Resume of Bhaskar DasGupta

Curriculum Vitae of Bhaskar DasGupta

(does not contain all information and may not be up-to-date. Please check other items of my homepage http://www.cs.uic.edu/~dasgupta for more up-to-date information.)

Table of contents

Basic Resume
Research Grants
Editorial and Other Administrative Responsibilities
Teaching Experience in University of Illinois at Chicago
- Teaching Assignments
- Course Evaluations
Teaching Experience in Rutgers-Camden
- Teaching Assignments
- Course Evaluations
Other activities in University of Illinois at Chicago
- Supervising Undergraduate/MS/PhD students
- Services to the department or university
Other activities in Rutgers-Camden
- Supervising Independent Study projects
- Services to the department or university
List of Recent Publications
Some softwares that have been developed
Other Professional Activities/Awards

Present Employment

Associate Professor, Department of Computer Science, University of Illinois at Chicago, Chicago, IL 60607-7053.

Education

PhD in Computer Science, received on January, 1995 from Department of Computer Science, University of Minnesota, Minneapolis, MN 55455-0159, USA.

MS in Computer Science, received on August, 1992 from Department of Computer Science, The Pennsylvania State University, University Park, PA 16802, USA.

Master of Engineering (ME) in Computer Science & Automation, received on December, 1987 from Indian Institute of Science (IISc), Bangalore, India.

Bachelor of Engineering (BE) in Computer Science & Engineering, received on July, 1986 from Jadavpur University, Calcutta, India.

Employment History and Professional Experiences

Associate Professor, in Department of Computer Science of University of Illinois at Chicago, from August 22, 2005 (continued presently).

Research Visitor, DIMACS (Center for Discrete Mathematics and Theoretical Computer Science), Rutgers University, New Brunswick, from August 2008 until May 2009.

Visiting Fellow, Lewis-Sanger Institute for Integrative Genomics, Princeton University, from August 2008 until May 2009.

Assistant Professor, in Department of Computer Science of University of Illinois at Chicago, from August 22, 2001 until August 22, 2005.

Assistant Professor, in Department of Computer Science of Rutgers-Camden, from July 1st 1997 until August 22, 2001.

Visiting Assistant Professor, in Department of Computer Science of Rutgers-Camden, from September, 1996 To June, 1997.

Joint Post-Doctoral Fellowship in University of Waterloo and in McMaster University in Canada, from July, 1995 to August, 1996.
I did post-doctoral research with the research groups of Prof. Ming Li (Waterloo) and Prof. Tao Jiang (McMaster) on Design and Analysis of algorithms in Computational Molecular Biology.

Part-time Professor in Wilfrid-Laurier University in Canada from January, 1996 to April, 1996.
I taught a course titled Advanced Data Structures.

Post-doctoral Fellowship in DIMACS center of Rutgers University, from January, 1995 to June, 1995.
I did post-doctoral research with Prof. Eduardo T. Sontag on Neural Networks and Learning Theory with application to Control Theory.

Teaching/Research Assistant in University of Minnesota from August, 1992 to December, 1994.

Instructor in Pennsylvania State University from June, 1992 to August, 1992.
I taught a course on Introduction to Computer Programming in PASCAL.

Teaching/Research Assistant in Pennsylvania State University from August, 1989 to May, 1992.

Industrial Experience

Software Application Engineer/Math Specialist, in Infinite Graphics Incorporated, Minneapolis, MN 55406, from June 1994 to August 1994.
I mostly worked on developing software for VLSI applications using the C language and other necessary software tools.

Research & Development Engineer, CMC Ltd., India, from February, 1988 to July 1989.
I mainly worked on developing software for Image Processing applications, including development of a complete system for Automatic Fingerprint Identification. We used a ZIP-3216 array processor and the ZIP-C language (which is a mixture of C and low-level assembly language).

Research Grants (click the link)

Editorial and Other Administrative Responsibilities
Current:

Member of editorial board, International Journal of Data Mining and Bioinformatics (IJDMB)
Associate editor, Discrete Mathematics, Algorithms and Applications (DMAA)
Member of editorial board, Advances in Bioinformatics
Member of editorial board, Theoretical Biology Insights
Member of editorial board, International Journal of Information Sciences and Computer Engineering
Member of editorial board, Biomedical Engineering and Computational Biology
Member of editorial advisory board, The Open Bioinformatics Journal
Reviewer, NIH study group on Small Business: Computational Biology, Image Processing, and Data Mining [IMST (14)]
Chairperson, Chicago Chapter of IEEE Computational Intelligence Society (CIS)

Past:

Associate editor, IEEE Transactions on Neural Networks (2009-2010)
Guest editor (with Piotr Berman and Jie Liang), special issue of Algorithmica (Volume 48, Number 4, August 2007) on Algorithmic Methodologies for processing Protein Structures, Sequences and Networks

Teaching Assignments in University of Illinois at Chicago

Sem/Yr Course Title Course Number Credits Enrollments

S13 Introduction to Computational Molecular Biology CS 502 4

F12 Computer Algorithms II CS 501 4 28

F12 Computer Algorithms I CS 401 3 (undergraduate) 18

4 (graduate) 48

S12 Introduction to Computational Molecular Biology CS 502 4 26

S12 Computer Algorithms II CS 501 4 28

MCS 501 4

F11 Computer Algorithms II CS 501 4 30

MCS 501 4

S11 Computer Algorithms I CS 401 3/4 (undergraduate/graduate) 45

F10 Computer Algorithms II CS 501 4 30

MCS 501 4 2

F10 Computer Algorithms I CS 401 3/4 (undergraduate/graduate) 47

S10 Introduction to Computational Molecular Biology CS 502 4 29

F09 Languages and Automata CS 301 3 36

F09 Computer Algorithms II CS 501 4 23

MCS 501 4 5

F08 and S09 Sabbatical leave (DIMACS and Princeton)

