CURRICULUM VITAE
Alexander Zelikovsky
Professor
Department of Computer Science
Georgia State University
Office: 1443, Peachtree Str. 34
Phone: (404) 413 5730
Fax: (404) 413-5717
E-mail: alexz@cs.gsu.edu
Web page: http://www.cs.gsu.edu/~cscazz
Personal Data
Date of Birth:
Sex:
Citizenship:
03/25/1960
Male
U. S. A.
Education
03/89
09/82
09/80
Ph.D. in Computer Science, Institute of Mathematics, Byelorussian Academy of
Sciences, Minsk, Belarus
M. S. in Computer Science and Mathematics, Department of Mathematics and
Cybernetics, Moldova State University, Kishinev, Moldova
B. S. in Mathematics, Department of Mathematics and Cybernetics, Moldova
State University, Kishinev, Moldova
Professional Experience
08/09–
08/04-07/09
01/99-07/04
09/97-01/99
11/95-09/97
09/95-11/95
01/89-09/95
04/90-09/95
12/88-03/90
09/82-11/85
Professor, Department of Computer Science,
Georgia State University, Atlanta, Georgia
Associate Professor, Department of Computer Science,
Georgia State University, Atlanta, Georgia
Assistant Professor, Department of Computer Science,
Georgia State University, Atlanta, Georgia
Postdoctoral Scholar, Computer Science Department,
University of California at Los Angeles, Los Angeles, California
Research Scientist, Computer Science Department,
University of Virginia, Charlottesville, Virginia
Visitor, Intl Computer Science Institute,
University of California at Berkeley, California
Senior Research Scientist, Department of Mathematics and Cybernetics,
Moldova State University, Kishinev, Moldova
Senior Research Scientist, Institute of Mathematics,
Moldova Academy of Sciences, Kishinev, Moldova
Junior Research Scientist, Institute of Mathematics,
Moldova Academy of Sciences, Kishinev, Moldova
Software Engineer, Institute of Mathematics,
Moldova Academy of Sciences, Kishinev, Moldova
Research Interests
Bioinformatics, Discrete Algorithms and Combinatorial Optimization; Ad Hoc and Sensor
Networks; Computer-Aided Design for Very Large System Integration: Physical Design & Design
for Manufacturing; Computational Biology; Graph Theory; Computational Geometry.
Funding
Internal Grants
1. GSU Research Initiation Grant “New Approaches in Optimizing Layout Manufacturability”,
$5,000, 1999-2000, PI
2. GSU Research Initiation Grant “Computational Methods for Genetic Association Search and
Susceptibility Prediction for Common Diseases”, $10,000, 2007-2008, PI
3. GSU Team Grant $15,000, 2009-2010, co-PI
External Grants
1. LifeTech Grant “Viral Metagenome Reconstruction Software for Ion Torrent PGM Sequencer”
$30K, 07/01/2012-30/06/2013, PI
2. NSF Grant IIS-1116001 “Travel Support: 7th International Symposium on Bioinformatics
Research and Applications, ” $20K, 04/01/2011-03/31/2013, PI
3. Subcontract of National Institute of Food and Agriculture award 2011-67016-30331
“Bioinformatics tools for viral quasispecies reconstruction from next-generation sequencing
data and vaccine optimization”, $120K, 3/01/2011-2/28/2014, PI
4. NSF Grant IIS-0916401 “III: Small: Collaborative Research: Reconstruction of Haplotype
Spectra from High-Throughput Sequencing Data”, $224K, 9/01/2009-8/01/2013, PI
5. U.S. Civilian Research & Development Foundation Award #MOM2-3049-CS-03 ``Algorithms
for Solving Optimization problems on Networks’’ $5.5K, 07/01/2005-06/30/2007, PI
6. NSF Grant CCF-0429735 ``Collaborative Research: New Directions for Advanced VLSI
Manufacturability'', $93K, 8/15/2004-7/31/2007, PI
7. Subcontract of NIH Award 1 P20 GM065762-01A1, $36K, 9/01/2003-8/31/2006, PI
8. U.S. Civilian Research & Development Foundation Award #MM2-3018 ``Algorithms for
Solving Optimization problems on Networks’’ $4K, 09/01/2001-05/31/2003, PI
9. Subcontract of NSF Grant CCR-9988331``Research in Layout Optimization for Advanced
Manufacturability Considerations'', $127K, 8/15/2000-7/31/2004, PI
10. Yamacraw, State of Georgia Grant "A Middleware for Collaborative Applications and
Handheld Devices", $318K, 07/01/2002 – 2004, co-PI.
Honors/Awards
1.
2.
3.
4.
5.
6.
Society of Industrial & Applied Mathematics (SIAM) Outstanding Paper Prize, 2007.
Best Poster Award, Fifth Georgia Tech Intl Conf on Bioinformatics, November 2005.
Best Poster Award, 25th BACUS Symp on Photomask Technology and Management, 2005.
Best Paper Award, Joint Intl VLSI Design / Asia & South Pacific Design Autom Conf, 2002.
Humboldt Scholarship, Saarbrücken, Germany, 1995
Moldova Academy of Sciences Young Investigator Award, Kishinev, Moldova, 1993
Professional Service
Conference Chair
1.
2.
3.
4.
5.
6.
7.
8.
9.
10.
11.
(Publication) IEEE Intl Conference on Bioinformatics and Biomedicine (BIBM 2011)
Workshop on Computational Advances in Molecular Epidemiology (CAME 2011)
Workshop on Computational Advances in Next-Generation Sequencing (CANG 2011-12)
(Workshop) IEEE Intl Conference on Bioinformatics and Biomedicine (BIBM 2009)
Workshop on Computational Issues in Genetic Epidemiology (CIGE 2008, 2009)
Intl Symposium/Workshop on Bioinformatics Research and Applications (ISBRA’05-11)
(Publication) IEEE Intl Symposium on Bioinformatics and Bioengineering (BIBE’07)
ACIS Intl Workshop on Self-Assembling Wireless Networks (SAWN’05, ’06, ’07)
Intl Workshop on Bioinformatics Research and Applications (IWBRA’05, ’06)
(Poster) SECABC Workshop on Biocomputing 2005
(Session) Intl Symposium on Mathematical Programming (ISMP 2000)
Program Committee Member
1. RECOMB Satellite Workshop on massively parallel sequencing (RECOMB-seq 2012)
2. Workshop on Algorithms in Bioinformatics (WABI 2011-12)
3.
4.
5.
6.
7.
8.
9.
10.
11.
12.
13.
14.
15.
16.
17.
Intl Computer Science Symposium in Russia (CSR 2010)
Intl Conference on Bioinformatics and Computational Biology (BICoB 2009-11)
IEEE Intl Workshop on Wireless Network Algorithm and Theory (2009)
ACM Intl Workshop on Foundations of Wireless Ad Hoc and Sensor Networking and
Computing (FOWANC 2009)
Brazilian Symposium on Bioinformatics (BSB 2009-11)
17th Intelligent Systems for Molecular Biology / 8th European Symposium on Computational
Biology, Population Genomics Track (ISMB/ECCB 2009)
The 6th Workshop on Algorithms and Models for the Web Graph (WAW 2009)
Intl Conference on BioMedical Engineering and Informatics (BMEI2008)
Intl Conference on Wireless Algorithms, Systems and Applications (WASA'08)
IEEE Intl Conference on Bioinformatics and Biomedicine (BIBM 2007-2009,11)
Intl Conference on Combinatorial Optimization and Applications (COCOA 2007, 2010)
ACM Intl Workshop On System-Level Interconnect Prediction (SLIP’02, ’07, ’08)
Annual Intl Computing and Combinatorics Conference (COCOON’07)
Intl Workshop on Mobile Ad-hoc and Ubiquitous Sensor Networks (MASN’05)
Intl Workshop on Approximation Algorithms for Comb. Optimization Problems (APPROX’02)
Panelist
1. NSF: 7/12, 12/10, 04/08, 01/07, 10/05, 03/05, 02/05
2. NIH: 09/06
3. UC-Labs 04/12
Editorial Activity
Editorial Board Member
1.
2.
3.
4.
5.
6.
7.
Intl Journal of Bioinformatics Research and Applications, Inderscience Publishers, 2006Advances in Bioinformatics, Hindawi Publishing Corporation, 2008 –
Advanced Studies in Biology, Hikari Ltd, 2009Discrete Mathematics, Algorithms and Applications, World Scientific, 2009 –
Journal of Biomedicine and Biotechnology, Hindawi Publishing Corporation, 2008 –
Intl Journal of Data Mining and Bioinformatics, Inderscience Publishers, 2009Frontiers in Statistical Genetics and Methodology, 2011-
Special Issue/Section Guest Editor
1. BMC Bioinformatics, Volume 13 Supplement 10, (2012)
2. BMC Proceedings, Volume 5, Supplement 5, (2011)
3. IEEE/ACM Trans. on Computational Biology and Bioinformatics, 9(4) (2012), 8(4) (2011),
6(2) (2009), 5(3) (2008), 4(4) (2007)
4. International Journal on Sensor Networks, 6(1) (2009)
5. Journal of Universal Computer Science, 13(1) (2007)
6. IEEE Trans. on Nanobioscience, 6(1) (2007)
Patents
[P1]
C. Albrecht, A. B. Kahng, I. Mandoiu and A. Zelikovsky, "Floorplan Evaluation with TimingDriven Global Wireplanning, Pin Assignment and Buffer/Wire Sizing," United States Patent
#7,062,743, June 2006.
