Sander Timmer, PhD

Sander Timmer, PhD

Brussels, Brussels Region, Belgium
5K followers 500+ connections

About

Seasoned global leader in AI, digital innovation, and cloud technology with a proven…

Articles by Sander

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Activity

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Experience

  • GSK Graphic

    GSK

    London, UK | Wavre, Belgium

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    Cambridge, United Kingdom

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    Nijmegen Area, Netherlands

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    Brussels Area, Belgium

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    Brussels Area, Belgium

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    Europe, the Middle East, and Africa

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    Europe, the Middle East and Africa

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    Amsterdam Area, Netherlands

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    Heidelberg Area, Germany

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    Cambridge, United Kingdom

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    Cambridge, United Kingdom

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    Eindhoven Area, Netherlands

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    Nijmegen Area, Netherlands

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    Nijmegen Area, Netherlands

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Education

  • University of Cambridge Graphic

    University of Cambridge

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    Activities and Societies: College rep for the Cambridge Union Society, Social Officer for the Clare Hall Boat Club

    Graduate student at Clare Hall

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    Activities and Societies: Advanced Bioinformatica course @ AMC, Biomolecular Mass Spectrometry course @ Netherlands Proteomics Centre

    Minor project: The influence of protein dynamics on structural alignments (supervised by Walter Pirovano, Anton Feensta and Jaap Heringa)

    Optional master course:

    Advanced Bioinformatics (12 ECTS)
    Academic Medical Center and University of Amsterdam
    by Prof. Dr. A.H.C. van Kampen and Dr. Ir. P.D. Moerland.
    Central in this course is the statistical program R and statistical research on cancer data and genomic data.


    Biomolecular Mass Spectrometry course 2008…

    Minor project: The influence of protein dynamics on structural alignments (supervised by Walter Pirovano, Anton Feensta and Jaap Heringa)

    Optional master course:

    Advanced Bioinformatics (12 ECTS)
    Academic Medical Center and University of Amsterdam
    by Prof. Dr. A.H.C. van Kampen and Dr. Ir. P.D. Moerland.
    Central in this course is the statistical program R and statistical research on cancer data and genomic data.


    Biomolecular Mass Spectrometry course 2008
    Utrecht University (Netherlands Proteomics Centre)
    by Prof. Dr. Albert Heck
    22-09-2008 - 26-09-2008

Licenses & Certifications

Volunteer Experience

  • Social Officer

    Clare Hall Boat Club

    - 2 years 4 months

    Organised social swaps and boat club dinners.

  • The Cambridge Union Society Graphic

    Clare Hall College representative

    The Cambridge Union Society

    - 1 year 9 months

    Discussing success previous week events on weekly meetings during full term.
    Promoting events at Clare Hall College.
    Persuading new students at the College to join the Cambridge Union Society.

  • EMBL-EBI Graphic

    Student representative

    EMBL-EBI

    - 1 year 2 months

    Civil Rights and Social Action

    Lobbied for improvements in social securities at European Council to get political backing.
    Negotiated improvements in social securities with EMBL senior management.
    Successful inclusion of fellows in social securities (similar to 12% salary increase).
    Meetings with head of graduate studies, discussing improvements to the PhD program.
    Organised two PhD interview weeks: hosting night out and introducing institue to candidates. Organised three day introduction course for new PhD…

    Lobbied for improvements in social securities at European Council to get political backing.
    Negotiated improvements in social securities with EMBL senior management.
    Successful inclusion of fellows in social securities (similar to 12% salary increase).
    Meetings with head of graduate studies, discussing improvements to the PhD program.
    Organised two PhD interview weeks: hosting night out and introducing institue to candidates. Organised three day introduction course for new PhD students.

Publications

  • Improving Process Yield Through Manufacturing Digital Twin Using Conditional Synthetic Data Engine (COSYNE)

    ECAI 2024

    The pharmaceutical industry must adhere to rigorous regulations to meet specific quality standards. Additionally, the intricate nature of pharmaceutical manufacturing processes and long time to production necessitates timely detection of batch failures. AI/ML models are used for predictive maintenance in an automated and data-driven manner to detect these failures and aid timely intervention. However, these models require substantial amount of data for model training. This can lead to extended…

    The pharmaceutical industry must adhere to rigorous regulations to meet specific quality standards. Additionally, the intricate nature of pharmaceutical manufacturing processes and long time to production necessitates timely detection of batch failures. AI/ML models are used for predictive maintenance in an automated and data-driven manner to detect these failures and aid timely intervention. However, these models require substantial amount of data for model training. This can lead to extended time-to-value before a predictive monitoring system can be deployed for any new process due to long process lead times. The current research proposes COSYNE, a generative AI-based approach to generate manufacturing digital twin, reducing the model development time by augmenting synthetic data with real data. The proposed solution is validated on a large pharmaceutical company’s batch manufacturing dataset, and the results are benchmarked across multiple dimensions of generation quality. Empirical results demonstrate that the proposed COSYNE outperforms the state-of-the-art approach by 2-3 times on average across all the generation quality metrics. Moreover, COSYNE enhances downstream AI/ML performance significantly through data augmentation and reduces time-to-value by creating high-fidelity digital twins with only 10% of real data and still achieve similar performance as current baseline trained on entire real data.

