Welcome to the Kober Lab
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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 use machine learning approaches to 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 available 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, data science, 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. We also teach the Master's core course N294D "Essentials of Human Genomics for Nurses" and the DNP core course NAP 202 Essentials of Human Genomics for the Advanced Practice Nurse. If you are a UCSF student interested in learning more about Artificial Intelligence, Dr. Yoshimi Fukuoka and Dr. Kord Kober have launched a new survey course N296 entitled "Introduction to AI in Health Care and Research". Finally, if you are a UCSF PhD or DNP student interested in learning more about using large datasets related to health and healthcare, including electronic health records and national research initiatives, Dr. Elena Flowers and Dr. Kord Kober have launched a new survey course N256 entitled "Leveraging Large Data to Advance Research and Health Care". |
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In the news...
Annesa Flentje's manuscript entitled "Differential Gene Expression in Response to AWARENESS: A Randomized Control Trial of an Intersectional Minority Stress Intervention" was accepted for publication in Health Psychology. Congratulations, Annesa! (September 25, 2024)
Khai Kober's (UC Irvine undergraduate, Alexandre Chan Lab) pitch entitled "Prediction of CDK 4/6 Inhibitor Outcomes in Metastatic Breast Cancer Patients Using Exosomal miRNAs" was selected as a finalist in the UCI Undergraduate Research Opportunities Program (UROP) 2024 Fall Project Pitch Challenge. Congratulations Khai, Quinton, Julia, and Alex! (September 16, 2024)
Lily Xu's abstract entitled "Advanced Practice Nurses' Knowledge Gap in Human Genomics” was accepted for a poster presentation at the 2024 ISONG World Congress. Congratulations, Lily and Elena! My presentation “An Introduction to the Use of Cloud Computing Resources for Omics and Prediction Modeling Studies” has been reviewed and selected for an expert lecture at the 2024 ISONG World Congress. See you there! (July 26, 2024)
Nidhi Thati presented the work she completed in our lab this summer at the Summer Programs for Undergraduate Research (SPUR) Research Showcase 2024. Her presentation was entitled "Evaluating DNA Extraction from Stool for Use in Combined Chemotherapy and Radiation Therapy (CCRT) Symptom Study". The University of California Leadership Excellence through Advanced Degrees (UC LEADS) summer research program seeks to develop students by providing research and educational experiences to further prepare them to assume positions. Congratulations, Nidhi! (August 15, 2024)
Michael Sayer's (UC Irvine) abstract "Utilizing Epigenetic Ageing Metrics To Quanitify Biological Changes In Adolescent And Young Adult Cancer Patients Over Time" was presented at the MASCC/JASCC/ISOO 2024 conference. Congratulations Michael, Quinton, and Alex! (June 27, 2024)
Michael Sayer's (UC Irvine) manuscript "Current Evidence Supporting Associations of DNA Methylation Measurements with Survivorship Burdens in Cancer Survivors: A Scoping Review" was accepted for publication in Cancer Medicine. Congratulations, Micheal and Alex! (June 27, 2024)
Matt Glasenapp (UC Santa Cruz) successfully defended his dissertation entitled "The Evolutionary Consequences of Introgression Among Strongylocentrotid Sea Urchins", Congratulations, Dr. Glasenapp! (May 24, 2024)
Alumni Kate Oppegaard and Joosun Shin received the 2024 Distinguished Dissertation Award in Nursing and were recognized at the School of Nursing graduation ceremony. Congratulations, Kate and Joosun! (May 23, 2023)
