Dr Namshik Han

University of Cambridge

University departments
Department of Applied Mathematics and Theoretical Physics
University institutes
Milner Therapeutics Institute
Wellcome Trust MRC Cambridge Stem Cell Institute

Position: Associate Faculty, Head of Computational Research & AI, Affiliated Principal Investigator
Personal home page: https://www.bio.cam.ac.uk/staff/namshik-han
Email:   nh417@cam.ac.uk

PubMed journal articles - click here

Dr Namshik Han is pleased to consider applications from prospective PhD students.

Research description

I am a computational drug discovery scientist, coming from a background in machine learning, computational biology, cancer genomics and cancer epigenomics. I am Head of Computational Research & AI at Milner Therapeutics Institute in University of Cambridge and also Associate Faculty at Cambridge Centre for AI in Medicine in the same University. I also have an Adjunct Professor position at Yonsei University College of Medicine. My lab develop and apply dedicated and bespoke Artificial Intelligence technologies that deal with the uncertainty and complexity of biological datasets to reveal novel disease pathways and mechanisms. Projects within the lab include (1) identification of new therapeutic targets in a variety of diseases, (2) stratification of patients to improve personalised medicine, (3) prediction of efficacy and safety of new and existing drugs and (4) identification of drug (re)positioning opportunities.

In addition to my academic research, I have a passion for working at the interface between academia and industry to apply my research to real-world problems. In my case this is in therapeutics and patient care where AI promises to revolutionize the ability to identify disease mechanisms and potential drug targets, informing patient care from disease diagnosis through to treatment. Towards this aim, I facilitate access of the Milner Therapeutics Consortium partner organizations to cutting-edge AI technology and to develop new computational methods fulfilling the global mission of identifying new or better therapies from the analysis of biological data. Furthermore, I contributed to the establishment of Storm Therapeutics. I co-founded two start-ups: (1) KURE.ai to develop immune-oncology NK cell therapy and (2) CardiaTec to develop innovative drugs for cardiovascular diseases.

Research Programme or Virtual Institute
Early Cancer Institute
Secondary Programme
Not applicable
Strategic Resources
The Milner Therapeutics Institute and Consortium
Methods and technologies
Computational modelling
DNA sequencing
Gene expression profiling
Public health
Statistical analysis
X-ray crystallography
Tumour type interests
Brain and central nervous system
Computational Biology
Machine Learning
Artificial Intelligence
Drug Discovery
Recent publications:
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Key publications

Predicting genes associated with RNA methylation pathways using machine learning
G Tsagkogeorga, H Santos-Rosa, A Alendar, D Leggate, O Rausch, T Kouzarides, H Weisser§ and Namshik Han§ (2022, in print) Communications Biology - preprint https://doi.org/10.1101/2021.12.10.472055

dialogi: Utilising NLP with chemical and disease similarities to drive the identification of Drug-Induced Liver Injury literature
N M Katritsis§, A Liu, G Youssef, S Rathee, M MacMahon, W Hwang, L Wollman, and N Han§ (2022, in print) Frontiers in Genetics - preprint https://doi.org/10.1101/2022.03.11.483929

Computational Discovery of Cancer Immunotherapy Targets by Intercellular CRISPR Screens
S Yim, W Hwang, N Han§, D Lee§ (2022) Frontiers in Immunology

DILIc: An AI based classifier to search for Drug-Induced Liver Injury literature
S Rathee*,§, M MacMahon*, A Liu, N Katritsis, G Youssef, W Hwang, L Wollman, N Han§ (2022) Frontiers in Genetics

Deriving time-concordant event cascades from gene expression data: A case study for Drug-Induced Liver Injury (DILI)
A Liu, N Han, J Munoz-Muriedas, A Bender (2022) PLOS Computational Biology

Identification of potential pan-coronavirus therapies using a computational drug repurposing platform
W Hwang and N Han (2021) Methods

Identification of SARS-CoV-2 induced pathways reveal drug repurposing strategies
N Han*§, W Hwang*, Tzelepis K*, … F Weber and T Kouzarides§ (2021) Science Advances

