Welcome to the Kober Lab

Welcome to our lab!

We are interested in using rich demographic, clinical and molecular data to improve our understanding of the molecular mechanisms underlying common symptoms (e.g., fatigue) or neurotoxic side effects (e.g., peripheral neuropathy) experienced by patients with cancer.

In addition, we develop and improve prediction models that would assist clinicians to identify high risk patients and provide recommendations for activity modifying interventions.

Finally, we develop new methods, tools, and resources as we explore new research space and strive to make them avaialable to the research community.

We are fortunate to have a well established track-record of successful collaborations and mentorships with transdisciplinary research teams. We believe this approach is needed to develop future symptom scientists who work with genomics and big data. For additional graduate student and post-doctoral opportunities, please look at the UCSF School of Nursing T32 Biobehavioral Research Program in Symptom Science.

If you are interested in studying genomics here at UCSF, the School of Nursing offers a Genomics Concentration that provides a spectrum of content related to human genomics and clinical implications for nurses taught by Dr. Elena Flowers and Dr. Kord Kober.

In the news...

[Open Position] Join our lab! We seek a dynamic and self-motivated Lead Molecular Biologist/Lab Manager who is looking to grow as a researcher, be supported, contribute to wet and dry lab work, and contribute to the success of a collaborative research lab. The Lead Molecular Biologist/Lab Manager assists the principal investigator (PI) and other staff with active experiments and the daily tasks related to the operation of a research laboratory and biorepository eventually assume lab manager and biorepository administrator roles. Interested candidates can see the full job description and apply here: 60348BR

Carolyn Harris's manuscript "Symptom Clusters in Patients Receiving Chemotherapy: A Systematic Review" was accepted for publication at BMJ Supportive and Palliative Care. Congratulations, Carolyn! (November 23, 2021)

We are excited that Esther Chavez-Inglesias has joined our lab as a Staff Research Associate I. Welcome, Esther! (November 16, 2021)

Congratulations to our research team who all presented research in virtual podium presentations at the 2021 ISONG Virtual World Congress. There were five studies looking at molecular pathways associated with symtom severity in patients undergoing treatment for cancer. The studies were presented by Dr. Chris Miaskowski (sleep), Carolyn Harris (evening fatigue), Kate Oppegaard (state anxiety), Joosun Shin (worst pain), and myself (morning fatigue). We are also excited that the analyses of the demographic and clinical characteristics in all five projects was performed by our data science trainee Vasuda Dokiparthi. (November 5-7, 2021)

Congratulations to Dr. Lucy Kornblith, Dr. Bainton Roland, Dr. Man-Cheung Lee and team on receiving the Canizaro award at the American Association of the Surgery of Trauma for their work on platelet genomics titled "A New Trauma Frontier: Exploratory Pilot Study of Platelet Transcriptomics in Trauma Patients". It was a pleasure to collaborate with you all. The manuscript was recently accepted for publication at The Journal of Trauma. (October 23, 2021)

Congratulations to Dr. Jim Brunner for presenting our collaborative work in a talk entitled "A dynamical system model for predicting gene expression from the epigenome" today at the Institute-wide Lab Meeting at the UCSF Bakar Computational Health Sciences Institute. (September 13, 2021)

Carolyn Harris passed her qualifying exam, advanced to candidacy, and successfully defended her dissertation proposal. Congratulations, Carolyn! (August 20, 2021)

Congratulations to Carolyn Harris for her election as the Student Representative to the International Society of Nurses in Genetics (ISONG) 2021-2022 Board of Directors! (July 30, 2021)

Carolyn Harris and Kate Oppegaard's manuscript, "Cancer-Related Cognitive Impairment is Associated with Perturbations in Inflammatory Pathways", was accepted for publication in Cytokine. Congratulations! (July 17, 2021)

Dr. Jim Brunner's abstract was accepted for a poster presentation at the ISMB/ECCB 2021 conference in the Regulatory and Systems Genomics (RegSys) COSI track. Jim will be presenting our collaborative work titled "A Stochastic Dynamical System Identifies Genes With Variable Transcription Factor Binding Activities". Congratulations, Jim! (May 25, 2021)

Our work developing prediction models for and evaluating for the molecular mechanisms of cancer-related fatigue was discussed today in the Science of Caring article: How Nurses Are Using Big Data and Genomics to Transform Patient Care. (May 25, 2021)

The genomics training in the T32 workshops and the genomics concentration were highlighted in the Science of Caring today: Preparing Nurses to Revolutionize Care Through Genomics . (May 25, 2021)

