About

Jan Berry Baker is an associate dean of faculty mentoring and community relations, a professor of saxophone, head of the woodwinds area, and vice chair of the Department of Music Performance, Education & Composition at the UCLA Herb Alpert School of Music. She is a Canadian-American saxophonist with extensive performance experience as a concerto soloist, chamber musician, and orchestral musician on many of the world’s great stages. Her recent engagements have taken her across the United States, Canada, Mexico, Japan, France, Germany, Scotland, England, Switzerland, Austria, Ukraine, and Czechia. A passionate advocate of contemporary music, cross-disciplinary collaborations, and community engagement, Baker is co-artistic director of the chamber ensemble Bent Frequency. As part of the BF Duo Project, she and Stuart Gerber have commissioned over 50 new works for saxophone and percussion, performing across the US, Canada, Mexico, and Europe, including a debut at Carnegie Hall in 2016. Her efforts to fund the creation, performance, and recording of new music have been supported by numerous foundations and arts organizations. In addition to her chamber work, she moves fluently in the orchestral world, regularly performing with the LA Phil and having spent nearly two decades as principal saxophonist with the Lyric Opera of Chicago, Grant Park Festival Orchestra, Chicago Philharmonic, Atlanta Ballet, and Atlanta Opera. She has also appeared with the LA Opera, Chicago Symphony Orchestra, Atlanta Symphony Orchestra, Joffrey Ballet, Paris Opera Ballet, Chicago Chamber Players, and American Ballet Theater. Baker’s extensive discography includes chamber and orchestral recordings on various labels, and she is featured on notable recordings such as American Orchestral Works with the Grant Park Orchestra, Atlanta Opera’s world premiere of The Golden Ticket, and the three-time GRAMMY-winning Gabriela Ortiz: Revolución Diamantina with the LA Phil. She has held residencies at numerous festivals and institutions worldwide, and is highly sought after as a guest artist and speaker, offering presentations on contemporary music, entrepreneurship, nonprofits, grant writing, community engagement, socially conscious programming, career development, and mentoring. Committed to education and mentorship, Dr. Baker is a professor of saxophone and woodwind area head at UCLA, serving as vice chair of the department and special assistant to the dean for faculty mentoring. Her academic background includes studies with Frederick L. Hemke, William H. Street, and Barbara Lorenz, culminating in a Doctor of Music degree in saxophone performance from Northwestern University. She is a founding member of the North American Saxophone Alliance’s Committee on Gender Equity and creator of its mentoring program. Baker is a Selmer Paris, Vandoren, and Key Leaves performing artist.

Research topics

• Gynecology
• Family medicine
• Internal medicine
• Medicine
• Pathology
• Oncology
• Medical physics

Selected publications

• ASO Visual Abstract: Analysis of the 2024 Breast Surgical Oncology Fellowship Match: Survey of Applicants and Program Directors’ Preferences Regarding In-Person Versus Virtual Interviews

  Annals of Surgical Oncology · 2025-09-10

  articleCorresponding
  PublisherDOI

• Analysis of the 2024 Breast Surgical Oncology Fellowship Match: Survey of Applicants’ and Program Directors’ Preferences Regarding In-Person Versus Virtual Interviews

  Annals of Surgical Oncology · 2025-08-23

  articleOpen accessCorresponding
  PublisherOA PDFDOI

• Weight gain trajectories from birth to 12 months and cardiovascular risk factors in middle adulthood

  Nutrition Metabolism and Cardiovascular Diseases · 2025-10-15

  articleOpen access

  BACKGROUND AND AIM: Infant weight gain is positively associated with fat and lean mass later in life, but whether it relates to adult cardiovascular disease (CVD) risk factors is ambiguous. We examined associations between infant weight gain trajectories and adult CVD risk factors. METHODS AND RESULTS: We included 739 individuals from the Copenhagen Perinatal Cohort. Repeated infant weight measurements and information on adult CVD risk factors at age 48-51 years were available. Five infant weight gain trajectories were estimated using latent class modelling (very low-moderately increasing; low-markedly increasing; low-stable increasing; average-stable increasing [reference group]; high-moderately increasing). Linear regression models were adjusted for parental and infant factors and additionally for birthweight. Compared with the average-stable increasing weight gain trajectory, in men, the very low-moderately increasing trajectory was associated with higher systolic and diastolic blood pressure (DBP), triglycerides, low-density lipoprotein and total cholesterol. In women, the low-markedly increasing trajectory was associated with higher DBP and the low-stable increasing trajectory was associated with lower body mass index and body fat percentage. The high-moderately increasing trajectory was associated with higher waist circumference in men and lower total cholesterol in women. Additional adjustment for birthweight attenuated some, but not all, associations. CONCLUSION: Infant weight gain trajectories were not consistently associated with CVD risk profiles during adulthood. In men, the very-low moderately increasing weight trajectory had a worse CVD risk profile. Women with the low-stable increasing weight trajectory tended to have a better CVD risk profile.