Publications
(Inverse chronological order, the authors are in the alphabet order except for papers in bioinformatics)
Edited Books & Proceedings
J. Chen, J. Wang and A.Z. Zelikovsky (Eds.), Proceedings of 7rd International Symposium
on Bioinformatics Research and Applications, Springer-Verlag, Lecture Notes in
Bioinformatics 6674, 2011.
[B2] I.I. Mandoiu and A.Z. Zelikovsky (Eds.), Bioinformatics Algorithms: Techniques and
Applications, John Wiley & Sons, 2008.
[B1]
I.I. Mandoiu, R. Sunderraman and A.Z. Zelikovsky (Eds.), Proceedings of 4rd International
Symposium on Bioinformatics Research and Applications, Springer-Verlag, Lecture Notes
in Bioinformatics 4983, 2008.
[B4] I.I. Mandoiu and A.Z. Zelikovsky (Eds.), Proceedings of 3rd International Symposium on
Bioinformatics Research and Applications, Springer-Verlag, Lecture Notes in Bioinformatics
4463, 2007.
[B5] A.Z. Zelikovsky (Ed.), LNCS Transactions on Computational Systems Biology, Volume II,
Springer, Lecture Notes in Bioinformatics 3680, 2005.
[B3]
Editorials in Journals
[E1]
[E2]
[E3]
[E4]
[E5]
[E6]
[E7]
[E8]
[E9]
J. Chen, I. Mandoiu, R. Sunderraman, J. Wang, A. Zelikovsky, "Guest Editors'
Introduction," BMC Bioinformatics 13(Suppl10):S1 (2012).
J. Chen and A. Zelikovsky, “Guest Editors’ Introduction to the Special Section on
Bioinformatics Research and Applications,” IEEE/ACM Transactions on Computational
Biology and Bioinformatics (TCBB), 9(4) (2012) pp. 1002-1003.
M. Borodovsky, T. M. Przytycka, S. Rajasekaran, and A. Zelikovsky, “Guest Editors’
Introduction to the Special Section on Bioinformatics Research and Applications,”
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB), 8(4) (2011),
865-866.
Yingshu Li, I.I. Mandoiu and A. Zelikovsky, “Editorial,” International Journal on Sensor
Networks, 6(1) (2009), pp. 1-2.
I.I. Mandoiu, Yi Pan, R. Sunderraman and A. Zelikovsky, “Guest Editors' Introduction to the
Special Section on Bioinformatics Research and Applications,” IEEE/ACM Transactions on
Computational Biology and Bioinformatics (TCBB), 6(2) (2009), pp. 178-179.
I.I. Mandoiu, Yi Pan and A. Zelikovsky, “Guest Editors' Introduction to the Special Section
on Bioinformatics Research and Applications,” IEEE/ACM Transactions on Computational
Biology and Bioinformatics (TCBB), 5(3) (2008), pp. 321-322.
I.I. Mandoiu, Yi Pan and A. Zelikovsky, “Guest Editors' Introduction to the Special Section
on Bioinformatics Research and Applications,” IEEE/ACM Transactions on Computational
Biology and Bioinformatics (TCBB), 4(4) (2007), pp. 513-514.
I.I. Mandoiu, Yi Pan and A. Zelikovsky, “Introduction to the Special Section on
Computational Nanobioscience,” IEEE Transactions on NanoBioscience, 6(1) (2007), 1-3.
G. Călinescu, I.I. Măndoiu, A. Zelikovsky and M. Zimand, “Selected Papers from the 1st
ACIS International Workshop on Self-Assembling Wireless Networks,” Journal of Universal
Computer Science, 13(1) (2007), pp. 1-3.
Book Chapters
[C1] G. Robins and A.Z. Zelikovsky, “Minimum Steiner Tree Construction,” in C. J. Alpert, D. P.
[C2]
[C3]
[C4]
[C5]
[C6]
[C7]
Mehta, and S. S. Sapatnekar, editors, The Handbook of Algorithms for VLSI Physical
Design Automation, CRC Press, 2009, 487-508.
Q. Cheng and A. Zelikovsky, “Network Mapping of Metabolic Pathways,” in M. Dehmer
and F. Emmert-Streibto (eds.), Analysis of Complex Networks: From Biology to Linguistics,
WILEY-VCH Verlag GmbH & Co., 2009, 271-293.
D. Brinza, J. He, and A. Zelikovsky, “Optimization Methods for Genotype Data Analysis in
Epidemiological Studies,” In I.I. Mandoiu and A.Z. Zelikovsky, editors, Bioinformatics
Algorithms: Techniques and Applications, Wiley, 2008, pp. 395- 415.
A.B. Kahng, I.I. Mandoiu, and A.Z. Zelikovsky, “Practical approximations of Steiner trees in
uniform orientation metrics,” In T.E. Gonzalez, editor, Approximation Algorithms and
Metaheuristics. CRC Press, 2007, pp. 43-1 – 43-13.
I.I. Mandoiu, A. Olshevsky, and A.Z. Zelikovsky, “QoS multimedia multicast routing,” In
T.E. Gonzalez, editor, Approximation Algorithms and Metaheuristics. CRC Press, 2007, pp. 711 – 71-16.
C. Albrecht, A.B. Kahng, I.I. Mandoiu, and A.Z. Zelikovsky, “Multicommodity flow
algorithms for buffered global routing,” In T.E. Gonzalez, editor, Approximation Algorithms and
Metaheuristics. CRC Press, 2007, pp. 80-1 – 80-18.
A.B. Kahng, I.I. Mandoiu, S. Reda, X. Xu, and A.Z. Zelikovsky, “Computer-aided
optimization of dna array design and manufacturing,” In K. Chakrabarty and J. Zeng,
[C8]
[C9]
[C10]
[C11]
editors, Design Automation Methods and Tools for Microfluidics-Based Biochips. Springer
Verlag, 2006, pp. 235-269.
P. Berman, G. Calinescu, C. Shah and A. Zelikovsky, "Efficient Energy Management in
Sensor Networks," In Ad Hoc and Sensor Networks, Wireless networks and Mobile
Computing Vol. 2, Y. Xiao and Y. Pan (Eds.), Nova Science Publishers, 2006, pp. 71-90.
A. Zelikovsky, “Bottleneck Steiner Tree Problems,” In Encyclopedia of Optimization, C. A.
Floudas and P. M. Pardalos eds., June 2001, Kluwer Academic Publishers.
P. Berman and A. Zelikovsky, “On the Approximation of Power-p and Bottleneck Steiner
Trees,” In: Advances in Steiner Trees, D-Z. Du, J.H. Rubinstein and J.M. Smith eds.,
Kluwer Academic Publishers, 2000, pp. 117-135.
M. Karpinski and A. Zelikovsky, “Approximating Dense Cases of Covering Problems,” In
DIMACS Workshop on Network Design: Connectivity and Facilities Location, Princeton
University, DIMACS series in Discrete Mathematics and Theoretical Computer Science 40,
1998, pp. 169-178.
Journal Articles
[J1]
[J2]
[J3]
[J4]
[J5]
[J6]
[J7]
[J8]
[J9]
[J10]
[J11]
[J12]
[J13]
[J14]
[J15]
N. Mancuso, B. Tork, P. Skums, L. Ganova-Raeva, I.I. Mandoiu and A. Zelikovsky,
"Reconstructing viral quasispecies from NGS amplicon reads, In Silico Biology 11, pp. 237249, (2012)
Mangul, A. Caciula, O. Glebova, I.I. Mandoiu and A. Zelikovsky, “Improved transcriptome
quantification and reconstruction from RNA-Seq reads using partial annotations,” In Silico
Biology 11, pp. 251-261, (2012)
P. Skums, Z. Dimitrova, D. S. Campo, G. Vaughan, L. Rossi, J. C. Forbi, J. Yokosawa, A.
Zelikovsky, Y. Khudyakov, "Efficient error correction for next-generation sequencing of
viral amplicons," BMC Bioinformatics 13 (Suppl10):S6 (2012).
G. Calinescu, C. G. Fernandes, H. Kaul and A. Zelikovsky. “Maximum Series-Parallel
Subgraph,” Algorithmica 63:137-157 (2012),
I. Astrovskaya, B. Tork, S. Mangul, K. Westbrooks, I. Mandoiu, P. Balfe and A. Zelikovsky,
“Inferring Viral Quasispecies Spectra from 454 Pyrosequencing Reads,” BMC
Bioinformtaics 12(Suppl 6):S1 (2011).
