Fall 2026 Setup

src/archive/2026/2026-09-17.md

@@ -0,0 +1,65 @@
+# Sep - Muhammad “Tuan” Amith
+
+!!! info "Event Details"
+
+    **Date/Time:**
+
+    Thursday, September 17th, 2026 :material-clock: 6:00pm - 8:00pm
+
+    **Location:**
+
+    :material-map-marker: **Location:** Vancouver General Hospital, Jimmy Pattison Pavilion South ([899 West 12th Ave., Vancouver, BC V5Z 1M9](https://maps.app.goo.gl/pvM16Frig5VjA9e69)), 1891 Lecture Theatre
+
+/// html | div[class="bio"]
+
+![headshot](./images/muhammad-amith.jpg)
+
+/// html | div
+
+**Featured Speaker**: Dr. Muhammad “Tuan” Amith
+
+**Talk Title:**  Examining semantic-driven distributed computing systems for the management of vaccine information
+
+<!---![type:video](https://www.youtube.com/embed/JcN11lVhwos)-->
+
+**Affiliation:**
+
+Assistant Professor in the Department of Health Information Science at University of Victoria
+
+///
+
+///
+
+**Bio:**
+
+Dr. Tuan Amith is an assistant professor with School of Health Information Sciences from the University of Victoria. He received his PhD in Biomedical Informatics from the McWilliams School of Biomedical Informatics at the University of Texas Health Science Center at Houston (UTHealth), under the supervision of Dr. Cui Tao. 
+
+He also has BS and MS in Computer Science and Software Engineering from the University of Houston. He previously served as faculty at UTHealth and University of Texas Medical Branch. His primary research focus is on the application of semantic web technologies and biomedical ontologies for clinical and public health subjects. 
+
+His past research has received best paper distinctions AMIA, MedInfo, and IEEE, and his dissertation was a finalist for the American Medical Informatics Association for best dissertation. He has served as PI and Co-I on past and current NIH-funded research. In addition, Dr. Amith is a member of the editorial board for Nature's Scientific Reports (Digital Health), BMC Medical Informatics and Decision Making, and the Journal of Clinical Informatics.
+
+**Abstract:**
+
+Distributed computing systems offer some advanced benefits to share and manage data and information. Theoretically, if these systems are coupled with semantics they can further improve and promote the aforementioned benefits for archiving data and information for bioinformatics. 
+
+In this talk, I will discuss two exploratory research ventures for vaccine informatics. One vision involves the development and the application of semantic blockchains to manage human papillomavirus (HPV) vaccine immunization information between clinics. The other venture explores the potential of using the nanopublication network to archive and distribute vaccine information from the Vaccine Investigation and Online Information Network (VIOLIN). 
+
+I will share initial findings and outputs with these two projects and lay out our future direction to continue this work.
+
+---
+
+/// html | div[class="bio"]
+
+![headshot](./images/kristi-fourie.png)
+
+/// html | div
+
+**Trainee Speaker:** Kristi Fourie
+
+**Affiliation:** MSc student in Bioinformatics, Karsan Lab, UBC & BC Cancer Research Centre
+
+**Talk Title**: Clonal and epigenetic evolution in acute myeloid leukemia at relapse
+
+///
+
+///

