This is a personally curated list of my peer-reviewed publications. Other sources include PubMed query, Google Scholar, and ORCID.

Personal top 10 list (rev. chronological order)

  • Omberg L, Chaibub Neto E, Perumal TM, Pratap A, Tediarjo A, Adams J, Bloem BR, Bot BM, Elson M, Goldman SM, Kellen MR, Kieburtz K, Klein A, Little MA, Schneider R, Suver C, Tarolli C, Tanner CM, Trister AD, Wilbanks J, Dorsey ER, Mangravite LM. Remote smartphone monitoring of Parkinson’s disease and individual response to therapy. Nature Biotechnology. 2021. doi:10.1038/s41587-021-00974-9

  • Doerr M, Moore S, Barone V, Sutherland S, Bot BM, Suver C, Wilbanks J. Assessment of the All of Us research program’s informed consent process. AJOB Empirical Bioethics. 2020. doi:10.1080/23294515.2020.1847214

  • Bot BM, Wilbanks JT, Mangravite LM. Assessing the consequences of decentralizing biomedical research. Big Data & Society. 2019. doi:10.1177/2053951719853858

  • Doerr M, Maguire Truong A, Bot BM, Wilbanks J, Suver C, Mangravite L. Formative evaluation of participant experience with mobile eConsent in the app-mediated parkinson mPower study: a mixed methods study. JMIR Mhealth Uhealth. 2017. doi:10.2196/mhealth.6521

  • Bot BM, Suver C, Chaibub Neto E, Kellen M, Klein A, Bare C, Doerr M, Pratap A, Wilbanks J, Dorsey ER, Friend S, Trister A. The mPower study, parkinson disease mobile data collected using researchKit. Nature Scientific Data. 2016. doi:10.1038/sdata.2016.11

  • 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. The consensus molecular subtypes of colorectal cancer. Nature Medicine. 2015. doi:10.1038/nm.3967

  • Derry J, Mangravite L, Suver C, Furia M, Henderson D, Schildwachter X, Bot B, Izant J, Sieberts S, Kellen M, Friend S. Developing predictive molecular maps of human disease through community-based modeling. Nature Genetics. 2012. doi:10.1038/ng.1089

  • Bot B, Eckel-Passow J, LeGrand, Hilton T, Cheville J, Igel T, Parker A. Expression of Endothelin-2 and Localized Clear Cell Renal Cell Carcinoma. Hum Pathol. 2012. doi:10.1016/j.humpath.2011.07.011

  • de Gramont A, Hubbard J, Shi Q, O’Connell M, Buyse M, Benedetti J, Bot B, O’Callaghan C, Yothers G, Goldberg R, Blanke C, Benson A, Deng Q, Alberts S, Andre T, Wolmark N, Grothey A, Sargent D. Association between disease-free survival and overall survival when survival is prolonged after recurrence in patients receiving cytotoxic adjuvant therapy for colon cancer: simulations based on the 20,800 patient ACCENT data set. J Clin Oncol. 2010. doi:10.1200/JCO.2009.23.1407

  • Sargent D, Kohne C, Sanoff H, Bot B, Seymour M, de Gramont A, Porschen R, Saltz L, Rougier P, Tournigand C, Douillard J, Stephens R, Grothey A, Goldberg R. Pooled safety and efficacy analysis examining the effect of performance status on outcomes in 9 first line treatment trials using individual patient data from 6,286 patients with metastatic colorectal cancer. J Clin Oncol. 2009. doi:10.1200/JCO.2008.20.2879


The rest of the best (rev. chronological order)

  • Chaibub Neto E, Perumal TM, Pratap A, Tediarjo A, Bot BM, Mangravite L, Omberg L. Disentangling personalized treatment effects from ‘time-of-the-day’ confounding in mobile health studies. PLoS One. 2022. doi:10.1371/journal.pone.0271766