S08 Introduction to Computational Molecular Biology CS 502 4 10

F07 Languages and Automata CS 301 3 25

F07 Discrete Structures I CS 201 4 56

S07 Computer Algorithms I CS 401 3/4 (undergraduate/graduate) 19

S07 Introduction to Computational Molecular Biology CS 502 4 19

F06 Computer Algorithms II CS 501 4 24

S06 Discrete Structures I CS 201 4 39

F05 Discrete Structures I CS 201 4 38

F04 Computer Algorithms I CS 401 3/4 (undergraduate/graduate) 30

F04 Computer Algorithms II CS 501 4 22

S04 Introduction to Computational Molecular Biology CS 502 4 27

F03 Computer Algorithms I CS 401 3/4 (undergraduate/graduate) 32

S03 Computer Algorithms II CS 501 4 20

F02 Computer Algorithms I CS 401 3/4 (undergraduate/graduate) 50

S02 Introduction to Computational Molecular Biology CS 594 4 32

F01 Computer Algorithms I CS 401 3/4 (undergraduate/graduate) 50

Sem/Yr	Course Title	Course Number	Credits	Enrollments
S13	Introduction to Computational Molecular Biology	CS 502	4
F12	Computer Algorithms II	CS 501	4	28
F12	Computer Algorithms I	CS 401	3 (undergraduate)	18
			4 (graduate)	48
S12	Introduction to Computational Molecular Biology	CS 502	4	26
S12	Computer Algorithms II	CS 501	4	28
		MCS 501	4
F11	Computer Algorithms II	CS 501	4	30
		MCS 501	4
S11	Computer Algorithms I	CS 401	3/4 (undergraduate/graduate)	45
F10	Computer Algorithms II	CS 501	4	30
		MCS 501	4	2
F10	Computer Algorithms I	CS 401	3/4 (undergraduate/graduate)	47
S10	Introduction to Computational Molecular Biology	CS 502	4	29
F09	Languages and Automata	CS 301	3	36
F09	Computer Algorithms II	CS 501	4	23
		MCS 501	4	5
F08 and S09	Sabbatical leave (DIMACS and Princeton)
S08	Introduction to Computational Molecular Biology	CS 502	4	10
F07	Languages and Automata	CS 301	3	25
F07	Discrete Structures I	CS 201	4	56
S07	Computer Algorithms I	CS 401	3/4 (undergraduate/graduate)	19
S07	Introduction to Computational Molecular Biology	CS 502	4	19
F06	Computer Algorithms II	CS 501	4	24
S06	Discrete Structures I	CS 201	4	39
F05	Discrete Structures I	CS 201	4	38
F04	Computer Algorithms I	CS 401	3/4 (undergraduate/graduate)	30
F04	Computer Algorithms II	CS 501	4	22
S04	Introduction to Computational Molecular Biology	CS 502	4	27
F03	Computer Algorithms I	CS 401	3/4 (undergraduate/graduate)	32
S03	Computer Algorithms II	CS 501	4	20
F02	Computer Algorithms I	CS 401	3/4 (undergraduate/graduate)	50
S02	Introduction to Computational Molecular Biology	CS 594	4	32
F01	Computer Algorithms I	CS 401	3/4 (undergraduate/graduate)	50

Course Evaluations in University of Illinois at Chicago

S/Yr and Course Title Overall Comparison

Other UIC Courses Other UIC Instructors

(Max=5) (Max=5)

F12, Computer Algorithms I (CS 401), graduate students 4.04 4.09

                                                             undergraduate students 3.33 3.67

F12, Computer Algorithms II (CS 501) 4.13 4.19

S12, Introduction to Computational Molecular Biology (CS 502) 4.50 4.30

S12, Computer Algorithms II (CS/MCS 501) 4.35 4.43

F11, Computer Algorithms II (CS/MCS 501) 4.33 4.70

S11, Computer Algorithms I (CS 401) 4.23 4.47

F10, Computer Algorithms II (CS/MCS 501) 3.80 4.00

F10, Computer Algorithms I (CS 401) 4.05 4.38

S10, Introduction to Computational Molecular Biology (CS 502) 4.54 4.69

F09, Languages and Automata (CS 301) 4.39 4.78

F09, Computer Algorithms II (CS 501) 4.25 4.50

                                           (MCS 501) 4.40 4.20

F08 and S09    Sabbatical leave (DIMACS and Princeton)