M. Nicolae, S. Mangul,
I.I. Mandoiu and
A. Zelikovsky,”Estimation
of
alternative
splicing isoform frequencies from RNA-Seq data”, Algorithms for Molecular Biology 6:9
(2011).
Q. Cheng and A. Zelikovsky, Combinatorial Optimization Algorithms for Metabolic
Networks Alignments and Their Applications,” International Journal of Knowledge Discovery
in Bioinformatics (IJKDB) 2(1):1-23 (2011).
B. Pasaniuc, R. Garfinkel, I. Mandoiu and A. Zelikovsky, “Optimal Testing of Digital
Microfluidic Biochips,” INFORMS Journal of Computing 23(4):518-529 (2011).
Q. Cheng, R. Harrison and A. Zelikovsky, “MetNetAligner: a web service tool for metabolic
network alignments,” Bioinformatics, 25(15):1989-1990 (2009).
D. Brinza and A. Zelikovsky, “2SNP: Scalable Phasing Method for Trios and Unrelated
Individuals,” Journal of IEEE/ACM Transactions on Computational Biology and
Bioinformatics (TCBB), 6(1):313-318 (2008).
D. Brinza and A. Zelikovsky, “Design and Validation of Methods Searching for Risk Factors
in Genotype Case-Control Studies,” Journal of Computational Biology 15(1):81-90 (2008).
I.M. Nolte, A.R. de Vries, G.T. Spijker, R.C. Jansen, D. Brinza, A. Zelikovsky, and G.J. te
Meerman, “Association testing by haplotype-sharing methods applicable to whole-genome
analysis,” BMC Proceedings 1(Suppl 1):S129 (2007).
R. Albert, B. DasGupta, R. Dondi, E. Sontag, A. Zelikovsky, K. Westbrooks, "A Novel
Method for Signal Transduction Network Inference from Indirect Experimental Evidence",
Journal of Computational Biology 14(7):927-949 (2007).
N. Hundewale, S. Jung and A. Zelikovsky, “Energy Efficiency of Load Balancing in MANET
Routing Protocols,” Journal of Universal Computer Science, 13(1):110-132 (2007).
J. He and A. Zelikovsky, "Informative SNP Selection Based on SNP Prediction", IEEE
Transactions on NanoBioscience 6(1):60-67 (2007).
[J16] A. B. Kahng, I. I. Mandoiu, X. Xu and A. Zelikovsky, "Enhanced Design Flow and
[J17]
[J18]
[J19]
[J20]
[J21]
[J22]
[J23]
[J24]
[J25]
[J26]
[J27]
[J28]
[J29]
[J30]
[J31]
[J32]
[J33]
[J34]
[J35]
[J36]
Optimizations for Multi-Project Wafers", IEEE Transactions on Computer-Aided Design of
Integrated Circuits and Systems, 26(2):301-311 (2007).
C. Chiang, A. B. Kahng, S. Sinha, X. Xu, and A. Zelikovsky, "Fast and Efficient Bright-Field
AAPSM Conflict Detection and Correction," IEEE Transactions on Computer-Aided Design
of Integrated Circuits and Systems, 26(1):115-126 (2007).
J. He and A. Zelikovsky, “MLR-Tagging: Informative SNP Selection for Unphased
Genotypes Based on Multiple Linear Regression,” Bioinformatics, 22(20):2558–61 (2006).
E. Althaus, G. Calinescu, I. Mandoiu, S. Prasad, N. Tchervenski and A. Zelikovsky, "Power
Efficient Range Assignment for Symmetric Connectivity in Ad-hoc Wireless Networks,"
Wireless Networks, 12(3):287-299 (2006).
A. B. Kahng, I. I. Mandoiu, S. Reda, X. Xu and A. Zelikovsky, "Computer-Aided
Optimization of DNA Array Design and Manufacturing," IEEE Transactions on ComputerAided Design of Integrated Circuits and Systems, 25(2):305-320 (2006).
D. Brinza and A. Zelikovsky, "2SNP: Scalable Phasing Based on 2-SNP Haplotypes,"
Bioinformatics, 22(3):371-373 (2006).
D. Lozovanu, D. Solomon, and A. Zelikovsky, "Multiobjective games and determining
Pareto-Nash equilibria,” Buletinul Academiei de Stiinte a Republicii Moldova, Math, 3(49):
115-122 (2005).
J. He, K. Westbrooks and A. Zelikovsky, "Linear Reduction Methods for Tag SNP
Selection,” Intl Journal on Bioinformatics Research & Applications, 1(3):249-260 (2005).
D. Brinza, J. He, W. Mao and A. Zelikovsky, "Phasing and Missing data recovery in Family
Trios,” Intl Journal on Bioinformatics Research & Applications, 1(2):221-229 (2005).
Y. Chen, A. B. Kahng, G. Robins, A. Zelikovsky and Y. Zheng, “Compressible Area Fill
Synthesis of Area Fill Layout Information,” IEEE Transactions on Computer-Aided Design of
Integrated Circuits and Systems 24(8):1169-1187 (2005).
Robins, G. and A. Zelikovsky, “Improved Steiner Tree Approximation in Graphs,” SIAM
Journal on Discrete Mathematics, 19(1):122-134 (2005). SIAM Outstanding Paper Prize
Awarded in 2007.
G. Calinescu and A. Zelikovsky, "The Polymatroid Steiner Problems," Journal of
Combinatorial Optimization 9(3):281-294 (2005).
M. Karpinski, I. Mandoiu, A. Olshevsky and A. Zelikovsky, “Improved Approximation
Algorithms for the Quality of Service Steiner Tree Problem,” Algorithmica 42(2):109-120
(2005).
A. B. Kahng, I. Mandoiu, P. Pevzner, S. Reda and A. Zelikovsky, "Scalable Heuristics for
Design of DNA Probe Arrays," Journal of Computational Biology 11(2):429-448 (2004).
G. Calinescu, I. Mandoiu, P.-J. Wan and A. Zelikovsky, “Selecting Forwarding neighbors in
Wireless Ad Hoc Networks,” ACM Mobile Networks&Applications 9(2):101-111 (2004).
C. H. Helvig, G. Robins and A. Zelikovsky, “Moving-Target TSP and Related Problems,”
Journal of Algorithms 49:153-174 (2003).
C. Albrecht, A. B. Kahng, B. Liu, I. Mandoiu and A. Zelikovsky, “On the Skew Bounded
Minimum-Buffer Routing Tree Problem,” IEEE Transactions on Computer-Aided Design of
Integrated Circuits and Systems 22(7):937-944 (2003).
G. Calinescu, C. G. Fernandes, H. Karloff and A. Zelikovsky, “A new approximation
algorithm for finding heavy planar subgraphs,” Algorithmica 36:179-205 (2003).
C. Alpert, A. B. Kahng, B. Liu, I. I. Mandoiu and A. Zelikovsky, “Minimum Buffered Routing
with Bounded Capacitive Load for Slew Rate and Reliability Control,” IEEE Transactions on
Computer-Aided Design of Integrated Circuits and Systems 22(3):241-253 (2003).
Y. Chen, A. B. Kahng, G. Robins and A. Zelikovsky, “Area Fill Synthesis for Uniform
Layout Density,” IEEE Transactions on Computer-Aided Design of Integrated Circuits and
Systems 21(10):1132-1147 (2002).
F. F. Dragan, A. B. Kahng, I. I. Mandoiu, S. Muddu and A. Zelikovsky, “Provably Good
Global Buffering by Generalized Multiterminal Multicommodity Flow Approximation,” IEEE
Transactions on Computer-Aided Design of Integrated Circuits and Systems 21(3):263-274
(2002).
[J37] D. Lozovanu, V. Voloshin and A. Zelikovsky, “A note on the colorability of a mixed
hypergraph using k colors,” Computer Science Journal of Moldova 1(28):92-95 (2002).
[J38] D. D. Lozovanu, E. Tataru and A Zelikovsky, “A generalization of the knapsack problem
[J39]
[J40]
[J41]
[J42]
[J43]
[J44]
[J45]
[J46]
[J47]
[J48]
[J49]
[J50]
[J51]
[J52]
[J53]
[J54]
[J55]
[J56]
[J57]
and finding the k-optimal tree in a weighted digraph,” Buletinul Academiei de Stiinte a
Republicii Moldova, Math, 1(38):111-117 (2002).
A. Zelikovsky and I. Mandoiu, “Practical Approximation Algorithms for Zero- and BoundedSkew Trees,” SIAM Journal on Discrete Mathematics, 15(1):97-111 (2002).
C. H. Helvig, G. Robins and A. Zelikovsky, “Improved Approximation Scheme for the
Group Steiner Problem,” Networks 37(1):8-20 (2001).
C. H. Helvig, G. Robins and A. Zelikovsky, “New Approximation Algorithms for Routing
with Multi-Port Terminals,” IEEE Transactions on Computer-Aided Design of Integrated
Circuits and Systems 19(10):1118-1128 (2000).