Congratulations to our research team trainees and visiting researchers who all presented research at the UCSF HDFCCC Symptom Science and Survivorship Symposium (SASS). Caroline Le's abstract was titled "Differential Methylation of Expression-Associated CpG Loci in an Enhancer Region is Associated with Morning Cancer-Related Fatigue Severity". Esther Chavez-Iglesias' abstract was titled "Dissociation of the Effects of Anticancer Agents Versus Cancer on Peripheral Blood Mononuclear Cells Through Bulk Transcriptomics – Status of the Preliminary Feasibility Study". Lisa Morse's abstract was titled "Stability and Consistency of Symptom Clusters in Younger Versus Older Patients Receiving Chemotherapy". Carolyn Harris' abstract was titled "Impact of Various Stressors on Psychological Symptom Cluster Severity Profiles in Postmenopausal Patients with Breast Cancer." Congratulations! (May 10, 2024)
A docker image is now available at Torch-eCpG (tecpg) tool to perform eQTM mapping analysis. This Docker image provides a pre-configured environment for running tecpg. Great work by Aaron Hechmer! (April 25, 2024)
The UCSF HDFCCC Symptom Science and Survivorship Symposium (SASS) is coming up on May 10, 2024. The SASS Symposium will feature talks and panel discussions on themes such as predicting toxicity of treatment and team-based/community-based research. Open to all members of the UCSF cancer community. Please register soon and bring a poster! (April 23, 2024)
Interested in learning more about research and artificial intelligence (AI) in the School of Nursing? Save the date for the AI Faculty Research Special Interest Group on June 10, 8 a.m.-1:30 p.m., in person in Mission Hall 1401, Mission Bay campus. Share your experience using AI in research with your faculty colleagues by submitting an abstract. See the flyer for more information and the abstract submission instructions. (April 17, 2024)
Esther Chavez Iglesias' abstract entitled "Dissociation of the Effects of Anticancer Agents Versus Cancer on Peripheral Blood Mononuclear Cells Through Bulk Transcriptomics – Status of the Preliminary Feasibility Study" was accepted for a poster presentation at the 2024 UCSF PROPEL Annual Symposium (May. 30, 2024). Congratulations, Esther! (April 16, 2024)
Caroline Le's abstract entitled "A Meta-Dimensional Approach to Identify Subgroups of Patients Undergoing Chemotherapy Associated with Morning Fatigue Severity" was accepted for a poster presentation at the 2024 UCSF PROPEL Annual Symposium (May. 30, 2024). Congratulations, Caroline! (April 16, 2024)
Kate Oppegaard has started a new position as a Clinical Nurse Specialist Scientist with the U.S. Department of Veterans Affairs at the Portland VA Health Care System. Congratulations, Kate! (April 10, 2024)
Caroline Le was awarded a UCSF Helen Diller Family Comprehensive Cancer Center (HDFCCC) Office of Diversity, Equity, Inclusion, and Accessibility (DEIA) mini grant for Conference Travel. Congratulations, Caroline! (April 8, 2024)
Kate Oppegaard's manuscript entitled "Neurodegenerative Disease Pathways are Perturbed in Patients with Cancer who Self-Report Cognitive Changes and Anxiety: A Pathway Impact Analysis" was accepted for publication in Cancer. Congratulations, Kate! (March 28, 2024)
Joosun Shin's manuscript entitled "Perturbations in Inflammatory Pathways Are Associated with Shortness of Breath Profiles in Oncology Patients Receiving Chemotherapy" was accepted for publication in Supportive Care in Cancer. Congratulations, Joosun! (March 18, 2024)
Thank you to School of Nursing at the University of Nevada Las Vegas for the invitation to speak as part of the Yucha Lecture Series. It was a tremendous opportunity to learn about their outstanding Nursing program and to share our research with the students and faculty. (March 4, 2024)
Torch-eCpG (tecpg) is our fast, reliable, and scalable computational tool to perform expression quantitative trait methylation (eQTM) mapping and identify expression-associated CpG loci (eCpGs). A manuscript describing the tool, "Torch-eCpG: A fast and scalable eQTM mapper for thousands of molecular phenotypes with graphical processing units", was accepted for publication in BMC Bioinformatics. The publication costs were subsidized by a Software and Publication Grant from the UCSF Chancellor's Fund (January 31, 2024). Congratulations, Liam, Ritu, and Adam! (January 22, 2024)
