Curriculum Vita Nitin Gupta

Senior Undergraduate Computer Science And Engineering Indian Institute of Technology Kanpur Email: nitingpt@iitk.ac.in

Personal Details
Current Address Room No D-203, Hall-I, IIT Kanpur Kanpur - 208016 C-30, Ranjeet Nagar, Bharatpur 321001 Rajasthan Phone +91-5644-236150 Personal URL http://home.iitk.ac.in/student/nitingpt Date of Birth Nationality Sex Marital Status 21 October, 1982 Indian Male Single Permanent Address

Academic Performance at IIT Kanpur

Semester 1 2 3 4 5 6 Cumulative Performace Index (GPA) Semester Performance Index 9.7 8.8 9.6 8.8 9.3 9.6 9.3/10.0 (equivalent to 3.72/4.0)

Schooling Information
Class Secondary Senior Secondary Institution Subjects St. Pauls Bharatpur Mathematics, English, Science, Hindi, Social Studies, Sanskrit D.A.V. Public Mathematics, Physics, Chemistry, School, Kota English, Hindi Percentage 90.34 88.40

Standard Test Scores

GRE TOEFL 1480 / 1600 Verbal : 680, Quant: 800, AWA : 5.5/6 290/300 (Computer Based Test)

Relevant Course-work
List incomplete, After each course the grade obtained in that course is indicated * means currently enrolled in that course, Fall 2003 ** means course is likely to be taken in the Spring 2004 CS210 CS220 CS245 CS301 CS350 CS330 CS340 CS315 CS335 CS355 CS397 CS498 CS674 CS497 CS365 Data Structures (A) Computer Organization (A) Algorithms (A) Discrete Mathematics (B) Priniciples of Prg. Lang. (A) Operating Systems (B) Theory of Computation (A) Database Systems (B) Compiler Design (A) Prog. Tools & Tech. (A) Spl. Topics in CS-I(A.I.)(A) B.Tech Project* Knowledge Discovery* Special Topics in CS II* Software Engineering** BSE633 Bioinformatics & Comp. Bio.(A) BSE613 Cell & Molecular Biology* BSE632 Biophysics & Structural Bio.* BSE634 Functional Genomics ** MTH101 Mathematics I (A) MTH102 Mathematics II (A) MTH203 Mathematics III (B) MTH320 Analysis I (A) PHY101 Physics I (A) PHY102 Physics II (B) CHM101 General Chemistry (A) BSO215 Industrial Organic Chemistry (B) ESC101 Fundamentals of Computing (A) ESO212 Fluid Mechanics (A) TA101 Engineering Graphics (A)

Academic Achievements
Secured All India Rank 1 in IITJEE2000 among more than 125,000 candidates. National Talent Search Exam (NTSE) Scholarship awarded by NCERT, a Govt. Of India undertaking. Listed in the Merit List of Class X at state level for outstanding performance. Won 5th prize in State Science Talent Search Exam organized by Dept. of Science & Tech, Govt. of Rajasthan in 1998. Semifinalist of Tech Olympiad, a part of technical festival of IIT Kanpur, 2001.

Areas of Interest

Computational Structural Biology Bioinformatics and Genomics. Machine Learning & Data Mining Artificial Intelligence

Publications
Nitin Gupta and Anders Irback. Coupled folding-binding versus docking: A Lattice model study. Journal of Chemical Physics, 120:3983-3989, 2004. Bhaduri, A., Pugalenthi, G., Gupta, N. and Sowdhamini, R. iMOT: an interactive package for the selection of spatially interacting motifs. Nucleic Acids Research (in press).

Term Papers & Presentations

Nitin Gupta and Nitin Mangal. Computational Approaches towards the protein folding problem. Supervisor: Prof. Somenath Biswas, Dept. of Computer Science and Engineering, IIT Kanpur. Nitin Gupta. Folding v/s non-folding polypeptides: A sequence based classification approach. Supervisor: Prof. Harish Karnick, Dept. of Computer Science and Engineering, IIT Kanpur. Nitin Gupta, Kamal Tiwari and Anupam Kumar. Spamivore: A two level email spam filter. Supervisor: Prof. Harish Karnick, Dept. of Computer Science and Engineering, IIT Kanpur. Nitin Gupta and Shantanu Sharma. Active Appearance Model based facerecognition system. Supervisor: Prof. Amitabha Mukherjee, Dept. of Computer Science and Engineering, IIT Kanpur. Nitin Gupta, Aseem Gupta and Sachin Kumar. Contemporary education system- Role of NGOs. Supervisor: Prof. B. Rath, Dept. of Humanities and Social Sciences, IIT Kanpur.