Congratulations to Nadia "Nate" Haas for successfully defended her thesis today entitled "Cytokine Gene Variations Are Associated With Levels Of Exercise In Women Prior To Breast Cancer Surgery". Congratulations, Nate! (May 19, 2021)

Recently, Dr. Sue Yom invited me to collaborate on an editorial highlighting the important role that cancer-related fatigue can play in influencing patients' treatment outcomes as well as their experiences and quality of life. I am excited to share that our editorial ("Doc, I Feel Tired ... Oh Really, So How’s Your Mucositis?") has been accepted by Cancer. It was a delight to work with Dr. Yom on this project. (April 26, 2021)

Man-Cheung Lee's abstract entitled "A New Trauma Frontier: Platelet Transcriptomics" was accepted for an oral presentation at the 80th Annual Meeting of AAST and Clinical Congress of Acute Care Surgery. Congratulations, Manch! (April 21, 2021)

Our research on the systems biology of symptoms was showcased in the Discovery Talks as part of the 2021 UCSF Alumni Weekend. (April 17, 2021)

Kate Oppegaard and Joosun Shin both were awarded the 2021 Oncology Nursing Foundation Doctoral Academic Scholarship. Congratulations to you both! (April 3, 2021)

Dr. Jim Brunner's abstract of our development of a dynamical system model for predicting gene expression from the epigenome was accepted for a lightning presentation at the 10th Annual Southern California Systems Biology Symposium. (March 3, 2021)

Carolyn Harris' manuscript "Multi-Staged Data-Integrated Multi-Omics Analysis for Symptom Science Research" was accepted by Biological Research for Nursing. Congratulations, Carolyn! (March 1, 2021)

Our paper using machine learning approaches to develop and evaluate models to predict evening cancer chemotherapy-related fatigue following chemotherapy was published today: Prediction of evening fatigue severity in outpatients receiving chemotherapy: less may be more. (February 23, 2021)

The UCSF School of Nursing is the top public recipient of 2020 federal research funding! See the whole article 'UCSF School of Nursing Ranks No. 1 Among Public Institutions in NIH Funding', (February 17, 2021).

Dr. Chris Miaskowski (Mentor) and I (Mentee) are honored and grateful to have received the Mentor-Mentee Research Award at the inaugural NINR-ONS-NCI Symptom Science Symposia. The purpose of the award is recognize an outstanding mentor and mentee dyad for their contributions to the Oncology Nursing Research program. (February 5, 2021)

Congratulations to Carolyn Harris, Kate Oppegaard, and Joosun Shin who all presented their research recently in virtual podium presentations at the inaugural NINR-ONS-NCI Symptom Science Symposia (February 4-5, 2021)

2020

Congratulations to Carolyn Harris and Kate Oppegaard who both presented their research recently in virtual podium presentations at the 2020 International Society of Nurses in Genetics (ISONG) Congress: "Genomic Nursing: Fulfilling Nightingale’s Legacy of Care" (November 13, 2020).

We are excited and honored to share that our work on "Morning Fatigue Severity Profiles in Oncology Outpatients Receiving Chemotherapy" (Wright et al. 2019, PMID 30024437) has received the annual Research Award from Cancer Nursing for 2019. Congratulations to our team! (August 5, 2020)

In support of the research community’s response to the COVID-19 pandemic, from March through June 2020 Kiley Charbonneau and Maureen Lewis performed literature reviews and provided annotations of human and viral genome mappable data for the SARS-CoV-2 Genome Browser for the Crowd-Sourced Data track. This browser is the world’s most comprehensive, publicly available and unrestricted tracking system for new strains of the SARS-CoV-2 virus. See the whole article in the UCSC Genome Browser News 'May 4th data release for SARS-CoV-2 genome browser' (May 4, 2020) and the associated manuscript.

Even with our (relatively) modest compute resources, we can do our part to support the computational efforts to evaluate for therapeutic compounds to treat COVID-19. Since March 2020, we have dedicated a GPU and CPU core to the [email protected] projects which includes COVID Moonshot Sprints to evaluate potential drugs. As of July 27, 2021 our over 1,500 completed work units moved us into the top 0.5% of contributors.

Previous

The Search for Mechanisms Underlying Fatigue Through Gene Expression Profiling. Our research was highlighted in a recent profile of the Fatigue Study Group of the Multinational Association of Supportive Care in Cancer (MASCC) Society. See the whole article in the MASCC Society News (January 4, 2017)

Bringing Big Data Analysis to the Search for Symptom Relief. Our research was highlighted in a recent profile in the UCSF Science of Caring. See more in The Science of Caring article (January 9, 2015) .

Photo Credit: Homepage artwork by Catherine Nguyen, RN as part of the SON N294A Introduction to Human Genomics course.