Registered Supplier (Hadassah, Clalit, HUJI)

Computational Analysis for Next-Generation Sequencing Data

Specializing in high-dimensional genomic data. From comprehensive Single-Cell transcriptomics to Spatial data mapping and bulk RNA-Seq/Epigenetics. Delivering rigorous, publication-ready bioinformatics pipelines for clinical and academic research.

View Technical Capabilities Contact for Consultation

Core Bioinformatics Services

Single-Cell RNA-Seq Analysis

  • Single Sample Analysis: Comprehensive QC, normalization, dimensional reduction (PCA, UMAP/t-SNE), clustering, and precise cell-type annotation using established markers and automated classifiers.
  • Multi-Condition/Sample Integration: Batch effect correction (Harmony, Seurat Integration) and robust Differential Expression of Genes (DEG) calculation per cell cluster across control vs. treated datasets.
  • Trajectory inference (pseudotime) and gene set enrichment analysis (GSEA).

Spatial Transcriptomics

Analysis of spatially resolved transcriptomic data generated by platforms such as 10x Genomics Visium and sub-cellular resolution platforms like 10x Xenium.

  • Mapping single-cell expression profiles to tissue architecture.
  • Identification of spatial domains and localized cell niches.
  • Cell-cell communication modeling based on spatial proximity.

Bulk RNA-Seq & Epigenetics

  • Bulk RNA-Seq: Read alignment, quantification, and rigorous differential expression analysis (DESeq2/edgeR).
  • ChIP-Seq / ATAC-Seq: Peak calling, motif discovery, and differential accessibility analysis.
  • Methylation: WGBS and targeted array analysis.

Custom Computational Workflows

  • Development of reproducible pipelines using R, Python, and Bash.
  • Integration of public datasets (GEO, TCGA) with proprietary lab data.
  • Generation of high-quality, publication-ready figures (Heatmaps, Volcano plots, Feature plots).

Methodology & Infrastructure

Institutional Supplier Integration

Officially registered as a supplier (Sapak Murshe) in Hadassah Medical Center, Hebrew University Faculty of Medicine, and Clalit Health Services. This eliminates administrative friction, allowing PIs to issue Purchase Orders (PO) immediately.

Data Backup

Genomic data and metadata are processed, stored, and backed up on dedicated workstations, with all code and intermediate objects thoroughly documented to ensure full reproducibility during peer review.

Tool Stack

Utilizing industry-standard R based and Python based frameworks such as Seurat, CellChat, clusterProfiler, methylKit and many more.

Extensive Experience

Successfully completed multiple tens of comprehensive Single-Cell and Spatial Transcriptomics (10x Xenium) projects.

Also completed multiple tens of Bulk RNA-Seq, Epigenetics, Methylation, Variant Calling, CHiP-Seq and more..

This extensive, hands-on exposure to diverse tissue types and experimental designs ensures robust pipeline execution, rapid troubleshooting, and the extraction of deep biological insights that only come from seasoned experience.

Selected Publications

View all 17 publications on LinkedIn

Co-authoring 17 academic papers as the bioinformatician, providing computational peer-reviewed pipelines, while collaborating with top researchers to deliver publication-ready analysis.

MicroRNA-122 functions as a rheostat regulating liver tolerance, inflammation and fibrosis

Journal of Hepatology, 2025

Superenhancers shape the landscape and repair dynamics of transcription-associated DNA breaks in cancer

Science Advances, 2026

WWOX maintains epidermal identity and suppresses EMT to prevent aggressive cutaneous squamous cell carcinoma

Proceedings of the National Academy of Sciences, 2026

The breakome of BRCA1 and BRCA2 pathway mutation carriers reveals early processes in breast oncogenesis

Cell Death & Disease, 2025

Tumor analysis of BRCA carriers reveals genomic similarities although separated by time

Discover Oncology, 2024

Muscle injury causes long-term changes in stem-cell DNA methylation

Proc Natl Acad Sci U S A., 2022

Contact & Project Inquiry

To discuss experimental design, analysis pipelines, or to request a formal quote, please reach out via email, phone, or the contact form.

jh.monin@gmail.com
(Israel) 054-569-8910
Registered In Hadassah Medical Center, Clalit Health Services, Hebrew University Faculty of Medicine