Oliver Bogen's manuscript entitled "Isolectin B4 (IB4)-conjugated streptavidin for the selective knockdown of proteins in IB4-positive (+) nociceptors" was accepted for publication in Molecular Pain. Congratulations, Oliver! (January 12, 2024)
Our project entitled "Differential Methylation of Expression-Associated CpG Loci in an Enhancer Region is Associated with Morning Cancer-Related Fatigue Severity" was presented as a poster at the 2024 Pacific Symposium in Biocomputing. This work highlights the efforts of our data science trainees Caroline Le, Maureen Lewis, and Liam Berger. This project is also the first to use our GPU accelerated eQTM mapping tool Torch-eCpG. Congratulations, all! (January 5, 2024)
2023
Oliver Bogen released a pre-print of his recent work "Isolectin B4 (IB4)-conjugated streptavidin for the selective knockdown of proteins in IB4-positive (+) nociceptors". Congratulations, Oliver! (December 19, 2023)
Applications are being accepted for the NIH-funded short course "Systems Biology – Foundations" offered by the UC Irvine Center for Complex Biological Systems (CCBS). Dr. Kober participated in this course in 2019. This short course is truly exceptional and is highly recommended for those looking to develop their skill across biological, biomedical sciences, quantitative and computational disciplines. (December 7, 2023)
Fay Wright's manuscript entitled "Adverse Stress Exposures Contribute to Worse Joint Morning and Evening Fatigue Profiles in Oncology Patients During Chemotherapy" was accepted for publication in Oncology Nursing Forum. Congratulations, Fay! (November 29, 2023)
Kate Oppegaard's manuscript entitled "Anxiety in oncology outpatients is associated with perturbations in pathways identified in anxiety focused network pharmacology research" was published in Supportive Care Cancer. Congratulations, Kate! (November 28, 2023)
Esther Chavez-Iglesias was admitted to the 2023/24 Post-baccalaureate Research Opportunity to Promote Equity in Learning (PROPEL) cohort. Congratulations, Esther! (November 14, 2023)
Congratulations to our research team trainees and visiting researchers who all presented research podium presentations at the 2023 ISONG World Congress. Caroline Le's abstract was titled "A Meta-Dimensional Approach to Identify Subgroups of Patients Undergoing Chemotherapy Associated with Morning Fatigue Severity". Esther Chavez-Iglesias' abstract was titled "An Exploratory Analysis of Associations Between Fatigue and Neuropathy with Plasma Cytokine Levels in Cancer Survivors". Joosun Shin's abstract was titled "Molecular mechanisms that underlie shortness of breath in patients with cancer may be similar to those associated with other respiratory conditions". Congratulations! (November 3, 2023)
Caroline Le's abstract entitled, “A Meta-Dimensional Approach Identifies Subgroups of Patients Receiving Chemotherapy Associated with Morning Fatigue Severity” has been accepted for a poster presentation at Annual Biomedical Research Conference for Minoritized Scientists (ABRCMS) 2023. Caroline was also selected to be an ambassador for the UCSF Post-baccalaureate Research Opportunity to Promote Equity in Learning (PROPEL) program. Congratulations, Caroline! (September 26, 2023)
We are very excited to have been awarded a grant from the NCI for our proposal entitled "An Evaluation of Cloud Computing for Symptom Science Research: Moving Genomics and Machine Learning Analyses of Cancer Chemotherapy-Related Fatigue to the Cloud". Congratulations, team! (September 8, 2023)
Congratulations to Sally Mortlock, Marina Sirota, Linda Guidice and team for our manuscript titled "Global Endometrial DNA Methylation Analysis Reveals Insights into mQTL Regulation and Associated Endometriosis Disease Risk and Endometrial Function" published in Communications Biology and highlighted at the NICHD news site. It was a pleasure to collaborate on this project. (August 16, 2023)
