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Ten simple rules for writing and sharing computational analyses in Jupyter Notebooks.

Rule A, Birmingham A, Zuniga C, Altintas I, Huang SC, Knight R, Moshiri N, Nguyen MH, Rosenthal SB, Pérez F, Rose PW.

PLoS Comput Biol. 2019 Jul 25;15(7):e1007007. doi: 10.1371/journal.pcbi.1007007. eCollection 2019 Jul. No abstract available.


Analyzing the symmetrical arrangement of structural repeats in proteins with CE-Symm.

Bliven SE, Lafita A, Rose PW, Capitani G, Prlić A, Bourne PE.

PLoS Comput Biol. 2019 Apr 22;15(4):e1006842. doi: 10.1371/journal.pcbi.1006842. eCollection 2019 Apr.


BioJava 5: A community driven open-source bioinformatics library.

Lafita A, Bliven S, Prlić A, Guzenko D, Rose PW, Bradley A, Pavan P, Myers-Turnbull D, Valasatava Y, Heuer M, Larson M, Burley SK, Duarte JM.

PLoS Comput Biol. 2019 Feb 8;15(2):e1006791. doi: 10.1371/journal.pcbi.1006791. eCollection 2019 Feb.


Investigation of protein quaternary structure via stoichiometry and symmetry information.

Korkmaz S, Duarte JM, Prlić A, Goksuluk D, Zararsiz G, Saracbasi O, Burley SK, Rose PW.

PLoS One. 2018 Jun 4;13(6):e0197176. doi: 10.1371/journal.pone.0197176. eCollection 2018. Erratum in: PLoS One. 2018 Jul 27;13(7):e0201403.


NGL viewer: web-based molecular graphics for large complexes.

Rose AS, Bradley AR, Valasatava Y, Duarte JM, Prlic A, Rose PW.

Bioinformatics. 2018 Nov 1;34(21):3755-3758. doi: 10.1093/bioinformatics/bty419.


GPs' understanding and practice of safety netting for potential cancer presentations: a qualitative study in primary care.

Evans J, Ziebland S, MacArtney JI, Bankhead CR, Rose PW, Nicholson BD.

Br J Gen Pract. 2018 Jul;68(672):e505-e511. doi: 10.3399/bjgp18X696233. Epub 2018 May 8.


Responsibility for follow-up during the diagnostic process in primary care: a secondary analysis of International Cancer Benchmarking Partnership data.

Nicholson BD, Goyder CR, Bankhead CR, Toftegaard BS, Rose PW, Thulesius H, Vedsted P, Perera R.

Br J Gen Pract. 2018 May;68(670):e323-e332. doi: 10.3399/bjgp18X695813. Epub 2018 Apr 23.


Recon3D enables a three-dimensional view of gene variation in human metabolism.

Brunk E, Sahoo S, Zielinski DC, Altunkaya A, Dräger A, Mih N, Gatto F, Nilsson A, Preciat Gonzalez GA, Aurich MK, Prlić A, Sastry A, Danielsdottir AD, Heinken A, Noronha A, Rose PW, Burley SK, Fleming RMT, Nielsen J, Thiele I, Palsson BO.

Nat Biotechnol. 2018 Mar;36(3):272-281. doi: 10.1038/nbt.4072. Epub 2018 Feb 19.


Supporting prostate cancer survivors in primary care: Findings from a pilot trial of a nurse-led psycho-educational intervention (PROSPECTIV).

Watson EK, Shinkins B, Matheson L, Burns RM, Frith E, Neal D, Hamdy F, Walter FM, Weller D, Wilkinson C, Faithfull S, Sooriakumaran P, Kastner C, Campbell C, Neal RD, Butcher H, Matthews M, Perera R, Wolstenholme J, Rose PW.

Eur J Oncol Nurs. 2018 Feb;32:73-81. doi: 10.1016/j.ejon.2017.12.002. Epub 2017 Dec 29.


