Acknowledgements

It gives me great pleasure in expressing my gratitude to all those people

who have supported me and had their contributions in making this thesis
possible. First and foremost, I must acknowledge and thank The Almighty
Allah for blessing, protecting and guiding me throughout this period. I could
never have accomplished this without the faith I have in the Almighty.
I express my profound sense of reverence to my supervisor and promoter
Prof. Dr. Rainer Breitling, for his constant guidance, support, motivation
and untiring help during the course of my PhD. His in-depth knowledge on
a broad spectrum of different Bioinformatics and Systems biology topics has
been extremely benecial for me. He has given me enough freedom during
my research, and he has always been nice to me. I will always remember his
calm and relaxed nature, and the way he asks YES! How can I help you?,
whenever I enter his ofce. I am thankful to the Almighty for giving me a
mentor like him.
I express my deepest gratitude to my second promoter and the Head of
the Groningen Bioinformatics Center Prof. Dr. Ritsert C. Jansen for boosting
my morale throughout the course of research. He has always been caring, a
source of wisdom and motivation. He is a great leader.
I would like to thank Prof. Dr. Eriko Takano for helping me in Microbi-
ology, and being available to guide me in my all projects and publications.
Being a Mathematical modeler, I always nd her comments, questions and
suggestions in the manuscripts very challenging and I always felt very re-
laxed after answering her concerns.
I thank Elena and Marnix for being very good friends and brilliant col-
laborators. Their critical remarks and suggestions have always been very
126 Acknowledgements
helpful in improving my skills and for strengthening our manuscripts. Both
of them have agreed to become my paranymphs, and that certainly makes
me feel condent during my defence. A special thank to Marnix for translat-
ing the thesis summary in to Dutch.
One person who has always been ready to help me was our secretary
Klazien Offens. She took care of all non-scientic works, including ofcial
procedure of PhD promotie. Thank you Klazien for all your support!
It is my pleasure to acknowledge all my current and previous colleagues
in GBiC, specially Marnix, Elena, Yang, Bruno, Andris, Richard, Frank, Anna,
Lying, Nino, Rene, Joeri, Danny, Morris, Martijn, Jingyuan, Rudi, Francien
and Gonzalo for their enormous support and providing a good atmosphere
in the lab. I will always be grateful to them for helping me to develop the
scientic approach and attitude. I would like to thank my colleagues in the
University of Glasgow, Fiona and Andris for helping me in latex!
I also would like to acknowledge my current supervisors Dr. W. koop-
man and Dr. P. Willems, and my colleagues at the CSBB, UMC Nijmegen.
Its very important to have a nice social environment out side the lab.
The city, Groningen, itself has taught me several good lessons and also has
given me several good friends. In Groningen, very rarely I have felt that I
am staying away from my home. In this regard, I would like to thank senior
Indian PhDstudents of RuGincluding Ratna, Deepa, Ranjeet, Shireesha, Raj,
Sriram, Kodanda, Aneesh, Samta, Hans, Anil, Vinay, Fiaz and many others
whose name is not mentioned here for creating a wonderful social platform
in the name of GISA. Inspired by the enthusiasm of GISA members, I started
participating in GISA activities, and also served as a cultural secretary of
GISA for the year 2009.
During my stay in Groningen, weekends were usually the times I recharged
myself by interacting with the friends around. These interactions aided in
improving my debating and culinary skills. I would like to thank my friends
Fiaz, Sasanka, Jyothi, Yamini, Gopi, Harsh, Divya Raj, Divya Sasanka, Deepa,
Bhushan, and Laksmi for the same. Although our debates typically ended
in a inconclusive fashion and for which credit needs to be given to Fiaz for
asking questions recursively. As a matter of fact, Jyothi answered all of them
Acknowledgements 127
with same enthusiasm and full references. These interactions helped to im-
prove my skills as a good listener, taught me how to organize my thoughts,
and phrase my points.
I am grateful to my school and college teachers, Late. Maulvi Idrees,
Master Rajendra babu, Prof. S. I. Ahson and Prof. Ram Ramaswamy, who
laid seeds of enthusiasm and passion in my pursuit of knowledge.
I cant imagine my current position without the love and support from
my family. I thank my parents, Mr. Md. Zaheer Alam and Mrs. Sajdah Kha-
toon, for striving hard to provide a good education for me and my siblings.
I always fall short of words and felt impossible to describe their support in
words. If I have to mention one thing about them, among many, then I would
proudly mention that my parents are very simple and they taught me how
to lead a simple life. I would simply say, Amma, Abba you are great!.
My sisters Nazli aapa, Rubi aapa and Sazli, and brothers, Tanweer Alam,
Tauseef Alam and Tafseer Alam, are great friends of mine. I would like
to thank them for guiding me throughout. My sisters-in-law Ghazala and
Tahseen, and brothers-in-law Tara bhai, Firoz bhai and Ijtaba Azam were
also supportive. I acknowledge Zainab for her efforts in proof reading Urdu
translation of the summary of the thesis.
Thanks to Hassan bhai for taking care of our family in the village. My
cousins Affan Badar, Suan Badar and Akhtar Nehal have always encour-
aged me to perform better. From my childhood, my uncles Late. Dr. Zafar
Alam sb., Late. Badre Alam sb., Late. Shamshuzzuha sb., Mahboob akhtar
sb., and Prof. Umar Ahsan sb. were very encouraging. My parents, brothers,
sisters and uncles are always excited to hear my success and that inspires
me to perform better and be successful. I acknowledge my entire family for
providing us a very educated atmosphere in our village.
Last but not the least I would like to remember and thank my paternal
grandfather Late. Haz Abdur Razzaque sahab and maternal grandfather
Late. Maulvi Mohibbul Hasan sahab for their prayers. I strongly believe that
their prayers played very important role in my life. They are not here with
me anymore but their prayers are, and Insha-Allah Taala everything will be
good (Ameen).