Advancing transcriptome analysis in models of disease and ageing
de Jong, Tristan Vincent
DOI:
10.33612/diss.99203371
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Publication date: 2019
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de Jong, T. V. (2019). Advancing transcriptome analysis in models of disease and ageing. Rijksuniversiteit Groningen. https://doi.org/10.33612/diss.99203371
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Acknowledgements
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At the end of this journey that has resulted in the thesis that lies here before you, I would like to thank everybody that helped me get to this point. It is important to remember I did not do this alone; I had the honor of working with some of the best and brightests of our generation. This is the end of the beginning, and so I would like to put credit where it is due.
First and foresmost, I would like to thank Victor Guryev, without who none of this would have been possible. You are a world class group leader, mentor and inspiration to those around you. Every time I entered your office lost in projects, I walked out full of new ideas and a sense of direction. Your friendship and comradery are of legendary proportions, whether is on a scientific retreat to Poland or just a casual Friday. Even now, the night before I send my thesis to the printing press, you are still up late, finding plots that need fixing and pages that need shuffling. Thank you.
Next I would like to thank my co-promotor Ellen Nollen. Your enthusiasm for collaboration has opened the path into RNA-sequencing analysis which now forms the cornerstone of my thesis. Thank you for introducing me to your wonderful group and floor.
Next, I would like to thank Yuri Moshkin; From no person have I learned more than from you. For every hour I spoke to you, my knowledge grew with my headache. I have never heard the words; “It’s simple”, so often with complex topics as with you, yet your explanation and understanding of mathematical concepts have allowed me to complete my papers, my thesis and eventually achieve my PhD. I am looking forward to our future research, our business venture and discussions. To many fruitful collaborations and many drinks.
I also want to thank Rob Williams, Pjotr Prins and Hao Chen. Thank you for believing in me and for making our international collaboration possible. My world would not be the same without this opportunity.
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As this chapter of the thesis goes from most important to the thesis to as many family and friends I can sneak in, I believe there are two people I should thank before any other PI, Co-author or colleague.
I believe there is no person on this list I owe more thanks to than Yanick
Hagemeijer. We have been friends from day 1 and we have brought every project
together to a successful conclusion ever since. We have travelled the world, worked on many projects and I owe my job to you. Finally, I would like to say that we are not a couple, have never been, no matter how many times people keep asking, we just make an amazing team.
Mark, without you I would not have made it this far. You have been the Bob to my Jay
and have picked me up every time I was down. Through the highest highs and the deepest lows, I have always been able to count on you and for that I am forever grateful. As long as life throws us balls, we’ll keep swinging for the fences. Thank you for everything, Pelican Keep Forever.
Next I would like to thank the PI’s who I had the pleasure of working with at ERIBA.
Eugene Berezikov, Cor Calkhoven, Floris Foijer, Marco Demaria and Peter Lansdorp. Your trust in me has resulted in many fruitful collaborations which have
allowed me to research far and wide in the spectrum of ageing research. Thanks to you I have been able to study protein aggregation, cellular senescence, aneuploidy, ageing related disease and have further opened the door to my theory of variation in gene expression with ageing with each field. Your efforts make this institute it is today; a place where good science comes together with good people to create the ideal working environment for a starting bioinformatician as myself.
Michael Chang, thank you for the solid writing advice on my thesis and being an
excellent PI within ERIBA.
Lenya Bystrykh, your harsh comments have kicked me into an understanding of my
own project that an un-critical view never would have given me, for that I am forever grateful.
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Olga Sin, thank you for everything, and thanks to the acquisition of the X-men by
Disney we might actually see whether a lightsaber can cut wolverine’s claws, though for the record; the answer is yes.
Christine Christine Müller and Amr Zaini, I have always enjoyed working with
both of you on projects within Cor’s group. You have always been polite, thankful and enthusiastic and your research has proven to be monumental to creating my own theories and grow my research.
Maaike de Vries and Alan Faiz, it was great being part of GRIAC and working with
you. Being part of this group has allowed me to broaden my knowledge on ageing related diseases and RNA-sequencing technologies.