Mapping genetic variations to three-dimensional protein structures to enhance variant interpretation: a proposed framework.

Glusman G, Rose PW, Prlić A, Dougherty J, Duarte JM, Hoffman AS, Barton GJ, Bendixen E, Bergquist T, Bock C, Brunk E, Buljan M, Burley SK, Cai B, Carter H, Gao J, Godzik A, Heuer M, Hicks M, Hrabe T, Karchin R, Leman JK, Lane L, Masica DL, Mooney SD, Moult J, Omenn GS, Pearl F, Pejaver V, Reynolds SM, Rokem A, Schwede T, Song S, Tilgner H, Valasatava Y, Zhang Y, Deutsch EW.

Genome Med. 2017 Dec 18;9(1):113. doi: 10.1186/s13073-017-0509-y. Review.


MMTF-An efficient file format for the transmission, visualization, and analysis of macromolecular structures.

Bradley AR, Rose AS, Pavelka A, Valasatava Y, Duarte JM, Prlić A, Rose PW.

PLoS Comput Biol. 2017 Jun 2;13(6):e1005575. doi: 10.1371/journal.pcbi.1005575. eCollection 2017 Jun.


Towards an efficient compression of 3D coordinates of macromolecular structures.

Valasatava Y, Bradley AR, Rose AS, Duarte JM, Prlić A, Rose PW.

PLoS One. 2017 Mar 31;12(3):e0174846. doi: 10.1371/journal.pone.0174846. eCollection 2017.


BioJava-ModFinder: identification of protein modifications in 3D structures from the Protein Data Bank.

Gao J, Prlic A, Bi C, Bluhm WF, Dimitropoulos D, Xu D, Bourne PE, Rose PW.

Bioinformatics. 2017 Jul 1;33(13):2047-2049. doi: 10.1093/bioinformatics/btx101.


Impact of genetic variation on three dimensional structure and function of proteins.

Bhattacharya R, Rose PW, Burley SK, Prlić A.

PLoS One. 2017 Mar 15;12(3):e0171355. doi: 10.1371/journal.pone.0171355. eCollection 2017.


The need for scientific software engineering in the pharmaceutical industry.

Luty B, Rose PW.

J Comput Aided Mol Des. 2017 Mar;31(3):301-304. doi: 10.1007/s10822-016-9997-x. Epub 2016 Dec 19.


The RCSB protein data bank: integrative view of protein, gene and 3D structural information.

Rose PW, Prlić A, Altunkaya A, Bi C, Bradley AR, Christie CH, Costanzo LD, Duarte JM, Dutta S, Feng Z, Green RK, Goodsell DS, Hudson B, Kalro T, Lowe R, Peisach E, Randle C, Rose AS, Shao C, Tao YP, Valasatava Y, Voigt M, Westbrook JD, Woo J, Yang H, Young JY, Zardecki C, Berman HM, Burley SK.

Nucleic Acids Res. 2017 Jan 4;45(D1):D271-D281. doi: 10.1093/nar/gkw1000. Epub 2016 Oct 27.


Integrating genomic information with protein sequence and 3D atomic level structure at the RCSB protein data bank.

Prlic A, Kalro T, Bhattacharya R, Christie C, Burley SK, Rose PW.

Bioinformatics. 2016 Dec 15;32(24):3833-3835. doi: 10.1093/bioinformatics/btw547. Epub 2016 Aug 22.


Variation in Direct Access to Tests to Investigate Cancer: A Survey of English General Practitioners.

Nicholson BD, Oke JL, Rose PW, Mant D.

PLoS One. 2016 Jul 22;11(7):e0159725. doi: 10.1371/journal.pone.0159725. eCollection 2016.


Symptoms of adult chronic and acute leukaemia before diagnosis: large primary care case-control studies using electronic records.

Shephard EA, Neal RD, Rose PW, Walter FM, Hamilton W.