Participation in Conferences
The International Symposium on Molecules, Machines and Networks (MMN) January 2004, National Centre for Biological Sciences, Bangalore. The International Conference on Mathematical Biology (ICMB), February 2004, Indian Institute of Technology, Kanpur.

Technical Skills
Programming Languages : C/C++, Java, Scheme, Prolog, Perl/Tk, Unix Shell Programming, Basic Assembly Language (i386) Platforms : Unix/Linux, MS DOS, Windows 95/98/NT/2000/XP, Solaris Tools and Technologies : Lex, Yacc, Make, HTML, CGI, Perl Scripts, LaTeX/TeX, Micorsoft VisualC++, VisualBasic Bioinformatics Tools : Blast, Malign, Comparer, Rasmol, BASE

Bioinformatics Databases : CATH, SCOP, TRANSFAC, KEGG, TRANSPATH

Research & Projects

Summer Internship I : Gene Expression Mapping on Signaling Pathways The first part of the project was to store the information about important signaling pathways in a machine readable format for which we used TRANSPATH and TRANSFAC to get the raw networks information. We also developed a GUI to create, edit, store and visualize the pathways. The next part of this project was to develop algorithms to find overlap between these pathways and gene expression data using clustered lists and evaluating the putative significance of different pathways in diseases like Breast Cancer. This project is now being further developed into an application to work together with BASE application developed by SWEGENE. Done under the guidance of Prof. Carsten Peterson, LUND University, Sweden and Dr. Jari Hakkinen, Lund Swegene Facility.

Summer Internship II :Monte Carlo Study of Coupled Folding & Binding We developed a simulation framework to study the coupled folding and binding of a small polymer to a target structure in HP Lattice Model. We consider two type of monomers hydrophobic and polar and the energy function considering adjacent HH monomers implicitly takes effects of the medium into account. We use this framework to compare the thermodynamic and kinetic properties of coupled foldingbinding to docking. Our findings are in accordance with Fly-Casting Mechanism given by Peter G Wolynes suggesting that unstructuredness actually speeds up the binding dynamics. Done under the guidance of Prof. Anders Irback, LUND University, Sweden. Accepted in the Journal of Chemical Physics. B.Tech Project : Devising new Fold Prediction Algorithms We are trying to develop new algorithms for automatic fold prediction based on the primary structure of a protein. Our first idea is to detect periodicity in hydrophobicity distribution along the sequence in frequency domain using Fourier analysis. In a second approach, we are using contact map prediction based on physically relevant parameters and a similarity measure between contact maps to identify the fold of a sequence. Being done under the guidance of Prof. Somnath Biswas, Dept. of Computer Science & Engineering, IIT Kanpur with my classmate Nitin Mangal. FOLDER: Comparative Protein Fold Recognition System Fully Automated threading based application for comparative fold recognition. Takes a amino acid sequence and predicts the secondary structure using PSIPRED. The output is then fed to THREADER3 to calculate the solvation potentials, pairwise residue potentials, similarity match etc against a template library of 5300 domains obtained from CATH database. A two layer feed forward neural network is used to obtain a single score to judge the appropriate fold from many various potentials and alignment scores. Done under the guidance of Dr. R. Sowdhamini, National Centre for Biological Sciences, Bangalore. Distinguishing proteins from random sequences We believe that biological sequences like DNA and proteins have different statistical properties from random sequences and have some inherent trends having physical relevance. We have developed a neural network based classification technique that uses a set of carefully chosen 27 sequence based parameters. These parameters represent properties like amino acid composition, hydrophobicity and charge distribution. Being done under the guidance of Prof. Harish Karnick, Dept. of Computer Science & Engineering, IIT Kanpur. Spamivore: A Two Layer Email Spam Filter Email spam are one of the most irritating problems faced by any email user. Our method is able to differentiate between legitimate mails and spam mails. The method is built upon Bayesian Filtering technique and a perceptron. Done under the guidance of Prof. Harish Karnick Dept. of Computer Science & Engineering, IIT Kanpur.

iMOT: Interacting Structural Motifs in Protein Superfamilies Developed an automated method of selecting interacting motifs for superfamilies based on their structural alignments. Conservation of motifs in homologues (obtained by BLAST) along with structural proximity, contributing to the favorable interaction among themselves is taken as the criterion for selecting family level motifs. Pseudo-potentials between motifs are evaluated to rank them. Structural motifs for the superfamily are then chosen from the family level motifs which are found at similar positions in the structural alignment of the superfamily. Done under the guidance of Dr. R. Sowdhamini, National Centre for Biological Sciences, TIFR, Bangalore. This work will shortly be submitted for publication.

