Computational Cancer Biology (CCBTP)

Computational Cancer Biology Training Program (CCBTP)

The Computational Cancer Biology Training Program brings together the principles of computational and physical science with cancer biology in research, and possibly even the clinic, to develop an emerging generation of postdoctoral computational cancer biologists with a unified quantitative outlook on the problems presented in fundamental cancer research.

This 5-year training grant renewal was awarded effective December 1, 2016.

Funding Source:
Cancer Prevention and Research Institute of Texas (CPRIT) RP170593


Director:
Dr. B. Montgomery Pettitt, The University of Texas Medical Branch at Galveston.
Co-Director:
TBA
Program Administrator:
Melissa Glueck



Call for Postdoctoral Applications

All application materials are due April 26 at 11:59 pm. This includes transcripts, letters of recommendation, and mentor recommendation forms.

Applicants must discuss their proposed project with the Steering Committee member at their home institutions before applying, so that the committee member can assess that the project is both well developed and applicable to CCBTP goals. See Steering Committee list below.

Interviews for selected applicants will be on May 16, with appointments to begin in June.

For more information, see “CCBTP Application Information,” and the trainee and mentor application forms below.

Please bear with us as we continue to improve this website.


CCBTP Overview

The complex interplay among often disparate clinical, laboratory, and computational science applications impacting cancer medicine and biology demands innovative and interdisciplinary methods of cancer research. Cancer biologists and clinicians must collaborate with leading researchers in mathematics,computational science and engineering to more effectively study cancer and develop cutting edge tools that will lead to creative solutions.

This postdoctoral training program in Computational Cancer Biology (CCBTP) brings together principles of computational and physical science with basic and clinical cancer biology to develop an emerging generation of computational cancer biologists with a unified computational/quantitative outlook on the problems presented in fundamental cancer research. Our goal
is to increase the number of skilled, multidisciplinary cancer researchers in Texas who are uniquely able to integrate the tools, ideas, and materials of computational science and biology.

CCBTP training and activities are weighted towards cancer-driven bioscience as opposed to purely clinical medicine. Postdoctoral fellows are required to:

  • Have dual faculty mentors from both cancer biology and computational areas; both mentors must be members of the CCBTP Training Faculty at the time of the application;
  • Complete a 2-4 month mini-sabbatical or internship in the secondary mentor's laboratory;
  • Mentor a summer undergraduate intern during a 10-week program;
  • Complete an approved Responsible Conduct of Research course as a postdoc, a grantsmanship workshop, professional and career development workshops including mentoring, an annual Independent Development Plan (IDP),  and any coursework assigned to strengthen skills in areas in which the postdoc was not previously trained;
  • Attend and present at required seminars, symposia, and journal clubs; attend and present at our own CCBTP annual trainee conference (if chosen), Keck Annual Research Conference, the CPRIT annual conference, and a national conference of comparable scope to an American Chemical Society national meeting.


We welcome applications from all qualified trainees, regardless of ethnicity, race, or disability status. All GCC member institutions are ADAAA compliant and have offices of disability support services that provide accommodations and support services to trainees, faculty, staff, and visitors.

 

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CCBTP Application Information

Both mentors must be members of the CCBTP training faculty at the time of the application.

Faculty interested in sponsoring a candidate in the upcoming round should apply to join the training faculty well before the application due date. See Faculty Eligibility section for details.

Faculty may only be a primary mentor for one CCBTP fellow at a time. If a faculty mentor is already a primary mentor to a current CCBTP trainee, s/he may sponsor a new applicant (as primary mentor) shortly before the current trainee's appointment will end, so that the two trainees' appointments will not overlap.

Prior to applying, all trainee applicants must contact the Steering Committee member from the applicant's institution, to ensure that the proposed project is relevant to this training program.

