You have various reasons for wanting to apply to graduate school. The programs to which you are applying want to know what those reasons are. So they ask you to write a statement, variously known as a Statement of Purpose, Statement of Intent, Statement of Reasons for Graduate Study, etc.
The statement also serves other purposes. It is an example of your ability to express yourself clearly in writing. It helps the program faculty to determine whether or not your goals and interests fit with theirs. And it can be expanded to include additional information which can affect your admissibility.
The statement is usually the only opportunity you as an applicant have to present yourself as a person distinct from your gradepoint average or test scores.
If there is additional information that you feel ought to be taken into consideration in the evaluation of your application, you can include it, either as part of the statement itself, or by attaching a supplementary statement. (Click here for some additional thoughts about discussing a "low" GPA in a reasons statement.)
The statement also serves other purposes. It is an example of your ability to express yourself clearly in writing. It helps the program faculty to determine whether or not your goals and interests fit with theirs. And it can be expanded to include additional information which can affect your admissibility.
The statement is usually the only opportunity you as an applicant have to present yourself as a person distinct from your gradepoint average or test scores.
What Information Should I Include?
The instructions which come with the application form should be your first guide as to what to include in your statement. The instructions should give you a good idea as to what information the program needs from you: your area of interest in the field (both what it is and why you are interested in studying it), your background preparation (education, training, work experience), and other relevant information. Often applicants are asked to list notable academic or work accomplishments that relate to the field of study.
You may also be asked to indicate possible thesis or dissertation topics or to indicate the names of faculty members with whom you would like to work. If you don't have a general idea of possible topics, you should at least mention about the area of concentration with in the field that you wish to pursue. If there is additional information that you feel ought to be taken into consideration in the evaluation of your application, you can include it, either as part of the statement itself, or by attaching a supplementary statement. (Click here for some additional thoughts about discussing a "low" GPA in a reasons statement.)
How Long Should My Statement Be?
Check the application instructions to see whether a minimum and/or maximum length is specified. If no guidelines are given, you need to balance two concerns:
- Providing your proposed program with the information sought, and
- Keeping your statement concise enough to be readable.
Is There a Preferred Format or Style?
All the rules of good writing apply to the writing of your statement. Unless you write final-draft quality prose on the first attempt, be prepared to revise your statement. It may be helpful to have other people read and critique a draft of your s tatement.
Format
Check the application instructions. In most cases, the specific format is left to the applicant. I use the term "statement" in these pages only because that's what we call it where I work. Unless you are instructed to the contrary, you can use a letter format if that helps you to write better. (It may help you to think of the statement as being similar in purpose to a cover letter that you would send with your resume to a prospective employer.) The best hint I can give is this: use the format that allows you to organize your thoughts to communicate to your best advantage.
The vast majority of statements which I see are at least typed, if not written with a word-processor. The wide availability of such technology means that it is easy to produce a statement that is free of typographical errors and easy to read. Even if you have very legible handwriting, it is probably better not to submit a hand-written statement. Style
The application instructions may or may not specify how the statement is to be written. As with any writing, it is important to consider your audience, but it is also important to write in your own voice. Affectation in word choice or syntax usually shows up very clearly.
Your chosen field of study will have a lot to do with what constitutes appropriate style. An applicant to a literature program will be expected to write in a different style than will an applicant to an engineering program. Another factor is whether or not you are required to submit work samples as part of your application. If you are not required to submit separate samples of academic w ork you have done, then it is more important that your statement be well written, as it will be your sole opportunity to demonstrate your writing proficiency. Statement of Purpose
Supratik Majumder
The quest for knowledge has always been a passion for me, a passion that just re- fuses to temper. So, its little surprise, that today, when I am faced with a plethora of choices for my career, I am determined to pursue research. A doctoral degree, I am sure, will empower me to give life to all those dreams that I have always nurtured: dreams of working onpath-breaking technology, dreams of not just walking the road, but leading it.
My sedulous hardwork during my school days ensured that I made it among the top
0.5% of more than 0.15 million students who took Indian Institute of Technology (IIT) joint entrance examination in India. During the four years of undergraduate study in the department of Electrical Engineering at IIT Kharagpur, a wide spectrum of courses in electrical circuits, microprocessors, computer architecture, etc, among others, haveprovided me with a firm theoretical foundation and introduced me to the vast and exciting field ofelectrical engineering. The field of Computer Systems has, however, enamored me the most.
My desire to expand myknowledge base led me to do a summer internship, after my junior year, at Cropmton Greaves Ltd., providing me with valuable experience. However myfirst exposure to real research wasduring mysenior year, when I took up the prob- lem of parameter estimation using a class of modulating functions known as the hartley modulating functions, as myB’Tech dissertation topic. The outcome of that effort was a publication in an international conference: Parameter Estimation of an Inverted Pendulum Model using Hartley Modulating Functions, Dr. Amit Patra1 & Supratik Majumder, International Conference on Energy Automation and Information Technology (EAIT) Dec 10-12, 2001, IIT Kharagpur.
Initially courses on microprocessors and computer architecture introduced me to the challenges in this area. Lured bythe prospect ofresearch in this exciting field, I joined mycurrent project, giving up an extremely lucrative job offer at IKOS India Pvt. Ltd. Presently I am employed in the Computer Science & Engg. Department at IIT Kharagpur as a graduate research consultant, working asapart ofafive member team, involved in the development of a flexible software development toolset for experi- menting with extensible processor architecture, like the CR16C processor2. We are now designing a processor description language that will allow us to automatically generate a cycle-accurate simulator, assembler, dis-assembler, patches for gcc and gdb, and test suites for any processor given its description in our language, as input.