src/archive/2026/2026-10-22.md

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+# Oct - Emilia Lim
+
+!!! info "Event Details"
+
+    **Date/Time:**
+
+    Thursday, October 22nd, 2026 :material-clock: 6:00pm - 8:00pm
+
+    **Location:**
+
+    :material-map-marker: **Location:** Gordon and Leslie Diamond Health Care Centre ([2775 Laurel St, Vancouver, BC V5Z 1M9](https://maps.app.goo.gl/bvXxcRMzUaC2cQkG7)), 1020 Lecture Theatre
+
+/// html | div[class="bio"]
+
+![headshot](./images/emilia-lim.jpg)
+
+/// html | div
+
+**Featured Speaker**: Dr. Emilia Lim
+
+**Talk Title:**  Mapping How Air Pollution Promotes Lung Cancer
+
+
+**Affiliation:**
+
+Assistant Professor in the Department of Biochemistry and Molecular Biology at the University of British Columbia and an Investigator at Edwin S.H. Leong Centre for Healthy Aging
+
+
+///
+
+///
+
+**Bio:**
+
+Emilia obtained her BSc in Bioinformatics at the University of Alberta, where she completed her thesis on the Human Metabolome Project with Dr. David Wishart. She then pursued her PhD in Bioinformatics under the mentorship of Dr. Marco Marra at UBC and the BC Cancer Genome Sciences Centre. She worked on epigenomic and transcriptomic biomarker discovery for treatment refractory hematological and pediatric cancers through the TCGA and TARGET NCI initiatives. She then completed her postdoctoral training with Dr. Charles Swanton at the Francis Crick Research Institute and University College London (UCL). She worked on the TRACERx and PEACE studies, examining chromosomal instability and how it shapes lung cancer evolution. Her interest in lung cancer in never smokers directed her to develop a framework for studying the environmental impact on cancer initiation. She discovered that air pollution triggers lung cancer initiation by promoting clonal expansion of cells harbouring oncogenic mutations which have accumulated due to aging. Her current research program concerns how environmental pollutants disrupt normal cells to accelerate the initiation of age-related disease states such as cancer.
+
+**Abstract:**
+
+Lung cancer in never-smokers is rising, particularly among women and individuals of Asian descent, and is frequently driven by EGFR mutations despite unusually low overall mutational burden. This pattern is difficult to reconcile with the classical model of carcinogenesis, in which carcinogens directly induce DNA mutations that drive tumour growth. This talk presents converging evidence—from epidemiology, mouse models, controlled human pollution exposures, and studies of normal lung tissue—supporting an alternative "tumour promotion" model, in which pre-existing oncogenic mutations (the initiator) are activated by air pollution exposure (the promoter) rather than being caused by it.
+
+Fine particulate matter (PM2.5) exposure is shown to drive IL1B-mediated inflammation and macrophage activation, expand the progenitor-cell capacity of EGFR-mutant lung cells, and promote clonal outgrowth of latent mutant clones already present in normal aging lung tissue. Clinical trial data (CANTOS) suggest this pathway may be therapeutically targetable.
+
+To directly visualize how pollution injures lung tissue, spatial transcriptomics is used to map gene expression across normal lung tissue in relation to anthracotic pigment—a histological marker of accumulated air pollution exposure. By comparing regions of interest overlapping anthracotic pigment to unaffected regions within the same tissue, this approach reveals localized shifts in epithelial cell composition, upregulation of oncogenic and inflammatory gene programs, suppression of lysosome/phagosome pathways, and impaired antiviral signalling specifically within "injured," pollution-exposed areas of the lung. A high-throughput image analysis workflow (SHADE) further enables systematic quantification of anthracosis across large tissue cohorts, linking pigment burden to an aggressive micropapillary-predominant lung cancer subtype.
+
+Together, these findings support a model in which air pollution promotes lung carcinogenesis primarily through localized, chronic inflammation acting on pre-existing mutations, rather than through new mutagenesis—reframing how environmental carcinogens should be studied and targeted for prevention.
+
+---
+
+/// html | div[class="bio"]
+
+![headshot](./images/asli-munzur.jpg)
+
+/// html | div
+
+**Trainee Speaker:** Asli Munzur
+
+**Affiliation:** PhD student in Genome Sciences and Technology, Wyatt Lab, UBC & Vancouver Prostate Centre
+
+**Talk Title**: TBD

src/archive/2026/2026-11-19.md

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+# Nov - Maria Tokuyama
+
+!!! info "Event Details"
+
+    **Date/Time:**
+
+    Thursday, September 17th, 2026 :material-clock: 6:00pm - 8:00pm
+
+    **Location:**
+
+    :material-map-marker: **Location:** Vancouver General Hospital, Jimmy Pattison Pavilion South ([899 West 12th Ave., Vancouver, BC V5Z 1M9](https://maps.app.goo.gl/pvM16Frig5VjA9e69)), 1891 Lecture Theatre
+
+/// html | div[class="bio"]
+
+![headshot](./images/maria-tokuyama.jpg)
+
+/// html | div
+
+**Featured Speaker**: Dr. Maria Tokuyama
+
+**Talk Title:**  TBD
+
+
+**Affiliation:**
+
+- Assistant Professor in the Department of Microbiology & Immunology at The University of British Columbia
+
+///
+
+///
+
+**Bio:**
+
+Dr. Tokuyama has always been interested in the interaction between viruses and the immune system. As an undergrad at University of California, Irvine, she worked in an infectious disease lab that focused on HIV research and obtained her B.S. in Molecular Biology and Biochemistry. She then worked at the National Institutes of Health at the Vaccine Research Center studying Ebola virus vaccines. Dr. Tokuyama obtained her Ph.D. in Molecular and Cellular Biology from University of California, Berkeley where she studied mechanisms of how natural kill cells recognize and kill cell infected by herpesviruses. Dr. Tokuyama trained at Yale University in the Department of Immunobiology, where she became fascinated by endogenous retroviruses and established the foundation for the research that she will carry out at UBC. In the past year, Dr. Tokuyama has also been part of the Yale IMPACT Team to develop a rapid saliva-based qPCR assay for SARS-CoV-2 and contributing to research on understanding immunological impacts of COVID-19.
+
+**Abstract:**
+
+TBD
+
+---
+
+/// html | div[class="bio"]
+
+![headshot](./images/moritz-aubermann.png)
+
+/// html | div
+
+**Trainee Speaker:** Moritz Aubermann
+
+**Affiliation:** MSc student in Bioinformatics, Pavlidis Lab, UBC
+
+**Talk Title**: Semantically Informed Embeddings of Differential Expression Data
+
+///
+
+///

src/index.md

@@ -10,4 +10,7 @@ Visit our sister groups for bioinformatics events in Montreal ([MonBUG](https://
 
