Ben Ainscough

Ben Ainscough

Ph.D. Candidate

  • e: b.ainscough@wustl.edu
  • a: Campus Box 8501
  • 4444 Forest Park Ave
  • Saint Louis, MO 63108
  • w: (314)747-9284

Education

Washington University in Saint Louis

Ph.D. Human Statistical Genetics

Advisors: Elaine R Mardis PhD, Obi L Griffith PhD

2012-2017(expected)

Brigham Young University

BS Bioinformatics

University Honors

2009-2012

Honors Thesis: Digging up the Molecular Relationships of the Freshwater Crayfish Fallicambarus (Decapoda: Astacidae)

Executive Summary

I am a data scientist anticipating completion of Ph.D. in Human and Statistical Genetics in mid to late 2017. I have a strong computational background with experience in big data, machine learning, statistics, data visualization, and communicating data insights verbally and in writing. I am interested in using cutting-edge data mining methodologies to solve disparate real world problems in academia and industry. Most recently in the academic sphere, I have been leveraging huge datasets to tranlate genetic data to clinical care. Specifically, I have lead a team of developers to produce a web resource, DoCM, that facilitates the curation of cancer-causing mutations in the academic literature. Similarly, I developed a machine learning model that automates the manual review of cancer mutations to eliminate false positives. Additionally, I created a start-up to produce an app that uses machine learning to allow users to easily create healthy meal plans which won a national student start-up competition. In my next position I am looking to apply and develop my data science skill set in a postdoctoral or industrial role.

Research Experience

Ph.D Candidate

Advisors: Elaine Mardis PhD, Obi Griffith PhD

2013-Present

My thesis is focused on using machine learning, data curation, and software development to identify and prioritize cancer mutations from whole genome sequence data. Specifically, this involved leading the development and curation of DoCM, the database of curated mutations, published in Nature Methods. Additionally, I developed a novel machine learning model that automates the laborious process of manually reviewing putative somatic cancer mutations for false positives.

Cancer Biology Pathway Fellow

Siteman Cancer Center

2014-2016

The Cancer Biology Pathway Fellowship is designed to train pre and postdoctoral students in interdisciplinary research relevant to cancer biology. Fellows shadow oncologists from various departments to give them an understanding in clinical cancer care. They also participate in coursework that teaches them about current clinical problems and how to bridge the gap between research and clinical practice.

Graduate Rotation Research Assistant

Advisors: Nancy Saccone PhD, Rob Mitra PhD, Rakesh Nagarajan PhD, Alison Goate PhD

2012-13

Rotated in both "wet" and "dry" lab environments performing a variety of tasks from cell culture to statistical/bioinformatic programming. Worked on a variety of disease systems and biological problems ranging from cell fate decisions to Alzheimer's disease.

Undergraduate Research Assistant

Advisor: John S. K. Kauwe PhD

2011 - 2012

Performed statistical analysis determine genetic relationshop of biomarkers in Alzheimer's Disease.

Undergraduate Research Assistant

Advisor: Keith A. Crandall PhD

2009 - 2011

Performed sanger sequencing and computation to estimate the phylogeny of the freshwater crayfish genus Fallicambarus. Results published in Zoologica Scripta and as Undergraduate Honors Thesis.

Work Experience

Founder/ Co-leader, SnapPEAs

September 2015 - Present

Assembled a team of 12 students to create SaaS-markeplace app, using machine learning, to promote healthy eating through meal planning and better management of grocers’ inventory.

  • Raised over $8,000 in funding
  • Won IDEA labs Demo Day 2016 - Idea Labs is a national student-run biotech incubator
  • Won the Washington University Skandalaris Center Fall 2015 Idea Bounce Competition.
  • Semi-finalist in 2016 Washington University Skandalaris Center Cup
  • Finalist in the 2016 Social Enterprise and Innovation Competition

Consultant, The BALSA Group

March 2015 - Present

Advised 3 companies in real estate, agriculture and ag-tech performing due diligence, profitability, and market entry analyses

Back-end Web Developer at BYU Broadcasting

April 2011 - November 2011

Worked on the back end web development of the BYUtv and BYUtv Sports website using the .Net framework and C#. Performed database creation, manipulation and modification with SQL and noSQL databases. Created and maintained web services.