1 Guide for mysenior year project
2 National Semiconductor USA, sponsor of the project; http://www.national.com/appinfo/compactrisc
1
Another project, which Iamcurrently doing, involves building an elementary form of internet radio, enabling voice-voice communication between two nodes and having features such as message store-and-forward, real-time connections, etc. I am looking into the hardware and kernel aspects ofsetting upsuch a network and the requirements thereof. These projects have actuated me to explore uncharted frontiers beyond the kenof regular work in Microprocessor architecture, Compilers and Embedded Systems and further strengthened myresolve to pursue research in these fields.3
I harbor a keen desire to undergo further learning at Rice University and study towards a Ph.D degree in the Computer Systems area. I feel that an advanced study will enable me to conduct research of redoubtable quality and make wholesome contribution to mychosen field. The genre of ongoing research carried out byrenowned faculties in the Computer Systems Laboratory interests mealot and Iwould consider myself extremely fortunate, given the chance to beinducted into one of the associated research groups, especially the Rice Computer Architecure Group. I am sure that the graduate program at Rice University would serve as an ideal stepping stone for a long and fruitful career in research. Last but not the least, at Rice University, I know mypeers and guides will bepeople, who share my curiosity and passion for knowledge, and that, more than anything else makes for successful research.
I have laid in front ofyou mydreams and future aspirations. I hope that youwill take a favourable decision regarding myadmission. I keenly lookforward to joining the university.
Supratik Ma jumder
December 22, 2001
STATEMENT OF PURPOSE
To accomplish great things we must first dream, then visualize, then plan... believe... act!
-Alfred A. Montapert
To dream is to move into the realms of the unknown, to step into where no one has gone before … research with it’s boundless reach promises all this and more.
Career Objective…
I believe that a career in research will offer the unique opportunity of working at the cutting edge of technology, with unparalleled intellectual challenges and creative satisfaction. To my mind an undergraduate education helps to comprehend the fundamental principles of science such that one is able to successfully apply these principles to real life situations. Graduate studies with a focus on my field of interest will without doubt fortify my academic foundation and increase the depth of my knowledge. This would constitute an ideal preparation for attaining my goal of a career in applied research.
In my view, Mathematics and Computing, the course that I am currently pursuing, is an eclectic blend of the core disciplines of both Mathematics and Computer Science. Thus it would be fair to say that, at this juncture of my undergraduate career, I am equipped with sufficient technical know-how to help me weather the challenges put forth during the course of my research endeavors. The 4 years of UG studies at the Indian Institute Of Technology ( IIT ) Kharagpur, have introduced me to a wide gamut of courses in Mathematics and Computer Science and has nurtured my inspiration to learn and create. The intellectual atmosphere and the spirit of scientific inquiry have been immensely invigorating as learning experiences, and have whetted my appetite to pursue original research. With this in mind, I intend pursuing a doctoral degree in my chosen field, Computer Networks.
It is my conviction that a correct decision can be made only after a first hand experience. This has driven me to explore quite a number of fields that I found exciting by taking up interesting research projects. I have dabbled with projects in the fields of optimization, statistics, networks and to a lesser extent in operating systems. I have followed these up after interesting undergraduate courses, discussions with researchers and extensive reading. Each of these projects has been instrumental in shaping my academic interests as they gradually converged to the field of Computer Networks. They have exposed me to a research oriented approach and have honed my analytical, computational and programming skills. I have had my share of successes and failures in these projects, and my experiences have made me realize the sort of temperament needed by researchers.
Research Experience and Background in Computer Networks…
My aptitude for learning and research is innate. This prompted me to take the initiative in the summer after my sophomore year (summer of 1999), and work under the guidance of Prof.R.N Banerjee of the Industrial Engineering Department at IIT Kharagpur. We addressed the problem of Genetic Algorithms: Applications in Machineshop Scheduling. The experience of first-hand research, though daunting at first, was extremely exciting and even at such an early stage of my undergraduate study; my interests zeroed in on research activity.
The defining period, which cemented my research interests in the field of Computer Networks, was when I undertook my training at Hughes Software Systems, this summer. I worked on Stream Control Transmission Protocol, a nascent protocol, designed to obviate the restrictions imposed by TCP on the transmission of PSTN signals. It exposed me, for the first time, to practical networking issues, infusing in me an understanding of the functioning of the various network layers, and also the concept of packet routing. I had to incorporate support for SCTP in the Linux kernel and this gave an insight to the network structure in Linux.
My final year dissertation, Routing and Wavelength Assignment in Optical Networks, under Prof. R. Badrinathof the Computer Science and Engineering Department, addresses the problem of embedding a virtual topology using the minimum number of wavelengths. We also propose to incorporate the additional constraint of fault tolerance.
All these exciting projects have given me a first-hand opportunity to participate in active, independent research and have brought to the fore, my latent abilities as a promising researcher.
Why Virginia Tech?
A journey of a thousand miles must begin with a single step.
-Confucius
Pursuing graduate studies is an obvious first step towards achieving my goal of a career in research. The Department Of Computer Science, with its renowned researchers offers excellent research opportunities in my area of interest with arguably some of the best faculty and facilities in the world. I have been amazed by the quality of work accomplished by the faculty. Working with such stalwarts in the field of Networks will be an honor and privilege and would no doubt be an invaluable experience towards realizing my career goals.
