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updated and cleaned up the papers logic
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‎_config.yml‎

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about_content: |
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**<sub>[CV](https://moneuron.github.io/assets/data/drive/cv.pdf) ·
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[CONTACT](#contact)</sub>**
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papers: |
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> I’m **Mo**, a NeuroAI researcher.
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---
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<span class="paper-item">
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· **Shakiba M**, Rokni R, Mohammadi M, Dehghani N. Harnessing cortical geometry, wiring, and function as inductive biases for recurrent neural networks. *arXiv*, 2026.
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<sub>**[HTML](https://arxiv.org/) ·
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[PDF](https://moneuron.github.io/assets/data/drive/preprint/) ·
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[CODE](https://github.com/moneuron/neuro-constrained-RNN) ·
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[BLOG](https://neurovium.github.io/)**</sub>
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<sub>**`Preprint`**</sub>
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</span>
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<span class="paper-item">
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· 34th Annual Computational Neuroscience Meeting: CNS\*2025. *J Comput Neurosci*, 2026.
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<sub>**[HTML](https://doi.org/10.1007/s10827-025-00915-4) ·
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[PDF](https://moneuron.github.io/assets/data/drive/article/cns-rnn.pdf)**</sub>
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<sub class="citation" id="cns-rnn" data-doi="10.1007/s10827-025-00915-4"></sub>
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<sub>**`Article`**</sub>
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</span>
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<span class="paper-item">
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· **Shakiba M**, Rokni R, Mohammadi M, Dehghani N. Anatomically and Functionally Constrained Bio-Inspired Recurrent Neural Networks Outperform Traditional RNN Models. *Kempner Institute Frontiers in NeuroAI Symposium*, 2025.
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<sub>**[HTML](https://www.researchgate.net/publication/393980916) ·
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[PDF](https://moneuron.github.io/assets/data/drive/poster/frnt-rnn.pdf)**</sub>
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<sub>**`Poster`**</sub>
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</span>
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<span class="paper-item">
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· **Shakiba M**, Rokni R, Mohammadi M. Neuro-constrained Bio-inspired Recurrent Neural Network. *Zenodo*, 2025.
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<sub>**[HTML](https://doi.org/10.5281/zenodo.15313132) ·
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[PDF](https://moneuron.github.io/assets/data/drive/preprint/neuro-bio.pdf)**</sub>
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<sub>**`Preprint`**</sub>
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</span>
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<span class="paper-item">
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· **Shakiba M**, Rassouli FB. Joining up the scattered anticancer knowledge on auraptene and umbelliprenin: a meta-analysis. *Scientific Reports*, 2024.
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<sub>**[HTML](https://doi.org/10.1038/s41598-024-62747-z) ·
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[PDF](https://moneuron.github.io/assets/data/drive/article/srep-meta.pdf) ·
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[CODE](https://github.com/moneuron/srep-meta-codes) ·
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[DATA](https://doi.org/10.5061/dryad.cvdncjt9k)**</sub>
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<sub class="citation" id="srep-meta" data-doi="10.1038/s41598-024-62747-z"></sub>
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<sub>**`Article`**</sub>
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</span>
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<span class="paper-item">
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· Talebian S, Shahnavaz B, **Shakiba M**, Rassouli FB. Illuminating new possibilities: Effects of copper oxide nanoparticles on gastrointestinal adenocarcinoma cells in hypoxic condition. *Heliyon*, 2024.
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<sub>**[HTML](https://doi.org/10.1016/j.heliyon.2024.e31414) ·
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[PDF](https://moneuron.github.io/assets/data/drive/article/hel-cuonp.pdf)**</sub>
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<sub class="citation" id="hel-cuonp" data-doi="10.1016/j.heliyon.2024.e31414"></sub>
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<sub>**`Article`**</sub>
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</span>
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intro: |
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> I’m **Mo**, a NeuroAI researcher.
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meta_title: Mo Shakiba · Home
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meta_url: moneuron.github.io