Caroline Le's abstract entitled "A Meta-Dimensional Approach to Identify Subgroups of Patients Undergoing Chemotherapy Associated with Morning Fatigue Severity" was accepted for a poster and podium presentation at the 2023 UCSF PROPEL Annual Symposium (Aug. 7, 2023). Congratulations, Caroline! (July 12, 2023)
Carolyn Harris's manuscript entitled "Neurotransmitter Gene Polymorphisms Are Associated with Symptom Clusters in Patients Undergoing Radiation Therapy" was published in Seminars Oncology Nursing. Congratulations, Carolyn! (July 5, 2023)
We are excited that Isha Kotalwar has joined our lab as a Data Science Trainee. Welcome, Isha! (June 14, 2023)
Alumni Carolyn Harris received the 2023 Distinguished Dissertation Award in Nursing and was recognized at the School of Nursing graduation ceremony. Congratulations, Caroline! (June 1, 2023)
Joosun Shin successfully defended her PhD today entitled "Clinical Characterization and Molecular Mechanisms of Dyspnea in Oncology Outpatients Undergoing Chemotherapy". Congratulations, Dr. Shin! (May 24, 2023)
Kate Oppegaard successfully defended her PhD today entitled "An Evaluation of Co-Occurring Cancer-Related Cognitive Impairment and Anxiety in Patients Receiving Chemotherapy Using Latent Variable Modeling and Pathway Impact Analysis". Congratulations, Dr. Oppegaard! (May 24, 2023)
The Scientific Workshop on Post-Dialysis Fatigue put together by the NIDDK was very engaging and provides a strong foundation for future research on this debilitating symptom. It was a privilege to share our experience evaluating for the molecular mechanisms of fatigue in patients with cancer. (May 22-23, 2023)
Our lab participated in the UCSF Sustainability Certification Program and received our Green Lab Gold Certification. The program helps UCSF provide a healthier planet by reducing emissions, saving energy, conserving water and reducing waste. Congratulations, Anatol, Esther, and Caroline! (May 12, 2023)
AJ Kwak successfully defended her Masters thesis title "Risk Factors for a Higher Symptom Burden in Oncology Patients During COVID-19". Congratulations, AJ! (May 2, 2023)
An excellent study titled "Chemotherapy for Pain: Reversing Inflammatory and Neuropathic Pain with the Anticancer Agent Mithramycin A" led by Zheyen Xu, Man-Cheung Lee and Mark Schumacher was accepted for publication in PAIN. It was a pleasure to collaborate on this project. Congratulations! (April 28, 2023)
I was honored to be a part of the faculty panel contributing to the Oncology Nursing Society supported Precision Health Symptom Science Mini-Symposium held in affiliation with the ONS Annual Congress in San Antonio. I was able to provide expertise on molecular mechanisms of cancer-related symptoms. It was an extremely productive and informative event. Congratulations to Jeannine Brant and Marilyn Hammer. (April 26, 2023)
Kate Oppegaard has accepted the University of Massachusetts Boston – Dana-Farber/Harvard Cancer Center Post-doctoral Fellowship. She will be working with Marilyn Hammer. Congratulations, Kate! (April 6, 2023)
Our abstract entitled "A Meta-Dimensional Approach Identifies Subgroups of Breast Cancer Survivors Associated with Chemotherapy-Induced Peripheral Neuropathy" was accepted for a presentation at the MASCC/JASCC/ISOO 2023 conference. Congratulations, Caroline! (April 3, 2023)
Our manuscript that developed a predictive model for morning fatigue severity one week following chemotherapy using demographic, clinical, and psychosocial predictors ("Prediction of Morning Fatigue Severity in Outpatients Receiving Chemotherapy: Less May Still Be More") was accepted for publication in Supportive Care in Cancer. Congratulations, all! (March 31, 2023)
Joosun Shin has accepted the University of Massachusetts Boston – Dana-Farber/Harvard Cancer Center Post-doctoral Fellowship. She will be working with Marilyn Hammer and Mary Cooley. Congratulations, Joosun! (March 30, 2023)
Carolyn Harris, Rachel Pozzar, and Sara Lahiguera's manuscript titled "Big Data in Oncology Nursing Research: State of the Science" was accepted for publication in Seminars in Oncology Nursing. Congratulations! (March 24, 2023)
