The Aparicio lab studies the genomic and phenotypic behaviour of breast and other cancers. Integrating leading edge technologies with patient-derived xenograft models of cancer, this research is working to better understand how cancer clones evolve and to identify novel strategies for cancer treatment and predictors of response.   

Dr. Aparicio’s research program encompasses the fields of cancer genomics, cancer evolution, single cell biology, mouse genetic models, high throughput screens, small molecule chemical probe development and translational breast cancer research. His work on the molecular taxonomy of breast cancer led to identification of new genes that could change the way breast cancer is diagnosed, and form the basis of next-generation treatments. This discovery was preceded by another breakthrough in decoding the genetic makeup of the most-deadly form of breast cancer, known as triple negative subtype (TNBC). Dr. Aparicio is also working to develop quantitative measures of clonal fitness in patients, including methods for single cell genome sequencing and PDX models of human cancer. He collaborates widely with other groups, with current projects including the genomic and biochemical analysis of lymphoma, ovarian cancer, and several rare pediatric cancers. He was a co-founder of Paradigm Therapeutics (now, Takeda Cambridge) and currently Contextual Genomics Ltd.

Website

Members

Faculty/Leaders

Staff

Husain Akbar

RESEARCH ADMINISTRATIVE COORDINATOR

Vinci Au

Research Assistant/Technician

Cherie Bates

Leader, Breast Cancer Provincial Clinical Research Program

Sean Beatty

Bioinformatics Scientist

Viviana Cerda Llanos

Research Assistant

Woongcheol (William) Choi

Research Assistant/Technician

Cynthia Ferguson

Research Projects and Operations Leader

Cristina Flores

Research Assistant/Technician

Shahid Haider

Programmer

BaRun Kim

RA/Technician

Esther Kong

Research Assistant

Daniel Lai

Senior Bioinformatics Scientist

So Ra Lee

Research Assistant/Technician

Joseph Micla

Front-end Web Developer

Ciara O'Flanagan, PhD

Research Associate

Benoit Prevost-Potvin

Software Developer

Robert Reinert

Data Manager

Yukta Thapliyal

Programmer

Michael Van Vliet

Research Assistant / Technician

Adrian Wan

Laboratory Research and Operations Manager

Jecy (Beixi) Wang

Research Assistant

Elena Zaikova

Bioinformatics Scientist

Ismat Zerin

Research Assistant

Post-Docs

Gurdeep Singh

Postdoctoral Fellow

Hoa Tran

Post-doctoral Fellow

Students/Trainees

Sanna Bhayana

Co-op Student

Vivien Dang

Summer Student

Jenna Liebe

Co-op Student

Yi Fei (Eric) Liu

Directed studies student

Isaac von Riedemann

Co-op Student

Chun Hei Yiu

Co-op Student

Open Positions

Research Grant Facilitator and writer

Application Deadline

Job Summary

The post holder will support and work closely with Dr. Samuel Aparicio, leader of Molecular Oncology, UBC Nan and Lorraine Robertson Chair of Breast Cancer, in developing scientific proposals, assisting in manuscript development and review, coordinating international multi-PI research studies and interacting with funders and advocates in reporting the activities of the single cell biology and drug development program. Demonstrated experience in authoring manuscripts and preparing funding applications and reports, is a requirement for the role. Preference will be given to candidates with experience in biosciences and cancer research. Ability to articulate science clearly in a written form and a high degree of independence and self organization are core skills for this post.

The Research Grants Facilitator and Writer will provide strategic planning and support for the program in single cell biology and drug development led by Dr. Samuel Aparicio. The incumbent will identify and communicate research award and funding opportunities from Canadian and international government funding agencies, private foundations and industry, as well as provide proposal development support for the Aparicio program’s research grant applications and award nominations, including writing significant portions of research proposals and grant applications. The incumbent will establish and maintain relationships with key points of contact with internal and external research and award sponsors. The incumbent will develop strategic research support plans for the single cell biology program. The incumbent will also provide authoritative advice and understanding of the mandates, priorities, processes and policies of internal UBC and major Canadian and international government and private research funding sponsors.

Organizational Status

This position reports directly to Dr. Aparicio and works closely with the program team members and collaborators to ensure that the Research Grants Facilitator and Writer's activities are integrated into the effective operation of the single cell biology research program. The position communicates directly with UBC faculty and staff, BC Cancer Research Institute (BCRI) researchers and external research sponsor personnel.