S08, Introduction to Computational Molecular Biology (CS 502) 4.00 4.50

F07, Discrete Structures I (CS 201) 4.45 4.55

F07, Languages and Automata (CS 301) 3.62 4.03

S07, Computer Algorithms I (CS 401) 3.93 3.93

S07, Introduction to Computational Molecular Biology (CS 502) 4.39 4.72

F06, Computer Algorithms II (CS 501) 4.59 4.71

S06, Discrete Structures I (CS 201) 3.45 3.82

F05, Discrete Structures I (CS 201) 3.94 4.06

F04, Computer Algorithms I (CS 401) 4.41 4.63

F04, Computer Algorithms II (CS 501) 4.71 4.76

S04, Introduction to Computational Molecular Biology (CS 502) 4.20 4.32

F03, Computer Algorithms I (CS 401) 3.94 4.00

S03, Computer Algorithms II (CS 501) 4.41 4.59

F02, Computer Algorithms I (CS 401) 3.89 4.18

S02, Introduction to Computational Molecular Biology (CS 594) 4.21 4.38

F01, Computer Algorithms I (CS 401) 3.86 4.14

S/Yr and Course Title	Overall Comparison
	Other UIC Courses	Other UIC Instructors
	(Max=5)	(Max=5)
F12, Computer Algorithms I (CS 401), graduate students	4.04	4.09
undergraduate students	3.33	3.67
F12, Computer Algorithms II (CS 501)	4.13	4.19
S12, Introduction to Computational Molecular Biology (CS 502)	4.50	4.30
S12, Computer Algorithms II (CS/MCS 501)	4.35	4.43
F11, Computer Algorithms II (CS/MCS 501)	4.33	4.70
S11, Computer Algorithms I (CS 401)	4.23	4.47
F10, Computer Algorithms II (CS/MCS 501)	3.80	4.00
F10, Computer Algorithms I (CS 401)	4.05	4.38
S10, Introduction to Computational Molecular Biology (CS 502)	4.54	4.69
F09, Languages and Automata (CS 301)	4.39	4.78
F09, Computer Algorithms II (CS 501)	4.25	4.50
(MCS 501)	4.40	4.20
F08 and S09 Sabbatical leave (DIMACS and Princeton)
S08, Introduction to Computational Molecular Biology (CS 502)	4.00	4.50
F07, Discrete Structures I (CS 201)	4.45	4.55
F07, Languages and Automata (CS 301)	3.62	4.03
S07, Computer Algorithms I (CS 401)	3.93	3.93
S07, Introduction to Computational Molecular Biology (CS 502)	4.39	4.72
F06, Computer Algorithms II (CS 501)	4.59	4.71
S06, Discrete Structures I (CS 201)	3.45	3.82
F05, Discrete Structures I (CS 201)	3.94	4.06
F04, Computer Algorithms I (CS 401)	4.41	4.63
F04, Computer Algorithms II (CS 501)	4.71	4.76
S04, Introduction to Computational Molecular Biology (CS 502)	4.20	4.32
F03, Computer Algorithms I (CS 401)	3.94	4.00
S03, Computer Algorithms II (CS 501)	4.41	4.59
F02, Computer Algorithms I (CS 401)	3.89	4.18
S02, Introduction to Computational Molecular Biology (CS 594)	4.21	4.38
F01, Computer Algorithms I (CS 401)	3.86	4.14

Teaching Assignments in Rutgers-Camden

S/Yr Course Title Number Credit Mode of Instruction Audience Responsibility Enrollment

S01 Introduction to Computer Science using C++ (Section 40) 50:198:111 3 Lec undergrad major total 50

F00 Design & Analysis of Algorithms 50:198:271 3 Lec undergrad major total 27

F00 Introduction to Computer Science using C++ (Section 1) 50:198:111 3 Lec undergrad major total 35

F00 Introduction to Computer Science using C++ (Section 2) 50:198:111 3 Lec undergrad major total 31

S00 Design & Analysis of Algorithms 50:198:271 3 Lec undergrad major total 32

S00 Senior Design Project 50:198:493 3 Lec undergrad major total 5

F99 None (FASP leave)

S99 Design & Analysis of Algorithms 50:198:271 3 Lec undergrad major total 17

S99 Computer Organization and Assembly Language 50:198:231 3 Lec undergrad major total 38

F98 Design & Analysis of Algorithms 50:198:271 3 Lec undergrad major total 30

F98 Introduction to Unix O/S 50:198:343 3 Lec undergrad major total 11

F98 Introduction to Programming Methods Using FORTRAN 50:198:151 3 Lec undergrad major total 11

Summ98 Advanced C & UNIX 50:198:243 3 Lec undergrduate major total 14

Summ98 Introduction to Programming Using C 50:198:152 3 Lec undergrduate total 30

S98 Introduction to Programming Methods Using FORTRAN 50:198:151 3 Lec undergrduate total 26

S98 Advanced C & UNIX 50:198:243 3 Lec undergrduate major total 35

F97 Introduction to Programming Methods Using FORTRAN 50:198:151 3 Lec undergrduate total 10

F97 Design & Analysis of Algorithms 50:198:344 3 Lec undergrduate major total 25

F97 Data Structures 50:198:228 3 Lec undergrduate major total 35

Summ97 Advanced C & UNIX 50:198:243 3 Lec undergrduate major total 13

Summ97 Introduction to Programming Using C 50:198:152 3 Lec undergrduate total 24

S97 Design & Analysis of Algorithms 50:198:344 3 Lec undergrd major total 33

S97 Introduction to Programming Using C 50:198:152 3 Lec undergrduate total 43

S97 Introduction to Programming Methods Using FORTRAN 50:198:151 3 Lec undergrduate total 29

F96 Introduction to Programming Using C (section 01) 50:198:152 3 Lec undergrduate total 34

F96 Introduction to Programming Using C (section 40) 50:198:152 3 Lec undergrduate total 15

S/Yr	Course Title	Number	Credit	Mode of Instruction	Audience	Responsibility	Enrollment
S01	Introduction to Computer Science using C++ (Section 40)	50:198:111	3	Lec	undergrad major	total	50
F00	Design & Analysis of Algorithms	50:198:271	3	Lec	undergrad major	total	27
F00	Introduction to Computer Science using C++ (Section 1)	50:198:111	3	Lec	undergrad major	total	35
F00	Introduction to Computer Science using C++ (Section 2)	50:198:111	3	Lec	undergrad major	total	31
S00	Design & Analysis of Algorithms	50:198:271	3	Lec	undergrad major	total	32
S00	Senior Design Project	50:198:493	3	Lec	undergrad major	total	5
F99	None (FASP leave)
S99	Design & Analysis of Algorithms	50:198:271	3	Lec	undergrad major	total	17
S99	Computer Organization and Assembly Language	50:198:231	3	Lec	undergrad major	total	38
F98	Design & Analysis of Algorithms	50:198:271	3	Lec	undergrad major	total	30
F98	Introduction to Unix O/S	50:198:343	3	Lec	undergrad major	total	11
F98	Introduction to Programming Methods Using FORTRAN	50:198:151	3	Lec	undergrad major	total	11
Summ98	Advanced C & UNIX	50:198:243	3	Lec	undergrduate major	total	14
Summ98	Introduction to Programming Using C	50:198:152	3	Lec	undergrduate	total	30
S98	Introduction to Programming Methods Using FORTRAN	50:198:151	3	Lec	undergrduate	total	26
S98	Advanced C & UNIX	50:198:243	3	Lec	undergrduate major	total	35
F97	Introduction to Programming Methods Using FORTRAN	50:198:151	3	Lec	undergrduate	total	10
F97	Design & Analysis of Algorithms	50:198:344	3	Lec	undergrduate major	total	25
F97	Data Structures	50:198:228	3	Lec	undergrduate major	total	35
Summ97	Advanced C & UNIX	50:198:243	3	Lec	undergrduate major	total	13
Summ97	Introduction to Programming Using C	50:198:152	3	Lec	undergrduate	total	24
S97	Design & Analysis of Algorithms	50:198:344	3	Lec	undergrd major	total	33
S97	Introduction to Programming Using C	50:198:152	3	Lec	undergrduate	total	43
S97	Introduction to Programming Methods Using FORTRAN	50:198:151	3	Lec	undergrduate	total	29
F96	Introduction to Programming Using C (section 01)	50:198:152	3	Lec	undergrduate	total	34
F96	Introduction to Programming Using C (section 40)	50:198:152	3	Lec	undergrduate	total	15

