Welcome to our website

A major roadblock in early drug design is the need to discover novel and potent small-molecule drug leads. Many projects do not achieve even one sub-micromolar lead and, in those that do, a single lead is typically obtained with nanomolar potency after several years of expert-led iterative optimisation work (thus, requiring extensive human and financial resources). Therapeutic targets are molecular, e.g. a disease-causing protein, or phenotypic, e.g. a cancer cell line or bacterial culture. For any of these targets, the more drug leads are discovered, the greater the likelihood that at least one will not have any preclinical issue and thus will eventually reach clinical trials.

Drugs overcoming clinical trials still face additional challenges after approval. In cancer, tumour heterogeneity and other inter-patient differences result in large response variability across patients despite having the same cancer type and being administered the same drug treatment. Precision oncology tackles this problem by attempting to identify drug-resistant patients early, so that they can be administered more effective therapies and they do not suffer unnecessary side effects. Unfortunately, most cancer drugs do not have response markers and most existing markers are far from being sufficiently predictive.

Our research aims at developing and applying computational methods to boost biomedical discoveries in these areas. We leverage three timely opportunities: artificial intelligence (AI) innovation, big data availability, and mature domain knowledge. This website introduces ourselves and the research we carry out in these fascinating areas.

The Ballester Group

Dr Pedro Ballester

Royal Society Wolfson Fellow & Senior Lecturer

Imperial College London

Following a first degree in Astrophysics and an MSc in Information Processing and Neural Networks, I completed a PhD at Imperial College on geophysical data mining and inference. After that, I was awarded a Junior Research Fellowship at the University of Oxford and then held a short postdoc at the University of Cambridge, both associated with their Chemistry departments. In 2010, I was awarded a 4-year MRC Methodology Research Fellowship, which funded my staff scientist position at the European Bioinformatics Institute, and also a Governing Body Fellowship at Wolfson College Cambridge. In 2014, I moved to the south of France for a position as a tenured group leader at INSERM with A*MIDEX Excellence Chair and ANR Tremplin-ERC awards. In 2022, I returned to the UK as an Associate Professor at Imperial College London and Wolfson Fellow of the Royal Society.

Awards

• 2022-27 Royal Society Wolfson Fellow, UK.
• 2019-22 INSERM scientific excellence merit award (PEDR), France.
• 2017-19 ANR Tremplin - ERC, France.
• 2015-17 A*MIDEX Excellence Chair, France.
• 2014 Civil Servant Qualifying Exams (INSERM CR1), France.
• 2011-14 JRF & Governing Body Fellow, Wolfson College Cambridge, UK.
• 2010-14 MRC Methodology Research Fellow, UK.
• 2007-08 Junior Research Fellow (JRF), St Cross College Oxford, UK.
• 2000-01 Scholar, Sa Nostra Foundation, Spain.
• 2000 Civil Servant Qualifying Exams (Physics Innovation Expert), Spain.

Funding

I have been awarded a total of €4,314,000 (€2,552,000 plus £1,554,782) to fund my research since 2010 (this includes the funding awarded to my group only, no total grant value). This is broken down into major project grants awarded as PI:
• 2023-26 EPSRC Healthcare Technologies (UK, £625,936).
• 2022-27 Royal Society Wolfson Fellowship (UK, £281,280).
• 2021-24 Plancancer MIC (France, €276,493).
• 2020-23 ANR PRC grant (France, €320,000).
• 2019-22 CEFIPRA (India-France bilateral projects, €77,000).
• 2017-20 ANR Tremplin-ERC (France, €130,000).
• 2015-17 A*MIDEX Excellence Chair (France, €235,000).
• 2010-14 MRC Methodology Research Fellowship (UK, £507,936).
Project grants awarded as co-I:
• 2022 ARC – SIGN'IT 2022 (France, €110,000).
• 2022 ANR – PEPR Digital health (France, €500,000).
• 2016 Canceropôle PACA (France, €83,000).
And also awarded grants for postdoctoral fellowships (ARC, FRM), PhD scholarships (Chulabhorn Royal Academy, ANR Artificial Intelligence, IPC, HEC, CONACyT, PTDF, USTH) and other purposes (Pfizer, PHC Merlion, INSERM).