  PublisherOA PDFDOI

• Abstract P1-01-30: Generation and validation of primary breast cancer epigenetic classifiers of pathologic nodal stage in a multi-center breast cancer cohort

  Clinical Cancer Research · 2025-06-13

  article

  Abstract Introduction: With increasingly effective systemic therapies and expanding indications for radiation, the role of axillary lymph node dissection (ALND) in the management of patients with node-positive breast cancer (BC) continues to evolve. However, while clinical trials have progressively demonstrated that ALND offers little to no added protection from local recurrence or death in various clinical scenarios, ALND remains the only method to fully stage the axilla and differentiate pN1 vs >pN1 disease. However, certain decisions for adjuvant therapies, such as CDK4/6 inhibitor therapy in patients with estrogen receptor (ER) positive BC, still rely on the nodal stage. In this study, we used machine learning algorithms to create epigenetic classifiers predictive of nodal stage (pN1 vs >pN1) based on DNA methylation profiling of primary BC tumors in two independent cohorts of patients (UCLA and Duke) with ER-positive, HER2-negative BC. Methodology: Eligibility criteria included women aged 18-80 years with ER+, HER2-negative BC, clinically node-positive, who underwent ALND without NAC. Tumoral tissue was microdissected from 8 µm Formalin-Fixed Paraffin-Embedded (FFPE) slides, previously annotated by a trained pathologist, and DNA was extracted using the Quick-DNA FFPE Miniprep kit (Zymo Research). DNAm profiling was performed using the Illumina Infinium Methylation EPIC BeadChip v1. DNAm data was processed using the R/ChAMP package (v.2.34.0), and the batch effect was corrected using the “champ.runCombat” function. The cohort was split into a training cohort (60%, n = 53) and a validation cohort (40%, n = 34). R/VarSelRF (v.0.7-8) was used to identify the combination of probes with the fewest sites and the highest potential to predict the pathological nodal stage. The best-performing classifiers were tested in the validation cohort. Results: DNAm profiling was performed on 91 primary BC samples, with four samples removed due to low data quality. The UCLA and Duke cohorts presented a significant batch effect, which was successfully corrected to avoid potential bias. We identified 1,653 differentially methylated sites between pN1 and >pN1 tumors in the training cohort, successfully stratifying both subgroups of patients. These sites were used to generate a Random Forest-based classifier with the minimum number of probes. We selected the three combinations of probes with the highest Area Under the Curve (AUC) and the fewest CpG sites. We identified three classifiers, comprising 8 to 12 genomic regions, with an AUC between 0.99 and 1 in the training cohort and between 0.81 and 0.82 in the validation cohort. Discussion: As randomized trial data support the omission of ALND in select clinical scenarios in patients with node-positive BC, clinicians will lose the pathologic nodal data that is provided by surgical dissection that guides adjuvant therapy decision-making. This study generated three classifiers that successfully identified patients with higher nodal stage (>pN1). These classifiers use a small number of genomic regions (8 to 12) and can be optimized for low-throughput techniques such as pyrosequencing or quantitative Methylation-Specific PCR, increasing the availability of this diagnostic tool in the clinical setting. Citation Format: Miquel Ensenyat-Mendez, Sandra Iñiguez-Muñoz, Julie Le, Sookyung Ahn, Isabel Eng, Peggy Sullivan, Pere Llinas-Arias, Jennifer L. Baker, Diego M. Marzese, Maggie L. DiNome. Generation and validation of primary breast cancer epigenetic classifiers of pathologic nodal stage in a multi-center breast cancer cohort [abstract]. In: Proceedings of the San Antonio Breast Cancer Symposium 2024; 2024 Dec 10-13; San Antonio, TX. Philadelphia (PA): AACR; Clin Cancer Res 2025;31(12 Suppl):Abstract nr P1-01-30.