I. Mandoiu and A. Zelikovsky, “A Note on the MST Heuristic for Bounded Edge-Length
Steiner Trees with Minimum Number of Steiner Points,” Information Processing Letters
75(4):165-167 (2000).
P. Berman, A. B. Kahng, D. Vidhani, H. Wang and A. Zelikovsky, “Optimal Phase Conflict
Removal for Layout of Dark Field Alternating Phase Shifting Masks,” IEEE Transactions on
Computer-Aided Design of Integrated Circuits and Systems 19(2):175-187 (2000).
A. B. Kahng, G. Robins, A. Singh, and A. Zelikovsky, "Filling Algorithms and Analyses for
Layout Density Control,” IEEE Transactions on Computer-Aided Design of Integrated
Circuits and Systems 18(4)):445-462 (1999).
A. Caldwell, A. B. Kahng, S. Mantik, I. L. Markov and A. Zelikovsky, “On Wirelength
Estimations for Row-Based Placement,” IEEE Transactions on Computer-Aided Design of
Integrated Circuits and Systems 18(9):1265-1278 (1999).
M. Karpinski and A. Zelikovsky, “New approximation algorithms for the Steiner tree
problems,” Journal of Combinatorial Optimization 1:47-65 (1997).
A. Zelikovsky, “A series of Approximation Algorithms for the Acyclic Directed Steiner Tree
Problem,” Algorithmica 18:99-110 (1997).
U. Fossmeier, M. Kaufmann and A. Zelikovsky, “Faster approximation algorithms for the
rectilinear Steiner tree problem,” Discrete & Computational Geometry 18:93-109 (1997).
A. Zelikovsky, “Later achievements in the Steiner tree approximations,” Journal of
Computer Science of Moldova 1:32-41 (1993).
A. Zelikovsky, “A faster approximation algorithm for the Steiner tree problem in graphs,”
Information Processing Letters 46:79-83 (1993).
A. Zelikovsky, “An 11/6-approximation algorithm for the network Steiner problem,”
Algorithmica 9:463-470 (1993).
A. Zelikovsky, “An approximation algorithm for matroids with coalitions,” Izvestia Akademii
Nauk Respublica Moldova 1:77-81 (1992).
A. Zelikovsky, “The Steiner tree problem in graphs without optimal vertices,”
Matematicheskie Issledovaniia 21:44-49 (1991).
A. Zelikovsky, “König's problem for Abelian permutation groups,” Izvestia Academii Nauk
Byelorusskoi Academii Nauk 5:34-39 (1989).
A. Zelikovsky, “Graph transformation categories which reconstruct graphs up to
isomorphism,” Matematicheskie Issledovaniia 76:24-29 (1984).
A. Zelikovsky and Le Thuk Zuk, “The contraction categories of graphs,” Matematicheskie
Issledovaniia 66:56-59 (1982).
A. Zelikovsky, “Graphs of particular contraction categories,” Matematicheskie Issledovaniia
66:50-55 (1982).
Refereed Conference Articles
[R1] J. Lindsay and H. Salooti and A. Zelikovsky and I.I. Mandoiu, “Scalable Genome
Scaffolding using Integer Linear Programming,” Proc. ACM Conference on Bioinformatics,
Computational Biology and Biomedicine (2012) pp 377-383.
[R2] S. Mangul and A. Caciula and S. Al Seesi and D. Brinza and A. Rouf Banday and R.
Kanadia and I.I. Mandoiu and A. Zelikovsky, “An Integer Programming Approach to Novel
[R3]
[R4]
[R5]
[R6]
[R7]
[R8]
[R9]
[R10]
[R11]
[R12]
[R13]
[R14]
[R15]
[R16]
[R17]
[R18]
[R19]
[R20]
Transcript Reconstruction from Paired-End RNA-Seq Reads”, Proc. ACM Conference on
Bioinformatics, Computational Biology and Biomedicine (2012) pp. 369-376.
T.Alsulaiman, S.K. Prasad, A. Zelikovsky, "Distributed Algorithms for TDMA Link
Scheduling in Sensor Networks", Parallel and Distributed Processing Symposium
Workshops & PhD Forum (IPDPSW) 2012, pp. 839 – 847.
L. Shi, W-Z. Song, M. Xu, A. Zelikovsky, L. Yu, “Collaborative Topology Control for
Lifetime Maximization,” Proc. 7th Mobile Ad-hoc and Sensor Networks (MSN), 2011, pp.
182-189.
S. Mangul, A. Caciula, I.I. Mandoiu and A. Zelikovsky, “RNA-Seq based discovery and
reconstruction of unannotated transcripts in partially annotated genomes,” Proc. 1st
Workshop on Computational Advances in Molecular Epidemiology, 2011, pp. 118-123.
N. Mancuso, B. Tork, I.I. Mandoiu and A. Zelikovsky and P. Skums, “Viral Quasispecies
Reconstruction from Amplicon 454 Pyrosequencing Reads,” Proc. 1st Workshop on
Computational Advances in Molecular Epidemiology, 2011, pp. 94-101.
S. Mangul, I. Astrovskaya, M. Nicolae, B. Tork, I.I. Mandoiu and A. Zelikovsky, “Maximum
Likelihood Estimation of Incomplete Genomic Spectrum from HTS Data,” Proc. 11th
Workshop on Algorithms in Bioinformatics, 2011, p. 213-224.
P. Berman, M. Karpinski, and A Zelikovsky, “A 3/2-Approximation Algorithm for
Generalized Steiner Trees in Complete Graphs with Edge Lengths 1 and 2,” Proc. of the
21st Intl Symp on Algorithms and Computation, (ISAAC 2010), Lecture Notes in Computer
Science 6506, 2010, pp. 15-24.
Q. Cheng, P. Berman, R. Harrison, and A. Zelikovsky, “Efficient Alignments of Metabolic
Networks with Bounded Treewidth,” Proc. 10th IEEE Intl Conf on Data Mining Workshops
(ICDMW), 2010, pp. 687-694.
Q. Cheng, J. Wei, A. Zelikovsky, and M. Ogihara, “Fixed-Parameter Tractable
Combinatorial Algorithms for Metabolic Networks Alignments,” Proc. 10th IEEE Intl Conf on
Data Mining Workshops (ICDMW), 2010, pp. 679-686.
Q. Cheng, M. Ogihara, J. Wei, and A. Zelikovsky, “WS-GraphMatching: a web service tool
for graph matching,” Proc. of the 19th ACM Conf on Information and Knowledge
Management (CIKM), 2010, pp. 1949-1950.
M. Nicolae, S. Mangul, I. I. Mandoiu and A. Zelikovsky, “Estimation of Alternative Splicing
isoform Frequencies from RNA-Seq Data,” Proc. Workshop on Algorithms in Bioinformatics
(WABI), 2010, Lecture Notes in Bioinformatics 6293, pp. 202-214.
X. Cao, Y. Wang and A. Zelikovsky, "Scheduling Bursts using Interval Graphs in Optical
Burst Switching Networks", Proc. IEEE GLOBECOM, 2009.
I. Astrovskaya and A. Zelikovsky, “Genotype Tagging with Limited Overfitting,” Proc. of
Brazilian Symposium on Bioinformatics (BSB), 2009, Lecture Notes in Bioinformatics 5676,
pp. 1-12.
P. Berman, M. Karpinski and A. Zelikovsky, “1.25-Approximation Algorithm for Steiner
Tree Problem with Distances 1 and 2,” Proc. of the 15th Intl Symp on Algorithms and Data
Structures (WADS), 2009, Lecture Notes in Computer Science 5664, pp. 86-97.
S. Gremalschi, G. Altun, I. Astrovskaya, A. Zelikovsky “Mean Square Residue Biclustering
with Missing Data and Row Inversions,” Proc. of International Symposium on Bioinformatics
Research & Applications (ISBRA), 2009, Lecture Notes in Bioinformatics 5542, pp. 28-40.
Q. Cheng, P. Berman, R. Harrison and A. Zelikovsky, “Fast Alignments of Metabolic
Networks,” Proc. of IEEE Intl Conf on Bioinformatics and Biomedicine (BIBM), 2008, pp.
147-152.
K. Wesbrooks, I. Astrovskaya, D. C. Rendon, Y. Khudyakov, P. Berman, and A.
Zelikovsky, “HCV Quasispecies Assembly using Network Flows,” Proc. of Intl Symp on
Bioinformatics Research & Applications (ISBRA), 2008, Lecture Notes in Bioinformatics
4983, pp. 159-170.
Q. Cheng, D. Kaur, R. Harrison, and A. Zelikovsky, “Mapping and Filling Metabolic
Pathways,” Proc. RECOMB Satellite Conference on System Biology, 2007.
D. Brinza and A. Zelikovsky, “Risk Factor Searching Heuristics for SNP Case-Control
Studies,” Proc. of IEEE Intl Conf on Bioinformatics and Biomedicine (BIBM), 2007, pp. 282
– 287.