FASSM: Family Annotation based on Substrate Specific Motifs Many protein families are characterized by poor sequence homology but have similar substrate binding sites. Family annotation of unknown sequences based on homology based methods is not suitable in such cases. We have developed a method to detect the possible substrate binding motifs in such families using PSI-Blast generated profiles and use these motifs for the family annotation. A feed forward backpropagation network is employed to evaluate the score for each family. Done under the guidance of Dr. R. Sowdhamini, National Centre for Biological Sciences, Bangalore. Active Appearance Model Based Face-Recognition System Active Appearance models represent a statistical system often employed for facial recognition. During training phase, we learn the relationship between model parameter displacements and the residual errors introduced between a training image and a synthesized model example. To match an image, we measure the current residuals and use the model to predict changes to the current parameters, leading to a better fit. Done under the guidance of Prof. Amitabha Mukherjee, Dept. of Computer Science & Engineering, IIT Kanpur as a part of Video Summarization Project sponsored by Adobe Systems Inc. Nachos: Operating Systems Simulation The project aimed at providing various functionalities to Nachos, instructional software that runs as secondary OS on Linux. Features like high level synchronization primitives, thread scheduling, system calls, console device driver and multiple-user programming support were successfully added and tested. Done under the guidance of Prof. Deepak Gupta, Dept. of Computer Science & Engineering, IIT Kanpur.

Pastoc : Pascal to C Converter Pastoc is a stand alone application which converts Pascal Code into its equivalent C code. We used Lex for lexical Analysis and Yacc for generating parser. Linked Lists and structures were used to simulate the symbol table. Done under the guidance of Prof. Sanjeev K. Agarwal, Head, Dept. of Computer Science & Engineering, IIT Kanpur.

Chinese Checkers Implementation Designed algorithm for this multiplayer board-game that can be played by 2, 3, 4 or 6 players, using modified alpha-beta Minimax Game Tree. Depth of tree was kept short to make the program faster and pruning at various levels and in varied amounts was done to optimize the performance. Our algorithm gave excellent results and was declared BEST PROJECT for the winning the knockout competition among 20 other similar implementations of the game. Done under the guidance of Prof. Manindra Agrawal, Dept. of Computer Science & Engineering, IIT Kanpur (Well known for his primality testing algorithm). Trie Based Search Engine The project used "Composite Trie" data structure for prefix pattern matching to implement a search engine for local data. Innovative indexing of files and preprocessing of data was done to make the engine fast at runtime. Parsing of HTML files made it possible to search webpages in addition to text files. Indexing allowed giving ranks to results and viewing them in the sorted order. Besides search engine, the project simulated automatic word completion facility and a spellchecker. Done under the guidance of Prof. R. K. Ghosh, Dept. of Computer Science & Engineering, IIT Kanpur.

About Myself
Myself: I am a sincere, hardworking and highly self-motivated individual with good communication skills and capacity to coordinate and take initiative. I have a strong work ethic and I am committed to highest levels of professional and personal excellence. Hobbies: My hobbies are acting, philately, quizzing, visiting places of historic importance and community service. Extra-curricular Participation: o o o o o Member of Student's Senate, the student representative body of the institute. Secretary, Mridaksh 2002 in Antaragni 2001, the cultural festival of IIT Kanpur. Member of Election Council for Gymkhana elections, 2001 Student Guide for year 2001-02 being a member of Student Counseling Service. Vice President of Shiksha Sopan, a registered NGO working for the upliftment of rural underdeveloped with emphasis on education and selfdependency. Represented my team in Skit and Play competitions of Galaxy 2001, the inter hall cultural competition. Secretary, T-Shirt Cell in Techkriti2001, the annual technical festival of the institute. Regular participation in sports - cricket, tennis and athletics.

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