-
Notifications
You must be signed in to change notification settings - Fork 0
Expand file tree
/
Copy pathindex.html
More file actions
289 lines (259 loc) · 13.8 KB
/
index.html
File metadata and controls
289 lines (259 loc) · 13.8 KB
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="UTF-8">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>Home | Bioinformatics Portfolio</title>
<!-- Link to fontawesome for inserting social media icons -->
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/7.0.1/css/all.min.css" integrity="sha512-2SwdPD6INVrV/lHTZbO2nodKhrnDdJK9/kg2XD1r9uGqPo1cUbujc+IYdlYdEErWNu69gVcYgdxlmVmzTWnetw==" crossorigin="anonymous" referrerpolicy="no-referrer" />
<link rel="stylesheet" href="style.css">
</head>
<body>
<!-- Navigation -->
<nav class="navbar">
<a href="#home" class="logo">
<img src="images/abc_logo.png" alt="Arthur Boffelli Castro Logo">
</a>
<button class="nav-toggle">
<i class="fas fa-bars"></i>
</button>
<ul class="nav-links">
<li><a href="#home" >Home</a></li>
<li><a href="#about"> About</a></li>
<li><a href="#skills">Skills</a></li>
<li><a href="#projects">Projects</a></li>
<li><a href="#contact">Contact</a></li>
</ul>
</nav>
<!-- Hero section -->
<section id="home" class="hero">
<div class="hero-content">
<h1>Arthur Boffelli Castro</h1>
<p class="subtitle">Bioinformatician & PhD Student</p>
<p class="division">Functional Breast Cancer Genomics, Lund University</p>
<p class="highlight">Investigating the functional impact of splicing factors in breast cancer using genomic and computational approaches.</p>
<a href="#contact" class="cta-button">
Let's Connect <i class="fas fa-paper-plane"></i>
</a>
</div>
<div class="hero-image">
<img src="images/anime_style_green.png" alt="Profile Photo" class="profile-img">
</div>
</section>
<!-- About me section -->
<section id="about" class="about">
<h2>About Me</h2>
<p>
I am a PhD student in the Functional Breast Cancer Genomics group at Lund University, where I study how splicing factors influence breast cancer biology. My research uses genomic data analysis to uncover new insights into gene regulation and cancer mechanisms.
</p>
<p>
Alongside my research, I work as a systems administrator for the Bioinformatics Masters Programme at Lund University, maintaining the computational infrastructure used for teaching. I enjoy coding and building tools, whether it's exploring biological data, creating workflows, or helping students get the most out of our teaching infrastructure.
</p>
<p class="hobbies">Outside of work, I enjoy playing tennis, practicing guitar, and drawing.</p>
</section>
<!-- Skills Section -->
<section id="skills" class="skills">
<h2>Technical Expertise</h2>
<div class="skills-grid">
<div class="skill-card">
<i class="fas fa-dna"></i>
<h3>Bioinformatics</h3>
<p>Genomics, Transcriptomics, Variant Analysis, Functional Annotation, Image Analysis</p>
</div>
<div class="skill-card">
<i class="fas fa-code"></i>
<h3>Programming</h3>
<p>R, Python </p>
</div>
<div class="skill-card">
<i class="fas fa-database"></i>
<h3>Data Analysis</h3>
<p>tidyverse, Pandas, Data Visualization</p>
</div>
<div class="skill-card">
<i class="fas fa-cogs"></i>
<h3>Workflow Management</h3>
<p>Snakemake, Conda</p>
</div>
<div class="skill-card">
<i class="fas fa-cloud"></i>
<h3>Version Control</h3>
<p>Git, GitHub</p>
</div>
<div class="skill-card">
<i class="fas fa-network-wired"></i>
<h3>Automation & Systems</h3>
<p>Linux, Ansible, Server Management</p>
</div>
<div class="skill-card">
<i class="fas fa-terminal"></i>
<h3>Command-line & HPC</h3>
<p>Bash scripting, AWK, SLURM</p>
</div>
<div class="skill-card">
<i class="fas fa-globe"></i>
<h3>Web Tools</h3>
<p>HTML, CSS, Shiny</p>
</div>
</div>
</section>
<!-- Projects Section -->
<section id="projects" class="projects">
<h2>Projects</h2>
<div class="project-grid">
<!-- 2023-2025 - ECC detection -->
<div class="project-card">
<h3>Enlarged Cancer Cell Detection</h3>
<p>
Developed a pipeline for detecting enlarged cancer cell nuclei in breast cancer tissue microarray (TMA) images.
The workflow combines <em>QuPath</em> and <em>Stardist</em> for nuclear detection and feature extraction, with a Snakemake-based automation pipeline to streamline analysis.
</p>
<p>
The project is ongoing and the pipeline will continue to be developed by other team members. The code is publicly available on GitHub.
</p>
<div class="project-tags">
<span class="tag">Snakemake</span>
<span class="tag">QuPath</span>
<span class="tag">Stardist</span>
<span class="tag">Image Analysis</span>
<span class="tag">Python</span>
<span class="tag">R</span>
<span class="tag">Bash</span>
<span class="tag">AWK</span>
<span class="tag">Groovy</span>
</div>
<a href="https://github.com/aboffelli/ecc-manual-analysis" class="project-link" target="_blank">
Source Code <i class="fab fa-github"></i>
</a>
</div>
<!-- 2021 - Interomics -->
<div class="project-card">
<h3>Interomics</h3>
<p>A Shiny-based web application for metagenomic data exploration and visualization.
Built in R using phyloseq, metacoder, and plotly, Interomics enables users to generate interactive diversity, abundance, and taxonomic tree plots directly from their data tables.