‎_data/papers.yml‎

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- key: rnn-inductive-biases
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authors:
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- name: Shakiba M
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highlight: true
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- name: Rokni R
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- name: Mohammadi M
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- name: Dehghani N
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title: Harnessing cortical geometry, wiring, and function as inductive biases for recurrent neural networks
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venue: arXiv
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year: 2026
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type: Preprint
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links:
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- label: HTML
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url: https://arxiv.org/
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- label: PDF
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url: https://moneuron.github.io/assets/data/drive/preprint/
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- label: CODE
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url: https://github.com/moneuron/neuro-constrained-RNN
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- label: BLOG
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url: https://neurovium.github.io/
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- key: cns-rnn
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title: "34th Annual Computational Neuroscience Meeting: CNS*2025"
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venue: J Comput Neurosci
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year: 2026
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type: Article
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doi: 10.1007/s10827-025-00915-4
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citation_id: cns-rnn
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links:
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- label: HTML
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url: https://doi.org/10.1007/s10827-025-00915-4
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- label: PDF
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url: https://moneuron.github.io/assets/data/drive/article/cns-rnn.pdf
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- key: frnt-rnn
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authors:
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- name: Shakiba M
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highlight: true
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- name: Rokni R
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- name: Mohammadi M
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- name: Dehghani N
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title: Anatomically and Functionally Constrained Bio-Inspired Recurrent Neural Networks Outperform Traditional RNN Models
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venue: Kempner Institute Frontiers in NeuroAI Symposium
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year: 2025
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type: Poster
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links:
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- label: HTML
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url: https://www.researchgate.net/publication/393980916
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- label: PDF
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url: https://moneuron.github.io/assets/data/drive/poster/frnt-rnn.pdf
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- key: neuro-bio
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authors:
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- name: Shakiba M
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highlight: true
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- name: Rokni R
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- name: Mohammadi M
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title: Neuro-constrained Bio-inspired Recurrent Neural Network
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venue: Zenodo
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year: 2025
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type: Preprint
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links:
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- label: HTML
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url: https://doi.org/10.5281/zenodo.15313132
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- label: PDF
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url: https://moneuron.github.io/assets/data/drive/preprint/neuro-bio.pdf
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- key: srep-meta
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authors:
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- name: Shakiba M
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highlight: true
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- name: Rassouli FB
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title: "Joining up the scattered anticancer knowledge on auraptene and umbelliprenin: a meta-analysis"
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venue: Scientific Reports
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year: 2024
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type: Article
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doi: 10.1038/s41598-024-62747-z
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citation_id: srep-meta
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links:
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- label: HTML
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url: https://doi.org/10.1038/s41598-024-62747-z
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- label: PDF
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url: https://moneuron.github.io/assets/data/drive/article/srep-meta.pdf
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- label: CODE
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url: https://github.com/moneuron/srep-meta-codes
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- label: DATA
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url: https://doi.org/10.5061/dryad.cvdncjt9k
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- key: hel-cuonp
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authors:
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- name: Talebian S
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- name: Shahnavaz B
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- name: Shakiba M
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highlight: true
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- name: Rassouli FB
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title: "Illuminating new possibilities: Effects of copper oxide nanoparticles on gastrointestinal adenocarcinoma cells in hypoxic condition"
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venue: Heliyon
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year: 2024
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type: Article
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doi: 10.1016/j.heliyon.2024.e31414
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citation_id: hel-cuonp
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links:
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- label: HTML
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url: https://doi.org/10.1016/j.heliyon.2024.e31414
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- label: PDF
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url: https://moneuron.github.io/assets/data/drive/article/hel-cuonp.pdf

‎_includes/about.html‎

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<div class="container">
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<div class="row clearfix">
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<div class="col-xs-12">
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{{ site.papers | strip | markdownify }}
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{%- if site.intro -%}
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{{ site.intro | strip | markdownify }}
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{%- endif -%}
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<hr>
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{%- include papers.html -%}
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</div>
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</div>
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</div>