I am aware of the high standards of academic excellence and research that Virginia Tech sets, and I am very confident of being able to live up to these standards. I envision myself making a significant contribution towards furthering the frontiers of existing knowledge and carving a niche for myself in the scientific community through an undying passion for research and unyielding commitment to the subject area. I hope that you will take a favorable decision regarding my application, and I look forward to joining your institute for a fruitful and exciting academic life.
My heart-thoughts urge me
to try the deep sea,
the play of the salt waves:
my mind moans out that I
journey my soul far from here,
to conquer the unexplored.
- Rabindranath Tagore(Nobel Laureate and poet)
R. Krishna Kumar
| Sagnik Mazumdar Ph.D Applicant, Fall 2005 Email: sagnik@mech.iitkgp.ernet.in |
STATEMENT OF PURPOSE
After a bachelor’s degree in Mechanical Engineering from the prestigious Indian Institute of Technology, Kharagpur, I joined Jindal Strips Limited, India’s largest producer and exporter of stainless steel as Project Engineer. It was during this tenure that I noticed how by incorporating simple changes in design for better utilization of thermal energy could lead to major cost benefits. The projects that I executed there not only enhanced my level of understanding of the area of thermal and fluid sciences but also increased my inquisitiveness about this field. I decided to pursue a career in research and development in the above area. My desire to excel in the above field suffered a setback due to my father’s sudden illness. I resigned from my position at Jindal to take charge of his civil engineering consultancy firm as well as household responsibilities. This period also transformed me into a much stronger, patient and responsible individual.
Subsequently, I rejoined IIT Kharagpur, to pursue my masters’ degree in the area of thermal and fluid sciences. I would like to thank Dr. S. Bhattacharyya and M. Ram Gopal for having faith in my abilities and letting me conduct my thesis research under their able supervision, even though my undergraduate grades in this area can never justify their acceptance. I justified their confidence by getting the highest grades in each and every course. Moreover, we have been able to communicate eleven research publications (6 accepted; 4 under review; 1 invited) over the course of my masters’ degree. Five more journal manuscripts are in preparation. As the first author on all of these research papers, I hope ample evidence is supplied to the fact that my low verbal score in GRE is more a stroke of ill fate rather than a question of aptitude. I have acquired the capability of doing intensive computational analysis as part of my graduate course and research work. I have become well versed with finite volume, finite difference and finite element methods. As a part of my MS thesis work I have solved a complicated mathematical system model to study the dynamic behavior of heat and mass (hydrogen) transfer of coupled reactor beds by taking into account the effect the transient nature the compressor, the conditioned space, and influence of the external fins on the reactor tubes which are used to enhance external heat transfer.
My term in the industry has also helped me develop an uncanny knack for experimentation as well. As mentioned in my curriculum vitae, I was an active member in major revamping projects such as designing and fitting of recuperators in reheating furnace, design modification and installation of hot coiler furnace, and the upgrade of roughing mill motor. Though all of these projects involved huge initial expenditure, the benefits gained by minimizing the heat and oil loss, and in improving product quality more than justified such outlay. The design and implementation period tested my team spirit and human management skills to the extreme. Due to the major cost benefits achieved, I was made the leader of the Total Productive Maintenance (TPM) team. I was also put in charge of production in Steckel Mill so that unnecessary expenditure incurred during production or breakdown could be reduced by systematic and proper understanding of the operating parameters. I used my experimental expertise during my masters’ work at IIT, Kharagpur. I developed an inexpensive thermal conductivity measurement device for non-metals using the inverse heat conduction technique. A device to measure permeability of porous compacts and powdered beds has also been developed. The permeability is obtained by fitting the experimental results with a closed form analytical solution of the momentum and mass balance equations of the porous bed. A number of in-house experimental setups have been made to study properties of metal hydrides, such as heat and entropy of formation, slope factor, hysteresis, and reaction kinetics. The results obtained from these setups will be published in technical literature in due course. My current work is focused on developing a laboratory scale compressor driven metal hydride cooling system.
With the above analytical, computational, and experimental background, I am eager to join the Heat Transfer; Fluid Mechanics; Heating, Ventilation, Air-conditioning & Refrigeration or Material Processing Group at your esteemed department. The work done by your faculty is reflective of the frontier topics of research interest in the world in this area. Macro-scalar phenomenon in heat and mass transfer and fluid mechanics is still widely researched. Also, fundamental research efforts in the above area are concentrating in the direction of micro-scale fluid mechanics, micro and nano-scale heat transport, combustion, biological transport and computational methods. The focus of applied research has converged on fuel cells, energy systems, micro-electromechanical systems (MEMS), micro fluidic devices, biomedical devices, optical diagnostics and manufacturing processes. I would love to explore any uncultured domain in the above fields for my doctorate.
“A successful person is a dreamer whom someone believed in” remarked Goethe. I do harbor dreams of becoming a successful researcher, and I will be hopeful that the Department of Mechanical Engineering at Purdue University recognize my achievements, and have faith in my abilities.
Ever optimistic,
(Sagnik Mazumdar)
I am Aroop Sircar studying in the Indian Institute of Technology Kharagpur in the Department of Biotechnology. IIT Kharagpur is the first of the seven IITs. It has been ranked first amongst all engineering institutes in India for three consecutive years (survey conducted by India Today). I shall be graduating in May 2004 with a Dual Degree (5-year combined Bachelors of Technology (Honors) & Masters of Technology) in Biotechnology & Biochemical Engineering. I have decided to pursue a research career in Computational Biology. I am applying to the Joint Ph.D. program in the area of Bioinformatics & Computational Biology of the Bioengineering department.