    See publication
  • Quantitative Genetics of CTCF Binding Reveal Local Sequence Effects and Different Modes of X-Chromosome Association

    PLOS Genetics

    Associating genetic variation with quantitative measures of gene regulation offers a way to bridge the gap between genotype and complex phenotypes. In order to identify quantitative trait loci (QTLs) that influence the binding of a transcription factor in humans, we measured binding of the multifunctional transcription and chromatin factor CTCF in 51 HapMap cell lines. We identified thousands of QTLs in which genotype differences were associated with differences in CTCF binding strength…

    Associating genetic variation with quantitative measures of gene regulation offers a way to bridge the gap between genotype and complex phenotypes. In order to identify quantitative trait loci (QTLs) that influence the binding of a transcription factor in humans, we measured binding of the multifunctional transcription and chromatin factor CTCF in 51 HapMap cell lines. We identified thousands of QTLs in which genotype differences were associated with differences in CTCF binding strength, hundreds of them confirmed by directly observable allele-specific binding bias. The majority of QTLs were either within 1 kb of the CTCF binding motif, or in linkage disequilibrium with a variant within 1 kb of the motif. On the X chromosome we observed three classes of binding sites: a minority class bound only to the active copy of the X chromosome, the majority class bound to both the active and inactive X, and a small set of female-specific CTCF sites associated with two non-coding RNA genes. In sum, our data reveal extensive genetic effects on CTCF binding, both direct and indirect, and identify a diversity of patterns of CTCF binding on the X chromosome.

    Other authors
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  • Understanding the epigenome using system genetics

    PhD thesis, Clare Hall College University of Cambridge

    Genetics has been successful in associating DNA sequence variants to both dichotomous and continuous traits in a variety of organisms, from plant and farm animal studies to human disease. With the advent of high-throughput genotyping, there has been an almost routine gen- eration of genome-wide association studies (GWAS) between human disease traits and genomic regions. Despite this success, a particular frustration is that the majority of associated loci are in non-coding regions of the genome…

    Genetics has been successful in associating DNA sequence variants to both dichotomous and continuous traits in a variety of organisms, from plant and farm animal studies to human disease. With the advent of high-throughput genotyping, there has been an almost routine gen- eration of genome-wide association studies (GWAS) between human disease traits and genomic regions. Despite this success, a particular frustration is that the majority of associated loci are in non-coding regions of the genome and thus interpretation is hard.
    To improve characterisation of non-coding regions, molecular as- says can be used as a phenotype, and subsequently be used to explain how genetics alter molecular mechanisms. In this thesis, the inter- play of three molecular assays that are involved in regulating gene expression is studied. On 60 individuals, several assays are performed: FAIRE-chip, CTCF- seq, RNA-seq and DNA-seq.
    In the first part, the discovery and characteristics of FAIRE-QTLs is presented. The identified FAIRE-QTLs show strong overlap with other molecular QTLs, histone modifications, and transcription factors.
    The second part consists of the integration of genome-wide molecu- lar assays in a human population to reconstruct the human epigenome. Each of the molecular assays is associated with each of the other assays to discover phenotype-to-phenotype correlations. Furthermore, QTL data are used to dissect the causality for these phenotype-to-phenotype correlations in a system genetic manner.
    The third part presents a comprehensive view of CTCF binding on the X chromosome, and its implications for X-chromosome inactivation. A novel X chromosome-wide CTCF effect is observed. Using the gender of each of the cell lines, observations are made about which CTCF sites are dosage-compensated, active on both chromosomes, or are only bound in females.

    See publication

Courses

  • Advanced Bioinformatica course - AMC, Amsterdam, NL

    2008

  • Basic Biology course - EMBL, Heidelberg, DE

    2009

  • Biomolecular Mass Spectrometry course - Netherlands Proteomics Centre, Utrecht, NL

    2008

  • Design and Analysis of Genetic-based Association Studies - Wellcome Trust Advanced Courses, Cambridge, UK

    2011

  • Sellings Skills - Cambridge University, Cambridge, UK

    2011

Honors & Awards

  • Data Insights COE Key IP contributor FY16

    Microsoft

  • EMBL International PhD Fellowship

    EMBL

    PhD fellowship with a total value of 􏰀115,000€.

Languages

  • English

    Native or bilingual proficiency

  • Dutch

    Native or bilingual proficiency

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