‎_includes/papers.html‎

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<section aria-label="Papers">
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{%- for paper in site.data.papers -%}
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<article class="paper-item">
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<header>
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<span>
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·
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{%- assign authors_count = paper.authors | size -%}
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{%- if authors_count > 0 -%}
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{%- for author in paper.authors -%}
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{%- if author.highlight -%}
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<strong>{{ author.name }}</strong>
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{%- else -%}
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{{ author.name }}
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{%- endif -%}
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{%- unless forloop.last -%}, {%- endunless -%}
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{%- endfor -%}.
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{%- endif -%}
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{%- assign title = paper.title | strip -%}
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{{ title }}{%- unless title | slice: -1 == '.' -%}.{%- endunless -%}
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<em>{{ paper.venue }}</em>, {{ paper.year }}.
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</span>
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</header>
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<footer>
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{%- assign links_count = paper.links | size -%}
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{%- if links_count > 0 -%}
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<div>
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<sub>
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<strong>
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{%- for link in paper.links -%}
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<a href="{{ link.url }}">{{ link.label }}</a>{% unless forloop.last %} · {% endunless %}
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{%- endfor -%}
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</strong>
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</sub>
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</div>
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{%- endif -%}
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{%- if paper.doi -%}
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<div>
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<sub class="citation"{% if paper.citation_id %} id="{{ paper.citation_id }}"{% endif %} data-doi="{{ paper.doi }}"></sub>
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</div>
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{%- endif -%}
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<div>
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<sub><strong><code>{{ paper.type }}</code></strong></sub>
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</div>
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</footer>
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</article>
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{%- endfor -%}
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</section>

‎assets/data/fetch_citations.py‎

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from scholarly import scholarly
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# -------------------------------------------------------------------
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# Load DOIs from _config.yml
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# Load DOIs from site files
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# -------------------------------------------------------------------
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def load_dois_from_config(config_path="_config.yml") -> list[str]:
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with open(config_path, encoding="utf-8") as f:
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config = yaml.safe_load(f)
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REPO_ROOT = Path(__file__).resolve().parents[2]
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PAPERS_DATA_FILE = REPO_ROOT / "_data" / "papers.yml"
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PAPERS_INCLUDE_FILE = REPO_ROOT / "_includes" / "papers.html"
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CONFIG_FILE = REPO_ROOT / "_config.yml"
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papers_html = config.get("papers", "")
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return re.findall(r'data-doi="([^"]+)"', papers_html)
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def extract_dois(text: str) -> list[str]:
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return re.findall(r'data-doi="([^"]+)"', text)
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PAPERS = load_dois_from_config()
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def unique_keep_order(values: list[str]) -> list[str]:
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seen: set[str] = set()
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out: list[str] = []
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for v in values:
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if v in seen:
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continue
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seen.add(v)
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out.append(v)
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return out
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def load_dois() -> list[str]:
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# Primary source: structured data file
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if PAPERS_DATA_FILE.exists():
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data = yaml.safe_load(PAPERS_DATA_FILE.read_text(encoding="utf-8")) or []
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papers: list[dict] = []
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if isinstance(data, list):
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papers = [p for p in data if isinstance(p, dict)]
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dois = [str(p.get("doi")) for p in papers if p.get("doi")]
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if dois:
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return unique_keep_order(dois)
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# Fallback: extract from include HTML (works if papers are still hard-coded)
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if PAPERS_INCLUDE_FILE.exists():
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dois = extract_dois(PAPERS_INCLUDE_FILE.read_text(encoding="utf-8"))
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dois = [d for d in dois if "{{" not in d and "}}" not in d]
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if dois:
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return unique_keep_order(dois)
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# Fallback: legacy config key (kept for backwards compatibility)
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if CONFIG_FILE.exists():
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config = yaml.safe_load(CONFIG_FILE.read_text(encoding="utf-8")) or {}
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papers_html = str(config.get("papers", ""))
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dois = extract_dois(papers_html)
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if dois:
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return unique_keep_order(dois)
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return []
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PAPERS = load_dois()
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# -------------------------------------------------------------------
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# Settings

‎assets/main.css‎

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transform: translateY(12px);
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animation: fadeUp 0.6s ease forwards;
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}
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.page-content .paper-item {
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font-size: 1.6rem;
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text-align: left;
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font-weight: 500;
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}
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@keyframes fadeUp {
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to {
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opacity: 1;

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