  PublisherDOI

• Epigenetic determinants of an immune-evasive phenotype in HER2-low triple-negative breast cancer

  npj Precision Oncology · 2025-08-16 · 5 citations

  articleOpen access

  Identifying molecular drivers in triple-negative breast cancer (TNBC) is crucial. While HER2-low expression predicts response to novel antibody-drug conjugates, its biological influence on TNBC biology is unknown. We performed a comprehensive multi-omics analysis, integrating genomic, epigenomic, transcriptomic, and proteomic profiling to characterize HER2-low TNBC. We generated genome-wide DNA methylation profiles from a multi-institutional cohort and integrated our data with three independent cohorts (TCGA, SCAN-B, I-SPY2). TNBC cases were categorized as HER2-zero (IHC 0) or HER2-low TNBC (IHC 1+/2+, ISH non-amplified). Among 506 patients (HER2-low, n = 288; HER2-zero, n = 218), HER2-low TNBC exhibited significantly lower tumor mutational burden (P = 0.02). Epigenetic analysis identified 5287 differentially methylated sites, with consistent hypermethylation of HLA genes in HER2-low tumors. Transcriptomic analyses revealed significant downregulation of genes enriched in immune response pathways (e.g., leukocyte activation, T-cell signaling) in HER2-low TNBC (adjusted P < 0.001). Immune cell deconvolution showed reduced immune cell infiltration in the HER2-low tumor microenvironment (P = 0.002). Higher expression of five immune-related genes, downregulated in HER2-low, correlated with improved relapse-free (HR = 0.52; P < 0.001) and overall survival (HR = 0.36; P < 0.001). HER2-low TNBC tumors display distinct molecular features compared to HER2-zero, imparting an immune-evasive phenotype. These findings provide critical insights into the unique biology of HER2-low TNBC, warranting further clinical investigation.

  PublisherOA PDFDOI

• The SHARE study – Survivorship After Head and Neck Cancer: evaluating patient care and adherence to follow up in Ontario, Canada: study protocol for a randomized controlled trial

  Trials · 2025-12-13

  articleOpen access

  BACKGROUND: Survivors of head and neck cancer (HNC) experience long-term physical and psychosocial effects post-treatment, however, often receive fragmented survivorship care. Evidence-based survivorship guidelines exist, but implementation remains limited. Poor coordination, insufficient communication, and lack of tailored support contribute to unmet patient needs. Treatment Summary and Survivorship Care Plans (TSSP) and Motivational Interviewing (MI) may improve self-efficacy and adherence to survivorship care recommendations. This study aims to evaluate whether a personalized TSSP along with a one-time MI counselling session improves physician implementation of survivorship care recommendations, patient satisfaction with post-treatment care, and quality of life (QoL) among HNC survivors. METHODS/DESIGN: This study is a prospective, single-centre, two-arm, superiority randomized controlled trial (RCT) with a 1:1 allocation ratio. Outcomes will be evaluated at baseline, 3, 6, and 12 months post-baseline visit. A total of 252 HNC survivors (stage I-IVA, aged ≥ 18 years, 3-6 months post-definitive treatment, English-speaking, with no metastatic or residual disease) will be recruited by a trained research assistant through the Survivorship Clinic at Victoria Hospital in London, Canada. Recruitment began in May 2025. Participants will be randomized to either the intervention group (TSSP and MI session) or the control group (usual care only). The intervention consists of a 45-min MI session delivered by a trained nurse practitioner, focused on exploring the top 3 patient survivorship symptoms/concerns, providing resources and referrals, and goal-setting related to survivorship care recommendations. The primary outcome is the proportion of patient-identified survivorship symptoms/concerns addressed by primary care providers (PCP) at 12 months post-baseline between study groups, with secondary assessments at 3 and 6 months. Secondary outcomes include patient satisfaction with the TSSP and MI session, patient satisfaction with care and information, QoL, and PCP feedback on the utility of the TSSP. Descriptive statistics will be reported, and intention-to-treat analyses will be conducted using mixed-effects models to evaluate group differences over time. DISCUSSION: This study will contribute new evidence on the feasibility and effectiveness of integrating a scalable, combined TSSP and MI counselling intervention into routine HNC survivorship care. By promoting patient-centered communication, this approach may empower survivors to engage in self-management and improve long-term health outcomes. Findings will inform best practices for survivorship care planning and support the implementation of patient-tailored interventions across various oncology settings. TRIAL REGISTRATION: ClinicalTrials.gov NCT06127784. Registered on Nov. 6, 2023; https://www. CLINICALTRIALS: gov/study/NCT06127784 .

