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Title Author Journal Reference_Subject Link for Proxy Access Link for Open Access
A Framework for Capturing Clinical Data Sets from Computerized Sources McDonald, C. J., Overhage, J. M., Dexter, P., Takesue, B. Y., Dwyer, D. M. Ann Intern Med CR_Data Collection   http://www.annals.org/content/127/8_Part_2/675.long
A Methodology for Conducting Retrospective Chart Review Research in Child and Adolescent Psychiatry Gearing, R. E., Mian, I. A., Barber, J., Ickowicz, A. J Can Acad Child Adolesc Psychiatry Residency_Education   http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2277255/?tool=pubmed
A Practical Guide for Health Researchers WHO Report: WHO Residency_Education   http://www.emro.who.int/publications/Book_Details.asp?ID=187
A consortium-based research education program for residents Neale, A. V., Pieper, D., Hammel, E. Acad Med Residency_Education   http://journals.lww.com/academicmedicine/pages/articleviewer.aspx?year=2000&issue=03000&article=00025&type=abstract
A curriculum for producing resident researchers Crooks, K. A., Pato, M. T., Berger, R. C. Acad Med Residency_Education http://dx.doi.org/10.1097/00001888-199905000-00093  
A novel curriculum for teaching research methodology Fraker, L. D., Orsay, E. M., Sloan, E. P., Bunney, E. B., Holden, J. A., Hart, R. G. J Emerg Med Residency_Education http://dx.doi.org/10.1016/0736-4679(96)00090-X  
A review of five cardiology journals found that observer variability of measured variables was infrequently reported Gow, R. M., Barrowman, N. J., Lai, L., Moher, D. J Clin Epidemiol Medical_Records_Review, CR_Data Collection http://dx.doi.org/10.1016/j.jclinepi.2007.05.010  
A systematic review of resident research curricula Hebert, R. S., Levine, R. B., Smith, C. G., Wright, S. M. Acad Med Residency_Education http://dx.doi.org/10.1097/00001888-200301000-00012  
Adaptive Design Methods in Clinical Trials - A Review Chow, S.-C., Chang, M Orphanet Journal of Rare Diseases Adaptive_Design   http://www.ojrd.com/content/pdf/1750-1172-3-11.pdf
Adaptive designs for binary treatment responses in phase III clinical trials: controversies and progress Atanu Biswas Statistical Methods in Medical Research Biostat_Ethics    
Adaptive designs: Looking for a needle in the haystack - A new challenge in medical researc Bauer, P Statist. Med. Adaptive_Design http://onlinelibrary.wiley.com/doi/10.1002/sim.3090/pdf  
Advanced statistics: understanding medical record review (MRR) studies Worster, A., Haines, T. Acad Emerg Med Medical_Records_Review http://dx.doi.org/10.1111/j.1553-2712.2004.tb01433.x  
After Three Months I Cannot Reproduce My Own Book Yihui Xie R-bloggers Reproducible_Research   (http://www.r-bloggers.com/after-three-months-i-cannot-reproduce-my-own-book/)
An experimental design for the development of adaptive treatment strategies Murphy, S. A. Statist. Med. Adaptive_Design http://onlinelibrary.wiley.com/doi/10.1002/sim.2022/pdf  
An experimental design for the development of adaptive treatment strategies various Drug Inf J. Adaptive_Design http://onlinelibrary.wiley.com/doi/10.1002/sim.v25:19/issuetoc  
Are All Economic Hypotheses False? De Long, J, Lang, K Journal of Political Economy   http://www.jstor.org/stable/2138833  
Are large clinical trials in rapidly lethal diseases usually unethical? Horrrobin, DF Lancet Biostat_Ethics    
Bayesian adaptive non-inferiority with safety assessment: Retrospective case study to highlight potential benefits and limitations of the approach Spann, M; Lindborg, S; Seaman, J; Baker, R; Dunayevich, E; Breier, A Journal of Psychiatric Research Adaptive_Design http://10.1016/j.jpsychires.2008.07.009  
Being successful with family medicine residency research: lessons learned from others Carek, P. J. Ann Fam Med Residency_Education   http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1466612/?tool=pubmed