Work Performed

Facilitation of Grant Application Process and Advising

  • Acts as a knowledge resource for Dr. Aparicio for research funding opportunities and actively seeks out and encourages applications for funding to improve the research program’s success in grants.
  • Establish and maintain productive relationships with internal and external research sponsors in order to maintain current knowledge of the research award and funding landscape.
  • Establish and maintain productive relationships with UBC and BCRI researchers, postdoctoral fellows, students and/or staff and maintain in-depth knowledge and understanding of their research within the single cell biology program.
  • Identify and disseminate information regarding various granting agencies requests for applications and research funding opportunities from various agencies to the research program. When requested, investigate potential funding opportunities on a specific topic or given area.
  • Provide authoritative advice to researchers and Dr. Aparicio on the eligibility criteria, deadlines, submission processes, budget requirements and other important details regarding internal and external research funding and award opportunities.
  • Ensure Dr. Aparicio is aware of, and address within the program’s funding applications, University and external agency policies and procedures.
  • Review research grant applications for key institutional requirements prior to the provision of Faculty­ level signatures.
  • Work with faculty in the development of research grant or award nomination proposals, which may include research team coordination; grant writing; copy editing; reviewing and providing feedback on proposal design and content; providing advice on grant budgets; assisting in the writing of letters of intent and proposal support letters; and assisting faculty to ensure that key components of grant applications are complete prior to submission.
  • Advise faculty and trainees within the single cell biology research program of research funding and award opportunities and research support services.
  • Identify potential funding opportunities to support identified research program strategic research plans.
  • Develop digital resources (e.g. budget templates, web content) to aid in the development of research proposals.
  • Develop, manage, collect, and coordinate relevant grant information, research budgets, statistics, and curriculum vitae.
  • Liaise effectively with UBC Office of Research Services, VP Research and Innovation, SPARC, research sponsor personnel, Research and Trust Accounting, University Industry Liaison Office, Institutional Programs Office, BCRI Office of Research Administration and Faculty and administrative staff on questions related to the acquisition and administration of research funding.
  • Manage and develop necessary agreements for the single cell biology research program in conjunction with the UBC Office of Research Services/University-Industry Liaison Office and BC Cancer Technology Development Office.
  • Respond to ongoing requests for regular reports by maintaining and updating information to ensure compliance with granting agencies and other external organizations.
  • Develop Research Ethics Board applications and amendments as required, and ensures compliance with Research Ethics Board guidelines.
  • Conduct regular literature reviews relating to research areas.  Contributes intellectual and scientific input to manuscripts for publications, provides scientific proofreading.

Facilitation of Research Knowledge Transfer and Exchange/Education

  • Develop and maintain a clear engagement and communication plan for both internal and external audiences.  This includes promotion and representation of the single cell biology research program through websites and social media platforms, and the development and facilitation of workshops, conferences, guest lecturers, etc.
  • Provide partners and Communications personnel with information on current research projects, recent grant awards and publications; ability to understand and effectively communicate complex scientific issues to the non-expert public, both verbally and in writing.
  • Develop and implement grant writing supports for the single cell biology research program (e.g. educational sessions and workshops on grant writing, open access, partnered research, award nomination, adopting researcher digital identifiers).

Strategic Planning

  • Monitor the research grant writing and research infrastructure support needs of the research program and, based on these needs, provide recommendation to Dr. Aparicio, on the ongoing requirements and possible avenues of research support.
  • In collaboration with Dr. Aparicio, plays a leadership role in identifying, developing, and applying for large and complex research grant funding from various funding agencies including provincial, federal and international programs.
  • Initiate and facilitate collaborations and initiatives between researchers, develop research partnerships, and identify funding opportunities.
  • Identify new translational pathways, such as commercial partnerships, licencing etc. for new technologies and encourage entrepreneurial activities as appropriate.

Supervision Received

The position works with a high degree of independence under the direction of Dr. Aparicio. Works independently in accordance with objectives established by the single cell biology research program.

Supervision Given

This position does not include supervision of other staff.

