Summary: Publications intended to be issued on an ongoing basis, generally more frequently than annually, containing separate articles, stories, or writings.

Top Publications

  1. Sladek R, Tieman J, Fazekas B, Abernethy A, Currow D. Development of a subject search filter to find information relevant to palliative care in the general medical literature. J Med Libr Assoc. 2006;94:394-401 pubmed
    ..Further research, such as frequency analysis of text-words and MeSH terms, is required to increase the sensitivity of searching in this subset of the literature. ..
  2. Schwartz L, Woloshin S, Dvorin E, Welch H. Ratio measures in leading medical journals: structured review of accessibility of underlying absolute risks. BMJ. 2006;333:1248 pubmed
    ..0, 2.1 to 4.3). Absolute risks are often not easily accessible in articles reporting ratio measures and sometimes are missing altogether-this lack of accessibility can easily exaggerate readers' perceptions of benefit or harm. ..
  3. Plint A, Moher D, Morrison A, Schulz K, Altman D, Hill C, et al. Does the CONSORT checklist improve the quality of reports of randomised controlled trials? A systematic review. Med J Aust. 2006;185:263-7 pubmed
    ..10-15.83), and total CONSORT items (standardised mean difference, 3.67 items; 95% CI, 2.09-5.25) were improved after adoption of CONSORT by the journal. Journal adoption of CONSORT is associated with improved reporting of RCTs. ..
  4. Lewis J, Ossowski S, Hicks J, Errami M, Garner H. Text similarity: an alternative way to search MEDLINE. Bioinformatics. 2006;22:2298-304 pubmed A variety of other derivative systems and visualization tools provides the user with an enhanced experience and additional capabilities. ..
  5. Jensen L, Saric J, Bork P. Literature mining for the biologist: from information retrieval to biological discovery. Nat Rev Genet. 2006;7:119-29 pubmed
    ..However, the latter will require the integration of literature and high-throughput data, which should encourage close collaborations between biologists and computational linguists. ..
  6. Skusa A, Ruegg A, Köhler J. Extraction of biological interaction networks from scientific literature. Brief Bioinform. 2005;6:263-76 pubmed
    ..This paper summarises the most important steps in network extraction and reviews common approaches and solutions for the extraction of biological networks from scientific literature. ..
  7. Scherf M, Epple A, Werner T. The next generation of literature analysis: integration of genomic analysis into text mining. Brief Bioinform. 2005;6:287-97 pubmed
  8. Kirsch H, Gaudan S, Rebholz Schuhmann D. Distributed modules for text annotation and IE applied to the biomedical domain. Int J Med Inform. 2006;75:496-500 pubmed
    ..The server and the underlying software are available to the public. ..
  9. Saric J, Jensen L, Ouzounova R, Rojas I, Bork P. Extraction of regulatory gene/protein networks from Medline. Bioinformatics. 2006;22:645-50 pubmed
    ..The revised GENIA corpus, the POS tagger, the extraction rules and the full sets of extracted relations are available from ..

More Information


  1. Michalopoulos A, Falagas M. A bibliometric analysis of global research production in respiratory medicine. Chest. 2005;128:3993-8 pubmed
    ..Although leaders of production of respiratory medicine research were from Western Europe and the United States, Canada, and Oceania had the best performance after adjustment for population and GNIPC. ..
  2. Rice S, Nenadic G, Stapley B. Mining protein function from text using term-based support vector machines. BMC Bioinformatics. 2005;6 Suppl 1:S22 pubmed
    ..The most promising results are for combined document retrieval and GO term assignment, which calls for the integration of methods developed in BioCreAtIvE Task 1 and Task 2. ..
  3. Soteriades E, Rosmarakis E, Paraschakis K, Falagas M. Research contribution of different world regions in the top 50 biomedical journals (1995-2002). FASEB J. 2006;20:29-34 pubmed
    ..Canada and Western Europe share the second place while the rest of the world is far behind. ..
  4. Eysenbach G. Citation advantage of open access articles. PLoS Biol. 2006;4:e157 pubmed
    ..OA is likely to benefit science by accelerating dissemination and uptake of research findings. ..
  5. Vergidis P, Karavasiou A, Paraschakis K, Bliziotis I, Falagas M. Bibliometric analysis of global trends for research productivity in microbiology. Eur J Clin Microbiol Infect Dis. 2005;24:342-6 pubmed
    ..The three regions in which research productivity increased the most were Asia, Latin America, and Eastern Europe. ..
  6. Wren J. Open access and openly accessible: a study of scientific publications shared via the internet. BMJ. 2005;330:1128 pubmed
    ..Decentralised sharing of scientific reprints through the internet creates a degree of de facto open access that, though highly incomplete in its coverage, is none the less biased towards publications of higher popular demand. ..