 ## VanBUG Monthly Event
 
-Stay tuned for announcements!
+{%
+   include-markdown "./archive/2026/2026-09-17.md"
+   start="# Sep - Muhammad “Tuan” Amith"
+%}

src/schedule.md

@@ -1,84 +1,49 @@
 # Schedule
 
-## Fall 2025
+## Fall 2026
 
 /// html | div[class="timeline"]
 
-- ### [Sep 18th, 2025, Thursday](./archive/2025/2025-09-18.md)
+- ### [Sep 17th, 2026, Thursday](./archive/2026/2026-09-17.md)
 
     :material-clock: 6:00pm - 8:00pm
 
-    :material-map-marker: **Location:** Gordon and Leslie Diamond Health Care Centre ([2775 Laurel St, Vancouver, BC V5Z 1M9](https://maps.app.goo.gl/bvXxcRMzUaC2cQkG7)), 1020 Lecture Theatre
-
-    Featured Speaker: Dr. Ewan Gibb
-
-    Trainee Speaker: Giuli Sucar
-
-- ### Oct 16th, 2025, Thursday
-
-    :material-clock: 6:00pm - 8:00pm
-
-    :material-map-marker: **Location:** Gordon and Leslie Diamond Health Care Centre ([2775 Laurel St, Vancouver, BC V5Z 1M9](https://maps.app.goo.gl/bvXxcRMzUaC2cQkG7)), 1020 Lecture Theatre
+    :material-map-marker: **Location:** Vancouver General Hospital, Jimmy Pattison Pavilion South ([899 West 12th Ave., Vancouver, BC V5Z 1M9](https://maps.app.goo.gl/pvM16Frig5VjA9e69)), 1891 Lecture Theatre
 
-    Featured Speaker: TBA
+    Featured Speaker: Dr. Muhammad “Tuan” Amith
 
-    Trainee Speaker: TBA
+    Trainee Speaker: Kristi Fourie
 
-- ### Nov 20th, 2025, Thursday
+- ### [Oct 22nd, 2026, Thursday](./archive/2026/2026-10-22.md)
 
     :material-clock: 6:00pm - 8:00pm
 
     :material-map-marker: **Location:** Gordon and Leslie Diamond Health Care Centre ([2775 Laurel St, Vancouver, BC V5Z 1M9](https://maps.app.goo.gl/bvXxcRMzUaC2cQkG7)), 1020 Lecture Theatre
 
-    Featured Speaker: TBA
-
-    Trainee Speaker: TBA
-
-
-///
-
-## Spring 2026
-
-/// html | div[class="timeline"]
-
-- ### Jan 15th, 2026, Thursday
-
-    :material-clock: 6:00pm - 8:00pm
+    Featured Speaker: Dr. Emilia Lim
 
-    :material-map-marker: **Location:** Vancouver General Hospital, Jimmy Pattison Pavilion South ([899 West 12th Ave., Vancouver, BC V5Z 1M9](https://maps.app.goo.gl/pvM16Frig5VjA9e69)), 1891 Lecture Theatre
-
-    Featured Speaker: Iman Hajirasouliha
-
-    Trainee Speaker: Mahdi Asmae
+    Trainee Speaker: Asli Munzur
 
-- ### [Feb 19th, 2026, Thursday](./archive/2026/2026-02-19.md)
+- ### [Nov 19th, 2026, Thursday](./archive/2026/2026-11-19.md)
 
     :material-clock: 6:00pm - 8:00pm
 
     :material-map-marker: **Location:** Vancouver General Hospital, Jimmy Pattison Pavilion South ([899 West 12th Ave., Vancouver, BC V5Z 1M9](https://maps.app.goo.gl/pvM16Frig5VjA9e69)), 1891 Lecture Theatre
 
-    Featured Speaker: Anne Condon
+    Featured Speaker: Dr. Maria Tokuyama
 
-    Trainee Speaker: Maxwell Douglas
+    Trainee Speaker: Moritz Aubermann
 
-- ### Mar 19th, 2026, Thursday
+- ### Dec 10th, 2026, Thursday
 
-    :material-clock: 6:00pm - 8:00pm
-
-    :material-map-marker: **Location:** Vancouver General Hospital, Jimmy Pattison Pavilion North ([899 West 12th Ave., Vancouver, BC V5Z 1M9](https://maps.app.goo.gl/pvM16Frig5VjA9e69)), 141 TF
+    :material-clock: TBD
 
-    Featured Speaker: Emilia Lim
-
-    Trainee Speaker: Asli Munzur
+    :material-map-marker: TBD
 
-- ### Apr 30th, 2026, Thursday
+    Special Event
 
-    :material-clock: 6:00pm - 8:00pm
-
-    :material-map-marker: **Location:** Vancouver General Hospital, Jimmy Pattison Pavilion North ([899 West 12th Ave., Vancouver, BC V5Z 1M9](https://maps.app.goo.gl/pvM16Frig5VjA9e69)), 141 TF
+///
 
-    Featured Speaker: David C. Clarke
 
-    Trainee Speaker: Neera Patadia
 
 ///