Consequence of Error/Judgement

The work of the incumbent is vital to the success of the development and acquisition of research grants and awards in the single cell biology research program. The position has significant influence on the quality and effectiveness of research support services within the research program. Failure to accurately adhere to external granting agency and University research policies and procedures can result in the subsequent rejection of grant applications, the return of awarded funds, the loss of future funds and/or the inability to collect funds owed to the University, and researchers. The loss of future opportunities and funds would call into question the perceived level of research competence of the research program and investigators.

Minimum Qualifications

A post-graduate degree or equivalent professional designation with a minimum of four years of related experience, or an equivalent combination of education and experience. Otherwise, an undergraduate degree in a relevant discipline is required with a minimum of six years of related experience, or an equivalent combination of education and experience.

Preferred Qualifications

  • Experience in a research environment with applied knowledge and demonstrated skill in successful research grant application development, facilitation, and administration (particularly in the health sciences) is preferred.
  • Strong understanding of the language and culture of the research community and research granting agencies.
  • Proven mastery of English grammar, punctuation, and scientific writing style is essential. Ability to communicate effectively verbally and in writing and to summarize relevant information in clear and succinct English, is essential.
  • High degree of analytical accuracy, sound judgment and the ability to work independently.
  • Superior communication skills (oral and written), excellent writing and copy-editing skills as well as experience in manuscript preparation are required.
  • Strong interpersonal skills and the ability to work effectively with internal and external stakeholders who possess a wide range of education and expertise.  Ability to use independent judgment and to manage and impart information to a diverse range of internal and external stakeholders.
  • Ability to exercise appropriate tact, discretion, confidentiality, and good judgment in all matters.
  • Knowledge of and/or experience in project management principles, accounting and fiscal management is preferable.
  • Very good knowledge of University policies and procedures related to research administration.
  • A broad knowledge of University structure and operations.
  • Demonstrated knowledge, skill and experience in research grant development, scientific technical writing, report writing and administration.
  • Excellent knowledge of policies and procedures of research funding sponsors and agencies.
  • Excellent organizational and time management skills, and demonstrated ability to coordinate research teams.
  • Ability to adapt to changing priorities, multitasking and meeting deadlines.
  • Experience in using a wide variety of word processing, spreadsheet, database and web applications essential; ability to learn/use sponsor grant application and reporting systems.
  • Strong presentation skills using PowerPoint and other multimedia.

This is a one year appointment and depending on funding and successful progress of the research it may be renewed for additional years.

Equity and diversity are essential to academic excellence. An open and diverse community fosters the inclusion of voices that have been underrepresented or discouraged.   We encourage applications from members of groups that have been marginalized on any grounds enumerated under the B.C. Human Rights Code, including sex, sexual orientation, gender identity or expression, racialization, disability, political belief, religion, marital or family status, age, and/or status as a First Nation, Metis, Inuit, or Indigenous person.

All qualified candidates are encouraged to apply; however Canadians and permanent residents will be given priority.

PDF (Molecular Biology), Single Cell Genomics, Aparicio lab

We are seeking a highly-motivated post-doctoral fellow (PDF) with strong leadership ability and expertise in single cell genomics and transcriptomics, and a strong background in molecular biology. The successful applicant will work full-time under the supervision of Dr. Samuel Aparicio. The position start date is flexible.

JOB SUMMARY

The Aparicio lab is developing new single cell genome and transcriptome methods for tracking clonal trajectories at single cell level in patient tissues and patient-derived xenografts (PDX). A PDF position is available in the Aparicio lab based at the BC Cancer Research Center in Vancouver, Canada, collaborating on an exciting project mapping clonal dynamics in human cancers with new single cell methods. The post holder will have the opportunity to interact as part of the international CRUK Grand Challenge IMAXT project, bringing new measurement methods and computational techniques to the 3D reconstruction of tumours, and mapping drug sensitivity and drug combinations using sgRNA/CRISPR methods in vivo. The program works closely with the Shah computational biology program, based at Memorial Sloan Kettering Cancer Centre, on the development of new models for single cell data and cancer evolution. Some experience with bioinformatics approaches to biological data and familiarity with handling of genomics data will be an advantage. 