  7. Cohen A, Hersh W. A survey of current work in biomedical text mining. Brief Bioinform. 2005;6:57-71 pubmed
  8. Lee A, Boldt H, Golnik K, Arnold A, Oetting T, Beaver H, et al. Structured journal club as a tool to teach and assess resident competence in practice-based learning and improvement. Ophthalmology. 2006;113:497-500 pubmed
    ..Although validity, reliability, and long-term efficacy studies are necessary, the structured journal club is one method of teaching and assessing resident competency in PBL and improvement. ..
  9. Mukherjea S. Information retrieval and knowledge discovery utilising a biomedical Semantic Web. Brief Bioinform. 2005;6:252-62 pubmed
    ..Finally, some of the challenges that have to be addressed to make the vision of a biomedical Semantic Web a reality are discussed. ..
  10. Rosmarakis E, Vergidis P, Soteriades E, Paraschakis K, Papastamataki P, Falagas M. Estimates of global production in cardiovascular diseases research. Int J Cardiol. 2005;100:443-9 pubmed
    ..3%). The data suggest a promising trend: developing world regions, with the important exception of Africa, achieved a higher rate of increase in the number of published articles in the studied period. ..
  11. Küffner R, Fundel K, Zimmer R. Expert knowledge without the expert: integrated analysis of gene expression and literature to derive active functional contexts. Bioinformatics. 2005;21 Suppl 2:ii259-67 pubmed
    ..The method allows for in-depth investigation of subsets of genes, the associated literature topics and publications. Supplementary data on clusters is available upon request. ..
  12. Shah R, Albert T, Bruegel Sanchez V, Vaccaro A, Hilibrand A, Grauer J. Industry support and correlation to study outcome for papers published in Spine. Spine (Phila Pa 1976). 2005;30:1099-104; discussion 1105 pubmed
  13. Mizuta Y, Korhonen A, Mullen T, Collier N. Zone analysis in biology articles as a basis for information extraction. Int J Med Inform. 2006;75:468-87 pubmed
    ..We also discuss our preliminary research on automatic zone analysis, and its incorporation into our IE framework. ..
  14. Blaschke C, Leon E, Krallinger M, Valencia A. Evaluation of BioCreAtIvE assessment of task 2. BMC Bioinformatics. 2005;6 Suppl 1:S16 pubmed
    ..The dataset generated in line with the BioCreative challenge is publicly available and will allow new possibilities for training information extraction methods in the domain of molecular biology. ..
  15. Ray S, Craven M. Learning statistical models for annotating proteins with function information using biomedical text. BMC Bioinformatics. 2005;6 Suppl 1:S18 pubmed
  16. Krallinger M, Padron M, Valencia A. A sentence sliding window approach to extract protein annotations from biomedical articles. BMC Bioinformatics. 2005;6 Suppl 1:S19 pubmed
    ..The combination of our approach with more refined statistical estimators and machine learning techniques might be a way to improve annotation extraction for future biomedical text mining applications. ..
  17. Sox H, Rennie D. Research misconduct, retraction, and cleansing the medical literature: lessons from the Poehlman case. Ann Intern Med. 2006;144:609-13 pubmed
    ..Finally, it requires authors to take pains to avoid citing retracted articles and to issue a correction when they inadvertently cite a retracted article. ..
  18. Spasic I, Ananiadou S, McNaught J, Kumar A. Text mining and ontologies in biomedicine: making sense of raw text. Brief Bioinform. 2005;6:239-51 pubmed
    ..The principal link between text and an ontology is terminology, which maps terms to domain-specific concepts. This paper summarises different approaches in which ontologies have been used for text-mining applications in biomedicine. ..
  19. Krallinger M, Erhardt R, Valencia A. Text-mining approaches in molecular biology and biomedicine. Drug Discov Today. 2005;10:439-45 pubmed
    ..Finally, we will consider the recent evolution of this field and the efforts for community-based evaluations. ..
  20. Ioannidis J. Contradicted and initially stronger effects in highly cited clinical research. JAMA. 2005;294:218-28 pubmed
    ..Controversies are most common with highly cited nonrandomized studies, but even the most highly cited randomized trials may be challenged and refuted over time, especially small ones. ..
  21. Morton L, Cahill J, Hartge P. Reporting participation in epidemiologic studies: a survey of practice. Am J Epidemiol. 2006;163:197-203 pubmed
    ..The authors conclude that epidemiologists need to address declining participation and to report participation consistently, including for biologic specimen collection. ..
