Lab of Cancer epi-proteomics and gene expression regulation
Dept. Exp. Oncology
European Institute of Oncology
Milano- Italy
W        https://www.ieo.it/it/RESEARCH/People/Researchers/Bonaldi-Tiziana/
            https://www.unimi.it/en/ugov/person/tiziana-bonaldi
            https://www.youtube.com/watch?v=zDroE0EtEPw
@        tiziana.bonaldi@ieo.it; Tiziana.bonaldi@unimi.it
 
TB is Tenured Group Leader at the European Institute of Oncology (IEO) in Milan, where she directs the “Cancer epi- proteomics and gene expression regulation” Group since 2008. Following a PhD in Molecular and Cellular Biology at the Dibit, San Raffaele Institute in Milan, she did a first post-doc at the LMU in Munich, in A. Imhof’s lab, where she started developing MS methods to study the histone code; then she carried out a second post-doc in the M. Mann’s group at the MPI of Biochemistry in Martinsried to strengthen her expertise in quantitative MS-based proteomics and its potential to study post-transcriptional regulation of gene expression. She received the “Armenise-Harvard Career Development Award” in 2007 that helped her to develop her career as independent investigator in Italy. In 2010, she won the “International Inner Wheel for Women, for scientific achievements”. She successfully completed her tenure-track in 2014 and was appointed as Associate Professor at IEO.
In 2021 she has also been appointed as Assistant Professor at the Department of Oncology and Haematology-Oncology of the University of Milan, where she coordinates the Proteomics and Metabolomics course for the Master Program in “Biomedical Omics” of the same University and she teaches Applied Biology at the Course Degree in “Health care professions”.
From a research point of view, at IEO TB coordinates a group comprising 10-12 students at various stages of their career path, from undergraduate students to senior post-docs. The group focuses on applying mass spectrometry (MS) –based proteomics to the investigation of the molecular mechanisms underpinning adaptive responses in cancer, with a specific interest towards the epigenetic regulation of gene expression. Her research is contributing both various technological innovations and several original findings in the MS-analysis of chromatin composition and modifications, on histones and beyond, in both pre-clinical models and, more recently, in primary cancer patient samples. As testified by her publication track, In the field of protein-methylation in cancer she is unravelling novel central roles of various epigenetic enzymes (e.g. LSD1, PRMT1) in the onset, progression and response to therapy for different cancer types and she has become a world-wide pioneer in the epi-proteomics analyses. 
She is involved in the gender balance program of her Institute, being founding member of the IEO GEP and IEO coordinator within the EU-Funded LIBRA project among members of the EU-LIFE consortium. She is active in various mentoring activities for young scientists, both locally and within the EU-LIFE. At IEO she is involved in different Institutional roles, such as Chair of the Scientific Council of the Dept. of Experimental Oncology, Member of the Educational Committee and of the Academic Council of the School of Molecular Medicine (SEMM) PhD Program. 
She took part as speaker to various Science Dissemination events at the local and regional level.  
She is partner of the EU-funded EPIC-XS consortium, to which she contributes both by developing novel analytical strategies for clinical epi-proteomics studies and by offering proteomics service for external user from EU.
She published more than 90 peer-review scientific papers (Google scholar h-index= 39, Citations: 10,584).
She’s married, with 2 children
 
Google scholar
https://scholar.google.it/citations?user=LjmxrbEAAAAJ&hl=en
PubMed
https://pubmed.ncbi.nlm.nih.gov/?term=bonaldi+t+&sort=date

I am a Professor of Medical Genetics and clinical geneticist with specific interest in neurodevelopmental disorders. I have extensive experience in next-generation and high-throughput molecular genetics, with special focus on the use of homozygosity mapping, linkage analysis and whole-exome sequencing in recessive forms of structural and functional abnormalities of the brain. I have successfully detected rare and somatic genetic variant identification in diverse range of diseases using high-throughput and next-generation genomics approaches at Yale. In the last ten years, I have published papers in Cell, Science, Nature, Nature Genetics and Neuron including one of the first successful applications of exome sequencing in the identification of genetic basis of recessive forms of structural and functional abnormalities of the brain. 

