Y. (Yunlei) Li, Assistant Professor

Dr. Yunlei Li studied data mining & bioinformatics at Delft University of Technology (TUD) under the supervision of Prof. Marcel Reinders and Prof. Lodewijk Wessels. She conducted her internship at the Netherlands Cancer Institute (NKI) under the supervision of Prof. Laura van ‘t Veer on breast cancer research. In 2004, she obtained her MSc degree with honor (cum laude). She performed her doctoral research at TUD with Prof. Marcel Reinders and Prof. Dick de Ridder and obtained her PhD in 2010 on “Exploiting noisy and incomplete biological data for prediction and knowledge discovery”. Since 2011, Dr. Li has been working at the Erasmus Medical Center (EMC) on multiple basic cancer research as well as health care-oriented projects covering a wide range of diseases (incl. leukemia, aneurysm, pancreatic cancer, lung cancer, glioblastoma, melanoma) and bioinformatics applications.

Currently she is leading the machine learning / artificial intelligence research line in the Department of Pathology & Clinical Bioinformatics at EMC. Her research focus is designing and applying novel artificial intelligence methods (data mining, machine learning, deep learning) in translational and clinical research settings to integrate and exploit multi-dimensional patient data (e.g. DNA, RNA, protein, image, clinical) for clinical cancer research and clinical trials, in order to gain insight of the diseases, discover biomarkers, improve diagnosis accuracies and stratification for personalized treatments.

• Jie Ju, Leonoor V. Wismans, Dana A.M. Mustafa, Marcel J.T. Reinders, Casper H.J. van Eijck, Andrew P. Stubbs & Yunlei Li. Robust deep learning model for prognostic stratification of pancreatic ductal adenocarcinoma patients. iScience 2021.
• Ana Silva, Afonso R.M. Almeida, Ana Cachucho, João L. Neto, Sofie Demeyer, Mafalda de Matos, Thea Hogan, Yunlei Li, Jules Meijerink, Jan Cools, Ana Rita Grosso, Benedict Seddon, João T. Barata. Overexpression of wild type IL-7Rα promotes T-cell acute lymphoblastic leukemia/lymphoma. Blood 2021.
• Willem de Koning, Diba Latifi, Yunlei Li, Casper van Eijck, Andrew Stubbs, Dana Mustafa. Identification, validation, and utilization of immune cells in pancreatic ductal adenocarcinoma based on marker genes. Frontiers in Immunology 2021.
• Fleur van der Sijde, Eveline Vietsch, Dana A Mustafa, Yunlei Li, Casper van Eijck. Serum miR-338-3p and miR-199b-5p expression are associated with the absolute neutrophil count in the blood of resectable pancreatic cancer patients. Clinica Chimica Acta 2020.
• Sai Ping Lau, Nadine van Montfoort, Priscilla Kinderman, Melanie Lukkes, Larissa Klaase, Menno van Nimwegen, Mandy van Gulijk, Jasper Dumas, Dana Mustafa, Sanne Lievense, Christianne Groeneveldt, Ralph Stadhouders, Yunlei Li, Andrew Stubbs, Koen Marijt, Heleen Vroman, Sjoerd van der Burg, Joachim Aerts, Thorbald van Hall, Floris Dammeijer, and Casper van Eijck. Dendritic cell vaccination and CD40-agonist combination therapy licenses T cell-dependent antitumor immunity in a pancreatic carcinoma murine model. Journal for ImmunoTherapy of Cancer 2020.
• Fleur van der Sijde, Yunlei Li, Rick Schraauwen, Willem de Koning, Casper van Eijck, Dana Mustafa. RNA from stabilized whole blood enables more comprehensive immune gene expression profiling compared to RNA from peripheral blood mononuclear cells. PLoS One 2020.
• Astrid Heikema, Willem de Koning, Yunlei Li, Andrew Stubbs, John Hays. Lessons learnt from the introduction of nanopore sequencing? Clinical Microbiology And Infection 2020.
• Liu Liu, Rogier van Wijck, Yunlei Li, Sigrid Swagemakers, Jill de Wit, Hester Langeveld-Benders, Peter de Laat, Martin van Hagen, Suzanne Pasmans, Peter van der Spek. Mesenchymal stromal cells and vascular morphogenesis: gene expression profiles and promoting pathways. Journal of Stem Cell Research & Therapy 2020.