ORGANIZATIONAL STATUS

The Postdoctoral Fellow will play a leadership role in the Aparicio lab, and will be reporting directly to Dr. Samuel Aparicio who is the primary investigator of the laboratory. More information on the lab, please visit https://aparicio.molonc.ca

WORK PERFORMED

  • Provide leadership, strategic direction, and translational research pertaining to single cell genomics and transcriptomics, and CRISPR methods.
  • Design and implement research plan to investigate the clonal dynamics in human cancer through single cell methods.
  • Design and conduct animal experiments.
  • Conduct in vivo testing or characterization of drugs, small molecules, knockouts or antibodies in relevant PDX animal models.
  • Foster research collaborations and work jointly with academic, clinical, industry, and other partners.
  • Scientifically document lab experiments, data analysis, interpretations.
  • Write manuscripts, present results at internal and external meetings.
  • Identify funding opportunities and if required write or assist with grant proposals.
  • Lead and mentor junior trainees/students in the laboratory.

CONSEQUENCE OF ERROR

This is a senior research position that plays a critical role in the development of this novel field. PDF is accountable for the quality and integrity of the research and data, including analyses and interpretation, as well as the effective and efficient management of research projects and deliverables. This position requires innovation, strategic planning, and adaptability. Incorrect decisions or actions may damage the reputation of the laboratory, lead to loss of credibility in this field, and be financially costly.

SUPERVISION RECEIVED

The PDF will work with a high degree of independence and set priorities under broad directives from Dr. Aparicio. The PDF will be expected to provide direction and mentoring in the laboratory under the supervision of Dr. Aparicio. This position will also provide the candidate with a high level of exposure to single cell genomics and translational research, as well as, providing opportunities to work collaboratively with industry partners and other researchers globally.

SUPERVISION GIVEN

The PDF will be expected to provide mentorship and guidance to undergraduate, graduate students and other research members as required.

QUALIFICATION

  • Ph.D. in biology, cell biology, molecular biology, biochemistry, genetics, genomics, or similar discipline.
  • The candidate should have a solid scientific and technical background with excellent written/oral communication, interpersonal and organizational skills.
  • Preference will be given to candidates with a proven track record with a minimum of 2-3 first author publications in reputable journals.
  • Proficiency in cell biology, molecular biology, histology, genetics, genomics, next-generation sequencing and biochemistry techniques.
  • Demonstrate the ability to work in a highly interdisciplinary environment.
  • Experience with cancer research.
  • Expertise and hands-on experience in animal studies, including all aspects of design, handling, breeding, tissue collection, histology, and analyses are essential.
  • Familiarity with testing/characterization of small molecule or drug in vivo is preferred.
  • Previous biochemical/cell biology and molecular biology experience with single cell genomics / transcriptomics, next generation sequencing, drugs screen and PDX modeling is an asset.
  • Experience with statistical analyses and scientific writing. Previous experience with grant writing is an asset.
  • Experience with bioinformatics approaches to biological data and familiarity with handling of genomics data is an asset.
  • Applicants with experience and a strong track record with large drug target screening, single cell methods, and PDX mouse models are especially encouraged to apply.

How to Apply

Exceptional candidates should submit a cover letter outlining your research interests and fit with the laboratory’s research, curriculum vitae, and the names of three referees willing to provide letters of reference.

To apply:  Please send the above documents to careersmolonc@bccrc.ca and put “PDF (Molecular Biology), Single Cell Genomics, Aparicio lab” and your family name in the subject line.

Due to the number of resumes we receive, we are unable to confirm receipt of submissions over the phone, or provide the status of the competition. Only shortlisted candidates will be contacted.

Equity and diversity are essential to academic excellence.  An open and diverse community fosters the inclusion of voices that have been underrepresented or discouraged.  We encourage applications from members of groups that have been marginalized on any grounds enumerated under the B.C. Human Rights Code, including sex, sexual orientation, gender identity or expression, racialization, disability, political belief, religion, marital or family status, age, and/or status as a First Nation, Metis, Inuit, or Indigenous person.

All qualified candidates are encouraged to apply; however Canadians and permanent residents will be given priority. 

PDF (Bioinformatics), Next-Generating Sequencing, Aparicio lab

Job Summary

The candidate would work within a dynamic and vibrant lab with a proven track record of outstanding achievements and contributions in breast oncology research. This position allows the candidate to contribute bold and innovative research that can be translated to new understanding in the evolutionary processes that drive cancers.