Publications and patents

As June 2023: 83 peer-reviewed papers since 2003, 79% as corresponding author. H-index restricted to papers where I am either first, last or corresponding author is 29.

Ballester, P.J. (2012) US Patent 8244483 “Shape Recognition Methods and Systems for Searching Molecular Databases”

Community service

Editorial roles: 2021-date Editorial Board Member of Briefings in Bioinformatics, 2019-date Associate Editor of npj Precision Oncology, among others. Peer-review: 500+ reviews of journal papers verified. Grant proposal evaluations for a range of funding agencies: Canada Research Chair, Medical Research Council (MRC, UK), DBT/Wellcome Trust India Alliance (India), Science Foundation (GACR, Czech Republic), National Research Foundation (NRF, South Africa), Ministry of Economy and Competitiveness (MINECO, Spain), Natural Sciences and Engineering Research Council (NSERC, Canada), Agency for Health Quality and Assessment of Catalonia (AQuAS, Spain), Engineering and Physical Sciences Research Council (EPSRC, UK), National Foundation for Science & Technology (FCT, Portugal), Health Research Board (HRB, Ireland), National Research Fund (FNR, Luxembourg), Israel Science Foundation (ISF), The Swiss National Science Foundation, Netherlands Organisation for Scientific Research, National Agency for Research (ANR, France), National Agency for Research (ANEP, Spain), Biotechnology and Biological Sciences Research Council (BBSRC, UK) and National Scientific Research Council (Romania). Times Higher Education’s World University Rankings: Invited to act as a reputation evaluator every year since 2018.

Members

Principal Investigator

pjb

Dr Pedro Ballester

Royal Society Wolfson Fellow & Senior Lecturer

Postdoctoral researchers

Avatar

Nivya James

February 2024-date

PhD Students

Avatar

Saiveth Hernández

Oct 2020 - date

Avatar

Chayanit Piyawajanusorn

Oct 2022 - date

Avatar

Hanqin Du

Oct 2022 - date

Avatar

Qianrong Guo

Jan 2023 - date

Avatar

Klaudia Caba

April 2023 - date

Avatar

Zerui Li

April 2023 - date

Avatar

Elizabeth Amelia

October 2023 - date

MRes Students

Avatar

Cosmin Ichim

MRes in Bioengineering (June 2023 - date)

Avatar

Sara Marsden

MRes in Bioengineering (October 2023 - date)

Avatar

Yuanjie Zou

MRes in Bioengineering (October 2023 - date)

Avatar

Seshagiri Sakthimani

MRes in Bioengineering (October 2023 - date)

Avatar

Jiatao Liu

MRes in Bioengineering (October 2023 - date)

Avatar

Tiantian He

MRes in Cancer Technology (October 2023 - date)

MSc Students

Avatar

Yue Cai

MSc in Biomedical Engineering (December 2023 - date)

Avatar

Alexis Dougha

MSc in Biomedical Engineering (December 2023 - date)

Alumni

MSc students at Imperial (UK): In Bioengineering (2023: Lucas He, Alec Reygrobellet), in Digital Chemistry (2023: Amrit Jandu, Nicola Chesterman), in Bioinformatics (2023: Rasmus Hildebrandt).

Undergraduate students at Imperial (UK): Jonathan Talbot-Martin (2023, primarily supervised by Dr Nicky Whiffin, University of Oxford), Aparna Loecher (2022, primarily supervised by Dr Nuria Oliva-Jorge, Imperial College).

Postdocs at CRCM (France): Jitendra Kuldeep (2021, 18 months), Viet-Khoa Tran-Nguyen (2021, 2 years), Ghita Ghislat (2022, 9 months), Junaid Muhammad (2021, 18 months), Saw Simeon (2019, 2 years), Pavel Sidorov (2017, 2 years), Stefan Naulaerts (2017, 1.5 years), Cuong Dang (2015, 2 years), Antonio Peon (2015, 2 years).