[R21] D. Brinza and A. Zelikovsky, “Discrete Methods for Association Search and Status
[R22]
[R23]
[R24]
[R25]
[R26]
[R27]
[R28]
[R29]
[R30]
[R31]
[R32]
[R33]
[R34]
[R35]
[R36]
[R37]
[R38]
Prediction in Genotype Case-Control Studies,” Proc. of IEEE 7-th International Symposium
on BioInformatics and BioEngineering (BIBE), 2007, pp. 270 – 277.
Q. Cheng, R. Harrison, and A. Zelikovsky, “Homomorphisms of Multisource Trees into
Networks with Applications to Metabolic Pathways,” Proc. of IEEE 7-th International
Symposium on BioInformatics and BioEngineering (BIBE), 2007, pp. 350-357.
R. Albert, B. DasGupta, R. Dondi, E. Sontag, A. Zelikovsky and K. Westbrooks, “Signal
Transduction Network Inference from Indirect Experimental Evidence,” Proc. Workshop on
Algorithms in Bioinformatics (WABI), 2007, Lecture Notes in Bioinformatics 4645, pp. 407419.
A. B. Kahng, P. Sharma, and A. Zelikovsky, “Fill for Shallow Trench Isolation CMP,” Proc.
IEEE/ACM Intl. Conference on Computer-Aided Design (ICCAD), 2006, pp. 661-668.
D. Brinza and A. Zelikovsky, “Combinatorial Analysis of Disease Association and
Susceptibility for Rheumatoid Arthritis SNP Data,” Proc. of Genetic Analysis Workshop
(GAW), 2006, 13: pp. 6-11.
A. R. de Vries, I. M. Nolte, Geert T. Spijker, D. Brinza, A. Zelikovsky, and G.J. te
Meerman, “Cross Haplotype Sharing Statistic: Haplotype length based method for whole
genome association testing,” Proc. Genetic Analysis Workshop (GAW), 2006, 13, pp. 1621.
D. Brinza, J. He, and A. Zelikovsky, “Combinatorial Search Methods for Multi-SNP Disease
Association,” Proc. International Conf. of the IEEE Engineering in Medicine and Biology
(EMBC), 2006, pp. 5802-5805.
J.He and A. Zelikovsky, “Multiple Linear Regression for Index SNP Selection on Unphased
Genotypes,” Proc. International Conf. of the IEEE Engineering in Medicine and Biology
(EMBC), 2006, pp. 5759-5762.
D. Brinza and A. Zelikovsky, “Combinatorial Methods for Disease Association Search and
Susceptibility Prediction,” Proc. Workshop on Algorithms in Bioinformatics (WABI), 2006,
Lecture Notes in Bioinformatics 4175, pp. 286-297.
D. Brinza, A. Perelygin, M. Brinton, A. Zelikovsky, “Search fo multi-SNP Disease
Association,” Proc. of the 5th International Conference on Bioinformatics of Genome
Regulation and Structure, 2006, pp. 122-125.
D. Brinza and A. Zelikovsky, “DEEPS: Deterministic Energy-Efficient Protocol for Sensor
networks,” Proc. 2nd ACIS International Workshop on Self-assembling Wireless Networks
(SAWN), 2006, pp. 261-266.
A. Dhawan, C. T. Vu, A. Zelikovsky, Y. Li, S. K. Prasad, “Maximum Lifetime of Sensor
Networks with Adjustable Sensing Range,” Proc. 2nd ACIS International Workshop on Selfassembling Wireless Networks (SAWN), 2006, pp. 285-289.
Q. Cheng , Y.Zhang, X. Hu, N. Hundewale and A. Zelikovsky, “Routing Using Messengers
in Sparse and Disconnected Mobile Sensor Networks,” Proc. of Advances in Web
Intelligence and Data Mining, June 2006, Studies in Computational Intelligence 23, pp. 3140.
D. Brinza and A. Zelikovsky, “Phasing of 2-SNP Genotypes based on Non-Random Mating
Model,” Proc. of Intl Conf on Computational Science, 2006, Lecture Notes in Computer
Science 3992, pp. 767-774.
J. He and A. Zelikovsky, “Tag SNP Selection Based on Multivariate Linear Regression,”
Proc. of Intl Conf on Computational Science, 2006, Lecture Notes in Computer Science
3992, pp. 750-757.
W. Mao, D. Brinza, N. Hundewale, S. Gremalschi and A. Zelikovsky, “Genotype
Susceptibility and Integrated Risk Factors for Complex Diseases,” Proc. IEEE Intl Conf on
Granular Computing, 2006, pp. 754-757.
J. He, J. Zhang, G. Altun, A. Zelikovsky and Y. Zhang, “Haplotype Tagging using Support
Vector Machines,” Proc. IEEE Intl Conf on Granular Computing, 2006, pp. 758-761.
J G. Altun, H.-J. Hu, D. Brinza, R.W. Harrison, A. Zelikovsky and Y. Pan, “Hybrid SVM
kernels for protein secondary structure prediction,” Proc. IEEE Intl Conf on Granular
Computing, 2006, pp. 762-765.
[R39] A. B. Kahng, X. Xu and A. Zelikovsky, "Fast Yield-Driven Fracture for Variable Shaped-
[R40]
[R41]
[R42]
[R43]
[R44]
[R45]
[R46]
[R47]
[R48]
[R49]
[R50]
[R51]
[R52]
[R53]
[R54]
[R55]
Beam Mask Writing," Proc. SPIE Symp on Photomask and NGL Mask Technology XIII,
2006, SPIE 6283, pp. 62832R-1 - 62832R-10.
P. Berman, M. Furer and A. Zelikovsky, “Applications of the Matroid Parity Problem to
Approximating Steiner Trees,” Proc. of Intl Computer Science Symp in Russia (CSR), 2006,
Lecture Notes in Computer Science 3967, pp. 70-79.
N. Hundewale, Q. Cheng, X. Hu, A. Bourgeois and A. Zelikovsky, "Autonomous
Messenger Based Routing in Disjoint Clusters of Mobile Sensor Networks," Proc. Spring
Simulation Multiconference, 2006, pp. 57-64.
A.B. Kahng, I.I. Mandoiu, X. Xu, and A. Zelikovsky, “Multi-project reticle design and wafer
dicing under uncertain demand,” Proc. 22nd European Mask and Lithography Conf, 2006,
SPIE 6281, pp. 628104-1 - 628104-11. Invited.
D. Brinza, G. Calinescu, S. Tongngam and A. Zelikovsky, "Energy-Efficient Continuous
and Event-Driven Monitoring," Proc. 2nd IEEE Intl Conf on Mobile Ad-Hoc and Sensor
Systems, 2005, 3pp.
A. B. Kahng, I. I. Mandoiu, X. Xu and A. Zelikovsky, "Yield-driven multi-project reticle design
and wafer dicing", Proc. 25th BACUS Intl Symp on Photomask Technology, 2005, SPIE
5992, pp. 599249-1 – 599249-11. Best Poster Award.
W. Mao, J.He, D. Brinza and A. Zelikovsky, "A Combinatorial Method for Predicting
Genetic Susceptibility to Complex Diseases" Proc. of the Intl Conf of the IEEE Engineering
in Medicine and Biology (EMBC), 2005, 224 - 227.
S. Jung, N. Hundewale and A. Zelikovsky, "Energy Efficiency of Load Balancing in MANET
Routing Protocols," Proc. of the First ACIS Intl Workshop on Self-assembling Wireless
Networks (SAWN), 2005, pp. 476-483.
D. Brinza, J. He, W. Mao and A. Zelikovsky, "Phasing and Missing data recovery in Family
Trios,” Proc. of Intl Conf on Computational Science, 2005, Lecture Notes in Computer
Science 3515, pp. 1011-1019.
S. Jung, N. Hundewale and A. Zelikovsky, "Node Caching Enhancement of Reactive Ad
Hoc Routing Protocols," Proc. IEEE Wireless Communication and Networking Conf
(WCNC), 2005, Volume 4, pp. 1970-1975.
C. Chiang, A. B. Kahng, S. Sinha, X. Xu and A. Zelikovsky, "Bright-Field AAPSM Conflict
Detection and Correction," Proc. Conf. on Design Automation and Test in Europe (DATE),
2005, Volume 2, pp. 908-913.
G. Calinescu and A. Zelikovsky, "The Polymatroid Steiner Problems," Proc. of the 15th Intl
Symp on Algorithms and Computation (ISAAC), 2004, Lecture Notes in Computer Science
3341, pp. 234-245.
Y. Chen, A. B. Kahng, G. Robins, A. Zelikovsky and Y. Zheng, "Evaluation of the New
OASIS Format for Layout Fill Compression," Proc. of the 11th IEEE Intl Conf on Electronics,
Circuits and Systems, 2004, pp. 377-382.
S. K. Prasad, V. Madisetti, S. Navathe, R. Sunderraman, E. Dogdu, A. G. Bourgeois, M.
Weeks, A. Zelikovsky, Y.-Q. Zhang, Y. Pan, S. Belkasim, R. Sivakumar, B. Liu, J.