As a person, I love hanging out with friends & family. With a passion for public speaking, I have stood third in Open IIT English debate & as a team we have won the Foundation Day debate of IIT Kharagpur. Having a flair to getting things done through proper co-ordination & motivation, I have taken part in the Autonomous section of the Robotix competition as a non-technical member. Our team had come third. I love traveling & have traveled extensively in India. I have spent a quarter of a year in Cambridge. I loved the openness & the way of life of the west. I would love to have the opportunity for more. I believe that to develop a true scientific temper, one has to overcome cultural biases & have an international exposure. Pursuing graduate studies in the US would be the ideal way to develop the perspective I need!
Fields of interest
I am interested in the field of Computational Biology, particularly in addressing various aspects of protein folding, sequence analysis & phylogeny. I am interested in drawing useful & meaningful statistics by parsing the vast amount of biological data already available. I am also interested in the development of software to address biological problems from a computational perspective. The trend today is to first apply bioinformatics tools to a problem & then corroborate the findings with experimental biology. I love carrying out wet lab biological experiments as well. I believe the fusion of computational biology with wet lab biology is the key to success of future biological research. Practical applicability of my findings is a great motivating factor for me. To that end, I believe that wet lab experiments are essential for the success of Bioinformatics. Bioinformatics helps to provide a very good initial guess, as to where to start from, when faced with a new problem. It also reduces the time taken to come up with a solution by providing a glimpse of what might actually be happening. This has already brought about tremendous changes in experimental design. My passion for computers & biology coupled with the desire to become a part of this revolution has led me to opt for a research career in this field.
Academic Background
The courses in Biochemistry, Genetics, Molecular Genetics, Cell & Molecular Biology and Protein Engineering have provided me a strong background in the fundamentals of biology. This coupled with courses like Introduction to Computing (C programming), Biostatistics, Biophysics & Modern Analytical Methods and Bioinformatics ensures a strong background for research work in my field. I have also taken the following courses: “Introductory Bioinformatics Course” & “Sequencing Project Management Using the Staden Package”, conducted by UK Human Genome Mapping Project Resource Center at the Dept of Genetics, Univ of Cambridge, UK. I would like to mention that I currently top my department. The damage to my eight semester GPA, can be attributed to my proficiency in Python, Perl, Regular Expressions & MySQL. Actually prior to visiting Cambridge, I had to master them, so I spent a significant amount of time during the eight semester experimenting with them!
Long Term Professional Goals
My personal experience has shown me that a career in research will keep me happy & excited. The essence of my research is, & will be, coming up with something novel, bearing in mind the relevance to the present-day world & the common man. I have found that developing nations like India, desperately need economically viable scientific knowledge that has practical applicability. In India, more often than not, cutting edge science is locked up in an ivory tower, far removed from the needs of the masses. In the long run I see myself as an active researcher, deploying my newly acquired scientific knowledge to address problems of practical importance. I feel that a Ph.D. degree is the first step to a successful scientific career & my endeavor to help the common man reap the benefits of modern science!
Research problems I have worked on
My first exposure to research was in the summer of my sophomore year (2001) when I was selected for the Visiting Summer Research Program fellowship at the Tata Institute of Fundamental Research (TIFR), Mumbai, India. I worked with Dr. K. S. Krishnan for two months on the project titled “An attempt to find genes responsible for synaptic transmission using Drosophila melanogaster as a model system”. The work involved extensive fly pushing & screening flies for phototactic & paralytic defects. I also worked on another project titled “Effect of Conus toxins on Drosophila melanogaster”. The work, though elementary, helped me realize the joys of challenging research & the excitement of coming up with something new!
My interest in computational biology arose mainly as a result of a training I underwent in National Centre for Biological Sciences (NCBS), Bangalore, India in the summer of 2002. I worked as a collaborator student with Dr. Satyajit Mayor & Dr. R. Sowdhamini on a project titled “Delving Deep into Deep Orange & Carnation from a Computational Viewpoint”. The work involved modeling (MODELLER) of the two Drosophila eye proteins Deep Orange & Carnation & finally docking them to find out the interacting residues (GRAMM).This experience proved to be a great learning experience & I felt I was finding a niche for my talents.
I then chose as my Bachelors dissertation topic: “Knowledge based cloning of regulatory sequence of Entamoeba histolytica genes” under Dr. S. K. Ghosh at IIT Kharagpur. I deployed my newly acquired techniques to establish a signature for the regulatory sequences of genes responsible for encystation & excystation. In our initial analysis, we chose some genes from the signal transduction cycle & tried to pick up homologues from Entamoeba histolytica using multiple alignment & phylogenetic tree analysis (PHYLIP). While working, we became interested in chitinases, which play an important role during encystation & excystation. We modeled these chitinases using homology modeling. A Chitin Box, i.e. conserved residues that have been observed to interact with chitin, was established.
In the summer of 2003, I worked as a visiting research student at the Dept of Biochemistry, Univ of Cambridge, UK with Dr. Kenji Mizuguchi, (Wellcome Trust Research Career Development Fellow) for ten weeks, in a project titled, “Structural assignment for the Drosophila genome & mapping of known mutations”. The work comprised of bioinformatics involving high throughput modeling & automatic analysis of results to generate useful statistics. We tried to optimize methods for automatic model evaluation. The programming was mainly carried out in Perl & Python, with MySQL being used to store the data. While working in this project, I also learnt to appreciate the power of Regular Expressions!