  • Chaibub Neto E, Pratap A, Perumal TM, Tummalacherla M, Snyder P, Bot BM, Trister AD, Friend SH, Mangravite L, Omberg L. Detecting the impact of subject characteristics on machine learning-based diagnostic applications. NPJ Digital Medicine. 2019. doi:10.1038/s41746-019-0178-x

  • Hershman SG, Bot BM, Shcherbina A, Doerr M, Moayedi Y, Pavlovic A, Waggott D, Cho MK, Rosenberger ME, Haskell WL, Myers J, Champagne MA, Mignot E, Salvi D, Landray M, Tarassenko L, Harrington RA, Yeung AC, McConnell MV, Ashley EA. Physical activity, sleep and cardiovascular health data for 50,000 individuals from the MyHeart Counts Study. Nature Scientific Data. 2019. doi:10.1038/s41597-019-0016-7

  • Radin JM, Steinhubl SR, Su AI, Bhargava H, Greenberg B, Bot BM, Doerr M, Topol EJ. The Healthy Pregnancy Research Program: transforming pregnancy research through a ResearchKit app. Digital Medicine. 2018. doi:10.1038/s41746-018-0052-2

  • Chan Y, Bot BM, Zweig M, Tignor N, Ma W, Suver C, Cedeno R, Scott ER, Hershman SG, Schadt EE, Wang P. The asthma mobile health study, smartphone data collected using ResearchKit. Nature Scientific Data. 2018. doi:10.1038/sdata.2018.96

  • Dienstmann R, Mason MJ, Sinicrope FA, Phipps AI, Tejpar S, Nesbakken A, Danielsen SA, Sveen A, Buchanan DD, Clendenning M, Rosty C, Bot B, Alberts SR, Milburn Jessup J, Lothe RA, Delorenzi M, Newcomb PA, Sargent D, Guinney J. Prediction of overall survival in stage II and III colon cancer beyond TNM system: a retrospective, pooled biomarker study. Ann Oncol. 2017. doi:10.1093/annonc/mdx052

  • Webster DE, Suver C, Doerr M, Mounts E, Domenico L, Petrie T, Leachman SA, Trister A, Bot BM. The Mole Mapper Study, mobile phone skin imaging and melanoma risk data collected using ResearchKit. Nature Scientific Data. 2017. doi:10.1038/sdata.2017.5

  • Munos B, Baker PC, Bot BM, Crouthamel M, de Vries G, Ferguson I, Hixson JD, Malek LA, Mastrototaro JJ, Misra V, Ozcan A, Sacks L, Wang P. Mobile health: the power of wearables, sensors, and apps to transform clinical trials. Annals of the New York Academy of Sciences. 2016. doi:10.1111/nyas.13117

  • Ho TH, Serie DJ, Parasramka M, Cheville JC, Bot BM, Tan W, Wang L, Joseph RW, Hilton T, Leibovich BC, Parker AS, Eckel-Passow JE. Differential gene expression profiling of matched primary renal cell carcinoma and metastases reveals upregulation of extracellular matrix genes. Annals of Oncology. 2016. doi:10.1093/annonc/mdw652

  • Guinney J, Wang T, Laajala TD, Kanigel Winner K, Bare JC, Chaibub Neto E, Khan SA, Peddinti G, Airola A, Pahikkala T, Mirtti T, Yu T, Bot BM, Shen L, Abdallah K, Norman T, Friend S, Stolovitzky G, Soule H, Sweeney CJ, Ryan CJ, Scher HI, Sartor O, Xie Y, Aittokallio T, Zhou FL, Costello JC. Prediction of overall survival for patients with metastatic castration-resistant prostate cancer: development of a prognostic model through a crowdsourced challenge with open clinical trial data. The Lancet Oncology. 2016. doi:10.1016/S1470-2045(16)30560-5

  • Lau E, Cao Q, Ng DCM, Bleakley BJ, Dincer TU, Bot BM, Wang D, Liem D, Lam MPY, Ge J, Ping P. A large dataset of protein dynamics in the mammalian heart proteome. Nature Scientific Data. 2016. doi:10.1038/sdata.2016.15

