Sebastian Zeki

Sebastian Zeki

Gastroenterology consultant

Guy's and St Thomas' NHS Trust


Dr Sebastian Zeki is a consultant gastroenterologist at St Thomas’ Hospital in London. His research interests include upper gastrointestinal physiology, upper gastrointestinal cancer, natural language programming and quality metrics in endoscopy. He co-leads the Gastroenterology data sciences Institute in London


  • Endoscopic therapy
  • Oesophageal and stomach cancers/Barrett’s oesophagus
  • Oesophageal physiology
  • Heartburn; chest pain; indigestion; bloating; spasm; dyspepsia; irritable bowel syndrome; swallowing disorders; hoarse voice; chronic cough and throat clearing
  • Eosinophilic oesophagitis
  • High quality endoscopy
  • Machine learning/R/Natural language programming
  • Genomics


  • PhD - Genomics of Barrett's related malignancy, 2013

    University of London

  • Member of the Royal College of Physician, 2006

  • MSc Health Informatics, 2003

    City University

  • MBBS MBChir Medicine, 2001

    University College London

  • MA in experimental psychology, 1998

    Cambridge University



Honorary Senior Clinical Lecturer, King’s College London

King’s College

Oct 2019 – Present London

Co-head of the Gastroenterology Data Sciences Institute

Guy’s & St Thomas’ NHS Trust

Jan 2017 – Present London

Honorary Senior Clinical Lecturer, Bart’s Cancer Institute

Bart’s Cancer Institute

Jan 2017 – Present London

Consultant Gastroenterologist

Guy’s & St Thomas’ NHS Trust

Apr 2015 – Present London

Clinical Lecturer

Cambridge University: MRC Hutchison

Jun 2013 – Apr 2015 Cambridge

PhD student

Queen Mary University of London

Jan 2010 – Jun 2013 London

Gastroenterology registrar

North West Thame’s Training Rotation

Jun 2006 – Jan 2016 London

Postgraduate internal medicine training

Jun 2001 – Jun 2006 London


Acid reflux and reflux related conditions

Reflux can cause a number of worrying symptoms such as heartburn, regurgitation, coughs, sore throats and a hoarse voice

Bloating, swollen abdomen, vomiting and feeling gassy

Feeling bloated and being gassy can be embarrassing but is usually avoidable with careful investigation and personalised treatment

Detection, surveillance and resection of early GI cancers and pre-cancers

Daycase endoscopic removal using mucosal and submucosal dissection

Eosinophilic oesophagitis and food allergies

The increasingly common condition called eosinophilic oesophagitis and its relationship to food

Swallowing problems

The feeling of food getting stuck after swallowing, or choking can be due to a number of different problems from obstructions, to weak or even overactive oesophageal muscles



A basic tutorial on data science methods as applied to gastroenterological data. This will explain the basic principles of natural language processing as applied to endoscopy and pathological text to allow information to be extracted in an automated way.

Improving Lesion Recognition using text

Health Foundation grant to use endoscopic and pathological free text merge with images to improve lesion recognition in trainees by automating individual metrics
Improving Lesion Recognition using text


A package written in R to automate extraction of endoscopic metrics from free text reports. R is a functional programming language and one of the most commonly used. Here it is applied to endoscopic and pathological natural language text. The open source package can execute on any body of text. The package comes with a well developed tutorial and plenty of examples.

MiFlo- a single page patient flow manager to help virtual consultations

A Shiny app that visually represents a patients timeline of investigations with summarised results as well as appointments. The excess of information that electronic data has brought with it means that there is now a desperate need to show only data that is needed to make a decision about a patient rather than to drown a clinician in a lot of unnecessary information. MiFlo provides this filter. It was initially developed for gastroenterology but is equally configurable to any clinical environment.
MiFlo- a single page patient flow manager to help virtual consultations

Gastroenterology book

A visual training manual for Gastroenterologists with automated MCQ’s. Gastroenterology training covers a huge number of subjects. The gastroenterology training book was the first online attempt to provide a comprehensive training book where each subject is treated as a single, visually represented page. Each page can automatically generate MCQ’s from the page so that there are an unlimited number of MCQs on the site. If you log in (which is free) you can get your performance on the MCQ’s as well as your reading metrics so you can discover your knowledge gaps.
Gastroenterology book

Recent & Upcoming Talks

Automation in endoscopy

A demonstration of EndoMineR to allow automated extraction of data from endoscopy and pathology free text reports.
Automation in endoscopy

IBS for general practice- how to approach, how to help and how to treat

IBS is common and needs a careful and sympathetic approach. Here I outline an approach that incorporates the latest evidence based guidance for diagnosis and treatment, with suggestions for empowering and sympathising with this patient group "

Natural language processing of endoscopic and pathological text

A demonstration of EndoMineR to allow automated extraction of data from endoscopy and pathology free text reports.
Natural language processing of endoscopic and pathological text


  • 02033014916
  • HCA The Shard,32 St Thomas Street, London, London SE1 9BS
  • Monday to Saturday evenings (18:00 to 20:00) or Tuesdays 09:00 to 12.30
  • Book an appointment

Endoscopy videos