Aaron Khodami

New Tool Added: BibTeX Generator

2026-04-30T09:00:00+00:00

We have added a new tool to the website: BibTeX Generator.

This DOI Metadata Tool lets you generate clean BibTeX from one DOI or many. You can paste DOI values, DOI URLs, or raw identifiers, and the tool will normalize them and build BibTeX entries.

Try it here:

BibTeX Generator

The tool works with trusted external metadata sources and is designed to keep output clean and practical for citation workflows.

ZotGit v0.0.30 Released

2026-04-29T09:00:00+00:00

ZotGit v0.0.30 is now available.

Following constructive user feedback, I addressed the caching issue related to hardcoded paths. This release includes improvements focused on speed and reliability across devices.

What’s new in v0.0.30

Optimized caching for faster performance.
Improved multi-device synchronization.

ZotGit update v0.0.30 with improved caching and sync.

The update is available at ZotGit.

Existing users will receive an update notification in Zotero shortly. As always, feedback is welcome.

LEACS Seminar Invitation

2026-04-15T08:00:00+00:00

Join my LEACS Seminar tomorrow, 17/04/2026, at 13:00 EET, either in person or online, where I will share my experiences and insights from my three-year PhD program.

The seminar will cover the following topics:

Our work with Parisa Kiyasati (incoming PhD student at Gissen) on the impact of short-term vigilance training on visual processing speed.
My mathematical and methodological research on trial-to-trial variability in processing speed in the Theory of Visual Attention (TVA).
Our collaborative work with Luca Battaglini and Parisa on the role of precision in fixation as a successful strategy for individuals with central vision loss.

How to Join

In person: Agora room Ag B222.1 (Gamma), University of Jyväskylä this event is finished

Online: via Zoom this event is finished

LEACS Seminar announcement.

Introducing ZotGit

2026-03-26T09:00:00+00:00

Excited to share ZotGit - an open-source Zotero plugin I built to make attachment management clean, automated, and GitHub-backed.

If you use Zotero heavily, you know how quickly PDF workflows can become messy, and how fast shared storage can fill up. ZotGit was designed to simplify that entire experience and keep your library easier to manage across devices.

What ZotGit does

Automatically move or copy imported attachments into a custom directory.
Auto-delete linked local files when they are removed in Zotero.
Attach the latest modified file from a folder to a Zotero item.
Optional Remote PDF Mode for GitHub-backed, on-demand recall.

Why this matters

ZotGit offers a practical way to synchronize files across multiple devices without worrying about storage limitations. By leveraging a GitHub repository, users can keep files in sync while maintaining a clean local setup.

It also optimizes local storage by using a cache workflow: files are synchronized and can be removed locally when Zotero closes, then recalled when needed for reading, editing, or highlighting.

ZotGit in action: clean attachment handling with GitHub-backed recall.

Explore ZotGit on GitHub

PhD Defense With Distinction

2026-03-23T09:00:00+00:00

In a personal milestone I am delighted to share that today I defended my PhD dissertation with distinction, and I am officially a PhD and Dr. Khodami at Universita degli Studi di Padova.

These three years with the International Research Office - University of Padua, under the Marie Sklodowska-Curie Actions, were full of both highs and lows, and they led to excellent results.

I am deeply grateful to everyone who supported me along the way. My supervisor, Prof. Battaglini, always trusted me at every step. My amazing mentor, Jeremy Wolfe from Harvard Medical School, was always available, even when I had a simple question. My second supervisor, Prof. Melissa Vo, welcomed me with open arms and gave me the chance to learn with her at Ludwig-Maximilians-Universitat Munchen.

This was not a simple achievement. It was a meaningful one, and I am proud of what I have done and of the path I have chosen. None of this would have been possible without the support of my family - my mom and dad, my wife, and definitely my cat, Kiki.

Finishing with excellence is not only an achieved goal; it motivates me to work even harder. I am excited for the path that has already begun at the University of Jyvaskyla.

This is one of the most important milestones of my life.

PhD defense day at the University of Padova.

New Heliyon Publication on Stress and Cognition

2026-03-04T09:00:00+00:00

I am pleased to share our recent publication in Heliyon:

“Stress effects on cognition: Evidence for stress-related disruption of attention and inhibitory control.”

In this study, we examined how perceived stress influences attention and inhibitory control in 91 participants using the Stroop and Go/No-Go tasks. The findings showed that individuals reporting higher perceived stress demonstrated slower reaction times, lower accuracy, and greater disruption under auditory or visual interference.

Many thanks to my colleagues Giulio Contemori, Maryam Jansarvatan, and my supervisor Luca Battaglini for the immense work and commitment that made this publication possible after two years of effort.