Br J Gen Pract. 2016 Mar;66(644):e182-8. doi: 10.3399/bjgp16X683989.


Stabilizing Pentacene By Cyclopentannulation.

Bheemireddy SR, Ubaldo PC, Rose PW, Finke AD, Zhuang J, Wang L, Plunkett KN.

Angew Chem Int Ed Engl. 2015 Dec 21;54(52):15762-6. doi: 10.1002/anie.201508650. Epub 2015 Nov 19.


International variation in adherence to referral guidelines for suspected cancer: a secondary analysis of survey data.

Nicholson BD, Mant D, Neal RD, Hart N, Hamilton W, Shinkins B, Rubin G, Rose PW.

Br J Gen Pract. 2016 Feb;66(643):e106-13. doi: 10.3399/bjgp16X683449. Epub 2016 Jan 6.


Diagnostic value of symptoms of oesophagogastric cancers in primary care: a systematic review and meta-analysis.

Astin MP, Martins T, Welton N, Neal RD, Rose PW, Hamilton W.

Br J Gen Pract. 2015 Oct;65(639):e677-91. doi: 10.3399/bjgp15X686941. Review. Erratum in: Br J Gen Pract. 2015 Dec;65(641):630.


Citing a Data Repository: A Case Study of the Protein Data Bank.

Huang YH, Rose PW, Hsu CN.

PLoS One. 2015 Aug 28;10(8):e0136631. doi: 10.1371/journal.pone.0136631. eCollection 2015.


Explaining variation in cancer survival between 11 jurisdictions in the International Cancer Benchmarking Partnership: a primary care vignette survey.

Rose PW, Rubin G, Perera-Salazar R, Almberg SS, Barisic A, Dawes M, Grunfeld E, Hart N, Neal RD, Pirotta M, Sisler J, Konrad G, Toftegaard BS, Thulesius H, Vedsted P, Young J, Hamilton W; ICBP Module 3 Working Group*; ICBP Module 3 Working Group.

BMJ Open. 2015 May 27;5(5):e007212. doi: 10.1136/bmjopen-2014-007212.


Quantifying the risk of Hodgkin lymphoma in symptomatic primary care patients aged ≥40 years: a case-control study using electronic records.

Shephard EA, Neal RD, Rose PW, Walter FM, Hamilton WT.

Br J Gen Pract. 2015 May;65(634):e289-94. doi: 10.3399/bjgp15X684805.


Quantifying the risk of non-Hodgkin lymphoma in symptomatic primary care patients aged ≥40 years: a large case-control study using electronic records.

Shephard EA, Neal RD, Rose PW, Walter FM, Hamilton WT.

Br J Gen Pract. 2015 May;65(634):e281-8. doi: 10.3399/bjgp15X684793.


The RCSB Protein Data Bank: views of structural biology for basic and applied research and education.

Rose PW, Prlić A, Bi C, Bluhm WF, Christie CH, Dutta S, Green RK, Goodsell DS, Westbrook JD, Woo J, Young J, Zardecki C, Berman HM, Bourne PE, Burley SK.

Nucleic Acids Res. 2015 Jan;43(Database issue):D345-56. doi: 10.1093/nar/gku1214. Epub 2014 Nov 26.


RCSB PDB Mobile: iOS and Android mobile apps to provide data access and visualization to the RCSB Protein Data Bank.

Quinn GB, Bi C, Christie CH, Pang K, Prlić A, Nakane T, Zardecki C, Voigt M, Berman HM, Bourne PE, Rose PW.

Bioinformatics. 2015 Jan 1;31(1):126-7. doi: 10.1093/bioinformatics/btu596. Epub 2014 Sep 2.


Development of a survey instrument to investigate the primary care factors related to differences in cancer diagnosis between international jurisdictions.

