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1,019 changes: 503 additions & 516 deletions _data/citations.yaml

Large diffs are not rendered by default.

3 changes: 2 additions & 1 deletion _includes/figure.html
Original file line number Diff line number Diff line change
Expand Up @@ -9,7 +9,8 @@
<img
src="{{ include.image | relative_url }}"
style="
width: {{ include.width | default: "auto" }};
width: {{ include.width | default: "25%" }};
max-width: 100%;
max-height: {{ include.height | default: "unset" }};
"
alt="{{ include.caption | default: "figure image" }}"
Expand Down
40 changes: 40 additions & 0 deletions _includes/gallery.html
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@@ -0,0 +1,40 @@
{% assign image_list = include.images | default: "" | split: "|" | array_filter %}
{% assign alt_list = include.alts | default: "" | split: "|" %}
{% assign caption_list = include.captions | default: "" | split: "|" %}
{% assign folder = include.folder | default: "" %}

{% if image_list.size > 0 %}
<div class="gallery">
{% for image_name in image_list %}
{% assign image_name = image_name | strip %}
{% assign alt_text = alt_list[forloop.index0] | default: "" | strip %}
{% assign caption_text = caption_list[forloop.index0] | default: "" | strip %}
{% if folder != "" %}
{% assign image_path = folder | append: "/" | append: image_name %}
{% else %}
{% assign image_path = image_name %}
{% endif %}

<figure class="figure gallery-item">
<a class="figure-image" aria-label="{{ caption_text | default: alt_text | default: 'gallery image' }}">
<img
src="{{ image_path | relative_url }}"
style="
width: 100%;
max-width: 100%;
max-height: {{ include.height | default: 'unset' }};
"
alt="{{ alt_text | default: caption_text | default: 'gallery image' }}"
loading="lazy"
{% include fallback.html %}
>
</a>
{% if caption_text != "" %}
<figcaption class="figure-caption">
{{ caption_text | markdownify | remove: "<p>" | remove: "</p>" }}
</figcaption>
{% endif %}
</figure>
{% endfor %}
</div>
{% endif %}
72 changes: 35 additions & 37 deletions _includes/list.html
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Expand Up @@ -21,42 +21,40 @@

{% for d in data %}
{% assign style = d.style | default: include.style %}

{%
include {{ include.component | append: ".html" }}
author=d.author
authors=d.authors
buttons=d.buttons
caption=d.caption
course_website=d.course_website
content=d.content
date=d.date
description=d.description
distribution=d.distribution
excerpt=d.excerpt
height=d.height
icon=d.icon
id=d.id
image=d.image
last_modified_at=d.last_modified_at
link=d.link
lookup=d.lookup
name=d.name
publisher=d.publisher
repo=d.repo
role=d.role
slug=d.slug
style=style
subtitle=d.subtitle
tags=d.tags
terms_offered=d.terms_offered
text=d.text
next_offered=d.next_offered
title=d.title
tooltip=d.tooltip
type=d.type
url=d.url
width=d.width
%}
{% include {{ include.component | append: ".html" }}
author=d.author
authors=d.authors
buttons=d.buttons
caption=d.caption
course_website=d.course_website
content=d.content
date=d.date
description=d.description
distribution=d.distribution
excerpt=d.excerpt
height=d.height
icon=d.icon
id=d.id
image=d.image
last_modified_at=d.last_modified_at
link=d.link
lookup=d.lookup
name=d.name
publisher=d.publisher
repo=d.repo
role=d.role
slug=d.slug
style=style
subtitle=d.subtitle
tags=d.tags
terms_offered=d.terms_offered
text=d.text
next_offered=d.next_offered
title=d.title
tooltip=d.tooltip
type=d.type
url=d.url
width=d.width
%}
{% endfor %}
{% endfor %}
13 changes: 13 additions & 0 deletions _includes/mentioned-people.html
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@@ -0,0 +1,13 @@
{% assign tagged_people = include.people | default: empty %}
{% assign tagged_people = tagged_people | join: "," | split: "," | array_filter %}