Currently, I am carrying out my final year dissertation with Dr. S. K. Ghosh at IIT. The project is titled “Structure determination& profiling of chitin binding proteins in Entamoeba histolytica& E. invadens”. In this project, we are looking more closely at chitin binding proteins. We are trying to establish new methods of visualization for chitin binding protein primary sequences. We are also trying to develop software for automatic identification of chitin binding proteins based on conserved residues across species, structural investigation& reports from existing literature.
Research Proposal
There are various problems which I have often thought of. However, being specifically asked for a research proposal, it has to be kept in mind that it is limited by my current knowledge& research experience. I would also like to add that I am open to different problems in related topics in biology keeping in mind my background& interest.
Given an opportunity, I intend to look into key residues of proteins & try to find out how the activity of the protein is affected by mutating them. These studies will go a long way in automatic identification of key residues in protein-protein or protein-ligand, interaction, a key issue in drug targeting. I would like to carry out this structural analysis from a bioinformatics perspective & initially use the Drosophila genome as a model system. After standardizing the procedure, I would be looking at other genomes as well, to identity interesting evolutionary relationships & also to increase the statistical significance of my results. Modelling of entire proteins is computationally very expensive & often incorrect. Thus each of the sequences will have to be broken down into domains, which are more conserved. These domains can be submitted to sequence searching & alignment tools similar to BLAST, but that include structural information as well (like Fugue). Based on templates so obtained, the domain sequences would be submitted for comparative modelling using Modeller. The models will have to be evaluated to eliminate the bad ones & refine the good ones. This set of structures (domains from wild type proteins) can be considered to be a control set. The same procedure can be carried out for the same set of genes, but this time the corresponding residues mutated based on already known mutations. Comparing these structures with those from the control set, the effect of mutations can be observed. Combining this result with output from other software, the structural regions (cavities, pockets, depressions) where these mutations exist can be found out. Conservation of these mutations across homologous sequences will have to be investigated as well. Thus useful statistics obtained for automatic identification of key residues. Simultaneously interesting evolutionary information can be drawn from phylogenetic & statistical analysis of the structure based search method.
Why Bioengineering at Berkeley?
Discussion with close friends who are PhD candidates in the US as well as my project guide at IIT, Dr. Sudip K. Ghosh , who has completed his postdoctoral research at the School of Public Health, Harvard University & Dr. Kenji Mizuguchi has given me an insight into how much more effective PhD studies in the US could be for my style of working than continuing in India. Both the computing equipment support & the level of educational care at the PhD level in the US in the fields in which I am interested are much superior to those available in India. Berkeley is one of the most reputed universities with renowned faculty in this field. Today Berkeley is a brand name & the name speaks for itself! I am especially interested in working with professors like Dr. Steven E. Brenner, Dr. Kimmen Sjolander, Dr. Lior Patcher, Dr. Teresa L. Head-Gordon & Dr. Richard Karp. I believe the approaches & problems addressed by their laboratories match very well with my research interests. I am sure that I will simply love working in their labs. Working with such renowned professors will be a privilege & will give me the opportunity to contribute something original to the field. Bioengineering at Berkeley has an interdisciplinary nature, which is evident from the joint appointments of faculty from various departments. I believe such an interdisciplinary nature is the key to its success & makes it one of the most coveted departments to be in!
STATEMENT OF PURPOSE & SIGNATURE
I am Aroop Sircar studying in the Indian Institute of Technology Kharagpur in the Department of Biotechnology. IIT Kharagpur is the first of the seven IITs. It has been ranked first amongst all engineering institutes in India for three consecutive years (survey conducted by India Today magazine). I shall be graduating in May 2004 with a Dual Degree (5-year combined Bachelors of Technology (Honors) and Masters of Technology) in Biotechnology and Biochemical Engineering. I have decided to pursue a research career in Computational Biology. I am applying to the Ph.D. program in the Computational Biology and Genomics group at the Department of Chemical and Biomolecular Engineering.
As a person, I love hanging out with friends and family. With a passion for public speaking, I have stood third in Open IIT English debate and as a team we have won the Foundation Day debate of IIT Kharagpur. Having a flair to getting things done through proper co-ordination and motivation, I have taken part in the Autonomous section of the Robotix competition as a non-technical member. Our team had come third. I love traveling and have traveled extensively in India. I have spent a quarter of a year in Cambridge. I loved the openness and the way of life of the west. I would love to have the opportunity for more. I believe that to develop a true scientific temper, one has to overcome cultural biases and have an international exposure. Pursuing graduate studies in the US would be the ideal way to develop the perspective I need!
Fields of interest
I am interested in the field of Computational Biology, particularly in addressing various aspects of protein folding, sequence analysis and phylogeny. I am interested in drawing useful and meaningful statistics by parsing the vast amount of biological data already available. I am also interested in the development of software to address biological problems from a computational perspective. The trend today is to first apply bioinformatics tools to a problem and then corroborate the findings with experimental biology. I love carrying out wet lab biological experiments as well. I believe the fusion of computational biology with wet lab biology is the key to success of future biological research. Practical applicability of my findings is a great motivating factor for me. To that end, I believe that wet lab experiments are essential for the success of Bioinformatics. Bioinformatics helps to provide a very good initial guess, as to where to start from, when faced with a new problem. It also reduces the time taken to come up with a solution by providing a glimpse of what might actually be happening. This has already brought about tremendous changes in experimental design. My passion for computers and biology coupled with the desire to become a part of this revolution has led me to opt for a research career in this field.