Balasooriya, A. Hariharan, W. Xie, P. Madiraju, S. Malladi, G. Johnson and J. He, "System
on Mobile Devices (SyD): A Middleware Testbed for Collaborative Applications over Small
Heterogeneous Devices and Data Stores," Proc. of the ACM/IFIP/USENIX 5th Intl
Middleware Conf, 2004, Lecture Notes in Computer Science 3231, pp. 352-371.
A. B. Kahng, X. Xu and A. Zelikovsky, "Yield and cost-driven fracturing for variable shaped
beam mask writing," Proc. 24th BACUS Intl Symp on Photomask Technology, 2004, SPIE
5567, 360-371.
J. He and A. Zelikovsky, "Linear Reduction for Haplotype Inference," Proc. of the
Workshop on Algorithms in Bioinformatics (WABI), 2004, Lecture Notes in Bioinformatics
3240, pp. 242-253.
M. Atlas, N. Hundewale, L. Perelygina and A. Zelikovsky, "Consolidating Software Tools
for DNA Microarray Design and Manufacturing," Proc. of the Intl Conf of the IEEE
Engineering in Medicine and Biology (EMBC), 2004, pp. 172-175.
[R56] J. He and A. Zelikovsky, "Linear Reduction Methods for Tag SNP Selection," Proc. of the
[R57]
[R58]
[R59]
[R60]
[R61]
[R62]
[R63]
[R64]
[R65]
[R66]
[R67]
[R68]
[R69]
[R70]
[R71]
[R72]
[R73]
[R74]
Intl Conf of the IEEE Engineering in Medicine and Biology (EMBC), 2004, pp. 2840-2843.
Regional student best paper award.
A. B. Kahng, I. Mandoiu, X. Xu and A. Zelikovsky, "Multi-Project Reticle Floorplanning and
Wafer Dicing," Proc. of the ACM/SIGDA Intl Symp on Physical Design, 2004, pp. 70-77.
P. Berman, G. Calinescu, C. Shah and A. Zelikovsky, "Power Efficient Monitoring
Management in Sensor Networks," Proc. of IEEE Wireless Communication and Networking
Conf (WCNC), 2004, pp. 2329-2334.
G. Calinescu, C. Fernandes, I. Mandoiu, A. Olshevsky, K. Yang and A. Zelikovsky,
“Quality of Service for Multimedia Multicast,” Proc. IEEE GLOBECOM, 2003, pp. 3631-35.
S. K. Prasad, M. Weeks, Y. Zhang, A. Zelikovsky, S. Belkasim, R. Sunderraman, and V.
Madisetti, "Toward an Easy Programming Environment for Implementing Mobile
Applications: A Fleet Application Case Study using SyD Middleware," Proc. IEEE Intl
Workshop on Web Based Systems and Applications (WEBSA), 2003, pp. 696-701.
A. B. Kahng, I. Mandoiu, S. Reda, X. Xu and A. Zelikovsky, “Evaluation of Placement
Techniques for DNA Probe Array Layout,” Proc. IEEE/ACM Intl Conf on Computer-Aided
Design (ICCAD), 2003, pp. 262-269.
A. B. Kahng, I. Mandoiu, S. Reda, X. Xu and A. Zelikovsky, “Design Flow Enhancements
for DNA Arrays,” Proc. of IEEE Intl Conf on Computer Design.2003, pp. 116-123.
G. Calinescu, S. Kapoor, A. Olshevsky and A. Zelikovsky, “Network Lifetime and Power
Assignment in Ad-Hoc Wireless Networks,” Proc. European Symp on Algorithms (ESA),
2003, Lecture Notes in Computer Science 2832, pp. 114-126.
M. Karpinski, I. Mandoiu, A. Olshevsky and A. Zelikovsky, “Improved Approximation
Algorithms for the Quality of Service Steiner Tree Problem,” Proc. Workshop on Algorithms
and Data Structures, 2003, Lecture Notes in Computer Science 2748, pp. 401-411.
A. B. Kahng, I. Mandoiu, P. Pevzner, S. Reda and A. Zelikovsky, “Engineering a scalable
placement heuristic for DNA probe arrays,” Proc. of the Seventh Annual Intl Conf on
Research in Computational Molecular Biology (RECOMB), 2003, pp. 148-156.
E. Althaus, G. Calinescu, I. Mandoiu, S. Prasad, N. Tchervenski and A. Zelikovsky,
“Power Efficient Range Assignment in Ad-hoc Wireless Networks,” Proc. of IEEE Wireless
Communication and Networking Conf (WCNC), 2003, Volume 3, pp. 1889-1894.
Y. Chen, A. B. Kahng, G. Robins, A. Zelikovsky and Y. Zheng, “Area Fill Generation with
Inherent Data Volume Reduction,” Proc. Intl Conf on Design Automation and Test in
Europe, 2003, pp. 868-873.
A. B. Kahng, I. Mandoiu and A. Zelikovsky, “Highly Scalable Algorithms for Rectilinear and
Octilinear Steiner Trees,” Proc. Asia and South Pacific Design Automation Conf, 2003, pp.
827-833.
Y. Chen, A. B. Kahng, G. Robins and A. Zelikovsky, "Monte-Carlo Methods for ChemicalMechanical Planarization on Multiple-Layer and Dual-Material Models," Proc. SPIE Intl
Symp on Microlithography, 2002, SPIE 4962, pp. 421-432.
S.K. Prasad, M. Weeks, Y.-Q. Zhang, A. Zelikovsky, S. Belkasim and R. Sunderraman, V.
Madisetti, “Mobile Fleet Application Using SOAP and System on Devices (SyD) Middleware
Technologies,” Proc. of IASTED Comm, Internet and Info Tech Conf, 2002, pp. 426-431.
A. B. Kahng, I. Mandoiu, P. Pevzner, S. Reda and A. Zelikovsky, “Border Length
Minimization in DNA Array Design,” Proc. Workshop on Algorithms in Bioinformatics
(WABI), 2002, Lecture Notes in Computer Science 2452, pp. 435-448.
G. Calinescu, I. Mandoiu and A. Zelikovsky, “Symmetric Connectivity with Minimum Power
Consumption in Radio Networks,” Proc. of 17th IFIP World Computer Congress, Stream
TC1/ 2nd IFIP Intl Conf on Theoretical Computer Science, 2002, R. Baeza-Yates and U.
Montaniri and N. Santoro (eds.), Kluwer Academic Publ., August 2002, pp. 119-130.
C. Bandela, Y. Chen, A. B. Kahng, I. Mandoiu and A. Zelikovsky, “Auctions with buyer
preferences,” Information Systems: the E-BUsiness Challenge – Proc. of 17th IFIP World
Computer Congress, Stream TC8, R. Traunmuller (ed.), 2002, pp. 223-238.
Y. Chen, A. B. Kahng, G. Robins and A. Zelikovsky, “Closing the Smoothness and
Uniformity Gap in Area Fill Synthesis,” Proc. ACM/IEEE Intl Symp on Physical Design,
2002, pp. 137-142.
[R75] C. Albrecht, A. B. Kahng, I. Mandoiu and A. Zelikovsky, “Floorplan Evaluation with Timing-
[R76]
[R77]
[R78]
[R79]
[R80]
[R81]
[R82]
[R83]
[R84]
[R85]
[R86]
[R87]
[R88]
[R89]
[R90]
[R91]
[R92]
[R93]
Driven Global Wireplanning, Pin Assignment and Buffer/Wire Sizing,” Proc. VLSI Design/
Asia and South Pacific Design Automation Conf, 2002, pp. 580-587. Best Paper Award.
C. Alpert, A. B. Kahng, B. Liu, I. Mandoiu and A. Zelikovsky, “Minimum-Buffered Routing of
Non-Critical Nets for Slew Rate and Reliability Control,” Proc. IEEE/ACM Intl Conf on
Computer-Aided Design (ICCAD), 2001, pp. 408-415.
C. Albrecht, A. B. Kahng, B. Liu, I. Mandoiu and A. Zelikovsky, “On the Skew Bounded
Minimum-Buffer Routing Tree Problem,” Proc. Workshop on Synthesis and System
Integration of Mixed Technologies, 2001, pp. 250-256.
F. Dragan, A. B. Kahng, I. Mandoiu, S. Muddu and A. Zelikovsky, “Practical Approximation
Algorithms for Separable Packing Linear Programs,” Proc. of Workshop on Algorithms and
Data Structures (WADS), 2001, Lecture Notes in Computer Science 2125, pp. 325-337.
G. Calinescu, I. Mandoiu, P.-J. Wan and A. Zelikovsky, “Selecting Forwarding neighbors in
Wireless Ad Hoc Networks,” Proc. of 5th Workshop on Discrete Algorithms and Methods for
Mobile Computing and Communications, 2001, ACM Press, pp. 34-43.
Y. Chen, A. B. Kahng, G. Robins and A. Zelikovsky, “Hierarchical Dummy Fill Synthesis for
Process Uniformity,” Proc. of the Asia and South Pacific Design Automation Conf 2001,
pp.139-144.