{% if tagged_people.size > 0 %}
<div class="mentioned-people">
<p class="mentioned-people-label">Mentioned</p>
<div class="mentioned-people-list">
{% for person in tagged_people %}
{% include portrait.html lookup=person style="tiny" %}
{% endfor %}
</div>
</div>
{% endif %}
7 changes: 7 additions & 0 deletions _includes/post-excerpt.html
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Expand Up @@ -52,5 +52,12 @@
<p data-search="{{ search }}">
{{ excerpt }}
</p>
{% if url %}
<p class="post-excerpt-more">
<a href="{{ url | relative_url }}">Click here for more</a>
</p>
{% endif %}
{% endif %}

{% include mentioned-people.html people=info_people %}
</div>
20 changes: 0 additions & 20 deletions _includes/post-info.html
Original file line number Diff line number Diff line change
Expand Up @@ -40,26 +40,6 @@
{% endunless %}
</div>

{% assign tagged_people = include.people | default: empty %}
{% assign tagged_people = tagged_people | join: "," | split: "," | array_filter %}

{% if tagged_people.size > 0 %}
<p class="center">
Mentioned:
{% for person in tagged_people %}
{% assign member = site.members
| where_exp: "member", "member.slug == person"
| first
%}
{% if member %}
<a href="{{ member.url | relative_url }}">{{ member.name }}</a>{% unless forloop.last %}, {% endunless %}
{% else %}
{{ person }}{% unless forloop.last %}, {% endunless %}
{% endif %}
{% endfor %}
</p>
{% endif %}

{% if include.tags %}
{% include tags.html tags=include.tags link="news" %}
{% endif %}
2 changes: 2 additions & 0 deletions _layouts/post.html
Original file line number Diff line number Diff line change
Expand Up @@ -20,6 +20,8 @@ <h1 class="center">{{ page.title }}</h1>

{{ content }}

{% include mentioned-people.html people=page.people %}

{% include section.html %}

{% include post-nav.html post=page %}
2 changes: 1 addition & 1 deletion _members/alina_yildirim.md
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Expand Up @@ -7,4 +7,4 @@ role: undergrad

Alina is a senior majoring in Computer Science and Statistics. She is interested in biomedical AI, especially how machine learning and language-based methods can help connect mouse and human disease. Her honors thesis focuses on comparing how experiments are described across species and what that means for translation.

After graduating in May '26, she will begin her PhD at UMass Amherst in the Hong Lab, where she plans to continue working on biomedical NLP and cross-species modeling.
After graduating in May '26, she will begin her [PhD in Computer Science at UMass Amherst](https://www.cics.umass.edu/) in the [Hong Lab](https://bio-nlp.github.io/), where she plans to continue working on biomedical NLP and cross-species modeling.
9 changes: 4 additions & 5 deletions _posts/2024-04-28-hildana-mckinley-honors-fellowship.md
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Expand Up @@ -4,14 +4,13 @@ author: halie_rando
people:
- hildana_shiferaw
tags:
- announcement
- honors
- fellowship
- McKinley
---

<!-- excerpt start -->
Hildana Shiferaw has been selected for the McKinley Honors Fellowship Program.
We are excited to share that Hildana Shiferaw has been selected as an Honors Fellow through the AEMES McKinley Fellowship Program!
<!-- excerpt end -->

We are excited to share that Hildana Shiferaw has been selected for the McKinley Honors Fellowship Program.

The fellowship will support Hildana's honors thesis work in the VBIL. More information about Smith's AEMES programs is available [here](https://www.smith.edu/academics/departments-programs-courses/aemes).
The fellowship will support Hildana's honors thesis work in the VBIL during her senior year. More information about Smith's AEMES programs is available [here](https://www.smith.edu/academics/departments-programs-courses/aemes).
23 changes: 23 additions & 0 deletions _posts/2024-07-24-CSIG.md
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@@ -0,0 +1,23 @@
---
title: Students present at CSIG
author: halie_rando
people:
- hildana_shiferaw
- tseegi_nyamdorj
tags:
- conference
- CSIG
- talks
---

Rising seniors Hildana Shiferaw and Tseegi Nyamdorj presented lightning talks at Computational Systems for Integrative Genomics at the Flatiron Institute in NYC!