Course Evluations (when available) in Rutgers-Camden

S/Yr and Course Title Evaluation Responses Teaching Effectiveness Course Quality

(Max=5) (Max=5)

Instructor Dept. Mean Instructor Dept. Mean

S01, Intro to Computer Science using C++ (Section 40) 35 4.55 4.2 4.3 4.1

F00, Design & Analysis of Algorithms 21 4.00 3.86 3.95 3.85

F00, Intro to Computer Science using C++ (Section 1) 24 3.79 3.86 3.63 3.85

F00, Intro to Computer Science using C++ (Section 2) 19 3.53 3.86 3.56 3.85

S00, Design & Analysis of Algorithms 28 3.88 4.02 3.8 3.93

S99, Design & Analysis of Algorithms 12 4.18 4.12 4.2 4.09

S99, Computer Organization and Assembly Language 21 3.48 4.12 3.45 4.09

F98, Intro. to UNIX Operating Systems 8 4.13 4.09 4.14 4.04

F98, Intro. to Prog. Methods Using FORTRAN 5 4.60 4.09 4.20 4.04

Summ98, Advanced C & UNIX 7 3.57 4.15 3.43 3.98

S98, Intro. to Prog. Methods Using FORTRAN 18 3.40 3.89 3.20 3.86

Summ97, Advanced C & UNIX 10 4.30 4.17 4.20 4.10

Summ97, Intro to Prog. Using C 24 4.08 4.17 4.13 4.10

S97, Design \& Analysis of Algorithms 19 4.26 3.81 3.84 3.72

S97, Intro to Prog. Using C 26 3.85 3.81 3.80 3.72

S97, Intro. to Prog. Methods Using FORTRAN 14 3.77 3.81 3.77 3.72

F96, Intro to Prog. Using C (Section 01) 19 3.44 4.05 3.28 3.97

F96, Intro to Prog. Using C (Section 40) 12 3.92 4.06 4.00 3.97

S/Yr and Course Title	Evaluation Responses	Teaching Effectiveness	Course Quality
		(Max=5)	(Max=5)
		Instructor	Dept. Mean	Instructor	Dept. Mean
S01, Intro to Computer Science using C++ (Section 40)	35	4.55	4.2	4.3	4.1
F00, Design & Analysis of Algorithms	21	4.00	3.86	3.95	3.85
F00, Intro to Computer Science using C++ (Section 1)	24	3.79	3.86	3.63	3.85
F00, Intro to Computer Science using C++ (Section 2)	19	3.53	3.86	3.56	3.85
S00, Design & Analysis of Algorithms	28	3.88	4.02	3.8	3.93
S99, Design & Analysis of Algorithms	12	4.18	4.12	4.2	4.09
S99, Computer Organization and Assembly Language	21	3.48	4.12	3.45	4.09
F98, Intro. to UNIX Operating Systems	8	4.13	4.09	4.14	4.04
F98, Intro. to Prog. Methods Using FORTRAN	5	4.60	4.09	4.20	4.04
Summ98, Advanced C & UNIX	7	3.57	4.15	3.43	3.98
S98, Intro. to Prog. Methods Using FORTRAN	18	3.40	3.89	3.20	3.86
Summ97, Advanced C & UNIX	10	4.30	4.17	4.20	4.10
Summ97, Intro to Prog. Using C	24	4.08	4.17	4.13	4.10
S97, Design \& Analysis of Algorithms	19	4.26	3.81	3.84	3.72
S97, Intro to Prog. Using C	26	3.85	3.81	3.80	3.72
S97, Intro. to Prog. Methods Using FORTRAN	14	3.77	3.81	3.77	3.72
F96, Intro to Prog. Using C (Section 01)	19	3.44	4.05	3.28	3.97
F96, Intro to Prog. Using C (Section 40)	12	3.92	4.06	4.00	3.97

Supervising PhD students at UIC:

Venkatkumar Srinivasan, Computer Science (currently continued)

Lakshmi Kaligounder, Computer Science (currently continued)

Guru Devanla, Computer Science (currently continued)

Supervising MS thesis at UIC:

Implementation of an Efficient Algorithm for Inferring Haplotype Configuration on Pedigrees

Name of student: Santhoshi Jagadeeshan
Status: Completed Fall 2007

Title: Experimental evaluation of an algorithm in reverse engineering of biological networks

Name of student: Tanu Garg
Status: Completed Summer 2007

Title: Model Driven Developments of Applications Based on Active Objects

Name of student: Paolo Beretta
Status: Completed Spring 2007.

Title: A Survey of the Protein Folding and the Inverse Protein Folding Problems

Name of student: Haripriya Rajamani
Status: Completed Spring 2006

Title: Inapproximability Results for the Lateral Gene Transfer Problem

Name of student: Sergio Ferrarini
Status: Completed Spring 2005

Title: CHISEL: Data Mining Tool for Clustering and Classification of Protein Functions

Name of student: Tanuja Bompada
Status: Completed Fall 2004

Title: Efficient Implementations of Combinatorial Algorithms for String Barcoding Problems in Bioinformatics

Name of student: Venkatram Vishwanath
Status: Completed Fall 2003

Supervising MS projects at UIC:

