Pushpa joins the lab

Pushpa Itagi joins as a postdoctoral fellow, jointly mentored by Dr. Andrew Hsieh. She received her PhD in Computational Biology at the University of Kansas and was a visiting graduate researcher at the UCLA. She will work on bladder cancer genome and liquid biopsy projects, spearheading the collaboration between the Ha and Hsieh Labs, as well as the Bladder Cancer Group at Fred Hutch and UW.

Patty and Anat join the lab

Anat Zimmer is a new postdoctoral fellow in the lab. She received her PhD in computational biology at the Weizmann Institute before joining the ISB in Seattle. Now, in the Ha lab, she will work on cell-free DNA projects including development of new computational methods to study treatment response in patients with cancer.

Patty Galipeau joins the lab as a Research Project Manager overseeing the experimental wet lab operations and provide management support for the lab’s overall research program and collaborations. We are excited to have Patty bring her wealth of management, research experience, and leadership to help drive forward our mission.

Abbey and Adam join the lab.

Welcome to Abbey Thorpe and Adam Kreitzman.

Abbey is a graduate student in the Genome Sciences department at UW and is rotating in the lab this summer semester. She will be working on a project to analyze cell-free DNA ultra-low pass sequencing data in prostate cancer to identify transcriptional signatures in response to treatments.

Adam is an undergraduate student in his senior year at UCSD. He joins the lab for this summer and fall as an undergrad research assistant working on developing improved methods for cancer detection from ctDNA.

Lab receives DoD Prostate Cancer Research Program Idea Development Award

The Ha lab is awarded a CDMRP Department of Defense Prostate Cancer Research Program Idea Development Award to develop innovative approaches using cell-free DNA. This is a 3 year grant which we propose to develop new algorithms to study different layers of the cellular machinery that regulates genes using standard sequencing of ctDNA molecules. By employing machine learning techniques, we will combine different strategies of analyzing of cell-free data to classify the tumor subtypes and to identify tumor changes when treatments fail.

Adil graduates with MSc from UW Lab Medicine Program

Congratulations to Adil for successfully completing his MSc degree in the UW Laboratory Medicine Graduate Program. Adil’s thesis was titled, "Accurate quantification of placental (fetal) fraction by tissue specific cell-free DNA analysis"

Robert Patton receives Trainee Grant from Brotman Baty Institute

Congratulations to Robert Patton on receiving a Trainee Grant from the Brotman Baty Institute for Precision Medicine.

Robert’s project will involve the study of prostate cancer phenotype classification using circulating tumor DNA. He proposes use machine learning techniques to develop predictive model to analyze genomic and nucleosome features from cell-free DNA fragmentation patterns. The outcome of his work will have important applications in tumor monitoring and diagnostics for men with advanced prostate cancer.

Eden and Adil join the lab.

A warm welcome to Eden Cruikshank and Mohamed Adil

Eden is a MCB graduate rotation student for this Winter 2021 semester. She will be developing models to detect breast cancer from DNA fragment analysis of circulationg tumor DNA.

Adil is a graduate student in the Master of Science in Laboratory Medicine program at UW Medicine. He will be completing his thesis research in the Ha Lab, under direct supervision with Dr. Jonathan Reichel and in close collaboration with Dr. Colin Pritchard and Shreeram Akilesh at UW Medicine.

Robert joins the lab.

A warm welcome to Robert Patton, who joins the lab as a postdoctoral fellow in the Computational Biology Program. He will be co-mentored by Dr. Peter Nelson of Fred Hutch.

Robert just finished his Ph.D. in theoretical biophysics at The Ohio State University. At Fred Hutch, he will leverage his unique expertise to study the cancer genomes of advanced prostate cancers from tissue and liquid biopsies.

Gavin named Top 40 Under 40 in Cancer - Emerging Leaders

Congratulations to Dr. Gavin Ha for being named a Top 40 Under 40 in Cancer in 2020, recognizing his achievements as a rising star and emerging leader in cancer research.

Kelsey and Hanna join the lab.