This position's primary focus in the lab will be to lead and to participate in projects involving the investigation of functional genomics using sequencing and expression data for breast oncology and cancer evolution. Using the wide network of connections and collaborations of the principal investigator, and extensive biomedical resources at the institution, candidates will be able to build on the existing research of the lab to quickly start up their own research projects.

The position will provide a unique opportunity for mentoring trainees, supervising analysts and interacting with industry. This is an excellent platform to receive outstanding training to gain the important skills for a successful medical research career in academia or industry.

This funded position with the University of British Columbia, at the BC Cancer Research Centre allows the candidate to flourish under the guidance of an experienced mentor

Organizational Status

The Postdoctoral Fellow will play a leadership role in the Aparicio lab, and will be reporting directly to Dr. Samuel Aparicio who is the primary investigator of the laboratory. More information on the lab, please visit https://aparicio.molonc.ca

Work Performed

  • Management and supervision of trainees;
  • May be involved in recruitment and training of trainees;
  • Performing regular reviews of the relevant literature;
  • Planning and designing of experiments;
  • Analyzing, interpreting and compiling data in study reports, presenting results, and participating in the preparation of scientific manuscripts and grant application packages;
  • Updating Dr. Aparicio and the group on the status of projects during lab meetings, in email correspondence and phone conferences;
  • Managing projects with key academic and industry partners.

Minimum Qualifications

  • PhD degree in the computer science, bioinformatics or equivalent
  • At least 4 years experience in bioinformatics research
  • Experience in genomics and next-generation sequencing
  • Extensive knowledge of cellular and molecular biology, biochemistry and genetics
  • Experience with cancer research a plus
  • Proven ability to multi-task in a deadline oriented environment with minimal supervision
  • Effective oral and written communication, analytical, and interpersonal skills
  • Excellent organizational skill and ability to learn new skills quickly
  • Ability to work independently and within a team environment.
  • Accuracy and attention to detail required
  • Candidates should demonstrate the ability to work in a highly interdisciplinary environment.

Supervision Received 

  • Works independently under direction of PI, Dr. Samuel Aparicio
  • Opportunities to work collaboratively with Industry partners and other researchers at UBC and globally

Supervision Given

  • Assists and oversees research assistants and students as required
  • Assists and provides guidelines to other research members, as required

How to Apply

Exceptional candidates should submit a cover letter outlining your research interests and fit with the laboratory's research, curriculum vitae, and the names of three referees willing to provide letters of reference.

To apply:  Please send the above documents to careersmolonc@bccrc.ca and put “PDF (Bioinformatics), Next-Generating Sequencing, Aparicio lab” and your family name in the subject line.

Due to the number of resumes we receive, we are unable to confirm receipt of submissions over the phone, or provide the status of the competition. Only shortlisted candidates will be contacted.

Equity and diversity are essential to academic excellence.  An open and diverse community fosters the inclusion of voices that have been underrepresented or discouraged.  We encourage applications from members of groups that have been marginalized on any grounds enumerated under the B.C. Human Rights Code, including sex, sexual orientation, gender identity or expression, racialization, disability, political belief, religion, marital or family status, age, and/or status as a First Nation, Metis, Inuit, or Indigenous person.

All qualified candidates are encouraged to apply; however Canadians and permanent residents will be given priority.

Selected Publications

Clonal Decomposition and DNA Replication States Defined by Scaled Single-Cell Genome Sequencing.

Cell, 2019
Laks, Emma, McPherson, Andrew, Zahn, Hans, Lai, Daniel, Steif, Adi, Brimhall, Jazmine, Biele, Justina, Wang, Beixi, Masud, Tehmina, Ting, Jerome, Grewal, Diljot, Nielsen, Cydney, Leung, Samantha, Bojilova, Viktoria, Smith, Maia, Golovko, Oleg, Poon, Steven, Eirew, Peter, Kabeer, Farhia, Ruiz de Algara, Teresa, Lee, So Ra, Taghiyar, M Jafar, Huebner, Curtis, Ngo, Jessica, Chan, Tim, Vatrt-Watts, Spencer, Walters, Pascale, Abrar, Nafis, Chan, Sophia, Wiens, Matt, Martin, Lauren, Scott, R Wilder, Underhill, T Michael, Chavez, Elizabeth, Steidl, Christian, Da Costa, Daniel, Ma, Yussanne, Coope, Robin J N, Corbett, Richard, Pleasance, Stephen, Moore, Richard, Mungall, Andrew J, Mar, Colin, Cafferty, Fergus, Gelmon, Karen, Chia, Stephen, , , Marra, Marco A, Hansen, Carl, Shah, Sohrab P, Aparicio, Samuel

Dissociation of solid tumor tissues with cold active protease for single-cell RNA-seq minimizes conserved collagenase-associated stress responses.