F. Dragan, A. B. Kahng, I. Mandoiu, S. Muddu and A. Zelikovsky, “Provably good global
buffering by multiterminal multicommodity flow approximation,” Proc. of the Asia and South
Pacific Design Automation Conf 2001, pp.120-125.
A. B. Kahng, S. Vaya and A. Zelikovsky, “New Graph Bipartizations for Double-Exposure,
Bright Field Alternating Phase-Shift Mask Layout,” Proc. of the Asia and South Pacific
Design Automation Conf 2001, pp.133-138.
A. Zelikovsky and I. Mandoiu, “Practical Approximation Algorithms for Zero- and BoundedSkew Trees,” Proc. of ACM/SIAM Symp on Discrete Algorithms (SODA), 2001, pp. 407416.
F. Dragan, A. B. Kahng, S. Muddu, I. Mandoiu and A. Zelikovsky, “Provably Good Global
Buffering Using an Available Buffer Block Plan,” Proc. IEEE/ACM Intl Conf on ComputerAided Design (ICCAD), 2000, pp. 104-109.
Y. Chen, A. B. Kahng, G. Robins and A. Zelikovsky, “Monte-Carlo Algorithms for Layout
Density Control,” Proc. Asia and South Pacific Design Automation Conf, 2000, pp. 523-528.
Y. Chen, A. B. Kahng, G. Robins and A. Zelikovsky, “Practical Iterated Fill Synthesis for
CMP Uniformity,” Proc. of ACM/IEEE Design Automation Conf, 2000, pp. 671-674.
G. Robins and A. Zelikovsky, “Improved Steiner Tree Approximation in Graphs,” Proc. of
ACM/SIAM Symp on Discrete Algorithms (SODA), 2000, pp. 770-779.
Y. Chen, A. B. Kahng, G. Qu, and A. Zelikovsky, “The Associative-Skew Clock Routing
Problem,” Proc. of IEEE/ACM Intl Conf on Computer-Aided Design (ICCAD), 1999, pp. 168172.
P. Berman, A. B. Kahng, D. Vidhani and A. Zelikovsky, “The T-join Problem in Sparse
Graphs: Applications to Phase Assignment Problem in VLSI Mask Layout,” Proc. of
Workshop on Algorithms and Data Structures (WADS), 1999, Lecture Notes in Computer
Science 1663, pp. 25-36.
P. Berman, A. B. Kahng, D. Vidhani, H. Wang and A. Zelikovsky, “Optimal Phase Conflict
removal for Layout of Dark Field Alternating Phase Shifting Masks,” Proc. of the
ACM/SIGDA Intl Symp on Physical Design, 1999, pp. 121-126.
A. B. Kahng, G. Robins, A. Singh and A. Zelikovsky, “New and Exact Filling Algorithms for
Layout Density Control,” Proc. of the 12th Intl Conf on VLSI Design, Goa, India, 1999, pp.
106-110.
A. B. Kahng, G. Robins, A. Singh, and A. Zelikovsky, “New Multi-Level and Hierarchical
Algorithms for Layout Density Control,” Proc. of the Asia and South Pacific Design
Automation Conf 1999, pp. 221-224.
A. B. Kahng, P. Tucker and A. Zelikovsky, “Optimization of Linear Placements for
Wirelength Minimization with Free Sites,” Proc. of the Asia and South Pacific Design
Automation Conf 1999, pp. 241-244 (nominated for Best Paper Award).
[R94] A. B. Kahng, H. Wang and A. Zelikovsky, “Automated Layout and Phase Assignment
Techniques for Dark Field Alternating PSM,” in Proc. of the SPIE 18th Annual BACUS
Symp on Photomask Technology, SPIE 3546,1998, pp. 222-231.
[R95] C. H. Helvig, G. Robins and A. Zelikovsky, “Moving-Target TSP and Related Problems,”
Proc. of European Symp on Algorithms (ESA). Lecture Notes in Computer Science 1461,
1998, pp. 453-464.
[R96] A. B. Kahng, G. Robins, A. Singh, H. Wang and A. Zelikovsky, “Filling and Slotting:
Analysis and Algorithms,” Proc. of the ACM/SIGDA Intl Symp on Physical Design,
Monterey, California, April, 1998, 95-102.
[R97] A. E. Caldwell, A. B. Kahng, S. Mantik, I. L. Markov and A. Zelikovsky, “On Wirelength
Estimations for Row-Based Placement,” Proc. of the ACM/SIGDA Intl Symp on Physical
Design, 1998, pp. 4-11.
[R98] C. H. Helvig, G. Robins and A. Zelikovsky, “Improved Approximation Bounds for the Group
Steiner Problem,” Proc. of the Intl Conf on Design Automation and Test in Europe, 1998,
pp. 406-413
[R99] M. Karpinski, G. Wirtgen and A. Zelikovsky, "An Approximation Algorithm for the
Bandwidth Problem on Dense Graphs," Proc. of RALCOM'97, 1997, pp. 1-14.
[R100] C. D. Bateman, C. H. Helvig, G. Robins and A. Zelikovsky, "Provably-Good Routing
Tree Construction with Multi-Port Terminals," Proc. of the ACM/SIGDA Intl Symp on
Physical Design, 1997, pp. 96-102.
[R101] H.-G. Cho and A. Zelikovsky, "Spanning closed trail and Hamiltonian cycle in grid
graphs," Proc. of 6th Intl Symp on Algorithms Automata and Combinatorics (ISAAC), 1995,
Lecture Notes in Computer Science 1002, pp. 342-351.
[R102] P. Berman, U. Fossmeier, M. Kaufmann, M. Karpinski and A. Zelikovsky, "Approaching
the 5/4-Approximations for Rectilinear Steiner Trees," Proc. of European Symp on
Algorithms (ESA), 1994 Lecture Notes in Computer Science 855, pp. 60-71.
[R103] U. Fößmeier, M. Kaufmann, and A. Zelikovsky, "Fast approximation algorithms for the
rectilinear Steiner tree problem,” Proc. of 6th Intl Symp on Algorithms Automata and
Combinatorics (ISAAC), 1993, Lecture Notes in Computer Science 762, pp. 533-542.
[R104] A. Zelikovsky, "A minimum base of weighted k-polymatroids and the Steiner tree
problem,” Proc. of Integer Programming and Combinatorial Optimization, 1993, pp. 89-98.
[R105] D. D. Lozovanu, and A. Zelikovsky, "Minimal and bounded trees," Tezele Congresului
XVIII al Academiei Romano-Americane, Kishinev, (1993), pp. 25-26.
[R106] A. Zelikovsky, "An 11/8-approximation algorithm for the Steiner problem on networks
with rectilinear distance,” Proc. of the Conf Sets, Graphs and Numbers, 1991. Colloquia
Mathematica Societatis J. Bolyai, 60, 1992, pp. 733-745.
[R107] A. Zelikovsky, "An 11/6-approximation algorithm for the Steiner problem on graphs,”
Proc. of IV Czechoslovakian Symp on Combinatorics, Prahatice (1990). Annals of Discrete
Mathematics 50, 1992, pp. 351-354.
[R108] A. Zelikovsky, "The solution of König's problem for Abelian permutation groups,” In Proc.
XIX All-union algebraic Conf, L'vov, part 2, (1989), pp. 98-99.
Invited Talks
2012/04
/07
/07
2011/08
/05
/04
/02
/01
2010/11
/10
/09
/05
2009/11
RECOMB-Seq, Barcelona, Spain (keynote)
University of Georgia, Athens, GA
Life Technologies, Menlo Park, CA
Life Technologies, Menlo Park, CA
ISBRA, Changsha, China (keynote)
Next-Gen Sequencing Congress, Boston, MS
ICCABS, Orlando, FL
UCLA, Los Angeles, CA
INFORMS Annual Meeting, Austin, TX
University of Connecticut, Storrs, CT
University of Birmingham, Birmingham, UK
University of Georgia, Athens, GA
Belarus State University, Minsk, Belarus
/10
/09
/02
2008/10
2007/12
/10
/03
/02
2006/09
/05
/04
2005/10
/05
/02
2004/08
/05
/04
2003/02
2002/06
2000/03
/04
1999/03
1998/09
1997/04
1996/12
1995/10
/06
1994/11
1992/06
University of Connecticut, Storrs, CT
Georgia Tech, Atlanta, GA
Kent State University, OH
INFORMS Annual Meeting, Washington, DC
Oak Ridge National Laboratory, Oak Ridge, TN
National Institute of Health, Washington, DC
University of Georgia, Athens, GA
University of Georgia, Athens, GA
National Institute of Cancer, Milan, Italy
IWAP Symposium, University of Connecticut, Storrs, CT
DIMACS, Rutgers Univ, Piscataway, NJ
Bonn University, Bonn, Germany
SECABC Symposium, GSU, Atlanta, GA
University of Connecticut, Storrs, CT
Kent State University, OH
Georgia Tech, Atlanta, GA
University of California at San Diego, La Jolla, CA
CEBC Symposium, GSU, Atlanta, GA
University of Georgia, Athens, GA
Georgia Tech, Atlanta, GA
Bonn University, Bonn, Germany
StarCore Technology Center, Lucent Technologies, Atlanta, GA
Integrated Device Technology, Inc., Atlanta, GA
Georgia Tech, Atlanta, GA
Pennsylvania State University, University Park, PA
Cadence Design Systems, Inc., San Jose, CA
Max-Plank-Institut fuer Informatik, Saarbrücken, Germany
University of Virginia, Charlottesville, VA
University of California at Berkeley, Berkeley, CA
Bonn University, Bonn, Germany
Max-Plank-Institut fuer Informatik, Saarbrücken, Germany
Max-Plank-Institut fuer Informatik, Saarbrücken, Germany
Membership
ACM, IEEE, SPIE, ISCB, INFORMS, ASHG
Industrial Contacts
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Cadence Design Systems, Inc., San Jose, CA
Intel Inc., Santa Clara, CA
Numerical Technologies, San Jose, CA
Rockwell Semiconductor Systems, Inc., Newport Beach, CA
Integrated Device Technology, Inc., Atlanta, GA
StarCore Technology Center, Lucent Technologies, Atlanta, GA
Affymetrix, Inc., San Jose, CA
Blaze, Sunnyvale, CA
Life Technologies, Fresno, CA
Refereeing
Journals
1.