Title: Compressed Graphs with Floyd-Warshall Algorithm

Name of student: Nihan Tokac
Status: Completed Summer 2012

Title: Parallel processing for protein structure alignment

Name of student: Mounika Mummaneni
Status: Completed Spring 2012

Title: Topology Independent Protein Structural Alignment

Name of student: Swapna Kolachina
Status: Completed Spring 2012

Title: Model of 3-Dimensional Electrocardiogram

Name of student: Tamar Makatsaria
Status: Completed Fall 2011

Title: Measure of Topological Redundancy of Networks

Name of student: Gowri Sangeetha Sivanthan
Status: Completed Fall 2011

Title: Transitive Reductions of Networks

Name of student: Kedsuda Apichonbancha
Status: Completed Fall 2009

Title: Generalizations and Applications of Secretary Problem

Name of student: Pavan K Maguluri
Status: Completed Summer 2008

Title: Random Variables, Strategies, and Hiring Problems

Name of student: Vamseedheeras Kanagala
Status: Completed Spring 2008

Title: A Study on Scheduling Problems

Name of student: Prasanth K. Goriparthi
Status: Completed Spring 2008

Title: The Complexity of Simplex Algorithm for Linear Programming -- A survey

Name of student: Kunduru Charanjithm
Status: Completed Spring 2008

Title: Search Algorithms with Local Sensory Information

Name of student: Vindhya Vunnam
Status: Completed Fall 2006

Title: String Barcoding Problem -- Analysis

Name of student: Sharad Choudhury
Status: Completed Fall 2006

Title: Phylogenetic Networks

Name of student: Nisha Raj Paryani
Status: Completed Fall 2006

Title: A survey on Algorithms for Imprefect Phylogeny Haplotyping (IPPH)

Name of student: Manoj Tulala
Status: Completed Fall 2006

Title: Online Algorithms for Scheduling Packets in Wavelength-Division Multiplexed Optical Networks

Name of student: Vinay Kumar Venkatachalapathy
Status: Completed Summer 2003

Title: Transmission Scheduling in Wavelength Division Multiplexed Optical Networks

Name of student: Balaji Gandhi
Status: Completed Spring 2003

Title: Scheduling Jobs Using the Two Phase Algorithm to Obtain Maximum Throughput

Name of student: Vandana Gummuluru
Status: Completed Spring 2003

Title: Implementation of a Two Phase Algorithm to Improve the Throughput of Off-line Scheduling Problem

Name of student: Gowri Venkatesh
Status: Completed Spring 2003

Title: Finding recurrent sources in sequences

Name of student: Reem Jaglith (Baridi)
Status: Completed Fall 2004

Title: Distributed Algorithm for Connected Sensor Cover Problems

Name of student: Sushma Dokku
Status: Completed Spring 2006

Co-supervising MS projects at UIC:

Title: Online Real-Time Preemptive Scheduling of Jobs With Deadlines on Multiple Machines

Name of student: Ravikumar Subramanian (ECE Graduate student, Primary adviser: Prof. Roland Priemar)
Status: Completed Spring 2003

Supervising Undergraduate Students Projects (CS 398) at UIC:

Title: Airline Reservation Systems

Name of students: Asna M. Khan and Alfonzo Clark
Status: Completed Spring 2010

Services to the department or university at UIC (selected few):

Chair of the Web and Public Relations committee.
Member of the graduate admissions committee
Member of the undergraduate committee.
Served as a member in the PhD thesis defense committee of a student (Andrei Turinsky) in the computer science department in 2002 (thesis title: Balancing cost and accuracy in distributed data mining, thesis adviser: Prof. Robert Grossman).
Served as a member in the PhD thesis defense committee of a student (Yaron Turpaz) in the bioengineering department in 2004 (thesis title: A novel method for discovery of gene function from protein surface patterns without known structures, thesis adviser: Prof. Jie Liang).
Served as a member in the PhD thesis defense committee of a student (Andrew Binkowski) in the bioengineering department in 2004 (thesis title: Inferring Structural and Functional Similarity in Proteins, thesis adviser: Prof. Jie Liang).
Served as a member in the PhD thesis defense committee of a student (Ying Cai) in the ECE department in 2005 (thesis title: Orthogonal Array-based Optimization Methods with Applications to Wireless Systems and Power Systems, thesis adviser: Prof. Derong Liu).

Undergraduate Independent Study projects at Rutgers-Camden:

Name of student:

Curtis Saal

Sem/Year:

Summer 2000 and Fall 2000.

Nature of project:

Implementing algorithms related to binary space partitioning of geometric objects.

Name of student:

Joseph P. Russell

Sem/Year:

Summer 1999 and Fall 1999.

Financial support:

Supported by my current NSF grant.

Nature of project:

Investigating properties of neural networks.

Name of students:

Valentino Lopez and Mingwei Wang.

Sem/Year:

Fall 1998 and Spring 1999.

Financial support:

Supported by a current NSF grant.

Nature of project:

Implementing (in C) an algorithm for State Equivalence in Hybrid PL Systems.

   Name of student:
   Antony Donlon
   Sem/Year:
   Spring 1998.
   Nature of project:
   Independent study on Java.


Services to the department or university at Rutgers-Camden:

Served as an external member in the PhD thesis defense committee of a student (Pirkko Kuusela) in the Mathematics department of Rutgers University (New Brunswick campus) in 1999 (thesis title: Learning Theory Techniques in Control Theory, thesis adviser: Prof. Daniel Ocone).

Participation in the operation of the Scholastic learning committee as a member.

Participation in the operation of faculty senate as a member.

Participation in the revision of the undergraduate curriculum and in the development of the anticipated Master's program in the department.

Acedemic advising and senior review of students.

(Selected) Invited Research Presentations:

"On Measuring and Evaluating Global Stability of Financial Networks", Department of Computer Science, Illinois Institute of Technology, Chicago, April 23, 2013.

"Models and Algorithmic Tools for Computational Processes in Cellular Biology: Recent Developments and Future Directions", Chinese Academy of Sciences, Beijing, China, July 18, 2012.

"Models and Algorithmic Tools for Computational Processes in Cellular Biology: Recent Developments and Future Directions", Northwestern Polytechnical University, Xi�an, China, July 15, 2012.

(Keynote speech) Models and Algorithmic Tools for Computational Processes in Cellular Biology: Recent Developments and Future Directions, in International Symposium on Bioinformatics Research and Applications, May 21-23, 2012

On Vulnerability of Banking Networks, in Mathematical Finance theme, 2012 Annual Meeting of the Canadian Applied and Industrial Mathematics Society, July 24-28, 2012

"Synthesizing and Simplifying Biological Networks from Pathway Level Information", SIAM Conference on Applications of Dynamical Systems, Snowbird, Utah, May 25, 2011.