Academic Background
The courses in Biochemistry, Genetics, Molecular Genetics, Cell & Molecular Biology and Protein Engineering have provided me a strong background in the fundamentals of biology. This coupled with courses like Introduction to Computing (C programming), Biostatistics, Biophysics & Modern Analytical Methods and Bioinformatics ensures a strong background for research work in my field. I have also taken the following courses: “Introductory Bioinformatics Course” and “Sequencing Project Management Using the Staden Package”. Both of these courses were conducted by United Kingdom Human Genome Mapping Project Resource Center at the Department of Genetics, University of Cambridge, United Kingdom. I would like to mention that I currently top my department. The damage to my eight semester GPA, can be attributed to my proficiency in Python, Perl, Regular Expressions and MySQL. Actually prior to visiting Cambridge, I had to master them, so I spent a significant amount of time during the eight semester experimenting with them!
Long Term Professional Goals
My personal experience has shown me that a career in research will keep me happy and excited. The essence of my research is, and will be, coming up with something novel, bearing in mind the relevance to the present-day world and the common man. I have found that developing nations like India, desperately need economically viable scientific knowledge that has practical applicability. In India, more often than not, cutting edge science is locked up in an ivory tower, far removed from the needs of the masses. In the long run I see myself as an active researcher, deploying my newly acquired scientific knowledge to address problems of practical importance. I feel that a Ph.D. degree is the first step to a successful scientific career and my endeavor to help the common man reap the benefits of modern science!
Research problems I have worked on
My first exposure to research was in the summer of my sophomore year (2001) when I was selected for the Visiting Summer Research Program fellowship at the Tata Institute of Fundamental Research (TIFR), Mumbai, India. There I worked with Dr. K. S. Krishnan for two months on the project titled “An attempt to find genes responsible for synaptic transmission using Drosophila melanogaster as a model system”. The work involved extensive fly pushing and screening flies for phototactic and paralytic defects. I also worked on another project titled “Effect of Conus toxins on Drosophila melanogaster”. The work, though elementary, helped me realize the joys of challenging research and the excitement of coming up with something new!
My interest in computational biology arose mainly as a result of a training I underwent in National Centre for Biological Sciences (NCBS), Bangalore, India in the summer of 2002. I worked as a collaborator student with Dr. Satyajit Mayor and Dr. R. Sowdhamini on a project titled “Delving Deep into Deep Orange and Carnation from a Computational Viewpoint”. The work involved modeling (using MODELLER) of the two Drosophila eye proteins Deep Orange and Carnation and finally docking them to find out the interacting residues (using GRAMM).This experience proved to be a great learning experience and I felt I was finding a niche for my talents.
I then chose as my Bachelors dissertation topic: “Knowledge based cloning of regulatory sequence of Entamoeba histolytica genes” under Dr. S. K. Ghosh at the Indian Institute of Technology Kharagpur. I deployed my newly acquired techniques to establish a signature for the regulatory sequences of genes responsible for encystation and excystation. In our initial analysis, we chose some genes from the signal transduction cycle and tried to pick up homologues from Entamoeba histolytica using multiple alignment and phylogenetic tree analysis (using PHYLIP). While working, we became interested in chitinases, which play an important role during encystation and excystation. We modeled these chitinases using homology modeling. A Chitin Box, i.e. conserved residues that have been observed to interact with chitin, was established.
In the summer of 2003, I worked as a visiting research student at the Department of Biochemistry, University of Cambridge, United Kingdom with Dr. Kenji Mizuguchi, (Wellcome Trust Research Career Development Fellow) for ten weeks, in a project titled, “Structural assignment for the Drosophila genome and mapping of known mutations”. The work comprised of bioinformatics involving high throughput modeling and automatic analysis of results to generate useful statistics. We tried to optimize methods for automatic model evaluation. The programming was mainly carried out in Perl and Python, with MySQL being used to store the data. While working in this project, I also learnt to appreciate the power of Regular Expressions!
Currently, I am carrying out my final year dissertation with Dr. S. K. Ghosh at the Indian Institute of Technology Kharagpur. The project is titled “Structure determination and profiling of chitin binding proteins in Entamoeba histolytica and E. invadens”. In this project, we are looking more closely at chitin binding proteins. We are trying to establish new methods of visualization for chitin binding protein primary sequences. We are also trying to develop software for automatic identification of chitin binding proteins based on conserved residues across species, structural investigation and reports from existing literature.
Research Proposal
There are various problems which I have often thought of. However, being specifically asked for a research proposal, it has to be kept in mind that it is limited by my current knowledge and research experience. I would also like to add that I am open to different problems in related topics in biology keeping in mind my background and interest.
Given an opportunity, I intend to look into key residues of proteins and try to find out how the activity of the protein is affected by mutating them. These studies will go a long way in automatic identification of key residues in protein-protein or protein-ligand, interaction, a key issue in drug targeting. I would like to carry out this structural analysis from a bioinformatics perspective and initially use the Drosophila genome as a model system. After standardizing the procedure, I would be looking at other genomes as well, to identity interesting evolutionary relationships and also to increase the statistical significance of my results. Modelling of entire proteins is computationally very expensive and often incorrect. Thus each of the sequences will have to be broken down into domains, which are more conserved. These domains can be submitted to sequence searching and alignment tools similar to BLAST, but that include structural information as well (like Fugue). Based on templates so obtained, the domain sequences would be submitted for comparative modelling using Modeller. The models will have to be evaluated to eliminate the bad ones and refine the good ones. This set of structures (domains from wild type proteins) can be considered to be a control set. The same procedure can be carried out for the same set of genes, but this time the corresponding residues mutated based on already known mutations. Comparing these structures with those from the control set, the effect of mutations can be observed. Combining this result with output from other software, the structural regions (cavities, pockets, depressions) where these mutations exist can be found out. Conservation of these mutations across homologous sequences will have to be investigated as well. Thus useful statistics obtained for automatic identification of key residues. Simultaneously interesting evolutionary information can be drawn from phylogenetic and statistical analysis of the structure based search method.