  22. Ding J, Hughes L, Berleant D, Fulmer A, Wurtele E. PubMed Assistant: a biologist-friendly interface for enhanced PubMed search. Bioinformatics. 2006;22:378-80 pubmed
  23. Shatkay H. Hairpins in bookstacks: information retrieval from biomedical text. Brief Bioinform. 2005;6:222-38 pubmed
    ..This paper introduces the basics of information retrieval, discusses its applications in biomedicine, and presents traditional and non-traditional ways in which it can be used. ..
  24. Couto F, Silva M, Coutinho P. Finding genomic ontology terms in text using evidence content. BMC Bioinformatics. 2005;6 Suppl 1:S21 pubmed
    ..From the performance obtained in BioCreative, we concluded that an automatic annotation system can effectively use our method to identify biological properties in unstructured text. ..
  25. Mills E, Wu P, Gagnier J, Heels Ansdell D, Montori V. An analysis of general medical and specialist journals that endorse CONSORT found that reporting was not enforced consistently. J Clin Epidemiol. 2005;58:662-7 pubmed
    ..General medical and specialist journals that endorse CONSORT do not enforce reporting issues consistently, with specialty journals lagging behind general medical journals. ..
  26. Weeber M, Kors J, Mons B. Online tools to support literature-based discovery in the life sciences. Brief Bioinform. 2005;6:277-86 pubmed
    ..This paper presents an overview of recent LBD research and discusses methodology, results and online tools that are available to the scientific community. ..
  27. Nail Chiwetalu B, Bernstein Ratner N. An assessment of the information-seeking abilities and needs of practicing speech-language pathologists. J Med Libr Assoc. 2007;95:182-8, e56-7 pubmed
  28. Jorge M, de Freitas C, Nóbrega M, Queiroz M. [Management in nursing: a critical view about the knowledge produced in Brazilian journals (2000-2004)]. Rev Bras Enferm. 2007;60:81-6 pubmed
    ..The confronts and reflections pointed out the need of transformation of management in direction to a participative and flexive posture, valuing the human potential. ..
  29. Kennedy J. [Celebration speech marking the 150th anniversary of the Vereniging Nederlands Tijdschrift voor Geneeskunde (Association Dutch Journal of Medicine)]. Ned Tijdschr Geneeskd. 2007;151:425-32 pubmed
    ..At present, there is a clear need for physician citizenship that engages in a broad spectrum of social responsibilities in a professional context. ..
  30. Monge Nájera J, Benavides Varela C, Morera B. [Which are the most influential journals, books and scientists in Latin American biology?]. Rev Biol Trop. 2004;52:1-17 pubmed
  31. Arney J, Rafalovich A. Incomplete syllogisms as techniques of medicalization: The case of direct-to-consumer advertising in popular magazines, 1997 to 2003. Qual Health Res. 2007;17:49-60 pubmed
    ..The researchers examine the implications of incomplete syllogisms in advertisements and suggest that their use might lead readers to redefine their physical and/or emotional problems to fit medical models of mental distress. ..
  32. Packer A, Meneghini R. Articles with authors affiliated to Brazilian institutions published from 1994 to 2003 with 100 or more citations: I - the weight of international collaboration and the role of the networks. An Acad Bras Cienc. 2006;78:841-53 pubmed
    ..It is evident that the role played by organizations in research networks as well as the international collaborations exerted strong influence in the impact of these articles, although with distinct amplitude in the different fields. ..
  33. Loh L, Ong H, Quah S. Impact of various continuing medical education activities on clinical practice - a survey of Malaysian doctors on its perceived importance. Ann Acad Med Singapore. 2007;36:281-4 pubmed
    ..Our findings provide an important first look at this under-explored area among Malaysian doctors and described a high degree of acceptance for the involvement of the pharmaceutical industry in CME activities. ..
  34. Barreto M. [Growth and trends in scientific production in epidemiology in Brazil]. Rev Saude Publica. 2006;40 Spec no.:79-85 pubmed
    ..Therefore, Brazilian scientific output in the epidemiology field is showing a growth pattern similar to that of other scientific areas in the country. ..
  35. Gatheral T, Bennett E. Year in review 2005: critical care--cardiology. Crit Care. 2006;10:225 pubmed
  36. Robinson J. Conservation Biology and real-world conservation. Conserv Biol. 2006;20:658-69 pubmed
  37. Rangachari P. Texts in context: Horace Davenport, carbonic anhydrase, and gastric acid secretion. Adv Physiol Educ. 2007;31:140-4 pubmed
    ..All three papers form part of the classic papers available through the American Physiological Society Legacy Project. ..