Research Skills

  • Machine Learning
  • Data Visualization
  • Data Analysis
  • Statistics
  • Supercomputing
  • Bioinformatics
  • Computational Biology
  • Molecular Biology
  • Phylogenetics
  • Genetics

Programming Skills

  • Python
  • R
  • C++
  • Java
  • C#
  • Perl
  • SQL
  • couchDB(noSQL)
  • Unix
  • XML
  • HTML
  • CSS
  • MVC
  • Agile Development
  • Git

Research Support

2014-2016 Cancer Biology Pathway Fellow, Siteman Cancer Center, $57,000

Scholarships and Awards

  • Best Application, 2014 NoB Hackathon
  • University Honors, BYU
  • S. Paul and Hilda F. Stewart Scholarship, BYU Biology Department
  • Honors Thesis Research Grant, BYU Honors Program
  • University Academic Scholarship, BYU
  • Phi Eta Sigma Honor Society, BYU
  • Eagle Scout Award

Publications

Nature Genetics

January 31, 2017

  • Griffith M,*
  • Spies NC,*
  • Krysiak K,*
  • McMichael JF,
  • Coffman AC,
  • Danos AM,
  • Ainscough BJ,
  • Ramirez CA,
  • Rieke DT,
  • Kujan L,
  • Barnell EK,
  • Wagner AH,
  • Skidmore ZL,
  • Wollman A,
  • Liu CJ,
  • Jones MR,
  • Bilski RL,
  • Lesurf R,
  • Feng YY,
  • Shah NM,
  • Bonakdar M,
  • Trani L,
  • Matlock M,
  • Ramu A
  • Campbell KM,
  • Spies GC,
  • Graubert AP,
  • Gangavarapu K,
  • Eldred JM,
  • Larson DE,
  • Walker JR,
  • Good BM,
  • Wu C,
  • Su AI,
  • Dienstmann R,
  • Margolin AA,
  • Tamborero D,
  • Lopez-Bigas N,
  • Jones SJM,
  • Bose R,
  • Spencer DH,
  • Wartman LD,
  • Wilson RK
  • Mardis ER,
  • Griffith OL

Experimental Hematology

May 15, 2016

  • Griffith M,
  • Griffith OL,
  • Krysiak K,
  • Skidmore ZL,
  • Christopher MJ,
  • Klco JM,
  • Ramu A,
  • Lamprecht TL,
  • Wagner AH,
  • Campbell KM,
  • Lesurf R,
  • Hundal J,
  • Zhang J,
  • Spies NC,
  • Ainscough BJ,
  • Larson DE,
  • Heath SE,
  • Fronick C,
  • O'Laughlin Shelly
  • Fulton R,
  • Magrini V,
  • McGrath S,
  • Smith SM,
  • Miller CA,
  • Maher CA,
  • Payton JE,
  • Walker JR,
  • Eldred JM,
  • Walter MJ,
  • Link DC,
  • Graubert TA,
  • Westervelt P,
  • Kulkarni S,
  • DiPersio JF,
  • Mardis ER,
  • Wilson RK,
  • Ley TJ

PLoS Computational Biology

July 9, 2015

*These authors contributed equally to this work

  • Griffith M*,
  • Griffith OL*,
  • Smith SM*,
  • Ramu A,
  • Callaway MB,
  • Brummett AM,
  • Kiwala M,
  • Coffmann AC,
  • Regier AA,
  • Oberkfell BJ,
  • Sanderson GE,
  • Mooney TP,
  • Nutter N,
  • Belter EA,
  • Du F,
  • Long RL,
  • Abbott TE,
  • Ferguson I,
  • Morton D,
  • Burnett M,
  • Weible JV,
  • Peck JB,
  • Dukes A,
  • McMichael JF,
  • Lolofie JT,
  • Derickson BR,
  • Hundall J,
  • Skidmore ZL,
  • Ainscough BJ,
  • Dees ND,
  • Schierding WS,
  • Kandoth C,
  • Kim K,
  • Lu C,
  • Harris CC,
  • Maher N,
  • Maher CA,
  • Magrini VJ,
  • Abbott BS,
  • Chen K,
  • Clark E,
  • Das I,
  • Fan X,
  • Hawkins AE,
  • Hepler TG,
  • Wylie TN,
  • Leonard S,
  • Schroeder WE,
  • Shi X,
  • Carmichael KL,
  • Weil M,
  • Wohldstadter RW,
  • Stiehr G,
  • McLellan MD,
  • Pohl CS,
  • Miller CA,
  • Koboldt DC,
  • Walker JR,
  • Eldred JM,
  • Larson DE,
  • Dooling DJ,
  • Ding L,
  • Mardis ER,
  • Wilson RK