Why Chemical and Bio-molecular Engineering at Johns Hopkins?
Discussion with close friends who are PhD candidates in the US as well as my project guide at IIT, Dr. Sudip K. Ghosh , who has completed his postdoctoral research at the School of Public Health, Harvard University and Dr. Kenji Mizuguchi (my supervisor at the University of Cambridge) has given me an insight into how much more effective PhD studies in the US could be for my style of working than continuing in India. Both the computing equipment support and the level of educational care at the PhD level in the US in the fields in which I am interested are much superior to those available in India. Johns Hopkins is one of the most reputed universities with renowned faculty in this field. Today JHU is a brand name and the name speaks for itself! I am especially interested in working with professors like DR. Michael E. Paulaitis, Dr. Jeffrey J. Gray and Dr. Steven Salzberg. I believe the approaches and problems addressed by their laboratories match very well with my research interests. I am sure that I will simply love working in their labs. Working with such renowned professors will be a privilege and will give me the opportunity to contribute something original to the field. Chemical and Biomolecular Engineering at JHU has an interdisciplinary nature, which is evident from the joint appointments of faculty from various departments. I believe such an interdisciplinary nature is the key to its success and makes it one of the most coveted departments to be in!
Aroop Sircar
29 October 2003
STATEMENT OF PURPOSE
I am Aroop Sircar studying in the Indian Institute of Technology Kharagpur in the Department of Biotechnology. IIT Kharagpur is the first of the seven IITs. It has been ranked first amongst all engineering institutes in India for three consecutive years (survey conducted by India Today magazine). I shall be graduating in May 2004 with a Dual Degree (5-year combined Bachelors of Technology (Honors) and Masters of Technology) in Biotechnology and Biochemical Engineering. I have decided to pursue a research career in Computational Biology. I am applying to the Ph.D. program in the area of development of New Tools for Genomics, Functional Genomics, Proteomics and Glycomics of the Biological Engineering department.
As a person, I love hanging out with friends and family. With a passion for public speaking, I have stood third in Open IIT English debate and as a team we have won the Foundation Day debate of IIT Kharagpur. Having a flair to getting things done through proper co-ordination and motivation, I have taken part in the Autonomous section of the Robotix competition as a non-technical member. Our team had come third. I love traveling and have traveled extensively in India. I have spent a quarter of a year in Cambridge. I loved the openness and the way of life of the west. I would love to have the opportunity for more. I believe that to develop a true scientific temper, one has to overcome cultural biases and have an international exposure. Pursuing graduate studies in the US would be the ideal way to develop the perspective I need!
Fields of interest
I am interested in the field of Computational Biology, particularly in addressing various aspects of protein folding, sequence analysis and phylogeny. I am interested in drawing useful and meaningful statistics by parsing the vast amount of biological data already available. I am also interested in the development of software to address biological problems from a computational perspective. The trend today is to first apply bioinformatics tools to a problem and then corroborate the findings with experimental biology. I love carrying out wet lab biological experiments as well. I believe the fusion of computational biology with wet lab biology is the key to success of future biological research. Practical applicability of my findings is a great motivating factor for me. To that end, I believe that wet lab experiments are essential for the success of Bioinformatics. Bioinformatics helps to provide a very good initial guess, as to where to start from, when faced with a new problem. It also reduces the time taken to come up with a solution by providing a glimpse of what might actually be happening. This has already brought about tremendous changes in experimental design. My passion for computers and biology coupled with the desire to become a part of this revolution has led me to opt for a research career in this field.
Academic Background
The courses in Biochemistry, Genetics, Molecular Genetics, Cell & Molecular Biology and Protein Engineering have provided me a strong background in the fundamentals of biology. This coupled with courses like Introduction to Computing (C programming), Biostatistics, Biophysics & Modern Analytical Methods and Bioinformatics ensures a strong background for research work in my field. I have also taken the following courses: “Introductory Bioinformatics Course” and “Sequencing Project Management Using the Staden Package”. Both of these courses were conducted by United Kingdom Human Genome Mapping Project Resource Center at the Department of Genetics, University of Cambridge, United Kingdom. I would like to mention that I currently top my department. The damage to my eight semester GPA, can be attributed to my proficiency in Python, Perl, Regular Expressions and MySQL. Actually prior to visiting Cambridge, I had to master them, so I spent a significant amount of time during the eight semester experimenting with them!
Long Term Professional Goals
My personal experience has shown me that a career in research will keep me happy and excited. The essence of my research is, and will be, coming up with something novel, bearing in mind the relevance to the present-day world and the common man. I have found that developing nations like India, desperately need economically viable scientific knowledge that has practical applicability. In India, more often than not, cutting edge science is locked up in an ivory tower, far removed from the needs of the masses. In the long run I see myself as an active researcher, deploying my newly acquired scientific knowledge to address problems of practical importance. I feel that a Ph.D. degree is the first step to a successful scientific career and my endeavor to help the common man reap the benefits of modern science!
