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)

Research Interests

I am interested in translational research with an emphasis on genomics and bioinformatics. Specifically, I would like to study how genomic information can influence personalized medicine. This has two key components, developing computational approaches to detect and predict effects of genetic mutations and utilizing these resources to analyze genomic information. In my current work I am involved in both of these areas with a specific focus on cancer.

Research Experience

Ph.D Candidate

Advisors: Elaine Mardis PhD, Obi Griffith PhD

2013-Present

Bioinformatics development and analysis for the MedSeq pipeline at the Genome Institute. The MedSeq pipeline automates analysis of cancer cases. This is done through combining whole genome, exome and transcriptome data to make accurate somatic mutation calls. My thesis work revolves around creating standalone tools that translate this information into clinically actionable data by improving variant detection and aiding clinicians in interpreting genomic information.

Cancer Biology Pathway Fellow

Siteman Cancer Center

2014-Present

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

Consultant, The BALSA Group

March 2015 - Present

Advised 3 companies in a variety of business problems including market entry and profitability.

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

  • Bioinformatics
  • Computational Biology
  • Supercomputing
  • Molecular Biology
  • Phylogenetics
  • Statistics
  • Genetics
  • Machine Learning

Programming Skills

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

Research Support

2012-2014 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

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

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

Founder/ Organizer, Cancer Informatics Journal Club

McDonnell Genome Institute

2014-present

Young Men President

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

2014-present

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.

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

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.

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.