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.

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...

Our manuscript "ShinyGAStool: A user-friendly tool for candidate gene association studies" was accepted for publication at SoftwareX. The tool was the result of a collaboration with Thomas Hoffmann and Chris Miaskowski. It is available online at: https://github.com/kordk/shinyGAStool Congratulations, Tom! (November 17, 2022)

Sandra Schimmel's manuscript entitled "Sleep Disturbance Is Associated With Perturbations In Immune-Inflammatory Pathways In Oncology Outpatients Undergoing Chemotherapy" has been accepted for publication in Sleep Medicine. Congratulations, Sandra! (November 14, 2022)

Congratulations to our research team who all presented research podium presentations at the 2022 ISONG World Congress. There were five studies looking at molecular pathways associated with symtom severity in patients undergoing treatment for cancer. Studies evaluating gene expression changes were presented by Dr. Chris Miaskowski (Symptom Cluster in patients with gynecological cancer diagonsis), Dr. Marilyn Hammer (Symptom Cluster in a heterogenous sample of patients with a cancer diagonsis), Dr. Sandra Schimmel (sleep disturbance) and Joosun Shin (shortness of breath). Studies evaluating methylation changes were presented by myself (morning fatigue) and Dr. Carolyn Harris (Symptom Cluster in patients with gynecological cancer diagonsis) and an evaluation of genotype data was presented by Dr. Ying Sheng (palpitations). We are also excited that the analyses of the demographic and clinical characteristics in a number of analyses were performed by our data science trainees Caroline Le and Maureen Lewis. Congratulations, all! (November 10-13, 2022)

Our manuscript entitled "Perturbations in Common and Distinct Inflammatory Pathways Associated with Morning and Evening Fatigue in Outpatients Receiving Chemotherapy" was accepted for publication in Cancer Medicine. Congratulations, team! (October 29, 2022)

Welcome to Caroline Le, our newest Research Data Analyst I, funded by the NCI to work on data-integrated multi-omic methods in cancer-related fatigue. (October 17, 2022)

Ying Sheng's manuscript "A Pilot Study of Associations Between the Occurrence of Palpitations and Cytokine Gene Variations in Women Prior to Breast Cancer Surgery" was accepted for publication in Biological Research for Nursing. Congratulations, Ying! (October 2, 2022)

Kate Oppegaard's manuscript "Blood-Based Biomarkers of Cancer-Related Cognitive Impairment in Non-Central Nervous System Cancer: A Scoping Review" was accepted for publication in Critical Reviews in Oncology / Hematology. Congratulations to Kate and Dr. Samantha Mayo! (September 21, 2022)

Carolyn Harris' manuscript titled "Epigenetic regulation of inflammatory mechanisms and a psychological symptom cluster in patients receiving chemotherapy" was accepted for publication in Nursing Research. Congratulations! (September 5, 2022)

Joosun Shin passed her qualifying exam, advanced to candidacy, and successfully defended her dissertation proposal. Congratulations, Joosun! (August 30, 2022)

Kate Oppegaard passed her qualifying exam, advanced to candidacy, and successfully defended her dissertation proposal. Congratulations, Kate! (August 19, 2022)

Joosun Shin's manuscript titled "Perturbations in Neuroinflammatory Pathways Are Associated with a Worst Pain Profile in Oncology Patients Receiving Chemotherapy" was accepted for publication in the Journal of Pain. Congratulations! (August 22, 2022)

Nate Hass' Masters thesis titled "Polymorphisms in Cytokine Receptor and Regulator Genes Are Associated With Levels of Exercise in Women Prior to Breast Cancer Surgery" was accepted for publication in Biologial Research for Nursing. Congratulations! (July 13, 2022)

Carolyn Harris' manuscript titled "Gastrointestinal Symptom Cluster is Associated with Epigenetic Regulation of Lymphotoxin Beta in Oncology Patients Receiving Chemotherapy" was accepted for publication in Biologial Research for Nursing. Congratulations! (July 19, 2022)

Our research group provided some comments used in a recent article written by Lindsay Modglin in Heal magazine: "Chemotherapy-Induced Peripheral Neuropathy: The Invisible Side Effect" (June 14, 2022)

Carolyn Harris successfully defended her PhD today entitled "Moving the Science of Symptom Cluster Research Forward: Phenotypic and Mechanistic Considerations". Congratulations, Dr. Harris! (May 27, 2023)

Delia Sass's manuscript titled "Differences in circulating extracellular vesicle and soluble cytokines in older versus younger breast cancer patients with distinct symptom profiles" was accepted for publication in Frontiers in Genetics. It was a great collaboration with Dr. Sass, Dr. Leo Saligan, and team. Congratulations! (March 23, 2022)

You-Juen (Jenny) Chou's manuscript titled "A pilot study of metabolomic pathways associated with fatigue in patients with colorectal cancer receiving chemotherapy" was published at European Journal of Oncology Nursing. Congratulations, Jenny! (January 27, 2022)

2021

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-Iglesias 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.