Nature

November 17, 2014

*These authors contributed equally to this work

  • Juric D*,
  • Castel P*,
  • Griffith M,
  • Griffith OL,
  • Won HH,
  • Ellis H,
  • Ebbesen S,
  • Ainscough BJ,
  • Ramu A,
  • Iyer G,
  • Shah RH,
  • Huynh T,
  • Mino-Kenudson M,
  • Sgroi D,
  • Isakoff S,
  • Thabet A,
  • Elamine L,
  • Solit D,
  • Lowe S,
  • Quadt C,
  • Peters M,
  • Adnan Derti,
  • Huang A,
  • Mardis ER,
  • Berger MF,
  • Baselga J,
  • Scaltriti M

Oral Presentations

DoCM: a database of curated mutations in cancer rescues clinically relevant mutations

Genome Informatics

Hinxton, Cambridgeshire, UK

September 21, 2016

Identifying clinically important somatic mutations through a knowledge-based approach

AACR Translation of the Cancer Genome

San Fransisco, Ca

February 7, 2015

Leveraging a curated variant database for knowledge-based variant detection

Human and Statistical Genetics Program Retreat

Washington University in Saint Louis

September 26, 2014

Poster Presentations

Rescuing somatic mutations using a knowledge-based approach

Advances in Genome Biology and Technology

Marco Island, FL

February 27, 2015

Identifying clinically important somatic mutations through a knowledge-based approach

AACR Translation of the Cancer Genome

San Fransisco, Ca

February 8, 2015

Clinical sequencing analysis using the Genome Modeling System

Human and Statistical Genetics Program Retreat (WashU)

Washington University in Saint Louis

October 11, 2013

Digging up the Molecular Relationships of the Freshwater Crayfish Fallicambarus (Decapoda: Astacidae)

Evolution 2010

Portland, OR

June 25-29, 2010

Teaching and Training Experience

Graduate Teaching Assistant

Bio 2950 - Introduction to Environmental Biology

Washington University in Saint Louis

Fall 2013

Graded term projects. Met with student groups individually and mentored them on improving term projects. Organized review sessions.

Student Mentoring

Jason Kunisaki, Undergraduate, Washington University

Mayank Choudhary, Graduate Rotation Student, Washington University

Service

Young Men President

Lindell Ward - The Church of Jesus Christ of Latter-day Saints

2014-2017

As the Young Men President I lead the Young Men organization, which consist of a presidency of 3-4 adult leaders and 5-9 youth leaders. Responsibilities include implementing the curriculum for activities and regular lessons, planning and overseeing activities to promote the growth and development of the boys in the program.

Committee Chairman

Boy Scouts of America

2012-present

In conjunction with the Lindell ward Young Men organization, implementing overseeing the scouting program in the Lindell ward.

Founder/ Organizer, Cancer Informatics Journal Club

McDonnell Genome Institute

2014-2016

Young Men Second Counselor

Lindell Ward - The Church of Jesus Christ of Latter-day Saints

2012-2014

Executed the plans and direction of the Young Men President. This includes teaching lessons, planning and arranging for quality activities and overseeing the boys individual development

College of Life Sciences Representative

BYU Student Advisory Council

2010-2011

Missionary

Washington Everett Mission - The Church of Jesus Christ of Latter-day Saints

2007-2009

Full time volunteer. Performed a variety of functions including teaching, proselyting and community service. Assigned to learn and speak Spanish. During my service I trained new missionaries, organized and taught english classes and organized spanish language congregations.