Believe it or not: how much can we rely on published data on potential drug targets? Prinz, F., Schlange, T. & Asadullah, K. Nature Rev. Drug Discov. Reproducible_Research http://dx.doi.org/10.1038/nrd3439-c1  
Chart documentation quality and its relationship to the validity of administrative data discharge records So, L., Beck, C. A., Brien, S., Kennedy, J., Feasby, T. E., Ghali, W. A., Hude, Q. Health Informatics J Medical_Records_Review http://dx.doi.org/10.1177/1460458210364784  
Chart review. A need for reappraisal Wu, L., Ashton, C. M. Eval Health Prof Medical_Records_Review http://dx.doi.org/10.1177/016327879702000203  
Choosing Your Workflow Applications Healy, K The Political Methodologist Reproducible_Research   Workflow paper
Source documents for paper
Clinical Trials--Are They Ethical? Passamani E. N Engl J Med Biostat_Ethics    
Clinical research during internal medicine residency: a practical guide Hamann, K. L., Fancher, T. L., Saint, S., Henderson, M. C. Am J Med Residency_Education http://dx.doi.org/10.1016/j.amjmed.2005.12.001  
Coding data from child health records: the relationship between interrater agreement and interpretive burden Hagelin, E.M. J Pediatr Nurs Medical_Records_Review http://dx.doi.org/10.1016/S0882-5963(99)80031-1  
Common Program Requirements for: Residency ACGME Report: ACGME Residency_Education   http://www.acgme.org/acWebsite/navPages/commonpr_documents/CompleteGuide_v2%20.pdf
Comparison of information content of structured and narrative text data sources on the example of medication intensification Turchin, A., Shubina, M., Breydo, E., Pendergrass, M. L., Einbinder, J. S. J Am Med Inform Assoc CR_Data Collection http://dx.doi.org/10.1197/jamia.M2777  
Conducting a successful residency research project Barletta, J. F. Am J Pharm Educ Residency_Education   http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2576431/?tool=pubmed
Contemporary Issues in Medicine: Basic Science and Clinical Research; Report IV of the Medical Schools Objective Project AAMC Report: AAMC Residency_Education   http://www.med.mun.ca/ugme/docs/msop4.pdf
Coordinating data monitoring committees and adaptive clinical trial designs Herson, J Drug Inf J. Adaptive_Design   http://www.diahome.org/productfiles/8357/diaj_23828.pdf
Data Application and Reproducibility   Science Reproducible_Research   http://www.sciencemag.org/content/334/6060.toc
Definition, structure, content, use and impacts of electronic health records: a review of the research literature Hayrinen, K., Saranto, K., Nykanen, P. Int J Med Inform Medical_Records_Review    
Development of a national course on research methodology for Canadian residents in obstetrics and gynecology Reid, R. L., Van Vugt, D. A., Hahn, P. M. Obstet Gynecol Residency_Education http://dx.doi.org/10.1016/S0029-7844(98)00367-6  
Do Pressures to Publish Increase Scientists’ Bias? An Empirical Support from US States Data Fanelli, D PLoS ONE Reproducible_Research   http://www.plosone.org/article/info:doi/10.1371/journal.pone.0010271
Drug development and clinical trials —the path to an approved cancer drug Rubin, E. H. & Gilliland, D. G. Nature Rev. Clin. Oncol. Reproducible_Research http://dx.doi.org/10.1038/nrclinonc.2012.22  
Enhanced Dynamic Documents for Reproducible Research Deborah Nolan, Roger D. Peng, Duncan Temple Lang   Reproducible_Research   https://www.ctspedia.org/wiki/pub/CTSpedia/ReproducibleResearchPapers/DynWord_1.pdf
Ensuring high accuracy of data abstracted from patient charts: the use of a standardized medical record as a training tool Pan, L., Fergusson, D., Schweitzer, I., Hebert, P. C. J Clin Epidemiol Medical_Records_Review http://dx.doi.org/10.1016/j.jclinepi.2005.02.004  
Ethical and Professional Expectations in Scientific Publication Peter B. Imrey IMS Bulletin Biostat_Ethics   http://bulletin.imstat.org/wp-content/uploads/Bulletin39_2.pdf
