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Items: 19


A large dataset of protein dynamics in the mammalian heart proteome.

Lau E, Cao Q, Ng DC, Bleakley BJ, Dincer TU, Bot BM, Wang D, Liem DA, Lam MP, Ge J, Ping P.

Sci Data. 2016 Mar 15;3:160015. doi: 10.1038/sdata.2016.15.


The mPower study, Parkinson disease mobile data collected using ResearchKit.

Bot BM, Suver C, Neto EC, Kellen M, Klein A, Bare C, Doerr M, Pratap A, Wilbanks J, Dorsey ER, Friend SH, Trister AD.

Sci Data. 2016 Mar 3;3:160011. doi: 10.1038/sdata.2016.11.



Chaibub Neto E, Bot BM, Perumal T, Omberg L, Guinney J, Kellen M, Klein A, Friend SH, Trister AD.

Pac Symp Biocomput. 2016;21:273-84.


The consensus molecular subtypes of colorectal cancer.

Guinney J, Dienstmann R, Wang X, de Reyniès A, Schlicker A, Soneson C, Marisa L, Roepman P, Nyamundanda G, Angelino P, Bot BM, Morris JS, Simon IM, Gerster S, Fessler E, De Sousa E Melo F, Missiaglia E, Ramay H, Barras D, Homicsko K, Maru D, Manyam GC, Broom B, Boige V, Perez-Villamil B, Laderas T, Salazar R, Gray JW, Hanahan D, Tabernero J, Bernards R, Friend SH, Laurent-Puig P, Medema JP, Sadanandam A, Wessels L, Delorenzi M, Kopetz S, Vermeulen L, Tejpar S.

Nat Med. 2015 Nov;21(11):1350-6. doi: 10.1038/nm.3967. Epub 2015 Oct 12.


Summary of the DREAM8 Parameter Estimation Challenge: Toward Parameter Identification for Whole-Cell Models.

Karr JR, Williams AH, Zucker JD, Raue A, Steiert B, Timmer J, Kreutz C; DREAM8 Parameter Estimation Challenge Consortium, Wilkinson S, Allgood BA, Bot BM, Hoff BR, Kellen MR, Covert MW, Stolovitzky GA, Meyer P.

PLoS Comput Biol. 2015 May 28;11(5):e1004096. doi: 10.1371/journal.pcbi.1004096. eCollection 2015 May.


Molecular markers identify subtypes of stage III colon cancer associated with patient outcomes.

Sinicrope FA, Shi Q, Smyrk TC, Thibodeau SN, Dienstmann R, Guinney J, Bot BM, Tejpar S, Delorenzi M, Goldberg RM, Mahoney M, Sargent DJ, Alberts SR.

Gastroenterology. 2015 Jan;148(1):88-99. doi: 10.1053/j.gastro.2014.09.041. Epub 2014 Oct 8.


ANKS1B is a smoking-related molecular alteration in clear cell renal cell carcinoma.

Eckel-Passow JE, Serie DJ, Bot BM, Joseph RW, Cheville JC, Parker AS.

BMC Urol. 2014 Jan 31;14:14. doi: 10.1186/1471-2490-14-14.


Somatic expression of ENRAGE is associated with obesity status among patients with clear cell renal cell carcinoma.

Eckel-Passow JE, Serie DJ, Bot BM, Joseph RW, Hart SN, Cheville JC, Parker AS.

Carcinogenesis. 2014 Apr;35(4):822-7. doi: 10.1093/carcin/bgt485. Epub 2013 Dec 28.


clearScience: Infrastructure for Communicating Data-Intensive Science.

Bot BM, Burdick D, Kellen M, Huang ES.

AMIA Jt Summits Transl Sci Proc. 2013 Mar 18;2013:27. eCollection 2013.


Comparison of outcomes after fluorouracil-based adjuvant therapy for stages II and III colon cancer between 1978 to 1995 and 1996 to 2007: evidence of stage migration from the ACCENT database.

Shi Q, Andre T, Grothey A, Yothers G, Hamilton SR, Bot BM, Haller DG, Van Cutsem E, Twelves C, Benedetti JK, O'Connell MJ, Sargent DJ.