I have served as a member of editorial boards, a reviewer in top-tier journals and conferences, and was invited to serve as a program committee member for international workshops and conferences as well. I established Medical Genetics Department and giving lectures to under and post graduate students, assisting in seminar groups or laboratories, and grading. Teaching activities are drawn from a diverse menu of lecture, laboratory, and seminar courses given at the undergraduate, graduate, and medical school level.

Certificates, Courses and Trainings
Vocational Training, Publons Academy Peer Reviewer, Publons Academy, 2020
 
Research Areas
Medicine, Childrens Mental Health and Disorders, Neurology, Medical Genetics, Obstretrics and Gynecology
 
Academic Titles /Tasks
Professor, Dokuz Eylul Universty, Sağlık Bilimleri Enstitüsü, Moleküler Tıp Anabilim Dalı (Disiplinlerarası),2019 - Continues
Professor, Demiroğlu Bilim Üniversitesi, Tıp Fakültesi, Dahili Tıp Bilimleri Bölümü,2018 -2019
Associate Professor, İstanbul Bilim University, School of Medicine, Department Of Internal Medicine,2015 -2017
 
Academic and Administrative Exprerience
Enstitü Yönetim Kurulu Üyesi, Dokuz Eylül Üniversitesi, Sağlık Bilimleri Enstitüsü,2022 – Continues
Asistant Director of the Institute, Dokuz Eylül University, Sağlık Bilimleri Enstitüsü,2022 - Continues
Ethics Committee Member, Dokuz Eylül University, Tıp Fakültesi, Dahili Tıp Bilimleri Bölümü,2021 – Continues
Director of the Center, Dokuz Eylül University, Tıp Fakültesi,Dahili Tıp Bilimleri Bölümü,2021 – Continues
Merkez Laboratuvar Başkan Yardımcısı, Dokuz Eylül Üniversitesi,Tıp Fakültesi, Dahili Tıp Bilimleri Bölümü, 2020 – Continues
Anabilim Dalı Akademik Kurul Üyesi, Dokuz Eylül Üniversitesi, Tıp Fakültesi, Dahili Tıp Bilimleri Bölümü,2019 - Continues
İstanbul Bilim Üniversitesi, 2015 -2019
İstanbul Bilim Üniversitesi,2015 -2017
 

Dr. Miral Dizdaroglu graduated from the University of Ankara, Faculty of Science, Chemistry Department in 1967. He received his doctorate in Physical Chemistry from the University of Karlsruhe in Germany in 1971, and then worked at the Max-Planck-Institute in Mülheim a.d. Ruhr, Germany for 7 years. Subsequently, Dr. Dizdaroglu received a stipend from the US National Academy of Sciences and moved to the USA to work at the Natick Research Center near Boston for 2 years. He then worked at the University of Maryland as an adjunct professor until 1986 when he joined the National Institute of Standards and Technology (NIST) in Maryland. Dr. Dizdaroglu established a renowned laboratory at NIST in the field of DNA Damage and Repair. He received a number of scientific awards for his work: Hillebrand Prize of the Washington DC Section of the American Chemical Society, 1989; Science Award of the Scientific and Technological Research Council of the Republic of Turkey, 1993; Silver Medal Award of the United States Department of Commerce, 1993; Turkish-American of the Year for Excellence in Science Award of the Assembly of the Turkish-American Associations in the USA, 1993; Doctor Honoris Causa (Honorary Doctorate) from Nicolaus Copernicus University, Collegium Medicum, Bydgoszcz, Poland, 2000; Gold Medal Award of the United States Department of Commerce, 2005; Fellow of the National Institute of Standards and Technology (NIST Fellow), 2006; Member of the Turkish Academy of Sciences, 2008; Doctor Honoris Causa from Dokuz Eylul University, Izmir, Turkey, 2009; Samuel Wesley Stratton Award of the National Institute of Standards and Technology, 2010. Dr. Dizdaroglu is one of the 40 NIST Fellows among 1500 scientists at NIST. Dr. Dizdaroglu published 265 peer-reviewed papers and edited two books. According to Web of Science, his h-index is 78 with 22879 citations. Google Scholar records his h-index as 92 with 33283 citations.
 