Ethics and Statistics in Randomized Clinical Trials Royall RM Stat Sci Biostat_Ethics    
Ethics and sample size. Bacchetti P, Wolf LE, Segal MR, McCulloch CE Am J Epidemiol Biostat_Ethics    
Evidence-based Data Analysis: Treading a New Path for Reproducible Research (Part 2) Roger Peng Simply Statistics Reproducible_Research   (http://simplystatistics.org/2013/08/28/evidence-based-data-analysis-treading-a-new-path-for-reproducible-research-part-2/)
Factors associated with citation of internal medicine residency programs for lack of scholarly activity Levine, R. B., Hebert, R. S., Wright, S. M Teach Learn Med Residency_Education http://dx.doi.org/10.1207/s15328015tlm1704_3  
First: The Earth Is Round (p <0.05) Cohen, J American Psychologist Online_Journal_Club    
From Single-SNP to Wide-Locus: Genome-Wide Association Studies Identifying Functionally Related Genes and Intragenic Regions in Small Sample Studies Wittkowski, KM, Sonakya, V, Song, T, Seybold, MP, Keddache, M, Dumer, M Pharmacogenomics Online_Journal_Club    
From adaptive design to modern protocol design for drug development: (Part I.) Editorial and summary of adaptive designs session at the Third FDA/DIA Statistics Forum Wang, S, Bretz, F Drug Inf J. Adaptive_Design   http://www.diahome.org/productfiles/8357/diaj_35919.pdf
From adaptive design to modern protocol design for drug development: (Part II.) Success probabilities and effect estimates for Phase 3 development programs Wang, S, Bretz, F Drug Inf J. Adaptive_Design   http://www.diahome.org/productfiles/8357/diaj_35919.pdf
Getting residents involved in research: a challenge in the era of managed care Collins, J., Meyer, R., Dawson, J. R. Acad Med Residency_Education    
Good Practices for Adaptive Clinical Trials in Pharmaceutical Product Development Brenda Gaydos , Eli Lilly , Keaven M. Anderson , Donald Berry , Nancy Burnham , Brenda Gaydos , Eli Lilly , KGaydos, B, Anderson, K, Berry, D, Burnham, N, Dudinak, J, Fardipour , P, Gallo , P, Givens, S, Lewis , R, Maca , J, Pinheiro , J, Pritchett , Y, Krams, M Drug Inf J. Adaptive_Design   http://www.diahome.org/productfiles/8357/diaj_31918.pdf
Guidelines were developed for data collection from medical records for use in retrospective analyses Jansen, A. C. van Aalst-Cohen, E. S. Hutten, B. A. Buller, H. R. Kastelein, J. J., Prins, M. H. J Clin Epidemiol Medical_Records_Review http://dx.doi.org/10.1016/j.jclinepi.2004.07.006  
Hellman S, Hellman DS.Problems of the Randomized Clinical Trial Hellman S, Hellman DS N Engl J Med Biostat_Ethics    
High drug attrition rates—where are we going wrong? Hutchinson, L. & Kirk, R. Nature Rev. Clin Oncol. Reproducible_Research http://dx.doi.org/10.1038/nrclinonc.2011.34  
How to develop and critique a research protocol Karlik, S. J. AJR Am J Roentgenol Residency_Education   http://www.ajronline.org/content/176/6/1375.long
Impact of a Scientific Presentation on Community Treatment Patterns for Primary Breast Cancer Giordano, S. H., Z. Duan, et al. Journal of the National Cancer Institute Biostat_Ethics    
Implementing Evidence-based Data Analysis: Treading a New Path for Reproducible Research (Part 3) Roger Peng Simply Statistics Reproducible_Research   (http://simplystatistics.org/2013/09/05/implementing-evidence-based-data-analysis-treading-a-new-path-for-reproducible-research-part-3/)
Integrating research training into residency: tools of human investigation Oxnard, G. R., Zinkus, T. M., Bazari, H., Wolf, M. Acad Med Residency_Education http://dx.doi.org/10.1097/ACM.0b013e3181b18861  
Magnitude of effects in clinical trials published in high-impact general medical journals Siontis, K. C., Evangelou, E., Ioannidis, J. P. Int J Epidemiol Content_of_Interest http://dx.doi.org/10.1093/ije/dyr095  
Medical record review conduction model for improving interrater reliability of abstracting medical-related information Engel, L., Henderson, C., Fergenbaum, J., Colantonio, A. Eval Health Prof Medical_Records_Review http://dx.doi.org/10.1177/0163278709338561  