Current and prospective computational approaches and challenges for developing COVID-19 vaccine
W Hwang*, W Lei*, NM Katritsis*, M MacMahon*, K Chapman and N Han (2021) Advanced Drug Delivery Reviews

Methylation of histone H3 at lysine-37 by Set1 and Set2 prevents spurious DNA replication
H Santos-Rosa*§, G Millan-Zambran*, N Han*, T Leonardi, M Klimontova, ... and T Kouzarides§ (2021) Molecular Cell

The inflammatory niche directs alveolar regeneration via Krt8+Cldn4+ regenerative progenitors
J Choi, J-E Park†, G Tsagkogeorga†, B-K Koo, N Han‡ and J-H Lee (2020) Cell Stem Cell

Differential expression of soluble receptor for advanced glycation end-products (sRAGE) in mice susceptible or resistant to chronic colitis
M Bramhall, K Rich, A Chakraborty, L Logunova, N Han†, ... and S Cruickshank (2020) Inflammatory Bowel Diseases

A novel long noncoding RNA Linc-ASEN represses cellular senescence through multileveled reduction of p21 expression
H C Lee*, D Kang*, N Han†, Y Lee, … and J Lee (2019) Cell Death & Differentiation

Genomic positional conservation identifies topological anchor point RNAs linked to developmental loci
P Amaral*, T Leonardi*, N Han*, E Vire, D K Gascoigne, … and T Kouzarides (2018) Genome Biology

Long non-coding RNA ChRO1 facilitates ATRX/DAXX-dependent H3.3 deposition for transcription-associated heterochromatin reorganization
J Park, H Lee, N Han†, S Kwak, … and E J Cho (2018) Nucleic Acid Research

DDX3X RNA helicase affects breast cancer cell cycle progression by regulating expression of KLF4
E Cannizzaro*, A J Bannister*, N Han†, and T Kouzarides (2018) FEBS Letters

TIGERi: Modeling and visualizing the responses to perturbation of a transcription factor network
N Han§, H Noyes, A Brass§ (2017) BMC Bioinformatics

Promoter-bound METTL3 maintains myeloid leukaemia by m6A-dependent translation control
I Barbieri*, K Tzelepis*, L Pandolfini*, … N Han†, … G Vassiliou§ and T Kouzarides§ (2017) Nature

FOXM1 and polo-like kinase 1 are co-ordinately overexpressed in patients with gastric adenocarcinomas
M Dibb, N Han†, J Choudhury, … and A D Sharrocks (2015) BMC research notes

Deregulation of the FOXM1 target gene network and its coregulatory partners in oesophageal adenocarcinoma
E F Wiseman, X Chen, N Han†, A Webber, … and A D Sharrocks (2015) Molecular Cancer

The forkhead transcription factor FOXK2 acts as a chromatin targeting factor for the BAP1-containing histone deubiquitinase complex
Z Ji, H Mohammed, … N Han, … and A D Sharrocks (2014) Nucleic acids research

The Forkhead TF FOXM1 Controls Cell Cycle-Dependent Gene Expression through an Atypical Chromatin Binding Mechanism
X Chen, G A Muller, … N Han, … and A D Sharrocks (2013) Molecular and Cellular Biology

Progressive lung cancer determined by expression profiling and transcriptional regulation
N Han*, Z Dol*, O Vasieva, … and J K Field (2012) International Journal of Oncology

The FOXM1-PLK1 axis is upregulated in oesophageal adenocarcinoma
M Dibb, N Han†, J Choudury, … and A D Sharrocks (2012) British Journal of Cancer

Protein kinase C regulates late cell cycle-dependent gene expression
Z Darieva, N Han†, K Doris, B A Morgan, A D Sharrocks (2012) Molecular and Cellular Biology

* Co-first author
§ Co-corresponding author
† Bioinformatics lead author
‡ Bioinformatics supervisor

Combining mathematics and biology in computer science can produce novel insights in the biology. Computational approaches not only ensure implementation of highly elaborated mathematical model using large scale genome-wide datasets generated by the high-throughput experiments, but also practicably analyse and visualize the results from the mathematical modelling process. The computationally derived results provide comprehensive understanding of biological mechanism. Image courtesy of Namshik Han