Daniel Geiszler is a Marie Curie TÜBITAK COFUND Postdoctoral Fellow in the lab of Prof. Nurhan Özlü at Koç University. He completed his doctorate in the lab of Prof. Alexey Nesvizhskii at the University of Michigan where he developed computational tools for the identification and characterization of post-translational modifications in mass spectrometry-based proteomics. His work is implemented in the computational proteomics platform FragPipe, which he helps maintain and contributes to. He continues to develop computational proteomics methods and applies them in biological and chemoproteomic contexts.
Daniel Geiszler is a Marie Curie TÜBITAK COFUND Postdoctoral Fellow in the lab of Prof. Nurhan Özlü at Koç University. He completed his doctorate in the lab of Prof. Alexey Nesvizhskii at the University of Michigan where he developed computational tools for the identification and characterization of post-translational modifications in mass spectrometry-based proteomics. His work is implemented in the computational proteomics platform FragPipe, which he helps maintain and contributes to. He continues to develop computational proteomics methods and applies them in biological and chemoproteomic contexts.

Dr. Melis Kant is presently working as a post-doctoral research scientist at the National Institute of Standards and Technology (NIST) in DNA damage and repair group.
She completed her B.Sc. at Ege University in 2006, later obtained a M.Sc. degree in Molecular Biology and Genetics at Izmir Institute of Technology in 2009 and Ph.D. degree in Biochemistry at Dokuz Eylul University in 2016. After She finished her Ph.D., she worked as a lecturer in Department of Genetics and Bioengineering at Izmir University of Economics.
During her career as a scientist, she authored 17 peer-reviewed scientific papers and two book chapters. She has been serving as reviewer in many scientific papers for Bioscience reports, Portland Press since 2017.
Her achievements were recognized by NIST Measurement Science Excellence Award 2022 for the outstanding measurements of the inhibition of a major human DNA repair enzyme by potential anticancer drugs, the products in DNA irradiated by Ne-22 ion beams in relation to cancer therapy, and DNA lesions in cooked food associated with cancer.
Her research is focused on the development and application of robust and accurate standardized techniques for DNA damage and repair measurements in biological systems. It is exceedingly important to understand, at the fundamental level, the mechanisms of oxidative DNA damage and its processing by DNA repair enzymes as well as how unrepaired DNA lesions may lead to cytotoxicity, mutagenesis and eventually to diseases such as cancer and aging. More detailed knowledge of mechanisms of DNA damage and repair might allow us to modulate DNA repair. This could lead to drug developments and clinical applications including the improvement of cancer therapy by inhibiting DNA repair in drug- or radiation-resistant tumors and/or the increase in the resistance of normal cells to DNA damage by overexpressing DNA repair genes.
She is currently collaborating several distinguished scientists both in the US and around the world on many aspects of oxidative DNA damage and its repair as related to mechanistic understanding of human disease processes.