Martijn and Nils, it was great working on cardiology projects with you and I am
looking forward to seeing our latest collaboration published :).
Bjorn Bakker, may the force be with you, always. It was great working, wampexing
and nerding out with you.
Aaron and David, thank you for being great bio-informatics support in the early
stages of my time at ERIBA (Also, Oh jah, 500…).
Alejandra, Unmasking Transcriptional Heterogeneity in Senescent Cells has turned
out to be a massive success in the community. It was nice working with you and wish you all the best in your marriage and career.
Henk Heidekamp, thank you for your faith in Victors decision to hire me and making
this all possible. It was great working with you and thank you for giving me the creative space to organize ERIBA activities that people today are still talking about.
Femke Reijnen, the PhD committee was only for PhD students, but once we changed
this rule and got you on board everything changed. Thank you for making the PhD committee great again. It was wonderful working with you.
Next I would like to extend my thanks to the absolute backbone of the institute; Sylvia
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myself with an infinite supply of missing pens, for always being there for a friendly talk and for helping me getting past every bureaucratic hurdle in my way.
During my time at ERIBA I had the pleasure of meeting a lot of interesting and fun people, many of them I thank personally. But before we get started, I would like to give you a special thanks, we had great lunches together filled with jokes and interesting discussions. We had waaay to much cake when it was time for another birthday, we partied hard until late at night at places like the pakhuis and had deep conversations at the end of defense parties. We went to movies together and I will never forget the awesome memories we have at the PhD committee events. I will always cherish the memories I have at ERIBA. You might have a personal thank you further down, but I think this was important.
Before I get to thanking friends, family and inspiring people whom I have so many fond memories with, I would like to thank one very special person;
Enikö, wise men say a lot of things, but I could not help falling in love with you.
Do I want to marry you? Yes, Yes I do.
Dear Frank and Stijn, it was awesome to have you guys as my colleagues. It was an honor to have you as my Viking brothers.
Sara Mouton, I am so happy to have you as my friend :) You’ve always been awesome,
you made ERIBA an epic workplace. You were my first friend in ERIBA and I am so glad to have you as my paranymph.
Katya Ovchinnikova, thank you for laughing at my jokes when I just got to ERIBA, I
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And ofcourse I have not forgotten about Simona Cantarella! Thank you for everything, thank you for the Prochutto, thank you for helping me clean the fridge, thank you for hosting us in Italy and say hi to your mom for me!
Jakub Wudarski, me Bruda, we have arrived at this part again. Thank you for helping
me save the world and get the girl. It was an amazing adventure and I will never forget all the wise lessons you’ve taught me over the years. Like… erm… never… plant beans on a field where onions have grown. Or… A duck with three wings and a loaf of bread is a brother to the turkey. Anyway; I gotta round up these monkeys for my circus. Please stay seated during the credits.
Klaske Schukken, thank you for driving the PhD committee with me to the amazing
success story it is today, thank you for joining my D&D campaign! Thank you for so many things, stay awesome!
Marindy, thank you for holding my hand at what was possibly the scariest moment
in my life. By that I mean; Thank you for teaching me ballroom dancing.
Kirill, добрый день товарищ, Спасибо за все. Я не говорю по-русски. Я люблю
водку. Медведь там. где шаслик? сколько стоит рыба? These are all important questions I am sure we can answer.
Satya Prakakash Pandey, the man, the legend, my guru. I am sure that some day I
will solve the mystery of why I hear wind chimes when you speak. Thank you for all the great memories. Until we meet again!
Gloria, watching you and Jakub argue is probably my favorite TV show and I will never
get bored with you around. Thank you for getting our team through Wampex and I will see you again next year 😉.
Anton, Irina, Margriet, Sonja, Daniele, Phillip, Magda, Lisa, Romeo, Clemance, Seka, Sonja, Joscha, Koen, Daniel, Sergio and many many many others, I have
indirectly thanked you before, but you guys are worth mentioning, the third floor was really a great place and you guys were a part of that.