 

APPLICANT ELIGIBILITY

Applicant eligibility:

  • Applicants may be US Citizens, Permanent Residents who have already received their Green Card, or Foreign Nationals with a current visa that allows them to work as a postdoc
  • Applicants must be employed by one of the 8 participating institutions (BCM, Rice, UH, UTHSC-H, MDACC, UTMB, IBT-TAMHSC, Methodist)
  • Applicants must be employed in the lab of their primary mentor on this application.

The Gulf Coast Consortia is committed to providing equal opportunity in training for individuals with disabilities and individuals from racial and ethnic groups who are currently under-represented in STEM fields. We welcome applications from all qualified trainees, regardless of ethnicity, race, or disability status. All GCC member institutions are ADAAA compliant and have offices of disability support services that provide accommodations and support services to trainees, faculty, staff, and visitors.

Application Requirements

  • Online Mentor Recommendation (link on home page) from your primary mentor
  • Online Mentor Recommendation (link on home page) from your secondary mentor
  • Online Trainee Fellowship Application (link on home page) - please ensure that your mentoring plan clearly describes how the two mentors will collaborate to give the trainee training in both of their disciplines, and what skills or techniques the trainee will learn from each
  • 2 Letters of Recommendation from people other than your mentors. They should email the letters directly to glueck@rice.edu. The letters do not have to be on letterhead, but must include title, institution, and contact information for the person writing the recommendation.
  • Current resume or Biosketch (in Word or PDF format) outlining your academic history and professional work experience: email to glueck@rice.edu
  • Individual Development Plan (IDP) such as AAAS myIDP: Save a detailed "my IDP Summary" that includes your plans for the upcoming two years, month by month (e.g. May 2017: attend grant writing class at XX). These plans should include curriculum, required seminars and conferences, national conferences you will attend, professional development like grant writing, and milestones for publications. Be detailed and specific: do not use vague "look into jobs" or "networking" for every month. You can anticipate being asked (in the review) whether you have discussed this completed IDP with your mentor, and if not, why not.
  • Current Proof of US Citizenship (birth certificate or passport), Permanent Residency (Green Card), or work visa for the United States: email a PDF scan to glueck@rice.edu or mail a clear photocopy to the address below. You must already have your work visa to be eligible to apply.
  • Transcripts: official copies preferred, but unofficial copies accepted. If the transcript is in a foreign language, you must submit an English translation. Email glueck@rice.edu the following as PDFs:
    • Undergraduate transcripts from all institutions you attended
    • PhD or MD Graduate transcript - if the date you received this diploma is not on the transcript, supply a PDF scan of your PhD diploma with the date on it (no photos of the diploma please).

Interviews:

Selected candidates will be invited to an interview, which both mentors are expected to attend. Here is the format:

Candidates will make a brief oral presentation (maximum 8 minutes, maximum 6 PowerPoint slides plus title slide), then answer questions from the committee.

Your presentation should provide an overview of your proposed research project, focusing on the first year. It should address the following:

  1. the interdisciplinary nature of the project and approached you propose to use, emphasizing quantitative aspects;
  2. features of the project that you consider particularly novel and/or innovative; and
  3. the importance of your project to the broad area of computational science and cancer biology This need not be lengthy or highly detailed but it should be explicit. Oftentimes this may be obvious to you and others in your specific area, but it may not be clear to the diverse, interdisciplinary Steering Committee which is reviewing you.

Your presentation should also outline the mentoring plan, and explicitly describe the roles that both your primary mentor and co-mentor will play in the plan as well as the proposed research. In particular, the committee is interested in hearing how the two mentors together enable you to conduct research that could not be accomplished with either alone. You may also comment on how this fellowship would enhance your training and career development.

We will provide the laptop for the presentation. Candidates will Dropbox their presentations to glueck@rice.edu, and bring a backup on a USB drive in a PC compatible format. Please do not include movies, as they generally do not work in this system.