Assoc.Prof. Gizem CALIBASI-KOCAL, graduated from Ege University, Biochemistry. Then she received her PhD degree of Basic Oncology from Dokuz Eylul University, and Biochemistry from Istanbul Medipol University, Turkey. From 2013 to 2015, she worked in Harvard University and Stanford, USA in the field of microfluidic technologies related with cancer metastasis as pre-doctoral research fellow. She has been a post-doctoral researcher in Koch Cancer Institute at Massachusetts Institute of Technology, in the field of diet-effected intestinal homeostasis and tumorigenesis. Her research interest has mainly focused on metastatic processes of cancer in terms of tumor microenvironment and cancer metabolism, as well as pharmacogenetic applications in cancer management. Her achievements were recognized by several awards and honors from The Scientific and Technological Research Council of Turkey (TUBITAK), Turkish Association for Cancer Research and Control, Organization of European Cancer Institutes (OECI), European Federation of Clinical Chemistry and Laboratory Medicine (EFLM). She is co-author of 35 publications and over 30 contributions to conferences. She also serves on editorial board of several journals including Artificial Intelligence in Cancer, Journal of Clinical and Basic Health Sciences, Journal of Biology. Knowledge transfer to the clinics with the ‘bench-to-bed’ approach to gain a better understanding for cancer management, is the main aim of Calibasi-Kocal Research Group.
 

Prof. Michael L. Nielsen is a professor at the Proteomics Section at the Novo Nordisk Center for Protein Research (since 2014), where he is heading a research group focusing on Proteomics Technology Development & Application. Dr. Nielsen obtained his PhD in ion-physics in 2007, and he did postdoctoral work at the Max-Planck Institute for Biochemistry in Munich (2007-2009), before joining the Novo Nordisk Center for Protein Research as an associate professor (2009-2014).
 
Research statement
An emerging concept of modern biology relates to the systematic understanding of cellular networks co-regulated via post-translational modifications (PTMs). However, despite the cellular ‘modificome’ being highly complex only a small subset of the estimated 200 possible types of PTMs are currently amenable for analysis on a system-wide scale. The research focus of the Nielsen group is on developing novel proteomics methods and technologies for studying obscure PTMs on a systems-level approach, with the aim of elucidating the biological roles these emerging PTMs play in human cells, while uncovering the functional impact they exert in cellular phenotypes and diseases. Key achievement in this field is the development of MS-based strategies enabling systems-wide analysis of endogenous protein modifications, including SUMOylation, Arginine methylation, and ADP-ribosylation.

Dr. Nurhan Özlü received her BS degree in Molecular Biology and Genetics in 2001 from the Bilkent University. She did her PhD at Max Planck Institute for Cell Biology and Genetics, Dresden Germany in 2005. Following her PhD, Dr. Ozlu worked as a Post Doctoral Researcher at the Harvard Medical School, Systems Biology Department and in Childrens Hospital  BostonProteomics Laboratory. Dr. Ozlu’s research is focused on the regulation of cell division using mass spectrometry based proteomics and anti-mitotic drugs in the treatment of cancer.

Dr. Güneş Özhan earned her Bachelor’s degree in Molecular Biology and Genetics at Middle East Technical University in 2003 and her PhD degree in 2009 with her thesis work on the molecular evolution of embryonic development in arthropods, which was carried out at the Max Planck Institute for Developmental Biology in Tübingen, Germany. She completed her post-doctoral studies on developmental biology and cell signaling using the zebrafish model at the Biotechnology Center of Dresden University of Technology. Afterwards Dr. Özhan joined Izmir Biomedicine and Genome Center in 2014 and established her independent research laboratory as well as a zebrafish facility. Upon her return to Türkiye, she has been successively awarded Reintegration Fellowship of TUBITAK, EMBO Installation Grant, L'Oréal Turkey For Women In Science award, Academy of Science BAGEP award, Turkish Academy of Sciences GEBIP award, METU Parlar Research and Technology Incentive Award and United Nations IOM Aegean Start-Ups Technology Based Entrepreneurship Program Award. Her major research interests include the regulatory mechanisms of Wnt signaling, the biology of tissue regeneration, and zebrafish models to understand the mechanisms of neurodegenerative diseases and cancer. Currently she is a faculty member at Dokuz Eylul University and a principal investigator at Izmir Biomedicine and Genome Center.