Research problems I have worked on
My first exposure to research was in the summer of my sophomore year (2001) when I was selected for the Visiting Summer Research Program fellowship at the Tata Institute of Fundamental Research (TIFR), Mumbai, India. There I worked with Dr. K. S. Krishnan for two months on the project titled “An attempt to find genes responsible for synaptic transmission using Drosophila melanogaster as a model system”. The work involved extensive fly pushing and screening flies for phototactic and paralytic defects. I also worked on another project titled “Effect of Conus toxins on Drosophila melanogaster”. The work, though elementary, helped me realize the joys of challenging research and the excitement of coming up with something new!
My interest in computational biology arose mainly as a result of a training I underwent in National Centre for Biological Sciences (NCBS), Bangalore, India in the summer of 2002. I worked as a collaborator student with Dr. Satyajit Mayor and Dr. R. Sowdhamini on a project titled “Delving Deep into Deep Orange and Carnation from a Computational Viewpoint”. The work involved modeling (using MODELLER) of the two Drosophila eye proteins Deep Orange and Carnation and finally docking them to find out the interacting residues (using GRAMM).This experience proved to be a great learning experience and I felt I was finding a niche for my talents.
I then chose as my Bachelors dissertation topic: “Knowledge based cloning of regulatory sequence of Entamoeba histolytica genes” under Dr. S. K. Ghosh at the Indian Institute of Technology Kharagpur. I deployed my newly acquired techniques to establish a signature for the regulatory sequences of genes responsible for encystation and excystation. In our initial analysis, we chose some genes from the signal transduction cycle and tried to pick up homologues from Entamoeba histolytica using multiple alignment and phylogenetic tree analysis (using PHYLIP). While working, we became interested in chitinases, which play an important role during encystation and excystation. We modeled these chitinases using homology modeling. A Chitin Box, i.e. conserved residues that have been observed to interact with chitin, was established.
In the summer of 2003, I worked as a visiting research student at the Department of Biochemistry, University of Cambridge, United Kingdom with Dr. Kenji Mizuguchi, (Wellcome Trust Research Career Development Fellow) for ten weeks, in a project titled, “Structural assignment for the Drosophila genome and mapping of known mutations”. The work comprised of bioinformatics involving high throughput modeling and automatic analysis of results to generate useful statistics. We tried to optimize methods for automatic model evaluation. The programming was mainly carried out in Perl and Python, with MySQL being used to store the data. While working in this project, I also learnt to appreciate the power of Regular Expressions!
Currently, I am carrying out my final year dissertation with Dr. S. K. Ghosh at the Indian Institute of Technology Kharagpur. The project is titled “Structure determination and profiling of chitin binding proteins in Entamoeba histolytica and E. invadens”. In this project, we are looking more closely at chitin binding proteins. We are trying to establish new methods of visualization for chitin binding protein primary sequences. We are also trying to develop software for automatic identification of chitin binding proteins based on conserved residues across species, structural investigation and reports from existing literature.
Research Proposal
There are various problems which I have often thought of. However, being specifically asked for a research proposal, it has to be kept in mind that it is limited by my current knowledge and research experience. I would also like to add that I am open to different problems in related topics in biology keeping in mind my background and interest.
Given an opportunity, I intend to look into key residues of proteins and try to find out how the activity of the protein is affected by mutating them. These studies will go a long way in automatic identification of key residues in protein-protein or protein-ligand, interaction, a key issue in drug targeting. I would like to carry out this structural analysis from a bioinformatics perspective and initially use the Drosophila genome as a model system. After standardizing the procedure, I would be looking at other genomes as well, to identity interesting evolutionary relationships and also to increase the statistical significance of my results. Modelling of entire proteins is computationally very expensive and often incorrect. Thus each of the sequences will have to be broken down into domains, which are more conserved. These domains can be submitted to sequence searching and alignment tools similar to BLAST, but that include structural information as well (like Fugue). Based on templates so obtained, the domain sequences would be submitted for comparative modelling using Modeller. The models will have to be evaluated to eliminate the bad ones and refine the good ones. This set of structures (domains from wild type proteins) can be considered to be a control set. The same procedure can be carried out for the same set of genes, but this time the corresponding residues mutated based on already known mutations. Comparing these structures with those from the control set, the effect of mutations can be observed. Combining this result with output from other software, the structural regions (cavities, pockets, depressions) where these mutations exist can be found out. Conservation of these mutations across homologous sequences will have to be investigated as well. Thus useful statistics obtained for automatic identification of key residues. Simultaneously interesting evolutionary information can be drawn from phylogenetic and statistical analysis of the structure based search method.
Why Biological Engineering at Massachusetts Institute of Technology?
Discussion with close friends who are PhD candidates in the US as well as my project guide at IIT, Dr. Sudip K. Ghosh , who has completed his postdoctoral research at the School of Public Health, Harvard University and Dr. Kenji Mizuguchi (my supervisor at the University of Cambridge) has given me an insight into how much more effective PhD studies in the US could be for my style of working than continuing in India. Both the computing equipment support and the level of educational care at the PhD level in the US in the fields in which I am interested are much superior to those available in India. Massachusetts Institute of Technology is one of the most reputed universities with renowned faculty in this field. Today MIT is a brand name and the name speaks for itself! I am especially interested in working with professors like Dr.Michael Yaffe and Dr. Bruce Tidor. I believe the approaches and problems addressed by their laboratories match very well with my research interests. I am sure that I will simply love working in their labs. The work carried out at the BioMicro centre by people like Sanchita Bhattacharya, is also of special interest to me. Working with such renowned professors will be a privilege and will give me the opportunity to contribute something original to the field. Biological Engineering at MIT has an interdisciplinary nature, which is evident from the joint appointments of faculty from various departments. I believe such an interdisciplinary nature is the key to its success and makes it one of the most coveted institutions to be in!
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