Sun C, Liu HH, Torres R, Krauthammer M, Lau WW, Liu H, Hsu CN, Schuemie M, Cohen KB, Hirschman L.

Genome Biol. 2008;9 Suppl 2:S3. doi: 10.1186/gb-2008-9-s2-s3. Epub 2008 Sep 1.

45.

Mapping proteins to disease terminologies: from UniProt to MeSH.

Mottaz A, Yip YL, Ruch P, Veuthey AL.

BMC Bioinformatics. 2008 Apr 29;9 Suppl 5:S3. doi: 10.1186/1471-2105-9-S5-S3.

46.

Gene Ontology density estimation and discourse analysis for automatic GeneRiF extraction.

Gobeill J, Tbahriti I, Ehrler F, Mottaz A, Veuthey AL, Ruch P.

BMC Bioinformatics. 2008 Apr 11;9 Suppl 3:S9. doi: 10.1186/1471-2105-9-S3-S9.

47.

A multi-sample automatic system for in situ electrochemical X-ray diffraction synchrotron measurements.

Rosciano F, Holzapfel M, Kaiser H, Scheifele W, Ruch P, Hahn M, Kötz R, Novák P.

J Synchrotron Radiat. 2007 Nov;14(Pt 6):487-91. Epub 2007 Oct 13.

PMID:
17960031
48.

Reconciliation of ontology and terminology to cope with linguistics.

Baud RH, Ceusters W, Ruch P, Rassinoux AM, Lovis C, Geissbühler A.

Stud Health Technol Inform. 2007;129(Pt 1):796-801.

PMID:
17911826
49.

Using discourse analysis to improve text categorization in MEDLINE.

Ruch P, Geissbühler A, Gobeill J, Lisacek F, Tbahriti I, Veuthey AL, Aronson AR.

Stud Health Technol Inform. 2007;129(Pt 1):710-5.

PMID:
17911809
50.

Challenges and methodology for indexing the computerized patient record.

Ehrler F, Ruch P, Geissbuhler A, Lovis C.

Stud Health Technol Inform. 2007;129(Pt 1):417-21.

PMID:
17911751
51.

Design of a decentralized reusable research database architecture to support data acquisition in large research projects.

Iavindrasana J, Depeursinge A, Ruch P, Spahni S, Geissbuhler A, Müller H.

Stud Health Technol Inform. 2007;129(Pt 1):325-9.

PMID:
17911732
52.

Using argumentation to extract key sentences from biomedical abstracts.

Ruch P, Boyer C, Chichester C, Tbahriti I, Geissbühler A, Fabry P, Gobeill J, Pillet V, Rebholz-Schuhmann D, Lovis C, Veuthey AL.

Int J Med Inform. 2007 Feb-Mar;76(2-3):195-200. Epub 2006 Jul 11.

PMID:
16815739
53.

Advancing biomedical image retrieval: development and analysis of a test collection.

Hersh WR, Müller H, Jensen JR, Yang J, Gorman PN, Ruch P.

J Am Med Inform Assoc. 2006 Sep-Oct;13(5):488-96. Epub 2006 Jun 23.

54.

Health search engine with e-document analysis for reliable search results.

Gaudinat A, Ruch P, Joubert M, Uziel P, Strauss A, Thonnet M, Baud R, Spahni S, Weber P, Bonal J, Boyer C, Fieschi M, Geissbuhler A.

Int J Med Inform. 2006 Jan;75(1):73-85. Epub 2005 Dec 27.

PMID:
16377235
55.

Automatic assignment of biomedical categories: toward a generic approach.

Ruch P.

Bioinformatics. 2006 Mar 15;22(6):658-64. Epub 2005 Nov 15.

PMID:
16287934
56.

Methodology to ease the construction of a terminology of problems.

Fabry P, Baud R, Ruch P, Despont-Gros C, Lovis C.

Int J Med Inform. 2006 Aug;75(8):624-32. Epub 2005 Oct 10.

PMID:
16219485
57.

Using argumentation to retrieve articles with similar citations: an inquiry into improving related articles search in the MEDLINE digital library.

Tbahriti I, Chichester C, Lisacek F, Ruch P.

Int J Med Inform. 2006 Jun;75(6):488-95. Epub 2005 Sep 13.

PMID:
16165395
58.

Extracting key sentences with latent argumentative structuring.

Ruch P, Baud R, Chichester C, Geissbühler A, Lisacek F, Marty J, Rebholz-Schuhmann D, Tbahriti I, Veuthey AL.

Stud Health Technol Inform. 2005;116:835-40.

PMID:
16160362
59.

Recent advances in natural language processing for biomedical applications.

Collier N, Nazarenko A, Baud R, Ruch P.

Int J Med Inform. 2006 Jun;75(6):413-7. Epub 2005 Aug 31. Review.

PMID:
16139564
60.

Data-poor categorization and passage retrieval for gene ontology annotation in Swiss-Prot.

Ehrler F, Geissbühler A, Jimeno A, Ruch P.

BMC Bioinformatics. 2005;6 Suppl 1:S23. Epub 2005 May 24.

61.

UMLF: a unified medical lexicon for French.

Zweigenbaum P, Baud R, Burgun A, Namer F, Jarrousse E, Grabar N, Ruch P, Le Duff F, Forget JF, Douyère M, Darmoni S.

Int J Med Inform. 2005 Mar;74(2-4):119-24.

PMID:
15694616
62.

Coping with the variability of medical terms.