Tseegi's talk was titled "Manubot: Incorporating MS Word track changes into version controlled writing workflows", and Hildana's was titled "Comparing semantic and biological representations of animal models."

We also got to take a tour of their in-house computing infrastructure!

{% include gallery.html
folder='images/news/2024-07-24-csig'
images='IMG_0610.jpeg|IMG_0612.jpeg|IMG_1048.jpeg'
alts='CSIG group photo 1|CSIG group photo 2|CSIG computing infrastructure tour'
%}
5 changes: 2 additions & 3 deletions _posts/2025-04-28-hildana-thesis-presentation.md
Original file line number Diff line number Diff line change
Expand Up @@ -4,13 +4,12 @@ author: halie_rando
people:
- hildana_shiferaw
tags:
- announcement
- honors
- thesis
---

<!-- excerpt start -->
Hildana Shiferaw gave an excellent presentation of her honors thesis on a urine-based screening approach for ovarian cancer.
Today Hildana Shiferaw gave an excellent presentation of her honors thesis on a urine-based screening approach for ovarian cancer!
<!-- excerpt end -->

On Monday, April 28, 2025, Hildana Shiferaw gave an excellent presentation of her honors thesis, "System Design of a Urine-Based Screening Approach for Ovarian Cancer Informed by Computational Identification of miRNAs as Biomarkers."
Her honors thesis is titled "System Design of a Urine-Based Screening Approach for Ovarian Cancer Informed by Computational Identification of miRNAs as Biomarkers" and is co-advised by Halie Rando (CSC) and Mike Kinsinger (EGR). Notably, Hildana completed a programming-heavy computational biology thesis without any CSC coursework after CSC 110! We are all so proud of her achievements -- congratulations Hildana!
9 changes: 4 additions & 5 deletions _posts/2025-04-29-alina-mckinley-honors-fellowship.md
Original file line number Diff line number Diff line change
Expand Up @@ -4,14 +4,13 @@ author: halie_rando
people:
- alina_yildirim
tags:
- announcement
- honors
- fellowship
- McKinley
---

<!-- excerpt start -->
Alina Yildirim has been selected for the McKinley Honors Fellowship Program.
We are excited to share that Alina Yildirim has been selected as an Honors Fellow through the AEMES McKinley Fellowship Program!
<!-- excerpt end -->

We are excited to share that Alina Yildirim has been selected for the McKinley Honors Fellowship Program.

The fellowship will support Alina's honors thesis work in the VBIL. More information about Smith's AEMES programs is available [here](https://www.smith.edu/academics/departments-programs-courses/aemes).
The fellowship will support Alina's honors thesis work in the VBIL during her senior year. More information about Smith's AEMES programs is available [here](https://www.smith.edu/academics/departments-programs-courses/aemes).
26 changes: 26 additions & 0 deletions _posts/2026-03-06-SAVY.md
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@@ -0,0 +1,26 @@
---
title: Students research accepted to SAVY
author: halie_rando
people:
- elaine_chen
- glenvelis_perez
- yixuan_he
- zihan_lyu
- caitlyn_kim
- halie_rando
tags:
- research
- conference
- poster
- talk
---

<!-- excerpt start -->
Exciting news: the lab had two abstracts accepted at the [third annual Symposium on AI in Veterinary Medicine (SAVY3.0)](https://web.cvent.com/event/aa14bd81-31f3-456b-8f5c-8a22e0fcf5cc/summary), which will be held at Cornell University in May.
<!-- excerpt end -->

Caitlyn Kim will present her poster "A New Benchmarking Dataset of AKC-Registered Dog Breeds for Fine-Grained Image Classification Tasks", describing the work her team has been doing to build a new dataset of images of dogs with confirmed breed labels. Co-authors include Nora and Frankie.