"On approximating quadratic optimization problems in modularity clustering and stochastic budget optimization", Workshop in Graph Theory and Combinatorics in memory of Uri Peled, Department of Mathematics, Statistics and Computer Science, University of Illinois at Chicago, Chicago, February 21-22, 2010.

"Synthesizing and simplifying biological networks from pathway level information", IEEE International Conference on Bioinformatics & Biomedicine, Washington D.C., November 1-4, 2009.

"Synthesizing and simplifying biological networks from pathway level information", Carnegie Mellon University, October 9, 2009.

"Transitive reduction problems on graphs and Horn formula optimization problems", Department of Computer Science, Columbia University, New York, April 13, 2009.

"Synthesizing and analyzing biological networks", Department of Biology, University of Pennsylvania, March 5, 2009.

"Transitive reductions, Horn formula optimizations and Parallel repetition theorem", DIMACS/CS Light Seminar: Theoretical Computer Science, DIMACS Center, Rutgers University, NJ 08854, December 3, 2008.

"Signal Transduction Network Inference from Double Causal Experimental Evidence", in INFORMS Annual meeting, Washington DC, October 13, 2008.

"Randomized approximations for offline and online set-multicover problems", in Department of Computer Science, University of Maryland, October 10, 2008.

"Synthesizing and Minimizing Signal Transduction (and Social) Networks" , DyDAn Homeland Security Seminar, DIMACS Center, Rutgers University, NJ 08854, October 6, 2008.

"Synthesizing and Minimizing Signal Transduction (and Social) Networks", Mount Sinai School of Medicine, NY 10029, September 30, 2008.

"Synthesizing and Minimizing Signal Transduction (and Social) Networks", Department of Industrial and Systems Engineering, Rutgers University, NJ 08854, September 16, 2008.

"On Approximating Four Covering and Packing Problems with applications to Bioinformatics", in Department of Computer Science, University of Toronto, Canada, July 21, 2008.

"On Approximating Four Covering and Packing Problems with applications to Bioinformatics", in Department of Computer Science, University of Waterloo, Waterloo, Canada, July 18, 2008.

"Reverse Engineering of Networks Via the Modular Response Analysis Method", in Networks: Biological, Social and Internet Workshop, 2008 SIAM Annual Meeting, San Diego, CA, July 11, 2008.

"Randomized approximations for offline and online set-multicover problems", Department of Computer Science, Universität Bonn, Bonn, Germany, January 2008.

"Signal Transduction Network Inference from Indirect Experimental Evidence", Department of Computer Science, Illinois Institute of Technology, Chicago, October, 2007.

"Signal Transduction Network Inference from Indirect Experimental Evidence", Department of Computer Science, Pennsylvania State University, University Park, PA 16802, July 27, 2007.

"A Novel Method for Signal Transduction Network Inference from Indirect Experimental Evidence", 1^st Bertinoro Systems Biology Meeting, Bertinoro, Italy, May 20-25, 2007.

"A Novel Method for Signal Transduction Network Inference from Indirect Experimental Evidence", DIMACS Workshop on Discrete Mathematical Problems in Computational Biomedicine New Brunswick, NJ, April 20, 2007.

"Randomized Approximation Algorithms for Set Multicover Problems with Applications to Reverse Engineering of Protein and Gene Networks", minisymposium on Identifiability and Inference in Biochemical Pathways, 2006 SIAM Conference on Life Sciences, Raleigh, NC, August 3, 2006.

"Grouped String Barcoding and related problems", DIMACS Workshop on Combinatorial Group Testing, DIMACS Center, Rutgers University, Piscataway, NJ, May 18, 2006.

"Inferring (Biological) Signal Transduction Networks via Transitive Reductions of Directed Graphs", Department of Computer Science, University of Connecticut, Storrs, CT, April 7 2006.

"Randomized Approximation Algorithms for Offline and Online Set Multicover Problems" , Toyota Technological Institute at Chicago, Chicago, IL March 3 2006.

"On Approximate Consistent Labeling of Biological Dynamical Systems", IEEE-EMBC 2005 Satellite Symposium on Bioinformatics and Computational Biology, Jiaotong University, Shanghai, China, August 30, 2005.

Invited tutorial on systems biology to selected undergraduate/graduate students in 5th International Summer School on Biocomplexity from System to Gene, Dartmouth College, Hanover, NH, June 28, 2005.

"Several Geometric Tiling and Packing Problems With Applications", Department of Computer Science, University of Massachusetts, Amherst, MA, November 22, 2004.

"Randomized Approximation Algorithms for Set Multicover Problems with Applications to Reverse Engineering of Protein and Gene Networks", Symposium on Computational Science of Biomolecules: Applications in Medicine and Therapeutics, University of Illinois at Chicago, October 8, 2004.

"Several Geometric Tiling and Packing Problems With Applications", Department of Computer Science, University of Wisconsin at Milwaukee, Milwaukee, WI, September 26, 2003.

"Several Geometric Tiling and Packing Problems With Applications", Department of Computer Science, Pennsylvania State University, University Park, PA 16802, February 27, 2003.

"Several Geometric Tiling and Packing Problem With Applications To Nonoverlapping local alignments, DNA microarray designs and Homology Searches", Department of Computer Science, Illinois Institute of Technology, Chicago, November 4, 2002.

"Algorithmic Problems Related to Sequences and Phylogentic Trees", UIC-UIUC Symposium on Bioinformatics in Medicine and Biology, April 13, 2002.

"Throughput Maximization Problems in Real-time Scheduling", Department of Mathematics/Computer Science, University of Osnabrück, Germany, September 8, 2000.

"On Approximate Learning by Multi-layered Feedforward Circuits", in the NeuroCOLT Workshop New Perspectives in the Theory of Neural Nets (organized by Prof. Wolfgang Maass), Schloß St. Martin, Graz, Austria, May 5, 2000.

"Improvements in Throughput Maximization for Real-Time Scheduling", Department of Computer Science, Yale University, New Haven, CT 06511, January 31, 2000.

