Brian Bot

Senior Scientist

Sage Bionetworks

Location
Seattle, Washington, United States
Discipline
Biological Sciences
Interests
challenging the scientific status quo
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  • 10 Followers

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About

I am currently a Senior Scientist at Sage Bionetworks working with large genetic, genomic and phenotypic datasets. This role requires advanced knowledge of a wide variety of subject matters including computational biology, biostatistics, bioinformatics, and a number of biological endpoints. Endpoints of particular interest are genetic mutations (SNP, CNV, etc.), RNA expression (miRNA, exon, gene-level), and protein production. Methods to integrate these endpoints are of particular interest and importance. We are currently working to create standardized open-source data structures and formats which will aid in increasing the accessibility and ease of analysis of biological data.

In providing open access to a large number of integrated datasets, we hope to stimulate the discovery and validation of biological networks that will help to explain disease specific etiology.
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Publications

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

    Oberg A, Bot B, Grill D, Poland G, Therneau T

    BMC genomics (2012)

    • -- Readers Readers not available. This publication is not currently accessible in the Mendeley catalog.
  • Developing predictive molecular maps of human disease through community-based modeling

    Derry J, Mangravite L, Suver C, Furia M, Henderson D, Schildwachter X et al.

    Nature Genetics (2012)

    • -- Readers Readers not available. This publication is not currently accessible in the Mendeley catalog.
  • Expression of endothelin 2 and localized clear cell renal cell carcinoma.

    Bot B, Eckel-Passow J, Legrand S, Hilton T, Cheville J, Igel T et al.

    Human pathology (2011)

    • -- Readers Readers not available. This publication is not currently accessible in the Mendeley catalog.
  • Integrated analysis of gene expression, CpG island methylation, and gene copy number in breast cancer cells by deep sequencing.

    Sun Z, Asmann Y, Kalari K, Bot B, Eckel-Passow J, Baker T et al.

    PloS one (2011)

    • -- Readers Readers not available. This publication is not currently accessible in the Mendeley catalog.
  • Comparative assessment of trial-level surrogacy measures for candidate time-to-event surrogate endpoints in clinical trials

    Shi Q, Renfro L, Bot B, Burzykowski T, Buyse M, Sargent D

    Computational Statistics & Data Analysis (2011)

    • -- Readers Readers not available. This publication is not currently accessible in the Mendeley catalog.
  • Evaluation of Guanylyl Cyclase C Lymph Node Status for Colon Cancer Staging and Prognosis.

    Sargent D, Resnick M, Meyers M, Goldar-Najafi A, Clancy T, Gill S et al.

    Annals of surgical oncology (2011)

    • -- Readers Readers not available. This publication is not currently accessible in the Mendeley catalog.
  • 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 Y, Okuno S, Schild S, Mandrekar S, Bot B, Martens J et al.

    International journal of radiation oncology, biology, physics (2007)

    • -- Readers Readers not available. This publication is not currently accessible in the Mendeley catalog.
  • Impact of pretreatment factors on adverse events: a pooled analysis of North Central Cancer Treatment Group advanced stage non-small cell lung cancer trials.

    Mandrekar S, Northfelt D, Schild S, Foster N, Bot B, Marks R et al.

    Journal of thoracic oncology : official publication of the International Association for the Study of Lung Cancer (2006)

    • -- Readers Readers not available. This publication is not currently accessible in the Mendeley catalog.
  • 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 D, Köhne C, Sanoff H, Bot B, Seymour M, de Gramont A et al.

    Journal of clinical oncology : official journal of the American Society of Clinical Oncology (2009)

    • -- Readers Readers not available. This publication is not currently accessible in the Mendeley catalog.
  • Two or three year disease-free survival (DFS) as a primary end-point 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.

    Sargent D, Shi Q, Yothers G, Van Cutsem E, Cassidy J, Saltz L et al.

    European journal of cancer (Oxford, England : 1990) (2011)

    • -- Readers Readers not available. This publication is not currently accessible in the Mendeley catalog.
  • 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 C, Bot B, Thomas D, Bleyer A, Kohne C, Seymour M et al.

    Journal of clinical oncology : official journal of the American Society of Clinical Oncology (2011)

    • -- Readers Readers not available. This publication is not currently accessible in the Mendeley catalog.
  • Evaluation of a new high-dimensional miRNA profiling platform.

    Cunningham J, Oberg A, Borralho P, Kren B, French A, Wang L et al.

    BMC medical genomics (2009)

    • -- Readers Readers not available. This publication is not currently accessible in the Mendeley catalog.
  • 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.

    de Gramont A, Hubbard J, Shi Q, O'Connell M, Buyse M, Benedetti J et al.

    Journal of clinical oncology : official journal of the American Society of Clinical Oncology (2010)

    • -- Readers Readers not available. This publication is not currently accessible in the Mendeley catalog.
  • Evaluation of the value of attribution in the interpretation of adverse event data: a North Central Cancer Treatment Group and American College of Surgeons Oncology Group investigation.

    Hillman S, Mandrekar S, Bot B, DeMatteo R, Perez E, Ballman K et al.

    Journal of clinical oncology : official journal of the American Society of Clinical Oncology (2010)

    • -- Readers Readers not available. This publication is not currently accessible in the Mendeley catalog.

Professional experience

Senior Scientist

Sage Bionetworks

December 2011 - Present

QC Statistical Geneticist

Sage Bionetworks

June 2011 - December 2011 (6 months)

Senior Statistical Analyst

Mayo Clinic

July 2008 - June 2011 (2 years 11 months)

Statistical Analyst II

Mayo Clinic

August 2006 - June 2008 (1 year 10 months)

Statistical Analyst

Mayo Clinic

May 2004 - August 2006 (2 years 3 months)

Education history

University of Minnesota - Twin Cities

Statistics

September 2000 - December 2003 (3 years 3 months)