Elaine Chen is the lead author on the abstract "Differentiating Effects of Neural Network Architecture versus Dataset in Computer Vision’s Dog Breed Identification Problem", which has been accepted as [one of five talks in the session on AI Applications in Companion Animal Health](https://web.cvent.com/event/aa14bd81-31f3-456b-8f5c-8a22e0fcf5cc/websitePage:98c370f0-c898-447a-aa1b-54632d0fd6e7). Co-authors include Glenvelis Perez and Yixuan (Quinn) He.

The teams are looking forward to attending this incredible symposium and sharing their work with the community!
24 changes: 24 additions & 0 deletions _posts/2026-04-09-ISMB.md
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@@ -0,0 +1,24 @@
---
title: Four student groups submit abstracts to ISMB
author: halie_rando
people:
- yuzhang_fu
- hildana_shiferaw
tags:
- research
- abstracts
- conference
---

<!-- excerpt start -->
Four student research teams submitted abstract to [Intelligent Systems in Molecular Biology](https://www.iscb.org/ismb2026/home), one of the major computational biology conferences, which will be held in Washington D.C. in July.
<!-- excerpt end -->

Some of the projects include:

- Natural language processing approaches for identifying the methods used in a study based on its metadata (submitted to [BOKR](https://www.bio-ontologies.org.uk/))
- Natural language processing approaches for comparing the similarity of experiments across species (submitted to [BOKR](https://www.bio-ontologies.org.uk/))
- An open-source tool for extracting fluorescent peak information from fragment analysis files in the ABIF format (submitted to [BOSC](https://www.open-bio.org/events/bosc-2026/))
- An analysis of alternative clustering approaches to understanding molecular phenotypes of high-grade serous ovarian cancer (submitted to [iRNA](https://irna.iscb.org/))

Notably, all of these submissions had at least one sophomore as a co-author! Fantastic work everyone!
30 changes: 30 additions & 0 deletions _posts/2026-04-10-CCSCNE.md
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@@ -0,0 +1,30 @@
---
title: Students present at CCSC-NE
author: halie_rando
people:
- yuzhang_fu
- halie_rando
tags:
- research
- conference
- poster
- talk
---

<!-- excerpt start -->
Our lab gave several presentations at [CCSC-NE](https://www.ccscne.org/), which was held this year here at Smith.
<!-- excerpt end -->

In the afternoon, Halie and Jade Lili (one of our amazing CSC 210 TAs) as well as two former data structures students presented the [unique data structures curriculum](https://handsondatastructures.github.io/) that Halie has been using in CSC 210 for the past few semesters. Their presentation was one of two tutorials offered at the conference this year.

In the evening, two groups from the lab also presented posters at the [undergraduate research poster session](https://www.ccscne.org/2026/StudentPosters.pdf):

- Ayesha & Yuzhang presented their poster "Mouse Model of Disease - Language, Metadata, and Cross-Species Comparison"
- Nargiz presented her poster "Microsatellites Made Accessible: An Open-Source Tool for Microsatellite Data Analysis"

{% include gallery.html
folder='images/news/2026-04-10-ccscne'
images='CCSCNE-YFAS.png|CCSCNE-NA.png'
alts='Ayesha and Yuzhang presenting their poster.|Nargiz presenting her poster.'
captions='Ayesha and Yuzhang presenting their poster.|Nargiz presenting her poster.'
%}
12 changes: 12 additions & 0 deletions _styles/figure.scss
Original file line number Diff line number Diff line change
Expand Up @@ -24,3 +24,15 @@
font-style: italic;
text-align: center;
}

.gallery {
display: grid;
grid-template-columns: repeat(auto-fit, minmax(180px, 1fr));
gap: 24px;
align-items: start;
margin: 40px 0;
}

.gallery-item {
margin: 0;
}
8 changes: 8 additions & 0 deletions _styles/post-excerpt.scss
Original file line number Diff line number Diff line change
Expand Up @@ -32,3 +32,11 @@
.post-excerpt > p {
width: 100%;
}

.post-excerpt-more {
text-align: center;
}

.post-excerpt-more a {
font-weight: var(--semi-bold);
}
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