Our abstract entitled "Prediction of fatigue severity in outpatients one week following administration of chemotherapy (CTX) using accessible data and two short questions" was accepted for a presentation at the MASCC/JASCC/ISOO 2023 conference.(March 13, 2023)
Our poster entitled "A Preliminary Evaluation of a Meta-Dimensional Approach to Combine Multimodal Omics Data to Identify Subgroups of Breast Cancer Survivors Associated with the Occurrence of Chemotherapy-Induced Peripheral Neuropathy" won Best Poster in Pain (Faculty) at the UCSF Pain and Addiction Research Center 2023 Retreat. The poster was a last minute sprint by Caroline Le and I and we are very excited to receive the recognition. Congratulations, Caroline! (March, 9, 2023)
Torch-eCpG is our fast, reliable, and scalable computational tool to perform expression quantitative trait methylation (eQTM) mapping and was released today (https://github.com/kordk/torch-ecpg). A pre-print version of the manuscript decribing the tool, "Torch-eCpG: A fast and scalable eQTM mapper for thousands of molecular phenotypes with graphical processing units", is available on bioRxiv. The manuscript is currently under peer review. Congratulations, Liam! (March 7, 2023).
The UCSF School of Nursing is the top public recipient of 2022 federal research funding! See the whole article 'UCSF School of Nursing Ranks No. 1 Among Public Institutions in NIH Funding', (February 17, 2023).
Fay Wright's manuscript entitled "Distinct Profiles of Morning and Evening Fatigue Co-occurrence in Patients During Chemotherapy" was accepted for publication in Nursing Research. Congratulations, Fay and Chris! (January 18, 2023)
2022
Kate Oppegaard's abstract "Co-occurring Cancer-Related Cognitive Impairment (CRCI) and Anxiety Are Associated with Perturbations in Neurodegenerative Pathways" has been accepted for Poster presentation at the 8th International Cognition & Cancer Task Force Conference 2023. Congratulations!
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 that 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. This study describes perturbations in common and distinct inflammatory pathways associated with morning and/or evening fatigue. Using a knowledge network approach, PI3K-Akt was identified as a bottleneck pathway. Congratulations, team! (October 29, 2022)
Welcome to Caroline Le, to her new role as a Research Data Analyst I, funded by the NCI to work on data-integrated multi-omic methods in cancer-related fatigue. Caroline is an NCI Diversity Supplement Awardee and UCSF PROPEL trainee (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, Carolyn! (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, Joosun! (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, Nate! (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, Carolyn! (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, 2022)
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)
Carolyn Harris has accepted a post doc position in the T32 Postdoctoral Training Program for Nurses in Genomics at the University of Pittsburgh. She will be working with Yvette Conley. Congratulations, Carolyn! (February 8, 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)
You-Juen (Jenny) Chou's manuscript titled "A Pilot Study of Metabolomic Pathways Associated With Fatigue in Survivors of Colorectal Cancer" was published at Biological Research for Nursing. Congratulations, Jenny! (July 22, 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 Folding@Home 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.
Fay Wright's manuscript entitled "Higher levels of stress and different coping strategies are associated with greater morning and evening fatigue severity in oncology patients receiving chemotherapy" was published in Supportive Care Cancer. Congratulations, Fay! (January 20, 2020)
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, MS as part of the SON N294A Introduction to Human Genomics course.