  • Dienstmann R, Jang IS, Bot B, Friend S, Guinney J. Database of genomic biomarkers for cancer drugs and clinical targetability in solid tumors. Cancer Discovery. 2015. doi:10.1158/2159-8290.CD-14-1118

  • Cokelaer T, Bansal M, Bare C, Bilal E, Bot BM, Chaibub Neto E, Eduati F, Gönen M, Hill SM, Hoff B, Karr JR, Küffner R, Menden MP, Meyer P, Norel R, Pratap A, Prill RJ, Weirauch MT, Costello JC, Stolovitzky G, Saez-Rodriguez J. DREAMTools: a Python package for scoring collaborative challenges. F1000Research. 2015. doi:10.12688/f1000research.7118.1

  • Commo F, Guinney J, Ferté C, Bot B, Lefebvre C, Soria JC, André F. rCGH: a comprehensive array-based genomic profile platform for precision medicine. Bioinformatics. 2015. doi:10.1093/bioinformatics/btv718

  • Karr JR, Williams AH, Zucker JD, Raue A, Steiert B, Timmer J, Kreutz C, DREAM8 Parameter Estimation Challenge Consorium, Wilkinson S, Allgood BA, Bot BM, Hoff BR, Kellen MR, Covert MW, Stolovitzky GA, Meyer P. Summary of the DREAM8 parameter estimation challenge: toward parameter identification for whole-cell models. PLoS Comput Biol. 2015. doi:10.1371/journal.pcbi.1004096

  • Sinocrope FA, Shi Q, Smyrk TC, Thibodeau SN, Dienstmann R, Guinney J, Bot BM, Tejbar S, Delorenzi M, Goldberg RM, Mahoney MR, Sargent DJ, Alberts SR. Molecular markers identify subtypes of stage III colon cancer associated with patient outcomes. Gastroenterology. 2015. doi:10.1053/j.gastro.2014.09.041

  • Eckel-Passow JE, Serie DJ, Bot BM, Joseph RW, Cheville JC, Parker AS. ANKS1B is a smoking-related molecular alteration in clear cell renal cell carcinoma. BMC Urology. 2014. doi:10.1186/1471-2490-14-14

  • Eckel-Passow JE, Serie DJ, Bot BM, Joseph RW, Hart S, Cheville JC, Parker AS. Somatic expression of ENRAGE is associated with obesity status among patients with clear cell renal cell carcinoma. Carcinogenesis. 2014. doi:10.1093/carcin/bgt485

  • Ferté C, Fernandez M, Hollebecque A, Koscielny S, Levy A, Massard C, Balheda R, Bot B, Gomez-Roca C, Dromain C, Ammari S, Soria JC. Tumor growth rate is an early indicator of anti-tumor drug activity in phase I trials. Clin Cancer Res. 2014. doi:10.1158/1078-0432.CCR-13-2098

  • Shi Q, Andre T, Grothey A, Yothers G, Hamilton S, Bot B, Haller D, Van Cutsem E, Twelves C, Benedetti J, O’Connell M, Sargent D. Comparison of outcomes after 5-fluorouracil-based adjuvant therapy for stage II and III colon cancer between 1978-1995 and 1996-2007: findings from the ACCENT database. J Clin Oncol. 2013. doi:10.1200/JCO.2013.49.4344

  • Ferté C, Trister A, Huang E, Bot B, Guinney J, Commo F, Sieberts S, Andre F, Besse B, Soria JC, Friend S. Impact of bioinformatic procedures in the development and translation of high-throughput molecular classifiers in oncology. Clin Cancer Res. 2013. doi:10.1158/1078-0432.CCR-12-3937