"On Computing Distances Between Evolutionary Trees", DIMACS Workshop on Discrete Mathematical Problems and Medical Applications, DIMACS Center, Rutgers University, Piscataway, NJ, December 8 - 10, 1999.

"Provably Good Algorithms for Transmission Scheduling in WDM Optical Networks", in Department of Computer Science, University of Waterloo, Waterloo, CANADA; July 1999.

"On distances between phylogenetic trees", DIMACS Workshop on Computational Biology as part of the 50th Anniversary for ENIAC, Princeton University, May 17 - 19, 1996.

"Complexity of Algorithms (in Segmented-Channel Routing)", CALCE Electronic Packaging Research Center, University of Maryland, College Park, USA; September 19, 1995.

"Analog versus Discrete Neural Networks", Department of Computer Science, McMaster University, Hamilton, CANADA; June 1995.

"Analog versus Discrete Neural Networks", Department of Computer Science & Engineering, IIT Kharagpur, India; April 1995.

"Approximation by Neural Networks", Workshop in Advances in Neural Information Processing Systems 4, Vail, Colorado; December 1991.

"Approximation and Learning by Neural Networks with Continuous Activation Functions", Workshop in Advances in Neural Information Processing Systems 6, Vail, Colorado; December 1993.

"Segmented-Channel Routing Problems", Department of Electrical Engineering, Purdue University; July 1993.

Honors/Affiliations etc.:

NSF CAREER grant, 2004

UIC COE Faculty Teaching Award, 2012

Senior Member of IEEE

Member of ACM, SIGACT (special interest group on Algorithms and Complexity Theory in ACM)

Past member of SIAM
Other Professional Activities:

Organizing workshops

DIMACS Workshop on Information Processing by Protein Structures in Molecular Recognition, June 13 - 14, 2005, DIMACS Center, CoRE Building, Rutgers University (co-organizer: Jie Liang)

Program committee activities

Chair

Best Student Paper Competition Chair, 2014 IEEE World Congress on Computational Intelligence, Beijing, China, July 6-11, 2014.
Organizing Committee co-Chair, 2013 International Conference on Brain Inspired Cognitive Systems, Beijing, China, June 9-11, 2013.
Program Co-Chair, 5^th International Conference on Bioinformatics and Computational Biology (BICoB), Hawaii, March 4-6, 2013.
Plenary Sessions co-Chair, 9^th International Symposium on Neural Networks, Shenyang, China, July 11-14, 2012
Co-Program Chair, 2011 International Symposium on Neural Networks (ISNN) , Gullin, China, May 29-June 1, 2011.
Co-Vice Chair, Cross-Cutting Computational Methods and Bioinformatics Infrastructure track, 2009 IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2009), Washington DC, November 1-4, 2009.
Finance chair, 2009 IEEE/INFORMS International Conference on Service Operations, Logistics and Informatics (SOLI), Chicago, IL, July 22-24, 2009.
Workshop co-Chair, 9^th IEEE International Conference on Bioinformatics and Bioengineering (BIBE 2009), Taichung, Taiwan, June 22-24, 2009.
Finance chair, 2008 IEEE International Conference on Networking, Sensing and Control, International Asia Pacific Convention Center and HNA Resort Sanya, China, April 6-8, 2008.
Registration co-chair of fourth International Symposium on Neural Networks, June 3-7, 2007, Nanjing, China.
Co-Chair of the Algorithm and software system for bioinformatics technical track (Track 3.1) of the Computational Biology and Bioinformatics theme (Theme 3) of the 28th Annual International Conference IEEE Engineering in Medicine and Biology Society (EMBS 2006), August 30--Spetember 3, 2006, New York City, NY.
Co-Chair (with Dong Xu) of the Algorithm and software system for bioinformatics technical track (Track 11.1) of the Computational Biology and Bioinformatics theme (Theme 11) of 27^th Annual International Conference IEEE Engineering in Medicine and Biology Society (EMBS'05), September 1-4, 2005, Shanghai, Chiana.
Co-Chair (with Dong Xu) of the Algorithm and software system for bioinformatics technical track of the 26^th Annual International Conference IEEE Engineering in Medicine and Biology Society (EMBS'04), Bioinformatics and Computational Biology Theme (Theme 6), September 1-5, 2004, San Francisco, USA.
Here is the call for papers for this theme.

