Karim Rahimi, PhD

My research background combines expertise in molecular and computational biology along with machine learning and statistical modeling. Currently, I am focused on modeling single-cell genomics and various biological metadata alongside multimodal AI agents and NLP-LLMs. ​​​​Additionally, I am keen on utilizing cutting-edge AI, machine learning, and NLP-LLM technologies to enhance our understanding of biological pathways and gene regulation, while also advocating for the protection and promotion of all mother languages, including Kurdish.

​

During my PhD I studied the role of non-coding RNAs in cancer stem cells and breast cancer mouse model. In particular I investigated the impact of microRNA miR-302 cluster on the stemness state of these cells. This interest later extended to lnc-RNAs and circular RNAs and their functions within neuronal system.​​

​

Circular RNAs represent an important class of non-coding RNA molecules that have emerged as crucial regulators in multiple biological process. These unique RNA structures have demonstrated significant roles in neuronal development, cancer progression, and immunity etc. In recent years, the scientific community has increasingly recognized circRNAs as promising candidates for therapeutic applications. My research has focused specifically on understanding both the formation mechanisms of circular RNAs and their functional roles within neurons followed by designing synthetic circRNAs as a sponging molecule for targeted therapy. Recently, we revealed brain-derived circRNAs exon composition and splicing complexity using Nanopore long-read sequencing. This project was published recently in Nature Communications (https://www.nature.com/articles/s41467-021-24975-z).

​​​

I am experienced and interested in Nanopore long-read sequencing and yet there are lots of questions at the genomic and transcriptomic level about the variations, repeat elements, and splicing events that need to be addressed. Additionally, Nanopore direct sequencing of DNA and RNA results in profiling the epigenetic markers and methylation patterns. This era of genome and transcriptome studies are highly interesting and potentially can reveal lots of complexities behind the gene expression regulation in response to stress, aging, cancer and any other environmental changes.

​

As a groundbreaking technology, I have been interested in CRISPR as a great tool for complex functional assays and pool screens and have a strong experience in working with and customizing CRISPR-Cas9, CRISPR-Cas13 and inactivated versions of these magic enzymes. This technology is very useful for high throughput research studies and I believe it is a promising tool for therapeutics approaches and precision medicine in the near future.

 

Single-cell genomics is another fascinating area in biology and integrating more metadata at the single-cell level would be extraordinary, such as long-read RNA isoforms, small RNAs, DNA sequencing and epigenome informations. I am interested to design and develop new methods for single-cell long-read RNA and DNA sequencing. Recently, I have collaborated on projects to study the full length RNA isoforms at the single cell resolution and at the tissue specific level and also cancerous versus normal samples. I have developed deep learning approaches to use the potential power of transformer technology for understanding the complexity of biological and biomedical metadata. Additionally, I am interested in AI-ML for better understanding the complexity of biological pathways and gene regulations. 

​

As a long-term nonprofit interest and commitment, I have worked and developed expertise in multiple aspects of Natural Language Processing (NLP) to protect, serve and promote mother languages started with my native Kurdish (kurdai.org). Very similar to global genome repositories, linguistic resources are a vital component of our shared human heritage, and safeguarding them is essential to preserving cultural identity. Recent advancement in NLP-LLM AI technology, offer immense potential not only to document and protect these languages but also to foster broader, cross-cultural understanding. By leveraging cutting-edge NLP capabilities, we can help each language share its unique insights, traditions, and perspectives with the world. This exchange of knowledge and ideas contributes to a more interconnected global society, one in which empathy transcends linguistic and cultural boundaries, ultimately reducing the likelihood of conflict and helping us move toward a more harmonious future while keeping the beauties of diversity.