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CCBTP Curriculum

Computational Cancer Biology Training Program Curriculum

1. Responsible Conduct of Research: Per CPRIT policy, all postdocs must fulfill the NIH Responsible Conduct of Research course training requirements. Even if a trainee has completed a course as a graduate student, or as a postdoc more than four years ago, per NOT-OD-10-019 the NIH requires that the trainee re-take an ethics course that meets all of its requirements. Online courses such as CITI do not meet the requirements.

Trainees must provide the GCC with a transcript, certificate, or other form of proof of completion of an approved course. If a trainee has not taken a course that meets all of the requirements (including time), s/he is required to complete it within the first year of appointment. The following are approved Responsible Conduct of Research courses:

1.BCM: Ethics for Postdocs
2.UTHSC-H: Postdoctoral Ethics course (part of postdoc certificate)
3.Rice University: UNIV 594 Training in the Responsible Conduct of Research; offered in the Fall semester
4.MDACC: Postdoctoral Ethics course
5.UTMB: MEHU 6101 Ethics in Scientific Research - offered twice per year for 2 consecutive days each in May and November
6.UH: take the UTMB course
7.IBT - TAMHSC: take the UTMB course.
 
2. Grantsmanship training: all CCBTP postdocs will have to complete a workshop on writing grants. Specifics will be communicated directly with the trainees.

3. Coursework: Depending on their background and previous coursework, coursework may be assigned to individual postdocs in order to strengthen skills or knowledge.

For instance a trainee with a biological or medical background may benefit from course work in computational science areas such as:
Probabilistic and Statistical Methods in Bioinformatics (UTMB BMB 6326)
Large Scale Machine Learning (RU COMP 441)
Advanced Machine Learning (UH COSC 7362)
Advanced Software Engineering (RU COMP 505 or UH COSC 6351)
Computational Mathematics for Quantitative Biomedicine (BCM GS-401)
Bioinformatics: Sequence Analysis (RU COMP 571)
Bioinformatics: Network Analysis (RU COMP 572)
Computational Molecular Bioengineering (RU BIOC 589)
Fundamentals of Medical Imaging (RU ELEC 485 or UH COSC 6370)
Cloud Computing (UH COSC 6376), or
Introduction to High-Performance Computing (UH COSC 6365).

For those coming from a mathematical or physical science background, essentially every campus involved has appropriate courses in biochemistry, cell and/or molecular biology, and the Steering Committee might recommend offerings such as Structural Basis of Human Disease (BCM BC 423J) or Systems Biology (RU SSPB 502).

For those seeking more advanced cancer-specific didactic work, they might choose from:
Cancer (BCM GS 508)
Bioinformatics and Genomic Analysis (BCM CB 459J)
Translational Cancer Biology (BCM MB 431)
Introduction to Molecular Carcinogenesis (BCM CB 457J)
Cancer Epidemiology (UTH PHM 2745)
DNA, Mutagenesis, Replication, and Environmental Toxicology (UTMB BMB 6209)
Genomics, Proteomics and Bioinformatics (UTMB BMB 6208)
Cell Signaling for Growth, Differentiation, Death (UTMB BMB 6316), or
Cancer Biology (RU BIOC 560).

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CPRIT Summer Undergraduate Fellowship

CCBTP Summer Undergraduate Fellowship in Computational Cancer Biology
The application deadline for the Summer 2017 program has ended.

Funded by Cancer Prevention and Research Institute of Texas (CPRIT) RP170593

Program Dates: May 31 - August 4, 2017

Our Computational Cancer Biology Training Program offers selected summer research undergraduates the chance to work one-on-one in labs with postdoctoral fellows who have mentors at the interface of two different research disciplines: one computational and one biological. This unique program offers you the opportunity to gain an interdisciplinary outlook on the problems presented in fundamental cancer research.

