Brian Bot

  • Senior Scientist
  • Sage Bionetworks

Research Interests

challenging the scientific status quo

Followers (10)

Explore network

Following (9)

Explore network

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.

Publications

Developing predictive molecular maps of human disease through community-based modeling

Derry J, Mangravite L, Suver C, Furia M, Henderson D, Schildwachter X, Bot B, Izant J, Sieberts S, Kellen M, Friend S

Nature Genetics (2012)

  • Get full text at journal
  • -- Readers Readers not available. This publication is not currently accessible in the Mendeley catalog.

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)

  • Get full text at journal
  • -- 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)

  • Get full text at journal
  • -- 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, Siemons G, Shi Q, Bot B, Wu T, Beaudry G, Haince J, Fradet Y

Annals of surgical oncology (2011)

  • Get full text at journal
  • -- 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, Parker A

Human pathology (2011)

  • Get full text at journal
  • -- 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, de Gramont A, Goldberg R, Sargent D

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

  • Get full text at journal
  • -- 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, Carr J, Khrebtukova I, Luo S, Zhang L, Schroth G, Perez E, Thompson E

PloS one (2011)

  • Get full text at journal
  • -- 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, Wolmark N, Bot B, Grothey A, Buyse M, de Gramont A

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

  • Get full text at journal
  • -- 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, 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

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

  • Get full text at journal
  • -- 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, Nelson H, Buckner J, Sargent D

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

  • Get full text at journal
  • -- 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, Bot B, Morlan B, Silverstein K, Staggs R, Zeng Y, Lamblin A, Hilker C, Fan J, Steer C, Thibodeau S

BMC medical genomics (2009)

  • Get full text at journal
  • -- 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, Porschen R, Saltz L, Rougier P, Tournigand C, Douillard J, Stephens R, Grothey A, Goldberg R

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

  • Get full text at journal
  • -- 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, Wender D, Soori G, Moore D, Kozelsky T, Jett J

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

  • Get full text at journal
  • -- 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, Mailliard J, Krook J, Maksymiuk A, Adjei A, Jett J

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.

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 Cancer Center Department of Molecular Pharmacology and Experimental Therapeutics

July 2008 - June 2011 (2 years 11 months)

Statistical Analyst II

Mayo Clinic Cancer Center Department of Molecular Pharmacology and Experimental Therapeutics

August 2006 - June 2008 (1 year 10 months)

Statistical Analyst

Mayo Clinic Cancer Center Department of Molecular Pharmacology and Experimental Therapeutics

May 2004 - August 2006 (2 years 3 months)

Education history

University of Minnesota Twin Cities

Statistics

September 2000 - December 2003 (3 years 3 months)