Genome biology, 2019
O'Flanagan, Ciara H, Campbell, Kieran R, Zhang, Allen W, Kabeer, Farhia, Lim, Jamie L P, Biele, Justina, Eirew, Peter, Lai, Daniel, McPherson, Andrew, Kong, Esther, Bates, Cherie, Borkowski, Kelly, Wiens, Matt, Hewitson, Brittany, Hopkins, James, Pham, Jenifer, Ceglia, Nicholas, Moore, Richard, Mungall, Andrew J, McAlpine, Jessica N, , , Shah, Sohrab P, Aparicio, Samuel

CX-5461 is a DNA G-quadruplex stabilizer with selective lethality in BRCA1/2 deficient tumours.

Nature communications, 2017
Xu, Hong, Di Antonio, Marco, McKinney, Steven, Mathew, Veena, Ho, Brandon, O'Neil, Nigel J, Santos, Nancy Dos, Silvester, Jennifer, Wei, Vivien, Garcia, Jessica, Kabeer, Farhia, Lai, Daniel, Soriano, Priscilla, Banáth, Judit, Chiu, Derek S, Yap, Damian, Le, Daniel D, Ye, Frank B, Zhang, Anni, Thu, Kelsie, Soong, John, Lin, Shu-Chuan, Tsai, Angela Hsin Chin, Osako, Tomo, Algara, Teresa, Saunders, Darren N, Wong, Jason, Xian, Jian, Bally, Marcel B, Brenton, James D, Brown, Grant W, Shah, Sohrab P, Cescon, David, Mak, Tak W, Caldas, Carlos, Stirling, Peter C, Hieter, Phil, Balasubramanian, Shankar, Aparicio, Samuel

CLK-dependent exon recognition and conjoined gene formation revealed with a novel small molecule inhibitor.

Nature communications, 2017
Funnell, Tyler, Tasaki, Shinya, Oloumi, Arusha, Araki, Shinsuke, Kong, Esther, Yap, Damian, Nakayama, Yusuke, Hughes, Christopher S, Cheng, S-W Grace, Tozaki, Hirokazu, Iwatani, Misa, Sasaki, Satoshi, Ohashi, Tomohiro, Miyazaki, Tohru, Morishita, Nao, Morishita, Daisuke, Ogasawara-Shimizu, Mari, Ohori, Momoko, Nakao, Shoichi, Karashima, Masatoshi, Sano, Masaya, Murai, Aiko, Nomura, Toshiyuki, Uchiyama, Noriko, Kawamoto, Tomohiro, Hara, Ryujiro, Nakanishi, Osamu, Shumansky, Karey, Rosner, Jamie, Wan, Adrian, McKinney, Steven, Morin, Gregg B, Nakanishi, Atsushi, Shah, Sohrab, Toyoshiba, Hiroyoshi, Aparicio, Samuel

Divergent modes of clonal spread and intraperitoneal mixing in high-grade serous ovarian cancer.

Nature genetics, 2016
McPherson, Andrew, Roth, Andrew, Laks, Emma, Masud, Tehmina, Bashashati, Ali, Zhang, Allen W, Ha, Gavin, Biele, Justina, Yap, Damian, Wan, Adrian, Prentice, Leah M, Khattra, Jaswinder, Smith, Maia A, Nielsen, Cydney B, Mullaly, Sarah C, Kalloger, Steve, Karnezis, Anthony, Shumansky, Karey, Siu, Celia, Rosner, Jamie, Chan, Hector Li, Ho, Julie, Melnyk, Nataliya, Senz, Janine, Yang, Winnie, Moore, Richard, Mungall, Andrew J, Marra, Marco A, Bouchard-Côté, Alexandre, Gilks, C Blake, Huntsman, David G, McAlpine, Jessica N, Aparicio, Samuel, Shah, Sohrab P

The somatic mutation profiles of 2,433 breast cancers refines their genomic and transcriptomic landscapes.