2.
3.
4.
5.
6.
Journal on Parallel and Distributed Computing
Bioinformatics
IEEE Transactions on Bioinformatics & Computational Biology
Journal of Combinatorial Optimization
Algorithmica
Information Processing Letters
7.
8.
9.
10.
11.
12.
13.
14.
15.
16.
17.
18.
19.
20.
21.
22.
23.
Intl Journal of Computational Geometry & Applications
Computational Geometry: Theory and Applications
IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems
Networks
Discrete Applied Mathematics
IEEE Transactions on VLSI
Discrete & Computational Geometry
IEE Proc. - Computers and Digital Techniques
IEE Electronics Letters
IEEE Systems, Man and Cybernetics - Part B
ACM Mobile Networks and Applications
IEEE/ACM Transactions on Networking
Geometriae Dedicata
IEEE Transactions on Computational Biology & Bioinformatics
IEEE Transactions on Nanobioscience
BMC Bioinformatics
Human Genetics
Conferences
24.
25.
26.
27.
28.
29.
ACM/SIAM Symposium on Algorithms
ACM European Symposium on Algorithms
ACM/IEEE Design Automation Conf
ACM/SIGDA Intl Symposium on Physical Design
IEEE INFOCOM, Annual Joint Conf of the IEEE Computer and Communication Societies
IEEE GLOBECOM, Communications: The Global Bridge
Grant proposals
30. Australian research council
31. Israel Science Foundation
32. Marsden Fund (New Zealand)
Teaching
CS 180
“Introduction to Algorithms and Complexity”, Spring 1998, UCLA
CSc 2010
“Introduction to Computer Science”, Spring/Fall 1999, GSU
CSc 4210/6210 “Computer Architecture”, Spring/Fall 1999-2003, GSU
CSc 4520/6520 “Algorithms: Design and Analysis”, Spring/Fall 2000-, GSU
CSc 8520
“Applied Combinatorics and Graph Theory”, Spring 2000, GSU
CSc 3420
“UNIX and C”, Summer 2000, GSU
CSc 4230/6230 “VLSI Design”, Fall 2000, GSU
CSc 8550
“Advanced Algorithms for VLSI CAD and Networks”, Spring/Fall 2001-, GSU
CSc 8221
“Optical and Wireless Networks”, Spring 2005, GSU
CSc 8980
“Topics in Computer Science: Algorithms in Bioinformatics”, Fall 2005, GSU
CSc 8540
“Algorithms in Bioinformatics”, Fall 2006-, GSU
CSc 9810
Seminar “Introduction to Systems Biology”, Summer 2007, GSU
CSc 8980
“Topics in Computer Science: Approximation Algorithms”, Fall 2007, GSU
CSc 8980
“Topics in Computer Science: Statistical Learning Tools”, Summer 2009, GSU
CSc 8980
“Topics in Computer Science: Next-Generation Sequencing”, 2010-, GSU
Course and Program Development
2000
2001
2005
2005
2005
2007
2007
2009
CSc 4230/6230 “VLSI Design”
CSc 8550 “Advanced Algorithms for VLSI CAD and Communication Networks”
CSc 8980 “Topics in Computer Science: Algorithms in Bioinformatics”
CSc 6540/4540 “Algorithms in Bioinformatics”
CSc 8540 “Algorithms in Bioinformatics”
CSc 9810 Seminar “Introduction to Systems Biology”
CSc 8980 “Topics in Computer Science: Approximation Algorithms”
CSc 8980 “Topics in Computer Science: Statistical Learning Tools”
2010
CSc 8980 “Topics in Computer Science: Next-Generation Sequencing”
Students Supervised
Ph. D. students:
S. Mantik, Y. Chen (UCLA), B. Liu (UCSD), I. Mandoiu (Georgia Tech), J. Nale, W. Mao, N.
Hundewale, J. He, D. Brinza, S. Gremalschi, I. Astrovsakaya, Q. Cheng, K. Westbrooks, S.
Mangul, Nick Mancuso, Bassam Tork, Olga Glebova, Adrian Caciula, Blanche Temate, Hamed
Salooti (all GSU)
Master students:
C. H. Helvig (University of Virginia), D. Vidhani, H. Wang, S. Vaya (UCLA), Y. Qin, C. Bandela, F.
Xu, C. Shah, O. Mbowe, M. Atlas, L. Ma, K. Yang, S. Jung, D. Vidal, F. Hussein, C Gardner, S.
Jun, D. Mohanbabu, D. Kaur (GSU)
Undergraduate students:
C. D. Bateman (University of Virginia), A. Olshevsky (Georgia Tech), S. Zavulunova (GSU)
Dissertations/Theses Committee Chair
PhD Dissertations
1. J. He, “Algorithms for Computational Genetic Epidemiology,” Summer 2006.
2. W. Mao, “Prediction of Genetic Susceptibility to Complex Diseases,” Summer 2006.
3. N. Hundewale, “CAD Tools for DNA Micro-Array Design, Manufacture and Application,” Fall
2006.
4. D. Brinza, “Discrete Methods for Analysis of Genotype Data,” Summer 2007.
5. K. Westbrooks, “Biological Inference Using Flow Networks,” Spring 2009.
6. Q. Cheng, “Metabolic Network Alignments and Their Applications,” Fall 2009.
7. S. Gremalschi, “Optimization Techniques for Protein-Protein Co-Regulation and Interaction
Prediction,” Fall 2009.
8. I. Astrovskaya, “Inferring Genomic Sequences,” Spring 2011.
9. S. Mangul, “Algorithms for Transcriptome Quantification and Reconstruction from
RNA-Seq Data”, Fall 2012.
Master Theses
1.
2.
3.
4.
5.
6.
7.
8.
9.
10.
11.
12.
13.
14.
15.
F. Xu, “Power Efficient Monitoring Schedules in Sensor Networks,” Summer 2003.
O. Mbowe, “Dynamic Power Assignment in Static Ad Hoc Networks,” Summer 2003.
L. Ma, “An Enhanced DSR Routing Protocol for Wireless Ad Hoc Network,” Summer 2003.
K. Yang, “Network Life Time Maximization and Power Assignment in Ad Hoc Wireless
Networks,” Fall 2003.
C. Shah, “Distributed Algorithms in Wireless Networks,” Fall 2003.
M. Atlas, “Consolidating Software Tools for DNA Micro-array Design and Manufacturing,”
Spring 2004.
S. Jung, “Node Caching Enhancement of Ad hoc Routing Protocols,” Summer 2005.
D. Vidal, “Approximation and Exact Algorithms for the Steiner Forest Problem,” Spring 2006
(project).
K. Westbrooks, “Inferring the Structure of Signal Transduction Networks from Interactions
Between Cellular Components and Inferring Haplotypes from Informative SNPs,” Summer
2006.
F. Hussein, “QOS Multimedia Multicast Routing: A Component Based Primal Dual Approach,”
Fall 2006.
C. Gardner, “Solving the Large Parsimony Problem: Converging Iterative Neighbor Joining,”
Spring 2007 (project).
S. Jun, “Genotype/Haplotype Tagging Methods and Their Validation,” Summer 2007.
D. Mohanbabu, “Informative SNP Selection and Validation,” Summer 2007.
D. Kaur, “Filling Holes in Metabolic Pathways,” Spring 2008.
S. Saachi, “Informative SNP Selection,” Summer 2009 (project).
Internal Service
Georgia State University
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Member of University Panel for Internal Proposals (former)
College of Arts and Sciences
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Member of Award Committee (former)
Member of A&S T&P Committee
Department of Computer Science
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Chair of Assessment Committee
Chair of Faculty Search Committee
Chair of Triennial Chair Evaluation Committee (former)
Member of Executive Committee