Publication page: /publications/
Paper link: https://lnkd.in/ectH67kP

Abstract

While stress can impair cognitive functions, including attention and inhibition, it is not always deleterious; e.g., stress could also increase alertness, motivation, and concentration. Limited research has examined these effects in clinical populations experiencing high perceived stress. The current study investigated the impact of perceived stress levels, as measured by the Perceived Stress Scale (PSS), on attention and inhibition in 91 participants grouped into high, moderate, and low perceived stress levels. Participants completed online versions of the Stroop and Go/No-Go tasks to assess attention and inhibition. Results revealed that participants with higher perceived stress exhibited longer reaction times and fewer correct responses than those reporting lower stress across both tasks. ANOVA revealed significantly poorer performance on the Stroop and Go/No Go tasks among individuals in the high-stress group compared with the moderate- and low-stress groups. Introducing auditory or visual interference further disrupted cognitive performance in the high-stress group. These findings indicate that raised perceived stress negatively impacts attention and inhibition. The study provides evidence that chronic stress may impede cognitive abilities and suggests that further research should examine stress effects in clinical cohorts. This investigation makes a meaningful contribution by demonstrating the deleterious impacts of high perceived stress on cognition in a clinical sample, addressing a gap in the literature.

How to Set Up and Use This Template

2026-02-10T09:00:00+00:00

This post explains how to fork, deploy, and customize the site. It also covers where to edit content, how to add images, and how to publish new posts.

Updates

Apr 12, 2026
- Updated versioning.
- Updated the footer layout.
- Added site-wide font switching.
- To change the website font, open _data/site.yml and set appearance.font to one of these options: times, ubuntu, or roboto.
- Added editable menu labels.
- To rename the menu items, open _data/site.yml and edit the values under navigation, such as home, about, research, publications, blog, and cv.
Apr 10, 2026
- Update versioning has been added to the website.

1) Fork the repository

Click Fork on GitHub to copy the template into your account.
Open your forked repo.

Direct link to the repository:

https://github.com/Aaronkhodami/Academic-web-with-blog

2) Configure GitHub Pages

Go to Settings -> Pages.
Source: Deploy from a branch.
Branch: main (or master), folder / (root).
Save and wait 1-3 minutes for the site to build.

Set the URL and base URL

Open these files and edit the values:

_config.yml
_data/site.yml

If your site is a project site (username.github.io/repo), use:

url: https://YOUR_USERNAME.github.io
baseurl: /YOUR_REPO

If your site is a user/org site (username.github.io), use:

url: https://YOUR_USERNAME.github.io
baseurl: ""

Commit and push. GitHub Pages will rebuild automatically.

3) Update site identity

Edit _data/site.yml to replace the placeholder info:

title and description
author.name, author.title, author.bio
social links
cv file path

Profile photo

Add your photo to assets/images/.
In _data/site.yml, set:

author:
	photo: your-photo.jpg

This image appears on the homepage and About page.

4) Update pages

Edit these Markdown files:

Home: index.md
About: about.md
Research: research.md
Publications: publications.md

5) Add and edit blog posts

Posts live in _posts/ and must follow the naming format:

YYYY-MM-DD-title.md

Each post has front matter at the top:

---
layout: post
title: "Your Post Title"
date: 2026-02-10 10:00:00 +0100
categories: updates
tags: [News, Lab]
excerpt: "Short summary shown in the blog list."
---

6) How the blog list works

The blog list page lives at blog.md. It loops through site.posts and renders each post card. When you add a new file in _posts/, it will automatically appear in the blog list.

If you want to change the blog layout or card design, edit blog.md.

7) How tags work

Tags come from each post’s front matter:

tags: [News, Lab, Publication]

On the blog page, clicking a tag appends ?tag=YourTag to the URL. The blog page reads that parameter and shows only posts that include the tag.

If you want a post to appear under multiple topics, add more tags to its list.

The template uses jekyll-seo-tag and jekyll-feed (enabled in _config.yml). SEO data comes from the site and page front matter.

To improve SEO and sharing previews:

Set title and description in _config.yml and _data/site.yml.
Ensure each page has a clear title.
For posts or pages, add a custom image in the front matter if needed:

image: /assets/images/your-share-image.jpg

The default layout will use this image for social previews when available. If no image is provided, it falls back to the profile photo from _data/site.yml.

9) Update publications

Edit _data/publications.yml to add or update entries. Each item supports:

title, type, authors, journal, abstract
doi (optional)
pdf (local file or external link)

10) Update research interests

Edit _data/interests.yml to change the cards on the homepage.

11) Add images

Place images in assets/images/ and reference them like this:

![Alt text](/assets/images/your-image.jpg)

For your profile image, place the file in assets/images/ and set author.photo in _data/site.yml.

12) Update technical skills (tools)

The Technical Skills section is driven by _data/about.yml:

tools:
	- Python
	- R
	- MATLAB

Add tool icons (custom)

You can use any image file (PNG, JPG, or SVG).

Upload icon files to assets/images/.
Edit _data/icons.yml to map tool names to icon files. Example:

python: python.png
matlab: matlab.svg
r: r.png

Make sure the tool name in _data/about.yml matches the key (case-insensitive).

The template lowercases the tool name to find the icon key. If no icon is found, it tries toolname.png automatically.

13) Add education entries and logos

Education entries live in _data/about.yml:

education:
	- degree: Ph.D. in [Field]
		university: "[University Name]"
		logo: "university_logo.png"
		url: "https://university.edu"
		year: "[Year]"
		details: |
			Dissertation: "[Your dissertation title here]"<br>
			Advisors: [Advisor names]

Add an education logo

Upload the logo file to assets/images/.
Set logo to the file name (for example, university_logo.png).

The logo will appear next to the university name on the About page.

14) Add experience entries and logos

Experience entries are also in _data/about.yml:

experience:
	- position: "Current Position"