  38. Serrant Green L. 'You could have been a doctor'. Nurse Res. 2007;14:76-8 pubmed
  39. Garry R. An invitation to recent graduates: publish your dissertation/thesis background section as a review in Virology Journal. Virol J. 2007;4:46 pubmed
    ..Virology Journal will publish background sections of approved dissertations or theses as Review Articles. ..
  40. Regidor E, de la Fuente L, Gutierrez Fisac J, de Mateo S, Pascual C, Sanchez Paya J, et al. The role of the public health official in communicating public health information. Am J Public Health. 2007;97 Suppl 1:S93-7 pubmed
    ..However, they must do so within the bureaucracy. Any actions that public health officials wish to take as advocates of particular public health activities should be carried out independent of their role as government officials. ..
  41. Ioannidis J. Limitations are not properly acknowledged in the scientific literature. J Clin Epidemiol. 2007;60:324-9 pubmed
    ..To facilitate this, journals should give better guidance and promote the discussion of limitations. Otherwise, we are facing an important loss of context for the scientific literature. ..
  42. Hill A. Motivation for eating behaviour in adolescent girls: the body beautiful. Proc Nutr Soc. 2006;65:376-84 pubmed
    ..For those working in adolescent nutrition it is a reminder that adolescent food choice and intake are subject to many competing, contradictory and non-health-related determinants. ..
  43. Turato E, Machado A, Silva D, de Carvalho G, Verderosi N, de Souza T. Research publications in the field of health: omission of hypotheses and presentation of common-sense conclusions. Sao Paulo Med J. 2006;124:228-33 pubmed
    ..Conclusions from scientific articles are often confounded with common-sense statements. Quantitative research is suggested, for studying the frequency of occurrence of these dubious methodological points. ..
  44. Roposch A, Moreau N, Uleryk E, Doria A. Developmental dysplasia of the hip: quality of reporting of diagnostic accuracy for US. Radiology. 2006;241:854-60 pubmed
    ..Authors tended to overinterpret their results. Overall, there was imperfect reporting of diagnostic accuracy in studies on the use of US for diagnosis of DDH. ..
  45. Mildenberger F. [The birth of acknowledgement: Michel Foucault and Werner Leibbrand]. Sudhoffs Arch. 2006;90:97-105 pubmed
    ..Thus, when Foucault was accepted by the latter, they were not prepared to examine the work of Leibbrand and realize how close some of the ideas developed by Leibbrand and Foucault had been. ..
  46. Edens J, Douglas K. Assessment of interpersonal aggression and violence: introduction to the special issue. Assessment. 2006;13:221-6 pubmed
    ..The authors conclude with a summary of the key findings of the articles that appear in this special issue. ..
  47. Donat S. Standards for surgical complication reporting in urologic oncology: time for a change. Urology. 2007;69:221-5 pubmed
    ..quot; The disparity in the quality of surgical complication reporting in urologic oncology makes it impossible to compare the morbidity of surgical techniques and outcomes. Standard guidelines need to be established. ..
  48. Figueira I, da Luz M, Braga R, Cabizuca M, Coutinho E, Mendlowicz M. The increasing internationalization of mainstream posttraumatic stress disorder research: a bibliometric study. J Trauma Stress. 2007;20:89-95 pubmed
    ..These findings suggest a growing international acceptance of this diagnostic category. However, the immaturity of PTSD research is demonstrated by the concentration of publications in a few countries. ..
  49. Kurtz J, Blais M. Introduction to the special issue on the personality assessment inventory. J Pers Assess. 2007;88:1-4 pubmed
    ..Finally, the authors offer several suggestions for future research with the PAI. ..
  50. Yue W, Wilson C, Boller F. Peer assessment of journal quality in clinical neurology. J Med Libr Assoc. 2007;95:70-6 pubmed
    ..Likewise, biomedical librarians may use these results for serials collection development. ..
  51. Stark M. A passion for nursing. In memoriam of Dr. Sharron Smith Humenick. J Obstet Gynecol Neonatal Nurs. 2006;35:681-3 pubmed
    ..Lessons from her life's work can inspire nurses in our specialty to be tireless and passionate advocates in practice, education, and public policy for supportive nursing care. Dr. Humenick died on September 9, 2006. ..
  52. Yang H, Pan B. Citation classics in Fertility and sterility, 1975-2004. Fertil Steril. 2006;86:795-7, 797.e1-6 pubmed
    ..Identification of the citation classic articles provides resourceful perspectives on the evolution of Fertility and Sterility and reproductive medicine. ..
  53. Wilson M, Itagaki M. Characteristics and trends of published emergency medicine research. Acad Emerg Med. 2007;14:635-40 pubmed
    ..The United States is the largest producer of EM research, only a small fraction of which is supported by the NIH. The majority of research published by emergency researchers is published in non-EM journals. ..