• Chantal van Houten, K. Oved, E. Eden, A. Cohen, D. Engelhard, Stefan Boers, Robert Kraaij, R. Karlsson, D. Fernandez, E. Gonzalez, Yunlei Li, Andrew Stubbs, E. Moore, John Hays, Louis Bont. Observational multi-centre, prospective study to characterize novel pathogen-and host-related factors in hospitalized patients with lower respiratory tract infections and/or sepsis - The "TAILORED-Treatment" Study. BMC Infectious Diseases 2018.
• Jordy van Der Zwet, Jules Meijerink, Jessica Buijs-Gladdines, Yunlei Li and Rob Pieters. Breaking IL7R signaling-induced glucocorticoid resistance by small molecule inhibitors in T-Cell Acute Lymphoblastic Leukemia. Blood 2017.
• Kirsten Canté-Barrett, Eric Vroegindeweij, Yunlei Li, Hans Clevers and Jules Meijerink. T-ALL oncogenes function in the context of pre- and post T-Cell commitment programs. Blood 2017.
• Kirsten Canté-Barrett, Rui Mendes, Yunlei Li, Eric Vroegindeweij, Karin Pike-Overzet, Tamara Wabeke, Anton Langerak, Rob Pieters, Frank Staal, Jules Meijerink. Loss of CD44dim expression from early progenitor cells marks T-cell lineage commitment in the human thymus. Frontiers in Immunology 2017.
• Kostandin V. Pajcini, Lanwei Xu, Lijian Shao, Jelena Petrovic, Karol Palasiewicz , Yumi Ohtani , Will Bailis, Curtis Lee, Gerald B Wertheim, Rajeswaran Mani, Natarajan Muthusamy, Yunlei Li, Jules P P Meijerink, Stephen C. Blacklow, Robert B. Faryabi, Sara Cherry, Warren S. Pear. MAFB enhances oncogenic Notch signaling in T cell acute lymphoblastic leukemia. Science Signaling 2017.
• Yunlei Li, Jessica Buijs-Gladdines, Kirsten Canté-Barrett, Andrew Stubbs, Eric Vroegindeweij, Wilco Smits, R. van Marion, W.N.M. Dinjens, M. Horstmann, R.P. Kuiper, R.C. Buijsman, G.J.R. Zaman, Peter van der Spek, Rob Pieters, Jules Meijerink. IL-7 receptor mutations and steroid resistance in pediatric T cell Acute Lymphoblastic Leukemia: A genome sequencing study. IL-7 receptor mutations and steroid resistance in pediatric T cell Acute Lymphoblastic Leukemia: A genome sequencing study. PLoS Medicine 2016.
• Gloria Milani, Kaat Durinck, Filip Matthijssens, Sofie Peirs, Tim Pieters, Lindy Reunes, Béatrice Lintermans, Niels Vandamme, Tim Lammens, Yunlei Li, Claire Schwab, Susana Raimondi, Barbara De Moerloose, Yves Benoit, Geert Berx, Christine Harrison, Giuseppe Basso, Helene Cave, Rosemary Sutton, Vahid Asnafi, Charles Mullighan, Jules Meijerink, Mignon Loh and Pieter Van Vlierberghe. Genetic characterization and therapeutic targeting of MYC translocated pediatric T-cell acute lymphoblastic leukemia. Cancer Research 2016.
• Sarah J. Stein, Ethan A. Mack, Kelly S. Rome, Kostandin V. Pajcini, Takuya Ohtani, Lanwei Xu, Yunlei Li, Jules P. P. Meijerink, Robert B. Faryabi, Warren S. Pear. Trib2 Suppresses Tumor Initiation in Notch-Driven T-ALL. PLoS One. 2016.
• Anna-Sophia Wiekmeijer, Karin Pike-Overzet, Martijn H. Brugman, Marja C.J.A. van Eggermond, Martijn Cordes, Edwin F.E. de Haas, Yunlei Li, Edwin Oole, Wilfred F.J. van IJcken, R Maarten Egeler, Jules P Meijerink, Frank J.T. Staal. Overexpression of LMO2 causes aberrant human T-cell development in vivo by three potentially distinct cellular mechanisms. Exp Hematol. 2016.
• H.K. Brand, I.M.L. Ahout , D. de Ridder, A. van Diepen, Yunlei Li, M. Zaalberg, A. Andeweg, N. Roeleveld, R. de Groot, A. Warris, P.W.M. Hermans, G. Ferwerda, F.J.T. Staal. Olfactomedin 4 Serves as a Marker for Disease Severity in Pediatric Respiratory Syncytial Virus (RSV) Infection. PLoS One 2015.