Baud RH, Ruch P, Gaudinat A, Fabry P, Lovis C, Geissbuhler A.

Stud Health Technol Inform. 2004;107(Pt 1):322-6.

PMID:
15360827
63.

UMLF: a Unified Medical Lexicon for French.

Zweigenbaum P, Baud R, Burgun A, Namer F, Jarrousse E, Grabar N, Ruch P, Le Duff F, Thirion B, Darmoni S.

AMIA Annu Symp Proc. 2003:1062.

64.

A frame-based representation of ICD-10.

Fabry P, Baud R, Ruch P, Le Beux P, Lovis C.

Stud Health Technol Inform. 2003;95:433-8.

PMID:
14664025
65.

Towards a unified medical lexicon for French.

Zweigenbaum P, Baud R, Burgun A, Namer F, Jarrousse E, Grabar N, Ruch P, Le Duff F, Thirion B, Darmoni S.

Stud Health Technol Inform. 2003;95:415-20.

PMID:
14664022
66.

Using lexical disambiguation and named-entity recognition to improve spelling correction in the electronic patient record.

Ruch P, Baud R, Geissbühler A.

Artif Intell Med. 2003 Sep-Oct;29(1-2):169-84.

PMID:
12957786
67.

Controlling the vocabulary for anatomy.

Baud RH, Lovis C, Rassinoux AM, Ruch P, Geissbuhler A.

Proc AMIA Symp. 2002:26-30.

68.

Evaluating and reducing the effect of data corruption when applying bag of words approaches to medical records.

Ruch P, Baud R, Geissbühler A.

Int J Med Inform. 2002 Dec 4;67(1-3):75-83.

PMID:
12460633
69.

The future of natural language processing for biomedical applications.

Baud R, Ruch P.

Int J Med Inform. 2002 Dec 4;67(1-3):1-5. No abstract available.

PMID:
12460627
70.

Looking back or looking all around: comparing two spell checking strategies for documents edition in an electronic patient record.

Ruch P, Baud RH, Geiddbühler A, Lovis C, Rassinoux AM, Rivière A.

Proc AMIA Symp. 2001:568-72.

71.

A light knowledge model for linguistic applications.

Baud RH, Lovis C, Ruch P, Rassinoux AM.

Proc AMIA Symp. 2001:37-41.

72.

Comparing general and medical texts for information retrieval based on natural language processing: an inquiry into lexical disambiguation.

Ruch P, Baud R, Geissbühler A, Rassinoux AM.

Stud Health Technol Inform. 2001;84(Pt 1):261-5.

PMID:
11604745
73.

Conceptual search in electronic patient record.

Baud RH, Lovis C, Ruch P, Rassinoux AM.

Stud Health Technol Inform. 2001;84(Pt 1):156-60.

PMID:
11604724
74.

A toolset for medical text processing.

Baud RH, Lovis C, Ruch P, Rassinoux AM.

Stud Health Technol Inform. 2000;77:456-61.

PMID:
11187593
75.

Tagging medical texts: a rule-based experiment.

Ruch P, Bouillon P, Robert G, Baud R, Rassinoux AM.

Stud Health Technol Inform. 2000;77:448-55.

PMID:
11187592
76.

Medical document anonymization with a semantic lexicon.

Ruch P, Baud RH, Rassinoux AM, Bouillon P, Robert G.

Proc AMIA Symp. 2000:729-33.

77.
78.

MEDTAG: tag-like semantics for medical document indexing.

Ruch P, Wagner J, Bouillon P, Baud RH, Rassinoux AM, Scherrer JR.

Proc AMIA Symp. 1999:137-41.

79.

Model-based semantic dictionaries for medical language understanding.

Rassinoux AM, Baud RH, Ruch P, Trombert-Paviot B, Rodrigues JM.

Proc AMIA Symp. 1999:122-6.

80.

The power and limits of a rule-based morpho-semantic parser.

Baud RH, Rassinoux AM, Ruch P, Lovis C, Scherrer JR.

Proc AMIA Symp. 1999:22-6.

81.

Mutagen sensitivity of wild type and recombination deficient c(3)G strains of Drosophila melanogaster.

Würgler FE, Graf U, Ruch P, Beck A, Steiner T.

Arch Genet (Zur). 1978;51(3):217-42. No abstract available.

PMID:
121955
82.

RNA polymerases from a rat hepatoma. Partial purification and comparison of properties with corresponding liver enzymes.

Rose KM, Ruch PA, Morris HP, Jacob ST.

Biochim Biophys Acta. 1976 Apr 15;432(1):60-72.

PMID:
177077
83.
84.
85.

X-ray-induced loss of the maternal second chromosome in inseminated eggs of Drosophila melanogaster.

Würgler FE, Ruch P, Graf U.

Mutat Res. 1972 May;15(1):31-40. No abstract available.

PMID:
4623570
86.

Rapid microassay of gentamicin, kanamycin, neomycin, streptomycin, and vancomycin in serum or plasma.

Sabath LD, Casey JI, Ruch PA, Stumpf LL, Finland M.

J Lab Clin Med. 1971 Sep;78(3):457-63. No abstract available.

PMID:
4999161
87.

Rapid microassay for circulating nephrotoxic antibiotics.

Sabath LD, Casey JI, Ruch PA, Stumpf LL, Finland M.

Antimicrob Agents Chemother (Bethesda). 1970;10:83-90. No abstract available.

PMID:
5000271

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