  PublisherDOI

• Reference intervals for serum immunoglobulin A, G, and M in a Danish paediatric population-based cohort

  Clinical Biochemistry · 2025-04-02 · 3 citations

  articleOpen access

  OBJECTIVES: To determine age- and sex-specific reference values for serum immunoglobulins (IgA, IgG, and IgM) in a population-based cohort of 6 to 18 years old Danish children and adolescents and investigate if immunoglobulin concentrations vary with body mass index standard deviation score (BMI SDS). MATERIALS AND METHODS: A total of 2171 school children and adolescents (median age 12.0 years) were recruited. BMI SDS was calculated, and health status was assessed by questionnaire and blood samples. Fasting serum concentrations of IgA, IgG, and IgM were determined by immunonephelometry. Sex- and age-specific percentiles were generated and partitioned following the Clinical and Laboratory Standards Institute (CLSI) EP28-A3c guidelines. Multiple linear regression models were used to investigate associations betweenIgA, IgG, IgM, and BMI SDS adjusted for age and sex. RESULTS: Concentrations of IgA increased with age but did not differ between boys and girls. An age-dependent increase was also detected for concentrations of IgG and IgM, although for IgG it was more pronounced in boys than girls. Girls had higher concentrations of IgG and IgM than boys at all ages. Concentrations of IgM were inversely associated with BMI SDS independent of age and sex. CONCLUSIONS: We generated age- and sex-specific reference intervals for IgA, IgG, and IgM based on children and adolescents from a Danish/North-European Caucasian population-based cohort. The findings can help evaluate alterations seen in primary and secondary immunodeficiencies and autoimmune diseases.

  PublisherDOI

• Impact of Honors Pass/Pass/Fail vs Traditional Letter Grading on EPA-Based Assessment of Student APPE Performance

  American Journal of Pharmaceutical Education · 2025-06-25

  articleOpen access

  OBJECTIVE: This retrospective, observational study evaluated the impact of honors/pass/fail grading (HPFG) implementation compared to traditional letter grading (TLG) on student performance assessed using entrustable professional activity (EPA)-based Advanced Pharmacy Practice Experience (APPE) rotation evaluations. Insights gleaned from a transition from Center for the Advancement of Pharmacy Education (CAPE)-based to EPA-based experiential assessments are also shared. METHODS: A total of 6679 raw student performance scores (RSPS) were collected from 2 colleges of pharmacy (COPs) across a 2-year period during which both COPs used an identical CAPE-based APPE evaluation tool with traditional letter grading (TLG), and a 2-year post-EPA implementation period during which one COP also implemented HPFG (COP 1), while the other (COP 2) continued using TLG. The change in RSPS from baseline was compared between the years 1-2 timeframe and years 3-4 at both institutions to assess for significant differences following HPFG implementation. A multiple linear regression model also evaluated associations between RSPS and several independent variables, including COP, time frame of evaluation, evaluation type (EPA vs CAPE-based), rotation category, and grading system (TLG vs HPFG). The distribution of grade prevalences was also compared across the 2 timeframes at both institutions. RESULTS: The COP transitioning to HPFG experienced a similar decline in RSPS following EPA-based evaluation implementation as the COP maintaining TLG. A multiple regression model identified no significant association between RSPS and the grading system, while controlling for COP, rotation category, and the timeframe of evaluation. CONCLUSION: Implementation of HPFG did not appear to have a detrimental impact on student rotation performance at a COP implementing EPA-based APPE evaluations.

  PublisherOA PDFDOI

• Surgical outcomes following neoadjuvant chemotherapy with and without immunotherapy in patients with triple-negative breast cancer