PhD students at CRCM (France): Hongjian Li (visiting from CUHK), Linh Nguyen, Adeolu Ogunleye, Sachin Vishwakarma, Saiveth Hernández.

Master students at CRCM (France): Louai Kassa-Baghdouche, Dina Ouahbi, Pablo Gomez, Louison Fresnais, Amad Diouf, Michal Zulcinski, Nicola Jaume.

Master students at EMBL-EBI (UK): Raquel Romero, Saumya Kumar.

Examples of current alumni positions: lecturers/assistant professors (Linh Nguyen and Cuong Dang at Vietnam National University, Pavel Sidorov at Hokkaido University, Viet-Khoa Tran-Nguyen at Paris Cite University), pharmaceutical companies (Sachin Vishwakarma at Evotec), senior Horizon Europe Marie Curie fellowships (Ghita Ghislat at Imperial College London).

News

 
 
 
 
 
What doesn’t help much with the structure-based identification of small-molecule inhibitors for PD1/PDL1? Simple protein-ligand interaction fingerprint search or deep learning models. What actually helps much more? Mining patents with PD1/PDL1 actives, training with large volumes of docked inactives, enabling inactive-enriched regression and large-scale machine-learning analysis.
 
 
 
 
 
Further evidence of the usefulness of large-scale machine learning analysis for precision oncology, here reporting predictors of pancreatic cancer patient response to gemcitabine.
 
 
 
 
 
Letter to Editor published
12 December 2023
While AI experts tend to overestimate the current impact of their models when applied to chemistry, it is equally true that chemistry experts tend to underestimate them. Nature wrote an editorial on the underestimation side. They expect an AI revolution in chemistry but argue that this will only happen when more labelled data becomes available, which is too simplistic. I highlighted some promising research topics in my response above, but there are of course many others underway. Time scales are hard to anticipate, but whether these are short (revolution) or large (evolution), I am convinced that one has much to learn by considering knowledge from experts at both extremes.
 
 
 
 
 
Social event
7 December 2023
Some pictures by clicking on the handle above.
 
 
 
 
 
Report published
25 October 2023
The UK Government Office for Science has released a paper on Future risks of frontier AI to inform the forthcoming AI Safety Summit. Pedro Ballester is one of the AI experts who was invited to contribute to this report.
 
 
 
 
 
We have released and explained our user-friendly protocol to train and rigorously validate target-specific machine-learning scoring functions for structure-based virtual screening.
 
 
 
 
 
Group update
9 October 2023
We welcome one PhD student awarded with the James West Scholarship (Elizabeth Amelia), five students from the MRes in Bioengineering (Cosmin Ichim, Sara Marsden, Yuanjie Zou, Seshagiri Sakthimani, Jiatao Liu) and one student from the MRes in Cancer Technology (Tiantian He). Thanks for choosing our group to carry out your research projects, we are excited for you to join us!
 
 
 
 
 
Postdoc available
Deadline: 24 July 2023
The link contains all the required information to apply. Please note the deadline above.
 
 
 
 
 
Paper published
March 2023
For virtual screening of chemically diverse libraries, your predictive model should be trained, tuned and validated using different clusters of molecules. But not anything goes here, as clustering quality can vary strongly with the employed algorithm and outlier detection method.
 
 
 
 
 
Here we show how virtual screening performance can still be overestimated when using simple methods or training-test data partitions designed to be unbiased.
 
 
 
 
 
Large-scale machine learning analysis leading to the discovery of highly predictive, robust and even interpretable predictors of breast cancer patient response to doxorubicin.

Contact

Email: p.ballester@imperial.ac.uk

Address: Sir Michael Uren Hub, Imperial College White City campus, 86 Wood Lane, London - W12 0BZ, UK

How to get here: https://www.imperial.ac.uk/visit/campuses/white-city/

About this campus: https://www.imperial.ac.uk/white-city-campus/

The Ballester Group