  • Haralambieva IH, Oberg AL, Ovsyannikova IG, Kennedy RB, Grill DE, Middha S, Bot BM, Wang VW, Smith DI, Jacobson RM, Poland GA. Genome-wide characterization of transcriptional patterns in high and low antibody responders to rubella vaccination. PLoS One. 2013. doi:10.1371/journal.pone.0062149

  • Wu W, Bot B, Hu Y, Geyer S, Sargent D. A phase II flexible screening design allowing for interim analysis and comparison with historical control. Contemporary Clinical Trials. 2013. doi:10.1016/j.cct.2013.05.007

  • Oberg A, Bot B, Grill D, Poland G, Therneau T. Technical and biological variance structure in mRNA-Seq data: life in the real world. BMC Genomics. 2012. doi:10.1186/1471-2164-13-304

  • Sargent D, Shi Q, Yothers G, Van Cutsem E, Cassidy J, Saltz L, Wolmark N, Bot B, Grothey A, Buyse A, de Gramont A. Two or three tear disease free survival (DFS) as a primary endpoint in stage III adjuvant colon cancer trials with fluoropyrimidines with or without oxaliplatin or irinotecan: data from 12,676 patients from MOSAIC, X-ACT, PETACC-3, C-06, C-07, and C89803. Eur J Cancer. 2011. doi:10.1016/j.ejca.2010.12.015

  • Blanke C, Bot B, Thomas D, Bleyer A, Kohne C, Seymour M, de Gramont A, Goldberg R, Sargent D, LIVESTRONG Young Adult Alliance (LSYAA). Impact of young age on efficacy and safety in advanced colorectal cancer: a pooled analysis examining 6,286 patients from nine first-line phase III chemotherapy trials. J Clin Oncol. 2011. doi:10.1200/JCO.2010.33.5281

  • Sargent D, Resnick M, Meyers M, Goldar-Najafi A, Clancy T, Gill S, Siemons G, Shi Q, Bot B, Wu T, Beaudry G, Desaulniers M, Haince J, Fradet Y. Evaluation of Guanylyl Cyclase C lymph node status for colon cancer staging and prognosis. Ann Surg Oncol. 2011. doi:10.1245/s10434-011-1731-2

  • Shi Q, Renfro L, Bot B, Burzykowski T, Buyse M, Sargent D. Comparative assessment of trial-level surrogacy measures for candidate time-to-event surrogate endpoints in clinical trials. Computational Statistics and Data Analysis. 2011. doi:10.1016/j.csda.2011.03.014

  • Sun Z, Asmann Y, Kalari K, Bot B, Eckel-Passow J, Baker T, Carr J, Khrebtukova I, Luo S, Zhang L, Schroth G, Perez E, Thompson A. Integrated analysis of gene expression, CpG island methylation, and gene copy number in breast cancer cells by deep sequencing. PLoS One. 2011. doi:10.1371/journal.pone.0017490

  • Hillman S, Mandrekar S, Bot B, DeMatteo R, Perez E, Ballman K, Nelson H, Buckner J, Sargent D. An evaluation of the value of attribution in the interpretation of adverse event data: a North Central Cancer Treatment Group (NCCTG) and American College of Surgeons Oncology Group (ACOSOG) investigation. J Clin Oncol. 2010. doi:10.1200/JCO.2009.27.4282

  • Cunningham J, Oberg A, Borralho P, Kren B, French A, Wang L, Bot B, Morlan B, Silverstein K, Staggs R, Zeng Y, Lamblin A, Hilker C, Fan J, Steer C, Thibodeau S. Evaluation of a new high dimensional miRNA profiling platform. BMC Med Genomics. 2009. doi:10.1186/1755-8794-2-57

  • Mandrekar S, Northfelt D, Schild S, Foster N, Bot B, Marks R, Mailliard J, Krook J, Maksymiuk A, Adjei A, Jett J. Impact of pretreatment factors on adverse events: a pooled analysis of North Central Cancer Treatment Group advanced stage non-small cell lung cancer trials. J Thorac Oncol. 2006. doi:10.1016/S1556-0864(15)30359-2