</p>
<div class="project-tags">
<span class="tag">R</span>
<span class="tag">Shiny</span>
<span class="tag">metacoder</span>
<span class="tag">phyloseq</span>
<span class="tag">plotly</span>
</div>
<a href=" https://aboffelli.shinyapps.io/interomics/." class="project-link" target="_blank">
Live App <i class="fas fa-external-link-alt"></i>
</a>
<a href="https://github.com/aboffelli/interomics" class="project-link" target="_blank ">Source code <i class="fab fa-github"></i></a>
</div>
<!-- 2022 - Runemark Lab -->
<div class="project-card">
<h3>Runemark Lab Website</h3>
<p>
Designed and developed the official website for the Runemark Lab from scratch using HTML, CSS, and JavaScript.
I handled the design, setup, and deployment, creating a fully functional and publicly accessible site for the lab.
</p>
<div class="project-tags">
<span class="tag">HTML</span>
<span class="tag">CSS</span>
<span class="tag">JavaScript</span>
<span class="tag">Web Design</span>
</div>
<a href="https://runemarklab.com/" class="project-link" target="_blank">
Visit Site <i class="fas fa-external-link-alt"></i>
</a>
</div>
<!-- 2022-2023 - scWGS Data analysis -->
<div class="project-card">
<h3>Copy Number Analysis of scWGS Data</h3>
<p>
Performed single-cell whole-genome sequencing (scWGS) analysis to investigate genomic instability in
drug-resilient breast cancer cells. This project contributed to the publication
<em>"Drug-resilient Cancer Cell Phenotype Is Acquired via Polyploidization Associated with Early Stress Response Coupled to HIF2α Transcriptional Regulation"</em>.
</p>
<p>
The analysis pipeline was developed in Bash using established bioinformatics tools for alignment and copy number inference.
</p>
<div class="project-tags">
<span class="tag">Bash</span>
<span class="tag">bwa</span>
<span class="tag">samtools</span>
<span class="tag">eagle</span>
<span class="tag">CHISEL</span>
</div>
<a href="https://aacrjournals.org/cancerrescommun/article/4/3/691/735078/Drug-resilient-Cancer-Cell-Phenotype-Is-Acquired" class="project-link" target="_blank">
Publication <i class="fas fa-external-link-alt"></i>
</a>
<a href="https://github.com/aboffelli/pacc-copy-number" class="project-link" target="_blank">
Source Code <i class="fab fa-github"></i>
</a>
</div>
<!-- 2021-2022 - Synonymous variants project -->
<div class="project-card">
<h3>Identification of Functional Synonymous Variants in Breast Cancer</h3>
<p>
Initially developed during my Master's thesis and now extended in my PhD, this computational pipeline identifies potentially functional synonymous variants across breast cancer cohorts.
The workflow integrates variant calling, annotation, and predictive modeling using GATK, VCFtools, VEP, MMSplice, and custom Python and R scripts.
The pipeline pinpointed candidate variants for experimental validation and forms the foundation for ongoing functional studies.
</p>
<div class="project-tags">
<span class="tag">GATK</span>
<span class="tag">VCFtools</span>
<span class="tag">VEP</span>
<span class="tag">MMSplice</span>
<span class="tag">Python</span>
<span class="tag">R</span>
<span class="tag">Breast Cancer</span>
</div>
<a href="https://github.com/aboffelli/variant_annotation" class="project-link" target="_blank">
Source Code <i class="fab fa-github"></i>
</a>
</div>
<!-- 2025-present - Splicing factors project -->
<div class="project-card">
<h3>Deregulation of the Splicing Machinery in Breast Cancer</h3>
<p>
This ongoing project investigates the expression and function of splicing factors across breast cancer subtypes using SCAN-B RNA-seq data.
The analysis integrates gene expression, alternative isoform usage, and somatic variant data to identify regulatory changes in splicing factors
and their potential impact on target gene networks.
</p>
<div class="project-tags">
<span class="tag">R</span>
<span class="tag">Python</span>
<span class="tag">RNA-seq</span>
<span class="tag">edgeR</span>
<span class="tag">Majiq</span>
<span class="tag">Variant Calling</span>
<span class="tag">Gene Set Enrichment Analysis</span>
<span class="tag">Pathway Enrichment Analysis</span>
</div>
<a href="#" class="project-link" title="Private Repository">
Available upon request <i class="fas fa-lock"></i>
</a>
</div>
</div>
</section>
<!-- Contact -->
<section id="contact" class="contact">
<div class="contact-container">
<h2>Contact Me</h2>
<form action="https://formspree.io/f/myzndwbw" method="POST" class="contact-form">
<input type="text" name="name" placeholder="Your Name" required>
<input type="email" name="_replyto" placeholder="Your Email" required>
<textarea name="message" rows="5" placeholder="Your Message" required></textarea>
<button type="submit">Send Message</button>
</form>
</div>
</section>
<!-- Footer -->
<footer>
<p>© 2026 Arthur Boffelli Castro — designed & built by me</p>
<div class="social-links">
<a href="https://github.com/aboffelli" target="_blank"><i class="fab fa-github"></i></a>
<a href="https://www.linkedin.com/in/arthur-boffelli-castro" target="_blank"><i class="fab fa-linkedin"></i></a>
<a href="https://orcid.org/0000-0002-2511-5301" target="_blank"><i class="fab fa-orcid"></i></a>
<a href="https://portal.research.lu.se/en/persons/arthur-boffelli-castro" target="_blank"><i class="fa-solid fa-graduation-cap"></i></a>
</div>
</footer>
<!-- Link to javascript file -->
<script src="script.js"></script>
</body>
</html>