You will be matched for a research experience in one of the participating labs of the Gulf Coast Consortia, which is comprised of multiple institutions (see list at the bottom of this page) in Houston and Galveston, Texas, according to your interests, previous knowledge and/or experience, and the availability of positions. You will work full time (~40 hours/week) during this 10-week period on an ongoing project in the lab, learn lab protocol and techniques, attend workshops (including but not limited to proper lab notebook keeping, research ethics, constructing effective abstracts, scientific reports, and PowerPoint presentations) and prepare a final report and present a poster on your project at the end of the program.

Who is eligible?
• Rising sophomores, juniors, or seniors majoring in either quantitative or biological sciences, such as:

  • statistics  
  • computational & applied math    
  • computer science   
  • biology   
  • biochemistry   
  • bioengineering  
  • chemistry     
  • physics 

• Preferred: students interested in interdisciplinary research and in pursuing graduate or medical school; those having relevant coursework, and computational/programming knowledge and skills
• We particularly encourage applications from members of diverse backgrounds including under-represented minority students, students from economically disadvantaged backgrounds, and students with disabilities.
• US Citizenship or Permanent Residency required.

What is the stipend?
• $5,000 stipend total for the 10-week full-time summer research experience + up to $1,000 reimbursement for travel and housing (if needed).

What is the application process?
Please prepare and submit your application package to include the following material:
• Resumé: include your contact information (i.e. cell phone number), the name of your college or university, your year and major, and current GPA; list all previous jobs you have had (including jobs in a lab, if any), and any computer language / programming courses taken or experience you have.
• One-page statement about why you are interested in computational cancer biology, what you hope to gain from this summer research experience, and your preference for a ‘wet’ lab or a computational lab (NOTE: the availability of ‘wet’ labs is limited, therefore your choice may not be guaranteed).            
*Statement format: 11 pt, single spaced, 1” margins; include your name at the top.
• Academic Transcripts from all undergraduate institutions attended, including course enrollment in current semester. Unofficial copies are acceptable.
• 2 letters of recommendation from faculty member(s)/former employer(s) emailed directly to herrera@rice.edu.

All application materials, including transcripts and recommendation letters, must be received on or before Friday, February 24, 2017 by email to Vanessa Herrera (preferred method) at herrera@rice.edu or to the address shown below.  All applicants will be notified of an acceptance decision no later than April 7, 2017.

Physical address for sending in your application materials:
Gulf Coast Consortia, MS 141
Attn: Vanessa Herrera
6100 Main St.
Houston, Texas 77005

For more information contact Vanessa Herrera at herrera@rice.edu.

The Gulf Coast Consortia administering this program is comprised of Baylor College of Medicine, Rice University, University of Houston, UT Health Science Center at Houston, UT Medical Branch at Galveston, UT MD Anderson Cancer Center, and the Institute of Biosciences & Technology of Texas A&M Health Science Center.

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CCBTP Training Faculty

Please note that this training grant was renewed in December 2016 with a new training faculty.

If a faculty member who was on the previous grant's faculty is not on this list, or if the faculty member has not yet been on the training faculty, when s/he wishes to sponsor a candidate in the current round of applications, the faculty member will need to follow the directions on the Faculty Eligibility page to request joining the faculty.

Link to Current CCBTP Faculty

PDF of Current CCBTP Faculty

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CCBTP Steering Committee

CCBTP Steering Committee

B. Montgomery Pettitt, Program Director
The University of Texas Medical Branch at Galveston

Elmer Bernstam
The University of Texas Health Science Center at Houston

Wah Chiu
Baylor College of Medicine

Ioannis Kakadiaris
University of Houston 


Lydia Kavraki
Rice University


David Tweardy
The University of Texas MD Anderson Cancer Center


TBA
IBT-TAMSHC

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What the CCBTP postdoctoral fellowship provides

  • 12 month fellowship
  • the opportunity to compete for re-appointment (for up to a total of three years) if progress is satisfactory
  • NIH-level stipend of $47,484 per year and above (depending on the years of science-related experience since receipt of the doctoral degree)
  • partial support for fringe benefits
  • travel funds

    Note: The primary mentor/department is responsible for the remainder of any fringe, and if applicable, stipend supplementation to reach the postdoc's current pay level.