Methodology to improve data quality from chart review in the managed care setting Cassidy, L. D., Marsh, G. M., Holleran, M. K., Ruhl, L. S. Am J Manag Care Medical_Records_Review    
Methods to achieve high interrater reliability in data collection from primary care medical records Liddy, C., Wiens, M., Hogg, W. Ann Fam Med Medical_Records_Review   http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3022047/?tool=pubmed
Mindless Statistics Gerd Gigerenzer The Journal of Socio-Economics Online_Journal_Club   Open Access PDF
Pharma Blasts EMA Draft Policy On Disclosing Clinical Trial Data, via Pharmalot Ed Silverman Pharmalot Reproducible_Research   Pharma Blasts EMA Draft Policy On Disclosing Clinical Trial Data, via Pharmalot:
Pragmatic strategies that enhance the reliability of data abstracted from medical records Eder, C., Fullerton, J., Benroth, R., Lindsay, S. P. Appl Nurs Res Medical_Records_Review http://dx.doi.org/10.1016/j.apnr.2004.04.005  
Principles for the ethical analysis of clinical and translational research Gelfond, JAL, Heitman, E, Pollock, BH, Klugman, CM Statistics in Medicine Online_Journal_Club    
Problems of stopping trials early. Guyatt GH, Briel M, Glasziou P, Bassler D, Montori VM BMK Biostat_Ethics    
Promoting Translational and Clinical Science: The Critical Role of Medical Schools and Teaching Hospitals AAMC Report: AAMC Residency_Education    
Quality control in multicentric clinical trials. An experience of the EORTC Gynecological Cancer Cooperative Group Favalli, G., Vermorken, J. B., Vantongelen, K., Renard, J., Van Oosterom, A. T., Pecorelli, S. Eur J Cancer CR_Data Collection    
Raise standards for preclinical cancer research Begley, CG, Ellis, L Nature Reproducible_Research http://dx.doi.org/10.1038/483531a  
Raising the bar for cancer therapy models Francia, G. & Kerbel, R. S. Nature Biotechnol Reproducible_Research http://dx.doi.org/10.1038/nbt0610-561  
Reference Guide on Epidemiology Green, MD, Freedman, DM, Gordis, L   CR_Education   http://www.fjc.gov/public/pdf.nsf/lookup/sciman06.pdf/$file/sciman06.pdf
Repeatability of published microarray gene expression analyses Ioannidis, J. P., Allison, D. B., Ball, C. A., Coulibaly, I., Cui, X., Culhane, A. C., Falchi, M., Furlanello, C.. Game, L., Jurman, G., Mangion, J., Mehta, T., Nitzberg, M., Page, G. P., Petretto, E., van Noort, V Nat Genet Reproducible_Research http://dx.doi.org/10.1038/ng.295  
Reproducible Research Baggerly, KA, Berry, DA Amstat News Reproducible_Research   http://magazine.amstat.org/blog/2011/01/01/scipolicyjan11/
Research strategies that result in optimal data collection from the patient medical record Gregory, K. E., Radovinsky, L. Appl Nurs Res Medical_Records_Review, CR_Data Collection   http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3030926/pdf/nihms194480.pdf
Resident research and scholarly activity in internal medicine residency training programs Levine, R. B., Hebert, R. S., Wright, S. M. J Gen Intern Med Residency_Education   http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1490049/?tool=pubmed
Resident research education in physical medicine and rehabilitation: a practical approach Boninger, M. L., Chan, L. Harvey, R.. Pine, Z. M., Helkowski, W., Garrison, C. J., Tran, T., Levin, H., Levy, C. E. Am J Phys Med Rehabil Residency_Education    
Resident research in internal medicine training programs Alguire, P. C., Anderson, W. A., Albrecht, R. R., Poland, G. A. Ann Int Med Residency_Education   http://www.annals.org/content/124/3/321.full.pdf+html
Reversals of established medical practices: evidence to abandon ship Prasad, V., Cifu, A., Ioannidis, J. P JAMA Reproducible_Research http://dx.doi.org/10.1001/jama.2011.1960  
Science and Its Skeptics Marcus, Gary The New Yorker Reproducible_Research   http://www.newyorker.com/online/blogs/elements/2013/11/science-and-its-skeptics.html
