Improving the reliability of peer-reviewed publications: We are all in it together

Biomolecular Detection and Quantification

Volumn 7, Issue , 2016, Pages A1-A5

  Bustin, Stephen A ^a,b   Nolan, Tania ^b,c  

^a ANGLIA RUSKIN UNIVERSITY   (United Kingdom)

^b The Gene Team Ltd   (United Kingdom)

^c UNIVERSITY OF MANCHESTER   (United Kingdom)

Author keywords

Biomedicine; Microarrays; Next generation sequencing; QPCR; Reproducibility; Research

Indexed keywords

EDITORIAL; INTERNAL CONSISTENCY; PEER REVIEW; PRIORITY JOURNAL; PUBLICATION; RELIABILITY; REPRODUCIBILITY; SCIENTIFIC LITERATURE;

EID: 84960802125     PISSN: None     EISSN: 22147535     Source Type: Journal    
DOI: 10.1016/j.bdq.2015.11.002     Document Type: Editorial

References (55)

1. Mobley A., Linder S.K., Braeuer R., Ellis L.M., Zwelling L. A survey on data reproducibility in cancer research provides insights into our limited ability to translate findings from the laboratory to the clinic. PLoS One 2013, 8:e63221.
2. Begley C.G., Ellis L.M. Drug development: raise standards for preclinical cancer research. Nature 2012, 483:531-533.
3. Prinz F., Schlange T., Asadullah K. Believe it or not: how much can we rely on published data on potential drug targets?. Nat. Rev. Drug Discov. 2011, 10:712.
4. Chalmers I., Bracken M.B., Djulbegovic B., et al. How to increase value and reduce waste when research priorities are set. Lancet 2014, 383:156-165.
5. Gunn I.P. Evidence-based practice, research, peer review, and publication. CRNA 1998, 9:177-182.
6. Bustin S.A. The reproducibility of biomedical research: sleepers awake!. Biomol. Detect. Quantif. 2014, 2:35-42.
7. Liumbruno G.M., Velati C., Pasqualetti P., Franchini M. How to write a scientific manuscript for publication. Blood Transfus. 2013, 11:217-226.
8. Kallet R.H. How to write the methods section of a research paper. Respir. Care 2004, 49:1229-1232.
9. Brazma A., Hingamp P., Quackenbush J., et al. Minimum information about a microarray experiment (MIAME)-toward standards for microarray data. Nat. Genet. 2001, 29:365-371.
10. Bustin S.A. Why there is no link between measles virus and autism. Recent Advances in Autism Spectrum Disorders 2013, vol. I. Intech-Open Access Company, pp. 81-98.
11. Bustin S.A. RT-qPCR and molecular diagnostics: no evidence for measles virus in the GI tract of autistic children. Eur. Pharm. Rev. Dig. 2008, 1:11-16.
12. Fang F.C., Casadevall A. Retracted science and the retraction index. Infect. Immun. 2011, 79:3855-3859.
13. Fang F.C., Steen R.G., Casadevall A. Misconduct accounts for the majority of retracted scientific publications. Proc. Natl. Acad. Sci. U. S. A. 2012, 109:17028-17033.
14. Bustin S.A., Benes V., Garson J.A., et al. The MIQE guidelines: minimum information for publication of quantitative real-time PCR experiments. Clin. Chem. 2009, 55:611-622.
15. Bustin S.A., Benes V., Garson J., et al. The need for transparency and good practices in the qPCR literature. Nat. Methods 2013, 10:1063-1067.
16. Sykes P.J., Neoh S.H., Brisco M.J., Hughes E., Condon J., Morley A.A. Quantitation of targets for PCR by use of limiting dilution. Biotechniques 1992, 13:444-449.
17. Huggett J.F., Foy C.A., Benes V., et al. The digital MIQE guidelines: minimum information for publication of quantitative digital PCR experiments. Clin. Chem. 2013, 59:892-902.
18. Sultan M., Amstislavskiy V., Risch T., et al. Influence of RNA extraction methods and library selection schemes on RNA-seq data. BMC Genom. 2014, 15:675.
19. Wu P.Y., Phan J.H., Wang M.D. Assessing the impact of human genome annotation choice on RNA-seq expression estimates. BMC Bioinform. 2013, 14(Suppl. 11):S8.
20. Seyednasrollah F., Laiho A., Elo L.L. Comparison of software packages for detecting differential expression in RNA-seq studies. Brief Bioinform. 2015, 16:59-70.
21. Li P., Piao Y., Shon H.S., Ryu K.H. Comparing the normalization methods for the differential analysis of illumina high-throughput RNA-Seq data. BMC Bioinform. 2015, 16:347.
22. t Hoen P.A., Friedländer M.R., Almlöf J., et al. Reproducibility of high-throughput mRNA and small RNA sequencing across laboratories. Nat. Biotechnol. 2013, 31:1015-1022.
23. Castel S.E., Levy-Moonshine A., Mohammadi P., Banks E., Lappalainen T. Tools and best practices for data processing in allelic expression analysis. Genome Biol. 2015, 16:195.
