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Reference Material on CTSpedia

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
Data Quality of General Practice Electronic Health Records: The Impact of a Program of Assessments, Feedback, and Training	Porcheret, M., Hughes, R., Evans, D., Jordan, K., Whitehurst, T., Ogden, H., Croft, P.	J Am Med Inform Assoc	Medical_Records_Review		http://www.ncbi.nlm.nih.gov/pmc/articles/PMC305461/?tool=pubmed
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\x92 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 \x97the 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\x97where 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 Document a Data Collection	UC San Diego Supercomputer Center	Online	CR_Data Collection		http://www.caida.org/data/how-to/how-to_document_data.xml
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
ICES Report: Using Data from Electronic Medical Records: Theory versus Practice	Mitiku, TF, Tu, K	Healthcare Quality	Medical_Records_Review		http://www.longwoods.com/content/20088
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
Measuring diagnoses: ICD code accuracy	O'Malley, K. J., Cook, K. F., Price, M. D., Wildes, K. R., Hurdle, J. F., Ashton, C. M.	Health Serv Res	CR_Data Collection		http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1361216/?tool=pubmed
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?
Using your electronic medical record for research: a primer for avoiding pitfalls	Terry, A. L., Chevendra, V., Thind, A., Stewart, M., Marshall, J. N., Cejic, S.	Fam Pract	Medical_Records_Review	http://dx.doi.org/10.1093/fampra/cmp068
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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