Second: P-Values and Confidence Intervals: Two Sides of the Same Unsatisfactory Coin Feinsten, AR Journal of Clinical Epidemiology Online_Journal_Club http://dx.doi.org/10.1016/S0895-4356(97)00295-3  
Simply Statistics Roger Peng Simply Statistics Reproducible_Research   http://simplystatistics.org/
https://groups.google.com/forum/#!forum/reproducible-research
Special Issue on Adaptive Design varioys Drug Inf J. Adaptive_Design http://onlinelibrary.wiley.com/doi/10.1002/sim.v25:19/issuetoc  
Statistical Analyses and Reproducible Research Gentleman, R, Lang, DT Bioconductor Project Working Papers Reproducible_Research   All Bioconductor Papers

Statistical Analysis and Reproducible Research

Statistics and ethics in medical research Misuse of statistics is unethical Altman D.G. British Medical Journal Biostat_Ethics    
Structured research training in residency training programs. The impact on the level of resident research activity Blake, D. J., Lezotte, D. C., Yablon, S., Rondinelli, R. D. Am J Phys Med Rehabil Residency_Education    
The Ottawa Statement on the Ethical Design and Conduct of Cluster Randomized Trials Weijer C, Grimshaw JM, Eccles MP, McRae AD, White A, et al PLoS? Med Biostat_Ethics    
The PRIME curriculum clinical research training during residency: response to Kohlwes et al Gangat, N. J Gen Intern Med Residency_Education   http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1831599/?tool=pubmed
The PRIME curriculum. Clinical research training during residency Kohlwes, R. J., Shunk, R. L., Avins, A., Garber, J., Bent, S., Shlipak, M. G. J Gen Intern Med Residency_Education   http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1484802/?tool=pubmed
The Truth Wears Off Lehrer, J The New Yorker Reproducible_Research   http://www.newyorker.com/reporting/2010/12/13/101213fa_fact_lehrer
The art and science of chart review Allison, J. J., Wall, T. C., Spettell, C. M., Calhoun, J., Fargason, C. A., Jr., Kobylinski, R. W., Farmer, R., Kiefe, C. Jt Comm J Qual Improv Medical_Records_Review   Abstract: http://www.ncbi.nlm.nih.gov/pubmed/10709146
The continuing unethical conduct of underpowered clinical trials Halpern SD, Karlawish JHT, Berlin JA Halpern SD, Karlawish JHT, Berlin JA: The continuing unethi JAMA-Journal of the American Medical Association Biostat_Ethics    
The research rotation: competency-based structured and novel approach to research training of internal medicine residents Kanna, B., Deng, C., Erickson, S. N., Valerio, J. A., Dimitrov, V., Soni, A. BMC Med Educ Residency_Education   http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1630691/?tool=pubmed
Third: P-Values: What They Are and What They Are Not Schervish, MJ The Americian Statistician Online_Journal_Club   http://links.jstor.org/sici?sici=0003-l305%28199608%2950%3A3%3C203%3APVWTAA%3E2.0
Training physician-scientists: a model for integrating research into psychiatric residency Back, S. E., Book, S. W., Santos, A. B., Brady, K. T. Acad Psychiatry Residency_Education   http://ap.psychiatryonline.org/data/Journals/AP/1830/jap00111000040.pdf
Treading a New Path for Reproducible Research: Part 1 Roger Peng Simply Statistics Reproducible_Research   (http://simplystatistics.org/2013/08/21/treading-a-new-path-for-reproducible-research-part-1/)
Unreliable research: Trouble at the lab   The Economist Reproducible_Research   http://www.economist.com/news/briefing/21588057-scientists-think-science-self-correcting-alarming-degree-it-not-trouble?
Why Most Published Research Findings Are False Ioannidis, J. P. PLoS Med Reproducible_Research   http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1182327/pdf/pmed.0020124.pdf
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Topic revision: r15 - 01 Apr 2013 - 15:15:29 - MaryBanach
 

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