Rose PW, Hamilton W, Aldersey K, Barisic A, Dawes M, Foot C, Grunfeld E, Hart N, Neal RD, Pirotta M, Sisler J, Thulesius H, Vedsted P, Young J, Rubin G; ICBP Module 3 Working Group*.

BMC Fam Pract. 2014 Jun 17;15:122. doi: 10.1186/1471-2296-15-122.


Systematic detection of internal symmetry in proteins using CE-Symm.

Myers-Turnbull D, Bliven SE, Rose PW, Aziz ZK, Youkharibache P, Bourne PE, Prlić A.

J Mol Biol. 2014 May 29;426(11):2255-68. doi: 10.1016/j.jmb.2014.03.010. Epub 2014 Mar 26.


The effects of pelvic radiotherapy on cancer survivors: symptom profile, psychological morbidity and quality of life.

Adams E, Boulton MG, Horne A, Rose PW, Durrant L, Collingwood M, Oskrochi R, Davidson SE, Watson EK.

Clin Oncol (R Coll Radiol). 2014 Jan;26(1):10-7. doi: 10.1016/j.clon.2013.08.003. Epub 2013 Aug 29.


Educational interventions for primary healthcare professionals to promote the early diagnosis of cancer: a systematic review.

Schichtel M, Rose PW, Sellers C.

Educ Prim Care. 2013 Jul;24(4):274-90. Review.


Trendspotting in the Protein Data Bank.

Berman HM, Coimbatore Narayanan B, Di Costanzo L, Dutta S, Ghosh S, Hudson BP, Lawson CL, Peisach E, Prlić A, Rose PW, Shao C, Yang H, Young J, Zardecki C.

FEBS Lett. 2013 Apr 17;587(8):1036-45. doi: 10.1016/j.febslet.2012.12.029. Epub 2013 Jan 18. Review.


The risk of oesophago-gastric cancer in symptomatic patients in primary care: a large case-control study using electronic records.

Stapley S, Peters TJ, Neal RD, Rose PW, Walter FM, Hamilton W.

Br J Cancer. 2013 Jan 15;108(1):25-31. doi: 10.1038/bjc.2012.551. Epub 2012 Dec 20.


The RCSB Protein Data Bank: new resources for research and education.

Rose PW, Bi C, Bluhm WF, Christie CH, Dimitropoulos D, Dutta S, Green RK, Goodsell DS, Prlic A, Quesada M, Quinn GB, Ramos AG, Westbrook JD, Young J, Zardecki C, Berman HM, Bourne PE.

Nucleic Acids Res. 2013 Jan;41(Database issue):D475-82. doi: 10.1093/nar/gks1200. Epub 2012 Nov 27.


BioJava: an open-source framework for bioinformatics in 2012.

Prlić A, Yates A, Bliven SE, Rose PW, Jacobsen J, Troshin PV, Chapman M, Gao J, Koh CH, Foisy S, Holland R, Rimsa G, Heuer ML, Brandstätter-Müller H, Bourne PE, Willis S.

Bioinformatics. 2012 Oct 15;28(20):2693-5. doi: 10.1093/bioinformatics/bts494. Epub 2012 Aug 9.


Cancer outcomes and all-cause mortality in adults allocated to metformin: systematic review and collaborative meta-analysis of randomised clinical trials.

Stevens RJ, Ali R, Bankhead CR, Bethel MA, Cairns BJ, Camisasca RP, Crowe FL, Farmer AJ, Harrison S, Hirst JA, Home P, Kahn SE, McLellan JH, Perera R, Plüddemann A, Ramachandran A, Roberts NW, Rose PW, Schweizer A, Viberti G, Holman RR.

Diabetologia. 2012 Oct;55(10):2593-2603. doi: 10.1007/s00125-012-2653-7. Epub 2012 Aug 10. Review. Erratum in: Diabetologia. 2012 Dec;55(12):3399-400.


The risk of pancreatic cancer in symptomatic patients in primary care: a large case-control study using electronic records.