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CCBTP faculty eligibility

  • Primary and secondary mentors must be tenure-track faculty, and members of the CCBTP Training Program faculty. Please note that membership in the Gulf Coast Consortia or in one of its other training programs does not automatically confer membership in the CCBTP Training Program. 
  • Primary mentors are usually expected to have prior training experience, for example by having previously been a primary or secondary mentor in a training program.
  • A faculty member may be the primary mentor for only one CCBTP trainee at a time; the faculty member may sponsor another applicant in a call for applications shortly before the current trainee will end his/her fellowship.
  • Junior faculty who have secured external funding but have only a limited training record may be considered as secondary mentors initially, with a required commitment to participate in our mentor training programs.
  • Requests to join the training faculty will be considered only when they are sponsoring a candidate in response to the current call for applications. This must be completed prior to the application due date.

    Please contact the CCBTP Steering Committee member from your institution (see separate CCBTP Steering Committee list), as a member must nominate you. Email the Committee member the following items, and copy 
    Melissa Glueck at glueck@rice.edu:  
      • a current 5-page NIH Biosketch (in Word format) including peer-reviewed funding; faculty are expected to be PI on an NIH R01 grant or equivalent peer-reviewed federal funding, and to have a training history;
      • a few sentences about how the faculty's research interests relate to the goals of the CCBTP;
      • whether you wish to sponsor a predoctoral/postdoctoral candidate as primary/secondary mentor; and
      • the name and institution of the proposed co-mentor.

    This will be forwarded to the Program Director for consideration. The faculty member will be reviewed and notified of eligibility to join prior to the application due date.

    Should his/her applicant be appointed to a CCBTP postdoctoral fellowship, only then the faculty member will be added to the training faculty. If his/her applicant is not appointed, then the faculty member will not be added to the training faculty at that time.

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Who is eligible to apply for a postdoctoral fellowship

  • US Citizens, Permanent Residents, or Foreign Nationals with a visa that allows them to work as a postdoc
  • must be in possession of their PhD or MD when they apply for a postdoctoral fellowship. Those who have completed the requirements for their PhD but will be awarded it at a later date must supply a letter from their institution verifying this.
  • must be currently employed by a participating institution, have a job offer from an eligible mentor, or be in a position to accept a job from them soon after the interview
  • must be employed in the lab of their primary mentor on this application, not another lab
  • must live and perform their research in Texas during the training.

The Gulf Coast Consortia is committed to providing equal opportunity in training for individuals with disabilities and individuals from racial and ethnic groups who are currently under-represented in STEM fields. We welcome applications from all qualified trainees, regardless of ethnicity, race, or disability status. All GCC member institutions are ADAAA compliant and have offices of disability support services that provide accommodations and support services to trainees, faculty, staff, and visitors.

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Monthly Fellows’ Meeting dates

CCBTP fellows meet every 4th Friday of the month in BioScience Research Collaborative (BRC), 6500 Main St. @ University, in Suite 172 from 3:00-3:50 pm, prior to the Keck Seminar. Fellows from UTMB are expected to attend these meetings in person.

Two fellows will be chosen to coordinate the choice of speakers and topics.

Meeting dates for 2017:
March 24, April 28, May 26, June 23, August 4 (special time), Sept. 22, and Oct. 27.
Nov. 24 and Dec. 24 are holidays so alternate dates will be chosen by the fellows in advance.

The June 23 meeting will be with the CCBTP Summer Undergraduate students, and instead of a July meeting, CCBTP fellows will be poster judges at the Summer Undergraduate poster session on Friday, August 4, from 10:00 am - 2:30 pm (including lunch and poster awards).

Any changes due to holidays or speaker availability will be communicated by email.

Previously appointed CCBTP fellows are always welcome to attend.

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Application Forms