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Next I would like to thank all the members of the PhD committee, those who came before me, those who helped me make it awesome, and those who kept up the good work. This includes Eike, Arthur, Danielle, Hidde, Alexander and many people whom I will forget to thank, but fear not, please read the generic thank you!
Jorge Garcia Martinez, I don’t know where you are, or if you will ever read this, but
I will never forget the legend of Jorge.
I also would like to thank my students, who have taught me a thing or two during their time here; Juliana Goh, Thamar J. Lobo, Sharlie van der Heide, David vd
Veerdonk, Anastasia Steshina, Sanjana Ravindran, and Rene Bults, You guys
were all unique and you will all go on to achieve great things! Thamar, it was also great seeing you become my collegue :).
We have now arrived at the point that I retrace my steps, thank some friends and family who have helped me along the way. It was a long journey and I would not be here today if it wasn’t for the love, friendship and support of these people.
A long time ago, in lokaal 17, it seems so far away now. I would like to thank the other Broformatics, a ragtag group of Bio-informaticians who have always stood by my side.
Rick, Arjen, Gonny, Herder, Lisanne, Cizar and Joop. I could not have done this
without you guys. You made my journey here a kick ass adventure and I owe you a million thanks. A special thanks to Gabriel and Laurens, I truly wish you could still be with us today.
This group of Bio-informaticians would not exists if it wasn’t for Martijn van der
Brugge, our Bio-informatics teacher. You are an amazing inspiration for us all. Your
enthusiasm has laid the foundation for my scientific career and I will always be thankful for that. I’m pretty sure nobody will ever forget your laugh.
Also, a special thanks to Ingrid Paffen, Tillman Todt and many other teachers along the way.
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A special thank you to Lars, the guy I went to Australia with, who is totally real… A long time ago, at the end of my bachelor’s degree, I did an internship at Plant Research International (PRI) at the Wageningen University. Here I met Gert Kema who was an amazing inspiration for me and who’s group set the tone for the rest of my career. Gert, you were a great mentor and I am forever grateful for the opportunity you gave me. I also want to extend a special thanks to your team at the time; Rafael
and Esperanza, Caucasella, Amir, Viviane, Mahmod, and Sarrah. Thank you all
for the fond memories!
Next I would like to thank the people of the Thursday group. You guys are amazing and have taught me so much about the wonderful world of special beers. Thank you
Heleen, Paul, Eric, Ittman, Petra, Rico, Martijn, Benoit and ofcourse Carel Oomes.
I would like to thank two very special people I met during my studies in Wageningen, You have both incited a passion for adventuring and storytelling in me that I will never let go; Bart Steen, we met on a non-descript Monday in some course and we were partnered up for some statistics project. Now we traverse the world together and for that I am forever thankful. Dunya Cleijne, after my studies in Nijmegen I thought my days of Dungeons and Dragons were over. They weren’t… Thanks to you we have built a rich world with exciting characters that I will use to tell cheap bedtime stories to my children. Thank you so much for that.
Dear Brendan, I am glad to inform you my latest endevour was successful. By October 28th I will be a PhD in Sciences. My wedding is on the horizon and I expect you to be
my best man simply because you are the best man I know. Thank you for your eternal support, Lots of love.
A big thanks to my family members; Nico, Margaret, Max and Nella. Thank you for supporting me in this adventure and I am sorry for barely visiting during my PhD.
I would like to give a quick shoutout to my family members in Australia, thanks for letting me stay and for supporting me in my journey! Daclun, thank you for
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introducing me to Minecraft, for keeping me company and for being fair dinkum aussie bloke!
Dear Timothy, Centaine and Charlaine, You guys know me better than anyone else. So please do not tell anybody there must have been a mistake. I’m going to be a doctor and I’m sure everything will be fine. It was awesome growing up with you guys. Now if you excuse me, I will do adult things, like staple papers together and pretending to read stuff.
Dear Mom and Dad, you have raised me, supported me, paid for my expenses, threatened me and gave me everything I needed to succeed. If somebody ever writes a book on how to raise children, they can take a page from yours. You did everything right. Thank you, and I love you.
Dear mr Pieter, I did everything you said I could, and this is just the start, thank you for believing in me.