A warm welcome to Kelsey Luu and Hanna Liao

Kelsey is a Master’s student in the Harvard Biomedical Informatics and she is working in the lab as a Bioinformatics Intern to study the complex rearrangements of prostate cancer genomes.

Hanna is a MCB graduate rotation student for this Fall 2020 semester. She will be studying the transcriptional regulation of breast cancer and neuroblastoma from circulationg tumor DNA.

Gavin is supported by the NCI Transition Career Development Award (K22)

We are very grateful to the NCI for supporting Dr. Gavin Ha with a Transition Career Development Award (K22). This award will help support his research for the next 3 years to develop computational methods for emerging technologies to analyze tumor and cell-free DNA and will provide insights into the mechanisms underpinning treatment resistance in metastatic castration resistant prostate cancer. The K22 award will allow Gavin to further develop his scientific, professional, and leadership skills and prepare him to become a well-rounded independent investigator, leading a multi-disciplinary cancer research group.

Gavin receives The V Foundation - V Scholar Grant

We are very grateful for the support of The V Foundation for awarding our lab the V Scholar Grant to develop liquid biopies approaches for identifying molecular signatures of treatment resistance in advanced prostate cancer.

Here is the story and the description of the project.

This project aims to better characterize the genetic landscape of castration-resistant prostate cancer (CRPC) to uncover genomic alterations implicated in therapeutic resistance. We are using leading research approaches to leverage “liquid biopsies” to address the challenges of tissue inaccessibility and to study the complex evolving genomic landscape of CRPC during the course of therapy.

The ultimate goal of the proposed work is to help reduce mortality from advanced prostate cancer by using innovative approaches and exploiting non-invasive biomarkers in ctDNA to predict treatment outcomes. Metastatic castration-resistant prostate cancer (CRPC) is a lethal disease with no cure. Because the majority of metastases spread to the bone, obtaining tissue biopsies are painful. Furthermore, it is not always feasible to repeatedly perform surgical biopsies during the course of treatment to assess the cancer.

The proposed approaches aim to leverage liquid biopsies as a non-invasive and sensitive screen for circulating tumor DNA (ctDNA) in cancer from patient blood. The detection of ctDNA can be used for monitoring changes in disease burden such as during progression while on treatment or disease relapse. We also propose that ctDNA can be used to identify genetic signatures in CRPC, which can pinpoint specific vulnerabilities of the cancer to therapies.

The translational impact for successfully achieving the goals of this proposed research is three-fold: (1) the development of methods will help to accelerate the use ctDNA for clinical applications; (2) the identification of genomic signatures from ctDNA can be incorporated into the design of new biomarker-guided clinical trial for CRPC; (3) the insights into therapeutic response and resistance learned from this study may reveal new directions in diagnostics and treatment of CRPC. The ability to use minimally-invasive liquid biopsies has the potential to complement or replace tissue biopsies, which will transform the standard-of-care and improve the lives of men with prostate cancer.

This research requires the strong collaborative efforts between computational, experimental, and clinical scientists, embodying the paradigm of “computer-to-bench-to-bedside.” Our key collaborators and partners at the Fred Hutch, Seattle Cancer Care Alliance, and University of Washington Medicine will be instrumental to the success of this project.

Minjeong and Yuzhen join the lab.

A warm welcome to Minjeong Ko, a new Bioinformatics Analyst, and to Yuzhen Liu, an MCB graduate rotation student.

Maggie and Will join the lab for their MCB rotations.

A warm welcome to rotation students Maggie Russell and Will Hannon.

Maggie and Will are graduate students in the MCB Program rotating for this Winter semester. They will be studying signatures of structural alterations in advanced prostate cancer.

30 Aug 2019 by Gavin Ha
Anna Hoge joins the lab.

A warm welcome to new lab member Anna Hoge.

Anna joins us as a Bioinformatics Analyst. She will be performing analysis on a variety of cancer datasets from on-going projects in the lab and through collaborations. We are delighted to have her start working on exciting research questions to study the genomes of advanced cancer patients.

Jonathan Reichel joins the lab.