Stapley S, Peters TJ, Neal RD, Rose PW, Walter FM, Hamilton W.

Br J Cancer. 2012 Jun 5;106(12):1940-4. doi: 10.1038/bjc.2012.190. Epub 2012 May 22.


Implementing evidence in practice: do action lists work?

Haley M, Lettis A, Rose PM, Jenkins LS, Glasziou P, Rose PW.

Educ Prim Care. 2012 Mar;23(2):107-14.


A qualitative study exploring the experience of the partners of cancer survivors and their views on the role of primary care.

Adams E, Boulton M, Rose PW, Lund S, Richardson A, Wilson S, Watson EK.

Support Care Cancer. 2012 Nov;20(11):2785-94. doi: 10.1007/s00520-012-1400-4. Epub 2012 Feb 22.


Personalised cancer follow-up: risk stratification, needs assessment or both?

Watson EK, Rose PW, Neal RD, Hulbert-Williams N, Donnelly P, Hubbard G, Elliott J, Campbell C, Weller D, Wilkinson C.

Br J Cancer. 2012 Jan 3;106(1):1-5. doi: 10.1038/bjc.2011.535. No abstract available.


Cancer survivors' experiences of discharge from hospital follow-up.

Harrison SE, Watson EK, Ward AM, Khan NF, Turner D, Adams E, Forman D, Roche MF, Rose PW.

Eur J Cancer Care (Engl). 2012 May;21(3):390-7. doi: 10.1111/j.1365-2354.2011.01312.x. Epub 2011 Nov 17.


A qualitative study of unmet needs and interactions with primary care among cancer survivors.

Khan NF, Evans J, Rose PW.

Br J Cancer. 2011 Nov 8;105 Suppl 1:S46-51. doi: 10.1038/bjc.2011.422.


Long-term health outcomes in a British cohort of breast, colorectal and prostate cancer survivors: a database study.

Khan NF, Mant D, Carpenter L, Forman D, Rose PW.

Br J Cancer. 2011 Nov 8;105 Suppl 1:S29-37. doi: 10.1038/bjc.2011.420.


Cancer survivorship: the impact on primary care.

Watson EK, Rose PW, Loftus R, Devane C.

Br J Gen Pract. 2011 Nov;61(592):e763-5. doi: 10.3399/bjgp11X606771. No abstract available.


Defining cancer survivorship: a more transparent approach is needed.

Khan NF, Rose PW, Evans J.

J Cancer Surviv. 2012 Mar;6(1):33-6. doi: 10.1007/s11764-011-0194-6. Epub 2011 Sep 9.


Interpretation and acceptance of the term 'cancer survivor': a United Kingdom-based qualitative study.

Khan NF, Harrison S, Rose PW, Ward A, Evans J.

Eur J Cancer Care (Engl). 2012 Mar;21(2):177-86. doi: 10.1111/j.1365-2354.2011.01277.x. Epub 2011 Aug 18.


Aspirin for prevention of cancer and cardiovascular disease.

Rose PW, Watson EK, Jenkins LS.

Br J Gen Pract. 2011 Jun;61(587):412-5. doi: 10.3399/bjgp11X578133. No abstract available.


Views of health professionals on the role of primary care in the follow-up of men with prostate cancer.

Watson EK, O'Brien R, Campbell C, Weller D, Neal RD, Wilkinson C, Rose PW; Prostate Cancer Follow-Up Study Group.

Fam Pract. 2011 Dec;28(6):647-54. doi: 10.1093/fampra/cmr034. Epub 2011 Jun 21.


Primary health and supportive care needs of long-term cancer survivors: a questionnaire survey.

Harrison SE, Watson EK, Ward AM, Khan NF, Turner D, Adams E, Forman D, Roche MF, Rose PW.

J Clin Oncol. 2011 May 20;29(15):2091-8. doi: 10.1200/JCO.2010.32.5167. Epub 2011 Apr 25.


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