• Linda Zuurbier, Alejandro Gutierrez, Charles G. Mullighan, Kirsten Canté-Barrett, A Olivier Gevaert, Johan de Rooi, Yunlei Li, Willem K. Smits, Jessica G.C.A.M. Buijs-Gladdines, Edwin Sonneveld, A Thomas Look, Martin Horstmann, Rob Pieters, Jules P.P. Meijerink. Immature MEF2C-dysregulated T-cell leukemia patients have an early T-cell precursor acute lymphoblastic leukemia gene signature and typically have non-rearranged T-cell receptors, Haematologica 2014.
• Yunlei Li, Jessica Buijs-Gladdines, Andrew Stubbs, Peter van der Spek, Rob Pieters, Jules Meijerink. Integration of whole genome sequencing and targeted exome sequencing data with gene copy-number analysis for pediatric T-cell acute lymphoblastic leukemia. 9^th Childhood Leukemia Symposium, Prague 2014.
• Yunlei Li, Jan Bot, Marcel J.T. Reinders and Dick de Ridder. A pathway approach to align regulatory-metabolic networks. Oral presentation at the 8^th Annual International Conference on Computational Systems Bioinformatics, Stanford University, USA, 2009.
• Yunlei Li, Dick de Ridder, Marco J.L. de Groot, Marcel J.T. Reinders. Metabolic pathway alignment between species using a comprehensive and flexible similarity measure, BMC Systems Biology 2008. Featured article, highly accessed.
• Yunlei Li, Dick de Ridder, Marco J.L. de Groot, Marcel J.T. Reinders. Metabolic Pathway Alignment (M-Pal) reveals diversity and alternatives in conserved networks. Advances in Bioinformatics & Computational Biology, vol. 6, pp. 273-285, Imperial College Press, 2008. Oral presentation at the 6^th Asia-Pacific Bioinformatics Conference (Kyoto, Japan).
• Yunlei Li, Dick de Ridder, Robert P.W. Duin, Marcel J.T. Reinders. Integration of prior knowledge of measurement noise in kernel density classification. Pattern Recognition 2008.
• Yunlei Li, Lodewijk F.A. Wessels, Dick de Ridder, Marcel J.T. Reinders. Classification in the presence of class noise using a probabilistic Kernel Fisher method. Pattern Recognition 2007.
• Erik H. van Beers, Tibor van Welsem, Lodewyk F.A. Wessels, Yunlei Li, Rogier A. Oldenburg, Peter Devilee, Cees J. Cornelisse, Senno Verhoef, Frans B.L. Hogervorst, Laura J. van't Veer, Petra M. Nederlof. Comparative Genomic Hybridization profiles in human BRCA1 and BRCA2 breast tumors highlight differential sets of genomic aberrations.  Cancer Research 2005.

• EU FP7: TTT - Tailored Antimicrobial Treatment: Patient stratification to reduce antibiotic use
• EU EUROSTARS: iKnowIT - Integrated knowledge discovery IT: Clinical Decision Support platform for Pancreatic Cancer
• EU H2020 & MSCA ITN: GlioTrain: Exploiting GLIOblastoma intractability to address European research TRAINing needs in translational brain tumour research, cancer systems medicine and integrative multi-omics
• EU H2020: CINECA: Common Infrastructure for National Cohorts in Europe, Canada, and Africa
• ESPID: Local host response defines patient clusters that reveal the pneumonia-causing pathogen
• Kika: Detection of novel mutations and deregulated signaling pathways in T-cell acute lymphoblastic leukemia
• KWF: IMPROVE study: Integration of clinical data, Multi-omics and pathomics by artificial intelligence to imPROVe prognostic prediction of Early stage melanoma
• Hanarth: Artificial Intelligence-Driven Clinical Decision Support for Pancreatic Cancer
• Hanarth: Histogenomic biomarker identification to improve neuroendocrine lung tumor diagnostics on biopsies, using multiplex immunohistochemistry and artificial intelligence assisted histomorphological classification
• ZonMW ETH: PancCanNet: A knowledge resource for EU pancreatic cancer translational research projects
• NWO Corona: Immune monitoring in COVID-19 patients
• Support Casper: The role of immune system in pancreatic cancer
• Stichting Lever Onderzoek: LAPC-2: Feasibility and efficacy of the addition of IMM-101 to standard stereotactic radiotherapy in locally advanced pancreatic cancer patients
• Hartwig Foundation: Developing Personalised Treatment Strategies Driven by the Genomic Landscape of Metastatic Pancreatic Cancer