24. Landt S.G., Marinov G.K., Kundaje A., et al. ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia. Genome Res. 2012, 22:1813-1831.
25. Bustin S. Transparency of reporting in molecular diagnostics. Int. J. Mol. Sci. 2013, 14:15878-15884.
26. Anon Announcement reducing our irreproducibility. Nature 2013, 496:398.
27. Anon Enhancing reproducibility. Nat. Methods 2013, 10:367.
28. Anon Raising reporting standards. Nat. Cell Biol. 2013, 15:443.
29. Anon Raising standards. Nat. Biotechnol. 2013, 31:366.
30. Anon Raising standards. Nat. Med. 2013, 19:508.
31. Anon Raising standards. Nat. Struct. Mol. Biol. 2013, 20:533.
32. Anon Raising standards. Nat. Genet. 2013, 45:467.
33. Anon Raising standards. Nat. Neurosci. 2013, 16:517.
34. Anon Raising standards. Nat. Immunol. 2013, 14:415.
35. Anon Journals unite for reproducibility. Nature 2014, 515:7.
36. Silginer M., Burghardt I., Gramatzki D., et al. The aryl hydrocarbon receptor links integrin signaling to the TGF-β pathway. Oncogene 2015, (in press).
37. Jing H., Liao L., An Y., et al. Suppression of EZH2 prevents the shift of osteoporotic MSC fate to adipocyte and enhances bone formation during osteoporosis. Mol. Ther. 2015.
38. Kim S.K., Joe Y., Chen Y., et al. Carbon monoxide decreases interleukin-1β levels in the lung through the induction of pyrin. Cell. Mol. Immunol. 2015.
39. Grünewald T.G., Bernard V., Gilardi-Hebenstreit P., et al. Chimeric EWSR1-FLI1 regulates the ewing sarcoma susceptibility gene EGR2 via a GGAA microsatellite. Nat. Genet. 2015, 47:1073-1078.
40. Xu C., Liberatore K.L., MacAlister C.A., et al. A cascade of arabinosyltransferases controls shoot meristem size in tomato. Nat. Genet. 2015, 47:784-792.
41. DeNicola G.M., Chen P.H., Mullarky E., et al. NRF2 regulates serine biosynthesis in non-small cell lung cancer. Nat. Genet. 2015.
42. Dijkstra J.R., van Kempen L.C., Nagtegaal I.D., Bustin S.A. Critical appraisal of quantitative PCR results in colorectal cancer research: can we rely on published qPCR results?. Mol. Oncol. 2014, 8:813-818.
43. Tricarico C., Pinzani P., Bianchi S., et al. Quantitative real-time reverse transcription polymerase chain reaction: normalization to rRNA or single housekeeping genes is inappropriate for human tissue biopsies. Anal. Biochem. 2002, 309:293-300.
44. Vandesompele J., De Paepe A., Speleman F. Elimination of primer-dimer artifacts and genomic coamplification using a two-step SYBR green I real-time RT-PCR. Anal. Biochem. 2002, 303:95-98.
45. Whittle M.C., Izeradjene K., Rani P.G., et al. RUNX3 controls a metastatic switch in pancreatic ductal adenocarcinoma. Cell 2015, 161:1345-1360.
46. Park H.W., Kim Y.C., Yu B., et al. Alternative wnt signaling activates YAP/TAZ. Cell 2015, 162:780-794.
47. Saito Y., Chapple R.H., Lin A., Kitano A., Nakada D. AMPK protects leukemia-initiating cells in myeloid leukemias from metabolic stress in the bone marrow. Cell Stem Cell 2015, (in press).
48. Kubaczka C., Senner C.E., Cierlitza M., et al. Direct induction of trophoblast stem cells from murine fibroblasts. Cell Stem Cell 2015, (in press).
49. Matkar S., Sharma P., Gao S., et al. An epigenetic pathway regulates sensitivity of breast cancer cells to HER2 inhibition via FOXO/c-myc axis. Cancer Cell 2015, 28:472-485.
50. Stromnes I.M., Schmitt T.M., Hulbert A., et al. T cells engineered against a native antigen can surmount immunologic and physical barriers to treat pancreatic ductal adenocarcinoma. Cancer Cell 2015, (in press).
51. Pfister S.X., Markkanen E., Jiang Y., Sarkar S., et al. Inhibiting WEE1 selectively kills histone H3K36me 3-deficient cancers by dNTP starvation. Cancer Cell 2015, (in press).
52. Vincent E.E., Sergushichev A., Griss T., et al. Mitochondrial phosphoenolpyruvate carboxykinase regulates metabolic adaptation and enables glucose-independent tumor growth. Mol. Cell 2015, 60:195-207.
53. Elia A.E., Wang D.C., Willis N.A., et al. RFWD3-dependent ubiquitination of RPA regulates repair at stalled replication forks. Mol. Cell 2015, 60:280-293.
54. de Wit E., Vos E.S., Holwerda S.J., et al. CTCF binding polarity determines chromatin looping. Mol. Cell 2015.
55. Begley C.G., Ioannidis J.P. Reproducibility in science: improving the standard for basic and preclinical research. Circ. Res. 2015, 116:116-126.