Nature communications, 2016
Pereira, Bernard, Chin, Suet-Feung, Rueda, Oscar M, Vollan, Hans-Kristian Moen, Provenzano, Elena, Bardwell, Helen A, Pugh, Michelle, Jones, Linda, Russell, Roslin, Sammut, Stephen-John, Tsui, Dana W Y, Liu, Bin, Dawson, Sarah-Jane, Abraham, Jean, Northen, Helen, Peden, John F, Mukherjee, Abhik, Turashvili, Gulisa, Green, Andrew R, McKinney, Steve, Oloumi, Arusha, Shah, Sohrab, Rosenfeld, Nitzan, Murphy, Leigh, Bentley, David R, Ellis, Ian O, Purushotham, Arnie, Pinder, Sarah E, Børresen-Dale, Anne-Lise, Earl, Helena M, Pharoah, Paul D, Ross, Mark T, Aparicio, Samuel, Caldas, Carlos

The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups.

Nature, 2012
Curtis, Christina, Shah, Sohrab P, Chin, Suet-Feung, Turashvili, Gulisa, Rueda, Oscar M, Dunning, Mark J, Speed, Doug, Lynch, Andy G, Samarajiwa, Shamith, Yuan, Yinyin, Gräf, Stefan, Ha, Gavin, Haffari, Gholamreza, Bashashati, Ali, Russell, Roslin, McKinney, Steven, , , Langerød, Anita, Green, Andrew, Provenzano, Elena, Wishart, Gordon, Pinder, Sarah, Watson, Peter, Markowetz, Florian, Murphy, Leigh, Ellis, Ian, Purushotham, Arnie, Børresen-Dale, Anne-Lise, Brenton, James D, Tavaré, Simon, Caldas, Carlos, Aparicio, Samuel

The clonal and mutational evolution spectrum of primary triple-negative breast cancers.

Nature, 2012
Shah, Sohrab P, Roth, Andrew, Goya, Rodrigo, Oloumi, Arusha, Ha, Gavin, Zhao, Yongjun, Turashvili, Gulisa, Ding, Jiarui, Tse, Kane, Haffari, Gholamreza, Bashashati, Ali, Prentice, Leah M, Khattra, Jaswinder, Burleigh, Angela, Yap, Damian, Bernard, Virginie, McPherson, Andrew, Shumansky, Karey, Crisan, Anamaria, Giuliany, Ryan, Heravi-Moussavi, Alireza, Rosner, Jamie, Lai, Daniel, Birol, Inanc, Varhol, Richard, Tam, Angela, Dhalla, Noreen, Zeng, Thomas, Ma, Kevin, Chan, Simon K, Griffith, Malachi, Moradian, Annie, Cheng, S-W Grace, Morin, Gregg B, Watson, Peter, Gelmon, Karen, Chia, Stephen, Chin, Suet-Feung, Curtis, Christina, Rueda, Oscar M, Pharoah, Paul D, Damaraju, Sambasivarao, Mackey, John, Hoon, Kelly, Harkins, Timothy, Tadigotla, Vasisht, Sigaroudinia, Mahvash, Gascard, Philippe, Tlsty, Thea, Costello, Joseph F, Meyer, Irmtraud M, Eaves, Connie J, Wasserman, Wyeth W, Jones, Steven, Huntsman, David, Hirst, Martin, Caldas, Carlos, Marra, Marco A, Aparicio, Samuel

Projects

Tumour heterogeneity and clonal dynamics of breast cancer

Cancer is a dynamic disease, and as a result a single tumour mass may comprise a diverse collection cancer clones with distinct phenotypes, mutations or sensitivity to treatment. Integrating deep and single cell genomic and transcriptomic sequencing with statistical modeling of clonal fitness, our lab is developing methods to study and predict the clonal dynamics of cancer in PDX and cell models, under natural and selective pressures such as drug intervention or CRISPR knockout.

Methods for studying cancers at single cell resolution

Single cell sequencing technologies allow the study of phenomena such as tumour heterogeneity, clonal dynamics, tissue microenvironments as well as the identification of novel and intermediary cell types, which may not be easily resolved with bulk sequencing strategies. Our lab has developed methods for the surveying of single cell genomics, and integrates them with methods to study the epigenome and transcriptome at single cell resolution, as well as with imaging techniques for spatial context

Sponsors

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