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A list of all the posts and pages found on the site. For you robots out there is an XML version available for digesting as well.
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About
Associate Director, Bioinformatics & Predictive AI
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Posts
books
Validating gene signatures in locally advanced HNSCC patients treated by PORT-C and in xenografts.
Published:
projects
Reproducing GPT-2
Published:
🧠💬 ChatGPT has become an integral part of my daily life. I became increasingly intrigued to understand what was going on under the hood of the GPT model and spent my weekends 🛠️ building a GPT model — aiming to replicate OpenAI’s GPT-2 (124M) model.
LLMs + Foundational models for Single Cell Analysis
Published:
🚀 We’re entering an exciting era where Biological Foundation Models are being integrated with Large Language Models (LLMs) — opening up powerful new ways to model cellular biology.
EVO2 DNA Foundational model Demo
Published:
🧬 EVO2 DNA FOUNDATIONAL MODEL Demo Summary 🚀
GPT-OSS Architecture: Implementation
Published:
GPT-OSS: Architecture Implementation
DeepSeek-V3 Model Architecture: Educational Deep Dive
Published:
DeepSeek-V3 Model Architecture: Educational Deep Dive
MultiOmicsBind: Deep Learning framework for Multi-Omics Data Integration
Published:
Deep learning framework applying ImageBind’s binding modality concept to integrate genomics, transcriptomics, proteomics, and metabolomics data.
AlphaGenome’s U-Net Architecture Implementation
Published:
Complete implementation of DeepMind’s 450M parameter model for genomic sequence analysis and multi-modal predictions.
OmicsNet: Integrating data from multiple omics modalities to build and analyze feature-level networks.
Published:
Introducing OmicsNet: Multi-Omics Integration Without Sample Overlap
OmicsFormer: Transforming Multi-Omics Data Integration with Deep Learning.
Published:
OmicsFormer is an open-source PyTorch framework that uses transformer architectures to integrate multi-omics data from multiple studies, handling missing modalities and batch effects. Validated on real-world SLE data achieving 91% accuracy across 8 independent studies.
Pokemon Agent: AI-Powered Pokemon Battle Agent.
Published:
Building an AI-Powered Pokemon Battle Agent: When LLMs Meet Strategic Gaming 🎮⚡
BulkRNA-Agent: AI-Powered Transcriptomics Analysis.
Published:
Open-source AI tool combining dual LLM architecture for intelligent bulk RNA-seq analysis with 100% local processing.
ScAdver: Adversarial Batch Correction for Single-Cell Data
Published:
Train once, project forever batch correction for single-cell RNA-seq with probe-gated adaptive query projection and robust domain adaptation.
publications
Male calling and spacing in natural chorus of Platygryllus sp. Implications for masking interference and mate choice.
Published in , 2015
This master thesis is about Male spacing in natural choruses of Platygryllus sp. of crickets and its implications on male and female crickets. The acoustic spaces of male crickets overlapped to a large extent and it is likely that the female could hear multiple males at a time. The study focuses on the strategy the female would choose to mate.
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The Role of the Virome in the Gut-Liver Axis.
Published in Springer, Cham, 2019
This is chapter in the book “The Human Gut-Liver-Axis in Health and Disease”.
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Assessing the in vitro resistance development in Enterovirus 71 in the context of combination antiviral treatment.
Published in ACS Infectious Diseases, 2020
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Analyses of molecular subtypes and their association to mechanisms of radioresistance in patients with HPV-negative HNSCC treated by postoperative radiochemotherapy.
Published in Radiotherapy and oncology, 2022
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Plasticity within aldehyde dehydrogenase–positive cells determines prostate cancer radiosensitivity.
Published in Molecular cancer research, 2022
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Development and validation of a 6-gene signature for the prognosis of loco-regional control in patients with HPV-negative locally advanced HNSCC treated by postoperative radio(chemo)therapy.
Published in Radiotherapy and Oncology, 2022
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A Novel 2-Metagene signature to identify high-risk HNSCC patients amongst those who are clinically at intermediate risk and are treated with PORT.
Published in Cancers, 2022
Developed a novel 2-metagene signature for risk stratification in head and neck squamous cell carcinoma (HNSCC) patients receiving postoperative radiotherapy, enabling personalized treatment decisions.
Recommended citation: Patil, S., et al. (2022). "A Novel 2-Metagene signature to identify high-risk HNSCC patients." Cancers, 14(12), 3031. https://www.mdpi.com/2072-6694/14/12/3031
Molecular characterisation of tumours and biomarker identification for personalised radiation oncology using genomic data of patients with locally advanced head and neck squamous cell carcinoma.
Published in Technical University of Dresden, 2022
This is my PhD thesis conducted in the Modeling and Biostatistics in Radiation Oncology group at OncoRay – National Center for Radiation Research in Oncology under the supervision of Prof. Dr. Steffen Löck.
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ALDH1A1 drives prostate cancer metastases and radioresistance by interplay with AR-and RAR-dependent transcription.
Published in Theranostics, 2024
Identified ALDH1A1 as a key driver of prostate cancer metastasis and radioresistance through its interaction with androgen receptor and retinoic acid receptor-dependent transcription pathways.
Recommended citation: Patil, S., et al. (2024). "ALDH1A1 drives prostate cancer metastases and radioresistance." Theranostics, 14, 714-732. https://www.thno.org/v14p0714.htm
The value of subcutaneous xenografts for individualised radiotherapy in HNSCC: Robust gene signature correlates with radiotherapy outcome in patients and xenografts.
Published in Radiotherapy and Oncology, 2024
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Unlocking Biological Insights Through AI-driven Multi-Omics Integration.
Published in Spanish Drug Discovery Network conference 2025, 2025
Poster presented at the Spanish Drug Discovery Network conference 2025.
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