A warm welcome to new lab member Jonathan Reichel.

Jonathan is a Lead Scientist at the Brotman Baty Institute (BBI) for Precision Medicine focused on cell-free DNA research. He is working with Dr. Colin Pritchard and the Ha Lab to develop new approaches for studying tissue-of-origin from circulating tumor DNA. He is facilitating its implementation into the BBI Clinical Diagnostic Platform.

Eliza Barkan joins the lab for her rotation.

A warm welcome to new lab member Eliza Barkan.

Eliza joins us as a graduate rotation student in the MCB Program for this spring semester. She will be studying signatures of structural alterations in advanced prostate cancer.

Anna-Lisa Doebley joins the lab. Welcome, Anna-Lisa!

A warm welcome to the newest lab member Anna-Lisa Doebley.

Anna-Lisa Doebley is joining us as an MSTP student in the MCB Program. She will be developing and applying novel approaches to analyze cell-free DNA from advanced cancer patients.

Welcome to the lab, Katharine Chen and Megan Chiang

A warm welcome to new lab members Katharine Chen and Megan Chiang.

Katharine joins us as a graduate rotation student in the MCB Program for this winter semester. She will be investigating approaches to analyze cell-free DNA from advanced cancer patients.

Megan join us as a bioinformatics intern from Northeastern University where she is completing her MSc. She will be analyzing tumor whole genome sequencing data from castration-resistant prostate cancer.

We are excited for them to start working on these exciting projects.

Computational Biologist/Bioinformatics Analyst position available

A computational biologist/bioinformatics analyst position in the laboratory of Dr. Gavin Ha and the Computational Biology Program is available immediately. We are seeking a highly motivated individual who is interested in studying the genetics and epigenetics of cancer using computational approaches. Candidates who are excited about large/complex ‘omics’ data analysis and cancer research are encouraged to apply. The position has a competitive salary with great benefits.

Please apply through the job posting here

Applicants must have at least a Bachelor’s degree in one of these disciplines:

  • Computational biology, bioinformatics, computer science, data science, statistics, biostatistics, biomedical engineering, computer/electrical engineering, physics, or other related fields

Applicants should have some of the following skills and experience:

  • Work well in team environments; strong communication skills; detail-oriented
  • Strong programming experience (R, Python, Matlab, Java, C/C++, Perl or other languages for research)
  • Experience with high performance computing environments or cloud computing environments is a plus
  • Experience with analyzing sequencing data is considered an asset
  • A background in cancer biology is considered an asset.

To apply, please submit your application with the following:

  • Cover letter describing your experience and/or research interests
  • CV
  • Example of your code either as (1) an attachment or (2) link(s) to public repositories (e.g. GitHub)
Postdoc position available

A postdoctoral position in the laboratory of Dr. Gavin Ha and the Computational Biology Program is available immediately. We are seeking a highly motivated individual who is interested in studying cancer and understanding the genetic and epigenetic basis driving cancer progression. Candidates who are excited about large/complex ‘omics’ data analysis and methods development for cancer research are encouraged to apply. The position has a competitive salary and great benefits.

Please apply through the job posting here

Applicants must have a PhD in one of these disciplines:

  • Computational biology, bioinformatics, computer science, data science, statistics, computer/electrical engineering, physics, or other related fields

Applicants should have some of the following skills and experience:

  • Work well in team environments; strong communication/organization skills; detail-oriented
  • Strong programming experience (R, Python, Matlab, Java, C/C++, Perl or other languages for research)
  • Experience with high performance computing environments and cloud computing environments is a plus
  • Experience with analyzing sequencing data is considered a strong asset
  • Applicants must have a demonstrated publication track record.
  • A background in cancer biology (esp in prostate or breast cancer) is considered a strong asset.

To apply, please submit your application with the following:

  • A statement of research interests and past accomplishments
  • CV
  • Names and email addresses of three references
  • Two representative publications or preprints (if available)
Paper on structural alterations in prostate cancer published in Cell

Check out the paper here

New website for the (Gavin) Ha Lab

Under construction – Please check back later for updates.