  Discover Oncology · 2024-09-20 · 2 citations

  articleOpen access

  PURPOSE: Adding pembrolizumab to neoadjuvant chemotherapy (NAC) for triple-negative breast cancer (TNBC) improves pathologic complete response (pCR) rates and event-free survival. The impact of adding immunotherapy to NAC on surgical outcomes is unknown. This study compares 90-day post-surgical complications (PSCs) and time to adjuvant treatment among patients undergoing NAC for TNBC with and without immunotherapy. METHODS: Patients treated with NAC alone or with immunotherapy (NAC-I) for stage I-III TNBC between 2018 and 2022 were retrospectively identified at a single academic institution. Kruskal-Wallis rank sum and Fisher's exact tests compared patient sociodemographic and clinical characteristics. Multivariable logistic regression determined odds ratios (OR) predicting PSCs. RESULTS: Of 54 patients, 29 received NAC alone and 25 received NAC-I. Compared to NAC patients, NAC-I patients had more advanced stage tumors (p = 0.038), and had slightly higher rates of mastectomy with reconstruction (p = 0.193). 72.0% of NAC-I patients experienced a pCR, compared with 44.8% of NAC patients (p = 0.193). There were 10 PSCs (34.5%) in NAC patients compared to 9 PSCs (36.0%) in NAC-I patients (p > 0.99). Regression analysis demonstrated no association of PSCs with NAC-I (OR 0.83, 95% CI 0.19-3.60). Time to adjuvant therapy was shorter for NAC-I patients (28 days vs 36 days, p = 0.013). CONCLUSIONS: Patients with TNBC receiving NAC-I have higher pCR rates and do not appear to have added 90-day PSCs or delays to adjuvant therapy despite trending toward more extensive surgical procedures compared to NAC alone. Larger studies are needed to further evaluate the surgical safety of immunotherapy.

  PublisherOA PDFDOI

• Safety and margin positivity rates of surgeon-performed intraoperative ultrasound-guided wire localization for breast cancer

  Surgical Oncology Insight · 2024-05-14 · 3 citations

  articleOpen access

  <h2>Abstract</h2><h3>Background</h3> Surgeon-performed intraoperative ultrasound-guided wire localization (IOL) offers an improved patient experience and decreased cost compared to preoperative localization by radiology, yet literature on this technique is sparse. Here we evaluate the safety and margin positivity rate after surgeon-performed IOL for breast cancer. <h3>Methods</h3> Patients with biopsy-proven breast malignancy and planned breast conservation who underwent IOL by a single breast surgeon between 2017–2023 and had follow-up at our institution were retrospectively identified. Patient and tumor characteristics, method of diagnosis, imaging findings, use of oncoplastic surgery, and follow-up data were analyzed. <h3>Results</h3> A total of 137 IOLs were performed for biopsy-proven ductal carcinoma in situ (DCIS) or invasive cancer. The median patient age was 69 years. Most patients had a non-palpable tumor (n = 104, 76.5%). 84.6% of patients underwent pre-operative biopsy by ultrasound guidance, 12.5% by stereotactic guidance, and 2.9% by MRI. In total, 7.3% of patients (n = 10) had positive margins, including 2 with invasive disease at the margin and 8 with DCIS at the margin. Nine patients underwent re-excision for positive or close margins, of which 8 had successful margin-negative breast conservation and 1 patient underwent mastectomy. Thirty-day postoperative complications occurred in 21 patients (15.3%). Of these, most (n = 19, 90.4%) had minor complications including seroma (n = 14), cellulitis (n = 3), and skin allergy (n = 2). At median follow-up of 20.4 months, no patients experienced recurrence. <h3>Conclusions</h3> In our single-surgeon series, IOL is a safe technique for localization of invasive carcinoma and DCIS with margin positivity, re-excision, and postoperative complication rates within previously published ranges. <h3>Synopsis</h3> This study evaluates the safety of and re-excision rates after intraoperative surgeon-performed ultrasound-guided wire localization (IOL) for breast cancer. Results demonstrate margin positivity and re-excision rates equivalent to or lower than rates reported in literature utilizing preoperative localization techniques.

  PublisherOA PDFDOI

Frequent coauthors

• Maggie L. DiNome

  Duke University

  19 shared

• Carlie K. Thompson

  University of California, Los Angeles

  15 shared

• Deanna J. Attai

  Centre for the Observation and Modelling of Earthquakes, Volcanoes and Tectonics

  12 shared

• Minna K. Lee

  University of California, Los Angeles

  11 shared

• Donna Plecha

  University Hospitals of Cleveland

  9 shared

• Rachael Lancaster

  University of Alabama at Birmingham

  9 shared

• Jennifer K. Plichta

  Durham University

  9 shared

• Liane E. Philpotts

  Yale University

  6 shared

Awards & honors

• Selmer Paris, Vandoren, and Key Leaves performing artist
• founding member of the North American Saxophone Alliance’s C…