Program committee member

3^rd IEEE International Conference on Computational Advances in Bio and medical Sciences (ICCABS), June 12-14, 2013, New Orleans, LA.
IASTED International Conference on Advances in Computer Science and Engineering (ACSE 2013), April 10-12, 2013, Phuket, Thailand.
23^rd International Symposium on Algorithms and Computation (ISAAC), National Taiwan University, Taipei, Taiwan, December 19-21, 2012.
23^rd International Conference on Genome Informatics (GIW), Tainan, Taiwan, December 12-14, 2012
2012 IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2012), Philadelphia, October 4-7, 2012.
International Symposium on Network Enabled Health Informatics, Biomedicine and Bioinformatics, Istanbul, Turkey, August 27-28, 2012.
8^th International Symposium on Bioinformatics Research and Applications (ISBRA), May 21-23, 2012, Dallas,Texas.
7^th IASTED International Conference on Advances in Computer Science and Engineering (ACSE 2012), April 2-4, 2012. Phuket, Thailand.
4^th International Conference on Bioinformatics and Computational Biology (BICoB-2012), Las Vegas, Nevada, March 12 -14, 2012.
2^nd IEEE International Conference on Computational Advances in Bio and Medical Sciences (ICCABS), February 23-25, 2012, Las Vegas, Nevada.
Foundations of Computer Science track, 38^th International Conference on Current Trends in Theory and Practice of Computer Science (SOFSEM 2012), Spindleruv Mlyn, Czech Republic, January 21-27, 2012.
IEEE International Conference on Bioinformatics & Biomedicine (BIBM), Atlanta, GA, 12-15 November 2011.
5^th International Conference on Combinatorial Optimization and Applications (COCOA), Zhangjiajie, China, August 4-6, 2011.
The 6^th International Conference on Future Information Technology (FutureTech 2011), Crete, Greece, June 28-30, 2011.
7^th International Conference on Algorithmic Aspects in Information and Management (AAIM), Jinhua, China, May 28-31, 2011.
7^th International Symposium on Bioinformatics Research and Applications (ISBRA 2011), Changsha, China, May 27-29, 2011.
2011 IEEE Symposium on Foundations of Computational Intelligence (FOCI'2011) . Paris, France, April 11-15, 2011.
3^rd International Conference on Bioinformatics and Computational Biology (BICoB-2011), New Orleans, Louisiana, March 23-25, 2011.
IEEE International Conference on Bioinformatics & Biomedicine, Hong Kong, 19-22 Dec 2010.
10^th Workshop on Algorithms in Bioinformatics (WABI), University of Liverpool, UK, 6-8 September 2010.
8^th International Bioinformatics Workshop (IBW2010), Wuhan University, Wuhan, China , June 4-6, 2010.
FutureTech 2010, Busan, Korea, May 21-23, 2010.
Algorithms and Bioinformatics Track, 2010 ACS/IEEE International Conference on Computer Systems and Applications, Hammamet, Tunisia, May 16-19th, 2010.
2010 IEEE International Conference of Networking, Sensing and Control, Chicago, April 11-13, 2010.
2^nd International Conference on Bioinformatics and Computational Biology (BICoB-2010), Honolulu, Hawaii, March 24-26 2010.
IASTED International Conference on Advances in Computer Science and Engineering (ACSE 2010), Sharm El Sheikh, Egypt, March 15-17, 2010.
20^th International Symposium on Algorithms and Computation (ISAAC 2009), Oahu, Hawaii, December 16-18, 2009.
20^th International Conference on Genome Informatics (GIW2009), Pacifico Yokohama, Japan, December 14-16, 2009.
8^th Computational Systems Bioinformatics Conference (CSB 2009), Stanford, CA, August 10-13, 2009.
5^th International Symposium on Bioinformatics Research and Applications (ISBRA 2009), Ft. Lauderdale, Florida, May 13-May 16, 2009.
3^rd International Frontiers of Algorithmics Workshop (FAW 2009), Hefei, China, June 20-23, 2009.
15^th International Conference on Computing and Combinatorics (COCOON'2009), Niagara Falls, New York, U.S.A., July 13--15, 2009.
1^st International Conference on Bioinformatics and Computational Biology (BICoB2009), New Orleans, March 25-27, 2009.
The IASTED International Conference on Computational Biology and Bioinformatics (CBB 2008), Orlando, Florida, November 16-18, 2008.
19^th International Conference on Genome Informatics (GIW2008), Brisbane, Queensland, Australia, December 1-3, 2008.
2008 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), Philadelphia, PA, November 7-9, 2008.
The International Conference on Wireless Algorithms, Systems and Applications (WASA'08), October 26-28, 2008, Dallas, TX.
4^th International Symposium on Bioinformatics Research and Applications, Atlanta, GA, May 6-8, 2008.
Second International Frontiers of Algorithmics Workshop (FAW'08), Changsha, China, June 19-21, 2008.
Third International Conference on Algorithmic Aspects in Information and Management, Portland, Oregon, June 20-22, 2007.
2007 International Symposium on Bioinformatics Research and Applications, May 6--9, 2006, Atlanta, GA.
2007 IEEE International Conference On Networking, Sensing and Control, London, United Kingdom, April 15-17, 2007.
The IASTED International Conference on Computational and Systems Biology , November 13-15, 2006, Dallas, Texas.
18th annual IEEE International Conference on Tools with Artificial Intelligence (ICTAI), 13th--15th November, 2006, Washington D.C.
2nd International Workshop on Bioinformatics Research and Applications (IWBRA 2006) University of Reading, UK, May 28-31, 2006.
2006 IEEE International Conference on Networking, Sensing and Control, Ft. Lauderdale, Florida, April 23-25, 2006.
4^th Asia Pacific Bioinformatics Conference (APBC), 13--16 February, 2006, Taiwan.
17^th annual IEEE International Conference on Tools with Artificial Intelligence (ICTAI), 14th--16th November, 2005, Hong Kong.
Intelligent Systems in Design and Manufacturing VI (SA108), 23-26 October, 2005, Boston, MA.
11th International Computing and Combinatorics Conference (COCOON 2005), August 16-19, 2005, Kunming, Yunnan, P. R. China.
2005 International Workshop on Bioinformatics Research and Applications, Emory University, Atlanta, GA, May 22-25, 2005 (in conjunction with International Conference on Computational Science 2005).
The 16th IEEE International Conference on Tools with Artificial Intelligence, November 15-17, 2004 Boca Raton, Florida.
2nd International Workshop on Biological Data Management (BIDM 2004) , September 1, 2004, Zaragoza, Spain.

Local organizing committee member

Symposium on Theory of Computing (STOC 2004) , 13-15 June, 2004, Chicago, IL.

Chairing sessions in conferences/workshops (selected few)

DIMACS Workshop on Discrete Mathematical Problems and Medical Applications, DIMACS Center, Rutgers University, Piscataway, NJ, December 8-10, 1999
2004 American Control Conference (ACC 2004), Boston MA, July 2004
26th Annual International Conference IEEE Engineering in Medicine and Biology Society (EMBS 2004), San Francisco CA, September 2004
27th Annual International Conference IEEE Engineering in Medicine and Biology Society (EMBS 2005), Shanghai, August-September 2005
28th Annual International Conference IEEE Engineering in Medicine and Biology Society (EMBS 2006), New York, NY, August-September 2006
DIMACS Workshop on Discrete Mathematical Problems in Computational Biomedicine New Brunswick, NJ, April 20, 2007.

External committee membership outside UIC

Served as an external member in the PhD thesis defense committee of a student (Kelly Westbrooks) in the Computer Science department of Georgia State University in April 2009 (thesis title: Biological Inference Using Flow Networks, adviser: Prof. Alexander Zelikovsky).
Served as an external member in the PhD thesis defense committee of a student (Mannan Sanghi) in the Electrical Engineering & Computer Science department of Northwestern University in April 2006 (thesis title: Sequence Design and Discovery, adviser: Prof. Ming-Yang Kao).