J Clin Oncol. 2013 Oct 10;31(29):3656-63. doi: 10.1200/JCO.2013.49.4344. Epub 2013 Aug 26.


Impact of bioinformatic procedures in the development and translation of high-throughput molecular classifiers in oncology.

Ferté C, Trister AD, Huang E, Bot BM, Guinney J, Commo F, Sieberts S, André F, Besse B, Soria JC, Friend SH.

Clin Cancer Res. 2013 Aug 15;19(16):4315-25. doi: 10.1158/1078-0432.CCR-12-3937. Epub 2013 Jun 18. Review.


Genome-wide characterization of transcriptional patterns in high and low antibody responders to rubella vaccination.

Haralambieva IH, Oberg AL, Ovsyannikova IG, Kennedy RB, Grill DE, Middha S, Bot BM, Wang VW, Smith DI, Jacobson RM, Poland GA.

PLoS One. 2013 May 1;8(5):e62149. doi: 10.1371/journal.pone.0062149. Print 2013.


Technical and biological variance structure in mRNA-Seq data: life in the real world.

Oberg AL, Bot BM, Grill DE, Poland GA, Therneau TM.

BMC Genomics. 2012 Jul 7;13:304. doi: 10.1186/1471-2164-13-304.


Expression of endothelin 2 and localized clear cell renal cell carcinoma.

Bot BM, Eckel-Passow JE, LeGrand SN, Hilton T, Cheville JC, Igel T, Parker AS.

Hum Pathol. 2012 Jun;43(6):843-9. doi: 10.1016/j.humpath.2011.07.011. Epub 2011 Nov 1.


Impact of young age on treatment efficacy and safety in advanced colorectal cancer: a pooled analysis of patients from nine first-line phase III chemotherapy trials.

Blanke CD, Bot BM, Thomas DM, Bleyer A, Kohne CH, Seymour MT, de Gramont A, Goldberg RM, Sargent DJ.

J Clin Oncol. 2011 Jul 10;29(20):2781-6. doi: 10.1200/JCO.2010.33.5281. Epub 2011 Jun 6.


Evaluation of guanylyl cyclase C lymph node status for colon cancer staging and prognosis.

Sargent DJ, Resnick MB, Meyers MO, Goldar-Najafi A, Clancy T, Gill S, Siemons GO, Shi Q, Bot BM, Wu TT, Beaudry G, Haince JF, Fradet Y.

Ann Surg Oncol. 2011 Nov;18(12):3261-70. doi: 10.1245/s10434-011-1731-2. Epub 2011 May 1.


Evaluation of a new high-dimensional miRNA profiling platform.

Cunningham JM, Oberg AL, Borralho PM, Kren BT, French AJ, Wang L, Bot BM, Morlan BW, Silverstein KA, Staggs R, Zeng Y, Lamblin AF, Hilker CA, Fan JB, Steer CJ, Thibodeau SN.

BMC Med Genomics. 2009 Aug 27;2:57. doi: 10.1186/1755-8794-2-57.


Pooled safety and efficacy analysis examining the effect of performance status on outcomes in nine first-line treatment trials using individual data from patients with metastatic colorectal cancer.

Sargent DJ, Köhne CH, Sanoff HK, Bot BM, Seymour MT, de Gramont A, Porschen R, Saltz LB, Rougier P, Tournigand C, Douillard JY, Stephens RJ, Grothey A, Goldberg RM.

J Clin Oncol. 2009 Apr 20;27(12):1948-55. doi: 10.1200/JCO.2008.20.2879. Epub 2009 Mar 2. Erratum in: J Clin Oncol. 2009 Jul 10;27(20):3410-1.


Phase I North Central Cancer Treatment Group Trial-N9923 of escalating doses of twice-daily thoracic radiation therapy with amifostine and with alternating chemotherapy in limited stage small-cell lung cancer.

Garces YI, Okuno SH, Schild SE, Mandrekar SJ, Bot BM, Martens JM, Wender DB, Soori GS, Moore DF Jr, Kozelsky TF, Jett JR.

Int J Radiat Oncol Biol Phys. 2007 Mar 15;67(4):995-1001.

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